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1. H He Li Be B Ne Na Mg Al Cl Ar SVP SV P f k f f f k f f k TZVP TZVPP f k f f f k f f k QZVP QZVPP k def2 SV P fik m f f k m f k def2 SVP fik im f f k m f k def2 TZVP def2 TZVPP f k fim f k m m k aug cc pVXZ X D Q h h k k h h k h h aug cc pV5Z k k k k k k ce pwCVXZ X D 5 k k k k N Note the auxiliary basis sets for the aug cc pV X d Z basis sets for Al Ar are identical with the aug cc pVXZ auxiliary basis sets Auxiliary basis sets for RI MP2 and RI CC2 elements K Kr K Ca Sc Zn Ga Br Kr SVP SV P fI f f f k TZVP TZVPP f f k QZVP QZVPP k def2 SV P m f f f k def2 SVP m f m f k def2 TZVP def2 TZVPP m f m i k aug cc pVXZ X D Q h h aug cc pV5Z p p cc pCWVXZ X D 5 p p aug cc pVXZ PP X D 5 p p cc pwCVXZ PP X D 5 p p Auxiliary basis sets for RI MP2 and RI CC2 elements Rb Rn Rb Sr Y Cd In Xe Cs Ba La Hg Tl At Rn def SVP def SV P f m def2 SVP def2 SV P m f f m mo f m m def TZVP def TZVPP f m def2 TZVP def2 TZVPP m def2 QZVP def2 QZVP m aug cc pVXZ PP X D 5 p p p cc pwCVXZ PP X D 5 p p p 1 3 HOW TO QUOTE USAGE OF TURBOMOLE 21 a Fully Optimized
2. auxiliary basis sets for RI DFT c d e auxiliary basis sets for RI MP2 f k h for Dunning basis sets Further references of papers not from the TURBOMOLE group are given in the bibliog raphy The following publications describe details of the methodology implemented in TURBOMOLE Methods I Electronic Structure Calculations on Workstation Computers The Program System TURBOMOLE R Ahlrichs M Bar M Haser H Horn and C K lmel Chem Phys Letters 162 165 1989 II Improvements on the Direct SCF Method M Haser and R Ahlrichs J Com put Chem 10 104 1989 III Semi direct MP2 Gradient Evaluation on Workstation Computers The MP GRAD Program F Haase and R Ahlrichs J Comp Chem 14 907 1993 IV Efficient Molecular Numerical Integration Schemes O Treutler and R Ahlrichs J Chem Phys 102 346 1995 V Stability Analysis for Solutions of the Closed Shell Kohn Sham Equation R Bauern schmitt and R Ahlrichs J Chem Phys 104 9047 1996 16 VI VII VIII IX XI XII XIII XIV XV XVI XVII XVIII CHAPTER 1 PREFACE AND GENERAL INFORMATION Treatment of Electronic Excitations within the Adiabatic Approximation of Time Dependent Density Functional Theory R Bauernschmitt and R Ahlrichs Chem Phys Letters 256 454 1996 Calculation of excitation energies within time dependent density functional the ory using auxiliary basis set expansion
3. natoms 9 Number of atoms in system current file mdlog aa The file containing the current position velocity time and timestep that is the 20 2 log FORMAT OF KEYWORDS AND COMMENTS 365 input configuration During an MD run the current information is generally kept at the end of the log file file mdlog ZZ The file to which the trajectory should be logged i e the output t time a u atomic positions x y z Bohr and symbols at t timestep au At atomic symbols and velocities x y z au at t At 2 kinetic energy H interpolated at t ab initio potential energy H calculated at t and pressure recorded at the barrier surface atomic units 1 au 29 421 TPa during the corresponding timestep ab initio potential energy gradients x y z H Bohr at t This file can be manipulated with LOG2 tools after the MD run Section 1 5 turbomole file control Where to look for TURBOMOLE keywords grad etc md_status The status of the MD run is a record of the action carried out during the previous MD step along with the duration of that step The format matches that of md_action below Canonical dynamics is supported using the Nos Hoover thermostat This option can be enabled in Mdprep or by the following syntax md_status canonical T 500 t 100 from t 25 0000000000 until t 0 00000000000 Here T specifies the temperature of the thermostat in K 500 K in the ex ample and t specifies
4. qudlen quadrupole operator u r r v all six components individual components can be specified with the labels xxqudlen xyqudlen xzqudlen yyqudlen yzqudlen zzqudlen If all six components are present the program will automatically give the electronic second moment tensor which involves only the electronic contributions M the isotropic second moment a 338 CHAPTER 20 KEYWORDS IN THE CONTROL FILE itrM and the anisotropy ly B 415 do Mii Misri 37 M x i x Furthermore the traceless quadrupole moment 1 Oi z 8rits ri including nuclear contributions is given angmom angular momentum ju L2 v all three components individual components can be specified with the labels xangmom yangmom zangmom I nef electronic force on nuclei u Le v where Zz is the charge of the nucleus J and r7 is the position vector of the electron relative to the nucleus all three components for all nuclei the labels are xnef001 ynef001 znef001 xnef002 etc where the number depends on the order in the coord file states all specification of states for which transition moments or first order properties are to be calculated The default is all i e the calculations will be done for all excited states for which excitation energies have been calculated Alternatively one can select a subset of these listed in parentheses e g states ag 3 1 3 5 biuf 1 1 3 b2u4 This will select the triple
5. 2 d 1 337006 0 599535 1 d 0 280427 1 d 0 133078 1 f 1 1428211 1 f 0 4395465 1 f 0 1758186 3 g 1 630421 0 747093 0 349040 1 g 0 164143 cl def SVP 8 s 4097 080409 1203 083193 386 280948 135 337690 51 567046 21 261034 9 420135 4 445228 1 s 2 209399 1 s 1 141575 1 s 0 604182 1 s 0 322378 4 p 51 8499902611 17 5847835188 190072032D 01 155214344D 01 138946250D 01 895263676D 02 100251139D 00 737448223D 01 276219913D 01 546316580D 02 198054511D 01 530973450D 01 1382352655D 02 107149960D 02 132565114D 01 271180364D 01 754640511D 01 173603618D 01 140197496D 01 982719736D 00 464178589D 00 8369336889D 00 359335506D 01 869599318D 01 391 392 CHAPTER 21 SAMPLE CONTROL FILES 6 49227239618 721211200D 01 2 55889114714 634201864D 01 1 p 1 05118767781 264152293D 01 1 p 437994865757 197670692D 01 4d 34 705550 548703710D 01 10 704427 619019402D 02 3 568067 337450480D 01 1 249848 905232209D 01 1 d 0 445360 418680075D 01 1 f 1 1872146118 1 0000000 1 g 1 30000000 1 0000000 end 21 5 BASISSET OPTIMIZATION FOR NITROGEN 393 21 5 Basisset optimization for Nitrogen Main File control title Basisset optimization for nitrogen SV P operating system unix symmetry oh uncomment following line to clean the basis file after optimization dump basis set coord file coord u
6. where x k u and AY C V Mk are the mass normalized normal modes ob tained from the eigenvectors CY of the dynamical matrix as calculated from the aoforce module 230 14 2 EVIB FEATURES 231 14 2 evib features The evib module implemented in TURBOMOLE allows to calculate the matrix elements of the first order derivative of the Kohn Sham operator dH A Hla v 14 4 which are required to obtain the first order electron vibration coupling constant as given in Eq 14 3 Features and limitations e LDA GGA and mGGA functionals supported e RHF and UHF SMP parallelization only cl symmetry at the moment e derivatives of the quadrature weights not supported use of large grids recom mended e just direct calculation no ri approximation at the moment 14 3 General usage of evib Calculating the matrix elements given in Eq 14 4 consists of 2 steps First a force constant calculation using aoforce is performed where the following control flags have to be added nosalc sijuai_out This will save the derivative of the density matrix The subsequent evib requires the following control flags no weight derivatives in dft section usage of large grids is therefore recommend and mgrid should be avoided The elements of the upper part of triangular matrix Eq 14 4 are stored binary in dfdxi dat dfdxi_a dat and dfdxi_b dat for UHF using formatted fortran output with record length of 8 bytes for each matr
7. PT2 is evaluated afterwards and added to the total energy For B2 PLYP B88 exchange 61 and LYP correlation 62 are used with the param eters a 0 53 and a 0 27 Due to the relatively large Fock exchange fraction self interaction error related problems are alleviated in B2 PLYP while unwanted side effects of this reduced account of static correlation are damped or eliminated by the PT2 term How to use B2 PLYP 6 2 EXCHANGE CORRELATION FUNCTIONALS AVAILABLE 129 O e during preparation of your input with DEFINE select b2 plyp in the DFT menu e carry out a DScF run Prepare and run a RI MP2 calculation with either RIMP2 or RICC2 program modules e the RI MP2 program directly prints the B2PLYP energy if this functional has been chosen before use the b2plypprep script to setp up the calculation e define coord and basis set e optional switch on ri or rijk and define jbasis or jkbasis run b2plypprep e run DSCF or RIDFT and RICC2 130 CHAPTER 6 HARTREE FOCK AND DFT CALCULATIONS 6 3 Restricted Open Shell Hartree Fock 6 3 1 Brief Description The spin restricted open shell Hartree Fock method ROHF can always be chosen to systems where all unpaired spins are parallel The TURBOMOLE keywords for such a case one open shell triplet e are open shells type 1 eg 1 1 roothaan 1 a 1 b 2 It can also treat more complicated open shell cases as indicated in the tables below In partic
8. e molecular point groups that contain reducible e representations are not sup ported Cn Cran with n gt 2 e as in mpgrad basis sets with a contraction that is greater than 10 are currently not supported e PBE and PBEO DFT functionals are not implemented in mpshift Chapter 16 Molecular Properties Wavefunction Analysis and Interfaces to Visualization Tools 16 1 Wavefunction analysis and Molecular Properties Molecular properties electrostatic moments relativistic corrections population anal yses for densities and MOs construction of localized MOs etc can be calculated with the module moloch Note that this program does not support unrestricted open shell input a script called moloch2 can currently be used as a work around type moloch2 help for further information Moreover analyses of densities apart from those calculated from molecular orbitals e g MP2 densities densities of excited states are not possible For the current version of moloch we refer to the keywords listed in Section 20 2 20 which partly can also be set by define see also Chapter 4 Note moloch is no longer supported but most functionalities of moloch now are integrated in programs that generate MOs or densities and can be done directly within the modules dscf ridft rimp2 mpgrad ricc2 and egrad If some of following keywords are set corresponding operations will be performed in the end of these programs If one desires to skip the MO
9. 177 178 179 180 181 F Della Sala Orbital dependent exact exchange mmethods in density func tional theory In M Springborg Ed Chemical Modelling Applications and Theory Band 7 Pages 115 161 Royal Society of Chemistry 2010 A Hefelmann A W Gotz F Della Sala A Gorling Numerically stable optimized effective potential method with balanced gaussian basis sets J Chem Phys 127 5 054102 2007 J B Krieger Y Li G J Iafrate Construction and application of an accurate local spin polarized kohn sham potential with integer discontinuity Exchange only theory Phys Rev A 45 101 1992 O V Gritsenko E J Baerends Orbital structure of the kohn sham ex change potential and exchange kernel and the field counteracting potential for molecules in an electric field Phys Rev A 64 042506 2001 A F Izmaylov V N Staroverov G E Scuseria E R Davidson G Stoltz E Canc s The effective local potential method Implementation for molecules and relation to approximate optimized effective potential techniques J Chem Phys 126 8 084107 2007 F Della Sala A Gorling The asymptotic region of the Kohn Sham exchange potential in molecules J Chem Phys 116 13 5374 5388 2002 F Della Sala A G rling Asymptotic behavior of the Kohn Sham exchange potential Phys Rev Lett 89 033003 2002 W Hieringer F Della Sala A Go rling Density functional calc
10. AB C AB AC B AC BC A BC rather than Energy ABC A BC A B AC B C AB C note that the first term neglects the BSSE in the dimer setup Interrupt calculation after the initial setup step to check and possibly correct the control files for the fragments and the su permolecule To continue start jobbsse without the setup option help shows a short description of the commands above 5 6 2 Output There will be an output written to file bsse_out In this file you will find all indi vidual energies computed which were used to calculate the last cp corrected energy The same holds true for the last gradients which are written to grad_out The convergence criteria and their current values are written out at the not converged file For the possible options to control convergence check the subsection for the opti mization program used statpt which is used by default or relax Since for weak complexes the force constants for intra and intermolecular bonds very strongly in magnitude it is recommended to use whenever possible redundant internal coordi nates 5 7 REACTION PATH OPTIMIZATION 119 5 7 Reaction Path Optimization 5 7 1 Background and Program structure The goal of self consistent optimization of the reaction path RP is usually to ob tain an initial guess for Transition State Search or an approximation to the barrier Methods that use reactant and product structure to compute the RP are oft
11. GGA an additional variable is used the Kohn Sham kinetic energy density which allows e g to construct self correlation free functionals Functionals in the above rungs can have high accuracy for different class of problems in chemistry and solid state physics but their main limitation is the self interaction error SIE 168 171 To avoid the SIE the exchange must be treated exactly and this can be achieved by functionals in the fourth rung which depend explicitly on all the occupied KS orbitals In the KS formalism the EXX exact exchange energy is for closed shell systems ns 2 168 171 occ Occ KS KS KS AKS q ei 2 5 f f drdr Da ror ro r oy r 18 1 a b le r i e the same functional form of the Hartree Fock HF exchange but computed with KS orbitals which are obtained using a self consistent local EXX potential At this point we should recall that hybrid DFT functionals including HF exchange doesn t belong to the KS formalism in hybrid DFT in fact the non local HF 259 256 CHAPTER 18 ORBITAL DEPENDENT DFT fhe Se Galt dalr ig employed in the self consistent a r r Generalized Kohn Sham equations LE the orbitals While LDA GGA meta GGA and hybrid functionals are implemented for ground state calculations in the dscf and ridft the odft module considers functionals of the fourth rung Currently exchange only orbital dependent approaches are im plemented in the odft modul
12. Manual setting of the integral block size in subroutine rirhs f for developers In order to run a geometry optimization jobex must be invoked with the level set to rirpa and the ri option E g jobex ri level rirpa In order to run a numerical frequency calculation NumForce must be invoked with the level set to rirpa e g NumForce d 0 02 central ri level rirpa 12 3 Further Recommendations e The direct RPA correlation energy is defined in a Kohn Sham context without inclusion of exchange integrals and therefore the use of self consistent KS or bitals obtained from semi local functionals is recommended HF orbitals or KS orbitals obtained form hybrid functionals lead to inferior results 222 CHAPTER 12 RANDOM PHASE APPROXIMATION e Experience has demonstrated that the difference in RPA correlation energies obtained from different semi local functionals is very small much smaller than the inherent error of the method Like MP2 RIRPA results are known to converge very slowly with increasing basis set size in particular slowly with increasing l quantum number of the basis set For reliable results the use of QZVP basis sets or higher is recom mended For non covalently bound systems larger basis sets especially with more diffuse functions are needed It is recommended to exclude all non valence orbitals from RIRPA calculations as neither the TURBOMOLE standard basis sets SVP TZVPP and QZVPP nor the cc p
13. Please check your user limits If one or several tests of the test suite fail it is very likely that your user limits for stack size and or memory are too small sh bash ksh users please do a ulimit a to get your actual limits The output should look like core file size blocks 0 data seg size kbytes unlimited file size blocks unlimited max locked memory kbytes unlimited max memory size kbytes unlimited open files 1024 pipe size 512 bytes 8 stack size kbytes unlimited cpu time seconds unlimited max user processes 8191 virtual memory kbytes unlimited The most important entries are data size stack size max memory size and virtual memory Those should be either unlimited or as big as your total RAM To set e g the stack size to the maximum allowed size on your system the so called hard limit do ulimit s hard csh tcsh users please do limit instead of ulimit and check the output Again like given above the limits should be at least as high as your memory avail able The syntax for changing the limits to unlimited using csh tesh is limit stacksize hard And please note that on 32bit machines unlimited can be the same as 4GB 4194303 kbytes If you are using a queuing system 32 CHAPTER 2 INSTALLATION OF TURBOMOLE Note that if you are submitting jobs to a queue the user limits might be different from what you get when you log in on the machines To check your limits you have to
14. TURBOMOLE Program Package for ab initio Electronic Structure Calculations USER S MANUAL TURBOMOLE Version 6 6 June 2 2014 Contents 1 Preface and General Information 1 1 Contributions and Acknowledgements 12 Features of TURBOMOLE oes a soe de a eee eo ee ee 1 3 How to Quote Usage of TURBOMOLE 2 4 1 4 Modules and Their Functionality iy gt MOONS o a ee 4 Ao Bd AA ROS oe eS EE ey e i 2 Installation of TURBOMOLE 2 1 Install TURBOMOLE command line version 2 2 1 1 Settings for each user sa sesa bea kaiaa ee ee 2 1 2 Setting system type and PATH by hand 2 1 3 Testing the installation 2 6 poe eee ee bea e RES 2 2 Installation problems How to solve 2 0004 3 How to Run TURBOMOLE z1 AAjnick and Dirty Tutorial s s 4 sot ea a ok ea a 24 e442 bee 3 1 1 Single Point Calculations Running TURBOMOLE Modules 3 1 2 Energy and Gradient Calculations 3 1 3 Calculation of Molecular Properties 3 1 4 Modules and Data Flow 20 mee Parallel RUNS cec 24 4 29445 e a h eed ek Oe ae ee we hd 3 2 1 Running Parallel Jobs MPI case 3 2 2 Running Parallel Jobs SMP case 2 um 2b ee es 4 Preparing your input file with DEFINE Non oo Ir 19 23 23 23 24 24 25 27 af 29 29 31 31 31 33 38 41 4 1 4 2 4 3 4 4 CONTENTS 4 0 3 Univers
15. Teller distortions The molecule is automatically reoriented if necessary Example Ty gt Dog gt Coy gt Cs You may enter Cartesian atomic coordinates and atomic symbols inter actively After entering an atomic symbol you will be asked for Carte sian coordinates for this type of atom until you enter If you enter amp the atom counter will be decremented and you may re define the last atom but you surely won t make mistakes will you After entering define asks for the next atom type Entering amp here will allow you to re define the last atom type and to leave this mode and return to 4 1 THE GEOMETRY MAIN MENU 53 a file aa file sub the geometry main menu Enter q as atom symbol if you want to use a dummy center without nuclear charge Symmetry equivalent atoms are created immediately after you entered a set of coordinates This is a convenient tool to provide e g rings exploit symmetry group Dyn to create an n membered planar ring by putting an atom on the x axis You may also read atomic coordinates and possibly internal coordinates from file where file must have the same format as the data group coord in file control The Cartesian coordinates and the definitions of the internal coordinates are read in free format you only have to care for the keywords coord and optionally intdef and important for the end at the end of the file The atomic symbol follows the Cartesian coordinates se
16. axis of 20 A along y semi major of 15 A on z and minor of 10A on x constant is the Hooke s Law force constant in atomic units of force H Bohr per length unit Here it is 2 0 H Bohr Angstrom a bastard combination of units 20 2 FORMAT OF KEYWORDS AND COMMENTS 367 springlen is the effective limit to the restorative force of the barrier For this system an atom at 5A into the barrier will feel the same force as at 1 0A temperature denotes the temperature of the cavity walls in Kelvin If the system quasi temperature is below this setpoint particles will be accelerated on their return to the interior Alternately they will be retarded if the system is too warm A temperature of 0 0K will turn off wall temperature control returning molecules to the system with the same momentum as when they encountered the barrier constraints angstroms tolerance 0 05 adjpercyc 0 25 type H 0 0 9 1 2 type F C 0 0 1 7 type HC 1 0 1 2 210 0 3 1 1 54 4 1 1 0 constraints specifies and or automatically generates atomic distance constraints The op tional flag angstroms can be used to indicate that data will be entered in ngstr ms rather than Bohr tolerance is the convergence criterion for application of constraints All distances must be within tolerance of the specified constraint Additionally the RMS deviation of all constrained distances must be below 2 3 of tolerance adjpercyc is the fraction of
17. closed shells a 1 4 2 ti 1 3 2 h 1 2 open shells type 1 a 5 1 h 2 4 5 roothaan 1 rohf 5a 5a 0 b 0 5a 2h 1 b 2 2h 2h a 15 16 b 15 8 Example 2 The 4d 5s 7S state of Mo symmetry I see Section 6 3 3 can also be done as follows roothaan 1 rohf 5a 5a a 0 b 0 5a 2h a 1 b 2 2h 2h a 1 b 2 6 3 RESTRICTED OPEN SHELL HARTREE FOCK 135 closed shells a 1 4 2 t1 1 3 2 h 1 2 open shells type 1 a 5 1 h 2 1 The shells 5s and 4d have now been made inequivalent Result is identical to 6 3 3 which is also more efficient Example 3 The 4d 5s 3D state of Ni symmetry I closed shells a 1 3 2 ti 1 2 2 open shells type 1 a 4 1 h 1 9 5 roothaan 1 rohf 4a 4a a 0 b 0 1h 1ih a 80 81 b 80 81 4a 1h a 1 b 10 9 see basis set catalogue basis SV 3D requires this input and gives the energy you must get 6 3 4 Miscellaneous Valence states Valence states are defined as the weighted average of all CSFs arising from an elec tronic configuration occupation MO This is identical to the average energy of all Slater determinants _ 2nip n 1 a b _ Nir 1 n This covers e g the cases n 1 and n 2nir 1 pt p d d etc since there is only a single CSF which is identical to the average of configurations 136 CHAPTER 6 HARTREE FOCK AND DFT CALCULATIONS Totally symmetric singlets for 2 or 2n 2 electrons
18. leaving rir12 unchanged corresponds to the choice of Qo Almost all modern MP2 F12 calculations use ansatz 2 default which gives much improved energies over ansatz 1 see Ref 114 for details The principal additional cost of using ansatz 2 over ansatz 1 is concerned with the coupling between the F12 and conventional amplitudes This is avoided by choosing 2 which corresponds to neglecting EBC Extended Brillouin Condition terms in the Fock matrix elements is the method of computing the matrices B see Ref 114 for details The cost and accuracy increases from A to B It is rec 9 5 RI MP2 F12 CALCULATIONS 177 comaprox cabs examp ri2orb corrfac cabsingles ommended to use B default The energies computed using A are then also printed out in the output is the method for approximately computing the integrals for the operator Tt fiz where the matrix representations of F K or T V are used F K the core Hamiltonian plus Coulomb term is rec ommended and is the default refers to the method of orthogonalising the orbitals in the com plementary auxiliary basis Singular value decomposition svd or Cholesky decomposition cho are available svd is recommended and is the default with a threshold of 1 0d 08 The basis set used for CABS is set from the cc menu refers to the choice of excitation space inv is the orbital invariant merhod of Ref 115 with amplitudes c kl noinv is the orig i
19. pop nbo to perform a natural population analyses 154 The possible options specified in the same line are AO must be provided the CAO case is not implemented tw real Threshold t to circumvent numerical difficulties in computing Ow default tw 1 d 6 idbgl integer Debug level default idbgl 0 ab For UHF cases Print alpha and beta density results short Print only natural electron configuration and summary Example pop nbo AO ab short atoms 1 2 6 leads to a natural population analysis AO basis with printing the results of alpha and beta densities only the electron configuration and the summary for the atoms 1 2 and 6 To change the NMB set for atoms one has to add a nbonmb block in the control file Example nbonmb ni s 4 p 2 d l o s 2 p l leads to a NMB set for Ni of 4 s 2 p and 1d functions and for O of 2 s and 1 p functions pop paboon to perform a population analyses based on occupation numbers 155 yielding shared electron numbers SENs and multicenter contributions For this method always the total density is used i e the sum of alpha and beta densities in case of UHF the SCF MP2 density in case of MP2 and the GHF total density for two component GHF 358 CHAPTER 20 KEYWORDS IN THE CONTROL FILE The results of such an analysis may depend on the choice of the number of modified atomic orbitals MAOs which can be specified by an additional line without further speci
20. tures to be used for discretization of the path and maxit is the number of cycles to run If maxit 0 structures will be rotated translated to minimize the cartesian distance for maxit 1 strutures will be used as provided Using method qg instead of method q a reaction path will be grown as in the growing string method To start a RP optimization you need to provide at least a reactant and a product struc ture ncoord gt 2 You may provide more structures if you have a guess for the reaction path The input structures will be used to compute an initial guess with ninter structures that is then optimized Reactant and product structure will stay fixed throughout the optimization All structures have to have the same ordering of atoms The input structures are provided in a file coords which contains merged coord files All ncoord structures are given in the right order in the typical TURBOMOLE coord format 5 7 3 How it works Minimum Input Quick and Dirty 1 Make a usual TURBOMOLE input using the coord file of either reactant of product structure 2 Join the coord files of reactant and product in a file coords 3 Run woelfling job 4 Check the output and the path path xyz to extract a TS guess It is usually a good idea to check the initial path before starting the calculation Once you have prepared the input simply run woelfling directly and check path xyz If it looks reasonable just run the woelfling job script Unsucce
21. 1 08597397921317 o symmetry d3d closed shells alg 1 3 2 a2u 1 2 2 eu 1 2 open shells type 1 eg 1 1 roothaan 1 a 1 b 2 energy SCF SCFKIN SCFPOT 1 149 4774402753 149 4799190239 298 9573592992 Reference singlet delta in D3d This is a Roothaan case as is D infinity h coord 0 0 0 0 1 08597397921317 o 0 0 0 0 1 08597397921317 o symmetry d3d closed shells alg 1 3 2 a2u 1 2 2 eu 1 2 open shells type 1 eg 1 1 roothaan 1 a 1 2 b 0 energy SCF SCFKIN SCFPOT 1 149 4297623470 149 4298692899 298 8596316369 21 6 ROHF OF TWO OPEN SHELLS 397 Extracts from control for O in D Symmetry HF SCF SVP Triplet sigma in D2h coord 0 0 0 0 1 08597397921317 o 0 0 0 0 1 08597397921317 o symmetry d2h closed shells ag 1 3 2 biu 1 2 2 b2u 1 2 b3u 1 2 open shells type 1 b2g 1 1 b3g 1 1 roothaan 1 a 1 b 2 energy SCF SCFKIN SCFPOT 1 149 4774402750 149 4798706643 298 9573109393 Singlet delta in D2h xx yy component where x b2g and y b3g In D infinity h b2g and b3g combine to eg coord 0 0 0 0 1 08597397921317 o 0 0 0 0 1 08597397921317 o symmetry d2h closed shells ag 1 3 2 biu 1 2 2 b2u 1 2 b3u 1 2 open shells type 1 b2g 1 1 b3g 1 Ci roothaan 2 rohf 1b2g 1b3g a 0 b 2 398 CHAPTER 21 SAMPLE CONTROL FILES 1b2g 1b2 a 1b3g 1b3 g a energy SCF SCFKIN SCFPOT 1 149 4297623516 1
22. 123 2005 074101 e for the SCS and SOS variants of MP2 S Grimme J Chem Phys 118 2003 9095 SCS or Y Jung R C Lochan A D Dutoi M Head Gordon J Chem Phys 121 2004 9793 SOS e for the SCS and SOS variants of CC2 and ADC 2 A Hellweg S Griin C Hattig Phys Chem Chem Phys 10 2008 4119 4127 Implementation e please include always a reference to the publication reporting the imple mentation of the core part of the ricc2 program C Hattig and F Weigend J Chem Phys 113 2000 5154 186 CHAPTER 10 RI CC2 e for transition moments and excited state first order properties C Hattig and A Kohn J Chem Phys 117 2002 6939 e for triplet excited states include C Hattig and K Hald Phys Chem Chem Phys 4 2002 2111 C Hattig A Kohn and K Hald J Chem Phys 116 2002 5401 e for ground state geometry optimizations include C Hattig J Chem Phys 118 2003 7751 e for geometry optimizations for excited states include A Kohn and C Hattig J Chem Phys 119 2003 5021 e for calculations with RI ADC 2 RI CIS D RI CIS D include C Hattig Adv Quant Chem 50 2005 37 e if the parallel version of ricc2 is used include a reference to C Hattig A Hellweg A Kohn Phys Chem Chem Phys 8 2006 1159 e for transition moments between excited states M Pabst and A Kohn J Chem Phys 129 2008 214101 e for RI MP2 F12 calculations R A Bachorz F
23. 2 e 1 10 2 a2 1 8 2 e 1 4 2 end File coord coord 00000000000000 00000000000000 00000000000000 ta 388 CHAPTER 21 2 19392179448315 3 79998401587749 00000000000000 2 19392179448315 3 79998401587749 00000000000000 4 38784358896629 00000000000000 00000000000000 00000000000000 00000000000000 4 46615918865523 00000000000000 00000000000000 4 46615918865523 intdef definitions of internal coordinates 1 k 1 0000000000000 stre 1 2 2 k 1 0000000000000 stre 1 5 end File basis basis ta def SVP ta 7s6p5d 6s3p2d 211111 411 41 2 s 14 400000000 12 000000000 1 os 5 0701477302 1 s 86033356487 1 s 37158938894 1 s 10745336254 1 s 39142776556E 01 4 p 7 4188720000 5 6984100000 1 1777211960 54478533555 1 p 22309270117 1 p 43100000000E 01 4 d 3 9738796278 1 4528884813 99343296745 1 6510077975 1 0000000000 1 0000000000 1 0000000000 1 0000000000 1 0000000000 26979695152 46968874449 50905100155 52298161137 1 0000000000 1 0000000000 52799310714E 01 18558319471 val 4 38784 val 4 46616 SAMPLE CONTROL FILES cl cl cl cl cl 21 4 TACLs INPUT FOR AN RI DFT CALCULATION WITH ECPS 61042908544 24216276510 1 d 87909318337E 01 cl def SVP cl 7s5p 6s2p 5 s 10449 827566 1571 7365221 357 12065523 100 25185935 30 812727554 3 s 51 923789434 5
24. 3 1 2 Dy 4 5 4 5 ZP 2 3 0 3P 15 16 9 8 4 2 3 Iper 69 80 27 40 I5 3 4 0 5 5 6 2p 24 25 24 25 only irrep g T mainly high spin available n f g a b 1 1 8 2G 0 0 2 1 4 TF 2 3 4 3 TA 0 4 3 3 8 4G 8 9 16 9 4 1 2 5A 1 2 5 5 8 4G 24 25 32 25 6 3 4 t 26 27 28 27 TA 8 9 4 9 7 7 8 2G 48 49 48 49 continues on next page 132 CHAPTER 6 HARTREE FOCK AND DFT CALCULATIONS Table 6 1 Roothaan coefficients a and b for cases with de generate orbitals continued d O3 h mainly high spin cases work n f d a b 1 1 10 2D 0 0 2 1 5 3F 3P T 5 8 5 4 IS 0 5 3 3 10 4p 4pit 5 6 5 3 4 2 5 5D H 15 16 15 8 5 1 2 6S 5A 1 2 6 3 5 D H 35 36 25 18 7 7 10 F4 P 95 98 55 49 8 4 5 3F 5P 125 128 65 64 rs 15 16 5 8 9 9 10 D H 80 81 80 81 except cases e g Daq or D4 where e gives only one dimensional irreps which are not Roothaan cases t only p given the state for groups Ty etc follows from S gt A T O I P gt T 7 0 1 D gt H J E T T 0 This is not a CSF in T or O a b describes average of states resulting from E T tt a b describes weighted average of high spin states not a CSF Example The 4d 5s 2D state of Ag in symmetry I closed shells a 1 5 2 ti 1 3 2 h 1 2 open shells type 1 h 2 9 5 roothaan 1 a 80 81 b 80 81 6 3 RESTRICTED OPEN SHELL HART
25. 97 100 102 107 116 130 141 145 148 164 166 167 173 187 222 224 227 231 238 271 290 294 298 305 308 309 353 O00 aid ITT TURBOMOLE installation 29 modules 23 quotation of 13 tools 25 Turbotest 30 twoint 34 40 41 UFF keywords 277 uff 23 51 100 101 111 112 277 279 uffgradient 112 INDEX uffhessian0 0 112 ufftopology 112 279 281 nxtn12 279 uhfuse 28 vector function 187 velocity 368 vibration 27 224 Vibrational Frequencies 224 wave function analysis keywords 354 woelfling 25 28 119 121 woelfling job 25 28 x2t 28 33 49 xxx map 199 435
26. Chir Qos 11 17 Ha This is the recommended approach which is used by default if not any other approch has been chosen with the examp option in rir12 see Sec 9 5 for further details on the options for F12 calculations note that the examp noinv option should not be combined with CCSD calculations CCSD F12 SP calculations are computation ally somewhat less expensive that CCSD F12 calculations which solve Eq 11 16 while both approaches are approximately similar accurate for energy differences The SP approach becomes in particular very efficient if combined with the neglect of certain higher order explicitly correlated contributions which have a negligible effect on the energies but increase the costs during the CC iterations The most accurate and recommeded variant is the CCSD F12 approximation 138 which gives essentially identical energies as CCSD F12 Also available are the CCSD F12 Ref 138 CCSD F12a Ref 139 and CCSD F12b Ref 140 approximations as well as the perturbative corrections CCSD 2 py and CCSD 2 pr see Refs 212 CHAPTER 11 CCSD CCSD F12 AND CCSD T 138 141 142 Note that these approximations should only be used with ansatz 2 and the SP approach i e fixed geminal amplitudes For MP3 the approximations F12 and F12 to a full F12 implementation be come identical they include all contributions linear in the coefficients ct The explicitly correlated MP4 method MP4 F12 is defined
27. For further details call MECPopt h prepares MP2 calculations interactively by adjusting parameters of the control file according to your system resources calculates numerically force constants vibrational frequencies and IR intensities Note that the name of the shell script is NumForce with capital F example outp 1 2 3 4 displays the out of plan angle between atom1 and the plane that is defined by the last three atoms atom is fixed at atom4 translates and rotates coordinates in the principal axis system and prints out the rotational constants calculates vibrational frequencies and Raman intensities See Sec tion 13 2 for explanation distorts a molecule along a vibrational mode prepares a series of control files with frozen internal coordinates The data group constraints e g provided by TmoleX is evaluated For further details call scanprep h distorts a molecule along a vibrational mode or generates a plot of an IR spectrum gnuplot required 28 sdg sysname stati t2x tm2aomix tm2molden tors tbtim tblist uhfuse CHAPTER 1 PREFACE AND GENERAL INFORMATION shows data group from control file for example sdg energy shows the list of calculated energies returns the name of your system used in almost all TURBOMOLE scripts prepares the control file for a statistics run converts TURBOMOLE coordinates to xyz format creates an input file for the AOMix program AOMix a software the
28. MP2 gradients necessary for optimisation of structure parameters at the MP2 level are calculated as analytical derivatives of the MP2 energy with respect to nuclear coordinates calulation of these derivatives also yields the first order perturbed wave function expressed as MP2 density matrix in analogy to the HF density matrix MP2 corrections of properties like electric moments or atomic populations are ob tained in the same way as for the HF level the HF density matrix is just replaced by the MP2 density matrix The resolution of the identity RI approximation means expansion of products of virtual and occupied orbitals by expansions of so called auxiliary functions Calculation and transformation of four center two electron integrals see above is replaced by that of three center integrals which leads to computational savings of rimp2 compared to mpgrad by a factor of ca 5 small basis sets like SVP to ca 10 large basis sets like TZVPP or more for cc pVQZ basis sets The errors dif ferences to mpgrad of rimp2 in connection with optimised auxliliary basis sets are small and well documented 9 107 The use of the mpgrad modul is recommended rather for reference calculations or if suitable auxiliary basis sets are not available 9 3 How to Prepare and Perform MP2 Calculations Prerequisites Calculations with mpgrad rimp2 or ricc2 require e a converged SCF calculation with the one electron density convergence thres ho
29. Moloch see Section 16 2 This can be done by calling ricc2 with the option fanal which bypasses the usual wavefunction calculation and triggers the program into an analysis mode for densities In this mode the program interpretes anadens and the keywords described in Section 16 2 To plot for example the difference density of the two above mentioned total densities you have to add the following lines in your control file anadens calc my_favourite_diffden from 1d0 ccitd cc2 xs 3a2 001 1d0 ccitd cc2 gs 1a1 001 10 4 TRANSITION MOMENTS 201 pointval and invoke ricc2 fanal This will generate the files my_favourite_diffden and my_favourite_diffden map The latter can be converted into gOpenMol format as described in Section 16 2 10 3 4 Fast geometry optimizations with RI SCF based gradients If geometry optimizations on MP2 or CC2 level are performed with large basis set especially with diffuse basis functions the N steps might become the dominant part of the overall timings In these cases the integral screening in the Hartree Fock part often becomes inefficient The resolution of the identity can be applied here to speed up the calculation of the HF reference wavefunction as well as the solution of the coupled perturbed Hartree Fock CPHF equations in the MP2 or CC2 gradient calculation An additional auxiliary basis denoted jkbas set has to be assigned via the General Options Menu in the define program In
30. The MP2 and all CC calculations for ROHF reference wavefunctions are done by first trans forming to a semi canonical orbital basis which are defined by the eigenvectors of the occupied occupied and virtual virtual blocks of the Fock matrices of alpha and beta spin No spin restrictions are applied in the cluster equations This approach is sometimes also denoted as ROHF UCCSD Note that if a frozen core approximation is used the semicanonical orbitals depend on whether the block diagonalization of the Fock matrices is done in space of all orbitals or only in the space of the correlated valence orbitals The two approaches lead thus to slightly different energies but none of two is more valid or more accurate than the other The ricc2 program uses the former scheme with the block diagonalization done in the space of all molecular orbitals The same scheme is used e g in the CFOUR program suite but other codes as e g the implementation in MOLPRO use a block diagonalization restricted to the active valence space Perturbative triples corrections To achieve ground state energies a high ac curacy which systematically surpasses the acccuracy MP2 and DFT calculations for reaction and binding energies the CCSD model should be combined with a perturba tive correction for connected triples The recommended approach for the correction 11 1 COMPUTATIONAL DEMANDS 213 is the CCSD T model Eccsp t Ecesp ES EY 11 18 which includes the
31. The file where the MOs are written on output default mos These two options can also be used for uhfmo_alpha and uhfmo_beta to use a core guess and write the molecular orbitals to file After running define or a TURBOMOLE calculation additional options may ap pear specifying the origin of the MOs expanded These MOs were obtained by projection form another basis set They should not be used for wavefunction analysis scfconv integer The MOs are converged SCF MOs the convergence criterion applied was 1Q7 integer scfdump znteger The MOs are unconverged SCF MOs which were written on this data group after iteration integer The latter three options are mutually ex clusive format format string This specifies the FORTRAN format specification which was used for MO output The standard format is 4d20 14 See data group mo output format Example Your data group scfmo could look like this after a successful TURBOMOLE run scfmo scfconv 7 format 3 1x d19 13 1 al eigenvalue 524127 nsao 6 1234567890123d 01 1234567890123d 00 1234567890123d 01 1234567890123d 01 1234567890123d 00 3 a2 eigenvalue 234810 scforbitalorder on off Order SCF MOs with respect to their energies default on scforbitalshift options To assist convergence either the energies of unoccupied MOs can be shifted to higher energies or in open shell cases the energies of closed shell MOs to lower energies In general a large shi
32. analysis of molecular orbitals For more information see http www sg chem net aomix creates a molden format input file for the Molden program Molden is a graphical interface for displaying the molecular density MOs nor mal modes and reaction paths For more information about molden see http www cmbi ru nl molden molden htm1 is a script to query a dihedral angle in a molecular structure e g tors 1 2 3 4 gives the torsional angle of atom 4 out of the plane of atoms 1 2 and 3 is used to convert timings output files from TURBOBENCH calculations to ATFXtables for options please type TBTIM help is used to produce summaries of timings from TURBOBENCH calcula tions to ATeXformat for options please type TBLIST help transforms the UHF MOs from a given symmetry to another sym metry which is C1 by default just enter uhfuse but can be speci fied e g as Cay by entering uhfuse s c2v Now this functionality is included in the MO definition menu of define program see Sec tion 4 3 1 woelfling job optimizes a reaction path with woelfling x2t For further information please type woelfling job h converts standard xyz files into TURBOMOLE coordinates Chapter 2 Installation of TURBOMOLE 2 1 Install TURBOMOLE command line version Installation requires familiarity with some simple UNIX commands The TURBOMOLE package is generally shipped as one tar file This has to be uncompressed gunzip turbomo
33. from the ground to an excited state is given by the direct product of the IRREPs of the two states For example to calculate the first Ag state in a Cy symmetric molecule with a By open shell ground state it is necessary to specify 160 CHAPTER 7 HF AND DFT RESPONSE CALCULATIONS soes bi 1 The number of excitations that have to be calculated in order to cover a certain spec tral range is often difficult to determine in advance The total number of excitations within each IRREP as provided by the define ex menu may give some hint A good strategy is to start with a smaller number of excitations and if necessary perform a second escf run on a larger number of states using the already converged excitation vectors as input To compute absorption and CD spectra it is often sufficient to include optically allowed transitions only This leads to substantial reduction of computational effort for molecules with higher symmetry For example in the UV VIS spectrum of an Op symmetric molecule only ti excitations are optically allowed The IRREPs of the electric and magnetic dipole moments as well as of the electric quadrupole moment are displayed automatically in the define ex menu If a large number of states is to be calculated it is highly recommended to provide extra memory by specifying rpacor m the integer m being the core memory size in megabytes default is 20 The larger m the more vectors can be processed simultaneously with
34. i e the old vector will be taken other wise scfmo none will be inserted into your output file which forces a calculation without start vector to be performed When you leave this menu the data groups closed shells open shells optionally and scfmo will be written to file You will then reach the last of the four main menus the General Menu which is described in Section 4 4 4 3 2 Assignment of Occupation Numbers If an automatic assignment of occupation numbers is not possible or you do not except the occupation numbers generated by the EHT you enter the following menu OCCUPATION lt int gt lt list gt lt list gt lt list gt lt list gt lt list gt ePdcooerpnoedtdere ct Nn dis e f lt int gt lt index gt lt list gt lt index gt lt index gt NUMBER ASSIGNMENT MENU e 60 c 0 o0 0 CHOOSE UHF SINGLET OCCUPATION CHOOSE UHF TRIPLET OCCUPATION CHOOSE UHF WITH lt int gt UNPAIRED ELECTRONS PRINT MO S FROM EHT IN lt list gt DEFAULT ALL PRINT MO COEFFICIENTS OF SHELL lt index gt CHOOSE SHELLS IN lt list gt TO BECOME CLOSED SHELLS CHOOSE SHELL lt index gt TO BECOME AN RHF OPEN SHELL CHOOSE SHELLS IN lt list gt TO BECOME UHF ALPHA SHELLS CHOOSE SHELLS IN lt list gt TO BECOME UHF BETA SHELLS CHOOSE SHELLS IN lt list gt TO BECOME EMPTY SHELLS REPEAT THE EXTENDED HUECKEL CALCULATION SAVE OCCUPATION NUMBERS amp GO TO NEXT ITEM GEOME
35. in this direction The unit cell dimensions are specified in A using cell ang The positions of the point charges in the unit cell are specified as Cartesian coordinates in A content ang The values of point charges for Al and O are given in the subsection charges embed periodic 2 cell angs 4 8043 4 8043 24 0000 90 0000 90 0000 120 0000 content ang Al 2 402142286 1 386878848 5 918076515 Al 0 000013520 0 000003382 7 611351967 146 CHAPTER 6 HARTREE FOCK AND DFT CALCULATIONS Al 0 000008912 2 773757219 8 064809799 Al 2 402041674 1 386946321 0 061230399 Al 0 000005568 0 000003223 10 247499466 Al 2 402137518 1 386872172 9 977437973 Al 0 000000070 2 773757935 5 390023232 Al 0 000006283 0 000005607 3 696748018 Al 2 402151346 1 386879444 3 243290186 Al 0 000100868 2 773690462 11 246870041 Al 0 000001982 0 000005796 1 060600400 Al 0 000004853 2 773764610 1 330662251 0 0 731205344 1 496630311 6 749288559 0 0 743527174 1 296469569 8 957922935 0 1 588027477 0 104536049 11 127140045 0 1 471626759 2 779079437 6 749288559 0 3 309734344 0 004341011 8 957920074 0 3 919768333 1 323050499 11 127141953 0 0 740424335 4 045563698 6 749289513 0 1 651123047 2 868478537 8 957910538 0 1 698525310 2 733071804 11 127161026 0 3 133347750 2 664006472 4 558811665 0 1 658615232 2 864167213 2 350177050 0 0 814115047 4 056100845 0 180959582 0 0 930515707 1 381557465 4 558811188 0 1 494558096 0 004332162 2 350180149 0 1 51762
36. including all and none Then you will be asked to enter the nickname of the basis set to be assigned There are two principal ways to do this 1 If you are in the append mode the nickname you entered will be appended to the atomic symbol of the element under consideration This is especially useful if you want to assign basis sets to different atoms with one command For example if you want to assign basis sets to hydrogen and oxygen atoms and you enter only DZ the basis sets h DZ and o DZ will be read from the basis set library 64 bb bl bm bp ecp ecpb ecpi ecpl CHAPTER 4 PREPARING YOUR INPUT FILE WITH DEFINE 2 If you are in the non append mode no atomic symbol will be in serted in front of the nickname entered Therefore you have to enter the full basis set nickname e g h DZ This mode is advantageous if you want to assign basis sets to dummy centers i e points without nuclear charge but with basis functions e g for counterpoise calcu lations or if you want to use the basis set nickname none which means no basis functions at this atom You can switch between the two modes with switches to append mode and switches to non append mode Once you have specified your basis set nickname define will look in the standard input file normally control for this basis set If it can not be found there you can switch to the standard basis set library if you did not use a standard input
37. internal off These lines switch on the non default optimization in cartesian coordinates and switch off the optimization in internal coordinates this has to be done explicitly As input data groups you need only grad as provided by on of the gradient programs For the first coordinate update an approximate force constant matrix is needed in data group forceapprox Output will be the updated coordinates on coord and the updated force constant matrix on forceapprox The coordinates for any single atom can be fixed by placing an f in the third to eighth column of the chemical symbol flag group As an example the following coordinates specify acetone with a fixed carbonyl group coord 2 02693271108611 2 03672551266230 O 00000000000000 c 1 08247228252865 0 68857387733323 O 00000000000000 c f 2 53154870318830 2 48171472134488 O 00000000000000 o 108 end 780637 90034738 64348282517094 23779643042546 64348282517094 31008893646566 31008893646566 12184425921830 1 0 0 w CHAPTER 5 STRUCTURE OPTIMIZATIONS 04586399389434 13141435997713 09026673535431 13141435997713 07002878668872 07002878668872 06288409251899 0 00000000000000 1 68855816889786 0 00000000000000 1 68855816889786 1 68840815751978 1 68840815751978 0 00000000000000 5 3 7 Optimization of Basis Sets SCF only For this task you have to specify optimize basis on internal off rrppppoa Th
38. job start 98 jobbsse 54 116 118 JOBEX 125 jobex 25 26 30 34 49 77 80 97 98 100 101 111 116 119 152 161 184 185 217 221 329 347 375 c 97 117 dscf 97 energy 97 117 ex 97 gceart 97 117 grad 97 gradient 117 keep 97 1 97 117 level 97 117 1s 97 117 md 97 mdfile 97 mdmaster 97 mem 117 opt 117 relax 97 117 ri 97 117 rijk 97 setup 117 432 statpt 97 trans 97 trimer 117 kdg 26 kinetic energy 368 lalp 359 lbet 359 Leapfrog Verlet algorithm 115 364 Lhfprep 261 301 lhfprep 27 261 301 lhfprep asy 262 lhfprep kli 262 lhfprep num 262 1mo 359 log2egy 27 log2rog 27 log2x 27 LT SOS RI MP2 45 179 mdens 200 mdlog 115 mdmaster 364 mdmaster 115 Mdprep 115 364 365 mdprep 364 mdprep 27 MECPopt 27 MECPprep 27 menu atomic attributes 60 63 general 74 75 geometry main 50 geometry menu 52 internal coordinate 55 56 occupation number assignment 68 69 start vectors 65 66 molecular dynamics 114 364 INDEX molecular orbitals binary format 66 MOLOCH keywords 350 moloch 88 91 92 94 95 235 350 MP2 RL 325 Mp2prep 35 172 mp2prep 27 36 172 MP3 325 MP4 325 MPGRAD keywords 322 mpgrad 14 23 24 36 38 39 80 98 104 108 117 166 167 169 172 174 199 234 236 238 272 283 296 307 311 323 324 346 354 355 373 375 MPSHIFT keywords 371 mpsh
39. k Opm 20pm 40pm 60pm 80pm and r gw are the van der Waals radii of the atoms pointval drives the calculation of space dependent molecular quantities at 3D grids planes lines or single points Without further specifications the values of densities are plotted on a three dimensional grid adapted to the molecular size Data are deposed to output files suffix plt that can be visualized directly with the gOpenMol program In case of RHF dscf ridft calculations you get the total density on file td plt for UHF dscf ridft calculations one gets both values for the total density D D on td plt and the spin density D D on sd plt For mpgrad rimp2 calculations one gets in the RHF case the total density D SCF MP2 on td plt and the MP2 contribution on mp2d plt and in the UHF case one obtains the total density D SCF M P2 D SCF MP2 on td plt the spin density D SCF M P2 D SCF MP2 on td plt and the respective MP2 contributions on files mp2d plt and mp2sd plt For egrad it is similar just replace in the filenames mp2 by e Integration of density if absolute value greater than eps within a sphere origin x y z radius r is performed for 20 2 FORMAT OF KEYWORDS AND COMMENTS 361 pointval integrate ry zr eps By default the origin is at 0 0 0 the radius is chosen large enough to include the whole 3D box and all contributions are regarded eps 0 Data different from total and spin densit
40. maximum number of itera tion maxit 20 output level output 0 3 asymptotic continuation in each iteration cgasy 1 With slater dtresh 1 d 9 default the calculations of the numerical integrals for the Slater potential is performed only if it changes more than 1 d 9 Asymptotic regions specification corrct region Rr Ar 0 Rp Ar basis set correction potential Rp Ar Rp Ar smooth region Rr Apr co asymptotic correction Defaults Rp 10 Ap 0 5 slater region Ry Ayn Rp AF 0 Ryn Ay basis set Slater potential Ry Ay Ry An smoothing region Ryn Ayn Rp Ap numerical Slater Rp A Rip At smoothing region 7 Alp 00 asymptotic Slater Note Ri Al lt RF AF Defaults Ry 7 Ay 0 5 Rp 10 A 0 5 Use correct b region and slater b region for the beta spin 304 CHAPTER 20 KEYWORDS IN THE CONTROL FILE Two component SCF GHF Self consistent two component calculations e g for spin orbit interactions can be carried out using the module ridft The following keywords are valid soghf enforces two component SCF calculations this option is combinable with rij rik and dft kramers switches on Kramers restricted formalism collinear switches on collinear two component formalism not rotational invariant gdiis enforces DIIS for complex Fock operator All electron relativistic approaches X2C BSS DKH Relativistic all electron calcula
41. or den sity generating step in case of programs dscf ridft rimp2 and mpgrad it is possible to directly jump to the routine performing analyses by typing lt program gt proper Currently the respective keywords have to be inserted in the control file by hand not by define Here we briefly present the functionalities i e the default use of keywords non default suboptions are described in detail in Section 20 2 21 235 236 CHAPTER 16 PROPERTIES AND ANALYSIS AND GRAPHICS Electrostatic moments up to quadrupole moments are calculated by default for the above modules Relativistic corrections mvd leads to calculation of relativistic corrections for the SCF total density in case of dscf and ridft for the SCF MP2 density in case of rimp2 and mpgrad and for that of the calculated excited state in case of egrad Quantities calculated are expectation values lt p gt lt pt gt and the Darwin term 9 1 Z4 p Ra Note that at least the Darwin term requires an accurate descrip tion of the cusp in the wave function thus the use of basis sets with uncontracted steep basis functions is recommended Moreover note that the results for these quantities are not too reasonable if ECPs are used a respective warning is written to the output Population analyses Population analyses are driven by the keyword pop Without any extension Mulliken population analyses MPA are carried out for all densities present in the respectiv
42. sweeps integer maximum number of orbital rotations to get LMOs default value is 10000 sometimes not enough in particular for highly delocalised sys tems thrcont real lower threshold for displaying MO and Mulliken contributions default 0 1 CAO LMOs are written to file in the CAO basis instead of AO pipmez Pipek Mezey localization is used esp_fit fits point charges at the positions of nuclei to electrostatic potential arising from electric charge distribution also possible for two component calculations for 360 CHAPTER 20 KEYWORDS IN THE CONTROL FILE UHF cases also for spin density For this purpose the real electrostatic potential is calculated at spherical shells of grid points around the atoms By default Bragg Slater radii rgs are taken as shell radii for each atom the number of points is given by 1000 Tag the total number of points is the sum of points for each atom reduced by the number of points of overlapping spheres Non default shells one or more can be specified as follows esp_fit shell i1 s1 shell i2 s2 Integer numbers 7 define the number of points for the respective shell real numbers s constants added to radii default corresponds to one shell with s 1 0 A parameterization very close to that by Kollman U C Singh P A Kollman J Comput Chem 5 2 129 145 1984 may be obtained by esp_fit kollman Here five shells are placed around each atom with r 1 4 ry qw k
43. the trace of the total shielding tensors its anisotropy and the CPHF contribution for each symmetry distinct atom are written into the control file after the keyword nmr lt rhf dft gt shielding constants This data group is write only for mpshift but you can utilize it for graphical render ing of the calculated NMR spectra and for a quick overview of the results A more detailed output with the complete shielding tensors can be found in the output of mpshift so it is recommended to put the output in a file when calling the program 15 3 How to Perform a MP2 calculation To perform an MP2 calculation of the NMR shieldings you have to prepare the input with mp2prep c mpshift will then calculate both the SCF and MP2 shielding constants The result is written into the control file after the keyword nmr mp2 shielding constants The script mp2prep will create the keywords csmp2 thize LOOOOOOOE 10 mointunit type intermed unit 61 size 0 file halfint type 1112 unit 63 size 0 file moint 1 type 1122 unit 64 size 0 file moint j type 1212 unit 65 size 0 file moint k type 1212a unit 70 size 0 file moint a type gamma 1 unit 71 size 0 file gamma t type gamma 2 unit 72 size 0 file gamma 2 type dtdb 1 unit 76 size 0 file dtdb 1 type dtdb 2 unit 77 size 0 file dtdb 2 traloop 1 statistics mpshift and starts a statistics run of mpshift by calling mpshift If the resulting disk space requirement exceeds the automatically detecte
44. thrmaxdispl threshold for maximal displacement element default 1 0d 3 350 CHAPTER 20 KEYWORDS IN THE CONTROL FILE thrmaxgrad threshold for maximal gradient element default 1 0d 3 thrrmsdispl threshold for RMS of displacement RMS root mean square default 5 0d 4 thrrmsgrad threshold for RMS of gradient default 5 0d 4 All values are in atomic units 20 2 20 Keywords for Module MOLOCH properties specifies the global tasks for program moloch by virtue of the following options properties trace off moments active potential off cowan griffin off localization off population analyses off plot off firstorder off fit off a missing option or a option followed by the flag off will not be taken into account The flag active may be omitted For most of these options with the only exceptions of trace and cowan griffin there are additional data groups allowing for more detailed specifications as explained below moments if moment is active you need moments Oth ist 2nd 3rd point 0 0 0 to compute the Oth 1st 2nd and 3rd moment at the reference point 0 0 0 potential if potential is active you need 20 2 FORMAT OF KEYWORDS AND COMMENTS 301 points 1 pot fld fldgrd shld point 0 0 0 to compute the electrostatic potential pot and or electrostatic field 1d and or electrostatic field gradient fldgrd and or the zeroth order contribu tion to the diamagnetic shielding shld at ref
45. with Ti J E and T2 dos j T Eivi with Eai and Faibj in the spin orbital basis They are printed in the summaries for excitation energies under the headings t1 and t2 For spin adapted excitation amplitudes 7 and 72 have to be computed from respective linear 10 2 CALCULATION OF EXCITATION ENERGIES 193 combinations for the amplitudes which reproduce the values in the spin orbital basis For ADC 2 which has a symmetric secular matrix with identical left and right normalized eigenvectors 7 and J2 are identical with the contributions from the singles and doubles parts for the eigenvectors to the trace of the occupied or virtual block of the orbital unrelaxed difference density between the ground and the excited state i e the criterium proposed in ref 12 Compared to the suggestion from ref 12 7i and 72 have the additional advantage of that they are for all methods guaranteed to be postive and can be evaluated with the same insignificantly low costs as T and T They are invariant with respect to unitary transformations of the occupied or the virtual orbitals and give by construction identical results in spin orbital and spin free calculations For CC2 and CIS D the diagnostics 7 and Tz agree for left and right eigenvectors usually with a few 0 01 for CIS D and ADC 2 they are exactly identical For singlet excitations in spin free calculations XT is typically by a factors of 1 5 2 larger than 7T gt The second order metho
46. 0 0 200000 18 2 Jenpleni entahiow e e 024244 24 Hh OA REED RSE eR Be 12 OEP EXA ate Ae ah eG we oe ee a ee eS 1a 2 DHE eree ok ce kk A a a A aE A ge TA 229 237 237 239 243 247 CONTENTS 9 Iso How to Forio e 6 6s eee a eR ROR Ae ae oe ee 252 18 4 How to plot the exchange potential 257 1S0 HOV OQUO e a e a el Be e e oe e a a e Sh ee 257 19 Treatment of Solvation Effects with Cosmo 258 20 Keywords in the control file 265 20 1 Inteoduction so ecs e cedri ou TERE E D E REE e ES 265 20 2 Format of Keywords and Comments oaoa ae 265 20 2 1 General Keywords aaau a 265 20 2 2 Keywords for System Specification 267 20 2 3 Keywords for redundant internal coordinates in redund_inp 269 20 2 4 Keywords for Module Uff aoaaa aaae 271 20 2 5 Keywords for woelfling euo sos 06 we po ee ee E oi 276 20 2 6 Keywords for Modules Dscf and Ridft 277 20 2 7 Keywords for Periodic Electrostatic Embedded Cluster Method 299 20 2 8 Keywords for Cosimo e eco s co bec r ike ed eee eee be 301 20 2 9 Keywords for Modules Grad and Rdgrad 307 20 2 10 Keywords for Module Aoforce 2 308 20 2 11 Keywords for Module evib 2 311 20 2 12 Keywords for Module Escf aaau a ald 20 2 13 GW Keywords 2 2 5 5 4 2b 5 ee bee ee Ea EROS 314 20 2 14 Keywords for Module rirpa 315 20 2 15 Keywords for Module Egrad 2 316
47. 000282 ENERGIES a u Total energy 76 0296831863 Total energy OC corr 76 0297567835 Dielectric energy 0 0118029468 Diel energy OC corr 0 0118765440 The following value is included for downward compatibility Total energy corrected 76 0297199849 The dielectric energy of the system is already included in the total energy OC corr denotes the outlying charge correction The last energy entry gives the total out lying charge corrected energy in the old definition used in TURBOMOLE 5 7 and older versions The Cosmo result file which contains the segment information energies and settings can be set using cosmo_out file filename cosmo 310 CHAPTER 20 KEYWORDS IN THE CONTROL FILE Isodensity Cavity This option can be used in HF DFT single point calculations only The cosmo_isodens section defines the settings for the density based cavity setup see also chapter 19 If the cosmo_isodens keyword is given without sub options a scaled iosodensity cavity with default settings will be created Possible options are cosmo_isodens activates the density based cavity setup The default values of nspa and nsph are changed to 162 and 92 respectively This values are superseded by the user defined nspa value of the cosmo section By default the scaled density method is used The atom type dependent density values are read from the radii cosmo file located in TURBODIR parameter dx real spacing of the marchi
48. 1 ricctools ntos CCREO 2 1 1 The results for the occupied and virtual NTOs will be stored in files named re spectively ntos_occ and ntos_vir Note that the NTO analysis ignores for the correlated methods CIS D ADC 2 CC2 CCSD etc the double excitation con tributions and correlation contributions to the ground state This is no problem for single excitation dominated transition out of a good single reference ground state in particular if only a qualitative picture is wanted but one has to be aware of these omission when using NTOs for states with large double excitation contributions or when they are used for quantitative comparisons Fit of charges due to the electrostatic potential esp_fit fits point charges at the positions of nuclei to electrostatic potential arising from electric charge dis tribution for UHF cases also for spin density also possible in combination with soghf For this purpose the real electrostatic potential is calculated at spher ical shells of grid points around the atoms By default Bragg Slater radii rgs are taken as shell radii A parametrization very close to that suggested by Kollman a multiple shell model with shells of radii ranging from 1 4 r gw to 2 0 r aw Tvaw is the van der Waals radius U C Singh P A Kollman J Comput Chem 5 2 129 145 1984 is used if the keyword is extended esp_fit kolman 238 CHAPTER 16 PROPERTIES AND ANALYSIS AND GRAPHICS 16 2 Inte
49. 17 5 EPPE pa B Tslha Ts o TS a Ba Veat A B J 6a fp Exclpa pa 17 6 Note that this energy differs from the KS total energy of the total system due to the approximation in Eq 17 4 as well as the approximated kinetic potential see Eq 17 5 which lead to approximated embedded densities 64 pa and pp pg With the current state of the art GGA kinetic approximations the error in the binding energy for weakly interacting systems is close to chemical accuracy Using the Generalized Kohn Sham GKS theory also hybrid exchange correlation functionals can be used in embedding calculations To obtain a practical computa tional method the obtained embedding potential must be approximated by a local expression as shown in Ref 163 This corresponds to performing for each subsys tem hybrid calculations including the interaction with other subsystems through an embedding potential derived at a semilocal level of theory When orbital dependent exchange correlation functionals e g hybrid functional and LHF are considered within the FDE method the embedding potential includes a non additive exchange correlation term of the form Eze p4 pB Excl pa ppl Evel 4 p Excl PB 17 7 where 64 p 4 pp denotes the Slater determinant which yields the total density pa ppg Since such a determinant is not easily available the non additive exchange 17 2 FROZEN DENSITY EMBEDDING CALCULATIO
50. 212 235 237 239 307 325 327 337 346 RIDFT keywords 283 Ridft 299 ridft 14 23 24 34 35 37 40 42 44 46 67 TT 78 98 117 123 125 127 139 141 149 156 157 165 170 171 184 185 199 209 219 222 232 230 236 238 209 241 256 267 268 273 299 300 304 305 307 311 313 353 355 373 375 RIMP2 keywords 322 434 rimp2 23 24 36 38 62 63 80 98 104 117 166 167 169 170 173 174 182 235 236 238 323 325 328 346 353 355 Rimp2prep 35 170 325 326 rimp2prep 36 rirpa 25 217 219 222 223 321 Roothaan parameters 71 rpagrad 221 222 rpaprof 223 scanprep 27 screwer 27 102 scs 178 206 330 SCS ADC 2 23 SCS CC2 23 SCS MP2 205 sdg 28 Simulated Annealing 369 SMP 44 sos 206 SOS ADC 2 23 SOS CC2 23 SOS MP2 205 SOS RI MP2 45 fourth order scaling 179 spectra Raman 227 spin flipping spins on atoms 68 Stati 125 stati 28 STATPT keywords 348 statpt 24 38 78 97 99 101 116 119 steepest descent 102 STOP 98 stop 98 structure library 53 INDEX structure optimization 97 substitution 53 Sysname 30 400 401 sysname 28 30 t2x 28 238 Tblist 401 tblist 28 Tbtim 401 tbtim 28 temperature 368 time 115 364 timestep 364 tm2aomix 28 tm2molden 28 238 Tors 26 tors 28 transformation Laplace 179 TTEST 399 400 402 TURBOMOLE 11 13 15 19 25 26 28 30 33 35 41 44 47 49 52 62 64 66 74 75
51. 395 n def SV P n 7s4pid 3s2p1d 511 31 1 use expopt to optimize exponents and contopt to optimize contractions 5 s expopt contopt 1712 8415853 0 53934125305E 02 257 64812677 0 40221581118E 01 58 458245853 0 17931144990 16 198367905 0 46376317823 5 0052600809 0 44171422662 1 s expopt 0 58731856571 1 0000000000 1 s expopt 0 18764592253 1 0000000000 3 p expopt contopt 13 571470233 0 40072398852E 01 2 9257372874 0 21807045028 0 79927750754 0 51294466049 1 p expopt 0 21954348034 1 0000000000 1d 1 0000000000 1 0000000000 File mos scfmo scfconv 10 format 4d20 14 SCF energy is 54 3329250250 a u virial theorem 2 000000001 1 alg eigenvalue 15623888057347D 02 nsaos 3 99166890864040D 00 28420294406651D 010 91519592317893D 02 2 alg eigenvalue 92524548524703D 00 nsaos 3 0 305068697 15453D 00 65051761026701D 00 44610487551870D 00 3 alg eigenvalue 0 74881229854801D 00 nsaos 3 0 30759302935434D 00 16295969601691D 010 16126161147521D 01 1 tiu eigenvalue 56865046629517D 00 nsaos 2 0 67926397018841D 000 46005039868410D 00 2 tiu eigenvalue 0 96169069264790D 00 nsaos 2 95675659621171D 000 10794148212163D 01 end 396 CHAPTER 21 SAMPLE CONTROL FILES 21 6 ROHF of Two Open Shells Extracts from control for O2 in D3 Symmetry HF SCF SVP Reference triplet sigma in D3d This is a Roothaan case as is D infinity h coord 0 0 0 0 1 08597397921317 o 0 0 0 0
52. 5I 5 51 4 combined method BFGS DFP If S1 lt S 1 S1 and 1 gt 0 perform DFP update otherwise BFGS The meaning of the symbols above is as follows PS A approximate inverse force constant matrix in the k th iteration s q general coordinates in the k th iteration GF gradients in the k th iteration dq gt gt dgk 1 gk gk Zk 1 dgk 1 FR 1ggk 1 S1 dg 1 tdgk S 1 dg t Fe laG 1 An alternative is to use update algorithms for the hessian H itself Ehrig Ahlrichs Diagonal update for the hessian by means of a least squares fit HE HE h di with the new estimate h for the diagonal elements obtained by _ Ek dG dq Die da and the error d obtained by the regression i 106 CHAPTER 5 STRUCTURE OPTIMIZATIONS Another alternative is to use DIIS like methods structure optimization by direct inversion in the iterative subspace See ref 33 for the description of the algorithm The DUS procedure can often be applied with good success using static or updated force constant matrices Any of the algorithms mentioned above may be chosen Recommended is the macro option ahlrichs which leads to the following actions n is the maximum number of structures to be included for the update default is n 4 ncycles lt n geometry update by inter extrapolation using the last 2 geometries ncycles gt n diagonal update for the hessian as described above
53. 7045760975 2 3508376809 1 s 44605124672 1 s 16848856190 5 p 307 66790569 72 102015515 22 532680262 7 8991765444 2 8767268321 1 p 77459363955 1 p 21037699698 1 d 65000000000 ecp ta def ecp ncore 60 coefficient 12 0179609 42959071631 43497228232 1 0000000000 19708362484E 02 14754727977E 01 66679112875E 01 17228924084 15883786100 10009298909 60841752753 54352153355 1 0000000000 1 0000000000 87801484118E 02 63563355471E 01 24016428276 47798866557 38515850005 1 0000000000 1 0000000000 1 0000000000 211111 41 3 exponent 2 0178811 389 390 s f 1345 36 12 p f 378 22 12 d f 104 8 12 end 8806470 7668062 0179609 4253015 2930909 0179609 8839557 7558481 0179609 File auxbasis jbas ta def SVP 3 s 15 52133 7 555743 3 699576 1 s 1 820141 1 s 0 898838 1 s 0 445062 1 s 0 220729 1 s 0 109530 1 p 1 502495 1 p 0 562985 1 p 0 228188 1 p 0 095078 5 8 5 0 35 1 ale di 1 CHAPTER 21 14 5464077 7 2732038 2 0178811 9 9355653 4 9677824 2 0178811 6 3473769 3 1736885 2 0178811 493702989D 00 259256574D 01 523168657D 01 262393615D 01 157711902D 01 200789711D 00 185974307D 00 765184411D 01 SAMPLE CONTROL FILES 21 4 TACLs INPUT FOR AN RI DFT CALCULATION WITH ECPS
54. An arbitrary combination of them can lead to very good total energy i e very close to the 18 3 HOW TO PERFORM 259 Hartree Fock one but unphysical OEP potential In the present release we strongly recommend to use the d aug cc pVTZ oep basis set and the corresponding auxiliary basis set directory xbasen The following options can modify the quality time and output of an OEP calculation All the options can be set by define Every option has a reasonable default value so the user does not need to select any of the options below to run a proper OEP calculation oep options Listing of all possible options for the flag oep charge vector integer The Charge condition expansion coefficients in auxiliary basis set repre sentation can be calculated in different kinds The selection of integer 1 will use the following ansatz to calculate the coefficients r r CP Niy Gp if Cag a 0 if Gp 0 Gp is the integral over a normalized Gaussian auxiliary basis function N x is the number of auxiliary basis functions with Gp 0 The selection of integer 2 will use the following ansatz to calculate the coefficients i CP P 0 if Gp 0 The variable integer must have an integer value The default value is 2 condition string2 string In the OEP method two constraints can be applied in the OEP equation This is the HOMO condition and the Charge condition The variable string can have the values none HOMO Charge
55. Contracted Gaussian Basis Sets for Atoms Li to Kr A Schafer H Horn and R Ahlrichs J Chem Phys 97 2571 1992 b Fully Optimized Contracted Gaussian Basis Sets of Triple Zeta Valence Quality for Atoms Li to Kr A Schafer C Huber and R Ahlrichs J Chem Phys 100 5829 1994 c Auxiliary Basis Sets to Approximate Coulomb Potentials K Eichkorn O Treut ler H Ohm M Haser and R Ahlrichs Chem Phys Letters 242 652 1995 d Auxiliary basis sets for main row atoms and transition metals and their use to approximate Coulomb potentials K Eichkorn F Weigend O Treutler and R Ahlrichs Theor Chem Acc 97 119 1997 e Accurate Coulomb fitting basis sets for H to Rn F Weigend Phys Chem Chem Phys 8 1057 2006 f RI MP2 Optimized Auxiliary Basis Sets and Demonstration of Efficiency F Weigend M Haser H Patzelt and R Ahlrichs Chem Phys Letters 294 143 1998 g Contracted all electron Gaussian basis sets for Rb to Xe R Ahlrichs and K May Phys Chem Chem Phys 2 943 2000 h Efficient use of the correlation consistent basis sets in resolution of the identity MP2 calculations F Weigend A K hn and C Hattig J Chem Phys 116 3175 2002 i Gaussian basis sets of quadruple zeta valence quality for atoms H Kr F Weigend F Furche and R Ahlrichs J Chem Phys 119 12753 2003 j Balanced basis sets of split valence triple zeta valence and quadruple zeta va lence
56. DIIS like update for the geometry G lt thr BFGS type update of the hessian and quasi Newton update of gener alized coordinates References for the algorithms mentioned above 30 33 37 5 3 4 Definition of Internal Coordinates If structure optimizations are to be performed in the space of internal coordinates optimize internal is the default setting appropriate internal coordinate defi nitions have to be provided on data block intdef The types available and their definitions are described in Section 4 1 2 For recommendations about the choice of internal coordinates consult ref 24 Nevertheless the structure of intdef will shortly be described The syntax is in free format 1 k 1 00000000 bend 1 2 3 val 1 9500 fdiag 6666 The first items have been explained in Chapter 4 Two additional items val real fdiag real may be supplied for special purposes val serves for the input of values for internal coordinates for the intercon version internal gt cartesian coordinates it will be read in by relax if the flag for interconversion of coordinates has been activated interconversion on or by the interactive input program define within the geometry spec ification menu fdiag serves for the input of diagonal force constants for the individual in ternal coordinates to initialize forceapprox 5 3 5 Structure Optimizations Using Internal Coordinates This is the default task of relax optimize interna
57. Hartree Fock and density functional methods Markus K Armbruster Florian Weigend Christoph van W llen Wim Klopper Phys Chem Chem Phys 10 1748 1756 2008 Quintuple quality coupled cluster correlation energies with triple basis sets David P Tew Wim Klopper Christian Neiss Christof Hattig Phys Chem Chem Phys 9 921 1930 2007 Benchmarking the performance of spin component scaled CC2 in ground and electronically excited states Arnim Hellweg Sarah A Griin Christof Hattig Phys Chem Chem Phys 10 4119 4127 2008 Scaled opposite spin CC2 for ground and excited states with fourth order scaling computational costs Nina O C Winter Christof Hattig J Chem Phys 134 184101 2011 and Quartic scaling analytical gradients of scaled opposite spin CC2 Nina O C Winter Christof Hattig Chem Phys 401 2012 217 The MP2 F12 Method in the TURBOMOLE Programm Package Rafal A Bachorz Florian A Bischoff Andreas Glo Christof Hattig Sebastian H6fener Wim Klopper David P Tew J Comput Chem 32 2492 2513 2011 Accurate and efficient approximations to explicitly correlated coupled cluster singles and doubles CCSD F12 Christof Hattig David P Tew Andreas K hn J Chem Phys 132 231102 2010 Large scale polarizability calculations using the approximate coupled cluster model CC2 and MP2 combined with the resolution of the identity approxima tion Daniel H Friese Nina O C Winter Patr
58. He Li Ne Na Ar K Ca Ga Kr cc pV6Z only for H He B Ne Al Ar for Al Ar also the recom mended newer cc pV X d Z sets are available cc pwCVXZ PP weighted core valence x tuple zeta basis sets X D T Q 5 are available for post d main group elements Ga Kr In Xe and Tl Rn also pure valence basis sets cc pVXZ PP are available for these ele ments but it is not recommended to use them cc pwCVXZ_ weighted core valence X tuple zeta basis sets X D T Q 5 avail able for H He B Ne Al Ar and Ga Kr for Al Ar also the recommended combination of the cc pV X d Z sets with the core valence functions wC i e the cc pwCV X d Z basis set are available aug diffuse functions for combination with the basis sets cc pVXZ cc pV X 4d Z cc pwCVXZ cc pV X d Z cc pVXZ PP or cc pwCV XZ PP available for H He B Ne Al Ar with X D 6 and Ga Kr In Xe and Tl Rn with X D 5 cce pVXZ F12 with X D T Q for use with the explicitly correlated F12 variants of wavefunction methods MP2 F12 CCSD F12 etc For calculations with the programs rimp2 and ricc2 optimized auxiliary basis sets are available for most of the correlation consistent basis set series 4 2 1 Description of the commands b With b you can specify basis sets for all atoms in your molecule After entering b you will be asked to specify the atoms to which you want to assign basis sets You can do this in the usual ways refer to Sec tion 4 0 4
59. Input for an RI DFT Calculation with ECPs Main File control title operating system unix symmetry d3h coord file coord intdef file coord atoms ta 1 jbas ta def SVP basis ta def SVP ecp ta def ecp cl 2 6 jbas cl def SVP basis cl def SVP pople AO basis file basis ecp file basis rundimensions dim fock dens 7662 natoms 6 nshell 51 nbf CAO 122 nbf AQ 115 dim trafo SA0 lt gt A0 CAO 346 scfmo none file mos none hamilton core guess will be made file mos will be generated by the program scfiterlimit 30 scfconv 6 thize LOOOOO00E 04 thime 5 scfdamp start 900 step 050 min 100 scfdump scfintunit unit 30 size 0 file twoint scfdiis start 0 5 drvopt cartesian on basis off global off 21 4 TACLs INPUT FOR AN RI DFT CALCULATION WITH ECPS 387 hessian on dipole on nuclear polarizability interconversion off qconv 1 d 10 maxiter 25 optimize internal on cartesian off global off basis off logarithm coordinateupdate dqmax 0 3 interpolate on statistics 5 forceupdate ahlrichs numgeo 0 mingeo 3 maxgeo 4 modus lt g dq gt dynamic fail 0 1 threig 0 005 reseig 0 005 thrbig 3 0 scale 1 00 damping 0 0 forceinit on diag default energy file energy grad file grad forceapprox file force lock off dft functional b p gridsize m3 last step define ricore 20 ridft jbas file auxbasis closed shells al 1 11 2 a2 1 2
60. J sp K sp ttyp 11 like ttyp 1 but one or both atoms are in Group 16 ttyp 2 J sp K sp or vice versa ttyp 21 like ttyp 2 but one or both atoms are in Group 16 ttyp 22 like ttyp 2 but J or K is next a sp atom ttyp 3 J sp K sp ttyp 9 all other cases is the value of the torsion angle in degree 677 is the angle value of I J K and j xK 1 is the cwone for J K L The hybridizations of J and K determine ttyp 20 2 FORMAT OF KEYWORDS AND COMMENTS 281 The inversion terms follow starting with the number of inversion terms e g the pyramidalisation of NH3 In each line is one inversion term I J K L itypl ityp2 ityp3 Wy we w3 I J K and L are the atom numbers Atom J is the central one itypl ityp2 ityp3 are the types of the inversions ityp 10 atom I is C and atom L is O ityp 11 like ityp 10 but L is any atom ityp 2 Lis P ityp 3 I is As ityp 4 I is Sb ityp 5 I is Bi ityp 9 all other cases w1 w2 and w3 are the values of the inversion angles in degree The nonbond terms follow starting with the number of the non bonded terms In each line is one nonbond term I J d Here I and J are the atom numbers d the distance in a u Then the partial charges follow If the determination of the molecule connectivity failed you can specify the block nxtneil2 in the file ufftopology Then the program calculates the other blocks Based on the nu
61. KEYWORDS AND COMMENTS 291 since e are not available The keyword prediag provides e of the zeroth iteration by diagonalization of occ occ and virt virt part of the first Fock matrix to allow for level shifting etc See scfdiis below restart dscf twoint Try a dscf restart The program will read the data group restartd which must exist also scfmo has to exist and continue the calculation at the point where it ended before If the additional option twoint is appended the program will read the two electron integrals from the files specified in scfintunit so there will be almost no loss of cpu time All this information is normally provided by the previous dscf run if the key word scfdump see there was given restartd data Data provided by a previous dscf run that has been interrupted This keyword is created when scfdump was given rundimensions data is set by define so usually no changes are necessary The dimensions must be greater or equal to those actually required i e you can delete basis functions and keep rundimensions This keyword is not necessary for small cases Example dim fock dens 6072 natoms 6 nshel1 34 nbf CA0 108 nbf A0 98 dim trafo SAO lt gt A0 CAO 256 rhfshells 1 scfconv integer SCF convergency criterion will be 107 9 for the energy Gradients will only be evaluated if integer gt 6 scfdamp start lt 500 gt step lt 050 gt min lt 100 gt
62. NL in a non self consistent way just add donl to the control file For a self consistent treatment of the dispersion correction add doscnl instead Note that dispersion corrections of DFT DN and NL DFT type must not be combined The grid size for the non local integration is set automatically by adapting the grid for the quadrature of the functional evaluation Currently only C1 symmetry and serial jobs are possible DF T NL is an interesting scientific alternative to DFT D3 but we recommend to use DFT D3 for applications instead Chapter 7 Hartree Fock and DFT Response Calculations Stability Dynamic Response Properties and Excited States 7 1 Functionalities of ESCF and EGRAD escf and egrad are designed as efficient tools for response and excited state calcu lations on large molecules escf serves to compute the following properties for HF and KS reference states e Eigenvalues of the electronic Hessian stability analysis e Frequency dependent polarizabilities and optical rotations e Vertical electronic excitation energies e Transition moments oscillator and rotatory strengths of electronic excitations UV VIS and CD spectra Spin restricted closed shell and spin unrestricted ground states except for stabil ity analysis are supported The RI J approximation in conjunction with LDA GGA and meta GGA MGGA functionals is implemented for all properties Exci tation energies and transition moments can be compu
63. OPTION OR q TO QUIT 80 CHAPTER 4 PREPARING YOUR INPUT FILE WITH DEFINE If you have selected an option e g rpas and quit this menu you will get another menu SELECT IRREP AND NUMBER OF STATES ENTER FOR HELP OR Q TO QUIT amp TO GO BACK This should be self evident MP2 and RI MP2 We recommend to use MP2 together with the RI technique program rimp2 or ricc2 This is more efficient and supports the frozen core option in the gradient calculation The entry mp2 leads to a submenu which allows to set some keywords for MP2 and RI MP2 calculations e g defining frozen orbitals maximum memory usage or as sign auxiliary basis sets for RI MP2 calculations etc If you want to use ricc2 you have to use the entry cc2 and the submenu ricc2 in order to assign MP2 as wave function model It covers all keywords required for rimp2 calculations Mandatory for rimp2 runs is the specification of the auxiliary basis set using the menu entry cbas Alternatively the rimp2prep tool can be used to set the keywords needed for rimp2 calculations Conventional MP2 calculations with mpgrad require a number of additional settings for which it is recommended to invoke the interactive tool mp2prep For geometry optimizations with jobex use nohup jobex level mp2 ri CC2 calculations The entry cc2 leads to a submenu which allows to set a number of keywords essential for calculations with the program ricc2 In particular it allows the as
64. Specification of position and magnitude of point charges to be included in the Hamiltonian Each point charge is defined in the format lt x gt lt y gt lt z gt lt q gt with lt x gt lt y gt lt z gt being the coordinates and lt q gt its charge e g point_charges thr lt real gt selfenergy nocheck list 2 2 2 Bs 5 0 0 2 5 In addition the following optional arguments may be given thr real distance threshold for discarding redundant point charges default value 1076 selfenergy if given the selfenergy of the point charge array will will be included in the energy and the gradient nocheck switches off the check for redundant point charges and the default sym metrization This option can significantly speed up the point charge treatment if many of them are involved use only if the point charges are well distributed and symmetry is C e g when they stem from proper MM runs list print all point charges in the output default is to print the point charges only if less than 100 charges given prediag concerns the first SCF iteration cycle if start MOs from an EHT guess are used The SCF iteration procedure requires control mechanisms to ensure fast con vergence in TURBOMOLE these are based on orbital energies e of the preceeding iteration used for level shifting and damping besides DIIS see below This feature cannot be used in the first iteration if EHT MOs are employed as start 20 2 FORMAT OF
65. Start Vectors 4 3 1 The MO Start Vectors Menu This menu serves to define the occupation numbers and to generate the start vectors for HF SCF and DFT calculations They may be constructed from earlier SCF calculations perhaps employing another basis set type use by Hamilton core guess hcore or by an extended H ckel calculation which can be performed automatically eht An occupation of the start orbitals will be proposed and can be modified if desired OCCUPATION NUMBER amp MOLECULAR ORBITAL DEFINITION MENU CHOOSE COMMAND infsao OUTPUT SAO INFORMATION atb Switch for writing MOs in ASCII or binary format eht PROVIDE MOS amp amp OCCUPATION NUMBERS FROM EXTENDED HUECKEL GUESS use lt file gt SUPPLY MO INFORMATION USING DATA FROM lt file gt man MANUAL SPECIFICATION OF OCCUPATION NUMBERS hcore HAMILTON CORE GUESS FOR MOS flip FLIP SPIN OF A SELECTED ATOM amp MOVE BACK TO THE ATOMIC ATTRIBUTES MENU THE COMMANDS use OR eht OR OR q uit TERMINATE THIS MENU FOR EXPLANATIONS APPEND A QUESTION MARK TO ANY COMMAND 66 CHAPTER 4 PREPARING YOUR INPUT FILE WITH DEFINE Recommendation You will normally only need to enter eht For the EHT guess define will ask for some specifications and you should always choose the default i e just lt enter gt Of importance is only the molecular charge specified as 0 neutral default 1 or 1 etc Based on the EHT orbital energies define proposes an
66. T e Vrele Jlo Erlo Eclo Vnuc 6 2 where T p is the kinetic energy Vne p is the nuclei electron interaction E p and E p are the exchange and correlation energy functionals The exchange and correlation functionals normally used in DFT are integrals of some function of the density and possibly the density gradient In addition to pure DFT methods dscf and grad modules support hybrid functionals in which the exchange functional includes the Hartree Fock exchange e g B3 LYP 6 2 Exchange Correlation Functionals Available The following exchange correlation functionals are available e LDAs S VWN PWLDA e GGAs B VWN B LYP B P PBE e MGGA TPSS M06 using XCFun e hybrid functionals BH LYP B3 LYP PBE0 TPSSh M06 2X using XCfun e double hybrid functional B2 PLYP energy calculations only For EXX and LHF see Chapter 18 The XCFun library Arbitrary Order Exchange Correlation Functional Library by Ulf Ekstr m and co workers has been included 55 and some of the functionals implemented there can now be utilized Among them are the empirically fitted MGGAs M06 and M06 2X from the Truhlar group 56 XCFun functionals are available for energy gradient vib frequencies and TDDFT excited state energy calculations with and without RI approximation For details and the license of XCFun please refer to its web site https repo ctcc no projects xcfun wiki In detail the Turbomole own functional library
67. The amount of stored integrals is controlled by simply specifying the amount of free memory using the keyword ricore e Multipole accelerated RI for Coulomb MARI J linear scaling O V method for large molecules It significantly reduces calculation times for molecules with more than 1000 basis functions All algorithms implemented in dscf grad ridft and rdgrad modules can exploit molecular symmetry for all finite point groups Typically the CPU time is pro portional to 1 Ng where Ng is the order of the nuclear exchange group Another important feature is a parallel implementation using the MPI interface Additionally dscf and ridft modules include the following common features e An UHF implementation 52 with automatic generation of optimal start vec tors by solving the HF instability equations 53 in the AO basis see the key word scfinstab for detailed information e Occupation number optimization using pseudo Fermi thermal smearing RI techniques can also be used for the Hartree Fock exchange part of the Fock matrix RI HF This is done by the ridft module if the keyword rik is found in the control file In this case ridft performs a Hartree Fock SCF calculation using the RI approximation for both J and K if suitable auxiliary basis sets which differ from that used for fitting of the Coulomb part only are specified This is efficient only for comparably large basis sets like TZVPP cc pVTZ and larger HF e
68. Theory Comput 0 just accepted DOI 10 1021 ct4008553 0 BIBLIOGRAPHY 417 147 148 149 150 151 152 153 154 155 156 157 158 M K hn Correlation Energies from the Two component Ran dom Phase Approximation J Chem Theory Comput Page http pubs acs org doi abs 10 1021 ct400994x 2014 F Furche Molecular tests of the random phase approximation to the exchange correlation energy functional Phys Rev B 64 195120 2001 F Furche Developing the random phase approximation into a practical post Kohn Sham correlation model J Chem Phys 129 114105 2008 P Deglmann F Furche R Ahlrichs An efficient implementation of sec ond analytical derivatives for density functional methods Chem Phys Lett 362 5 6 511 518 2002 P Deglmann F Furche Efficient characterization of stationary points on potential energy surfaces J Chem Phys 117 21 9535 9538 2002 M H ser R Ahlrichs H P Baron P Weis H Horn Direct computation of second order SCF properties of large molecules on workstation computers with an application to large carbon clusters Theor Chim Acta 83 5 6 455 470 1992 T Ziegler G Schreckenbach Calculation of NMR shielding tensors using gauge including atomic orbitals and modern density functional theory J Phys Chem 99 2 606 611 1995 A E Reed R B Weinstock F Weinhold Natural population anal
69. XVI XVI RIJK ridft XX NMR chemical shifts mpshift IX MP2 parallel DFT ridft X geometry optimization in redundant internal coordinates relax XI RI integral evaluation XXV explicitly correlated F12 methods for ground state energies ricc2 MP2 F12 XXXIV MP3 F12 XXXV MP4 F12 XXXV CCSD F12 XXXI CCSD F12 XXXV CCSD F12 T XXXI CCSD F12 T XXXV e Orbital and auxiliary basis sets basis sets 1 3 HOW TO QUOTE USAGE OF TURBOMOLE 15 SV SV P SVP DZ a TZV TZVP TZVPP b TZVPP Rb Hg f QZV QZVP QZVPP i new balanced basis sets with smaller ECPs i e the def2 basis sets j x all electron basis sets for Rb to Xe SVPall SVPPall TZVPall TZVP Pall g references for the correlation consistent basis sets cc pV XZ etc can be found e g at http tyr0O chem wsu edu kipeters Pages cc_append html or http www emsl pnl gov forms basisform html Note that most of the correlation consistent basis sets in the basis set library of TURBOMOLE have been downloaded from the latter EMSL web site and therefore users are requested to include in addition to the original scientific reference an appropriate citation see web site in any publications resulting from the use of these basis sets property optimized augmentations def2 SVPD def2 TZVPD def2 TZVPPD def2 QZVPD def2 QZVPPD n basis sets for Dirac Fock ECPs i e the dhf basis sets o
70. Yalu Pa H is the projector onto the virtual spin orbitals The F12 correction is obtained by minimizing the functional Fro gt c Bijciz 2c vij 9 5 i lt j with respect to the amplitudes collected in the vector c The vectors v and the matrices B are defined as vij kl kl fi2Qi2rj9 lij 9 6 Bij kl mn kl fi2 i fo ci Qi2fi2 mn in the spin orbital formalism m n denote spin orbitals and mn is a two electron determinant f is the Fock operator for electron u and ex is a semi canonical Hartree Fock orbital energy A MP2 F12 calculation is defined through a number of choices concerning the nature of the geminals fiz and Q12 the geminal excitation space ijkl or ijij and approxi mations in computing the B matrix GBC EBC f12 These choices correspond to keywords in the rir12 data group explained below To run a MP2 F12 calculation one has to select the auxiliary basis sets cbas cabs and optionally jkbas The ricc2 program uses the robust fitting techniques of Ref 110 for the F12 integrals and the cbas basis is used for both the F12 and the usual MP2 Coulomb integrals For the density fitting of the Coulomb and exchange matrices of the Fock matrix the jkbas will be used instead of the cbas basis if it is included in the control file this is recommended and is achieved using the rijk menu in define For the RI approximation of the 3 and 4 electron integrals as
71. advantageous to consider a fully variational Lagrangian of the excited state energy 20 L X Y C Z W Ecs X Y A X Y 0 X YIAIX Y 1 ia pq Here Egs denotes the ground state energy F and S are the Fock and overlap ma trices respectively and indices p q run over all occupied and virtual MOs First L is made stationary with respect to all its parameters The additional La grange multipliers Z and W enforce that the MOs satisfy the ground state HF KS equations and are orthonormal Z is the so called Z vector while W turns out to be the excited state energy weighted density matrix Computation of Z and W requires the solution of a single static TDHF TDKS response equation 7 4 also called coupled and perturbed HF KS equation Once the relaxed densities have been computed excited state properties are obtained by simple contraction with deriva tive integrals in the atomic orbital AO basis Thus computation of excited state gradients is more expensive than that of ground state gradients only by a constant factor which is usually in the range of 1 4 TDHF TDDFT expressions for components of the frequency dependent polarizabil ity _g w can also be reformulated as variational polarizability Lagrangians 100 LP Xa Ya X6 Yo C ZP WP w Xa Ya A wA Xg Yo Xa Yalup ual Xp Ya B ga 5 Zito Tiao 7 5 W o pq tao PqO PSq 7 13 7 3 IMPLEMENTATION 155 The stationary point of L w
72. aibj aibjTaibj ALE augmented with double excitations into the explicitly correlated pairfunctions geminals which are described in Sec 9 5 T T To To 11 12 1 kl Ty 5 2 Cf rity 11 13 ijkl where Tkujlij Qiefi2 kl for the defintion Qi and fiz see Sec 9 5 This en hances dramatically the basis set convergence of CCSD calculations 134 Without any further approximations than those needed for evaluating the neccessary matrix elements this extension of the cluster operator T leads to the CCSD F12 method CCSD F12 is an approximation 134 135 to CCSD F12 which neglects certain computationally demanding higher order contributions of Ty This reduces the com putational costs dramatically while the accuracy of CCSD F12 is essentially identi cal to that of CCSD F12 136 137 In the CCSD F12 approximation the amplitudes are determined from the equations Qu val H T2 Tp HF 0 11 14 Qu m H T2 To H T2 2T T2 HF 0 11 15 Quy He F Ty H T2 HF 0 11 16 Similar as for MP2 F 12 also for CCSD F12 the coefficients for the doubles excita tions into the geminals ch using the rational generator also known as SP or fixed amplitude approach In this can be determined from the electronic cusp conditions case Eq 11 16 is not solved To account for this the energy is then computed from a Lagrange function as Eccsp F12 sp Locsp riz HF H CC
73. algorithm for self consistent field linear response theory and application to Ceo Excitation energies oscillator BIBLIOGRAPHY 413 99 100 101 102 103 104 105 106 107 108 109 strengths and frequency dependent polarizabilities J Chem Phys 99 2 1262 1270 1993 M K hn F Weigend Implementation of Two component Time Dependent Density Functional Theory in TURBOMOLE J Chem Theory Comput 9 5341 5348 2013 D Rappoport F Furche Lagrangian approach to molecular vibrational raman intensities using time dependent hybrid density functional theory J Chem Phys 126 20 201104 2007 F Furche Dichtefunktionalmethoden f r elektronisch angeregte Molek le Theorie Implementierung Anwendung PhD thesis Universit t Karlsruhe 2002 E R Davidson The iterative calculation of a few of the lowest eigenvalues and corresponding eigenvectors of large real symmetric matrices J Comp Phys 17 1 87 94 1975 F Wang T Ziegler Time dependent density functional theory based on a noncollinear formulation of the exchange correlation potential J Chem Phys 121 24 12191 12196 2004 M K hn F Weigend Phosphorescence energies of organic light emitting diodes from spin flip Tamm Dancoff approximation time dependent density functional theory Chem Phys Chem 12 3331 3336 2011 M J van Setten F Weigend F Evers The gw method for quantum ch
74. an exact two component X2C one It was developed by many groups starting with formal work in the mid 1980s X2C is related to the step wise Douglas Kroll Hess DKH approach which also achieves exact decoupling but sequentially The number of transformation steps is called the order of DKH X2C is also related to the Barysz Sadlej Snijders BSS method that first applies the free particle Foldy Wouthuysen transformation which is the first mandatory step in DKH and then constructs the one step exact decoupling trans formation of X2C These three approaches have been reviewed and directly compared in terms of formalism and results respectively in Ref 74 see also this reference for a complete bibliography on exact decoupling methods Essentially X2C methods change the one electron Hamiltonian in basis set repre sentation The Schriddinger one electron Hamiltonian including the external po tential of the atomic nuclei is replaced by the transformed upper left block of the Dirac Hamiltonian Since the transformation is carried out in the fully decontracted primitive basis all matrix operations needed for the generation of the relativistic one electron Hamiltonian can be cumbersome and even prohibitive if the size of the molecule is large In order to solve this unfavorable scaling problem a rigor ous local approach called DLU has been devised 75 and should be activated for large molecules However since the local atomic structur
75. analysis only analysis only to read a complete Hessian from the input file hessian and perform only the frequency analysis analysis only intcoord print printlevel to perform an analysis of normal modes in terms of internal coordinates Details about this option and the effect of the printlevel default is 0 are given in Section 13 The effect of the keyword only is the same as described above maxcor 50 fixes the RAM memory to be used by the run here 50 MB about 70 of available memory should be fine because maxcor specifies only the memory used to store derivatives of density and Fock matrices as well as the CPHF RHS Default is 200 MB 20 2 FORMAT OF KEYWORDS AND COMMENTS 315 forceconv 7 sets the convergence criterion for the CPHF equations to a residual norm of 1 0d 7 Normally the default value of 1 0d 5 already provides an accuracy of vibrational frequencies of 0 01 cm with respect to the values obtained for the convergence limit forceiterlimit 10 fixes the maximum number of Davidson iterations for the solution of the CPHF equations to a value of ten Normal calculations should not need more than eight iterations but as a precaution the default value is 25 nosalc forces the program in case of molecules with C1 symmetry not to use 3N 6 5 symmetry adapted but all 3N cartesian nuclear displacement vectors This option may lead to a moderate speed up for molecules notedly larger than 1000 basis fun
76. and both No condition is chosen when none is elected The HOMO condition is chosen when HOMO is elected The Charge condition is chosen when Charge is elected The HOMO condition and the Charge condition are chosen when both is elected The variable string2 is optional and only electable if a spin unrestric ted calculation is performed The variable string2 can have the values alpha and beta If string2 alpha then the condition is defined for the alpha spin channel If string2 beta then the condition is defined for the beta spin channel Both spin channels can have different values Example oep condition alpha HOMO condition beta Charge 260 LHF CHAPTER 18 ORBITAL DEPENDENT DFT If only one spin channel is defined the other spin channel uses the same condition automatically The default value in any case is string both core memory integer debug Core memory is the amount of main memory given to the OEP calcu lation to store the three index integrals calculated during the OEP cal culation The core memory amount is given MB The calculation runs as fast as possible if all three index integrals can be stored in the core memory The variable integer must have an integer value The default value is 200 Print further information about the OEP calculation especially matrices and vectors used during the OEP calculation Use this option carefully since a lot of data is written The default value is false eigenval
77. bas should provide no problems glb refers to a global scaling factor for all basis set exponents Imagine that you would like to replace your basis set which contains basis functions Xp 20 y yo z 20 exp n 7 70 by another basis set which contains basis functions Xu x0 y yo z 20 exp any r 70 where a is the same for all primitive basis functions y With command glb you are able to calculate analytical derivatives of the total energy with respect to a and can thus easily determine the optimum a dip enables you to calculate the first derivatives of the electric dipole moment with respect to nuclear displacements which gives you infrared intensities pol allows you to calculate the contribution of the nuclear rearrangement on the electric polariz ability fa finally performs only a frequency analysis which means that aoforce will read the force constant matrix hessian or hessian projected diagonalize it and give you the frequencies and normal modes tol is not a logical switch as the other options in this menu but a cutoff threshold for the derivative integrals i e integrals below this threshold will be neglected in the derivative calculations Entering will bring you to the second derivative submenu Debug Options for the Derivative Programs The following menu deals only with some debug options for grad Use them with caution each of them can produce
78. be modified with the iman command of the internal coordinate menu described earlier if internal coordinates has been defined Another option is to select m in the geometry main menu which provides the following submenu CARTESIAN COORDINATE MANIPULATION MENU move TRANSLATE AND OR ROTATE PART OF THE MOLECULE inert MOVE MOLECULE SO THAT COORDINATE AXES BECOME PRINCIPAL AXES OF INERTIA mback RESTORE PREVIOUS MOLECULAR GEOMETRY dis DISPLAY MOLECULAR GEOMETRY YOU MAY APPEND A QUESTION MARK TO ANY OF THESE COMMANDS FOR FURTHER EXPLANATIONS HIT gt return lt OR USE ANY GEOMETRY COMMAND NOT IN THIS LIST TO TERMINATE THIS MENU UPON TERMINATION THE MOLECULAR SYMMETRY WILL BE ENFORCED ACCORDING TO SYMMETRY GROUP c3v The meaning of the commands inert and mback should be clear command move allows you to manipulate the geometry of your molecule After entering move you will be asked to specify a set of atoms on which the command shall act You can use this to manipulate only a part of your molecule e g if you are building a structure from subunits and you want to adjust their relative arrangement As long as you stay in this menu the molecular symmetry needs not be correct so that you can try different movements and or rotations but as soon as you leave it the geometry will be symmetrized according to the present Sch nflies symbol After you specified the atomic set to be considered you get the following information INPU
79. calculated without RLJ approximation using dscf or with the RI JK approximation using ridft See Chapter 6 for a discussion of the RI approximations in SCF calculations and 20 2 6 for the required input In geometry optimizations with jobex and for the calculation of force constants and vibrational spectra with NumForce the ricc2 program is used in combination with the RI JK approximation for the Hatree Fock calculation using ridft if jobex and NumForce are invoked with the rijk option How to quote If results obtained with the ricc2 program are used in publications the following citations should be included if you have used the methods program parts auxiliary basis sets or results reported in therein Methods e for the approximate coupled cluster singles and doubles model CC2 O Christiansen H Koch P Jorgensen Chem Phys Lett 243 1995 409 418 e for CI singles with a perturb correct for connected double excitations CIS D M Head Gordon R J Rico M Oumi and T J Lee Chem Phys Lett 219 1994 21 and for the iterative CIS D variant M Head Gordon M Oumi and D Maurice Mol Phys 96 1999 593 e for the algebraic diagrammatic construction through second order ADC 2 J Schirmer Phys Rev A 26 1981 2395 A B Trofimov and J Schirmer J Phys B 28 1995 2299 e for MP2 F12 W Klopper and C C M Samson J Chem Phys 116 2002 6397 6410 D P Tew and W Klopper J Chem Phys
80. can be used only for the density matrix convergence or if Rydberg virtual orbitals are of no interest asymptotic on Full asymptotic treatment and use of the numerical Slater in the near asymptotic region asymptotic dynamic 1 d 3 Automatic switching on off to the special asymptotic treatment if the differential density matrix rms is below above 1 d 3 This is the default 20 2 FORMAT OF KEYWORDS AND COMMENTS 303 pot file save the converged Slater and correction potentials for all grid points are saved in the files slater pot and corrct pot respectively Using pot file load the Slater potential is not calculated but read from slater pot the cor rection potential is instead recalculated For spin unrestricted calcula tions the corresponding files are slaterA pot slaterB pot corrctA pot and correctB pot homo allows the user to specify which occupied orbital will not be included in the calculation of correction potential by default the highest occupied orbital is selected This option is useful for those systems where the HOMO of the starting orbitals e g EHT HF is different from the final LHF HOMO homob is for the beta spin correlation func functional a correlation functional can be added to the LHF potential use func lyp for LYP or func vwn for VWN5 correlation For expert users Options for the conjugate gradient algorithm for the computation of the correction potential rms convergence conj grad conv 1 d 7
81. consists of e The Slater Dirac exchange functional only S 57 58 e The 1980 correlation functional functional V in the paper of Vosko Wilk and Nusair only VWN 59 e A combination of the Slater Dirac exchange and Vosko Wilk and Nusair 1980 functional V correlation functionals S VWN 57 59 6 2 EXCHANGE CORRELATION FUNCTIONALS AVAILABLE 127 The S VWN functional with VWN functional III in the paper This is the same functional form as available in the Gaussian program 57 59 e A combination of the Slater Dirac exchange and Perdew Wang 1992 correla tion functionals 57 58 60 e A combination of the Slater Dirac exchange and Becke s 1988 exchange func tionals B88 57 58 61 Lee Yang and Parr s correlation functional LYP 62 The B LYP exchange correlation functional B88 exchange and LYP correla tion functionals 57 58 61 62 The B VWN exchange correlation functional B88 exchange and VWN V correlation functionals 57 59 61 The B P86 exchange correlation functional B88 exchange VWN V and Perdew s 1986 correlation functionals 57 59 61 63 The Perdew Burke and Ernzerhof PBE exchange correlation functional 57 58 60 64 The Tao Perdew Staroverov and Scuseria functional Slater Dirac TPSS exchange and Perdew Wang 1992 and TPSS correlation functionals 57 58 60 65 Additionally for all four modules dscf grad ridft and rdgrad following h
82. created each line containing one machine name nodel nodel node2 42 CHAPTER 3 HOW TO RUN TURBOMOLE node3 node4 node4 And the environment variable HOSTS_FILE has to be set to that file export HOSTS_FILE nfshome username hostsfile Note Do not forget to set PARNODES to the number of lines in HOSTS_FILE Note In general the stack size limit has to be raised to a reasonable amount of the memory or to ulimited In the serial version the user can set this by ulimit s unlimited on bash sh ksh shells or limit stacksize unlimited on csh tcsh shells However for the parallel version that is not sufficient if several nodes are used and the etc security limits conf files on all nodes might have to be changed Please see the following web site for details Turbomole User Forum Testing the parallel binaries The binaries ridft rdgrad dscf grad and ricc2 can be tested by the usual test suite go to TURBODIR TURBOTEST and call TTEST Note Some of the tests are very small and will only pass properly if 2 CPUs are used at maximum Therefore TTEST will not run any test if PARNODES is set to a higher value than 2 If you want to run some of the larger tests with more CPUs you have to edit the DEFCRIT file in TURBOMOLE TURBOTEST and change the defmaxnodes option Linear Algebra Settings The number of CPUs and the algorithm of the linear algebra part of Turbomole depends on the settings of parallel_platform cluster
83. define The type of stationary point optimization depends on the value of itrvec specified as an option within statpt By default itrvec is set to 0 which implies a structure minimization A value itrvec gt 0 implies a transition state optimization using the eigenvalue following TRIM algorithm where the index of the transition vector is specified by itrvec Note that statpt orders eigenvalues and 100 CHAPTER 5 STRUCTURE OPTIMIZATIONS eigenvectors of the Hessian in ascending order shifting six or five in the case of linear molecules zero translation and rotation eigenvalues to the end Note this order differs from that used for vibrational frequencies in the control file where rotational and translational eigenvalues are not shifted By default a structure optimization is converged when all of the following criteria are met e the energy change between two optimization cycles drops below the value given by threchange default 10 a u e the maximum displacement element drops below the value given by thrmax disp1 default 1073 a u e the maximum gradient element drops below the value given by thrmaxgrad default 1073 a u e the root mean square of the displacement elements drops below the value given by thrrmsdispl default 5 10 a u e the root mean square of the gradient elements drops below the value given by thrrmsgrad defaul t 5 10 4a u The default values for the convergence criteria can be changed
84. density difference between the distorted state and the initial state with density P The interaction is composed of three contributions the initial state dielectric energy the interaction of the potential difference with the initial state charges and the electronic screening energy that results from the density difference The energy expression can be used to derive the correspondent gradients which can be applied in a numerical frequency calculation Because the COSMO cavity changes for every distorted geometry the initial state potential has to be mapped onto the new cavity in every step The mapped potential of a segment of the new cavity is calculated from the distance weighted potentials of all segments of the old cavity that fulfill a certain distance criterion The mapped initial state screening charges are re calculated from the new potential Iterative MP2 Cosmo For ab initio MP2 calculations within the CSM frame work three alternatives can be found in the literature 184 The first approach often referred to as PTE performs a normal MP2 energy calculation on the solvated HF 267 wave function The response of the solvent also called reaction field is still on the HF level It is the only of the three approaches that is formally consistent in the sense of second order perturbation theory 185 186 In the so called PTD approach the vacuum MP2 density is used to calculate the reaction field The third approach often called PTED
85. excitation energies are obtained by standard coupled cluster linear response theory as eigenvalues of the Jacobian defined as derivative of the vector function with respect to the cluster amplitudes cez _ u _ mlll HT 2 JIHF val 12 HF w a ull rJIHF ual Fa HE oe Since the CC2 Jacobian is a non symmetric matrix left and right eigenvectors are different and the right left eigenvectors E Ei are not orthogonal among them selves but form a biorthonormal basis if properly normalized E E Ei Ei Et El by 10 9 To obtain excitation energies only the right or the left eigenvalue problem needs to be solved but for the calculation of transition strengths and first order properties both left and right eigenvectors are needed see below A second complication that arises from the non symmetric eigenvalue problem is that in the case of close degeneracies 190 CHAPTER 10 RI CC2 within the same irreducible representation symmetry it can happen that instead of two close lying real roots a degenerate complex conjugated pair of excitation energies and eigenvectors is obtained CC2 and also other standard coupled cluster response methods are thus not suited for the description of conical intersections etc For the general theory behind coupled cluster response calculations see e g ref 127 128 or other reviews The ricc2 program exploits that the doubles doubles block of the CC2 Jacobian is diagon
86. file sys data The file has the following simple format c h 2 2 h h 2 0 4 1 THE GEOMETRY MAIN MENU 59 The format of the entries is almost arbitrary the two element symbols have to be separated by a bar the new bond distance follows in free format in atomic units If the file cannot be read properly a warning message is displayed This command leaves this first main menu and writes all data generated so far to file The default output file is the file you choose in the first question during your define session usually control Now the data groups coord and intdef will be written to file After leaving this menu you will enter the atomic attributes menu which is described in Section 4 2 4 1 2 Internal Coordinate Menu INTERNAL COORDINATE MENU ideg 6 k 2 f 0 d 0 i 0 imet lt a gt PROVIDE B MATRIX FOR ACTIVE INTERNAL COORDINATES CHECK COMPLETENESS AND NUMERICAL QUALITY AND CHANGE REDUNDANT INTERNALS TO display idef SUB MENU FOR INTERACTIVE DEFINITION OF INTERNAL COORDINATES ideg lt a gt OUTPUT NUMBER OF TOT SYMMETRIC INTERNAL DEGREES OF FREEDOM iaut TRY AUTOMATIC DEFINITION OF INTERNAL COORDINATES iman lt a gt MANIPULATE GEOMETRY BY CHANGING INTERNAL COORDINATE VALUES imanat lt i gt AS iman BUT STARTING AT INTERNAL COORD NUMBER i ic lt i gt lt x gt CHANGE STATUS OF INTERNAL COORDINATE lt i gt TO lt x gt e g ic 5 d TO MAKE 5TH COORD display OR ic k d irem lt i gt REMOVE INTE
87. file the standard library will be searched immediately If the basis set cannot be found there you are asked either to enter a new standard library which will be standard only until you leave this menu or another input file where the basis set can be found If you do not know the exact nickname of your basis set you may abbreviate it by so you could enter h DZ to obtain basis sets like h DZ h DZP h DZ special etc define will give you a list of all basis sets whose nicknames match your search string and allows you to choose among them You may also use the command list to obtain a list of all basis sets cataloged bb does essentially the same as b but does not search your default input file for basis sets Instead it will look in the basis set library immediately bl gives you a list of all basis sets assigned so far This command is used to modify basis sets which are already assigned The corresponding submenu is self explanatory but we recommend to change directly the file basis The TURBOMOLE programs normally work with basis sets of 5d functions which means they delete the s component of the full 6d set bp allows to switch between the proper 5d 7f set and the Cartesian 6d 10f set This command allows you to specify effective core potentials for some atoms The assignment works exactly like the specification of basis sets see above This one does the same as command ecp but restricted to the basis set library
88. force constants is likely to fail if there are other states nearby in C1 because the roots may flip when the molecule is distorted Note also that it may be necessary to include higher excited states using exopt see above in C calculations of molecules with higher symmetry in order to enforce convergence to the correct state In any case it should be checked that the energy change due to the displacements available in the numforce KraftWerk 1log files is reasonably small For a Numforce run the convergence criteria should be tightened It is recommended to use at least 162 CHAPTER 7 HF AND DFT RESPONSE CALCULATIONS scfconv 8 in all Numforce calculations Other Numforce options such as central d np work in exactly the same way as they do for ground states 7 4 7 Polarizability Derivatives and Raman Spectra Calculations of polarizability derivatives by the egrad program use the same speci fications in the scfinstab data group as polarizability calculations by escf scfinstab polly specifies derivatives of the static polarizability while scfinstab dynpol unit frequency requests derivatives of the dynamical polarizability at the given frequency Note that unlike polarizability calculations multiple frequencies are not allowed Polarizability derivatives have to be projected onto vibrational normal modes to obtain Raman intensities see Chapter 13 for further details Chapter 8 Many body perturbation the
89. formulated by Boys and Bernadi S F Boys and F Bernardi Mol Phys 19 553 1970 to estimate the Basis Set Superposition Error BSSE For a dimer the cp correction takes the form for the monomers A and B E Eag Exp Ea Ega EB Where parentheses denote ghost basis sets without electrons or nuclear charges For a timer jobbsse used by default the conventional so called site site functional counterpoise corrections ESpo Easc Epc Ea Epcacy EB Ecqas Ec jobbsse works similar as the jobex script it cycles through the SCF DFT and if needed gradient and force relaxation programs and stops if either the maximum number of cycles is reached or the convergence criteria change in the total energy maximum norm of the gradient are fulfilled It does either only energy calculations or a full geometry optimization including up to three fragments By default the executable programs are taken from the load modules library within the TURBOMOLE directory Note that you need to set up the fragments and possibly their symmetries using define in the geometry menu beforehand The general structure of a jobbsse cal culation is as follows 1 bsseenergy is invoked to generate input files for define which is then used to prepare the control files including occupation numbers initial guess MOs etc for the different ghost and monomer calculations and shell scripts with commands for ca
90. hessian is a unit matrix However better choices are prefer able For structure optimizations using internal coordinates you may use structural information to set up a diagonal force constant matrix with elements chosen in ac cord to the softness or stiffness of the individual modes For detailed information refer to ref 36 For optimization of basis set parameters less information is avail able When neither data block forceapprox is available nor forceinit on is set the force constant matrix will be initialized as a unit matrix Specifying the force constant initialization key forceinit on diag will lead to diag real Initialization with real as diagonal elements diag default Initial force constant diagonals will be assigned the following default values 5 4 FORCE FIELD CALCULATIONS 111 internal coordinates stretches 0 50 angles 0 20 scaling factors S p 1 50 d 3 00 exponents uncontracted 0 15 contracted 10 00 contraction coefficients 100 00 global scaling factor 15 00 cartesian force constants 0 50 diag individual Initial force constant diagonals will be taken from intdef fdiag or global fdiag Similar initialization modes are NOT supported for geometry optimization in cartesian space and for the optimization of basis set parameters carthess Data group hessian projected is used 5 3 14 Look at Results The energy file includes the total energy of all cycles of a structure optimization c
91. is fairly common especially when using symmetry that at your TS there is a second imaginary frequency This means that you have not found the correct TS The proper procedure is to distort the structure along the extra imaginary normal mode using the tool screwer see Section 1 5 Very often such a distortion requires also lowering the point group symmetry The distortion must be large enough otherwise the next run will come back to the invalid structure 5 3 Program Relax 5 3 1 Purpose relax drives and controls a non linear optimization procedure to locate the minimum or a stationary point of a function f x In TURBOMOLE f is always the electronic energy and the coordinates x will be referred to as general coordinates They include e cartesian atomic coordinates e internal atomic coordinates e exponents contraction coefficients and scaling factors of basis functions e a global scaling factor a common scaling factor for all basis set exponents The optimization employs an iterative procedure based on gradients Vf of the cur rent and if available previous iterations Various procedures can be applied steep est descent Pulay s DIIS quasi Newton conjugate gradients as well as combina tions of them relax carries out e update of general coordinates e update of approximate hessians if needed e conversion of coordinates internal lt gt cartesian The mode of operation is chosen by the keywords optimi
92. is of non hybrid type we recommend B P86 but slightly better results are obtained for the hybrid functional B3 LYP 18 stability analysis of single determinant closed shell wave functions second derivative of energy with respect to orbital rotations 19 computes gradients and first order properties of excited states Well converged orbitals are required The following methods are available for spin restricted closed shell or spin unrestricted open shell reference states 1 5 TOOLS 25 rirpa mpshift freeh intense woelfling Cl Singles approximation TDA Time dependent Hartree Fock method RPA Time dependent density functional methods egrad can be employed in geometry optimization of excited states using jobex see Section 5 1 and in finite difference force constant calcula tions using Numforce Details see 20 calculates ground state energies and analytic first order properties within the random phase approximation RPA see Section 12 requires a converged SCF or DFT run for closed shells mpshift com putes NMR chemical shieldings for all atoms of the molecule at the SCF DFT or MP2 level within the GIAO ansatz and the CPHF SCF approximation From this one gets the NMR chemical shifts by compar ison with the shieldings for the standard compound usually employed for this purpose e g TMS for carbon shifts Note that NMR shielding typically requires more flexible basis sets than neces
93. its pathname in this data group as follows scratch files relax ftmp path file The first column specifies the program the second column the scratch file and the third column the pathname of the file to be used as scratch file Input Data Blocks Needed by RELAX intdef or redundant Definitions of internal coordinates and optionally values of internal coordi 346 CHAPTER 20 KEYWORDS IN THE CONTROL FILE nates val given in a u or degrees or force constant diagonal elements fdiag grad Cartesian coordinates and gradients calculated in subsequent optimization cy cles Entries are accumulated by one of the gradient programs grad mpgrad rimp2 ricc2 egrad etc egrad Basis set exponents scale factors and their gradients as calculated in subsequent optimization cycles Entries are accumulated by one of the gradient programs globgrad Global scale factors and gradients as calculated in subsequent optimization cycles Entries are accumulated by the grad or aoforce program corrgrad Allows to augment internal SCF gradients by approximate increments obtained from treatments e g correlation or relativistic on higher level See the exam ple below corrgrad coordinate increment 1 0 0600 8 0 0850 forceapprox options Approximate force constant matrix as needed for geometry optimization tasks The storage format may be specified by the available options format format the
94. leads to an efficient scheme for the calculation of RPA correlation energies 144 gormpa 7 W pcio 12 7 no 2T where the integrand contains Naux X Naux quantities only FC w For In Taux QW QW 12 8 Naux is the number of auxiliary basis functions The integral is approximated using Clenshaw Curtiss quadrature Prerequisites Calculations with rirpa require 12 2 GRADIENTS THEORY 219 e aconverged SCF calculation e rirpa options may be included by adding them in the lines below the keyword rirpa in the control file Possible options are npoints integer Number of frequency integration points default is 60 nohxx HF energy is skipped HXX Hartree eXact Fock eXchange rpaprof Generates profiling output e the maximum core memory the program is allowed to allocate should be defined in the data group maxcor in MB the recommended value is ca 3 4 of the available physical core memory at most e orbitals to be excluded from the correlation treatment have to be specified in data group freeze e an auxiliary basis defined in the data group cbas e an auxiliary basis defined in the data group jbas for the computation of the Coulomb integrals for the Hartree Fock energy e optional an auxiliary basis defined in the data group jkbas for the compu tation of the exchange integrals for the Hartree Fock energy rik should be added to the control file for RI JK to be effec
95. less diverse than the ones of the standard radii bases cav ity construction Because gradients are not implemented the radii based isosurface cavity can be used in single point calculations only 20 2 FORMAT OF KEYWORDS AND COMMENTS 311 cosmo_isorad dx real spacing of the marching tetrahedron grid in default 0 3 Cosmo in MP2 Calculations The iterative Cosmo PTED scheme see chapter 19 can be used with the mp2cosmo script Options are explained in the help message mp2cosmo h Both MP2 modules RIMP2 and mpgrad can be utilized The control file can be prepared by a normal Cosmo SCF input followed by a RIMP2 or mpgrad input The PTE gradients can be switched on by using the cosmo_correlated keyword RIMP2 only Again a normal SCF Cosmo input followed by a Rimp2 input has to be generated The cosmo_correlated keyword forces dscf to keep the Cosmo information needed for the following MP2 calculation and toggles on the CosMO gradient contribution Cosmo in Numerical Frequency Calculations NumForce can handle two types of CosMo frequency calculations The first uses the normal relaxed COSMO energy and gradient It can be performed with a standard dscf or ridft COSMO input without further settings This is the right method to calculate a Hessian for opti mizations The second type which uses the approach described in chapter 19 is implemented for ridft only The input is the same as in the first case but Numforce has t
96. logarithm 339 scale 339 cartesian 103 339 global 103 340 internal 103 106 339 345 redundant 103 339 paboon 352 parallel_parameters 374 parallel_platform 42 372 pardft 374 path 272 point_charges 156 290 points 90 91 95 350 pointval 201 238 239 360 dens 362 fld 240 362 INDEX fmt 362 cub 363 map 363 plt 363 txt 363 vec 363 xyz 363 geo 242 364 line 364 plane 364 point 364 integrate 361 Imo 241 362 mo 240 362 nao 241 nmo 362 nto 242 pot 239 362 xc 240 362 pop 236 355 356 atoms 356 dos 356 lall 356 mo 356 netto 356 overlap 356 thrpl 356 pop nbo 236 357 pop paboon 236 357 pople 274 prediag 290 293 printlevel 326 329 properties 88 350 ramanonly 316 rbss 139 304 rdkh 139 304 redund_inp 275 redundant 107 226 339 345 INDEX response 335 conv 335 fop 335 gradient 335 nosemicano 335 nozpreopt 335 semicano 335 sop 335 thrsemi 335 zconv 335 zpreopt 335 response 181 184 196 199 204 335 337 restart 293 restartd 291 293 ricc2 171 173 178 180 184 188 189 191 196 199 205 206 208 215 327 328 335 337 adc 2 328 cc2 328 ccs 328 ccsd 328 ccsd t 328 cis 328 cis d 328 cisdinf 328 conv 328 didiag 328 fmtprop 328 geoopt 196 328 gsonly 328 hard_restart 328 intcorr 216 328 iprint 328 lindep 328 maxiter 328 maxred 328 mp2 328 427
97. matrix elements The rijk menu of define can be used for this How To Perform a Calculation As presently no gradients are available only single point calculations are possible 1 Select in define within the menu cc the wavefunction model submenu ricc2 frozen core options submenu freeze an auxiliary basis for cbas submenue cbas the amount of main memory option memory and for CCSD F12 calculations in addition 11 1 CHARACTERISTICS OF THE IMPLEMENTATION AND COMPUTATIONAL DEMANDS209 the F12 options submenu 12 and a CABS basis submenu cabs By default a CCSD F12 with ansatz 2 and geminal amplitudes fixed by the cusp conditions is performed To switch to the computationally more efficient recommended CCSD F12 approximation add to the input group rir12 the linet ccsdapprox ccsd f12 The auxiliary JK basis must be chosed in menu rijk and the exponent for the correlation function must set by editing the 1cg data group of the control file 2 Do an SCF calculations using either the dscf or the ridft module 3 Invoke the ricc2 program on the command line or with a batch script How to quote e for all F12 calculations cite the implementation of RI MP2 F12 in TURBO MOLE The MP2 F12 Method in the TURBOMOLE Programm Package Rafal A Ba chorz Florian A Bischoff Andreas Glo Christof H ttig Sebastian H fener Wim Klopper David P Tew J Comput Chem 32 2492 2513 2011 e for MP3
98. module and requires setting of the ridft keyword marij precision 1 0D 06 lmaxmom 10 nbinmax 8 wsindex 0 0 extmax 20 0 thrmom 1 0D 18 The following options are available precision specifies precision parameter for the multipole expansions Low precision MARI J calculations require 1 1076 which is the de fault For higher precision calculations it should be set to 1 107 1 107 lmaxmom maximum l moment of multipole expansions It should be set to a value equal at least twice the maximum angular momentum of basis functions Default value is 10 and it should probably never be set higher than 18 thrmom Threshold for moment summation For highly accurate calcula tions it should be set to 1 10774 nbinmax number of bins per atom for partitioning of electron densities Default value is 8 and hardly ever needs to be changed wsindex minimum separation between bins Only bins separated more than the sum of their extents plus wsindex are considered as far field Default is 0 0 and should be changed only by the experts extmax maximum extent for charge distributions of partitioned densities Extents with values larger then this are set to extmax Hardly ever needs to be changed Seminumeric HF Exchange If the keyword senex is found in the control file ridft performs a Hartree Fock SCF calculation using the seminumerical approximation for HF exchange Standard dft grids can be used for the numerical integration
99. mp3 328 mp4 328 mxdiis 328 nohard_restart 328 norestart 328 oconv 328 restart 328 scs 328 sos 328 ricore 77 124 125 156 160 225 299 375 ricore_slave 375 ridft 156 160 299 300 rij 299 304 rik 124 219 299 304 ripop 299 rir12 170 174 176 178 184 208 209 211 330 ansatz 330 cabs 330 cabsingles 330 ccsdapprox 330 comaprox 330 corrfac 330 examp 330 pairenergy 330 r12model 330 r12orb 330 rirpa 219 221 321 rlocal 139 305 rlocpara 305 rohf 297 roothaan 275 297 rpaconv 155 319 320 rpacor 160 319 rsym 140 rundimensions 291 rx2c 139 304 428 scfconv 36 79 156 291 295 318 326 settings for AOFORCE 225 NUMFORCE 225 scfconv 7 222 scfdenapproxl 289 292 scfdiis 291 293 scfdump 289 291 293 scfinstab 124 155 320 ciss 318 cist 318 dynpol 319 non real 318 polly 319 rpas 318 rpat 318 singlet 318 soghf 318 spinflip 318 triplet 318 ucis 318 urpa 318 scfintunit 40 45 156 291 293 296 326 371 file 293 size 293 unit 293 scfiterinfo 293 scfiterlimit 293 scfiterlimit 1 222 scfmo 68 273 274 289 291 293 294 208 371 expanded 294 file 294 format 294 none 67 294 scfconv 294 scfdump 294 INDEX scfmo none 67 scforbitalorder 294 scforbitalshift 294 automatic 295 closedshell 295 individual 295 noautomatic 295 scftol 295 326 371 sc
100. necessary to switch on the field calculations manually Therefore edit the control file after having finished your define session and enter on after the entries of fields and geofield 4 4 5 Properties The program moloch used for this purpose is currently being revamped and will then be much simpler to use The subsequent description for an older version may not work in all cases sorry for that If you enter prop in the general menu define first will check whether the data group properties does already exist in your control file or in a file referenced therein If this is not the case you will be asked to specify the file on which properties shall be written data group properties has not yet been specified FOR INITIALIZING lt moloch gt KEYWORDS ENTER return WRITE TO CONTROL FILE control DEFAULT OR filename WRITE TO ANOTHER FILE Afterwards you will get the following submenu which allows you to control all possible actions of program moloch 4 4 THE GENERAL OPTIONS MENU 89 switch on one or more of the following options lt i gt lt i gt 1 9 for switching off option lt i gt specify lt i gt 1 trace off 2 moments off 3 potential off 4 cowan griffin off 5 localization off 6 population analyses off 7 plot off 8 firstorder off selecting an already active option indicates that suboptions shall be modified or q uit quit for help type help lt integer gt All option
101. noinv only the diagonal amplitudes are non zero and are either predetermined using the coalescence condi tions fixed or optimized noinv not orbital invariant If char inv the F12 energy contribution is computed using all three methods For open shell calculations noflip supresses the use of spin flipped geminal functions The fixed flip method is used if examp is absent pairenergy char char off or on If char off default the print out of the standard and F12 contribu tions to the pair energies is suppressed The summary of the RI MP2 F12 correlation energies is always printed out corrfac char char LCG or R12 332 CHAPTER 20 KEYWORDS IN THE CONTROL FILE The corrfac flag determines which correlation factor is used for the geminal basis LCG requires the data group 1cg which contains the in formation regarding exponents and coefficients of the linear combination of Gaussians cabsingles char char off or on The cabsingles flag determines whether or not the single excitations into the CABS basis are computed The CABS singles are computed in any case if the CABS Fock matrix elements are computed anyway for the F12 calculation i e for ansatz 2 or rl2model B or comaprox F K ri2orb char char hf rohf boys or pipek The r12orb flag controls which orbitals are used for the F12 geminal basis functions With hf the semi canonical Hartree Fock orbitals are used default For ROHF based UMP2 calcula
102. occupation If you accept you are done if not you get the occupation number assignment menu explained in 4 3 2 Description of Commands infsao Command infsao provides information about the symmetry adapted basis which is used for the SCF calculation To exploit the molecular symmetry as efficiently as possible TURBOMOLE programs do not use the simple basis which you specified during your define session Instead it builds linear combinations of equal basis functions on different but symmetry equivalent atoms This basis is then called the SAO basis Symmetry Adapted Orbital It has the useful property that each basis function transformed to this basis transforms belongs to one irreducible representation of the molecular point group that is the basis reflects the full molecular symmetry as specified by the Sch nflies symbol infsao gives you a listing of all symmetry adapted basis functions and their constituents either on file or on the screen This may help you if you want to have a closer look at the SCF vectors because the vector which is output by program dscf is written in terms of these SAQOs atb Molecular orbitals can be written either in ASCII or in binary format This command switches from one option to the other and it is highly recommended to read which setting is currently active ASCII format is portable and allows the usage of TURBOMOLEinput files on different systems with incompatible binary format Binary format
103. occupations are diposited in data group spinor All electron calculations The keywords rx2c rbss and rdkh Order of DKH are used to activate the X2C BSS or DKH Hamiltonian The default order of the DKH Hamiltonian is four It is not recommended to go beyond but to use X2C instead For details on the arbitrary order DKH Hamiltonians see Ref 78 for de tails on the infinite order DKH theory 79 for the implementation and 80 for a conceptual review of DKH theory The local approach DLU can be optionally ac tivated by rlocal for all one and two component all electron Hamiltonians For 140 CHAPTER 6 HARTREE FOCK AND DFT CALCULATIONS symmetric molecules point group symmetry is not exploited by default but can be used in the one component case by setting rsym 6 5 PERIODIC ELECTROSTATIC EMBEDDED CLUSTER METHOD 141 6 5 Periodic Electrostatic Embedded Cluster Method 6 5 1 General Information The Periodic Electrostatic Embedded Cluster Method PEECM functionality 81 provides electronic embedding of a finite quantum mechanical cluster in a periodic infinite array of point charges It is implemented within HF and DFT energy and gradient TURBOMOLE modules dscf grad ridft rdgrad and escf Unlike embed ding within a finite set of point charges the PEEC method always yields the correct electrostatic Madelung potential independent of the electrostatic moments of the point charges field It is also significantly faster
104. or the transition vector from the lowest eigenvalue search executes one molecular dynamics MD step Like relax it follows a gradient run these gradients are used as classical Newtonian forces to alter the velocities and coordinates of the nuclei requires a well converged SCF or DFT run by dscf or ridft see keywords and performs an analytic calculation of force constants vi brational frequencies and IR intensities aoforce is also able to calculate only the lowest Hessian eigenvalues with the corresponding eigenvectors which reduces computational cost The numerical calculation of force constants is also possible see tool Numforce in Section 1 5 requires a well converged SCF or DFT run and calculates time de pendent and dielectric properties spin restricted closed shell or spin unrestricted open shell reference static and frequency dependent polarizabilities within the SCF ap proximation static and frequency dependent polarizabilities within the time dependent Kohn Sham formalism including hybrid functionals such as B3 LYP electronic excitations within the RHF and UHF CI S restricted CI method electronic excitations within the so called SCF RPA approximation poles of the frequency dependent polarizability electronic excitations within the time dependent Kohn Sham for malism adiabatic approximation It can be very efficient to use the RI approximation here provided that the functional
105. other flags 20 2 FORMAT OF KEYWORDS AND COMMENTS 321 There are several options which can be added to the gw keyword the syntax is gw nl 1 gam 0 001 output qpe dat rpa With the optional entries nl lt integer gt Default 1 Number of orbitals to calculate gw for It is set to the number of occupied orbitals 5 if set smaller than the number of occupied orbitals gam lt real gt Default 0 001 Infinitesimal complex energy shift Negative value switches to cal culating at that value but extrapolating to 0 in linear approximation output lt filename gt Default qpe dat Output filename for the quasiparticle energies rpa Default false not set If added as option pure rpa responce function is calculated If not added the TDDFT response function is calculated and used to screen the coulomb interaction 20 2 14 Keywords for Module rirpa The keyword rirpa allows to specify the following options npoints n Number of frequency integration points n default is 60 nohxx HF energy calculation is skipped HXX Hartree eXact Fock eXchange 322 CHAPTER 20 KEYWORDS IN THE CONTROL FILE rpaprof Generates profiling output rpagrad Switches on the gradients calculation for RI RPA drimp2 Computes gradients in the direct RI MP2 limit niapblocks n Manual setting of the number of integral blocks n in subroutine rirhs f This is for developers the default is determined with the maxcor 20
106. parameters are also recommended in 16 for the SCS variants of CC2 CIS D CIS D and ADC 2 for ground and excited states Also just sos can be used as a keyword to switch to the SOS approach proposed by the Head Gordon group for MP2 with scaling factors of cos 1 3 and css 0 0 Y Jung R C Lochan A D Dutoi and M Head Gordon J Chem Phys 121 2004 9793 which are also recommended for the SOS variants of CC2 CIS D CIS D and ADC 2 The Laplace transformed algorithm for the SOS variants are activated by the additional data group laplace laplace conv 4 For further details on the Laplace transformed implementation and how one can estimated whether the O N scaling Laplace transformed or O N scaling con ventional RI implementation is efficieint see Sec 9 6 Since Version 6 6 the O N scaling Laplace transformed implementation is available for ground and excited state gradients with CC2 and ADC 2 Restrictions e the spin S expectation value for open shell calculation can not be evaluated in the SCS or SOS approaches e for LT SOS CC2 and the related CIS D and ADC 2 versions the following further limitations apply only parallelized with MPI no OpenMP parallelization incompatible with the calculation of the D and D diagnostics Chapter 11 CCSD CCSD F12 and CCSD T calculations The ricc2 module includes also an implementation of the full coupled cluster singles and
107. path xyz which is the output of the woelfling program woelfling job then creates folders to run the calculations of each structure in gathers coordinates and gradients and then calls woelfling again The aim of RP optimization is usually not to optimize the RP to some accuracy but to obtain an initial guess for a TS optimization It is in general not possible to find a convergence criterion and a corresponding threshold that guarantees a good initial guess The maximum number of iterations and the convergence threshold are therefore relatively high and tight One can extract a TS guess also during the course of the optimization If the TS search is successful or not you can stop or restart the RP optimization Apart from simply killing the program you can add a stop file in the scratch directory in which the script runs It will then terminate at the end of the current cycle and can easily be restarted 5 7 2 Input Structure Options can be modified using keywords in the woelfling data group The most important options are 120 CHAPTER 5 STRUCTURE OPTIMIZATIONS woelfling ninter 14 riter 0 ncoord 2 align 0 maxit 40 dist 3 00000000000000 thr 1 000000000000000E 004 method q The values above are the default values If woelfling is missing it will be added during the first woelfling run and default values will be set Most importantly ncoord is the number of input structures provided ninter is the number of struc
108. points are associated to the nearest segment grid centers and the segment coordinates are re defined as the center of area of their associated basis grid points while the segment area is the sum of the basis grid areas Segments without basis grid points are discarded In order to ensure nearest neighbor association for the new centers this procedure is repeated once At the end of the cavity construction the intersection seams of the spheres are paved with individual segments which do not hold associated basis grid points Density based Cavity Construction Instead of using atom specific radii the cavity can be defined by the electron density In such an isodensity cavity con struction one can use the same density value for all atoms types or the so called scaled isodensity values In the later approach different densities are used for the different atom types The algorithm implemented in TURBOMOLE uses a marching tetrahedron algorithm for the density based cavity construction In order to assure 266 CHAPTER 19 TREATMENT OF SOLVATION EFFECTS WITH COSMO a smooth density change in the intersection seams of atoms with different isodensity specification this areas are smoothened by a radii based procedure A Matrix Setup The A matrix elements are calculated as the sum of the contri butions of the associated basis grid points of the segments k and if their distance is below a certain threshold the centers of the segments are used otherwise
109. polyatomic molecules J Chem Phys 88 4 2547 2553 1988 BIBLIOGRAPHY 421 194 195 196 197 198 199 200 A Wolf M Reiher B Hess The generalized Douglas Kroll transformation J Chem Phys 117 9215 9226 2002 R Send F Furche First order nonadiabatic couplings from time dependent hybrid density functional response theory Consistent formalism implementa tion and performance J Phys Chem 132 044107 2010 J C Tully Molecular dynamics with electronic transitions J Chem Phys 93 1061 1990 E Tapavicza I Tavernelli U Rothlisberger Trajectory surface hopping within linear response time dependent density functional theory Phys Rev Lett 98 023001 2007 E Tapavicza A M Meyer F Furche Unravelling the details of vitamin D photosynthesis by non adiabatic molecular dynamics simulations Phys Chem Chem Phys 13 20986 2011 B G Levine C Ko J Quenneville T J Martinez Conical intersections and double excitations in density functional theory Mol Phys 104 1039 2006 E Tapavicza I Tavernelli U Rothlisberger C Filippi M E Casida Mixed time dependent density functional theory classical trajectory surface hopping study of oxirane photochemistry J Chem Phys 129 12 124108 2008 Index non append mode 64 47 central 228 fanal 200 frznuclei 227 228 level rirpa 98 relax 97 117 ri 221 r
110. procedures employed The output headers of TURBOMOLE modules include the relevant papers One may also use the following connections between method module number in the subsequent list For module ricc2 see also Section 10 CHAPTER 1 PREFACE AND GENERAL INFORMATION e Programs and methods general program structure and features I HF SCF dscf ridft II DFT quadrature dscf ridft escf aoforce IV d m grids RLDFT ridft aoforce escf c d XXIII marij VII escf XXIV aoforce MP2 mpgrad III RI MP2 ricc2 energies and gradients VIII XXIX f and static po larizabilities XXXVI stability analysis escf V electronic excitations by CIS RPA TD DFT escf VI VII XVIII XX VII excited state structures and properties with CIS RPA TD DFT egrad XIX XXVI XXVII RI CC2 ricc2 x singlet XII and triplet excitation energies XIII x transition moments and first order properties of excited states XV and first order properties for triplet states XIV ground state geometry optimizations X XI x excited state geometry optimizations and relaxed properties XXII x parallelization XXIX spin component scaled SCS variants XXXII SOS variants of MP2 CIS D ADC 2 and CC2 with O N scaling XXXIII x frequency dependent and static polarizabilities XXXVI RI ADC 2 RI CIS D and RI CIS D ricc2 XXVIII analytical second derivatives force fields aoforce
111. quantity set by step damp real default value is 0 10 The minimum value set by max damp real default value is 0 90 fde input options epsilon real max iter integer start damp real max damp real step damp real Embedding energy error The embedding error in the total energy is computed as AB EF p 4 pp EPFT p 17 12 where EPFT is the DFT total energy of total system with density p r In order to compute AF as well as its components the flag err energy must be used This flag will required also the DFT calculation on the total system In this case the converged SCF output file must be named output dscf 17 2 FROZEN DENSITY EMBEDDING CALCULATIONS USING THE FDE SCRIPT253 An example of session output for the computation of embedding energy and energy error decomposition when err energy flag is present is the following FDE ENERGY TOTAL SYSTEM 200 99720391651 Ha FDE BINDING ENERGY 4 960885 mHa 3 113002 kcal mol FDE ENERGY ERROR 2 003352 mHa ERROR ENERGY DECOMPOSITION coulomb contribution 0 693026 mHa nuclear contribution 3 136544 mHa exchange correlation contribution 1 156390 mHa kinetic contribution 6 989320 mHa where the FDE energy E P the FDE binding energy the embedding energy error AF and the error energy decomposition in its coulomb nuclear exchange correlation and kinetic contributions are reported This output is present at each FDE iteration fde input option err
112. referencing their pathnames in this data group All possible scratch files are listed in the following example scratch files dscf dens path1 filet dscf fock path2 file2 dscf dfock path3 file3 dscf ddens path4 file4 dscf statistics path7 file7 dscf errvec path8 file8 dscf oldfock path9 fileg dscf oneint path10 file10 The first column specifies the program type dscf stands for SCF energy cal culations i e the dscf program the second column the scratch file needed 296 CHAPTER 20 KEYWORDS IN THE CONTROL FILE by this program and the third column the pathname of the file to be used as scratch file statistics options The following options are allowed off Do not perform integrals statistics dscf Perform integrals statistics for dscf kora see KORA mpgrad see mpgrad polly see POLLY dscf parallel see PARALLEL PROCESSING Options kora dscf parallel grad mpgrad polly will be described in the related chapters If statistics dscf has been given integral prescreening will be performed which is an n step and may therefore be time consuming and a table of the number of stored integrals as a function of the two parameters thize and thime will be dumped Afterwards the filespace needed for the current com bination of thize and thime will be written to the data group scfintunit and statistics dscf will be replaced by statistics off thime integer Integral storage parameter which is related to the time needed to
113. rimp2 does the same upon request if tplot is added to control file More or less than five t amplitudes will be plotted for tplot n where n denotes the number of largest amplitudes to be plotted It is up to the user to decide from these quantities whether the SCF MP2 treatment is suited for the present problem or not Unfortunately it is not possible to define a threshold which distinguishes a good and a bad MP2 case since the value of indi vidual t amplitudes are not orbital invariant but depend on the orbital basis and thereby under certain circumstances even on the orientation Example the largest norm of t amplitudes for the Cu atom d s good MP2 case amounts to ca 0 06 that of the Ni atom d s bad MP2 case is ca 0 14 A more descriptive criterion may be derived from the MP2 density matrix The eigenvalues of this matrix reflect the changes in occupation numbers resulting from the MP2 treatment compared to the SCF density matrix where occupa tion numbers are either one two for RHF or zero Small changes mean small corrections to HF and thus suitability of the HF MP2 method for the given problem In case of gradient calculations rimp2 displays by default the largest eigenvalue of the MP2 density matrix i e the largest change in occupation numbers in All eigenvalues are shown if mp2occ is added to the control file For main group compounds largest changes in occupation numbers of ca 5 or less are ty
114. serves to specify the electrostatic moments to be calculated Oth charge 1st dipole moment 2nd quadrupole moment 3rd octuple moment The refer ence point is the origin of the coordinate system used in the calculation The value of any calculated moment will be independent of this reference point if all lower mo ments are zero The default for the reference point is the origin i e the coordinate system used for the calculation of the moments will be the same as the one in which the atomic coordinates are specified The reference point may be changed by typing point with the three new coordinates appended Alternatively you may choose the coordinates of one of the atoms as reference point by entering atom and the atom index Option potential This option collects all possible quantities related to the electrostatic field created by the molecular charge distribution This includes the following suboptions list of suboptions pot electrostatic potential fld electrostatic field fldgrd electrostatic field gradient shld diamagnetic shielding file file reference quit The meaning of the four suboptions pot fld fldgrd and shld will probably present no problems to you For each of them however you will have to specify at which point s this property should be calculated This is accomplished by one or more data groups points in file control After you chose one or more of the above options you will therefore reach the
115. shell molecules it is often helpful to increase the value for scforbitalshift closedshell a value of ca 1 0 may serve as a rough recommendation Effective core potentials The two component formalism may be most easily pre pared and applied in the following way e Run define choose Cl symmetry select ECPs and basis sets with suffices 2c for the respective elements For spin orbit treatments two component ECPs suffix 2c are required the use of extended basis sets accounting for the spatial splitting of inner p shells also suffix 2c is recommended see 77 ECPs and basis sets def2 XVP 2c X S TZ QZ are available for Ag I Au At they can be selected within the define session RI J and RI JK auxiliary basis sets of def2 type are of sufficient flexibility for two component treatments they are the same with and without suffix 2c The corrresponding auxiliary basis sets are provided automatically e Insert soghf in the control file as well as further desired keywords e Start the two component calculation with ridft e At the end of the SCF procedure real and imaginary parts of spinors are written to files spinor r and spinor i eigenvalues and spinor occupations are collected in the file EIGS the total energy is added to data group energy The data groups closed shells alpha shells and beta shells for open shell cases are no longer significant but nevertheless kept in the control file additionally the spinor
116. suite is that only the specific information about an individual test example is included in its local directory along with the input and reference files This information is stored in the criteria file CRIT which contains the program calls test criteria and specific reference timings Running the test script creates a new test subdirectory usually called like TESTDIR i786 pc linux gnu where the TURBOMOLE programs are run and the results are summarized in the protocol file TESTPROTOKOLL 399 400 CHAPTER 22 PERL BASED TEST SUITE 22 2 Running the tests Starting a single test example is simple Change to the test example of your choice and call the TTEST script without arguments The test is started in a subdirectory named TESTDIR sysname where sysname is the current platform name as returned by the Sysname script The tested executable a short description and the test summary are output to the screen Detailed information about the performed commands and results of all test criteria are found in the TESTPROTOKOLL file in the test subdirectory The default location for the binaries and scripts used for testing is the TURBODIR directory If you like to test some other e g your local version of the TURBOMOLE binaries or scripts you can specify the loading paths by the 1 or 1s options for the binaries and scripts respectively TTEST 1 usr local TURBOMOLE bin i786 pc linux gnu ls usr local TURBOMOLE scripts A specific exe
117. the 1hf group are off diag on The LHF exchange potential is computed default off diag off The KLI exchange potential is computed can be selected by lhfprep kli num slater on the Slater potential is calculated numerically everywhere this is more accurate but quite expensive When ECPs are used turn on this option It can be selected by 1hfprep num num slater off the Slater potential is computed using basis sets This leads to very fast calculations but accurate results are obtained only for first row elements or if an uncontracted basis set or a basis set with special additional contractions is used This is the default asymptotic for asymptotic treatment there are three options asymptotic off No asymptotic treatment and no use of the numerical Slater The total exchange potential is just replaced by 1 r in the asymptotic region This method is the fastest one but can be used only for the density matrix convergence or if Rydberg virtual orbitals are of no interest asymptotic on Full asymptotic treatment and use of the numerical Slater in the near asymptotic region It can be selected by 1hfprep asy asymptotic dynamic 1 d 3 Automatic switching on off to the special asymptotic treatment if the differential density matrix rms is below above 1 d 3 This is the default pot file save the converged Slater and correction potentials for all grid points are saved in the files slater pot and corrct pot respect
118. the input file will not be used ecpi gives you some general information about what type of pseudopo tentials is supported For more information we refer to 25 and references therein ecpl gives you a list of all pseudopotentials assigned so far 4 3 GENERATING MO START VECTORS 65 ecprm ecprm allows to remove a pseudopotential assignment from the list This command is useful if you want to perform an all electron calculation after an ECP treatment c Command c assigns a special nuclear charge to an atom This is useful to define dummy centers for counterpoise calculations where you set the nuclear charge to zero m This command allows you to assign non default atomic masses to an atom Use this if you want to analyze isotopic shifts of calculated har monic frequencies The standard masses are those of the natural isotope mix dat dat gives you a list of all data already specified This is again the usual command to leave a menu and write all data to file control or any other output file It is not possible to leave this menu unless basis sets have been specified for all atoms in your molecule If you do not want to use a basis set for one or more atoms use the basis set nickname none On leaving this menu the data groups atoms and basis will be written to the output file After you finished this menu you will enter the third main menu of define which deals with start vectors and occupation numbers 4 3 Generating MO
119. the less memory you give the more integrals are treated directly i e recomputed on the fly in every iteration jbas file auxbasis Cross reference for the file specifying the auxiliary basis as referenced in atoms We strongly recommend using auxbasis sets optimized for the respective MO basis sets e g use SVP or TZVP for the basis and the corresponding auxbasis as provided by define default file auxbasis ripop Calculation of atomic charges according to the s partial wave and atomic dipole moments according to the p partial wave as resulting from the auxbasis repre sentation of the density RI JK If the keyword rik is found in the control file ridft performs a Hartree Fock SCF calculation using the RI approximation for both Coulomb and HF exchange efficient for large basis sets For this purpose needed apart from ricore jkbas file auxbasis Cross reference for the file specifying the JK auxiliary basis as referenced in atoms This group is created by the rijk menu in define 300 CHAPTER 20 KEYWORDS IN THE CONTROL FILE MARI J Multipole Accelerated Resolution of Identity J This method partitions the Coulomb interactions in the near and far field parts The calculation of the far field part is performed by application of the multipole expansions and the near field part is eval uated employing the RI J approximation It speeds up calculation of the Coulomb term for large systems It can only be used with the ridft
120. the thermostat relaxation time in a u 100 a u in the example It is advisable to choose the thermostat relaxation 2 10 times larger than the time step Note that user defined actions are presently not supported in canonical dynamics mode These are optional keywords seed 123 Integer random number seed 366 title Arbitrary title log_history 100 mdlog P 71 mdlog Q ke_control length 50 response 1 CHAPTER 20 KEYWORDS IN THE CONTROL FILE To determine the trends in kinetic energy and total energy average values and overall drifts it is necessary to read the history of energy statistics over the recent MD steps The number of MD steps recorded so far in each log file are therefore kept in the log_history entry this is updated by the program each step The length of records needed for reliable statistics and the number of steps over which changes are made to kinetic energy response are specified in ke_control barrier angstroms type elps limits 5 0 10 0 7 5 constant 2 0 springlen 1 0 temperature 300 0 barrier specifies a virtual cavity for simulating condensed phases The op tional flag angstroms can be used to indicate that data will be entered in Angstroms rather than Bohr type can be one of orth elps or none for orthorhombic ellipsoidal or no barrier the default respectively limits are the x y z sizes of the cavity In this case an ellipsoid with a major
121. to generate cartesian coordinates file coord nothing else You can start an single point calculation calculation by typing uff To start an uff geometry optimization one has to change the number of cycles parameter maxcycle in the block uff in the file control The ouput is the optimized structure file coord the analytical gradient file uffgradient and the analytical cartesian hessian file uffhessian0 0 Furthermore the control file will be modified forceinit on carthess uffhessian file uffhesian0 0 These commands have the effect to inititialize the force constant matric for a geom etry optimization with the hessian one In some cases uff cannot recognize the connectivity then one can specify the connec tivity in the file ufftopology The program will calculate the bond angle torsion inverison and non bonded terms force field terms based on the connectivity speci fied in the topology file 5 4 3 The UFF implementation The uff implementation follows the paper by Rapp 7 The energy expression in uff is as follows 5 4 FORCE FIELD CALCULATIONS 113 te 1 cos 40 Krk ce C4 cos 6 Cs cos 20 octahedral case general case NB 1 2 Eurr hi Ste 5 1 Krk 1 cos 20 linear case Na Alix 1 cos 30 trigonal planar case gt Aran 1 cos 40 quadratic planar case 40 26 Nr 1 fi pF Vg 1 cos ngo cos n I Vo ci C cosw C cos 2
122. unrestricted open shell run In this case the wavefunctions will not be spin eigenfunctions and multiplicities are not well defined 192 CHAPTER 10 RI CC2 case of convergence problems the first thing do is to verify that the ground state is not a multireference case by checking the D1 diagnostic If this is not the case the following situations can cause problems in the calculation of excitation energies e almost degenerate roots in the same symmetry class e complex roots break down of the CC approximation close to conical intersec tions e large contributions from double excitations The first two reasons can be identified by running the program with a print level lt 3 It will then print in each iteration the actual estimates for the eigenvalues If some of these are very close or if complex roots appear you should make sure that the DUS procedure is not switched on before the residuals of the eigenvectors are small compared to the differences in the eigenvalues For this thrdiis controlling the DUS extrapolation in the linear solver should be set about one order of magnitude smaller than the smallest difference between two eigenvalues and preopt controlling the switch to the DIIS solver again about one order of magnitude smaller then thrdiis Tighter thresholds or difficult situations can make it necessary to increase the limit for the number of iterations maxiter In rare cases complex roots might persist even with tight
123. which they have been evaluated If both ground and excited state densities are found on file both will be passed to the density analysis thereby providing a shortcut to the fanal and the anadens keyword for the analysis of differences between ground and excited state densities The general density analysis option In general ricc2 saves by default all relaxed densities generated during a calcula tion in files named cc1td lt type gt lt mult gt lt irrep gt lt number gt where ccltd stands for coupled cluster one electron total density lt type gt is one of mp2 gs MP2 ground state cc2 gs CC2 ground state ccs xs CCS excited state cc2 xs CC2 excited state or adc2 xs ADC 2 excited state and the other entries specify multiplicity irreducible representation and the number of the state Having specified the calcu lation of relaxed densities e g by requesting relaxed one electron properties or as a by product of a gradient calculation you will end up with two files named like ccltd cc2 gs 1a1 001 ccitd cc2 xs 3a2 001 In case of open shell molecules additional files with names ccisd for one electron spin densities will be generated These files are currently in a binary format similar as the files dens mdens and edens Therefore be aware that a transfer between different computer architectures may result in trouble The densities on these files can be analysed with the tools and interfaces provided by
124. with linear perturbation Int J Quantum Chem 47 6 469 483 1993 J G Angyan Choosing between alternative MP2 algorithms in the self consistent reaction field theory of solvent effects Chem Phys Lett 241 1 2 51 56 1995 R Cammi B Mennucci J Tomasi Second order Mgller Plesset analytical derivatives for the polarizable continuum model using the relaxed density ap proach J Phys Chem A 103 45 9100 9108 1999 G Scalmani M J Frisch B Mennucci J Tomasi R Cammi V Barone Geometries and properties of excited states in the gas phase and in solution Theory and application of a time dependent density functional theory polariz able continuum model J Chem Phys 124 9 094107 2006 S Sinnecker A Rajendran A Klamt M Diedenhofen F Neese Calcula tion of solvent shifts on electronic g tensors with the Conductor like Screening Model COSMO and its self consistent generalization to real solvents Direct COSMO RS J Phys Chem A 110 2235 2245 2006 F Eckert A Klamt Fast solvent screening via quantum chemistry COSMO RS approach AICHE Journal 48 369 385 2002 A Klamt V Jonas T B rger J C W Lohrenz Refinement and parametriza tion of COSMO RS J Phys Chem A 102 5074 5085 1998 O Treutler R Ahlrichs Efficient molecular numerical integration schemes J Chem Phys 102 1 346 354 1995 A D Becke A multicenter numerical integration scheme for
125. you keep a copy of the file hessian A general prerequisite for this option is that you have defined a set of non redundant coordinates for all 3N 6 3N 5 degrees of freedom of your molecule To make sure that this is the case you should switch off redundant coordinates currently this is only possible by manually removing the data group redundant and also removing the entry redundant on in optimize Run define to generate non redundant coordinates by using the iaut command in the internal coordinate menu or by creating them manually via idef We recommend to use the irem command first to delete all previous definitions of internal coordinates See Section 4 for further details If the molecules point group is not C4 define will set some of the coordinate to status d display or i ignore Use the ic command to change all coordinates to k You can also achieve this by editing in the intdef data group manually The analysis in internal coordinates is switched on by adding a line in the data group drvopt that has the following syntax analysis only intcoord print print level Keywords in square brackets are optional If only is added the program assumes that the file hessian exists and runs only the analysis part of aoforce The program will give the following output controlled by the print level given in parenthesis e diagonal elements of the Hessian in internal coordinates force constants of bonds angles etc print level
126. 0 e complete force constant matrix in internal coordinates print level 2 e normal modes in terms of internal coordinates print level 1 e Potential energy contributions V 7 defined as Vg LPL Fijo where L are the elements of the normal coordinate belonging to mode n and F j are the elements of the force constant matrix both expressed in the internal coordinate basis w is the related eigenvalue The program will list the diagonal contributions Ve print level 1 the off diagonal contributions Vp Vp h print level 2 for up to 10 atoms else print level 10 and the brutto contributions gt gt Vp print level 1 e Based on these quantities the program will give an assignment of normal modes by listing all internal coordinates with large diagonal or brutto contributions print level 0 13 2 CALCULATION OF RAMAN SPECTRA 227 Note that for large molecules or complicated topologies the B matrix that is used to transform from Cartesian coordinates into internal coordinates and vice versa may become singular In this case only the normal modes in the internal coordinate basis can be listed 13 2 Calculation of Raman Spectra Vibrational Raman scattering cross sections are computed in the approximation of the polarizability theory from derivatives of the frequency dependent polarizability tensor with respect to normal modes of vibration 5 ky cia w cay w Here a w and Y w denote the iso
127. 0 The generated file td vec will contain the quantity pe aeay o n u 2 20 1 20 2 22 Keywords for Module FROG The ab initio molecular dynamics MD program frog needs a command file named mdmaster The interactive Mdprep program manages the generation of mdmaster and associated files It is always a good idea to let Mdprep check over mdmaster before starting an MD run Mdprep has online help for all menus In this implementation of ab initio MD time is divided into steps of equal duration At Every step the energy and its gradient are calculated and these are used by the frog to work out the new coordinates for the next step along the dynamical trajectory Both the accuracy of the trajectory and the total computation time thus depend crucially on the time step chosen in Mdprep A bad choice of timestep will result in integration errors and cause fluctuations and drift in the total energy As a general rule of thumb a timestep At should be chosen which is no longer than one tenth of the shortest vibrational period of the system to be simulated Note that Mdprep will transform velocities so that the total linear and angular mo mentum is zero Actually for the Leapfrog algorithm initial velocities are At 2 before the starting time The following keywords are vital for frog nsteps 75 Number of MD time steps to be carried out nsteps is decreased by 1 every time frog is run and JOBEX md stops when nsteps reaches 0
128. 0 6 4ali 0 87046 2 16 0 0000 0 0000 TO CONTINUE ENTER lt return gt This allows you to get the linear combination of basis functions which form the MO index Note that this refers not to the basis set you spec ified but to the extended Hiickel basis index must be a single index not an index list This command allows you to specify closed shells Their occupation will be 2 per MO the total occupation the shell degeneracy which you can obtain by using command s list is a list of shell indices like 1 13 or 1 3 5 7 This command allows you to specify open shells index must be a single shell index not an index list You will then be asked for the number of electrons per MO which shall be contained in this shell For example for a fluorine atom you should choose o n where n is the index of the 70 CHAPTER 4 PREPARING YOUR INPUT FILE WITH DEFINE p shell and an occupation of 5 3 per MO You may enter the occu pation numbers as simple integers or as integer fractions e g 1 for the s occupation in sodium 5 3 for the p occupation in fluorine v list With this command you can remove an orbital occupation if you speci fied a wrong one list is again a list of shell indices in usual syntax amp This command has a different meaning in this menu than in the rest of define Here it will repeat the extended Hiickel calculation perhaps you want to change some Hiickel parameters for the next one will not bring you back to the
129. 0 00 0 00 18 1 000 0 357 0 01 0 00 0 98 0 20 0 27 0 01 0 50 0 00 0 00 20 1 000 0 335 0 00 0 00 1 00 0 00 0 00 0 00 0 00 1 00 0 00 22 1 000 0 333 0 01 0 00 0 99 0 13 0 03 0 32 0 00 0 00 0 51 23 1 000 0 333 0 01 0 00 0 99 0 14 0 03 0 34 0 00 0 00 0 49 BETA 39 1 000 0 326 0 00 0 00 1 00 0 33 0 08 0 09 0 00 0 00 0 50 41 1 000 0 326 0 00 0 00 1 00 0 33 0 08 0 09 0 00 0 00 0 50 43 1 000 0 321 0 00 0 00 1 00 0 00 0 00 0 00 0 00 1 00 0 00 46 1 001 0 318 0 05 0 00 0 95 0 00 0 43 0 51 0 00 0 00 0 00 RELEVANT LMOS FOR ATOM 2 cu ALPHA index occupation energy s p d f daxx dyy dzz dxy dxz dyz 16 1 000 0 357 0 01 0 00 0 98 0 20 0 27 0 01 0 50 0 00 0 00 17 1 000 0 357 0 01 0 00 0 98 0 20 0 27 0 01 0 50 0 00 0 00 19 1 000 0 335 0 00 0 00 1 00 0 00 0 00 0 00 0 00 1 00 0 00 21 1 000 0 333 0 01 0 00 0 99 0 13 0 03 0 32 0 00 0 00 0 51 24 1 000 0 333 0 01 0 00 0 99 0 14 0 03 0 34 0 00 0 00 0 49 BETA 40 1 000 0 326 0 00 0 00 1 00 0 33 0 08 0 09 0 00 0 00 0 50 42 1 000 0 326 0 00 0 00 1 00 0 33 0 08 0 09 0 00 0 00 0 50 4 3 GENERATING MO START VECTORS 73 44 1 000 0 321 0 00 0 00 1 00 0 00 0 00 0 00 0 00 1 00 O 45 1 001 0 318 0 05 0 00 0 95 0 00 0 43 0 51 0 00 0 00 O a2b FLIPPING ALPHA TO BETA default b2a FLIPPING BETA TO ALPHA r repeat atom choice As evident from the second column for each Cu atom five localized alpha and four localized beta orbitals were generated which are of d type the sixth column labelled d shows valu
130. 00 1 85766051386774 1 85766051386774 intdef definitions of internal coordinates 1 k 1 0000000000000 stre 2 d 1 0000000000000 stre 3 k 1 0000000000000 bend end File basis basis n def SVP n 7s4pid 5 s 1712 8415853 257 64812677 58 458245853 16 198367905 5 0052600809 1 s 58731856571 1 s 18764592253 3 p 13 571470233 2 9257372874 79927750754 1 p 21954348034 1 d 1 0000000000 def SVP 3s2p1d CHAPTER 21 SAMPLE CONTROL FILES 00000000000000 1 00494155217173 n 00000000000000 50247077608587 o 00000000000000 50247077608587 o 2 1 val 2 39232 3 1 val 2 39232 2 3 1 val 101 88429 511 31 1 563934125305E 02 40221581118E 01 17931144990 46376317823 4417 1422662 1 0000000000 1 0000000000 40072398852E 01 21807045028 51294466049 1 0000000000 1 0000000000 o 7s4pid 3s2p1d 511 31 1 21 3 NO INPUT FOR AN UNRESTRICTED DFT CALCULATION 2266 1767785 340 87010191 77 363135167 21 479644940 6 6589433124 1 s 80975975668 1 s 25530772234 3 p 17 721504317 3 8635505440 1 0480920883 1 p 27641544411 1 d 1 2000000000 end 53431809926E 02 39890039230E 01 17853911985 46427684959 44309745172 1 0000000000 1 0000000000 43394573193E 01 23094120765 51375311064 1 0000000000 1 0000000000 385 386 CHAPTER 21 SAMPLE CONTROL FILES 21 4 TaCl
131. 00000 1 0000000000 40072398852E 01 21807045028 51294466049 1 0000000000 1 0000000000 511 19682158000E 01 13796524000 47831935000 1 0000000000 1 0000000000 format 4d20 14 SAMPLE CONTROL FILES 21 2 NH3 INPUT FOR A RHF CALCULATION 1 al eigenvalue 15633041862301D 02 nsaos 10 98699003163455D 00 47221435341751D 01 55873125006179D 02 26746008768233D 02 20823779196149D 03 14270460008808D 01 58676121352806D 03 29091871198884D 03 2 ail eigenvalue 99896275238736D 00 nsaos 10 26412162337482D 00 51846472345768D 00 37623729061179D 00 47252329287316D 02 21494050853221D 02 11795673774658D 00 11229203933488D 01 27038186251429D 02 3 al eigenvalue 57101279949392D 00 nsaos 10 35584199011701D 01 96938258881594D 01 70254605702716D 01 44746149963029D 00 40094287741992D 03 51691151834284D 01 19189122068531D 02 56638497851180D 03 1 e eigenvalue 64374209294851D 00 nsaos 9 49313475446075D 00 33757893447603D 00 76142296567409D 04 26407572210452D 00 22619038902975D 00 50035170531670D 05 63021657663245D 04 end 48016374887169D 02 90849517503597D 02 77139882704089D 02 83316086019184D 01 65569041318341D 00 47722350097160D 01 74524664248740D 04 12199166245418D 03 381 382 CHAPTER 21 SAMPLE CONTROL FILES 21 3 NO input for an unrestricted DFT calculation Main File control title NO2 c2v UKS SVP operating system unix sy
132. 01 2011 R Bauernschmitt R Ahlrichs Treatment of electronic excitations within the adiabatic approximation of time dependent density functional theory Chem Phys Lett 256 4 5 454 464 1996 R Bauernschmitt R Ahlrichs Stability analysis for solutions of the closed shell Kohn Sham equation J Chem Phys 104 22 9047 9052 1996 F Furche R Ahlrichs Adiabatic time dependent density functional methods for excited state properties J Chem Phys 117 16 7433 7447 2002 BIBLIOGRAPHY 407 21 22 23 24 25 26 27 28 29 30 31 32 M Kollwitz J Gauss A direct implementation of the GIAO MBPT 2 method for calculating NMR chemical shifts Application to the naphthalenium and and anthracenium ions Chem Phys Lett 260 5 6 639 646 1996 C van Wiillen Shared memory parallelization of the TURBOMOLE programs AOFORCE ESCF and EGRAD How to quickly parallelize legacy code J Comp Chem 32 1195 1201 2011 M von Arnim R Ahlrichs Geometry optimization in generalized natural internal coordinates J Chem Phys 111 20 9183 9190 1999 P Pulay G Fogarasi F Pang J E Boggs Systematic ab initio gradient calcu lation of molecular geometries force constants and dipole moment derivatives J Am Chem Soc 101 10 2550 2560 1979 M Dolg U Wedig H Stoll H Preuf Energy adjusted ab initio pseudopo tentials for the first ro
133. 03 The parameters in this definition have the following meaning symb atom symbol list list of all atoms for which this definition should apply The syntax for this list is as usual in TURBOMOLE e g 2 3 8 10 12 nmao 2 means number of MAOs to be included method meth means selection criterion for MAOs meth can be occ default eig or man string where occ denotes selection of MAOs by occupation num bers eig selection by eigenvalues and man allows manual selection In the latter case the string max 8 characters appended to man serves as nickname for the definition of the MAOs to be chosen This nickname is expected to appear as the leftmost word in a line somewhere within data group mao selection and is followed by the indices of the modified atomic orbitals which are to be selected threshold r means the threshold to be applied for the selection criteria occ or eig default 0 1 Example mao selection threshold 0 09 atom c 1 3 5 nmao 5 method eig threshold 0 1 atom o 2 nmao 3 method man olabel olabel 3 5 option plot is out of fashion to plot quantities on a grid rather use pointval in connection with dscf ridft rimp2 or egrad as described below If never theless plot is active you need grid 1 mo 4aig origin 000000 000000 000000 vector1l 1 000000 000000 000000 vector2 000000 1 000000 000000 gridi range 5 000000 5 000000 points 100 grid2 range 5 000000 5 000000 points 100 30
134. 136 2003 XXIV Nuclear second analytical derivative calculations using auxiliary basis set ex pansion P Deglmann K May F Furche and R Ahlrichs Chem Phys Let ters 384 103 2004 XXV Efficient evaluation of three center two electron integrals over Gaussian func tions R Ahlrichs Phys Chem Chem Phys 6 5119 2004 XXVI Analytical time dependent density functional derivative methods within the RI J approximation an approach to excited states of large molecules D Rap poport and F Furche J Chem Phys 122 064105 2005 XXVII Density functional theory for excited states equilibrium structure and elec tronic spectra F Furche and D Rappoport Ch HI of Computational Pho tochemistry Ed by M Olivucci Vol 16 of Computational and Theoretical Chemistry Elsevier Amsterdam 2005 XXVIII Structure optimizations for excited states with correlated second order meth ods CC2 CIS D and ADC 2 Christof Hattig Adv Quant Chem 50 37 60 2005 XXIX Distributed memory parallel implementation of energies and gradients for second order Moller Plesset perturbation theory with the resolution of the identity ap proximation Christof Hattig Arnim Hellweg Andreas K hn Phys Chem Chem Phys 8 1159 1169 2006 18 XXX XXXI XXXII XXXIII XXXIV XXXV XXXVI CHAPTER 1 PREFACE AND GENERAL INFORMATION Self consistent treatment of spin orbit interactions with efficient
135. 2 1 OEP EXX In the present implementation the OEP EXX local potential is expanded as 172 VEX r wey oe ae 18 6 p where gp are gaussian functions representing a new type of auxiliary basis set see directory xbasen Inserting Eq 18 6 into Eq 18 2 a matrix equation is easily obtained for the coefficient cp Actually not all the coefficients cp are independent each other as there are other two conditions to be satisfied the HOMO condition see Eq 18 4 and the charge condition XE ooo 1 18 7 p which ensures that v X r approaches 1 r in the asymptotic region Actually Eq 18 6 violates the condition 18 5 on the HOMO nodal surfaces such condition cannot be achieve in any simple basis set expansion Note that for the computation of the final KS Hamiltonian only orbital basis set matrix elements of vEX are required which can be easily computes as three index Coulomb integrals Thus the present OEP EXX implementation is grid free like Hartree Fock but in contrast to all other XC functionals 258 CHAPTER 18 ORBITAL DEPENDENT DFT 18 2 2 LHF In the LHF implementation the exchange potential in Eq 18 3 is computed on each grid point and numerically integrated to obtain orbital basis sets matrix elements In this case the DFT grid is needed but no auxiliary basis set is required The Slater potential can be computed numerically on each grid point as in Eq 18 3 or using a basis set expansio
136. 2 15 Keywords for Module EGRAD egrad uses the same general keywords as escf and grad see Sections 20 2 9 and 20 2 12 The state to be optimized is by default the highest excited state specified in soes Note that only one IRREP can be treated at the same time in contrast to escf calculations When the desired excited state is nearly degenerate with another state of the same symmetry it may be necessary to include higher states in the initial calculation of the excitation energy and vector in order to avoid root flipping This is accomplished by means of the additional keyword exopt n which explicitly enforces that n th excited state is optimized n must not be larger than the number of states specified in soes nacme flag to compute Cartesian non adiabatic coupling vectors between the excited state of interest and the ground state 195 This option requires the use of weight derivatives in section dft It is only implemented for C1 symmetry 20 2 16 Keywords for Modules MPGRAD and RIMP2 If an MP2 run is to be performed after the SCF run the SCF run has to be done with at least 1 density convergence denconv 1 d 7 2 energy convergence scfconv 6 20 2 FORMAT OF KEYWORDS AND COMMENTS 323 Keywords Valid for Both MPGRAD and RIMP2 maxcor n The data group maxcor adjusts the maximum size of core memory n in MB which will be allocated during the MP2 run Recommendation 3 4 of the actual main memory at most If max
137. 20 2 FORMAT OF KEYWORDS AND COMMENTS 337 contain diffuse basis functions For calculations on large molecules with small or medium sized basis sets the preoptimization becomes inefficient compared to the large effects of integral screening for the conventional CPHF equations and should be disabled This option is automatically disabled for ricc2 calculations based on foregoing RI JK Hartree Fock calculation nozpreopt disable the preoptimization of the Z vector by a preceding RI CPHF calculation with the cbas basis set Note that the preoptimization is automatically deactivated if the ricc2 calculation is based on a foregoing RI JK Hartree Fock calculation Common options for keywords in the data groups ricc2 response and excitations operators diplen dipvel input of operator labels for first order properties transition moments etc Currently implemented operators labels are overlap overlap charge operator the integrals evaluated in the AO basis are ulv diplen dipole operator in length gauge r v with i z y z the index O indicates dependency on the origin for expectation values of charged molecules which in the present version is fixed to 0 0 0 all three components individual components can be specified with the labels xdiplen ydiplen zdiplen dipvel dipole operator in velocity gauge u V v all three components individual components can be specified with the labels xdipvel ydipvel zdipvel
138. 20 2 16 Keywords for Modules Mpgrad and Rimp2 316 20 2 17 Keywords for Module Ricc2 aaae 319 20 2 18 Keywords for Module Relax aoaaa 339 20 2 19 Keywords for Module Statpt 342 20 2 20 Keywords for Module Moloch 344 20 2 21 Keywords for wave function analysis and generation of plotting Mabe ents 4 oe Se oh Sk doe Bo he Ge gd 348 20 2 22 Keywords for Module Frog 22 358 20 2 23 Keywords for Module Mpshift 365 10 20 2 24 Keywords for Parallel Runs 21 Sample control files 21 1 introduction s o es eoe eh ee wee ee ee ee 21 2 NH3 Input for a RHF Calculation 21 3 NO input for an unrestricted DFT calculation 21 4 TaCls Input for an RI DFT Calculation with ECPs 21 5 Basisset optimization for Nitrogen 21 6 ROHF of Two Open Shells i o soser be ep eee 22 The Perl based Test Suite Structure Sool Genefal o e Shwe book we hd Soe ha be hd eG a 22 2 R mmng he este e e a ce es a ae eR A eG 22 3 Taking the timings and benchmarking 22 4 Modes and options of the TTEST script Bibliography Index CONTENTS Chapter 1 Preface and General Information 1 1 Contributions and Acknowledgements TURBOMOLE 1 is a development of University of Karlsruhe and Forschungszentrum Karlsruhe GmbH 1989 2007 TURBOMOLE GmbH since 2007 The following peo ple have made contributions R
139. 39 804400921 000008912 402049065 4 804400921 2 402136564 0 000013520 0 000008912 7 206440926 4 804286480 FowWworeFe oF OWW Oo I N O m m o 0O e O A N Q Nre N CO WWAHOANKPHTOBGB THF WOO AHA ROAA 547518253 934402943 160642624 547518253 934336185 321288109 708164215 321288109 156304836 483696461 893717766 457115650 265182018 029124260 893717766 617761612 425827980 316950798 644342422 029124260 094982147 773757219 934336185 773690462 160642624 321288109 095048904 934402943 321288109 N ONI 977437973 064809799 10 977437973 11 10 977437973 10 957920074 11 11 957922935 11 957910538 11 957922935 11 957920074 11 957910538 11 064809799 11 11 611351967 611351967 064809799 064809799 611351967 247499466 246870041 247499466 247499466 127141953 127161026 127140045 127161026 127140045 127141953 246870041 246870041 246870041 147 Finally you have to specify the coordinates of the QM cluster along with the sur rounding ECPs This is done in the usual way using the coord keyword coo rd 0 00002358760000 4 53939007480000 4 53939638280000 9 07879006320000 10 48329315900000 13 10412613690000 7 86247730390000 10 48329315900000 18 85463057110000 15 24028611330000 19 36497297520000 18 85463057110000 al al al al 148 CHAPTER 6 HARTR
140. 4 5 digits k can be changed by specifying rpaconv k Several roots i e several excited states or frequencies can be treated simultaneously which is very effective and permits the cal culation of whole excitation spectra and dispersion curves During the iteration the vectors are kept on scratch files vfile_ lt IR gt wfile_ lt IR gt and or rhs_ lt IR gt where IR denotes an IRREP of the point group see below Before the programs terminate the converged vectors are written onto formatted files type IR where type is an abbreviation for the type of response calculation performed cf scfinstab Given these files in the working directory escf and egrad calculations can be restarted or continued e g with a larger number of roots Integral direct algorithm In the iterative method outlined above the super matrices A and B never need to be set up explicitly only the products of A and B with some suitable basis vectors are required These matrix vector products are evaluated very efficiently in the AO basis because the required four index integrals can be computed on the fly and need not be transformed or stored on disk In addition prescreening techniques based on rigorous bounds are straightforward to 156 CHAPTER 7 HF AND DFT RESPONSE CALCULATIONS apply This leads to a low order scaling O N O N for the time determining steps Due to the similarity to ground state fock matrix construction the same keywords ar
141. 4 fit CHAPTER 20 KEYWORDS IN THE CONTROL FILE outfile 4alg to obtain two dimensional plot data of mo 4alg the plane is specified by origin and two vectors with grid range and number of grid points which is written to file 4alg Several plots may be obtained 1 2 etc at the same time Use tool konto to visualize the plot Note This is the old fashioned way to plot MOs and densities A new and easier one is to use pointval as described below if fit is active you need vdw_fit shell number_of_gridpoints distance_from_vdW_surface refine value_of_potential shell Each line refers to all atoms the line specifies a spherical layer of grid points around the atoms The number of points and their dis tance from the van der Waals surface Bohr are given the default is 1 0 refine one line only smoothing of the layers of grid points around the molecule the real number is used to define isopotential surfaces on which the points of the layers have to lie vdw_radii element_symbol van_d_waals_radius One line per element has to be specified it contains the name of the element and the van der Waals radius in Bohr 20 2 21 Keywords for wave function analysis and generation of plot ting data Properties of RHF UHF and two component GHF wave functions as well as those of SCF MP2 densities or such from excited state DFT calculations can be directly analyzed within the respective programs d
142. 49 4298351805 298 8595975321 i i e e O oT i i Oo Oo Singlet delta in D2h xy yx component an example of the general type xy singlet where in D2h x b2g and y b3g are of different symmetry In D infinity h b2g and b3g combine to eg see the reference calculation in D3d above coord 0 0 0 0 1 08597397921317 o 0 0 0 0 1 08597397921317 o symmetry d2h closed shells ag 1 3 biu 1 2 b2u 1 b3u 1 open shells type 1 b2g 1 b3g 1 1 roothaan 2 rohf 1b2g 1b3 g a 1 b 2 1b2g 1b2g a 0 b 0 1b3g 1b3g a 0 b 0 energy SCF SCFKIN SCFPOT 1 149 4297623501 149 4298391833 298 8596015334 EN NNN N N NN e a N m Chapter 22 The Perl based Test Suite Structure 22 1 General Testing the TURBOMOLE modules for correctness and speed is the first task once the coding is completed It is subject to automatization and thus requires a structure which is as simple and flexible as possible In the Perl based test suite this is im plemented by a Perl script TTEST which performs all the testing and benchmarking tasks and resides in the central scripts directory of the TURBOMOLE installation The test examples are located in subdirectories of the TURBOTEST directory grouped according to the modules modules to be tested and a rough short long classifica tion The benchmark suite shows the same directory structure and is rooted in the TURBOBENCH directory The central idea of the Perl based test
143. 5 3 Only experts should try to change default settings Optimization Methods The first of the relax subgenus deals with the type of optimization to be performed int F INTERNAL coordinates crt F CARTESIAN coordinates bas F BASIS SET exponents scale factors glb F GLOBAL scaling factor use lt opt gt for enabling lt opt gt for disabling option lt opt gt lt RETURN gt OR OR q uit WILL TERMINATE THIS MENU 84 CHAPTER 4 PREPARING YOUR INPUT FILE WITH DEFINE You can choose between a geometry optimization in the space of internal coordi nates in this case you will need definitions of internal coordinates of course or in the space of Cartesian coordinates these possibilities are mutually exclusive of course Furthermore optimizations of basis set parameters exponents contraction coefficients and scaling factors or of a global scaling factor is possible these options are also exclusive but can be performed simultaneous to a geometry optimization For the geometry optimization you should normally use internal coordinates as they provide better convergence characteristics in most cases Coordinate Updates The next submenu deals with the way relax updates the old coordinates You may choose a maximum change for the coordinates or you can allow coordinate updates by means of extrapolation dqmax lt real gt coordinates are allowed to change by at most lt real gt DEFAULT 0 3000 a u polish p
144. 5928 2 837586403 0 180958077 0 3 142566681 0 115072958 4 558810234 0 0 751034439 1 292158127 2 350189686 0 0 703617156 1 427564979 0 180938885 end charges 0 2 0 Al 3 0 end The above input defines a periodic perfect and infinite two dimensional lattice of point charges corresponding to the 0001 a Al20O3 surface In order to use the lattice for PEECM calculation we have to make space for our QM cluster and the surrounding ECP shell This is done by specifying the part of the lattice that is virtually removed from the perfect periodic array of point charges to make space for the cluster The positions of the removed point charges are specified in the subsection cluster of the embed keyword Note that the position of the QM cluster must exactly correspond to the removed part of the crystal otherwise positions of the cluster atoms would overlap with positions of point charges in the periodic lattice 6 5 PERIODIC ELECTROSTATIC EMBEDDED CLUSTER METHOD resulting in a nuclear fusion clus Al Al Al Al Al Al Al 2 OOO OF OPO OO 2S OG rrr rr Fr Se eS Se PPP PPP PP Pp end The positions of point charges are specified in A as Cartesian coordinates ter ang 0 000012482 2 402141094 2 402144432 4 804287434 2 402250767 0 000005568 2 402137518 4 804294586 0 907584429 1 517618299 703624666 145677090 990177393 751026928 100675106 743527174 588027477 309734344 919768333 5553269
145. 6939 2002 An efficient implementation of second analytical derivatives for density func tional methods P Deglmann F Furche and R Ahlrichs Chem Phys Let ters 362 511 2002 Efficient characterization of stationary points on potential energy surfaces P Deglmann and F Furche J Chem Phys 117 9535 2002 An improved method for density functional calculations of the frequency depen dent optical rotation S Grimme F Furche and R Ahlrichs Chem Phys Letters 361 321 2002 1 3 HOW TO QUOTE USAGE OF TURBOMOLE 17 XIX Adiabatic time dependent density functional methods for excited state proper ties F Furche and R Ahlrichs J Chem Phys 117 7433 2002 J Chem Phys 121 12772 2004 E XX A fully direct RI HF algorithm Implementation optimised auxiliary basis sets demonstration of accuracy and efficiency F Weigend Phys Chem Chem Phys 4 4285 2002 XXI Geometry optimizations with the coupled cluster model CC2 using the reso lution of the identity approximation C Hattig J Chem Phys 118 7751 2003 XXII Analytic gradients for excited states in the coupled cluster model CC2 employ ing the resolution of the identity approximation A K hn and C Hattig J Chem Phys 119 5021 2003 XXIII Fast evaluation of the Coulomb potential for electron densities using multipole accelerated resolution of identity approximation M Sierka A Hogekamp and R Ahlrichs J Chem Phys 118 9
146. 725683720000 92800239300000 25351019750000 24028611330000 25351019750000 25351019750000 38337475740000 38337475740000 24028611330000 24028611330000 38337475740000 between QM cluster and ECP shell is made in the atoms section atoms al 1 8 basis al def SV P o 9 20 basis o def SV P al 21 29 basis none ecp al ecp 10 hay amp wadt In the example above the Al atoms 1 8 and O atoms 9 20 are defined as QM atoms with def SV P basis sets The Al atoms 21 29 are pure ECPs and have no basis functions basis none This step ends the input definition for the PEECM calculation o 9 pp w Poe Pe oOo 002C0C00C060UC CUGDUUC UwMlLCOCO o op w pp Pp Pp M H PPP Pe PP Pp 6 6 DISPERSION CORRECTION FOR DFT CALCULATIONS 149 6 6 Dispersion Correction for DFT Calculations Based on an idea that has earlier been proposed for Hartree Fock calculations 84 85 a general empirical dispersion correction has been proposed by Stefan Grimme for density functional calculations 86 A modified version of the approach with extension to more elements and more functionals has been published in ref 87 The most recent implementation 88 is less empirical i e the most important parameters are computed by first principles and it provides a consistent description across the whole periodic system The first version DF T D1 can be invoked by the keyword olddisp in the control file The second version DFT D2 is used if the keywo
147. 8 Parameters 1 precision parameter 1 00E 06 2 maximum multipole 1 moment 10 3 maximum number of bins 8 4 minimum separation of bins 0 00 5 maximum allowed extension 20 00 6 threshold for multipole neglect 1 00E 18 Enter the number to change a value or lt return gt to accept all Just rely on the defaults Multiple auxiliary basis sets With the command trunc you can switch on this option Effect a reduced auxiliary or fitting basis to represent the electron density is employed during SCF iterations the final SCF iteration and the gradient are computed with the full auxiliary basis truncated RI ALREADY SWITCHED ON DO YOU WANT TO SWITCH OFF truncation default no 78 CHAPTER 4 PREPARING YOUR INPUT FILE WITH DEFINE Note trunc is presently not compatible with marij RI in SCF calculations Considerable savings in CPU times are achieved with the RI technique for both Coulomb J and exchange K terms in SCF calculations the RI JK method 29 provided large basis sets are employed e g TZVPP cc pVTZ or cc pVQZ With rijk you get STATUS OF RI OPTIONS RI IS NOT USED Memory for RI 200 MB Filename for auxbasis auxbasis ENTER RI OPTION TO BE MODIFIED m CHANGE MEMORY FOR RI f CHANGE FILENAME jkbas ASSIGN AUXILIARY RI JK BASIS SETS on TO SWITCH ON RI Use lt ENTER gt q end or to leave this menu For an explanation of the menu items see Section 4 4 1 RI JK calculations can be carried out w
148. 96 S Laricchia E Fabiano F Della Sala Frozen density embedding with hybrid functionals J Chem Phys 133 164111 2010 S Laricchia E Fabiano F Della Sala Frozen density embedding calcula tions with the orbital dependent localized Hartree Fock Kohn Sham potential Chem Phys Lett 518 114 2011 L A Constantin E Fabiano S Laricchia F Della Sala Semiclassical neutral atom as a reference system in density functional theory Phys Rev Lett 106 186406 2011 S Laricchia E Fabiano L A Constantin F Della Sala Generalized gradi ent approximations of the noninteracting kinetic energy from the semiclassical atom theory Rationalization of the accuracy of the frozen density embedding theory for nonbonded interactions J Chem Theory Comput 7 2439 2011 A Lembarki H Chermette Obtaining a gradient corrected kinetic energy functional from the Perdew Wang exchange functional Phys Rev A 50 5328 1994 F D Sala A G rling Efficient localized Hartree Fock methods as effective exact exchange Kohn Sham methods for molecules J Chem Phys 115 13 5718 5732 2001 A G rling Orbital and state dependent functionals in density functional the ory J Chem Phys 123 6 062203 2005 S K mmel L Kronik Orbital dependent density functionals Theory and applications Rev Mod Phys 80 1 3 2008 BIBLIOGRAPHY 419 171 172 173 174 175 176
149. A Bischoff A Glo C Hattig S H fener W Klopper D P Tew J Comput Chem 32 2011 2492 e for O N scaling calculations using the Laplace transformation ground state and excitation energies N O C Winter C Hattig J Chem Phys 134 2011 184101 transition moments first order properties and gradients N O C Winter C Hattig Chem Phys 401 2012 217 e for second order properties relaxed or unrelaxed D H Friese N O C Winter P Balzerowski R Schwan C Hattig J Chem Phys 136 2012 174106 Auxiliary basis sets e the appropriate reference for the auxiliary SVP TZVP and TZVPP basis sets for calculations with RI MP2 RI CC2 and related methods is F Weigend M Haser H Patzelt R Ahlrichs Chem Phys Lett 294 1998 143 e for the auxiliary cc pVXZ cc pV X d Z aug cc pV XZ aug cc pV X d Z basis sets with X D T or Q cite F Weigend A Kohn C Hattig J Chem Phys 116 2001 3175 e for the auxiliary cc pV5Z cc pV 5 d Z aug cc pV5Z aug cc pV 5 d Z cc pwCVXZ with X D T Q 5 and QZVPP basis sets the reference is C Hattig Phys Chem Chem Phys 7 2005 59 66 This reference should also be included if you employ the analytic basis set gradients implemented in the ricc2 program for the optimization of your own auxiliary basis set s 10 1 CC2 GROUND STATE ENERGY CALCULATIONS 187 e for the auxiliary def2 basis sets from Rb to Rn the reference is
150. A Hellweg C Hattig S H fener and W Klopper Theor Chem Acc 117 2007 587 597 e for the auxiliary cc pVXZ PP aug cc pVXZ PP cc pwCVXZ PP and aug cc pwCVXZ PP basis sets for Ga Kr In Xe and Tl Rn C Hattig G Schmitz J Ko amp fmann Phys Chem Chem Phys 14 2012 6549 6555 For more details on the references for the basis sets included in the basis set libraries of the TURBOMOLE distribution see Sec 1 3 and the library files 10 1 CC2 Ground State Energy Calculations The CC2 ground state energy is similarly to other coupled cluster energies ob tained from the expression Eco HF H CC HF Hexp T HF 10 1 Boor gt gt ti tati 2Caljb jalib 10 2 iajb where the cluster operator T is expanded as T Ti T gt with T Yoi 10 3 ai 1 Th 5 pe 10 4 aibj for a closed shell case in an open shell case an additional spin summation has to be included The cluster amplitudes tf and tJ are obtained as solution of the CC2 cluster equations 124 Qu nl TIF 0 10 5 Qu ul F T2 HF 0 10 6 with H exp T H exp T where u1 and u2 denote respectively the sets of all singly and doubly excited deter minants The residual of the cluster equations Q ta taibj is the so called vector function The recommended reference for the CC2 model is ref 124 the implementation with the resolution of the identity approximation RI CC2 was f
151. A Vydrov T V Voorhis Nonlocal van der waals density functional The simpler the better J Chem Phys 133 244103 2010 W Hujo S Grimme Comparison of the performance of dispersion corrected density functional theory for weak hydrogen bonds Phys Chem Chem Phys 13 13942 13950 2011 F Furche D Rappoport Density functional methods for excited states equi librium structure and electronic spectra In M Olivucci Ed Computational Photochemistry Band 16 von Computational and Theoretical Chemistry Kapi tel III Elsevier Amsterdam 2005 F Furche On the density matrix based approach to time dependent density functional theory J Chem Phys 114 14 5982 5992 2001 F Furche K Burke Time dependent density functional theory in quantum chemistry Annual Reports in Computational Chemistry 1 19 30 2005 D Rappoport F Furche Excited states and photochemistry In M A L Marques C A Ullrich F Nogueira A Rubio K Burke E K U Gross Eds Time Dependent Density Functional Theory Kapitel 22 Springer 2005 J E Bates F Furche Harnessing the meta generalized gradient approxi mation for time dependent density functional theory J Chem Phys 137 164105 2012 S Grimme F Furche R Ahlrichs An improved method for density functional calculations of the frecuency dependent optical rotation Chem Phys Lett 361 3 4 321 328 2002 H Weiss R Ahlrichs M Haser A direct
152. A energy is not directly differentiated in our method Instead we define the RI RPA energy Lagrangian LERPA E E D WIX Ve S EMIRPA C E X 0 Do CF ola Ex Wo CZSCo 1 12 10 C E D and W are independent variables LRIRPA is required to be stationary with respect to C E D and W D and W act as Lagrange multipliers enforcing that C and E satisfy the KS equations and the orbital orthonormality constraint QLRIRPA T Sa j C F ls 0 12 11 RIRPA Sa C7SC 1 0 12 12 o stat D and W are determined by the remaining stationarity conditions as 0 12 13 E stat an RIRPA L 0 12 14 ac stat It turns out from eqs 12 13 and 12 14 that the determination of D and W requires the solution of a single Coupled Perturbed KS equation Complete expres sions for D and W are given in 146 At the stationary point stat C C e D D4 W WY first order RI RPA properties are thus efficiently obtained from dERIRPA C X LRIRPA dX LRIRPA DAVOS dg 7 Ox i dg Ove o J LRIRPA dS a ade ee Finally the RPA energy gradients may be explicitly expanded as follows dEPPPA C e X prunes a x DA eu dg stat dg dg o dIt It dS re re Ww 12 16 where DRIRPA is the KS ground state one particle density matrix D plus the RI RPA difference density matrix D which corrects
153. Al Ar optimised F12 basis sets are not yet available In this case basis sets must be selected and or optimised carefully It is advised to contact the Theoretical Chemistry Group in Karlsruhe for support e mail to klopper kit edue 9 6 Laplace transformed SOS RI MP2 with O N scal ing costs The ricc2 module contains an implementation of SOS MP2 which exploits the RI approximation and a Laplace transformation of the orbital energy denominators 1 Ea b Ei j oo nL 1 e7 eaten ei ey t au 5 Woe Kate a ei te l 9 8 0 a 1 to achieve an implementation with O N scaling costs opposed to the conven tional O N scaling implementation In particular for large molecules the Laplace transformed implementation can reduce a lot the computational costs of SOS MP2 calculations without loss in accuracy The Laplace transformed implementation for SOS MP2 calculations is activated with the input laplace conv 5 where the parameter conv is a convergence threshold for the numerical integration in Eq 9 8 A value of conv 5 means that the numerical integration will be converged to a root mean squared error of 107 a u 180 CHAPTER 9 2ND ORDER M OLLER PLESSET PERTURB THEORY Whether the conventional or the Laplace transformed implementation will be more efficient depends firstly on the system size the number of occupied orbitals and secondly on the required accuracy the number of grid points for
154. Aoi 1 HE H Ty EF 50 if ul W T3 IHF 11 7 H2 with W H F To evaluate the fourth order energy one needs in addition to the first order also the second order amplitudes which are obtained from the solution of the equations all TP W THF 0 11 8 ual T W Ty JHE 0 11 9 ual FT W THF 0 11 10 From these the fourth order energy correction is computed as Bupa tia l W TP Dy 73 IW Ty TEF 11 11 H2 Eqs 11 5 and 11 7 11 11 are computational much more complex and demand ing than the corresponding doubles equations for the CC2 model If M is a measure for the system size e g the number of atoms the computational costs in terms of floating point operations for CCSD calculations scale as O N If for the same molecule the number of one electron basis functions N is increased the costs scale with O N For RI MP2 and RI CC2 the costs scale with the system size as O N and with the number of basis functions as O N The computational costs for an MP3 calculations are about the same as for one CCSD iteration For MP4 the com putational costs are comparable to those for two CCSD iteration plus the costs for the perturbation triples correction see below 11 1 COMPUTATIONAL DEMANDS 211 Explicitly correlated CCSD F12 methods In explicitly correlated CCSD cal culations the double excitations into products of virtual orbitals described by Ty 3
155. BASIS SETS bb b RESTRICTED TO BASIS SET LIBRARY bl LIST ATOMIC BASIS SETS ASSIGNED bm MODIFY DEFINITION OF ATOMIC BASIS SET bp SWITCH BETWEEN 5d 7f AND 6d 10f lib SELECT BASIS SET LIBRARY ecp ASSIGN EFFECTIVE CORE POTENTIALS ecpb ecp RESTRICTED TO BASIS SET LIBRARY ecpi GENERAL INFORMATION ABOUT EFFECTIVE CORE POTENTIALS ecpl LIST EFFECTIVE CORE POTENTIALS ASSIGNED ecprm REMOVE EFFECTIVE CORE POTENTIAL S c ASSIGN NUCLEAR CHARGES IF DIFFERENT FROM DEFAULTS cem ASSIGN NUCLEAR CHARGES FOR EMBEDDING m ASSIGN ATOMIC MASSES IF DIFFERENT FROM DEFAULTS dis DISPLAY MOLECULAR GEOMETRY dat DISPLAY ATOMIC ATTRIBUTES YET ESTABLISHED h EXPLANATION OF ATTRIBUTE DEFINITION SYNTAX TERMINATE THIS SECTION AND WRITE DATA OR DATA REFERENCES TO control GOBACK amp TO GEOMETRY MENU The headline gives you the number of atoms the number of atoms to which basis sets have already been assigned and the number of atoms to which effective core potentials have already been assigned Most of the commands in this menu deal with the specification of basis sets and pseudopotentials Basis sets available The following basis sets are available on TURBODIR basen which you may inspect to see which other basis sets are supported automatically The corresponding publi cations can be found here 1 3 SV P or def SV P for routine SCF or DFT Quality is about 6 31G TZVP or def TZVP for accurate SCF or DFT Qu
156. CF or DFT calculations for RHF or UHF runs natural orbitals natural orbital occupation keywords and data groups set by unrestricted dscf or ridft runs Contain natural MO vector and orbital occupation energy grad energies and gradients of all runs e g for documentation in a geometry opti mizations f orceapprox approximate force constant for geometry optimizations The control file must end with this keyword end 20 2 2 Keywords for System Specification General information defining the molecular system nuclear coordinates symmetry basis functions number of occupied MOs etc which are required by every module title give title of run or project here symmetry d4h Sch6nflies symbol of the point group All point groups are supported with the exception of NMR shielding and force constant calculations etc which do not work for groups with complex irreps C3 C3h T etc Use a lower symmetry group in this case atoms Example 274 CHAPTER 20 KEYWORDS IN THE CONTROL FILE atoms cu 1 4 basis cu ecp 18 arep jbas cu ecp 18 ecp cu ecp 18 arep se 5 6 basis se ecp 28 arep dzp jbas se ecp 28 ecp se arep note the backslash this is necessary For each type of atom one has to spec ify the basis set and the auxiliary fitting basis for RIDFT calculations the ECP if this is used The files basis ecp and jbas must provide the necessary information under the labels specified in at
157. DE gt lt real gt gt O DEFAULT NO SCALING min lt real gt DO NOT ALLOW EIGENVALUES OF HESSIAN TO DROP BELOW lt real gt DEFAULT 1000E 02 USE lt real gt AS A RESET VALUE FOR TOO SMALL EIGENVALUES CP min DEFAULT 1000E 02 DO NOT ALLOW EIGENVALUES OF HESSIAN TO BECOME LARGER THAN lt real gt DEFAULT 1000 WITH THE EXCEPTION OF min reset AND max ALL OPTIONS MAY BE DISABLED BY ENTERING lt opt gt lt RETURN gt OR OR q uit WILL TERMINATE THIS MENU reset lt real gt max lt real gt Initialization of the Hessian Finally there are some options to control the choice of the initial Hessian during your geometry optimization switch off initialization DEFAULT on l cart use analytical cartesian hessian provided by a 2nd derivatives calculation DEFAULT n diag use diagonal matrix with diagonal elements set individually within data groups intdef or basis or global DEFAULT n unit lt r gt use multiple of the unit matrix H lt r gt E l DEFAULT n DEFAULT lt r gt 1 000 NOTE THAT THESE OPTIONS ARE MUTUALLY EXCLUSIVE lt RETURN gt OR OR q uit WILL TERMINATE THIS MENU Option off will be used if you have already a good Hessian from a previous calcu lation which may be used cart describes an even better state where you have a Hessian from a calculation of the second derivatives available aoforce The other two options describe real procedures for initiali
158. Damping parameters for SCF iterations in order to reduce oscillations The old Fock operator is added to the current one with weight 0 5 as start if con vergence is good this weight is then reduced by the step 0 05 in each successive iteration until the minimum of 0 1 is reached These are the default settings of define for closed shell RHF DSCF automatically tries to adjust the weight to optimize convergence but in difficult cases it is recommended to start with a large weight e g 1 5 and to set the minimum to a larger value e g 0 5 scfdebug options Flags for debugging purposes Following options are available 292 CHAPTER 20 KEYWORDS IN THE CONTROL FILE vectors integer Output level concerning molecular orbitals integer O0 default means minimal output gt 1 will output all start MOs and all MOs in each iter ation density integer Output level concerning difference density matrices debug integer integer gt 0 will dump a lot of information hbe careful scfdenapproxl integer Direct SCF procedures build the Fock matrix by exploiting information from previous iterations for better efficiency With this keyword information from the last integer iterations will be used This feature is switched on with the default value 20 even if the keyword is absent The user may reduce the num ber of iterations employed to smaller values e g 10 in cases were numerical stability could become an issue With the value 0 this feature
159. E EE EE Rt ee E ES Subsystem B atomic coordinates and basis set information x y Zz atom basis set ecp Gh nA hh ah RAN a a hE Tete aaah ae 2 7537 0 0364 0 0000 f def2 TZVP none 1 0191 0 1789 0 0003 h def2 TZVP none Running Isolated subsystems FKK KK AE K K K 2K K K FK FK K K FK FK K KOK FK K ISOLATED SUBSYSTEM A FKK KK KK K K K 2K 2K K K 2K FK K K FK FK K K FK FK K Done DR KK KK K K K 2K FK K K 2K FK K K FK 2K K KOK FK K ISOLATED SUBSYSTEM B FE E ik k kk kk kk kk Done 248 CHAPTER 17 FROZEN DENSITY EMBEDDING CALCULATIONS Saved isolated subsystems data in isolated_energy ks mos_A ks mos_B ks FO kkk k Kk k Kk kk KK K FDE step 1 FR AK KK K Kg K K FK FK K 2 2g K K 2 2K K K FDE ENERGY TOTAL SYSTEM FDE BINDING ENERGY Dipole convergence 0 138071 EK KKK K kkk Kk Kk KK K FDE step 2 FR KK Kk 2K K 2K FK FK K 2K 2K K K 2K 2K K K FDE ENERGY TOTAL SYSTEM FDE BINDING ENERGY Dipole convergence 0 009246 EE KK k kkk KK Kk KK K FDE step 3 FR KK KK A Kg aK 2K FK K 2K 2K K K 2K 2K K K FDE ENERGY TOTAL SYSTEM FDE BINDING ENERGY Dipole convergence 0 004395 200 96417090754 Ha 5 865327 mHa 3 680548 kcal mol Damping 0 45 200 96418098234 Ha 5 875401 mHa 3 686870 kcal mol Damping 0 35 200 96418289036 Ha 5 877309 mHa 3 688067 kcal mol Damping 0 25 See embedded susbsystems calculations in STEP3 SUBSYSTEM_A STEP3 SUBSYS
160. ED o s es op i dcp 4 poi ee A ee A ee ee Re 93 52 1 General Information s pe s ses t Sep ee See eee ed 93 Daa Hessian Mati e s i a pe eR ho ee oe 94 523 Finding Minima s e asee ee ew Ble 95 CONTENTS 5 5 2 4 Finding transition states s Gop a eWoe a i e a e e e 95 no Program Relax ocer s oeg a ai e e Ahead hh ii a bus 96 Jal PODOI a oie g Bs ee ee E e Ge i a e E le 96 5 3 2 Optimization of General Coordinates aaa aaa aa 97 5 3 3 Force Constant Update Algorithms 98 5 3 4 Definition of Internal Coordinates 100 5 3 5 Structure Optimizations Using Internal Coordinates 100 5 3 6 Structure Optimization in Cartesian Coordinates 101 5 3 7 Optimization of Basis Sets SCF only 102 5 3 8 Simultaneous Optimization of Basis Set and Structure 102 5 3 9 Optimization of Structure and a Global Scaling Factor 103 5 3 10 Conversion from Internal to Cartesian Coordinates 103 5 3 11 Conversion of Cartesian Coordinates Gradients and Force Con stants to Internals so coure 8 be Mee RE EE 103 Poole The m Matik ec sa pae e o ee e 104 5 3 13 Initialization of Force Constant Matrices 104 Fodd Look at Resumes se eoor a eee dk ok ode ee ke Ga hee oo 105 54 Force Field Calculations os sse t 6 0 e 66 eb bebe hee we es 105 g amp l Purpose o c eime ecko amp biaeeae be ie ed See be ee 105 5 4 2 How to Perform a UFF Calculation 106 5 4 3 The UFF i
161. EE FOCK AND DFT CALCULATIONS iS 53959732680000 00001052200000 53938331720000 07880357850000 71508649490000 86788376470000 32965829240000 94446987180000 54034461170000 41923561090000 74915508620000 40506312580000 00093786570000 25449323900000 40729073370000 10 49804944110000 9 07900452260000 0 00001684120000 4 53921616520000 9 07900452260000 4 53938151440000 0 00002554910000 0 00001684120000 13 61820356690000 9 07878826040000 end I jo NOwWrRPNFPN ORFPNHP O PF This is the standard TURBOMOLE syntax for atomic coordinates The actual distinction 13 15 18 15 85428007030000 10 13 10 06002818410000 13 13 18 15 15 18 13 20 24164297480000 13 24151682240000 86247730390000 15 20 13 15 10399998250000 72496001430000 34577677080000 72496001430000 36268741690000 02724227310000 31245694970000 28312353520000 02724227310000 17494056150000 92251179600000 71676368210000 22517102690000 28312353520000 96648359440000 10399998250000 72496001430000 96660974680000 10412613690000 72496001430000 21 19 18 19 16 21 21 16 21 16 21 16 21 16 21 16 21 15 21 21 14 14 15 15 14 25351019750000 36497297520000 85463057110000 36497297520000 92802041340000 02725683720000 02729288000000 92802581990000 02725323160000 92800239300000 02729288000000 92802581990000 02725323160000 92802041340000 02
162. F energy with respect to elec trostatic field default off increment for numerical differentiation is edelt see below 2nd derivative on off Calculate numerical 2nd derivative of SCF energy with respect to elec trostatic field default off increment for numerical differentiation is edelt edelt real Increment for numerical differentiation default 0 005 fields on off Calculate SCF energy for non zero external electrostatic fields defined in electrostatic field geofield on off Calculate SCF energy for one external field definition and dump dis turbed MOs onto scfmo This enables to evaluate properties or perform geometry optimizations in the presence of an external field 20 2 FORMAT OF KEYWORDS AND COMMENTS 289 Caution don t use the RI approximation for all these calculations since this will lead to non negligible errors incore integer By using this option the two electron integrals are kept in RAM integer spec ifies how many megabytes should be allocated If the integrals exceed the RAM allocated the program reverts to the standard mode Supports all meth ods which process two electron integrals i e SCF and DFT including hybrid functionals RHF and UHF The following condition must be met scfdenapproxl 1 and rhfshells 1 or 2 It is advisable to set thize as small as possible e g thize 0 1d 08 and to remove the keyword scfdump Note this keyword does not work for parallel runs mo di
163. F12 and CCSD F12 Quintuple quality coupled cluster correlation energies with triple basis sets David P Tew Wim Klopper Christian Neiss Christof Hattig Phys Chem Chem Phys 9 921 1930 2007 e for MP4 F12 CCSD F12 CCSD F12 T Accurate and efficient approximations to explicitly correlated coupled cluster singles and doubles CCSD F12 Christof Hattig David P Tew Andreas K hn J Chem Phys 132 231102 2010 11 1 Characteristics of the Implementation and Compu tational Demands In CCSD the ground state energy is as for CC2 evaluated as Ecc HF H CC HE H exp T HF 11 1 For other avaible approximation and the corresponding input options see Sec 20 2 17 210 CHAPTER 11 CCSD CCSD F12 AND CCSD T where the cluster operator T Ti T consist of linear combination of single and double excitations T Yoa 11 2 ai 1 Th z D tai Tab A 11 3 aibj In difference to CC2 the cluster amplitudes ta and taj are determined from equa tions which contain no further approximations apart from the restriction of T to single and double excitations H T HF 0 11 4 H Ts T DIHF 0 11 5 Qu ul To Tv Qu uol where again H exp T exp T1 and u1 and jg are respectively the sets of all singly and doubly excited determinants For MP3 the energy is computed from the first order amplitudes i as Emp3 tot Eur Emp2 EMP3 11 6
164. For all segments that do not have associated basis grid points i e intersection seam segments the segment centers are used The diagonal elements A that represent the self energy of the segment are calculated via the basis grid points contributions or by using the segment area Akk 3 8 az if no associated basis grid points exist Outlying charge correction The part of the electron density reaching outside the cavity causes an inconsistency that can be compensated by the outlying charge correction This correction will be performed at the end of a converged SCF or an iterative MP2 calculation and uses an outer surface for the estimation of the energy and charge correction 182 The outer surface is constructed by an outward projection of the spherical part of the surface onto the radius R ROUT F RSOLV It is recommended to use the corrected values Numerical Frequency Calculation The calculation of harmonic frequencies raises the problem of non equilibrium solvation in the Cosmo framework because the molecular vibrations are on a time scale that do not allow a re orientation of the solvent molecules Therefore the total response of the continuum is split into a fast contribution described by the electronic polarization and a slow term related to the orientational relaxation As can be shown 183 the dielectric energy for the disturbed state can be written as Efa SOPE 5 F n a P4 B PS F e aP BP where P denotes the
165. GEOMETRY MAIN MENU 59 Dihedral angle tors abcd is the angle between the planes a b c and b c d This is a special coordinate type to describe the bending of a near linear system linc abcd describes the collinear bending of a b c where the angle is defined as for bend the apex atom appears last in the plane of b c d see also below command linp The system b c d has to be non linear of course This coordinate is similar to linc but describes the bending of a b c perpendicular to the plane b c d These two types of coordinates are in most cases sufficient to describe the bending of near linear systems An example may help you to understand these two coordinate types Consider ketene H2CCO which contains a linear system of three atoms Without symmetry this molecule has 9 degrees of freedom You could choose the four bond lengths two CCH angles and the out of plane an gle of the C C bond out of the CHH plane But then two degrees of freedom still remain which cannot be specified using these normal co ordinate types You can fix these by using linc and linp The two coordinates linc 1 3 2 4 and linp 1 3 2 4 where 1 oxygen 2 car bon 3 carbon 4 hydrogen would solve the problem The type comp describes a compound coordinate i e a linear combina tion of primitive internal coordinates This is often used to prevent strong coupling between primitive internal coordinates and t
166. I tpss tpssh Possible grids are 1 5 and m3 m5 where grid 1 is coarse least accurate and 5 most dense We recommend however the use of so called multiple grids m3 m5 SCF iterations with grid 1 3 final energy and gradient with grid 3 5 Usually m3 is fine for large or delicate systems try m4 For a reference calculation with a very fine grid and very tight thresholds use reference as grid specification instead of gridsize xy Note the functionals b3 lyp_ Gaussian and s vwn_ Gaussian are made available only for comparability with Gaussian The functional VWNIII is much less well founded than VWN5 and the TURBOMOLE team does not recommend the use of VWNIII 20 2 FORMAT OF KEYWORDS AND COMMENTS 299 RI Dscf does not run with the keyword rij you must call the RI modules Ridft and Rdgrad for energy and gradient calculations However it does run with the keyword rik but it will ignore all RI settings and do a conventional non RI Hartree Fock or DFT calculation rij Enforces an RI J calculation if module ridft is used can be used for Hartree Fock as well as for DFT calculations with pure or hybrid functionals ridft Obsolete keyword use rij instead rik Enforces a RI JK calculation if module ridft is used can be used for Hartree Fock as well as for DFT calculations with pure or hybrid functionals ricore integer Choose the memory core available in megabyte for special arrays in the RI calculation
167. MO amplitudes electrostatic potential this format is x y z f x y z In case of vectors components of the vector and its norm are displayed This format is valid for all types of grid 3D plane line points see below it is the default format in case of calculation of values at single points Output file suffix is xyz only for 3D default in this case Data are written to binary files that can be directly read by gOpenMol Note that this output is restricted to scalar quantities thus in case of vectors E field only the norm is plotted Output file suffix is plt only for 3D Data are written to ASCII files that can be imported by e g gOpenMol Note that this output is restricted to scalar quantities thus in case of vectors E field only the norm is plotted Output file suffix is map a format compatible with gOpenMol for visualization of vectors v The format is Y Z Vz Vy Uz for planes and lines default in these cases In case of a line specified by a y see below output is a f x y z for scalars for vectors compo nents and norm are displayed vectors Analogously in case of planes it is a P f x y z The output file suffix vec may be visualized by plot ting programs suited for two dimensional plots A command file termed gnuset to get a contour plot by gnuplot is automatically generated only for 3D writes out data in Cube format which can be imported by many external visualization pro
168. MP2 and the calculation of expectation values for Note that the memory specified with maxcor is for OpenMP parallel calculation the maximum amount of memory that will be dynamically allocated by all threads together To use your computational resources efficiently it is recommended to set this value to about 75 of the physical memory available for your calculations but to at most 16000 megabytes Due to the use of integerx4 arithmetics the ricc2 program is presently limited to 16 Gbytes In the dscf program the OpenMP parallelization covers presently only the Hartree Fock coulomb and exchange contributions to the Fock matrix in fully integral direct mode and is mainly intended to be used in combination with OpenMP parallel runs of ricc2 Nevertheless the OpenMP parallelization can also be used in DFT calcu lations but the numerical integration for the DFT contribution to the Fock matrix will only use a single thread CPU core and thus the overall speed up will be less good Localized Hartree Fock calculations dscf program are parallelized using OpenMP In this case an almost ideal speedup is obtained because the most expensive part of the calculation is the evaluation of the Fock matrix and of the Slater potential and both of them are well parallelized The calculation of the correction term of the grid will use a single thread Restrictions e In the ricc2 program the parts related to RI MP2 F12 LT SOS RI MP2 or calculatio
169. Mol available via http www csc fi gopenmol1 is driven by the keyword pointval This keyword is evaluated by all density matrix generating TURBOMOLE modules i e by dscf ridft rimp2 mpgrad ricc2 see Section 10 3 3 and egrad Note that all of the following quantities may be calculated simultaneusly and that for programs dscf ridft rimp2 and mpgrad the density matrix generating steps may be skipped by typing lt program gt proper Electron densities For the above mentioned programs setting of keyword pointval dens or simply pointval yields calculation of densities 16 2 INTERFACES TO VISUALIZATION TOOLS 239 p Rp X Dindr Rp dy Rp 16 3 vp dens on an orthogonal grid Rp the size of which is automatically adjusted to the size of the molecule and the resolution is adjusted to yield acceptable gOpenMol plots for specification of non default grid types planes lines and non default output formats see Section 20 2 21 Names of output files are td plt total density UHF a density plus 8 density sd plt spin density density minus density mp2d pl1t MP2 density mp2sd plt MP2 spin density ed plt differential density for excited state esd plt differential spin density for excited state lt myname gt pl1t general density passed e g by the ricc2 program The plt files may directly be visualized by gOpenMol the file coord xyz which is also necessary for gOpenMol is generated by the above pro
170. N TURBOMOLE export PATH TURBODIR bin sysname PATH The usual binaries are replaced now by scripts that prepare the input for a parallel run and start mpirun or poe on IBM automatically The number of CPUs that shall be used can be chosen by setting the environment variable PARNODES export PARNODES 8 The default for PARNODES is 2 Finally the user can set a default scratch directory that must be available on all nodes Writing scratch files to local directories is highly recommended otherwise the scratch files will be written over the network to the same directory where the input is located The path to the local disk can be set with export TURBOTMPDIR scratch username This setting is automatically recognized by the parallel ridft and ricc2 programs Note e This does not set the path for the integral scratch files for dscf see section below about twoint of keyword scfintunit e In MPI parallel runs the programs attach to the name given in TURBOTMPDIR node specific extension e g scratch username 001 to avoid clashes be tween processes that access the same file system The jobs must have the per missions to create these directories Therefore one must not set TURBOTMPDIR to something like scratch which would result in directory names like scratch 001 which can usually not created by jobs running under a standard user id If TURBOTMPDIR is not set by the user ridft will check for a tmp scr or work
171. ND OF DEFINE SESSION This menu serves very different purposes The next subsection deals with commands required to activate and or specify specific methods of calculation The subsequent subsection describes commands used to select non default options Standard SCF calculations do not require special action just leave the menu The final subsection describes the settings for property calculations 4 4 1 Important commands DFT calculations Command dft leads you to the menu STATUS OF DFT_OPTIONS DFT is NOT used functional b p gridsize m3 ENTER DFT OPTION TO BE MODIFIED func TO CHANGE TYPE OF FUNCTIONAL grid TO CHANGE GRIDSIZE on TO SWITCH ON DFT Just lt ENTER gt q or terminate this menu To activate DFT input on and then specify the grid for the quadrature of exchange correlation terms TURBOMOLE offers grids 1 coarse to 7 finest and the multiple grids m3 to m5 4 The latter employ a coarser grid during SCF iterations and grid 3 to grid 5 in the final SCF iteration and the gradient evaluation Default is grid m3 for clusters with more than 50 atoms use m4 The functionals supported are obtained with the command func 76 CHAPTER 4 PREPARING YOUR INPUT FILE WITH DEFINE SURVEY OF AVAILABLE EXCHANGE CORRELATION ENERGY FUNCTIONALS FUNCTIONAL TYPE EXCHANGE CORRELATION REFERENCES slater dirac LDA IS 1 2 exchange l l S VWn LDA IS VwWN V 1 3 vwn LDA VWNC V 3 s vwn_Ga
172. NS USING THE FDE SCRIPT245 correlation contribution cannot be determined directly and the non additive exchange correlation term can be approximated as 164 pnd 54 pp ESO 4 pp ESO pa ESS p 17 8 17 2 Frozen Density Embedding calculations using the FDE script The shell script FDE controls and executes automatically FDE calculations The script FDE prepares the input files running define runs the calculations only dscf is supported in the present versiob and combines the results running fdetools Because the FDE equations are coupled sets of one electron equations one for each subsystem full relaxation of the electron densities of both subsystems is obtained by using a freeze and thaw 162 procedure until convergence The converged FDE calculations are store in the subdirectories STEPN SUBSYSTEM_A and STEPN SUBSYSTEM_B where N is the number of the FDE iteration The sub directory ISOLATED_SUBSYSTEM_A and ISOLATED_SUBSYSTEM_B contain instead the calculations for isolated subsystems see also Section 17 2 1 Current functionalities and limitations of FDE are e only Ci point group e only for closed shell systems that consist of two closed shell subsystems e g weakly interacting closed shell dimers e only total and binding energy calculations no gradients e serial and OMP dscf runs no MPI e monomolecular and supermolecular basis set approach e LDA GGA kinetic energy functionals for weakl
173. NTERNAL COORDINATES disg lt range gt GRAPHICAL DISPLAY OF MOL GEOMETRY lt range gt IS A SET OF ATOMS REFERENCED lt real gt IS AN OPTIONAL DISTANCE THRESHOLD DEFAULT 5 0 AS AN EXAMPLE CONSIDER disc 1 3 6 10 11 WHICH DISPLAYS THE CARTESIAN COORDINATES OF ATOMS 1 3 4 5 6 10 and 11 HIT gt return lt TO CONTINUE OR ENTER ANY DISPLAY COMMAND Of course you may enter each of these display commands directly without entering the general command dis before The option disg needs special adaption to the computational environment however and will normally not be available 4 0 4 Specifying Atomic Sets For many commands in define you will have to specify a set of atoms on which that command shall act There are three ways to do that e You may enter all or none the meaning of which should be clear entering none makes not much sense in most cases however e You may specify a list of atomic indices like 1 or 3 5 6 or 2 4 6 7 8 10 or similar e You may also enter atomic identifiers which means strings of at most eight characters the first two contain the element symbol and the remaining six could be used to distinguish different atoms of the same type For example if you have several carbon atoms in your molecule you could label some c ring and others c chain to distinguish them Whenever you want to enter an atomic identifier you have to put it in double quotation marks c ring You should take into account that define also
174. NTS 317 The convergence of the macro iterations is strongly influenced by the size of the starting search subspace Generally all guess Hessian eigenvectors correspond ing to imaginary frequencies and at least two real ones are used as starting search subspace However it proved to be necessary to use even more vectors in the case of guess Hessians with very large conditioning numbers hesscond 8 0d 5 means that all eigenvalues with the quotient eigenvalue max eigenvalue lower than 0 00008 are added to the starting search subspace Default is 1 0d 4 hotfcht Triggers the generation of input files for hot FCHT program to calculate Franck Condon factors by R Berger and co workers See 13 4 sijuai_out Save the derivative of the density matrix for subsequent use in the module evib See 14 Force constant calculations on the DFT level prove to be numerically reliable only with large integration grids or if one includes the effects of quadrature weights This is done by default to prevent this insert no weight derivatives in dft 20 2 11 Keywords for Module EvIB dfdxi textout can be used to generate text output of the matrix elements of the derivative of the Fock operator For bigger systems this can however generate very large output files See 14 20 2 12 Keywords for Module ESCF ESCF calculations to perform an escf calculation converged molecular orbitals from a HF DFT or RIDFT calculation are needed The HF DFT
175. O SCF calculations for molecules embedded in an electric conductor i e using f 1 The liquid can be imagined as a dense packing of molecules in the perfect conductor the reference state For the statistical thermodynamic procedure this system is broken down to an ensemble of pair wise interacting surface segments The interactions can be expressed in terms of surface descriptors e g the screening charge per segment area o q az Using the information about the surface polarity o and the interaction energy functional one can obtain the so called o potential us o T This function gives a measure for the affinity of the system S to a surface of polarity o The system S might be a mixture or a pure solvent at a given temperature T Because the parabolic part of the potential can be described well by the COSMO model we subtract this portion form the COSMO RS potential jis o T ws o T 1 f e eo0 The parameter co can be obtained from the curvature of a COSMO RS o potential of a nonpolar substance e g hexane Thus the remaining part of the chemical potential of a compound i with mole fraction x in the mixture Si can be expressed 268 CHAPTER 19 TREATMENT OF SOLVATION EFFECTS WITH COSMO as m ix gt s o T Hos kT ln z where the combinatorial term Ho g accounts for effects due to the size and shape differences of the molecules in the mixture and az denotes the area of segment t The kT ln x can be skipp
176. ONDITIONS FOR UPDATE mingeo lt i gt START UPDATE IF THERE ARE AT LEAST lt i gt CYCLES DEFAULT min 3 maxgeo lt i gt USE LAST lt i gt CYCLES FOR UPDATE DEFAULT max 4 lt RETURN gt OR OR q uit WILL TERMINATE THIS MENU Special Boundary Conditions for Ahlrichs and Pulay Updates For the default update method ahlrichs some additional control parameters are available which can be defined in this menu DEFINE BOUNDARY CONDITIONS FOR AHLRICHS OR PULAY UPDATE modus lt i gt DEFINE MODUS FOR GDIIS PROCEDURE MINIMIZE lt dqldg gt IF lt i gt 0 lt gldqg gt IF lt i gt 1 lt glg gt IF lt i gt 2 lt dE gt IF lt i gt 3 DEFAULT lt i gt 1 IGNORE GDIIS IF lt gldq gt lt gldq gt IS LARGER THAN lt r gt DEFAULT lt r gt 0 1 lt RETURN gt OR OR q uit WILL TERMINATE THIS MENU For detailed description consult Section 5 3 diagonal RESTRICT UPDATE TO DIAGONAL ELEMENTS IF METHOD IS BFGS DFP OR MS DEFAULT n offreset DISCARD OFF DIAGONAL ELEMENTS DEFAULT n offdamp lt r gt DAMP OFF DIAGONAL ELEMENTS BY 1 1 lt r gt DEFAULT 1 000 DAMP UPDATE BY 1 1 lt real gt DEFAULT 0000E 00 SCALE INPUT HESSIAN BY lt real gt DEFAULT 1 000 l SCALE INPUT HESSIAN BY lt real gt DE IF IDEI damp lt real gt scale lt real gt allow lt real gt 4 4 THE GENERAL OPTIONS MENU 87 THE OBSERVED ABSOLUTE CHANGE IN ENERGY IS OBEYING THE CONDITION
177. OORDINATES ff UFF FORCEFIELD CALCULATION m MANIPULATE GEOMETRY frag DEFINE FRAGMENTS FOR BSSE CALCULATION w lt file gt WRITE MOLECULAR COORDINATES TO FILE lt file gt r lt file gt RELOAD ATOMIC AND INTERNAL COORDINATES FROM FILE lt file gt name CHANGE ATOMIC IDENTIFIERS del DELETE ATOMS dis DISPLAY MOLECULAR GEOMETRY banal CARRY OUT BOND ANALYSIS TERMINATE MOLECULAR GEOMETRY SPECIFICATION AND WRITE GEOMETRY DATA TO CONTROL FILE IF YOU APPEND A QUESTION MARK TO ANY COMMAND AN EXPLANATION OF THAT COMMAND MAY BE GIVEN This menu allows you to build your molecule by defining the Cartesian coordinates interactively ai or by reading the coordinates from an external file a aa The 4 1 THE GEOMETRY MAIN MENU 51 structure can be manipulated by the commands sub m name and del The com mand sy allows you to define the molecular symmetry while desy tries to determine automatically the symmetry group of a given molecule There exists a structure library which contains the Cartesian coordinates of selected molecules e g CH4 These data can be obtained by typing for example a ch4 or a methane The data files are to be found in the directory TURBODIR structures The library can be extended You can perform a geometry optimization at a force field level to preoptimize the geometry For this purpose the Universal Force Field UFF developed from Rapp et al in 1992 7 has been implemented in the uf
178. OS MP2 with O N scaling computation costs e Static polarizabilities currently restricted to closed shell reference wavefunc tions and the sequential and SMP versions cannot yet be combined with spin component scaling see Chapter 10 5 for a description of the input e See Chapter 10 for further details 9 1 1 How to quote e For calculations with mpgrad Semi direct MP2 Gradient Evaluation on Workstation Computers The MP GRAD Program F Haase and R Ahlrichs J Comp Chem 14 907 1993 e For calculations with rimp2 RI MP2 first derivatives and global consistency F Weigend and M Haser Theor Chem Acc 97 331 1997 168 CHAPTER 9 2ND ORDER M OLLER PLESSET PERTURB THEORY e For calculations with ricc2 CC2 excitation energy calculations on large molecules using the resolution of the identity approximation C Hattig and F Weigend e for MPI parallel calculations with ricc2 in addition Distributed memory parallel implementation of energies and gradients for second order Meller Plesset perturbation theory with the resolution of the identity ap proximation Christof Hattig Arnim Hellweg Andreas K hn Phys Chem Chem Phys 8 1159 1169 2006 e for MP2 F12 calculations in addition The MP2 F12 Method in the TURBOMOLE Programm Package Rafal A Ba chorz Florian A Bischoff Andreas Glof Christof Hattig Sebastian H6fener Wim Klopper David P Tew J Comput Chem 32 2492 2513 2011 e for O N sca
179. PATION NUMBER ASSIGNMENT Note that not all open shell systems can be handled in this way It is possible to specify a and b for atomic calculations with s p d and d configurations and for calculations on linear molecules with a and 6 configurations Furthermore it is possible to do calculations on systems with half filled shells where a 1 b 2 In the literature you may find tabulated values for individual states arising from d configurations but these are not correct Instead these are parameters for an average of all states arising from these configurations You can obtain these values if you enter val on the above question For a detailed description see Section 6 3 4 3 5 Start MOs for broken symmetry treatments flip Broken symmetry treatments suggested by e g Noodleman or Ruiz are a popular tool for the calculation of spin coupling parameters in the framework of DFT As an example one might consider two coupled Cu centers e g for a hypothetical arrangement like this coord 0 0 2 7 0 0 cu 0 0 2 7 0 0 cu 0 0 6 1 0 0 f 0 0 6 10 0 f 2 4 0 0 0 0 f 2 4 0 0 0 0 f end The high spin case a doublet with an excess alpha electron at each Cu atom aa in an obvious notation preserves Dj symmetry while the low spin state ba does 72 CHAPTER 4 PREPARING YOUR INPUT FILE WITH DEFINE not For a broken symmetry treatment it is advidsable to calculate the high spin state first and then broken symmetry sta
180. PI export PATH TURBODIR bin sysname PATH export PARNODES expr PBS_L_NODENUMBER else HHHHH Sequentiel job set the PATH for Turbomole calculations export PATH TURBODIR bin sysname PATH fi VERY important is to tell PBS to change directory to where the input files are 43 44 CHAPTER 3 HOW TO RUN TURBOMOLE cd PBS_O_WORKDIR HHHHHHHH ENTER YOUR JOB HERE HHHHHHHHHHHHHHHHHHHHHAE HEAR AE AE jobex ri gt jobex out FETE EH EEE EE EEE EE EE EE AAR ERREA HRHHHERHH 3 2 2 Running Parallel Jobs SMP case The SMP version of TURBOMOLE currently combines three different parallelization schemes which all use shared memory e dscf and ricc2 are also partially parallelized with OpenMP for applications on shared memory in particular multi CPU and multi core machines e aoforce escf and egrad are currently parallelized as described in 22 e ridft and rdgrad are parallelized with MPI using the Global Arrays toolkit but use shared memory on SMP systems Setting up the parallel SMP environment In addition to the installation steps described in Section 2 see page 23 you just have to set the variable PARA_ARCH to SMP i e in sh bash ksh syntax export PARA_ARCH SMP This will cause sysname to append the string _smp to the system name and the scripts like jobex will take the parallel binaries by default To call the parallel versions of the programs ridft rdgrad dscf ricc2 aoforce
181. REE FOCK 133 6 3 3 More Than One Open Shell A Half filled shell and all spins parallel All open shells are collected in a single open shell and Example The 4d 5s 7S state of Mo treated in symmetry I roothaan 1 a 1 b 2 closed shells a 1 4 2 t1 1 3 2 h 1 2 open shells type 1 a 5 1 h 2 1 Two electron singlet coupling The two MOs must have different symmetries not required for triplet coupling see example 6 3 3 We have now two open shells and must specify three sets of a b i e one for each pair of shells following the keyword rohf Example CH in the B state from 3a1 1b2 molecule in x z plane closed shells al 1 2 2 b1 1 2 open shells type 1 al 3 1 b2 1 1 roothaan 1 rohf 3ai 3ail a 0 b 0 1b2 1b2 a 0 b 0 3a1 1b2 a 1 b 2 134 CHAPTER 6 HARTREE FOCK AND DFT CALCULATIONS Two open shells This becomes tricky in general and we give only the most important case shell 1 is a Roothaan case see 6 3 2 shell 2 is one electron in an a s MO nir 1 with parallel spin coupling of shells This covers e g the p st 3P states or the dts 6D states of atoms The coupling information is given following the keyword rohf The a b within a shell are taken from above 6 3 2 the cross term shell 1 shell 2 is in this case a 1 always b 2 ifn lt nip b where nir and n refer to shell 1 Example 1 The 4d 5s D state of Nb in symmetry I
182. REPARING YOUR INPUT FILE WITH DEFINE redundant internals defined as linearly independent combinations of internals see ref 23 provided automatically by the command ired in the geometry main menw in Section 4 1 below This works in almost all cases and is efficient The disadvantage is that this is a black box procedure the coordinates employed have no direct meaning and cannot be modified easily by the user cartesians should always work but are inefficient more cycles needed for conver gence Cartesians are the last resort if other options fail they are as signed as default if one leaves the main geometry menu and no other internals have been defined 4 1 The Geometry Main Menu After some preliminaries providing the title etc you reach the geometry main menu SPECIFICATION OF MOLECULAR GEOMETRY ATOMS 0 SYMMETRY c1 YOU MAY USE ONE OF THE FOLLOWING COMMANDS sy lt group gt lt eps gt DEFINE MOLECULAR SYMMETRY default for eps 3d 1 desy lt eps gt DETERMINE MOLECULAR SYMMETRY AND ADJUST COORDINATES default for eps 1d 6 susy ADJUST COORDINATES FOR SUBGROUPS ai ADD ATOMIC COORDINATES INTERACTIVELY a lt file gt ADD ATOMIC COORDINATES FROM FILE lt file gt aa lt file gt ADD ATOMIC COORDINATES IN ANGSTROEM UNITS FROM FILE lt file gt sub SUBSTITUTE AN ATOM BY A GROUP OF ATOMS i INTERNAL COORDINATE MENU ired REDUNDANT INTERNAL COORDINATES red_info DISPLAY REDUNDANT INTERNAL C
183. RNAL COORDINATE lt i gt e g irem d TO REMOVE ALL display COORDS dis ANY DISPLAY COMMAND e g disi OR disc disiat lt i gt AS disi BUT STARTING AT INTERNAL COORD NUMBER i WHERE lt a gt OPTIONAL ATOMIC SET DEFAULT a11 lt i gt INDEX LIST OF INTERNAL COORDINATE S LIKE 3 6 8 OR lt i gt lt x gt lt x gt STATUS OF INTERNAL COORDINATE k f d OR i ADDING A QUESTION MARK TO ANY COMMAND MAY PROVIDE EXPLANATIONS ENTER COMMAND OR HIT gt return lt TO GET BACK TO GEOMETRY MAIN MENU The parameters in the headline of this menu have the following meanings ideg is the total number of symmetry restricted degrees of freedom k is the number of active internal coordinates specified up to now Only these coordinates are optimized during a geometry optimization f is the number of fized internal coordinates specified These coordinates will be included in the B matrix see command imet but their values will not be changed during geometry optimization 56 CHAPTER 4 PREPARING YOUR INPUT FILE WITH DEFINE d is the number of internal coordinates whose values will only be displayed e g by command disi but no gradients will be calculated for these coordinates nor will they be included in the geometry optimization i means the number of coordinates which are defined but will be com pletely ignored i e they are not even displayed on the screen and will not be used by any program this is the waste paper basket of de
184. Smaller grids 1 0 and the 20 2 FORMAT OF KEYWORDS AND COMMENTS 301 corresponding m grids m1 m2 have been defined as well Grids of at least size m3 are recommended for heavy atoms The gridsize can be modified just like in dft calculations The keyword dsenex activates seminumerical gradient calculations An example using the default grid for SCF m1 and grid 5 for gradients default grid 3 looks like this senex dsenex gridsize 5 LHF Use the Localized Hartree Fock LHF method to obtain an effective Exact Exchange Kohn Sham potential module dscf The LHF method is a serial implementation for spin restricted closed shell and spin unrestricted ground states dft functional lhf gridsize 6 With the LHF potential Rydberg series of virtual orbitals can be obtained To that end diffuse orbital basis sets have to be used and special grids are required gridtype 4 is the most diffuse with special radial scaling gridtype 5 is for very good Rydberg orbitals gridtype 6 default in Lhfprep is the least diffuse only for the first Rydberg orbitals Only gridsize 3 5 can be used no multiple grids Use test integ to check if the selected grid is accurate enough for the employed basis set How to do LHF runs 1 Do a Hartree Fock calculation using dscf 2 Use the script lhfprep to prepare the control file the old control file will be saved in control hf and the molecular orbitals in mos hf or in alpha hf and bet
185. T DIRECTION OF MOVEMENT OR LOCATION OF ROTATION AXIS EITHER AS A COORDINATE TRIPLE SEPARATED BY BLANKS OR AS TWO ATOMIC INDICES SEPARATED BY KOMMA OR x OR y OR z OR ENTER ANY DISPLAY COMMAND FIRST OR amp TO GO BACK You can thus specify the direction of movement or the rotational axis in the form 0 0 1 or simply z which both describes the z axis or 1 3256 3 333 0 2218 for an arbitrary axis If you want to specify an axis which is related to your molecule you may also enter two atomic indices which define it After having specified the axis you have to enter the distance of movement and the angle of rotation If you want to perform a simple rotation enter 0 for the distance of movement and if you want to simply move your structure enter 0 for the rotational angle You can leave this menu and return to the geometry main menu by hitting lt return gt or by entering any command of the geometry main menu 4 2 The Atomic Attributes Menu After you specified the molecular geometry and symmetry and wrote this data to file you will encounter the atomic attributes menu which is the second of the four 4 2 THE ATOMIC ATTRIBUTES MENU 61 main menus You will enter this menu if all necessary data cannot be read from your input file or if you do not use an input file This menu deals with the specification of basis sets and other data related to the atom type ATOMIC ATTRIBUTE DEFINITION MENU atoms 5 bas 5 ecp 0 b ASSIGN ATOMIC
186. TEM_B See total system in STEP3 ENERGY_SYSTEM 17 2 FROZEN DENSITY EMBEDDING CALCULATIONS USING THE FDE SCRIPT249 Sun Mar 25 23 00 21 CEST 2012 Total time 20 secs The final energies are stored in the file fde_energy The directory STEPN ENERGY_SYSTEM contains the total system with density pA ppg this directory can only be used for density analysis 17 2 1 Options All the options for the FDE can be specified as commandlines and are described below The options can be also be specified in file fde input which is read by the FDE script If fde input is not present it is created by the FDE script Command lines options overwrites options found in the fde input file Subsystem definition The flag p integer is required or it must be present in the fde input file Equivalent command pos cut integer fde input option pos cut integer Kinetic energy functionals In order to use different GGA approximations of the non additive kinetic potential the flag k string must be used Here string is the acronym used to identify a given GGA kinetic energy approximation that can be selected among the following functionals e string revapbek generalized gradient approximation with a PBE like en hancement factor obtained using the asymptotic expansions of the semiclassi cal neutral atom as reference 165 166 revAPBEk This is the default choice e string 1c94 Perdew Wang PW91 exchange functional reparametrized for kine
187. TIONS is a tight convergence criterion as the dipole moment is highly sensitive to small changes in electron density The convergence parameter f for the j th step in the freeze and thaw procedure is computed by means the following expression _ LAA Axl ed 2 17 10 where ai Axl lall i A B is the difference between the dipole moments of two consecutive steps for the i th subsystem Eq 17 10 allows to consider changes in both subsystems or one of them because of the relaxation of their electron densities By default FDE stops when ef lt 0 005 a u The default value for the convergence criteria can be changed using the flag epsilon real where real is a decimal number The maximum number of freeze and thaw cycles can be specified by max iter integer and the default value is 20 In order to make easy the convergence of the iterative solution of the KSCED coupled equations a damping factor 7 must be used for the matrix elements of the embedding potential Vemb as perturbation to a given subsystem d Vemb ig 1 1 Vemb ip 1 Vemb in 17 11 for the j th iteration Here dhemb is the matrix element effectively used in the j th iteration after the damping In FDE the starting value of 7 can be changed using start damp real default value is 0 45 where real is a decimal number The damping parameter can also dynamically change at each iterative step according to the convergence process of a
188. TRY DISPLAY COMMANDS CALCULATE EHT ENERGY FURTHER ADVICE INTEGER INDEX OF MO SHELL ACCORDING TO COMMAND s LIST OF MO SHELL INDICES LIKE 1 5 7 8 11 4 3 GENERATING MO START VECTORS 69 Recommendation Enter 1 to get a list of eht MO energies Then make up your mind on what to do closed shell RHF open shell not allowed for DFT or UHF Look at the examples below RHF UHF ROHF c 1 41 43 45 to define these levels to be doubly occupied a 1 5 alpha levels to be occupied b 1 3 5 beta levels to be occupied Or simply s t or u 1 to get singlet triplet or doublet occupation pattern c 1 41 43 45 levels to be doubly occupied o 42 level 42 should be partially occupied You will then be asked to specify the occupation If there are more open shells you have to repeat since only a single open shell can be specified at a time Watch the headline of the menu which tells you the number of electrons assigned to MOs Description of Commands s list p index c list o index This command gives you a listing of all MOs and their energies as ob tained from the extended Htickel calculation For NH3 in C3 and TZVP you get e g ORBITAL SYMMETRY ENERGY SHELL CUMULATED CL SHL OCC OP SHL OCC SHELL TYPE DEGENERACY SHELL DEG PER ORBITAL PER ORBITAL 1 tai 15 63244 2 2 0 0000 0 0000 2 2al 0 99808 2 4 0 0000 0 0000 3 te 0 64406 4 8 0 0000 0 0000 4 3al 0 57085 2 10 0 0000 0 0000 5 2e 0 30375 4 14 0 0000 0 000
189. TURBOMOLE syntax for atomic coordinates The actual distinction between QM cluster ECP shell and explicit point charges is made in the atoms section atoms f 1 6 23 basis f def TZVP ca 2 5 basis ca def TZVP ca 24 235 basis none ecp ca ecp 18 hay amp wadt f 236 605 basis none charge 1 00000000 In the example above the F atoms 1 and 6 23 as well Ca atoms 2 5 are defined as QM atoms with def TZVP basis sets The Ca atoms 24 235 are pure ECPs and have no basis functions basis none and F atoms 236 605 are explicit point charges with charge 1 with no basis functions and no ECP This step ends the input definition for the PEECM calculation Example 2 AlgOj2 cluster embedded in a Al203 0001 surface In this example a QM cluster with the composition AlgOj2 surrounded by 9 ECPs representing Al cations is embedded in a two dimensional periodic field of point charges 3 for Al and 2 for O corresponding to the 0001 surface of a AlgO3 As in the first example the program has to know that this is a two dimensional periodic system and this is specified by the keyword periodic 2 The dimensions of the unit cell for the 0001 a AlgO3 surface are given in the subsection cell of the embed keyword The aperiodic direction is always the z direction but you have to specify the unit cell as if it was a 3D periodic system This means that the third dimension of the unit cell must be large enough to enclose the entire surface
190. TURBOTEST dscf directory does the same TTEST long executes long examples for all modules TTEST ridft short performs all short examples from the ridft directory Recursive testing creates some additional files in the central TURBOTEST directory The global protocol file TESTPROTOKOLL sysname contains short result messages for all test and a list of errors occurred The list of failed tests is also written to the PROBLEMS sysname file and can be rerun by calling the test script with the r option TTEST r PROBLEMS i786 pc linux gnu The r may also be useful to create any user defined selection of test examples The full list of available examples is obtained by the TTEST list command Once you are done with testing you may wish to clean up afterwards To do it use the clean and realclean options of the TTEST script The difference between these two is that TTEST clean deletes only the test directories and protocols that were created for the current computer architecture as returned by Sysname In contrast the TTEST realclean wipes out all test directories and protocols that get in its way 22 3 Taking the timings and benchmarking Benchmarking differs from testing only in that program timings are computed and compared with reference timings Calling the script as TTEST timings performs the test calculates the CPU and wall clock timings and writes the raw results to the TESTTIMINGS sysname nodename file Auxiliary
191. VXZ basis set families with X D T Q 5 6 are designed for correlation treatment of inner shells for this purpose polarisation functions for the inner shells are needed The default selection for frozen core orbitals in Define or bitals below 3 a u are frozen provides a reasonable guess If core orbitals are included in the correlation treatment it is recommended to use basis sets with additional tight correlation functions as e g the cc pwCVXZ and cc pCVXZ basis set families We recommend the use of auxiliary basis sets optimized for the corresponding MO basis sets The auxiliary basis sets optimized for RI MP2 and RI CC2 are suitable for rirpa 144 correlation energy calculations For systems where ECPs are required as well as within the two component relativistic implementation RIRPA total energies HF KS correlation must be computed in two steps RIRPA correlation energies can be obtained using the nohxx option and the HF energy can then be computed separately e g in ridft if the RI J approximation is used for the Coulomb integrals To compute the HF KS energy compute the KS orbitals first then disable dft and set scfiterlimit 1 in the control file to perform a single SCF iteration Finally add the total HF KS energy from ridft to the correlation energy from the nohxx rirpa calculation to obtain the total RIRPA energy Note the molecular orbitals are altered by ridft after a single iteration so the HFQKS energy must be com
192. Vibrational Spectra 13 1 Analysis of Normal Modes in Terms of Internal Coordinates 13 2 Calculation of Raman Spectra ss rea sarea kaea kaa 13 3 Vibrational frequencies with fixed atoms using NumForce 134 Interface to hot FOCHT sja sios rapi pir e ua ee k eo R e E RE 14 First order electron vibration coupling 14 1 Theoretical background os e noses opne ee ee i E 14 2 vib features 2 2 ew enpa teue Ei Oe we G a eee ees 14 3 General usage of evib 2 0 ec ee ee 15 Calculation of NMR Shieldings 15 1 Prereguisiles o so to mose ak ee ae ea ke a eh ee Ee 15 2 How to Perform a SCF of DFT Calculation 15 3 How to Perform a MP2 calculation o cp s 6 02 ee eee ee 15 4 Chemical Shifts s s ipe ee ee ew he ere 15 5 Other Features and Known Limitations 0 CONTENTS 218 220 221 221 222 224 224 225 225 16 Molecular Properties Wavefunction Analysis and Interfaces to Vi sualization Tools 16 1 Wavefunction analysis and Molecular Properties 16 2 Interfaces to Visualization Tools 0 0 004 17 Frozen Density Embedding calculations tel Backeround Theory e os i644 sioak Ab Ges BE REED 17 2 Frozen Density Embedding calculations using the FDE script Veet Opon suck back ae Fe ke ake ae a oe ae 17 2 2 FDE with hybrid and orbital dependent functionals 18 Orbital Dependent Kohn Sham Density Functional Theory 18 1 Theoretical Background
193. WORDS IN THE CONTROL FILE Content of the unit cell where label is the label of the point charge Content of the unit cell where label is the label of the point charge type and x y z are correspond ing Cartesian or fractional crystal coordinates Defaults are Cartesian coordinates and atomic units You can specify Cartesian coordinates in A using content ang and fractional coordinates using content frac Note that Cartesian coordinates assume that the cell vector a is aligned along the x axis and the vector b on the xy plane cluster label x y z end Atomic coordinates of the piece of the crystal to be replaced by the QM cluster and surrounding isolation shell ECPs and explicit point charges where label is the point charge label and x y z are corresponding Cartesian or fractional crystal coordinates Defaults are Cartesian coordinates and atomic units You can spec ify Cartesian coordinates in A using cluster ang and fractional coordinates using cluster frac charges label charge end Values of point charges for each atom type where label is the point charge label and charge specifies charge in atomic units ch_list label charge end Values of point charges for each atom where label is the point charge label and charge specifies charge in atomic units Note that charges and ch_list are mutually exclusive An integer number n can also be appended to charges or ch_list to set the tolerance for charge neutrality violat
194. We briefly state the basic working equations in the following as far as required to understand the program output For a more detailed treatment of the theory see refs 20 92 95 and refs therein The following discussion is restriced to the one component nonrelativistic treatment for the sake of convenience The first order frequency dependent response of the density matrix can be expanded as y 2 dA Xaiei a ple YaiPa x 2 7 1 The real expansion coefficients Xa and Ya are conveniently gathered in a super vector X soe 7 2 on L the linear space of products of occupied and virtual ground state MOs yi x y x plus their complex conjugates X and Y describe the first order change of the ground state MOs due to an external perturbation which is represented by P Q on L For example if an oscillating electric dipole perturbation along the z axis is applied P Q w where u is the electric dipole operator 7 2 THEORETICAL BACKGROUND 153 Next we define the 2 x 2 super matrices ewe Rela as 7 3 where the four index quantities A and B are the so called orbital rotation Hessians Explicit expressions for the standard A and B can be found e g in ref 20 For MGGA functionals the linear response of the paramagnetic current density leads to additional XC kernel matrix elements and subsequently to modified defintions of A and B 96 The vector X Y is determined as th
195. X Script In its normal mode of operation the shell script jobex controls and executes au tomatic optimizations of molecular geometry parameters It will cycle through the direct SCF gradient and force relaxation programs and stop if either the maximum number of cycles is reached or the convergence criteria change in the total energy maximum norm of the gradient are fulfilled By default the executable programs are taken from the load modules library within the TURBOMOLE directory 5 1 1 Options Given a shell the usage is nohup jobex amp This command invokes structure optimization using the default program statpt Structure optimizations using program relax can be performed using relax flag nohup jobex relax amp nohup means that the command is immune to hangups logouts and quits amp runs a background command jobex accepts the following arguments controlling the level of calculation convergence criteria and many more for example nohup jobex gcart 4 amp energy integer converge total energy up to 10 lt integer gt Hartree default 6 97 98 gcart integer c integer dscf grad statpt relax trans level level ri rijk ex 1l lt path gt ls lt path gt md mdfile file mdscript file keep help 5 1 2 Output CHAPTER 5 STRUCTURE OPTIMIZATIONS converge maximum norm of cartesian gradient up to 10 lt integer gt atomic units default 3 perform up to in
196. a hf for the spin unrestricted case See lhfprep help for options 3 Run again dscf Otherwise the LHF functional can be selected in define in this case default options are used Options for the LHF potential can be specified as follows see also lhfprep help 302 CHAPTER 20 KEYWORDS IN THE CONTROL FILE lhf off diag on numerical slater off pot file save asymptotic dynamic 1 d 3 homo 1biu homob 1b1u ONLY UNRESTRICTED conj grad conv 1 d 7 maxit 20 output 1 cgasy 1 slater dtresh 1 d 9 slater region 7 0 0 5 10 0 0 5 corrct region 10 0 0 5 slater b region 7 0 0 5 10 0 0 5 ONLY UNRESTRICTED corrct b region 10 0 0 5 ONLY UNRESTRICTED correlation func lyp off diag off calculation of the KLI exchange potential By default the LHF exchange potential is computed off diag on numerical slater on the Slater potential is calculated numerically everywhere this is more accurate but much more expensive When ECP are used turn on this option numerical slater off leads to accurate results only for first row elements or if an uncontracted basis set or a basis set with special additional contractions is used in other cases numerical slater on has to be used this is default asymptotic for asymptotic treatment there are three options asymptotic off No asymptotic treatment and no use of the numerical Slater The total exchange potential is just replaced by 1 r in the asymptotic region This method is the fastest one but
197. aals terms with the Lennard Jones potential The partial charges needed for electrostatic nonbond terms are calculated with the Charge Equilibration Modell QEq from Rapp 39 There is no cutoff for the non bonded terms The relaxation procedure distinguishes between molecules wih more than 90 atoms and molecules with less atoms For small molecules it consists of a Newton step followed by a linesearch step For big molecules a quasi Newton relaxation is done The BFGS update of the force constant matric is done 34 40 42 Pulay s DIIS procedure is implemented for big molecule to accelarate the optimization 33 43 The coordinates for any single atom can be fixed by placing an f in the third to eighth column of the chemical symbol flag group As an example the following coordinates specify acetone with a fixed carbonyl group coord 2 02693271108611 2 03672551266230 0 00000000000000 c 1 08247228252865 0 68857387733323 0 00000000000000 c 2 53154870318830 2 48171472134488 0 00000000000000 o 1 78063790034738 1 04586399389434 O 00000000000000 c 2 64348282517094 0 13141435997713 1 68855816889786 h 2 23779643042546 3 09026673535431 O 00000000000000 h 2 64348282517094 0 13141435997713 1 68855816889786 h 1 31008893646566 3 07002878668872 1 68840815751978 h 1 31008893646566 3 07002878668872 1 68840815751978 h 4 12184425921830 2 06288409251899 O 00000000000000 h end 5 5 Molecular Dynamics Calculations Ab initi
198. add ulimit or limit in the script that is sent to the queue ulimit a gt mylimits out jobex ri c 200 statpt gt jobex out send it to the queue and check the file mylimits out to find out which limits are set Parallel version The parallel binaries are being started by the mpirun command which often uses ssh to start a process on a remote node The limits for the stack size can not be set by the user in such a case so everything in HOME profile HOME bashrc etc will not help to get rid of the problem To check the limits on a remote node try sh bash ksh syntax ssh lt hostname gt ulimit a If the ssh command gives a lower stack size than unlimited or a large number you have to change the file etc security limits conf on all nodes where the parallel binaries might run and add there the line example for 4GB limit soft stack 4194303 Redo ssh lt hostname gt ulimit a and you should get 4GB stack size limit as it is set in limits conf now Chapter 3 How to Run TURBOMOLE 3 1 A Quick and Dirty Tutorial A detailed tutorial for the usage of TURBOMOLE on the command line can be found in the DOC directory of your TURBOMOLE installation or on the web site of COSMOlogic see http www cosmologic de All TURBOMOLE modules need the control file as input file The control file provides directly or by cross references the information necessary for all kinds of runs and tasks see Section 20 define p
199. ag 344 carthess 345 default 344 individual 344 off 107 344 on 51 107 110 340 344 347 carthess 51 111 347 diag 110 forceiterlimit 315 316 forcestatic 347 forceupdate 107 341 347 ahlrichs 341 indgeo 342 maxgeo 341 numgeo 341 INDEX allow 343 bfgs 341 damping 344 dfp 341 dfp bfgs 341 diagonal 343 ms 341 offdamp 343 offreset 343 pulay 342 347 fail 343 maxpul 342 minpul 342 modus 342 numpul 342 reseig 344 scale 343 schlegel 341 thrbig 344 threig 344 freeze 156 169 170 172 180 183 184 208 219 323 325 326 gap_threshold 370 gdiis 139 304 gdiishistory 340 global 104 109 344 347 globgrad 104 109 346 grad 104 107 109 238 273 329 336 346 348 grad_send_dens 374 grid 95 354 gw 320 gw gam 321 gw nl 321 gw output 321 gw rpa 321 hOhessian 101 hessian 82 104 110 111 314 315 345 INDEX hessian projected 82 347 hotfcht 317 incore 45 289 intdef 53 55 106 107 226 272 339 341 344 345 integral_ex 370 interconversion 102 340 maxiter 341 on 106 340 341 qconv 341 ironly 316 isopts 316 isosub 315 316 jbas 125 219 221 273 299 jkbas 125 170 184 219 299 ke_control 366 368 kramers 139 157 159 219 304 laplace 171 180 183 184 204 206 326 327 conv 327 last MP2 energy change 345 last SCF energy change 345 last excitation energy change 161
200. agram only nirreps integer If this keyword is set the energies and symmetry labels of all occupied MOs will be dumped to this data group This may be helpful to draw mo diagrams If only has been set only the start MOs are dumped and the program quits nirreps will hold the total number of displayed orbitals after the successful run moprint If this keyword is present all occupied orbitals are dumped to standard output Be careful about this option as it can create huge output files in case of many basis functions mo output format format If this line is present the dscf program is forced to output the MOs using the new FORTRAN format format regardless of the format option in data group scfmo Otherwise the input format will be used Example mo output format 3 2x d15 8 natural orbitals This data group will be written after an UHF calculation together with nat ural orbital occupation and contains the natural space orbitals same syntax as scfmo natural orbital occupation This data group will be written after an UHF calculation together with natural orbitals and contains the occupation of natural orbitals syntax as any data group related with orbital occupation information e g closed shells e g a 1 5 2 00000000000000 290 CHAPTER 20 KEYWORDS IN THE CONTROL FILE a 6 1 99949836999366 a 7 1 99687490286069 a 8 1 00000000000000 a 9 00312509713931 a 10 00050163000634 point_charges
201. al 283 debug 283 dgrenze 287 diffuse 285 fgrenze 287 fullshell 286 functional 298 gridordering 287 gridsize 283 298 gridtype 283 nkk 283 nphi 284 ntheta 284 old_RbCs_xi 284 qgrenze 287 radsize 284 reference 286 rhostart 285 rhostop 285 sgrenze 287 symblock1 287 symblock2 287 test integ 286 301 weight derivatives 287 dkhparam 304 423 dkhparam 1 304 dkhparam 2 304 dkhparam 3 304 dkhparam 4 304 dkhparam 5 304 drvopt 82 226 313 314 basis on 108 drvtol 82 dsenex 301 ecp 156 273 egrad 104 108 339 346 348 electrostatic field 156 287 288 embed 142 143 145 146 305 307 cell 307 charges 307 cluster 307 content 307 epsilon 307 lmaxmom 307 periodic 307 potval 307 wsicl 307 end 53 273 energy 139 161 273 329 336 escfiterlimit 159 320 esp_fit 359 ex_energies 370 excitation 199 excitations 184 190 193 197 202 203 216 333 337 bothsides 333 conv 333 exprop 197 333 irrep 333 leftopt 333 oldnorm 333 preopt 333 spectrum 202 333 424 thrdiis 333 tmexc 203 333 xgrad 333 exopt 161 322 fermi 81 287 hicrt 287 nue 287 stop 287 tmend 287 tmfac 287 tmstrt 287 firstorder 288 fldopt 156 287 288 1st derivative 289 2nd derivative 289 edelt 289 fields 289 geofield 289 forceapprox 106 110 273 340 343 344 346 347 format 346 forceconv 315 316 forceinit 51 344 347 di
202. al and the linear eigenvalue problem in the singles and doubles space can be reformulated as a non linear eigenvalue problem in single substitution space only CC CC CC AST t w AC t T ATOZ t Ayers _ w Arn t AST 1902 u SNE wO Bp This allows to avoid the storage of the double substitution part of the eigen or excitation vectors E E The algorithms are described in refs 10 11 about the RI error see ref 126 The solution of the CC2 eigenvalue problem can be started from the solutions of the CCS eigenvalue problem see below or the trial vectors or solutions of a previous CC2 excitation energy calculation The operation count per transformed trial vector for one iteration for the CC2 eigenvalue problem is about 1 3 1 7 times the operation count for one iteration for the cluster equations in the ground state calculation depending on the number of vectors transformed simultaneously The disk space requirements are about O V N N double precision words per vector in addition to the disk space required for the ground state calculation CCS excitation energies are obtained by the same approach but here double sub stitutions are excluded from the expansion of the excitation or eigenvectors and the ground state amplitudes are zero Therefore the CCS Jacobian dQ Ane a gt mllE IIHF 10 10 Vv is a symmetric matrix and left and right eigenvectors are identical and form an orthonormal basis The configurati
203. al surface in the asymptotic region along direction r Considering together with condition 18 4 we finally obtain that Ux r will approach 1 r along all directions where romo r does not have a nodal surface in the asymptotic region e g this is the case of atoms 18 2 IMPLEMENTATION 257 on directions which belong to the nodal surface of the HOMO the vx r will approach m vx O m 1 r Both OEP EXX and LHF gives total energies very close to the Hartree Fock one actually Euf gt Epxx gt Eup thus without an appropriate correlation functional these methods are not suitable for thermochemistry On the other hand OEP EXX and LHF give very good KS orbital spectra In fact the eigenvalues of the HOMO is very close to the Hartree Fock and to exact ionization potential I P this is in contrast to functional of the first three rungs which underestimate the HOMO energy by several eVs In addition a continuum set of bound unoccupied orbitals are obtained Thus OEP EXX or LHF KS orbitals are very good input quantities for computing NMR shielding constants 178 energy levels in hybrid interfaces 179 and TD DFT excitation energies 180 the latter using LDA GGA kernels not the hybrid ones 18 2 Implementation Both the OKP EXX and LHF methods can be used in spin restricted closed shell and spin unrestricted open shell ground state calculations Both OEP EXX and LHF are parallelized in the OpenMP mode 18
204. alculations two choices of the examp fixed method are available These are controled by a keyword in the rir12 data group ump2fixed full diag full 9 6 LT SOS RI MP2 WITH O N SCALING COSTS 179 These differ in the treatment of the af block where either only the diagonal excita tions enter with amplitude 0 5 diag or the equivalent of the spin adapted singlet and triplet pair excitations enter as far as possible full Note that the diag method with UMP2 F12 yields a result different to that of fixed MP2 F12 even for identical RHF and UHF determinants However the diag method is somewhat less expensive than the full method Recommendations for orbital and auxiliary basis sets The best orbital basis sets to use for MP2 F12 calculations are probably the cc pVXZ F12 basis sets specially optimised for MP2 F12 calculations 113 for the atoms H He B Ne and Al Ar In conjunction with these cc pVXZ F12 basis sets we recommend to use the optimised cc pVXZ F12 sets of Yousaf and Peterson 112 as cabs Furthermore cbas and jkbas basis sets can be selected from the cbasen and jkbasen libraries respectively using the alias cc pVXZ F12 a jkbas is currently not available for He Ne and Ar This alias points to the corresponding aug cc pwCV X 1 Z cbas and aug cc pV X 1 Z jkbas These recommendations are on the side of caution and are likely to be refined as more experience is gained 121 123 For atoms other than H He B Ne and
205. alculations on large molecules using the resolution of the identity approximation J Chem Phys 113 13 5154 5161 2000 C H ttig K Hald Implementation of RI CC2 for triplet excitation energies with an application to trans azobenzene Phys Chem Chem Phys 4 11 2111 2118 2002 C H ttig A K hn K Hald First order properties for triplet excited states in the approximated coupled cluster model CC2 using an explicitly spin coupled basis J Chem Phys 116 13 5401 5410 2002 C Hattig Geometry optimizations with the coupled cluster model CC2 using the resolution of the identity approximation J Chem Phys 118 17 7751 7761 2003 A K hn C Hattig Analytic gradients for excited states in the coupled cluster model CC2 employing the resolution of the identity approximation J Chem Phys 119 10 5021 5036 2003 C Hattig A Hellweg A K hn Distributed memory parallel implementation of energies and gradients for second order Moller Plesset perturbation theory with the resolution of the identity approximation Phys Chem Chem Phys 8 10 1159 1169 2006 A Hellweg S Gr n C Hattig Benchmarking the performance of spin component scaled CC2 in ground and electronically excited states Phys Chem Chem Phys 10 1159 1169 2008 N O C Winter C Hattig Scaled opposite spin CC2 for ground and excited states with fourth order scaling computational costs J Chem Phys 134 1841
206. alculations on molecules containing heavy main group elements Theor Chem Acc 121 1 11 19 2008 BIBLIOGRAPHY 415 123 124 125 126 127 128 129 130 131 132 S H fener F A Bischoff A Glo W Klopper Slater type geminals in explicitly correlated perturbation theory application to n alkanols and anal ysis of errors and basis set requirements Phys Chem Chem Phys 10 23 3390 3399 2008 O Christiansen H Koch P J rgensen The second order approximate coupled cluster singles and doubles model CC2 Chem Phys Lett 243 5 6 409 418 1995 W Klopper F R Manby S Ten no E F Valeev R12 methods in explicitly correlated molecular electronic structure theory Int Rev Phys Chem 25 3 427 468 2006 C H ttig A K hn Transition moments and excited state first order properties in the second order coupled cluster model CC2 using the resolution of the identity approximation J Chem Phys 117 15 6939 6951 2002 T Helgaker P J rgensen J Olsen Molecular Electronic Structure Theory Wiley New York 2000 O Christiansen P J rgensen C H ttig Response functions from Fourier component variational perturbation theory applied to a time averaged quasienergy Int J Quantum Chem 68 1 1 52 1998 C H ttig P J rgensen Derivation of coupled cluster excited states response functions and multiphoton transition moments between two
207. ality is slightly better than 6 311G TZVPP or def TZVPP for MP2 or close to basis set limit SCF or DFT Comparable to 6 311G 2df QZVP and QZVPP for highly correlated treatments quadruple zeta 3d2flg or 4d2flg beyond Ne 3p2d1f for H These basis sets are available for atoms H Kr and the split valence SV and valence triple TZV basis sets types with ECPs also for Rb Rn except lanthanides 62 CHAPTER 4 PREPARING YOUR INPUT FILE WITH DEFINE For calculations with the programs rimp2 and ricc2 optimized auxiliary basis sets are available for the basis sets SV P SVP TZVP TZVPP and QZVPP NEW New sets of basis functions partly identical with those mention above de noted def2 XYZ are available for atoms H Rn 6 The def2 basis sets for 5p and 6p block elements are designed for small core ECPs ECP 28 ECP 46 and ECP 60 For each family SV TZV and QZV we offer two sets of polarisation functions leading to def2 SV P and def2 SVP def2 TZVP and def2 TZVPP def2 QZVP and def2 QZVPP We strongly recommended the new def2 basis since they have been shown to provide consistent accuracy across the periodic table Recommendation Use the same basis set type for all atoms use ECPs beyond Kr since this accounts for scalar relativistic effects New basis sets def2 XYZ MP2 implies RI MP2 and RICC2 exploratory MP2 SVP almost quantitative DFT SV P HF SVP MP2 TZVPP properties HF and DFT TZVPP q
208. alized using the threshold denconv which by default is set conservatively to the tight value of 1077 For single point energy calculations conv in laplace can savely be set to 4 which gives SOS MP2 energies converged within 1074 a u with com putational costs reduced by one third or more compared to calculations with the default settings for these thresholds For geometry optimizations with SOS MP2 we recommend to set conv in laplace to 5 e The spread of the orbital energy denominators depends on the basis sets and the orbitals included in the correlation treatment Most segmented contracted basis sets of triple or higher accuracy as e g the TZVPP and QZVPP basis sets lead to rather high lying anti core orbitals with orbital energies of 10 a u and more For the calculation of SOS MP2 valence correlation energies it is recom mended to exclude such orbitals from the correlation treatment see input for freeze in Sec 20 9 6 LT SOS RI MP2 WITH O N SCALING COSTS 181 Alternatively one can use general contracted basis sets as e g the cor relation consistent cc pVXZ basis sets But note that general contracted basis sets increase the computational costs for the integral evaluation in the Hartree Fock and for gradient calculations also the CPHF equations and related 4 index integral derivatives Also for the calculation of all electron correlation energies with core valence basis sets which in
209. ally Available Display Commands in DEFINE 42 4 0 4 Specifying Atomic Sets o e c 4 se eo roke ka 42 4 0 5 control as Input and Output File 2 42 AOG Be Prepared p scios 4 airia goeie eae aoe SR g eiki 43 The Geometry Main Menu 0 020000 44 4 1 1 Description of commands a sos ie s nye be ee eee Sd 46 4 1 2 Internal Coordinate Menu 49 4 1 3 Manipulating the Geometry aoaaa e 54 The Atomic Attributes Menu aoaaa aaa e 54 4 2 1 Description of the commands 57 Generating MO Start Vectors aoao 20000 59 4 3 1 The MO Start Vectors Menu 59 4 3 2 Assignment of Occupation Numbers 62 43 3 Orbital Specification Menu lt sa scs e 44 a ae a es 64 4 34 Roothaan Parameters o cno coms sacma erom iada 65 4 3 5 Start MOs for broken symmetry treatments flip 65 The General Options Menu 0 00 00005 68 AAi Important commands polip o oe Rae eR ee e g 69 AAD Special adjustments o cree e e e a Ae T A 75 4AS KelaxOpione ocea a aa d bce E a oe e ee ee 77 4 4 4 Definition of External Electrostatic Fields 81 WA Properties oa bank es hee hee eee eo BRE ee eS 82 5 Calculation of Molecular Structure and Ab Initio Molecular Dy namics 91 5 1 Structure Optimizations using the JOBEX Script 91 SLL OPUS 6 ang eae eR RSL R ee Ee ES 91 DLS Output pe so ea Rig eS lee eee a a we ee ee 92 52 Program STAT
210. amed e g 10a_d plt Visualization of the amplitudes of the different spinor parts is achieved e g by pointval mo 10 12 15 minco real where real is a plotting threshold that may take values between zero and one The corresponding part I of the spinor Re a Im a Re 8 Im will be written to file if NT see below is larger than that threshold Nt tr D S Tr Tx T Duw D Civ Cip i The filenames consist of the number of the spinor according to file EIGS and an additional number for the respective part of the spinor 1 for Re a 2 for Im a 3 and 4 for the corresponding 6 parts e g 10a_4 plt for the Im of spinor 10 Localised molecular orbitals If one has generated localized molecular orbitals LMOs see above they can also be visualized pointval lmo 3 6 8 as an example leads to calculation of amplitudes for LMOs 3 6 and 8 The coeffi cients are read from file 1mos UHF lalp and lbet the numbering is due to the output from the localizaton section For an UHF case this means If you included in the localization procedure e g 5 a type orbitals and 3 type orbitals then if you are interested in plotting the 6 type LMOs only you have to type pointval lmo 6 8 Natural molecular orbitals for two component wavefunctions only module ridft and only if soghf is set In two component calculations it is often useful to visualize natural molecular orbitals In contrast to one component calculations the occupation num
211. and print if SEN gt lt r gt DEFAULT 1000E 01 3c lt r gt T compute 3 center SEN and print if SEN gt lt r gt DEFAULT 1000E 01 4c lt r gt T compute 4 center SEN and print if SEN gt lt r gt DEFAULT 1000E 01 S2e2eere es oe e eee e e ee nosym F switch off use of symmetry orbs F compute orbital contributions to SEN irreps F compute irrep contributions to SEN caw Lise E A E E SEEE lt option gt switch off lt option gt or q uit leave this menu The procedure for changing the options is the same as described above By default calculation of 2 3 and 4 center SENs will be enabled with thresholds of 0 01 each Option plot This option allows you to prepare the data needed for contour plots of orbital ampli tudes or total electron densities We do not recommend to prepare plotting data this way an easier method with an easier syntax is to generate these data directly by the programs where densities also MP2 or excited ones and Molecular orbitals are calculated This is described in Chapter 16 If you nevertheless want to prepare the input for plotting data as needed by moloch using define on activating plot you get the following menu 4 4 THE GENERAL OPTIONS MENU 95 there are 1 data groups grid manipulate data group s grid a add another data group m lt integer gt modify lt integer gt th data group m all modify all data gr
212. ansition state optimizations involving large molecules where calculation of the full Hessian is too expensive Note that LES calculations for statpt in addition to the les keyword require the following keywords to be added manually in the control file hOhessian nomw The default Hessian update for minimization is bfgs which is likely to remain pos itive definite The powell update is the default for transition state optimizations since the Hessian can develop a negative curvature as the search progresses 5 2 3 Finding Minima Simply specify the statpt keyword in the control file and run jobex as explained above You can very often speedup the optimization by calculating the initial Hessian matrix using uff 5 2 4 Finding transition states Locating minima on a PES is straightforward In contrast transition state optimiza tion requires much more input The diagonal guess Hessian will almost never work so you must provide a computed one The Hessian should be computed at your best guess as to what the TS should be The real trick here is to find a good guess for the transition state structure The closer you are the better It is often difficult to guess these structures One way to obtain a good guess is to built an approximate TS and to perform a constrained minimization by freezing internal coordinates that change most during the reaction Alternatively you can generate several structures intermediate to reactants and product
213. antly improve geometries of bonded systems but still can improve the energetic de scription For non bonded systems larger basis sets especially with more diffuse functions are needed e It is recommended to exclude all non valence orbitals from MP2 calculations as neither the TURBOMOLE standard basis sets SVP TZVPP and QZVPP nor the cc pVXZ basis set families with X D T Q 5 6 are designed for correlation treatment of inner shells for this purpose polarisation functions for the inner shells are needed The default selection for frozen core orbitals in Define or bitals below 3 a u are frozen provides a reasonable guess If core orbitals are included in the correlation treatment it is recommended to use basis sets with additional tight correlation functions as e g the cc pwCVXZ and cc pCVXZ basis set families e RI MP2 We strongly recommend the use of auxiliary basis sets optimized for the corresponding MO basis sets Fast RI MP2 calculations with the ricc2 program As pointed out above the ricc2 program includes almost all functionalities of the rimp2 program Because of slightly refined batching algorithms screening and symmetry treatment the ricc2 program is usually somewhat faster than rimp2 This is in particular the case when the molecular point group is Dg or a subgroups thereof and a significant number of atoms is positioned on symmetry elements e g planar molecules and when because of memory restrictions the ri
214. are allowed to use on your system is large enough a few GB or 70 90 percent of the total memory should be sufficient cat proc sys kernel shmmax shows the amount of allowed shared mem ory use sysctl to set new values but you have to be root to do that the default shared memory that is used is per process for the matrices is 300 MB for heap and 10 MB for stack For large cases this can be too small and an error will be given in the output In order to increase the default values just set paroptions ga_memperproc lt stacksize gt lt heapsize gt stacksize and heapsize have to be given in word i e units of 8 Byte 1 MB is equivalent to 131072 word Chapter 4 Preparing your input file with DEFINE define is the general interactive input generator of TURBOMOLE During a session with define you will create the control file which controls the actions of all other TURBOMOLE programs During your define session you will be guided through four main menus 1 The geometry main menu This first menu allows you to build your molecule define internal coordinates for geometry optimizations determine the point group symmetry of the molecule adjust internal coordinates to the desired values and related operations Beyond this one can perform a geometry op timization at a force field level to preoptimize the geometry and calculate a Cartesian analytical Hessian After leaving this menu your molecule to be calculated should
215. as fourth order approxima tion to CCSD F12 T Note that MP4 F12 has to be used with the SP or fixed amplitude approache for the geminal coefficients ch MP3 F12 and MP4 F12 are currently only available for closed shell or unrestricted Hartree Fock reference wavefunctions The CPU time for a CCSD F12 calculation is approximately the sum of the CPU time for an MP2 F12 calculation with the same basis sets plus that of a conventional CCSD calculation multiplied by 1 Ncags N where N is the number of basis and Neoaps the number of complementary auxiliary basis CABS functions typically Noasps 2 3N If the geminal coefficients are determined by solving Eq 11 16 instead of using fixed amplitudes the costs per CCSD F12 iteration increase to 1 2Ncasgs N the costs for conventional CCSD iteration Irrespective how the geminal coefficients are determined the disc space for CCSD F12 calculations are approximated a factor of 1 2Ncaps N larger than the disc space required for a conventional CCSD calculation Note that this increase in the computational costs is by far outweighted by the enhanced basis set convergence In combination with the CCSD F12 approximation and also CCSD F12 CCSD F12a CCSD F12b CCSD 2 Fp and CCSD 2 q5 the CPU time for the SP ap proach is only about 20 or less longer than for a conventional CCSD calculation within the same basis set CC calculations with restricted open shell ROHF references
216. as methods to reduce the effort within each iteration when the calculation is almost converged integral prescreening and differential density scheme ridft and rdgrad are modules for very efficient calculation of energy and gradient at the Hartree Fock HF and DFT level 51 Both programs employ the Resolution 123 124 CHAPTER 6 HARTREE FOCK AND DFT CALCULATIONS of the Identity approach for computing the electronic Coulomb interaction RI J This approach expands the molecular electron density in a set of atom centered auxiliary functions leading to expressions involving three center ERI s only This usually leads to a more than tenfold speedup for non hybrid DFT compared to the conventional method based on four center ERI s for example the dscf or grad module The combination of RI J for Coulomb interactions with a case adapted conventional exchange treatment reduces the scaling behaviour of the conventional exchange evaluation required in HF SCF and hybrid DFT treatments Usage of ridft and rdgrad for HF and hybrid DFT is of advantage as compared to dscf and grad for larger systems where it reduces computational costs significantly The most important special features of the ridft and rdgrad modules are e A very efficient semi core algorithm for energy calculation The most expensive three center integrals are kept in memory which significantly reduces the com putational time for small and middle sized molecules
217. ata group for the numerical Laplace transformation laplace and that the sops option in the data group response is set Frequency dependent dipole polarizabilities with the CC2 model are obtained with the input ricc2 cc2 laplace conv 4 response sop operators diplen diplen freq 0 077d0 The frequency has to be given in atomic units Static orbital relaxed polarizabilities are obtained with response sop operators diplen diplen relaxed 10 6 Parallel RI MP2 and RI CC2 Calculations The ricc2 program is partially parallized for distributed memory architectures e g clusters of Linux boxes based on the message passing interface MPI standard In the present version parallel calculations can be carried out for ground state and excitation energies for all wavefunction models available in ricc2 The analytic gradients for RI MP2 and RI CC2 in the ground state and RI CC2 in excited states are also parallized While in general the parallel execution of ricc2 works similar to that of other paral lized Turbomole modules as e g dscf and grad there are some important difference concerning in particular the handling of the large scratch files needed for RI CC2 or RI MP2 As the parallel version dscf also the parallel version of ricc2 assumes that 10 7 SPIN COMPONENT SCALING APPROACHES SCS SOS 205 the program is started in a directory which is readable and writable on all compute nodes under the same path e g a NFS dire
218. ation of MP2 energies and or gradients for RHF and UHF wave functions within the efficient RI approximation RI MP2 166 9 1 FUNCTIONALITIES OF MPGRAD RIMP2 RICC2 167 e The frozen core approximation is implemented for both RI MP2 energies and gradients e RI MP2 needs optimised auxiliary basis sets which are available for all TURBOMOLE standard basis sets SVP TZVP TZVPP QZVPP as well as for the aug cc p wC VXZ X D T Q 5 basis sets series for Al Ar also for the aug cc p wC V X d Z series Exploitation of symmetry of all point groups e Can only be used for sequential calculations e Can be combined with the COSMO solvation model see chapter 19 for details Functionality of ricc2 e Includes all of the above rimp2 functionalities e Runs sequentially and parallel with MPI or OpenMP and supports at the MP2 level all point groups and can in geometry optimizations and vibrational frequency calculations with NumForce combined with RI JK SCF for the Hartre Fock reference calculation e Contains an implementation of explicitly correlated MP2 F12 methods present ly restricted to energies and the C point group e Can for open shell calculations be used with UHF and single determinant high spin ROHF reference wavefunctions ROHF MP2 presently limited to ener gies e Energies and gradients for the spin component scaled SCS and SOS MP2 ap proaches including a Laplace transformed implementation of S
219. ation of atomic neto populations and MO contributions to atomic brutto populations The status flags for these tasks will then change from F false to T true To switch off any option you simply have to enter the corresponding keyword preceded by a e g netto for disabling calculation of atomic netto populations After having left the Mulliken PA section you will be asked whether a population analysis based on occupation numbers a modified Roby Davidson PA should be performed by moloch When typing y you will see the following submenu where you can switch on several special options for the PA in the same manner as described above 4 4 THE GENERAL OPTIONS MENU 93 add or delete one or more special options for a population analysis based on occupation numbers option status description compute MO contributions to modified atomic orbital MA0 occupation numbers maodump F dump all MAOs onto standard output select F write only those MAOs which have been employed in the population analysis all F write all MAOs l l l l l l l l maofile F write MAOs onto a separate file l l l l l l l note that the options select and all are complementary lt option gt switch off lt option gt or q uit leave this menu Afterwards you have the possibility to change the criterion to be applied for the selection of modified atomic orbitals MAOs within the following little submenu global criterion for selection of Mo
220. ations irrep al nexc 2 irrep b1 nexc 2 The single substitution parts of the right eigenvectors are stored in files named CCREO s m azrz where s is the number of the symmetry class irreducible rep resentation m is the multiplicity and zzz the number of the excitation within the symmetry class For the left eigenvectors the single substitution parts are stored in files named CCLEO s m azz These files can be kept for later restarts Trouble shooting For the iterative second order methods CIS Dx ADC 2 and CC2 the solution of the nonlinear partitioned eigenvalue problem proceeds usu ally in three steps 1 solution of the CCS CIS eigenvalue problem to generate reasonable start vec tors the eigenvectors are converged in this step only to a remaining residual norm lt preopt 2 pre optimization of the eigenvectors by a robust modified Davidson algorithm see ref 10 using the LINEAR CC RESPONSE SOLVER until the norm of all residuals are below preopt combined with a DIIS extrapolation for roots as sumed to be converged below the threshold thrdiis 3 solution of the nonlinear eigenvalue problem with a DIIS algorithm using the DIIS CC RESPONSE SOLVER until the norm of the residuals are below the re quired threshold conv This procedure is usually fairly stable and efficient with the default values for the thresholds But for difficult cases it can be necessary to select tighter thresholds In Provided that it is not an
221. ations are somewhat faster excitation energies for the models CIS CCS CIS D CIS D ADC 2 and CC2 including spin component scaled SCS and SOS version of of the latter four methods transition moments for ground state excited and excited excited state tran sitions for the models CCS and CC2 for ADC 2 only moments for ground state excited state transitions are available first order properties for the ground state with SCF CCS MP2 and CC2 and for excited states with CCS CC2 ADC 2 and CIS Dx geometric gradients for the electronic ground state at the MP2 and the CC2 level for electronically excited states at the CIS D ADC 2 and CC2 level second order properties for the ground state with MP2 and CC2 and a closed shell RHF reference wavefunction currently restricted to the sequentical and SMP parallel versions 182 183 gradients for auxiliary basis sets for RI MP2 CC2 etc calculations based on the RI MP2 error functional F12 corrections to RI MP2 MP2 ground state energies can be computed in C1 symmetry using explicitly correlated two electron basis functions in the frame work of the MP2 F12 model 121 125 solvent effects for the methods and states for which orbital relaxed densities are available equilibrium solvent effects can be included in the framework of the cosmomode for details see Chapter 19 All functionalities at the MP2 and CC2 level are implemented for closed shell RHF and ope
222. ay In connection with the optional atomic set a this com mand can help you to find out in which part of a complicated molecule internal coordinates are missing if you fail to get the full number of ideg which equals the result of ideg all for the molecule as a whole iaut tries an automatic definition of internal coordinates This command relies on an recursive procedure which tries to simplify the molecule as far as possible and then starts the definition of internal coordinates At present not all molecular topologies are supported therefore it may hap pen that no internal coordinates can be assigned to your molecule or at least a part of it However for all cases in which an automatic assign ment of coordinates is possible iaut has up to now proved to provide very good internal coordinates If iaut works for your molecule and in most non pathological cases it will we recommend strongly to use these coordinates as they may help you to save several cycles in the geometry optimization procedure After creating internal coordinates with iaut you should always use imet see above because iaut may provide an overcomplete set of coordinates All coordinates which conflict with the molecular symmetry are set to ignore by iaut iman allows you to modify the values of internal coordinates If you specify a list of atoms a only those internal coordinates which refer to only these atoms will be handled You will get a list of all active and f
223. bd in the MO are precalculated and stored on file before the iterative solution of the coupled cluster equation 11 4 and 11 5 For larger systems however the storage and I O of the integrals ac bd leads to bottlenecks An alternatively this contribution can be evaluated in an integral direct was as tig gt tage ne gt taylan Opn gt a Ca cd KA pv 11 23 which depending on the implementation and system has formally a 2 3 times larger operation count but allows to avoid the storage and I O bottlenecks by processing the 4 index integrals on the fly without storing them Furthermore integral screen ing techniques can be applied to reduce the operation count for large systems to asymptotic scaling with O N 214 CHAPTER 11 CCSD CCSD F12 AND CCSD T In TURBOMOLE only the latter algorithm is presently implemented For small systems other codes will therefore be faster The other class of expensive contributions are so called ring terms in some publi cations denoted as C and D terms which involve contractions of the doubles am plitudes tgip with several 4 index MO integrals with two occupied and two virtual indeces partially evaluated with T dependent MO coefficients For these terms the implementation in TURBOMOLE employs the resolution of the identity or density fitting approximation with the cbas auxiliary basis set to reduce the overhead from integral transformation steps Due this approximation CCSD energ
224. be fully specified 2 The atomic attributes menu Here you will have to assign basis sets and or effective core potentials to all atoms The SV P basis is assigned automatically as default as well as ECPs small core beyond Kr 3 The occupation numbers and start vectors menu In this menu you should choose eht to start from Extended Hiickel MO vectors Then you have to define the number of occupied orbitals in each irreducible representation 4 The general menu The last menu manages a lot of control parameters for all TURBOMOLE programs Most of the menu commands are self explanatory and will only be discussed briefly Typing or q terminates the current menu writes data to control and leads to the next while typing amp goes back to the previous menu 47 48 CHAPTER 4 PREPARING YOUR INPUT FILE WITH DEFINE 4 0 3 Universally Available Display Commands in DEFINE There are some commands which may be used at almost every stage of your define session If you build up a complicated molecular geometry you will find the dis command useful It will bring you to the following little submenu ANY COMMAND WHICH STARTS WITH THE 3 LETTERS dis IS A DISPLAY COMMAND AVAILABLE DISPLAY COMMANDS ARE disc lt range gt DISPLAY CARTESIAN COORDINATES dist lt real gt DISPLAY DISTANCE LIST disb lt range gt DISPLAY BONDING INFORMATION disa lt range gt DISPLAY BOND ANGLE INFORMATION disi lt range gt DISPLAY VALUES OF I
225. bers are no longer close to zero one or two but can take any value between zero and two Therefor natural orbitals file natural natural orbital occupation file natural has to be set additionally to soghf also possible via define By setting pointval nmo 9 in control file a gOpenMol compatible file named nmo_9 p1t is written Natural atomic orbitals If one has generated natural molecular orbitals NAOs see above they can be visualized with the following command in the control file pointval nao 7 9 12 where the numbers of the NAOs are in the output of the population analysis 242 CHAPTER 16 PROPERTIES AND ANALYSIS AND GRAPHICS Natural transition orbitals If natural transition orbitals NTOs for electronic excitations are available in files named nto_nocc and nto_vir for respectively the occupied and virtual NTOs plot files for visualizing them can be generated by setting pointval nto 1 5 This will generate plot files for the first five occupied and virtual NTOs The plot file are named nto_vir_n plt where n is the NTO index Non default grids are decribed in detail in Sections 20 2 21 Calculation of the above quantities at single points is needed quite often thus an example is given here pointval geo point 753 007 123 calculates densities at points 7 5 3 0 0 7 and 1 2 3 Output is x y z density output file suffix is xyz We note in passing that calculation of electrostatic potential at po
226. calculate the integral The larger integer the less integrals will be stored The default value is integer 5 see also thize statistics thize real Integral storage parameter that determines together with thime the num ber of integrals stored on disc Only integrals larger than real will be stored The default value is real 0 100E 04 RHF ROHF closed shells Specification of MO occupation for RHF e g alg 1 4 2 a2g 1 2 open shells type 1 MO occupation of open shells and number of open shells type 1 here means that there is only a single open shell consisting e g of two MOs b2g 1 1 b3g 1 1 20 2 FORMAT OF KEYWORDS AND COMMENTS 297 rohf This data group is necessary for ROHF calculations with more than one open shell Example rohf 1 a a a 0 b 0 h h a 1 b 2 a h a 1 b 2 This example is for the 7S state of chromium 3d 4s in symmetry group T Note that for this option being activated roothaan also has to be specified in your control file although its parameter has no meaning in this case For more details see Section 6 3 roothaan For ROHF calculations with only one open shell the Roothaan parameters a and b have to be specified within this data group see also rohf Example roothaan a 3 4 b 3 2 This example is for the 3P ground state of carbon 2p in symmetry group I define recognizes most cases and suggests good Roothaan parameters For further information o
227. cation of the option interconversion on will over ride optimize coordinateupdate options define some variables controlling the update of coordinates Available options are dqmax real maximum allowed total change for update of coordinates The maximum change of individual coordinate will be limited to dqmaz 2 and the col lective change dq will be damped by ddmaz dq dq if dq dq gt ddmax4 default 0 3 interpolate on off calculate geometry update by inter extrapolation of geometries of the last two cycles the interpolate option is always switched on by default but it is only active ANY time if steepest descent update has been chosen i e forceupdate method none otherwise it will only be activated if the DUS update for the geometry is expected to fail statistics on integer off provide a statistics output in each optimization cycle by displaying all the last integer default setting by define is 5 subsequent coordinates gradient and energy values default on gdiishistory file char the presence of this keyword forces relax to provide informational output about the usage of DIIS for the update of the molecular geometry interconversion options default off special input related to the transformation of atomic coordinates between cartesian and internal coordinate spaces default off Available options are 20 2 FORMAT OF KEYWORDS AND COMMENTS 341 maxiter n maximum number of iterat
228. ccurate enough for the employed basis set by performing a numerical integration of the norm of all occupied and virtual orbitals Useful for LHF 295 batchsize integer Grid points are sorted into batches which are then processed This increases efficency This should be changed only by developers Default is batchsize 100 fullshell Standard grids have reduced number of spherical grid points near nu clei With the keyword fullshell this reduction is suppressed Refer ence grid see keyword reference always has full spherical grids with 1202 points Should be used to checked the influence of spherical grid reduction Example for the usage of fullshel11 dft functional b p gridsize m4 fullshell 20 2 FORMAT OF KEYWORDS AND COMMENTS 287 Se ee for developers only symblock2 real p y Values of real effects efficiency of the quadrature default is symblock1 0 001 and symblock2 0 001 one can try higher or smaller values xparameter integer not recommended for use Where xparameter default can be sgrenze 8 fgrenze 10 qgrenze 12 dgrenze 12 and fcut 14 These parameters control neglect of near zeros of various quantities With xparameter integer one changes the default integer larger than defaults will increase the numerical ac curacy Tighter threshold are set automatically with keyword scfconv see section 20 2 6 on page 285 weight derivatives Includes the derivatives of quadrature weights t
229. ced coordinates Additional keywords necessary for parallel runs with the MPI binaries are described in Chapter 20 However those keywords do not have to be set by the users When using the parallel version of TURBOMOLE scripts are replacing the binaries Those scripts prepare a usual input run the necessary steps and automatically start the parallel programs The users just have to set environment variables see Sec 3 2 1 below To use the OpenMP parallelization only an environment variable needs to be set But to use this parallelization efficiently one should consider a few additional points e g memory usage which are described in Sec 3 2 2 3 2 1 Running Parallel Jobs MPI case The parallel version of TURBOMOLE runs on all supported systems e workstation cluster with Ethernet Infiniband Myrinet or other connection e SMP systems e or combinations of SMP and cluster Setting up the parallel MPI environment In addition to the installation steps described in Section 2 see page 23 you just have to set the variable PARA_ARCH to MPI i e in sh bash ksh syntax export PARA_ARCH MPI This will cause sysname to append the string _mpi to the system name and the scripts like jobex will take the parallel binaries by default To call the parallel versions of the programs ridft rdgrad dscf grad ricc2 or mpgrad from your command line without explicit path expand your PATH environment variable to 40 CHAPTER 3 HOW TO RU
230. clude uncontracted steep functions it is rec ommended to check if extremely high lying anti core orbitals can be ex cluded Note that for large molecules it is recommended to disable for geometry optimizations or for gradient or property calculations in general the preoptimization for the Z vector equations with the nozpreopt option in the response data group see Sec 20 217 Restrictions e The Laplace transformed SOS MP2 implementation is presently only paral lelized with MPI The OpenMP parallelization is not yet recognized by the LT SOS RI MP2 related program parts e It is presently not compatible with the calculation of the D and D diagnostics The respective options will be ignored by program if the Laplace transformed implementation is used Chapter 10 Second Order Approximate Coupled Cluster CC2 Calculations ricc2 is a module for the calculation of excitation energies and response properties at a correlated ab initio level in particular the second order approximate coupled cluster model CC2 124 All calculations employ the resolution of the identity RD approximation for the electron repulsion integrals used in the correlation treatment and the description of excitation processes At present the following functionalities are implemented ground state energies for MP2 and CC2 and spin component scaled variants thereof the MP2 results are identical with those obtained with rimp2 but usually the calcul
231. constant Then from 2500 0a u gradual cool ing at the default rate annealing is to occur until the time 3000 0 a u when free Newtonian dynamics will resume Here are all the possible instructions md_action fix temperature from t lt real gt fix total energy from t lt real gt These commands cause velocities to be scaled so as to keep the average kinetic energy i e quasi temperature or the average total energy approximately con stant This is only possible once enough information about run history is available to give reliable statistics Keywords log_history ke_control md_action 20 2 FORMAT OF KEYWORDS AND COMMENTS 369 set temperature at t lt real gt to x lt real gt K set total energy at t lt real gt to x lt real gt H set kinetic energy at t lt real gt to x lt real gt H set position file lt filename gt at t lt real gt set velocity file lt filename gt at t lt real gt set velocity at t lt real gt random set velocity at t lt real gt zero At some time during the ab initio MD run the user can specify a new value for one of the dynamical variables The old value is discarded Single values are given by x real number Vectors must be read in frog format from file file md_action anneal from t lt real gt anneal from t lt real gt x lt real gt quench from t lt real gt quench from t lt real gt x lt real gt file lt file gt relax at t lt real gt In Simulated Anneal
232. conv 1 d 10 maxiter 25 optimize internal on cartesian off global off basis off logarithm coordinateupdate dqmax 0 3 interpolate on statistics 5 forceupdate ahlrichs numgeo 0 mingeo 3 maxgeo 4 modus lt g dq gt dynamic fail 0 1 threig 0 005 reseig 0 005 thrbig 3 0 scale 1 00 damping 0 0 forceinit on diag default energy file energy grad file grad forceapprox file force lock off last step define end File coord coord 00000000000000 00000000000000 54561506935122 n 87806233111566 1 52084856970468 18187168978374 h 87806233111566 1 52084856970468 18187168978374 h 1 75612466223131 00000000000000 18187168978374 h intdef definitions of internal coordinates 1 k 1 0000000000000 stre 4 1 val 1 90084 2 k 1 0000000000000 bend 4 3 1 val 106 27756 1 0000000000000 bend 3 2 1 1 0000000000000 bend 2 4 1 end 380 File basis basis h def SVP n 7s4pid 5 s 1712 8415853 257 64812677 58 458245853 16 198367905 5 0052600809 1 os 58731856571 1 s 18764592253 3 p 13 571470233 2 9257372874 79927750754 1 p 21954348034 1d 1 0000000000 def SVP h 7s 3s 3 s 13 010701000 1 9622572000 44453796000 1 s 12194962000 1 p 80000000000 end File mos scfmo expanded CHAPTER 21 3s2p1d 511 31 1 563934125305E 02 40221581118E 01 17931144990 46376317823 4417 1422662 1 00000
233. convergence thresholds This can happen for CC2 and CIS D close to conical intersections between two states of the same symmetry where CC response can fail due to its non symmetric Jacobian In this case one can try to use instead the ADC 2 model But the nonlinear partitioned form of the eigenvalue problem used in the ricc2 program is not well suited to deal with such situations Diagnostics for double excitations As pointed out in ref 12 the T diag nostic or T 100 T which is evaluated directly from the squared norm of the single and double excitation part of the eigenvectors T 100 7 T T with T ii Ei where the excitation amplitudes are for spin free calculations in a correspoding spin adapted basis which is not necessarily normalized has the disadvantage that the results depend on the parameterization of the spin adapted excitation operators This prevents in particular a simple comparison of the results for singlet and triplet excited states if the calculations are carried out in a spin free basis With the biorthogonal representation for singlet spin coupled double excita tions 127 results for T also differ largely between the left and right eigenvectors and are not invariant with respect to unitary transformations of the occupied or the virtual orbitals The ricc2 module therefore uses since release 6 5 an alternative double excitation diagnostic which is defined by ATi 100 Ti Ti 72
234. cor is not found its value is set to 200 MB mp2energy Calculation of MP2 gradient is omitted only MP2 energy is calculated In connection with this keyword you may also activate the spin component scaled SCS MP2 proposed by Grimme mp2energy SCS with the default values of 6 5 for pS and 1 3 for pT which may be modified this way mp2energy SCS pt vall ps val2 freeze alg 1 2 tiu 1 The data group freeze specifies frozen orbitals in the above syntax by irreducible representations The symmetry independent and for standard applications recommended syntax is freeze implicit core 5 virt 2 This will freeze the 5 lowest occupied and 2 highest virtual orbitals alpha and beta count as one in UHF cases Note that degenerate orbitals count twice e representations thrice t representations etc In case of mpgrad frozen orbitals have to be specified manually for rimp2 the preparation tool rimp2prep may be used to specify frozen core orbitals frozen virtuals have to be specified manually Note In case of gradient calculations frozen core orbitals are regarded only by rimp2 but not by mpgrad moreover freezing of virtual orbitals is generally not supported by mpgrad 324 MPGRAD Essential Keywords All essential data groups for mpgrad may be generated by the preparation tool CHAPTER 20 KEYWORDS IN THE CONTROL FILE mp2prep apart from maxcor see above these are the following traloop n specifies the
235. creates from the atoms you entered all others according to symmetry If necessary you will therefore have to lower the formal symmetry before executing a command 4 0 5 control as Input and Output File define may be used to update an existing control file which is helpful if only the basis set has been changed In this case just keep all data i e reply with lt enter gt on 49 all questions and only specify new start MOs The more general usage is described now At the beginning of each define session you will be asked to enter the name of the file to be created As mentioned earlier all TURBOMOLE programs require their input to be on a file named control but it may be useful at this moment to choose another name for this file e g if you have an old input file control and you do not want to overwrite it Next you will be asked to enter the name of an old file which you want to use as input for this session This prevents you from creating the new input from scratch if you want to make only minor changes to an old control file It is possible to use the same file as input and output file during a define session which means that it will only be modified This may lead to difficulties however because define reads from the input file when entering each main menu and writes the corresponding data when leaving this menu Therefore the input file may be in an ill defined status for the next main menu this will be the case for exampl
236. ctation value of the Cowan Griffin operator Option localization Specifying option localization will switch on a Boys localization of molecular or bitals define by default chooses a set of MOs to be localized according to a certain threshold for the orbital energy Information about these are displayed like this BOYS localization will be performed with respect to x y z number of sweeps 10000 subset of molecular orbitals to be localized gt all occupied molecular orbitals with orbital energy above 2 00000 Hartree you are employing default options for localization do you want to modify them DEFAULT n If you want to change the MO selection or other options for the localization enter y at this point By default or when typing n you will reach the moloch options menu again You will then be asked whether to change the MO selection method If you want this you will enter a little submenu where you can choose one of three possible selection procedures all selects all occupied orbitals thr selects all occupied orbitals with orbital energy larger than a certain threshold man enables you to select the MOs manually later in this section If the selection method thr is specified you then will be asked for the threshold to be applied for the selection Afterwards you have the possibility to change some other topics concerning the localization 92 CHAPTER 4 PREPARING YOUR INPUT FILE WITH DEFINE e specify other localization d
237. ctions and 100 atoms noproj forces the program not to project out translations and rotations when form ing a basis of symmetry adapted molecular displacements This option may be needed if a Hessian is required that contains translation and rotation contributions e g for coupling the system with low cost methods Output of the unprojected hessian is done on nprhessian format is the same as for con ventional hessian Output of the corresponding eigenvalues and eigenvectors is done analogously on nprvibrational spectrum and nprvibrational normal modes nomw causes the program to diagonalize a not mass weighted hessian Output is on nprhessian nprvibrational spectrum and nprvibrational normal modes because projection of rotations is not possible in this case isosub This keyword allows to trace back the effects of isotopic substitution on vibrational frequencies The atom s for which isotopic substitution is to be investigated are specified in subsequent lines of the form atom index mass in special isotope e g isosub 3 2 001 5 13 316 CHAPTER 20 KEYWORDS IN THE CONTROL FILE The interpolation then takes place between the mass es specified in atoms or the default mass es if none specified and the mass es in isosub Take care of symmetry equivalent atoms otherwise symmetry analysis will fail This feature can not be used in a lowest eigenvalue search keyword les isopts 6 Sets the number of poin
238. ctory The directory must contain all input files and will at the end of a calculation contain all output files Large scratch files e g for integral intermediates will be placed under the path specified in the control file with tmpdir see Section 20 2 17 which should point to a directory in a file system with a good performance All large files will be placed on the nodes in these file systems The local file system must have the same name on all nodes Note that at the end of a ricc2 run the scratch directories specified with tmpdir are not guaranteed to be empty To avoid that they will fill your file system you should remove them after the ricc2 calculation is finished Another difference to the parallel HF and DFT gradient programs is that ricc2 will communicate much larger amounts of data between the compute nodes With a fast network interconnection Gigabit or better this should not cause any problems but with slow networks the communication might become the limiting factor for performance or overloading the system If this happens the program can be put into an alternative mode where the communication of integral intermediates is replaced by a reevaluation of the intermediates at the expense of a larger operation count wherever this is feasible Add for this in the control the following data group mpi_param min_comm 10 7 Spin component scaling approaches SCS SOS By introducing individual scaling factors for the same sp
239. cts in CeOzg and CaF investigated using periodic electrostatic embedded cluster method J Chem Phys 130 17 174710 2009 K N Kudin G E Scuseria A fast multipole method for periodic systems with arbitrary unit cell geometries Chem Phys Lett 283 61 68 1998 P Ewald Die Berechnung optischer und elektrostatischer Gitterpotentiale Ann Phys 64 253 287 1921 J Hepburn G Scoles R Penco A simple but reliable method for the predic tion of intermolecular potentials Chem Phys Lett 36 451 456 1975 R Ahlrichs R Penco G Scoles Intermolecular forces in simple systems Chem Phys 19 119 130 1977 S Grimme Accurate Description of van der Waals Complexes by Density Func tional Theory Including Empirical Corrections J Comput Chem 25 12 1463 1473 2004 412 87 88 89 90 91 92 93 94 95 96 97 98 BIBLIOGRAPHY S Grimme Semiempirical GGA type density functional constructed with a long range dispersion contribution J Comput Chem 27 15 1787 1799 2006 S Grimme J Antony S Ehrlich H Krieg A consistent and accurate ab initio parametrization of density functional dispersion correction DFT D for the 94 elements H Pu J Chem Phys 132 154104 2010 S Grimme S Ehrlich L Goerigk Effect of the damping function in dispersion corrected density functional theory J Comp Chem 32 1456 1465 2011 O
240. cutable can be chosen by the x option TTEST x usr local TURBOMOLE bin i786 pc linux gnu dscf If a test output is already present e g in the TESTDIR directory you may wish to check the results This is accomplished by calling TTEST in check mode TTEST check TESTDIR which compares the results in TESTDIR with the reference and writes the results to the CHECKPROTOKOLL file in the test directory Testing parts of the TURBOTEST directory structure or the entire test suite at once is performed by calling the TTEST script from the appropriate place The test script works recursively executing all test examples underneath its starting directory This requires that the test examples be arranged in a TURBOTEST like directory structure progname short long example e g dscf short H20 SCF E1 and the TURBOTEST directory contain a DEFCRIT file with general test suite settings If TTEST is started in the central TURBOTEST without any options all available test examples are executed By giving the list of module names for full list check TTEST help as argument to the script the test can be restricted to these modules The short and long options allow the user to select only the short or long test examples respectively Some examples of usage are given in the following table 22 3 TAKING THE TIMINGS AND BENCHMARKING 401 TTEST dscf called in the TURBOTEST directory performs only the tests for DSCF module TTEST called in the
241. d crt exclude each other ENTER STATPT OPTIONS TO BE MODIFIED itve 0 itvc change INDEX OF TRANSITION VECTOR updte bfgs updte change method of HESSIAN UPDATE hsfrq 0 hsfrq frequency of HESSIAN CALCULATION kptm 0 kptm FREEZING transition vector INDEX hdiag 5 000000E 01 hdiag change DIAGONAL HESSIAN ELEMENTS rmax 3 000000E 01 rmax change MAX TRUST RADIUS rmin 1 000000E 04 rmin change MIN TRUST RADIUS trad 3 000000E 01 trad change TRUST RADIUS Just lt ENTER gt q or terminate this menu Excited states frequency dependent properties and stability analysis Excited state calculations with RPA or CIS based on HF SCF and TDDFT pro cedures as well as stability analyses SCF or DFT are carried out by the program escf You will need a well converged HF SCF or DFT calculation that were converged to at least scfconv 7 see Section 4 4 2 Details of calculations are specified with the command ex MAIN MENU FOR RESPONSE CALCULATIONS OPTION STATUS DESCRIPTION rpas off RPA SINGLET EXCITATIONS TDHF OR TDDFT ciss off TDA SINGLET EXCITATIONS CI SINGLES rpat off RPA TRIPLET EXCITATIONS TDHF OR TDDFT cist off TDA TRIPLET EXCITATIONS CI SINGLES dynpol off DYNAMIC POLARIZABILITY single off SINGLET STABILITY ANALYSIS triple off TRIPLET STABILITY ANALYSIS nonrel off NON REAL STABILITY ANALYSIS l l l l l l l l polly off STATIC POLARIZABILITY l l l l l l l l ENTER lt OPTION gt TO SWITCH ON OFF
242. d dump SCF MOs in each iteration onto scfmo scfdump iter Additionally a data block scfiterinfo will be dumped containing accumulated SCF total one and two electron energies of all previous SCF iterations Information that will allow you to perform a restart if your calculation aborts will be dumped on data group restartd see also restart scfintunit options Disc space specification for two electron integrals The following suboptions are available and necessary unit integer Fortran unit number for this file Unit numbers 30 31 are recom mended size integer Filespace in megabytes for this file size 0 leads to a fully direct run size is set by astatistics run see statistics DSCF switches to direct mode if the file space is exhausted file char Filename This may also be a complete path name if you want to store the integrals in a special directory Make sure the file is local otherwise integrals are transmitted over the network Thus your data group scfintunit may look like this scfintunit unit 30 size 35 file twointl unit 31 size 35 file users work twoint2 Maximal 30 files may be specified in this way scfiterlimit integer Maximum number of SCF iterations default 30 scfmo none file char Input output data group for SCF MOs You can specify 294 CHAPTER 20 KEYWORDS IN THE CONTROL FILE none To perform a calculation without a start vector i e use a core Hamilto nian guess file char
243. d free disk space on your system it will increase traloop and run a statistics run again This will be done as long as your free disk space is not sufficient for the calculation If the mp2prep script fails to run on your system try to use the p option or do the procedure described above by hand Call mp2prep h for more informations about mp2prep 234 CHAPTER 15 SHIELDINGS 15 4 Chemical Shifts NMR shifts are obtained by comparing nuclear shieldings of your test compound with a reference molecule subst Oref Gref Tsubdst Therefore you have to choose a reference molecule with a well known shift for which you can easily calculate the absolute shielding constant This implies a certainty about the geometry too Furthermore you have to use the very same basis set for corresponding atoms to minimize the basis set influence Keywords for the module Mpshift A list of keyword for the module mpshift can be found in Section 20 2 23 15 5 Other Features and Known Limitations e the mpshift program can be restarted at any stage of computing since all intermediate results are written into the file restartcs In case of an external program abort you have to remove the actual step flag by the command actual r or using an editor mpshift analyses this file and decides where to continue e ECPs can not be used since the electrons in the ECP cores are not taken into account e only closed shell calculations are currently supported
244. d the orbitals do not respond to the external field Orbital unrelaxed CC2 properties are calculated as first derivatives of the real part of the unrelaxed Lagrangian 124 Ee C4 8 HF H CC 5 gt ty l THF 10 12 H J fo Halt Fo BV Ta HF H2 with H Ho GV where V is the one electron operator describing the external field 6 the field strength and Ho and Fo are the Hamiltonian and Fock operators of the unperturbed system by the expression ur OL ea t p ur yj c02 n 5B j s3 D voy 10 13 Pq ve FH Stu l V T HF 10 14 H D atoll TARY u2 where R indicates that the real part is taken Relared CC2 properties and gradi ents are calculated from the the full variational density including the contributions from the orbital response to the external perturbation which are derived from the Lagrangian 13 128 LP CC2 4 HF A CC YXO tu l A T HF 10 15 H Y bua ml F THE XO Ryo Fun H2 Ho 10 3 FIRST ORDER PROPERTIES AND GRADIENTS 195 where F is the Fock operator corresponding to the Hamiltonian of the perturbed system H Ho BV One electron properties are then obtained as yes ne HFM S tu u V V T HF 10 16 H JO Ba al V THE Ruo Vio H2 Ho DO Vg 10 17 Pq The calculation of one electron first order properties requires that in addition to the cluster equations also the linear equations for the Lagrangian m
245. d to store any arrays with a size of N or O N or larger as complete array in main memory Therefore the mini mum memory requirements are relatively low although is difficult to give accurate estimate for them On should however be aware that if the amount of memory provided to the program in the data group maxcor becomes too small compared to O N 128 x 1024 MBytes loops will be broken in many small batches at the cost of increased I O operations and a decrease in performance As mentioned above it is recommended to set maxcor to 66 77 of the physical core memory available for the calculation 11 1 COMPUTATIONAL DEMANDS 215 Important options The options to define the orbital and the auxiliary basis sets the maximum amount allocatable core memory maxcor and the frozen core approximation maxcor have been mentioned above and described in the previous chapters on MP2 and CC2 calculations Apart from this CCSD and CCSD T calculations require very little additional input Relevant are in particular some options in the ricc2 data group ricc2 ccsd ccsd t conv 7 oconv 6 mxdiis 10 maxiter 25 The options ccsd and ccsd t request respectively CCSD and CCSD T calcu lations Since CCSD T requires the cluster amplitudes from a converged CCSD calculation the option ccsd t is implies the ccsd option The number given for mxdiis defines the maximum number of vectors included in the DIIS procedure for the solution
246. default 0 02 20 2 4 Keywords for Module UFF One has to specify only the Cartesian coordinates data group coord to start a uff run The program uff requires the data groups uff ufftopology uffgradient and uffhessian If these keywords do not exist in the control file the program will generate these data groups The data group uff contains the parameters described below The default values in the control file are 1 1 O maxcycle modus nqeq 111111 iterm 0 10D 07 0 10D 04 econv gconv 0 00 1 10 qtot dfac 0 10D 03 0 10D 04 0 30 epssteep epssearch dqmax 25 0 10 0 00 mxls dhis ahls 1 00 0 00 0 00 alpha beta gamma F F F transform lnumhess 1md The explanation of the variables are as follows maxcycle number of max optimization cycles maxcycle 1 single point calculation modus can have the values 1 or 1 If modus 1 only the topology will be calcu lated ngeq each ngeq cycle the partial charges will be calculated If nqeq 0 then the partial charges are calculated only in the first cycle if the file ufftopology does not exist iterm switch for the different types of force field terms 100000 bond terms will be calculated 010000 angle terms will be calculated 001000 torsion terms will be calculated 278 CHAPTER 20 KEYWORDS IN THE CONTROL FILE 000100 inversion terms will be calculated 000010 non bonded van der Waals terms will be calculated 000001 non bonded electrostatic terms w
247. default format is format 8f10 5 but other 10 digit f10 x formats e g x 4 6 are possible and will be used after being manually speci fied within forceapprox See the example below forceapprox format 8f10 4 0 9124 0108 0 3347 0 2101 0 0299 1 3347 0 0076 0 1088 0 0778 0 6515 20 2 FORMAT OF KEYWORDS AND COMMENTS 347 hessian projected this data block contains the analytical cartesian force constant matrix with translational and rotational combinations projected out as output by the aoforce program and may be used to supply a high quality force constant matrix forceapprox for geometry optimizations specifying forceinit on carthess or interconversion cartesian gt internal hessian RELAX Output Data Groups coord either updated cartesian coordinates if a successful coordinate update has been performed or cartesian coordinates for input internal coordinates if only a conversion from internal to cartesian coordinates has been performed basis updated basis set exponents basis sets contraction coefficients or scaling fac tors if optimize basis on has been specified global updated global scaling factor for all basis set exponents if optimize global on has been specified forceapprox an approximate force constant matrix to be used in quasi Newton type geom etry optimizations this matrix will be improved in subsequent optimization cycles if one of the variable metric methods forceupdate
248. dic array of point charges to make space for the cluster The positions of the removed point charges are specified in the subsection cluster of the embed keyword Note that the position of the QM cluster and the isolating shell must exactly correspond to the removed part of the crystal otherwise positions of the cluster atoms would overlap with positions of point charges in the periodic lattice resulting in a nuclear fusion cluster F O 00000000000000 O 00000000000000 O 00000000000000 Ca 2 61994465796043 2 61994465796043 2 61994465796043 Ca 2 61994465796043 2 61994465796043 2 61994465796043 Ca 2 61994465796043 2 61994465796043 2 61994465796043 Ca 2 61994465796043 2 61994465796043 2 61994465796043 144 os es es aies es e gt es e gt e es CHAPTER 6 HARTREE FOCK AND DFT CALCULATIONS 23988931592086 00000000000000 23988931592086 00000000000000 00000000000000 00000000000000 23988931592086 23988931592086 23988931592086 23988931592086 23988931592086 repeated for Caz16 F389 end 00000000000000 00000000000000 00000000000000 23988931592086 00000000000000 23988931592086 23988931592086 00000000000000 00000000000000 23988931592086 23988931592086 00000000000000 23988931592086 00000000000000 00000000000000 23988931592086 00000000000000 00000000000000 23988931592086 23988931592086 O 00000000000000 O 00000000000000 By defa
249. dified Atomic Orbitals MAQs MAOs are employed if atomic density eigenvalues exceed a threshold of 1000 specify the appropriate option if you want to use another global criterion for selecting MAQs option status description select by eigenvalues of the atomic density matrices select by occupation numbers lt r gt is the selection threshold DEFAULT 1000 or q uit leave this menu The criterion applied by default is the so called atomic density eigenvalue with a threshold of 0 1 You can switch the criterion to occupation numbers by entering occ If you also want to change the threshold you just have to append its new value to the selection keyword e g occ 2 Finally you can select or disable various options in connection with the computation of shared electron numbers SEN within the following menu 94 CHAPTER 4 PREPARING YOUR INPUT FILE WITH DEFINE actual settings for data group shared electron numbers 2 center shared electron numbers will be computed values are printed if absolute value exceeds 0100 3 center shared electron numbers will be computed values are printed if absolute value exceeds 0100 4 center shared electron numbers will be computed values are printed if absolute value exceeds 0100 add or delete one or more options for the computation of Shared Electron Numbers SEN option status description DAARNAAS lt ss 2525 4 oe eee ee 2c lt r gt T compute 2 center SEN
250. dilution of the COSMO RS model is given in the output The use of this energy makes sense if the molecule under consideration is different than the used solvent or not component of the solvent mixture respectively To be consistent one should only compare energies containing the same contributions i e same outlying charge correction and with or without combinatorial contribution Please note the COSMO RS contribution of the DCOSMO RS energy depends on the reference state and the COSMO RS parameterization used in the calculation of the chosen COSMO RS potential Therefore the DCOSMO RS energies should not be used in a comparision with the gas phase energy i e the calculation of solvation energies 20 2 9 Keywords for Modules GRAD and RDGRAD Many of the dscf and ridft keywords are also used by grad and rdgrad drvopt This keyword and corresponding options are required in gradient calculations only in special circumstances Just drvopt is fine no options needed to compute derivatives of the energy with respect to nuclear coordinates within the method specified SCF DFT RIDFT If running a DFT gradient calculation it is possible to include the derivatives of the quadrature weights to get more accurate results In normal cases however those ef fects are marginal An exception is numerical calculation of frequencies by Numforce where it is strongly recommended to use the weight derivatives option The biggest deviations from the uncor
251. dinates If you choose idef in the internal coordinate menu you will get the following infor mation ENTER INTERNAL COORDINATE DEFINITION COMMAND lt x gt lt type gt lt indices gt WHERE lt x gt k f d i lt type gt stre invr bend outp tors linc linp comp ring pyrm bipy pris cube octa THESE COMMANDS WILL BE EXPLAINED IN DETAIL IF YOU ENTER lt x gt lt type gt FOR SOME CHOICE OF lt x gt AND lt type gt E G k stre DEFAULT GO BACK TO INTERNAL MAIN MENU DISPLAY dis The lt x gt means the status see page 49 of the internal coordinate entered k f d i The syntax is k stre 1 2 d tors 362 7 f bend 3 4 5 i outp 3479 Note that in the third example atom 5 is the central atom of the angle Specification of available internal coordinates The following types of coordinates are available stre The stre for stretch describes a distance between two atoms It needs only two atomic indices to be given the order of which is arbitrary invr The invr coordinate for inverse r describes an inverse distance The declaration is the same as for stre but in some cases if you are far away from the minimum the use of invr may result in better convergence bend bend describes a bond angle It requires three atoms to be specified of which the third one is the atom at the apex outp Out of plane angle outp abcd is the angle between bond a d and plane b c d 4 1 tors linc linp comp ring THE
252. directory If one of those is found it will be used by default On all systems TURBOMOLE is using the MPI library that has been shipped with your operating system On Linux for PCs and Itanium2 systems Platform MPI formerly known as HP MPI is used see Platform MPI COSMOlogic ships TURBOMOLE with a licensed Platform MPI TURBOMOLE users do not have to install or license Platform MPI themselves Parallel binaries will run out of the box on the fastest interconnect that is found Infiniband Myrinet TCP IP etc The binaries that initialize MPI and start the parallel binaries mpirun are located in the TURBODIR mpirun_scripts HPMPI directory Note the parallel TURBOMOLE modules except ricc2 need an extra server running in addition to the clients This server is included in the parallel binaries and it will be 3 2 PARALLEL RUNS 41 started automatically but this results in one additional task that usually does not need any CPU time So if you are setting PARNODES to N N 1 tasks will be started If you are using a queuing system or if you give a list of hosts where TURBOMOLE jobs shall run on see below make sure that the number of supplied nodes match PARNODES e g if you are using 4 CPUs via a queuing system make sure that PARNODES is set to 4 In some older versions of the LoadLeveler on IBM systems the total number of tasks must be set to PARNODES 1 except for ricc2 Starting parallel jobs After set
253. doubles method CCSD and its explicitly correlated CCSD F12 and CCSD F12 variants CCSD and the F12 variants can be combined with a perturbative correction for connected triple excitations CCSD T As perturbative approximations beyond MP2 also the approximations MP3 MP3 F12 MP4 and MP4 F12 are available Presently the implementation of the F12 variants and of connected triple excitations is restricted to ground state energies and the CCSD implementation to ground state and excitation energies Closed shell RHF unrestricted UHF or single determi nant restricted ROHF open shell reference wavefunctions can be used for CCSD and CCSD T but no gradients or properties are yet available for these wavefunc tion models The MP3 and MP4 approximations can currently not be combined with ROHF reference wavefunctions Further limitations no MPI parallelization calculations at these levels can presently only carried out on a single compute node only the OpenMP see Sec 3 2 2 parallelization is available for calculations beyond CC2 use of symmetry restricted to D2 and its subgroups for the conventional im plementation no symmetry can be used for the F12 methods Please note that calculations with MP3 MP4 CCSD and methods beyond CCSD require considerably more disc space and core memory than MP2 or CC2 calculations See section below for more details and recommendations Note that for the explicitely correlated CCSD varia
254. ds CC2 ADC 2 CIS D and CIS D can usually be trusted for 72 lt 15 For compatibility the program can be switched to use of the old 7 and 7Jz diag nostics printed with the headers T1 and T21 by setting the flag oldnorm in the data group excitations Note that the choice of the norm effects the individ ual results left and right one and two photon transition moments while transition strengths and all other observable properties independent of the individual normal ization of the right and left eigenvectors The 7J2 and T diagnostics can not be monitored in the output of the quasi linear solver But it is possible to do in advance a CIS D calculation The CIS D results for the 72 and T gt correlate usually well with the results for this diagnos tic from the iterativ second order models as long as there is clear correspondence between the singles parts of the eigenvectors Else the DIIS solver will print the doubles diagnostics in each iteration if the print level is set gt 3 States with large double excitation contributions converge notoriously slow a consequence of the par titioned formulation used in the ricc2 program However the results obtained with second order methods for doubly excited states will anyway be poor It is strongly recommended to use in such situations a higher level method Visualization of excitations An easy way to visualize single excitations is to plot the natural transition orbi
255. dscf 14 23 24 30 35 42 44 45 66 67 76 98 104 115 117 123 127 141 156 165 171 172 184 185 199 204 209 232 235 236 288 256 261 267 268 272 273 291 295 296 301 304 305 307 311 313 353 355 371 373 375 dummy center 53 edens 200 EGRAD keywords 322 egrad 14 24 25 36 38 39 44 46 98 104 151 152 155 156 161 162 200 227 235 236 238 322 346 353 355 eigenvalue difference 260 Eiger 240 359 eiger 26 energy 111 environment variable OMP _NUM_ THREADS 44 INDEX PARA ARCH 44 PARNODES 44 ESCF keywords 317 escf 14 24 36 39 44 46 79 141 151 155 162 164 165 267 305 307 S11 317 319 322 evalgrad 26 EVIB keywords 317 evib 231 317 extended H ckel calculation 66 FDE 26 Freeh 38 225 freeh 25 FROG keywords 364 frog 24 38 98 115 364 367 369 frozen coordinates 227 geometries excited states 196 ground state 194 geometry manipulation of 60 GRAD keywords 313 grad 23 24 35 37 39 41 42 76 82 98 104 107 108 115 117 123 127 141 161 196 204 268 305 307 311 313 322 346 348 373 375 grad_out 118 gradient 199 gradients excited states 196 ground state 194 hcore 26 431 Infrared Spectra 224 intcorr 216 intense 25 227 internal coordinates linear combination of 59 manual definition of 58 types of 58 intersections conical 190 jmol 27 job lt cycle gt 98 job last 98
256. e scftol scfintunit scfmo have the save meaning as in dscf see Section 20 2 6 Since mpshift works semi direct it uses the same integral storage scratch files The scratch files allocated by mpshift can be placed anywhere in your file systems instead of the working directory by referencing their pathnames in this data group All possible scratch files are listed in the following example 372 CHAPTER 20 KEYWORDS IN THE CONTROL FILE scratch files mpshift csssmat path1 filet mpshift cshsmat path2 file2 mpshift csdgsmat path3 file3 mpshift csusmat path4 file4 mpshift dens path5 file5d mpshift fock path6 file6 mpshift dfock path7 file7 mpshift idvds1 path8 file8 mpshift idvds2 path9 file9 mpshift idvds3 path10 file10 mpshift jdvdsi path11 file11 mpshift jdvds2 path12 file12 mpshift jdvds3 path13 file13 mpshift cshmmat path14 file14 trast trand traloop number stands for traloop start and traloop end Each loop or pass in MP2 chemical shift calculations can be done individually by providing the keywords trast and trand This can be used to do a simple parallelization of the run Create separate inputs for each traloop Add trast lt number gt trand lt number gt in the control files number goes from 1 to the number of traloops Each calculation will create a restart file called restart mpshift To collect all steps and to do the remaining work copy all restart files to one directory and rename the
257. e The EXX KS local potential vEXX r can be ob tained using the optimized effective potential OEP method in each self consistent step 169 172 exchange operator 6 eE Ein 6a NY p EEE 18 2 where y r r 5 Qn dalr os r ds F dalF ig the non interacting density a Ea Es response An effective approximation to the OEP EXX potential is given by the Localized Hartree Fock LHF potential 168 which is given by rey ae I far ee r ano lt E gilo ot o 18 3 where the first term is called Slater potential and the second term correction term If terms i j are neglected in the correction term the Krieger Li Iafrate KLI potential 173 is obtained Note that the Eq 18 3 depends only on occupied orbitals whereas Eq 18 2 depends also on virtual orbitals The LHF total energy is assumed to be the EXX total energy even if LHF is not variational although the deviation from the EXX energy is very small usually below 0 01 The LHF potential is equivalent to the Common Energy Denominator Approximation CEDA 174 and to the Effective Local Potential ELP 175 Both OEP EXX and LHF in contrast to functionals of the first three rungs satisfy the HOMO condition 173 dH0Mo x nomo duomol r Homo 18 4 and the asymptotic relation 176 177 a 1 vx tr F oul vx Oe lfm 18 5 where m is the highest occupied orbital which do not have a nod
258. e if you add or change atoms in the first menu so that the basis set information is wrong in the second menu define takes care of most but not all of these problems For these reasons it is recommended to use a different filename for the input and the output file of the define session if you change the molecule to be investigated In most cases involving only changes in the last three of the four main menus no problem should arise when using the same file as input and output 4 0 6 Be Prepared Atomic Coordinates Molecules and their structures are specified by coordinates of its atoms within the program invariably by Cartesian coordinates in atomic units Angstrom would also do In TURBOMOLE these coordinates are contained in the file coord see Section 21 Sample control files for an example Recommendation We strongly recommend to create the coord file before calling define only for small molecules one should use the interactive input feature of define Set up the molecule by any program you like and write out coordinates in the xyz format XMol format which is supported by most programs Then use the TURBOMOLE tool x2t to convert it into a TURBOMOLE coord file see Section 1 5 Internal Coordinates Structure optimizations see jobex are most efficient if carried out in internal coor dinates and TURBOMOLE offers the following choices internals based on bond distances and angles see Section 4 1 2 50 CHAPTER 4 P
259. e 1 0d 6 thrmaxdispl 1 0d 3 thrmaxgrad 1 0d 3 thrrmsdispl 5 0d 4 thrrmsgrad 5 0d 4 Only non default values are written in the control file except statpt 20 2 FORMAT OF KEYWORDS AND COMMENTS 349 itrvec 0 Following options are available itrvec Index of the Hessian eigenvector to follow for transition structure search tran sition vector Eigenpairs are sorted in ascending order i e with increasing eigenvalues and start with index 1 The eigenpairs corresponding to transla tions and rotations are shifted to the end For minimization the value 0 has to be specified update Method of hessian update For minimization default is BFGS for TS search default is Powell and none is for no update hssfreq Recompute the full Hessian every N th step during a transition state search The default is zero and the Hessian is read in or computed in the first step only If the standard Hessian update methods fail it can help to use this keyword Warning This will make the calculation much more time demanding keeptmode Freezing transition vector index hssidiag diagonal hessian elements for diagonal Hessian guess default 0 5 radmax Maximum allowed value for trust radius default 0 3 radmin Minimum allowed value for trust radius default 1 0d 4 tradius Initial value for trust radius default tradius radmax 0 3 Convergence criteria threchange threshold for energy change default 1 0d 6
260. e cavity de symmetrization phsran real phase of the cavity de symmetrization refind real refractive index used for the calculation of vertical excitations and num frequencies the default 1 3 will be used if not set explicitly use_old_amat uses A matrix setup of TURBOMOLE 5 7 20 2 FORMAT OF KEYWORDS AND COMMENTS 309 use_contcav in case of disjunct cavities only the largest contiguous cavity will be used and the smaller one s neglected This makes sense if an unwanted inner cavity has been constructed e g in the case of fullerenes Default is to use all cavities If the cosmo keyword is given without further specifications the default parameter are used recommended For the generation of the cavity COSMO also requires the definition of atomic radii User defined values can be provided in Angstrom units in the data group cosmo_atoms e g for a water molecule cosmo_atoms radii in Angstrom units o 1 radius 1 7200 h 2 3 radius 1 3000 If this section is missing in the control file the default values defined in the radii cosmo file located in TURBODIR parameter are used A user defined value supersedes this defaults cosmo and cosmo_atoms can be set interactively with the COSMO input program cosmoprep after the usual generation of the TURBOMOLE input The COSMO energies and total charges are listed in the result section E g SCREENING CHARGE cosmo 0 003925 correction 0 003644 total 0
261. e is defined by the atom centered basis functions within DLU diffuse functions in the basis set should be handled with care and the use of tailored basis sets is recommended relativistic cal culations require refitted basis sets if these are not available for X2C or X2C DLU standard second order DKH basis sets could be used As in DKH theory X2C and BSS exist in full two component spin same orbit coupling including and in a one component scalar relativistic form Both have been implemented into the TURBOMOLE package and all details on the efficient implementation have been described in Ref 76 which should be cited when the module is activated 6 4 RELATIVISTIC EFFECTS 139 6 4 2 How to use The keyword soghf enforces the two component calculations Keywords for speci fication of the method of calculation are the same as for the one component case The DIIS scheme for complex Fock operators can be activated by inserting gdiis in the control file For closed shell species a Kramers invariant density functional formalism only pure density functionals can be switched on with the keyword kramers These keywords have to be inserted into the control file manually As start wavefunctions Hiickel UHF or RHF wavefunctions may be used The two component formalism supports Abelian point group symmetry if kramers is set Otherwise start wave functions may be transformed to Cl symmetry by define or the script uhfuse For open
262. e or two atoms might does lead to some artifical small but non zero frequencies e Zero point vibrational energies calculated with the frznuclei option are only meaningful for comparison of systems with the same mechanically active atoms and similar embedding as the contributions from the frozen coordinates are not included 13 4 Interface to hotFCHT aoforce supports the generation of input files for the hotFCHT code version 2 0 and later of R Berger and co workers see http fias uni frankfurt de berger group hotFCHT index html which allows for the calculation of Franck Condon factors Just include the keyword hotfcht in the control file The option is also active in analysis mode that is as long as you still have the data group hessian in the control file or in a file refer enced in the control file you can always use aoforce in analysis mode to quickly generate the hotFCHT input The program will write three files The first one hotfcht_header inp contains a collection of the most important keywords of hot FCHT set to some default values please adapt to your needs and list of all atomic masses either TURBOMOLE s default masses or the ones given in the atoms data group The other two hotfcht_data_i inp and hotfcht_data_f inp contain the vibrational frequencies normal modes and the names of the irreducible representa tions of the normal modes In the former file these data are associated with the hotFCHT keywords for
263. e program e g total and spin densities leading to Mulliken charges and unpaired electrons per atom in RHF UHF type calculations in dscf or ridft SCF MP2 densities in rimp2 or mpgrad excited state densities in egrad Suboptions see Section 20 2 21 also allow for calculation of Mulliken contributions of selectable atoms to selectable MOs including provision of data for graphical output simulated density of states With pop nbo a Natural Population Analysis NPA 154 is done Currently only the resulting charges are calculated With pop paboon a population analyses based on occupation numbers 155 is per formed yielding shared electron numbers SENs and multicenter contributions For this method always the total density is used i e the sum of alpha and beta densities in case of UHF the SCF MP2 density in case of MP2 and the GHF total density for two component GHF Note that the results of such an analysis may de pend on the choice of the number of modified atomic orbitals MAOs By default numbers of MAOs which are reasonable in most cases are taken see Section 20 2 21 Nevertheless it is warmly recommended to carefully read the information concerning MAOs given in the output before looking at the numbers for atomic charges and shared electron numbers For different ways of selecting MAOs see Section 20 2 21 Generation of localized MOs localize enables calculation of localized molec ular orbitals Per default a Boys
264. e residual vector in the solution of the Z vector equations will be set to 10779 semicano use semi canonical formulation for the calculation of transition one electron densities Switched on by default The semi canonical formu lation is usually computationally more efficient than the non canonical formulation Exceptions are systems with many nearly degenerate pairs of occupied orbitals which have to be treated in a non canonical way anyway See also explanation for thrsemi below nosemicano use non canonical formulation for the calculation of transition one electron densities Default is to use the semi canonical formulation thrsemi the threshold for the selection of nearly degenerate pairs of occupied orbitals which if contributing to the density have to be treated in a non canonical fashion will be set to 10 s If set to tight the semi canonical algorithm will become inefficient if the threshold is to large the algorithm will become numerical unstable zpreopt threshold for preoptimizating the so called Z vector i e the lagrangian multipliers for orbital coefficients with a preceding RI CPHF calcula tion with the cbas auxiliary basis The RI CPHF equations will be con verged to a residual error lt 10 7PreoP Default is zpreopt 4 This preoptimization can reduce significantly the computational costs for the solution of the Z vector equations for large basis sets in particular if they
265. e solution of the TDHF TDDFT response problem A wA X Y P Q 7 4 If Xq Ya arises from an electric dipole perturbation ua the electronic dipole polarizability at frequency w is Aap Ww Xa Yo Mg 7 5 a b x y z Similarly if mq is a component of the magnetic dipole moment operator the optical rotation is 97 baa w 3Im Xa Yalms 7 6 where c is the light velocity Excitation energies Q are the poles of the frequency dependent density matrix re sponse They are thus the zeros of the operator on the left hand side of Eq 7 4 A A Xn Yn 0 7 7 The corresponding eigenvectors X Yn are the transition density matrices for a given excitation also called excitation vectors in the following They are required to be normalized according to Xn Yn A Xn Yn 1 7 8 Transition moments are evaluated by taking the trace with one particle operators e g po Xn Yni p 7 9 for the electric and m Xn Yn M 7 10 for the magnetic transition dipole moments The full TDHF TDDFT formalism is gauge invariant i e the dipole length and dipole velocity gauges lead to the same transition dipole moments in the basis set limit This can be used as a check for basis set quality in excited state calculations The TDA can formally be derived as an approximation to full TDHF TDDFT by constraining the Y vectors to zero For TDHF the TDA is equivalent
266. e solvent charges should be equilibrated one inserts the keyword cosmorel state x where the ground state x is used normally but can be replaced by any requested excited state Make sure to request relaxed properties for any desired state otherwise the COSMO macro iteration will not work in ricc2 The off diagonal contributions mentioned above can be switched off by setting the keyword nofast in cosmo A typical input might look like ricc2 adc 2 excitations irrep a multiplicity 1 nexc 1 npre 1 nstart 1 irrep a multiplicity 1 nexc 1 npre 1 nstart 1 exprop relaxed states all response fop relaxed cosmo epsilon 50 000 rsolv 1 30 refind 3 0000 cosmorel state a 1 nofast cosmo_correlated cosmo_atoms This would deliver an excited state calculation for the lowest singlet A and A excitations using the ADC 2 method The solvent charges are equilibrated to state 11 A and the non equilibrium energy contributions for the MP2 ground state and the 1 A excited state are calculated furthermore All contributions to the one electron density are included since the proper keyword is commented out Note when doing solvent relaxations with the CCS CIS model no request of relaxed ground state properties are needed since the relaxed ground state is identical to the HF ground state A short summary of the COSMO input is given at the beginning of the ricc2 output as well as a summary of the energy contributi
267. e used to control these steps as in semi direct SCF namely thime thize scfintunit see Chapter 6 The same is true for DFT and RI keywords such as dft ridft ricore Point group symmetry escf and egrad can exploit point group symmetry for all finite point groups with up to 99 fold symmetry axes gt symmetry The re sponse and eigenvalue problems 7 4 and 7 7 decompose into separate problems for each IRREP that are solved independently For excited state and instability calculations it is thus necessary to specify the IRREPs to be treated soes see below For response calculations the perturbation is automatically subduced into irreducible components The overall speedup compared to C symmetry is approxi mately 1 g where g denotes the point group order For spin restricted closed shell ground states spin symmetry is used to further reduce the dimension of the response and eigenvalue problems by a factor of 2 Point group symmetry cannot be exploited in two component calculations Other features escf and egrad fully support external fields using the keyword electrostatic field specify geofield on in fldopt point charges using the keyword point_charges and effective core potentials using ecp In escf cal culations occupied and virtual MOs can be frozen using freeze 7 4 How to Perform The most convenient way to set up an escf or egrad calculation is to use the ex option of the last general define
268. e wavefunctions No additional input is required apart from the usual ROHF input for the dscf and ridft programs and a standard MPn or CC input for ricc2 TURBOMOLEs Hartree Fock codes can handle within the ROHF framework many cases which include beside common high and low spin configuration state functions also weighted averages of high spin CSFs see Sec 6 3 for further details The Moller Plesset perturbation theory and coupled cluster functionalities implemented in ricc2 require a single determinant reference state and can thus only deal with high spin open shell cases not averaged e The spins of all nopen unpaired electrons are parallel a spin will be assumed so that the ROHF reference state has the spin multiplicity Nopen 1 e There must be only one type of open shells and all orbitals in this shell must have the occupation number 1 e For the single electron case i e doublets the Roothaan parameters are a b 0 for high spin cases with more than one unpaired electron the Roothaan parameters must be set to a 1 and b 2 For non abelian points groups this implies that shells with degenerate orbitals as e g t in point group J must be half filled An average over the different symmetry equivalent or inequivalent high spin determinants that are obtained when a shell of degenerate orbitals is less than or more than half filled is not possible with single point ricc2 calculations For states with less than or more
269. ebug output default debug 1 means some output debug 2 means a lot more output Be careful nkk integer Specification of the sharpness of the partition function as proposed by Becke 193 default is nkk 3 The usage of nkk makes sense only in the range 1 lt nkk lt 6 Example 284 ntheta integer nphi integer CHAPTER 20 KEYWORDS IN THE CONTROL FILE dft nkk 3 not recommended for use Only for user specified Lobatto grids i e gridsize 9 ntheta specifies the number of 0 points and nphi specifies the number of points For the fixed Lobatto grid i e gridtype 8 the default value is ntheta 25 and nphi 48 When gridsize 9 is given you have to specify both ntheta and nphi see below otherwise the program will crash The restriction for user defined Lobatto grids is the number of grid points which must not exceed 2000 grid points Example dft gridsize 9 ntheta 30 nphi 60 old_RbCs_xi Original grids had not been carefully optimized for all atoms individually This has now been done which let to changes of for Rb and Cs only resulting in minor improvements If you have ongoing projects which have been started with the old grids you should continue using them with the keyword old_RbCs_xi Example dft old_RbCs_xi radsize integer Specifies the number of radial grid points Default values depend on type of atom and grid see keyword gridsize The formula for the radial egridsize is
270. ects due to the step length option ad real default value is 0 02a u It is strongly recommended to use Numforce in DFT calculations only with the option weight derivatives in dft since this provides more accurate gradients and thus frequencies see Section 20 2 9 5 The Numforce script can be run for different levels of theory which means that the binaries it calls have to be specified additionally To perform calculations using the RI approximation call Numforce with the option ri MP2 and CC2 calculations are requested via the options level mp2 and level cc2 respectively NumForce works also on the RI RPA level with level rirpa note the ri option must be used in this case To select the correct option s use the explanations you get by calling NumForce h For a review of theory and implementation see refs 150 151 Limitations The aoforce code has presently a number of limitations one should be aware of e It can only handle basis sets up to at most g functions e Point groups with reducible E representations such as Cn and Cpp with n gt 3 Sn with n gt 5 or T and Tq e Frozen internal or cartesian coordinates are not recognized aoforce will all ways evaluate the full hessian matrix 226 CHAPTER 13 VIBRATIONAL FREQUENCIES 13 1 Analysis of Normal Modes in Terms of Internal Co ordinates A note in advance The analysis of normal modes can at nearly no computational cost always be redone as long as
271. ed as follows 1 Dimensionality of the system is specified by the keyword periodic in the embed section periodic 3 means a bulk three dimensional system periodic 2 denotes a two dimensional surface with an aperiodic z direction 2 Definition of the unit cell of periodic point charges field is specified in the subsections cell and content of the embed section 3 Definition of the values of the point charges by specifying a charge value per species using the subsection charges or a charge value for each point charge using the subsection ch_list Note that only one of the subsections can be defined 4 Definition of the part of point charges field that will be replaced by the QM cluster together with the isolating shell ECPs explicit point charges is spec ified in the subsection cluster of the embed section 5 Definition of the quantum mechanical cluster as well as the surrounding ECPs and anionic point charges is included in the usual coord section The following two examples show the definition of the point charges unit cells Example 1 Ca Fi9 cluster embedded in bulk CaF2 In this example a QM cluster with the composition Ca4F 19 surrounded by 212 ECPs and 370 explicit point charges representing Ca cations and F anions is embedded in a periodic field of point charges 2 for Ca and 1 for F corresponding to the CaF fluorite lattice First the program has to know that this is a three dimensional periodic system T
272. ed for infinite dilution The free energy gained by the solvation process in the DCOSMO RS framework is the sum of the dielectric energy of the COSMO model and the chemical potential described above 1 diel RS iO ae Foote Eudiel foot The factor fpo has been introduced to account for the missing solute solvent back polarization The default value is one in the current implementation From the above expression the solvent operator V can be derived by functional derivative with respect to the electron density m 5 Je tS _ ve E r r a 1 Thus the solvation influence of the COSMO RS model can be viewed as a correction of the COSMO screening charges q The additional charges Serle as ghF5 ca be obtained from q4 5 A 4 5 where the potential PAES arises from chemical potential of the solute in the solvent s Pia fool At Es d q a In order to get a simple and differentiable representation of the COSMO RS potential us o T we use equally spaced cubic splines An approximate gradient of the method has been implemented DCOSMO RS can be used in SCF energy and gradient calculations geometry optimizations with dscf ridft grad and rdgrad Please regard the restriction of the DCOSMO RS energy explained in the keyword section 20 2 8 Because the DCOSMO RS contribution can be considered as a slow term contribution in vertical excitations it does not have to be taken into account in res
273. einhart Ahlrichs Markus Klaus Armbruster Rafat A Bachorz Michael Bar Hans Peter Baron R diger Bauernschmitt Florian A Bischoff Stephan B cker Nathan Crawford Peter Deglmann Fabio Della Sala Michael Diedenhofen Michael Ehrig Karin Eichkorn Simon Elliott Daniel Friese Filipp Furche Andreas GI6f Frank Haase Marco Haser Christof Hattig Arnim Hellweg Sebastian H 6fener Hans Horn Christian Huber Uwe Huniar Marco Kattannek Wim Klopper Andreas K hn Christoph K6lmel Markus Kollwitz Klaus May Paola Nava Christian Ochsenfeld Holger Ohm Mathias Pabst Holger Patzelt Dmitrij Rap poport Oliver Rubner Ansgar Schafer Uwe Schneider Marek Sierka David P Tew Oliver Treutler Barbara Unterreiner Malte von Arnim Florian Weigend Patrick Weis Horst Weiss Nina Winter 11 12 CHAPTER 1 PREFACE AND GENERAL INFORMATION We acknowledge help from e Michael Dolg University of Stuttgart now University of Cologne e J rgen Gauss University of Mainz e Christoph van Wiillen University of Bochum now TU Kaiserslautern e Stefan Brode BASF AG Ludwigshafen e Heinz Schiffer HOECHST AG Frankfurt e Ove Christiansen and Tobias Schwabe Aarhus University T S now Hamburg University and financial support by the University of Karlsruhe BASF AG BAYER AG HOECHST AG the DFG and the Fonds der Chemischen Industrie Contact address Abteilung fiir Theoretische Chemie Institut fiir Physikalische Chemie Karlsru
274. emistry applications Theory and implementation J Chem Theory Comput 9 232 2013 F Haase R Ahlrichs Semidirect MP2 gradient evaluation on workstation computers The MPGRAD program J Comp Chem 14 8 907 912 1993 F Weigend A Kohn C Hattig Efficient use of the correlation consistent basis sets in resolution of the identity MP2 calculations J Chem Phys 116 8 3175 3183 2001 C L Janssen I M B Nielsen New diagnostics for coupled cluster and M ller Plesset perturbation theory Chem Phys Lett 290 4 6 423 430 1998 I M B Nielsen C L Janssen Double substitution based diagnostics for coupled cluster and Mgller Plesset perturbation theory Chem Phys Lett 310 5 6 568 576 1999 414 110 111 112 113 114 115 116 117 118 119 120 121 122 BIBLIOGRAPHY F R Manby Density fitting in second order linear rj2 M ller Plesset pertur bation theory J Chem Phys 119 9 4607 4613 2003 E F Valeev Improving on the resolution of the identity in linear R12 ab initio theories Chem Phys Lett 395 4 6 190 195 2004 K E Yousaf K A Peterson Optimized auxiliary basis sets for explicitly correlated methods J Chem Phys 129 18 184108 2008 K A Peterson T B Adler H J Werner Systematically convergent basis sets for explicitly correlated wavefunctions The atoms H He B Ne and Al Ar J Che
275. en re ferred to as double ended methods or if the the RP is discretized chain of states methods 45 47 The RP connects reactant and product its highest point being the transition state It is a steepest descent path which means that its tangent t is always parallel to the gradient g The RP is in actual calculations discretized by a finite number of structures n The tangents are parallel to the gradients for all structures i 1 n Assuming normalized tangents tt 1 this can be written as 0 1 tit gi 5 5 Several approximations for the tangents t exist 47 48 usually using finite differ ence schemes The most common methods the Nudged Elastic Band NEB 47 48 and String Method SM 49 prevent the structures from sliding down the re action path towards products and reactants with additional springs or interpola tion redistribution algorithms The method used here achieves equal spacing via constrained optimization assuming a quadratic potential 50 An initial path is pro vided using a slight variation of the Linear Synchronous Transit 45 The structure of the optimization is the same as in other TURBOMOLE structure optimizations As the jobex script drives optimizations by calling statpt relax as well the SCF and gradient modules The woelfling job script drives optimizations by calling woelfling as well as the SCF and gradient modules The woelfling job scripts reads the current path from file
276. enMP or multi threaded techniques for shared memory and multi core machines Generally there are two hardware scenarios which determine the kind of paralleliza tion that is possible to use e On a single node with several CPUs and or cores using the same memory shared memory the user can run all parallelized modules of TURBOMOLE For some modules both shared memory and MPI versions are available but it is recommended not to use the latter ones for performance reasons How to run the parallel TURBOMOLE SMP version on multi core and or multi CPU systems Please see chapter 3 2 2 e On a cluster a parallel calculation can be performed using several distinct nodes each one with local memory and disks This can be done with the MPI version How to run the parallel TURBOMOLE MPI version on clusters Please see chapter Deel The list of parallelized programs includes presently e ridft parallel ground state Hartree Fock and DFT energies including RI J and the multipole accelerated RI MA RI J e rdgrad parallel ground state gradients from ridft calculations e dscf Hartree Fock and DFT ground state calculations for all available DFT functionals without the usage of RI J approximation e grad parallel ground state gradients from dscf calculations e ricc2 parallel ground and excited state calculations of energies and gradi ents at MP2 and CC2 level using RI as well as energy calculations of other wave functio
277. energy 1 Restarting The script FDE checks in the current directory for previous FDE calculations If these are present then the FDE calculation will be restarted from the last iteration found The directories ISOLATED_SUBSYSTEM_A and ISOLATED_SUBSYSTEM_B will be overwritten by the converged calculations from previous run The energy and the orbital from the isolated systems are saved in the current directory in the files isolated_energy ks mos_A ks and mos_B ks Note that a restart is possible only if the same subsystem definition and the same basis set are used e g the same p flag and the s or m flag Other flags e g kinetic and xc functionals and convergence paramters can be instead modified As all the options are saved in the fde input file to restart a FDE calculation the FDE script can be inkoved without any parameters To force a calculation from scratch use FDE p 3 scratch 17 2 2 FDE with hybrid and orbital dependent functionals In order to use local approximations 17 1 and 17 8 with FDE the flag f string must be add to the options of the script Here string denotes the local semilocal ap 254 CHAPTER 17 FROZEN DENSITY EMBEDDING CALCULATIONS Table 17 1 Other options in the shell script FDE d or dipole dipole 1 dipole moment each step v or verbose shows more informations save mos save mos 1 save the MOs of both subsystems for each step save matrix save matrix 1 save fde matrices i
278. ensity functional response theory from automatic differentiation J Chem Theory Comput 6 1971 1980 2010 56 Y Zhao D G Truhlar The M06 suite of density functionals for main group thermochemistry thermochemical kinetics noncovalent interactions excited states and transition elements two new functionals and systematic testing of four M06 class functionals and 12 other functionals Theor Chem Acc 120 215 241 2008 57 P A M Dirac Quantum mechanics of many electron systems Proc Royal Soc London A 123 792 714 733 1929 58 J C Slater A simplification of the Hartree Fock method Phys Rev 81 3 385 390 1951 59 S Vosko L Wilk M Nusair Accurate spin dependent electron liquid corre lation energies for local spin density calculations a critical analysis Can J Phys 58 8 1200 1211 1980 60 J P Perdew Y Wang Accurate and simple analytic representation of the electron gas correlation energy Phys Rev B 45 23 13244 13249 1992 410 61 62 63 64 65 66 67 68 69 70 71 72 73 BIBLIOGRAPHY A D Becke Density functional exchange energy approximation with correct asymptotic behaviour Phys Rev A 38 6 3098 3100 1988 C Lee W Yang R G Parr Development of the Colle Salvetti correlation energy formula into a functional of the electron density Phys Rev B 37 2 785 789 1988 J P Perd
279. equals to aag w The requirement that L w be stationary with respect to all variational parameters determines the Lagrange multi pliers 7 and W All polarizability components a are processed simultaneously which allows for computation of polarizability derivatives at the computational cost which is only 2 3 higher than for the electronic polarizability itself Within TDDFT and TDHF the X and Y coefficients are normalized as follows Gal Mal 1 7 14 ia where 7 and a label occupied and virtual MOs respectively Thus the squared coefficient of a single electron excitation from orbital 7 to orbital a can be defined as cial F Xial E Vaal 7 15 escf prints out Cia 100 starting with the largest coefficient until the sum of the coefficients is 0 9 or greater TDA is contained as special case with Y 0 7 3 Implementation Without giving details we discuss features of the implementation in escf and egrad that matter for applications The interested reader is referred to the refs given in the program headers as well as ref 101 Simultaneous vector iteration The solutions of Eqs 7 4 and 7 7 Eq 7 11 are expanded in a subspace of L which is iteratively expanded Davidson method 102 The iteration is stopped when the Euclidean norm of the residual vector is smaller than 107 The default for k is 5 which usually gives excitation energies accurate to 8 10 digits and properties accurate to
280. erence point 0 0 0 localization if localization is active you need boys to perform a boys localization of orbitals with orbital energies gt thresholad 2 Hartrees localize with respect to locxyz x y and z and write resulting orbitals to lmofile Imo At the most sweeps 10000 orbital rotations are performed Non defaults may be specified using the following suboptions Imofile filename locxyz dirl dir2 dir3 threshold real sweeps integer population analyses if population analyses is active you need mulliken spdf molap netto irpspd irpmol mommul to perform a Mulliken population analysis The options specify the output data spdf print molecular orbital contributions to atomic s p d populations molap print molecular orbital contributions to overlap populations netto print atomic netto populations irpspd print contributions of irreducible representations to atomic s p d populations irpmol print contributions of irreducible representations to overlap pop ulations or loewdin to perform a L wdin population analysis options are invalid here A L wdin 302 CHAPTER 20 KEYWORDS IN THE CONTROL FILE population analysis is based on decomposing VSDV S instead of DS in case of a Mulliken PA or paboon momao maodump maofile mao all to perform a population analysis based on occupation numbers the options are not necessary and produce some output data concerning the modified a
281. erform an interpolation or extrapolation of coordinates DEFAULT y polish disable inter extrapolation lt RETURN gt OR OR q uit WILL TERMINATE THIS MENU These options result in better convergence of your optimization in most cases Interconversion Between Internal and Cartesian Coordinates The interconversion between internal and Cartesian coordinates is not possible di rectly in this direction Instead it is performed iteratively The following options control this conversion 4 4 THE GENERAL OPTIONS MENU 85 on switch on interconversion DEFAULT off qconv lt r gt set convergence threshold for interconversion l l of coordinates to lt r gt DEFAULT lt r gt 1000E 09 iter lt i gt allow at most lt i gt iterations for interconversion of coordinates DEFAULT lt i gt 25 crtint transform cartesian into internal coordinates DEFAULT n intcrt transform internal into cartesian coordinates DEFAULT n grdint transform cartesian into internal gradients DEFAULT n hssint transform cartesian into internal hessian DEFAULT n use lt opt gt for disabling any interconversion option lt RETURN gt OR OR q uit WILL TERMINATE THIS MENU The options qconv and iter are used in each normal relax run to determine the char acteristics of the back transformation of coordinates into the internal space With the other options and interconversion switched on you can force relax to perform only the s
282. es close to 1 the other columns such close to 0 The six columns at the right show the individual contributions of the six cartesian d functions What has to be done to generate start MOs for the ba case Obviously one of the five localized alpha spin orbitals from the first Cu atom atom label 1 cu has to become a beta spin orbital These five orbitals have the indices 15 18 20 22 23 In order to avoid linear dependencies it is advisable to take the orbital that has no beta analogue This can be found by comparing the contributions of the six d functions In the present example this is the case for the localized alpha orbitals 15 and 18 in contrast to all localized beta orbitals they show significant contributions from dgy One thus enters a2b 15 and after confirming the replacement of original MOs with the generated start MOs one is finally asked It is advisable to modify damping and orbital shift in the following way scfdamp start 5 000 step 0 050 min 0 500 scforbitalshift automatic 1 0 scfiterlimit 999 Do you want to replace the corresponding entries in the control file y which should be confirmed as otherwise the prepared spin state might be destroyed during the SCF iterations From this input one may start the SCF HF DFT procedure For recommended choices of DFT functionals and formulae to calculate the coupling parameters from these energy differences please consult the papers of the above mentioned authors F
283. escf or egrad from your command line without explicit path expand your PATH environment variable to export PATH TURBODIR bin sysname PATH The usual binaries are replaced now by scripts that prepare the input for a parallel run and start the job automatically The number of CPUs that shall be used can be chosen by setting the environment variable PARNODES export PARNODES 8 The default for PARNODES is 2 NOTE Depending on what you are going to run some care has to be taken that the system settings like memory limits etc will not prevent the parallel versions to run See the following sections 3 2 PARALLEL RUNS 45 OpenMP parallelization of dscf and ricc2 The OpenMP parallelization does not need any special program startup The bi naries can be invoked in exactly the same manner as for sequential non parallel calculations The only difference is that before the program is started the environ ment variable PARNODES has to be set to the number or threads that should be used by the program the scripts will set OMP_NUM_THREADS to the same value and start the OpenMP binaries The number of threads is essentially the max number of CPU cores the program will try to utilize To exploit e g all eight cores of a machine with two quad core CPUs set export PARNODES 8 for csh and tcsh use setenv PARNODES 8 Presently the OpenMP parallelization of ricc2 comprises all functionalities apart from the recently LT SOS RI
284. escribed in refs 12 126 ref 126 also contains a discussion of the basis set effects and the errors introduced by the RI approximation The calculation of excited state first order properties thus requires the calculation of both the right and left E eigenvectors and of the excited state Lagrangian multipliers ier The disk space and CPU requirements for solving the equations for Ex and gler are about the same as those for the calculation of the excitation energies For the construction of the density matrices in addition some files with O Nroot N size are written where Nroot is the number of excited states The single substitution parts of the excited states Lagrangian multipliers n are saved in files named CCNLO s m zqrz For the calculation of first order properties for excited states the keyword exprop must be added with appropriate options to the data group excitations else the input is same as for the calculation of excitation energies ricc2 cc2 response fop unrelaxed_only operators diplen qudlen excitations irrep al nexc 2 exprop states all operators diplen qudlen Orbital relaxed first order properties and gradients To obtain orbital relaxed first order properties or analytic derivatives gradients the Lagrange functional for the excited state in Eq 10 18 is analogously to the treatment of ground states augmented by the equations for the SCF orbitals and the perturbations i
285. etermining reaction paths in large molecules application to myoglobin Chem Phys Lett 139 5 375 380 1987 M G H Jonsson Quantum and thermal effects in h 2 dissociative adsorption evaluation of free energy barriers in multidimensional quantum systems Phys Rev Lett 72 7 1124 1127 1994 BIBLIOGRAPHY 409 48 G Henkelman H Jonsson J Chem Phys 113 22 9978 9985 2000 49 E Weinan W Ren E Vanden Eijnden Phys Rev B 66 5 052301 2002 50 P Plessow Reaction Path Optimization without NEB Springs or Interpolation Algorithms J Chem Theory Comput 9 3 1305 1310 2013 51 K Eichkorn O Treutler H Ohm M Haser R Ahlrichs Auxiliary basis sets to approximate Coulomb potentials erratum 1995 242 283 Chem Phys Lett 242 6 652 660 1995 52 J A Pople R K Nesbet Self consistent orbitals for radicals J Chem Phys 22 3 571 572 1954 53 J Cizek J Paldus Stability conditions for solutions of Hartree Fock equations for atomic and molecular systems application to pi electron model of cyclic plyenes J Chem Phys 47 10 3976 3985 1967 54 F Neese F Wennmohs A Hansen U Becker Efficient approximate and parallel Hartree Fock and hybrid DFT calculations A chain of spheres algo rithm for the Hartree Fock exchange Chem Phys 356 98 109 2009 55 U Ekstr m L Visscher R Bast A J Thorvaldsen K Ruud Arbitrary order d
286. etry optimizations and molecular dynamics Invoke jobex with the level CC2 option see Section 5 1 for addi tional options and parameters of the jobex script that might be needed or useful for geometry optimizations and ab initio molecular dynamics calculations Force constants and vibrational frequencies Force constants can be calculated by numerical differentiation of the gradients Invoke for this NumForce with the level CC2 option see Chapter 13 for details about Numforce The usage of the Numforce interface for excited states is restricted to C symmetry Note using ricc2 in connection with jobex or Numforce requires that the method and the electronic state for which the gradient should be calculated and written to the interface files is specified in the option geoopt see Section 10 3 1 in datagroup ricc2 see Section 20 2 17 For calculations on excited states this state has in ad dition to be included in the input for excitation energies in datagroup excitations RI SCF reference wavefunctions The ricc2 program can be used in combina tion with conventional SCF or with the RI J and RI JK approximations for SCF with the exception that the calculation of gradients for reference wavefunctions which employ only the RI J approximation for the Coulomb matrix but 4 index integrals for the exchange matrix is presently not supported The implementation of gradients 185 in ricc2 assumes that the reference wavefunction has either been
287. ew Density functional approximation for the correlation energy of the inhomogenous electron gas Phys Rev B 33 12 8822 8824 1986 J P Perdew K Burke M Ernzerhof Generalized gradient approximation made simple Phys Rev Lett 77 18 3865 3868 1996 J Tao J P Perdew V N Staroverov G E Scuseria Climbing the den sity functional ladder Nonempirical meta generalized gradient approximation designed for molecules and solids Phys Rev Lett 91 14 146401 2003 A D Becke A new mixing of Hartree Fock and local density functional theo ries J Chem Phys 98 2 1372 1377 1993 A D Becke Density functional thermochemistry III The role of exact ex change J Chem Phys 98 7 5648 5652 1993 J P Perdew M Ernzerhof K Burke Rationale for mixing exact exchange with density functional approximations J Chem Phys 105 22 9982 9985 1996 V N Staroverov G E Scuseria J Tao J P Perdew Comparative assessment of a new nonempirical density functional Molecules and hydrogen bonded complexes J Chem Phys 119 23 12129 12137 2003 S Grimme Semiempirical hybrid density functional with perturbative second order correlation J Chem Phys 124 034108 2006 A Gorling M Levy Correlation energy functional and its high density limit obtained from a coupling constant perturbation expansion Phys Rev B 47 13105 1993 A Gorling M Levy Exact Kohn Sham sche
288. excited states as derivatives of variational functionals J Chem Phys 109 21 9219 9236 1998 C H ttig O Christiansen P J rgensen Multiphoton transition moments and absorption cross section in coupled cluster response theory employing varia tional transition moment functionals J Chem Phys 108 20 8331 8354 1998 C H ttig Structure optimizations for excited states with correlated second order methods CC2 CIS Doo and ADC 2 Adv Quant Chem 50 37 60 2005 S Grimme E Ugorodina Calculation of 0 0 excitation energies of organic molecules by CIS D quantum chemical methods Chem Phys 305 223 230 2004 416 133 134 135 136 137 138 139 140 141 142 143 144 145 146 BIBLIOGRAPHY Y M Rhee M Head Gordon Scaled second order perturbation corrections to configuration interaction singles Efficient and reliable excitation energy methods J Phys Chem A 111 5314 5326 2007 D P Tew W Klopper C Neiss C H ttig Quintuple quality coupled cluster correlation energies with triple basis sets Phys Chem Chem Phys 9 1921 1930 2007 H Fliegl C H ttig W Klopper Coupled cluster theory with simplified linear r 2 corrections The CCSD R12 model J Chem Phys 122 084107 2005 T Shiozaki M Kamiya S Hirata E F Valeev Explicitly correlated coupled cluster singles and doubles method based on c
289. f char lt g dq gt or lt dq dq gt fmode static use static force constants fmode dynamic use updated force constants fail real real defines the threshold for the quantity g dq g dq which defines the angle between gradient vector and coordinate change default 0 1 If pulay is used in connection with a multidimensional BFGS update for the hessian than the default is real 0 0 If waa gt real the pulay update for the geometry is expected to fail and will be ignored For example pulay numpul 4 maxpul 4 minpul 3 modus lt dql dq gt static fail 0 2 options for forceupdate diagonal update only the diagonal force constants update for off diagonals will be suppressed only active if method ms dfp bfgs offdamp real this allows to damp off diagonal force constants by 1 real compare of freset which discards off diagonals completely Only values gt 1 0 will be accepted This option is active only within one relax run and will be disabled automatically by relax This is useful in difficult cases where the non diagonal update has lead to too large non diagonal elements of the hessian offreset reset off diagonal force constants to zero This option will be active for the current optimization cycle only i e it will be removed by relax after having discarded off diagonals allow real optimization cycle specification of a maximum energy change allowed given in mHartree which will be accepted using the act
290. f module see also Section 5 4 This can also be used to calculate an analytical approximate cartesian Hessian If one does so the start Hessian for the ab initio geometry optimization is this Hessian instead of the diagonal one forceinit on carthess for relax module Recommendation Here is an easy way to get internal coordinates which should work Have coord ready before calling define In the main geometry menu proceed as follows to define redundant internals a coord read coord desy determine symmetry if you expect a higher symmetry repeat with in creased tolerance desy 0 1 you may go up to desy 1 ired get redundant internals quit main geometry menu To define internals a coord read coord desy determine symmetry i go to internal coordinate menu iaut automatic assignment of bends etc q to quit bond analysis imet to get the metric unnecessary internals are marked d now If ideg k in the head line you are done Otherwise this did not work lt enter gt go back to main geometry menu quit main geometry menu To define cartesians 52 a coord desy CHAPTER 4 PREPARING YOUR INPUT FILE WITH DEFINE read coord determine symmetry quit main geometry menu 4 1 1 Description of commands Main Geometry Menu In the headline of this menu you can see the current number of atoms and molecular symmetry we use an input for PH as example The commands in this menu will now be described br
291. fer to the basis set which is defined in this control file As a rough guide delete them whenever you have made changes in one of the first three main menus during your define session After that you will reach the last main menu of define which helps you to control the actions of all TURBOMOLE programs The meanings of the various options are explained in more detail in the description of the individual programs therefore only a short explanation will be given here Now have a look at the menu GENERAL MENU SELECT YOUR TOPIC scf SELECT NON DEFAULT SCF PARAMETER mp2 OPTIONS AND DATA GROUPS FOR rimp2 and mpgrad cc OPTIONS AND DATA GROUPS FOR ricc2 ex EXCITED STATE AND RESPONSE OPTIONS prop SELECT TOOLS FOR SCF ORBITAL ANALYSIS drv SELECT NON DEFAULT INPUT PARAMETER FOR EVALUATION OF ANALYTICAL ENERGY DERIVATIVES GRADIENTS FORCE CONSTANTS rex SELECT OPTIONS FOR GEOMETRY UPDATES USING RELAX stp SELECT NON DEFAULT STRUCTURE OPTIMIZATION PARAMETER e DEFINE EXTERNAL ELECTROSTATIC FIELD dft DFT Parameters ri RI Parameters rijk RI JK HF Parameters senex seminumeric exchange parameters 4 4 THE GENERAL OPTIONS MENU 75 hybno hybrid Noga Diag parameters dsp DFT dispersion correction trunc USE TRUNCATED AUXBASIS DURING ITERATIONS marij MULTIPOLE ACCELERATED RI J dis DISPLAY MOLECULAR GEOMETRY list LIST OF CONTROL FILE amp GO BACK TO OCCUPATION ORBITAL ASSIGNMENT MENU or q E
292. ficant computa tional savings in particular for geometry optimizations for small and medium sized molecules with large basis sets quadruple and beyond or basis sets with diffuse functions e g the aug cc pVXZ basis set families For large molecules with TZVPP or similar basis sets conventional direct SCF calcula tions are usually more efficient 9 3 HOW TO PREPARE AND PERFORM MP2 CALCULATIONS 171 8 With ricc2 spin component scaled SCS or SOS RI MP2 calculations can be carried out by adding in the ricc2 data group the line scs cos 1 2d0 css 0 3333d0 where the two parameters are the scaling factors for respectively the opposite and same spin contribution The specification of the scaling factors is optional the default values are cos 6 5 and css 1 3 as recommended by S Grimme in J Chem Phys 118 2003 9095 The abbreviation sos can be used for SOS MP2 calculations with cos 1 3 and css 0 0 Y Jung R C Lochan A D Dutoi and M Head Gordon J Chem Phys 121 2004 9793 SOS MP2 is in ricc2 implemented with O N scaling costs For such calculations the data group laplace has to be added 9 For technical recommendations and additional options for parallel RI MP2 cal culations with the ricc2 program see Secs 3 2 and 10 6 MP2 calculations with a ROHF reference state With the program ricc2 it is possible to compute MP2 and spin component scaled MP2 energies with single determinant restricted open shell referenc
293. fication their number is calculated by the method mix see below Note One should carefully read the information concerning MAOs given in the output before looking at the numbers for atomic charges and shared electron numbers mao selection options to specify how MAOs are selected per atom Available options are a for the way of sorting MAOs of each atom eig occ MAOs are sorted according to their eigenvalue those with largest EW finally are chosen This is the default MAOs are sorted according to their occupation note that the num ber of all occupation is NOT the number of electrons in the system This option is kept rather for historical reasons b for the determination of the number of MAOs fix A fixed number of MAOs is taken for each atom usually this is the number of shells up to the complete valence shell e g 5 for B Ne 6 for Na Mg etc Exceptions are Elements Sc Y La Ti Zr Hf V Nb Ta for which not all five d shells are included but only 2 3 or 4 respectively This modification leads to better agreement with partial charges calculated by an ESP fit thr lt real gt max mix All MAOs with an eigenvalue larger than lt real gt are chosen de fault is lt real gt 0 1 This and the following two options are not valid in connection with occ Maximum of numbers calculated from fix and thr 0 1 is taken 2 1 mixture of fix and thr 0 1 This choice gives best agreement
294. fine Note that the k plus f must equal the number of degrees of freedom ideg of your molecule if you want to perform a geometry optimization If you have less coordinates than degrees of freedom you will have to specify further ones commands idef or iaut see below if you have more coordinates than degrees of freedom you will have to throw away some of them commands irem or imet see below The commands in this menu allow you to define internal coordinates for your molecule adjust your geometry to special values of these internal coordinates and to control the numeric reliability of the chosen set of internal coordinates In detail the commands act as follows Description of commands imet a This command computes the so called B matrix which is the matrix of the derivatives of the active and fixed internal coordinates with re spect to Cartesian coordinates This matrix is used in program relax for the conversion from Cartesian coordinates and gradients to internal ones and vice versa If this matrix is singular or even nearly singular this indicates a linear dependency of your internal coordinate set As a consequence the geometry update more exactly the transformation of the updated internal coordinates into Cartesian ones will fail This may also happen in the course of a geometry optimization if the coordi nates run into linear dependency during their optimization imet checks the B matrix and removes linear dependent i
295. following two terms 4 2 Bop O eT BP 11 19 H2 5 2 ER aa a 11 20 H where the approximate triples amplitudes evaluated as 2 F LH T2 HF taibjck 11 21 Ea Ei b Ej c k In the literature one also finds sometimes the approximate triples model CCSD T also denoted as CCSD T CCSD which is obtained by adding only EY to the CCSD energy Usually CCSD T is slightly more accurate than CCSD T although for closed shell or spin unrestricted open shell reference wavefunctions the energies of both models CCSD T and CCSD T model are correct through 4 th order pertur bation theory For a ROHF reference however EY contributes already in 4 th order and only the CCSD T model is correct through 4 th order perturbation theory Integral direct implementation and resolution of the identity approxima tion The computationally most demanding in terms floating point operations steps of a CCSD calculation are related to two kinds of terms One of the most costly steps is the contraction Oar gt teiaj aclbd 11 22 cd where a b c and d are virtual orbitals For small molecules with large basis sets or basis sets with diffuse functions where integral screening is not effective it is time determing step and can most efficiently be evaluated with a minimal operation count of 30 V where O and V are number of respectively occupied and virtual orbitals if the 4 index integrals ac
296. for clusters with TCP IP interconnect Communication is avoided by using an algorithm that includes only one or few CPUs MPP for clusters with fast interconnect like Infiniband or Myrinet Number of CPUs that take part at the calculation of the linear algebra routines depends on the size of the input and the number of nodes that are used SMP all CPUs are used and SCALapack see http www netlib org scalapack routines are involved The scripts in TURBODIR mpirun_scripts automatically set this keyword depending on the output of sysname All options can be used on all systems but especially the SMP setting can slow down the calculation if used on a cluster with high latency or small bandwidth 3 2 PARALLEL RUNS Sample simple PBS start script bin sh Name of your run PBS N turbomole Number of nodes to run on PBS 1 nodes 4 Export environment PBS V Set your TURBOMOLE pathes HHHHHHHH ENTER YOUR TURBOMOLE INSTALLATION PATH HERE export TURBODIR whereis TURBOMOLE HHH HHHH HHH HHH HHH RE HEHEHE HHH HR aHH H export PATH TURBODIR scripts PATH set locale to C unset LANG unset LC_CTYPE set stack size limit to unlimited ulimit s unlimited Count the number of nodes PBS_L_NODENUMBER wc 1 lt PBS_NODEFILE Check if this is a parallel job if PBS_L_NODENUMBER gt 1 then H Parallel job Set environment variables for a MPI job export PARA_ARCH M
297. for correlation and orbital relaxation 12 3 FURTHER RECOMMENDATIONS 221 effects h is the one electron Hamiltonian T1 3 4 are 2 3 and 4 centre electron repulsion integrals and the T 3 4 are the corresponding 2 3 and 4 index relaxed 2 particle density matrices W may be interpreted as the energy weighted total spin one particle density matrix This result illustrates the key advantage of the Lagrangian method Total RI RPA energy derivatives featuring a complicated implicit dependence on the parameter X through the variables C and e are replaced by partial derivatives of the RI RPA Lagrangian whose computation is straightforward once the stationary point of the Lagrangian has been fully determined Gradients Prerequisites Geometry optimizations and first order molecular property calculations can be exe cuted by adding the keyword rpagrad to the rirpa section in the control file RPA gradients also require e an auxiliary basis defined in the data group jbas for the computation of the Coulomb integrals for the Hartree Fock energy e an auxiliary basis defined in the data group cbas for the ERI s in the corre lation treatment e zero frozen core orbitals RIRPA gradients are not compatible with the frozen core approximation at this time The following gradient specific options may be further added to the rirpa section in the control file e drimp2 computes gradients in the DRIMP2 limit e niapblocks integer
298. for other methods than CC2 The MP2 equa tions and the energy are obtained by restricting in the CC2 equations the single substitution amplitudes tai to zero In this sense MP2 can be derived as a simplifi cation of CC2 But it should be noted that CC2 energies and geometries are usually not more accurate than MP2 For CCS and CIS the double substitution amplitudes are excluded from the cluster expansion and the single substitution amplitudes for the ground state wavefunction are zero for closed shell RHF and open shell UHF reference wavefunctions and thus energy is identical to the SCF energy For the Methods CIS D CIS D and ADC 2 the ground state is identified with the MP2 ground state to define is total energy of the excited state which is needed for the definition of gradients and relaxed first order properties which are obtained as analytic derivatives the total energy Diagnostics Together with the MP2 and or CC2 ground state energy the pro gram evaluates the D diagnostic proposed by Janssen and Nielsen 108 which is 10 2 CALCULATION OF EXCITATION ENERGIES 189 defined as D y is 2 taili Amax bass 10 7 where Amax M is the largest eigenvalue of a positive definite matrix M For CC2 the D diagnostic will be computed automatically For MP2 is must explictly be requested with the didiag option in the ricc2 data group since for RI MP2 the calculation of D will contribute significantly to the compu
299. formation too If you enter the filename from which the structure is to be read starting with the file will be taken from the structure library see Section 4 1 Definitions of internal coordinates will be adjusted after substitution but no new internal coordinates are created This command offers a submenu which contains everything related to internal coordinates It is further described in Section 4 1 2 54 frag w file name del banal CHAPTER 4 PREPARING YOUR INPUT FILE WITH DEFINE This command offers a submenu which allows you to manipulate the molecular geometry i e to move and rotate the molecule or parts of it It is further described in Section 4 1 3 Here the fragments will be defined as being used by the jobbsse script in order to do a calculation osing the counter poise correction scheme In this menu up to three monomers can be defined together with their charges and their symmetry When assigning atom numbers to frag ments if x is entered instead of a number the program will request the first and last atoms of a range This will be useful for very large fragments The command w writes your molecular geometry and your internal coor dinates to file Afterwards you will be back in the geometry main menu If the filename entered starts with the structure will be written to the structure library name allows you to change atomic identifiers turning e g oxygen atoms into sulfur atoms A
300. ft may help to get better convergence Options are 20 2 FORMAT OF KEYWORDS AND COMMENTS 295 noautomatic Automatic virtual shell shift switched off automatic real Automatic virtual shell shift switched on the energies of virtual orbitals will be shifted if the HOMO LUMO gap drops below real such that a gap of real is sustained This is the default setting if the keyword is missing with real 0 1 closedshell real Option for open shell cases Closed shells are shifted to lower energies by real The default shift value is closedshel1 0 4 Note Normally this will disable the automatic shift of energies of virtual orbitals To override this you should append an exclamation mark to the automatic switch i e specify automatic real individual Set shifts for special occupied MOs To use this option start the line with the symmetry label and the list of MOs within this symmetry and append the desired shift in brackets as in the following example al 1 2 4 6 34 bi 8 3 scftol real Integral evaluation threshold Integrals smaller than real will not be evaluated Note that this threshold may affect accuracy and the convergence properties if it is chosen too large If scftol is absent a default value will be taken obtained from scfconv by real ee bf number of basisfunc tions scratch files The scratch files allocated by dscf can be placed anywhere in your file systems instead of the working directory by
301. fter entering the identifier to be changed remember the double quotation marks c ring you will be asked to enter the new one You can use question marks for characters not to be changed e g you enter ring to change c chain to c ring If you do not enter eight characters your input will be filled up with trailing blanks The command del allows you to delete one or more atoms After you entered the atomic list define will show you a list of all atoms con cerned and will ask you to confirm deleting these atoms If any internal coordinate definitions exist which rely on some of the deleted atoms these definitions will be deleted too The command banal allows you to perform a bonding analysis that is define will try to decide which atoms are bonded and which are not according to a table of standard bond lengths which is included in the code of define You must have performed this command before you can use the display commands disb display bonding information or disa display bond angle information The standard bond lengths and the bonding analysis available from these are also needed for the commands sub and iaut see internal coordinate menu Section 4 1 2 If you want to change the standard bond lengths or define more bond lengths because not for all possible combinations of elements a standard length is available you can do that by creating your own file with the non default values and by specifying its full pathname in
302. generated by the tool Rimp2prep Moreover you may specify by hand tmpdir work thisjob specification of directory for scratch files by default files are written to the working directory works also with capital letters for consistency with ricc2 clalgorithm avoids symmetry gymnastics in case of Cy symmetry rather for debugging cbasopt enforces calculation of lt ij ab gt exact lt ij ab gt RI eli elj ela e b necessary for characterization of auxiliary basis set quality and for auxiliary basis optimizations works only for C1 symmetry Note all integrals are kept in memory so this is for atoms and small molecules only tplot Enforces plotting of five largest t amplitudes as well as five largest norms of t amplitudes for fixed pair of occupied orbitals ij By additional integer this number may be changed mp2occ Enforces plotting of all eigenvalues of the MP2 density matrix 20 2 17 Keywords for Module Ricc2 Note that beside the keywords listed below the outcome of the ricc2 program also depends on the settings of most thresholds that influence the integral screening e g 326 CHAPTER 20 KEYWORDS IN THE CONTROL FILE denconv scfconv scftol and for the solution of Z vector equation with 4 index integrals for relaxed properties and gradients on the settings for integrals storage in semi direct SCF runs i e thime thize scfintunit For the explanation
303. ght eigenvectors for test purposes only bothsides The oldnorm flag switches the program to the old normalization of the 20 2 FORMAT OF KEYWORDS AND COMMENTS 335 response fop u sop o gradi conv zconv semic nosem thrse In thi eigenvectors and T and T diagnostics which were identical with those used in the CC response code of the Dalton program nrelaxed_only operators diplen perators diplen diplen freq 0 077d0 ent 6 6 ano icano mi 3 s data group you have to give additional input for the calculation of ground state properties and the solution of response equations fop sop gradi This flag switches on the calculation of ground state first order prop erties expectation values The operators flag can be followed by a list of operators see below for which the first order properties will be calculated Default is to compute the components of the dipole and the quadrupole moment The option unrelaxed_only suppress the calcula tion of orbital relaxed first order properties which require solution the CPHF like Z vector equations Default is the calculation of unrelaxed and orbital relaxed first order properties The unrelaxed_only option will be ignored if the calculation of gradients is requested see gradient option below and geoopt in data group ricc2 requests the calculation of ground state second order properties as e g dipole polarizabilities The operators flag has to be f
304. given as number of radial grid points ioffrad radsize 1 5 ioffrad is atom dependent the more shells of electrons the larger ioffrad elements ioffrad elements ioffrad for H He 20 for K Kr 40 for Li Ne 25 for Rb Xe 45 for Na Ar 30 for Cs Lw 50 The radial grid size increases further for finer grids 20 2 FORMAT OF KEYWORDS AND COMMENTS 285 gridsize 1 2 3 4 5 6 7 8 9 radsize 1 2 3 6 8 10 14 9 3 If you want to converge results with respect to radial grid size increase radsize in steps of 5 which is convenient see equation above diffuse integer Serves to increase quadrature grids this is recommended in case of very diffuse wavefunctions With the keyword diffuse grids are modified by changing the linear scaling factor of radial grid points and the radial eridsize radsize gt radsize incr E scal diffuse integer 1 2 3 4 5 6 incr 1 2 3 4 5 6 scal 1 5 2 0 2 8 4 0 5 0 6 0 For information about the linear scaling parameter see Eq 16 19 and Table 1 in Ref 192 In addition the reduction of spherical grid points near nuclei is sup pressed i e fullshell on is set see page 280 Note the keyword radsize integer overrules the setting of incr for more information see p 278 Recommendation For diffuse cases use gridsize m4 or larger in com bination with diffuse 2 and check the number of electrons for more difficult cases use diffuse 4 In case of doubt verify the calc
305. grad and globgrad the latter contains the global scaling factors and their gradients accumulated in all optimization cycles Out put will be on coord global also on forceapprox updated Note that for optimization of a global scaling factor a larger initial force constant element is rec ommended about 10 0 5 3 10 Conversion from Internal to Cartesian Coordinates Due to translational and rotational degrees of freedom and the non linear dependence of internal coordinates upon cartesian coordinates there is no unique set of cartesian coordinates for a given set of internal coordinates Therefore an iterative procedure is employed to calculate the next local solution for a given cartesian start coordinates This task may be performed using the relax program but it is much easier done within a define session 5 3 11 Conversion of Cartesian Coordinates Gradients and Force Constants to Internals To perform this tasks you have to activate the interconversion mode by interconversion on cartesian gt internal coordinate gradient hessian Note that any combination of the three options showed is allowed The default value is coordinate the two other have to be switched on explicitly if desired You need as input data groups intdef Definitions of redundant internal coordinates coord Cartesian coordinates for option coordinate grad Cartesian coordinates and gradients as provided and accumulated in subsequent optimizat
306. grams 20 2 FORMAT OF KEYWORDS AND COMMENTS 363 For 3D grids non default boundarys basis vector directions origin and resolu tions may be specified as follows pointval gridi vector 0 3 0 range 2 2 points 200 grid2 vector 0 0 7 range 1 4 points 300 grid3 vector 1 0 0 range 1 1 points 300 origin 1 1 1 Grid vectors automatically normalized now are 0 1 0 0 0 1 1 0 0 the grid is centered at 1 1 1 and e g for the first direction 200 points are dis tributed between 2 and 2 Grids of lower dimensionality may be specified in the same line as pointval by typing either geo plane or geo line or geo point The way to use is best explained by some examples pointval geo plane gridi vector 0 1 0 range 2 2 points 200 grid2 vector 0 0 1 range 1 4 points 300 origin 1 1 1 Values are calculated at a plane spanned by vectors 0 1 0 and 0 0 1 centered at 1 1 1 pointval geo line gridi vector 0 1 0 range 2 2 points 50 origin 0 0 1 Values are calculated at a line in direction 0 1 0 centered at 0 0 1 Output format as above pointval geo point 753 007 Values are calculated at the two points 7 0 5 0 3 0 and 0 0 0 0 7 0 Plane averaged density can be computed by 364 CHAPTER 20 KEYWORDS IN THE CONTROL FILE pointval dens averagez fmt vec gridi vector 1 0 0 range 10 10 points 100 grid2 vector 0 1 0 range 10 10 points 100 grid3 vector 0 0 1 range 20 20 points 200 origin 0 0
307. grams if pointval is set in the control1 file Two component wave functions only module ridft and only if soghf is set Total density is on file td plt like for one component wave functions this is also true for all other quantities depending only on the density matrix electrostatic potential etc sd plt contains the absolute value of the spin vector density which is the absolute value of the following vector s t a Uo g iene pointval fmt txt leads to a file containing the spin vector density vectors which can be used by gOpenMol It is advisable to choose ca one Bohr as the distance between two eridpoints Electrostatic potentials In an analogous way electrostatic potentials can be cal culated on grids pointval pot 240 CHAPTER 16 PROPERTIES AND ANALYSIS AND GRAPHICS leads to calculation of the electrostatic potential of electrons and nuclei and external constant electric fields and point charges Q if present V p ate 59 J BE z 16 4 7 Q Pr In order to prevent the calculation of singularities at the positions of nuclei for gridpoints that are closer to a nucleus than 1076 a u the charge of the respective nucleus is omitted in the calculation of the electrostatic potential for these points The output files are termed tp plt sp plt etc Electric fields as derivatives of potentials are calculated by pointval fld The absolute values of electric fields are written to files tf
308. h files option can be specified an example for a dscf run is given below The scratch directory must be accessible from all nodes scratch files dscf dscf dscf dscf dscf dscf dscf dscf dscf dscf dens fock dfock ddens XSV pulay statistics errvec oldfock oneint home dfs cd00 cd03_dens home dfs cd00 cd03_fock home dfs cd00 cd03_dfock home dfs cd00 cd03_ddens home dfs cd00 cd03_xsv home dfs cd00 cd03_pulay home dfs cd00 cd03_statistics home dfs cd00 cd03_errvec home dfs cd00 cd03_oldfock home dfs cd00 cd03_oneint For all programs employing density functional theory DFT i e dscf gradand ridft rdgrad pardft can be specified pardft 374 CHAPTER 20 KEYWORDS IN THE CONTROL FILE tasksize 1000 memdiv 0 The tasksize is the approximate number of points in one DFT task default 1000 and memdiv says whether the nodes are dedicated exclusively to your job memdiv 1 or not default memdiv 0 For dscf and grad runs you need a parallel statistics file which has to be generated in advance The filename is specified with 2e ints_shell_statistics file DSCF par stat or 2e ints _shell_statistics file GRAD par stat respectively The statistics files have to be generated with a single node dscf or grad run For a dscf statistics run one uses the keywords statistics dscf parallel 2e ints_shell_statistics file DSCF par stat parallel_parameters maxtask 400 maxdisk 0 d
309. h results are written to interface files e g control gradient or xxx map In ground state calculations ricc2 will pass to the density analysis routines the correlated total and for UHF based calculations also the spin density and the canonical SCF orbitals from which the SCF spin density is constructed All options described in chapter 16 are available from within the ricc2 program apart from the evaluation of electrostatic moments which would interfere with the calculation of expectation values requested through the fop option in response In excited state calculation ricc2 will pass the excited state total and for UHF based calculation in addition the spin density But no ground state densities and or 200 CHAPTER 10 RI CC2 uncorrelated densities or orbitals Thus for excited states the ricc2 program does in difference to egrad not print out a comparison with the ground state SCF density Also all some options which require orbitals as e g the generation and visualization of localized orbitals or some population analysis options and not available for excited states in ricc2 As other modules also ricc2 provides the proper flag to bypass a re calculation of the density and gradient to enter immediately the density analysis routines with a previously calculated density The ricc2 program will then pass the densities found on the interface file for the density analysis routines without further check on the method and state for
310. has been chosen See 5 3 13 and 20 2 18 forcestatic a static i e never updated approximate force constant matrix to be used in DIUS type geometry optimizations It will be initialized by relax specifying forceupdate pulay modus lt dq dq gt static The next data groups are output by relax depending on the optimization subject in order to control the convergence of optimization procedures driven by the shell script jobex maximum norm of cartesian gradient real maximum norm of internal gradient real 348 CHAPTER 20 KEYWORDS IN THE CONTROL FILE maximum norm of basis set gradient real real is the absolute value of the maximum component of the corresponding gradient Other Input Output data used by RELAX In order to save the effort for conversion of accumulated geometry and gradient data as needed for the force constant update or the DIIS update of the geometry to the optimization space within which the geometry has to be optimized one may specify the keyword oldgrad Then the relax program accumulates all subsequent coordinates and gradient as used in optimization in this data group or a referenced file This overrides the input of old coordinate and gradient data from data blocks grad egrad as accumulated by the grad program degrees 20 2 19 Keywords for Module STATPT statpt itrvec 0 update bfgs hssfreq 0 keeptmode hssidiag 0 5 radmax 0 3 radmin 1 0d 4 tradius 0 3 threchang
311. he RHF scheme of one component treatments is applicable Effective core potentials The most economic way to account for relativistic ef fects is via effective core potentials by choosing either the one or the two component 138 CHAPTER 6 HARTREE FOCK AND DFT CALCULATIONS ECP and for the latter additionally setting soghf in the control file The theo retical background and the implementation for the two component SCF procedure is described in 73 The backgrund theory of the more fundamental approach all electron relativistic electronic structure theory is given in the next paragraph Relativistic all electron approaches X2C DKH BSS Relativistic calcu lations are based on the Dirac rather than on the Schr dinger Hamiltonian Since the Dirac Hamiltonian introduces pathological negative energy states and requires extensive one electron basis set expansions methods have been devised which allow one to calculate a matrix representation of that part of the Dirac Hamiltonian which describes electronic states only For this a unitary transformation is employed to block diagonalize the Dirac Hamiltonian and thus to decouple the negative energy from the electronic states In order to be efficient this transformation is carried out only for the one electron part of the full Hamiltonian as a consequence the two electron interaction will then be affected by a picture change effect The resulting quantum chemical approach has been called
312. he blocks nxtneil2 nxteneil3 nxtneil4 connectivity angle torsion inversion nonbond and qpartial It starts with uff topology and ends with end The first three blocks nxtneil2 nxtneil3 nxtneil4 have the same form they start with the atom number and the number of its neigh bours in the next line are the numbers of the neighbour atoms Then the connec tivity block follows starting with the number of bond terms Each line contains one bond term I J d BO 280 CHAPTER 20 KEYWORDS IN THE CONTROL FILE Here are J and J the number of the atoms d the distance in a u and BO is the bond order The angle terms follow starting with the number of the angle terms In each line is one angle term J I K wtyp 0 nr JI nrg Here are J I and K the atoms number where atom J is in the apex wtyp is the angle type and has the following values wtyp 1 linear case wtyp 2 trigonal planar case wtyp 3 quadratic planar case wtyp 6 octahedral case wtyp 9 all other cases 0 is the angle value in degree nrjy and nrrg are the number of the bonds between J and I and the bond between J and K The hybridization of atom J determines wtyp Then the torsion terms follow starting with the number of the torsion terms Each line contains one torsion term I J K L NT IK ttyp 0 OLJK OJKL Here are I J K and L the atom numbers nryjg is the number of the bond between J and K ttyp is the torsion type ttyp 1
313. he directory dir default TESTDIR sysname and highlights the positions of the retrieved matches Loading path and naming options loaddir dir 1 dir scriptdir dir ls dir testprog prog X prog dir dir critfile file defcritfile file protfile file output file gprotfile file checkfile file errfile file probfile file Loading path for the TURBOMOLE binaries default TURBODIR bin sysname Loading path for the TURBOMOLE scripts default TURBODIR scripts Tests the given executable prog Name for the local test directory default TESTDIR sysname Name for the local criteria file default CRIT Name for the test suite settings file default DEFCRIT Name for the local protocol file default TESTPROTOKOLL Name for the global protocol file default TESTPROTOKOLL sysname Name for the check protocol file default CHECKPROTOKOLL Name for the local error output file default output err Name for the failed tests list Apnfarilt s DDNDT ECE anremnm y 404 CHAPTER 22 PERL BASED TEST SUITE Bibliography 1 2 3 _ 4 5 6 7 S 9 R Ahlrichs M Bar M H ser H Horn C K lmel Electronic structure cal culations on workstation computers The program system Turbomole Chem Phys Lett 162 3 165 169 1989 A Sch fer H Horn R Ahlrichs Fully optimized contracted Gaussian basis sets for atoms Li to Kr J C
314. he end of this run the actual GW calculation is performed Possible source of errors When dscf or ridft is repeated after escf the sing _a file may not be correct anymore this may happen when degenerate levels are present escf will however not recognize this and continue using the previously converged data in sing a leading to nonsense values for Xe Before running escf the old sing _a file has to be removed Chapter 9 Second order Moller Plesset Perturbation Theory Preliminary note TURBOMOLE offers three programs for MP2 energy and gradient calculations A con ventional implementation 106 mpgrad based on the calculation of four center in tegrals not further developed for several years and two implementations which use the resolution of the identity RI approximation the implementation from 1997 8 in rimp2 and a new implementation as part the CC2 program 10 ricc2 9 1 Functionalities of MPGRAD RIMP2 and RICC2 Functionality of mpgrad e Calculation of MP2 energies and or MP2 gradients for RHF and UHF wave functions e The frozen core approximation possibility to exclude low lying orbitals from the MP2 treatment is implemented only for MP2 energies e Exploitation of symmetry of all point groups e Can be used sequentially or parallel e Can be combined with the COSMO solvation model see chapter 19 for details Presently restricted to sequential calculations Functionality of rimp2 e Calcul
315. he use_old_amat option can be used to calculate energies not gradients using the old cavity algo rithm of TURBOMOLE 5 7 The basic COSMO settings are defined in the cosmo and the cosmo_atoms block Example with default values cosmo epsilon infinity nppa 1082 nspa 92 disex 10 0000 rsolv 1 30 routf 0 85 cavity closed ampran 0 1D 04 phsran 0 0 refind 1 3 the following options are not used by default allocate_nps 140 use_old_amat use_contcav 308 CHAPTER 20 KEYWORDS IN THE CONTROL FILE no_oc epsilon real defines a finite permittivity used for scaling of the screening charges allocate_nps integer skips the COSMO segment statistics run and allocates memory for the given number of segments no_oc skips the outlying charge correction All other parameters affect the generation of the surface and the construction of the A matrix nppa integer number of basis grid points per atom allowed values i 10 x 3 x 4 2 12 32 42 92 nspa integer number of segments per atom allowed values i 10 x 3 x 4 2 12 32 42 92 disex real distance threshold for A matrix elements Angstrom rsolv real distance to outer solvent sphere for cavity construction Angstrom routf real factor for outer cavity construction in the outlying charge correction cavity closed pave intersection seams with segments cavity open leave untidy seams between atoms ampran real amplitude of th
316. hem Phys 97 4 2571 2577 1992 A Sch fer C Huber R Ahlrichs Fully optimized contracted Gaussian basis sets of triple zeta valence quality for atoms Li to Kr J Chem Phys 100 8 5829 5835 1994 K Eichkorn F Weigend O Treutler R Ahlrichs Auxiliary basis sets for main row atoms and transition metals and their use to approximate Coulomb potentials Theor Chem Acc 97 1 4 119 124 1997 F Weigend F Furche R Ahlrichs Gaussian basis sets of quadruple zeta valence quality for atoms H Kr J Chem Phys 119 24 12753 12762 2003 F Weigend R Ahlrichs Balanced basis sets of split valence triple zeta valence and quadruple zeta valence quality for H to Rn Design and assessment of accuracy Phys Chem Chem Phys 7 18 3297 3305 2005 A K Rapp C J Casewit K S Colwell W A Goddard III W M Skiff UFF a full periodic table force field for molecular mechanics and molecular dynamics simulations J Am Chem Soc 114 25 10024 10035 1992 F Weigend M Haser RI MP2 first derivatives and global consistency Theor Chem Acc 97 1 4 331 340 1997 F Weigend M Haser H Patzelt R Ahlrichs RI MP2 Optimized auxiliary basis sets and demonstration of efficiency Chem Phys Letters 294 1 3 143 152 1998 405 406 10 11 12 13 14 15 16 17 18 19 20 BIBLIOGRAPHY C H ttig F Weigend CC2 excitation energy c
317. her Institut fiir Technologie Kaiserstr 12 D 76131 Karlsruhe E mail info turbomole com Web http www turbomole com Support is provided by COSMOlogic GmbH amp Co KG see http www cosmologic de Email turbomole cosmologic de 1 2 FEATURES OF TURBOMOLE 13 1 2 Features of TURBOMOLE TURBOMOLE has been specially designed for UNIX workstations and PCs and efficiently exploits the capabilities of this type of hardware TURBOMOLE consists of a series of modules their use is facilitated by various tools Outstanding features of TURBOMOLE are e semi direct algorithms with adjustable main memory and disk space require ments e full use of all point groups e efficient integral evaluation e stable and accurate grids for numerical integration e low memory and disk space requirements 1 3 How to Quote Usage of TURBOMOLE Please quote the usage of the program package under consideration of the version number TURBOMOLE V6 6 2014 a development of University of Karlsruhe and Forschungszentrum Karlsruhe GmbH 1989 2007 TURBOMOLE GmbH since 2007 available from http www turbomole com A LaTeX template could look like this misc TURBOMOLE title TURBOMOLE V6 6 2014 a development of University of Karlsruhe and Forschungszentrum Karlsruhe GmbH 1989 2007 TURBOMOLE GmbH since 2007 available from tt http www turbomole com Scientific publications require proper citation of methods and
318. his is specified by the keyword periodic 3 meaning periodicity in three dimensions The dimensions of the unit cell for bulk CaF are given in the subsection cell of the embed keyword By default the unit cell dimensions are specified in atomic units and can be changed to A using cell ang The positions of the point charges in the unit cell are specified in the subsection content In this example positions are given in fractional crystal coordinates content frac You can change this by specifying content for Cartesian coordinates in atomic units or content ang for 6 5 PERIODIC ELECTROSTATIC EMBEDDED CLUSTER METHOD 143 Cartesian coordinates in A The values of point charges for Ca and F are given in the subsection charges embed periodic cell 10 47977 10 47977 content frac 3 10 47977 90 0 90 0 90 0 F 0 00 0 00 0 00 Ca 0 25 0 75 0 75 F 0 50 0 50 0 00 F 0 50 0 00 0 50 F 0 00 0 50 0 50 F 0 50 0 50 0 50 F 0 00 0 00 0 50 F 0 50 0 00 0 00 F 0 00 0 50 0 00 Ca 0 25 0 25 0 25 Ca 0 25 0 75 0 25 Ca 0 25 0 25 0 75 end charges F 1 0 Ca 2 0 end The above input defines a periodic perfect and infinite three dimensional lattice of point charges corresponding to the bulk CaF structure In order to use this lattice for PEECM calculation we have to make space for our QM cluster and the isolating shell This is done by specifying the part of the lattice that is virtually removed from the perfect perio
319. his menu refer only to the corresponding type of orbitals The commands of this menu do not need much explanation lt label gt is the irrep label of one irre ducible representation of the molecular point group e g a1 b2 tig lt list gt is a list of orbital indices within this irrep e g 1 2 4 or 1 8 10 11 p or print will 4 3 GENERATING MO START VECTORS 71 give you the same listing of the orbital occupations as you saw before entering this menu After you leave this submenu you will be back in the occupation numbers main menu 4 3 4 Roothaan Parameters In open shell calculations within the restricted Hartree Fock ansatz ROHF the coupling between the closed and the open shells must be specified using two param eters a and b which depend on the type of the open shell the number of electrons in it the electron configuration but also on the state to be calculated For example there are three states arising from the s p configuration of an atom P 1D tS which have different values of a and b For the definition of these parameters and their use refer to Roothaan s original paper 26 For simple cases define sets these parameters automatically If not you have to enter them yourself In this case you will get the following message ROOTHAAN PARAMETERS a AND b COULD NOT BE PROVIDED TYPE IN ROOTHAAN a AND b AS INTEGER FRACTIONS OR ENTER val FOR AN AVERAGE OF STATES CALCULATION OR ENTER amp TO REPEAT OCCU
320. hod q or grow reaction path method qg Furthermore riter 0 counts the number of completed iteration no option 20 2 FORMAT OF KEYWORDS AND COMMENTS 283 20 2 6 Keywords for Modules DscF and RIDFT denconv real Convergency criterion for the root mean square of the density matrix If you want to calculate an analytical MP2 gradient program mpgrad real should be 1 d 7 or less dft options Listing of all possible sub keywords for dft cross references are given The user normally has to choose only the functional and the grid size see below All other parameters have proven defaults functional name Specification of the functional default is BP86 printed as functional b p For all possible and useful functionals please refer to page 292 and for definition of the functionals the section 6 2 on page 120 Example default input dft functional b p gridsize integer or minteger Specification of the spherical grid see section 20 2 6 on page 292 De fault is gridsize m3 Example dft gridsize m3 gridtype integer not recommended for use Specification of the mapping of the radial grid Possible values for gridtype are 1 6 but gridtype 4 to 6 is only for the use with functional lhf see page 295 For the definition of gridtype 1 3 please refer to Eq 16 17 and 19 in Ref 192 Example default value dft gridtype 3 debug integer Flag for debugging debug 0 means no d
321. i THERMAL SMEARING OF OCC NUMBERS fermi By the command fermi you can switch on smearing of occupation numbers and thus automatically optimize occupations and spin Menu drv The most important of the derivative menus is the first one which tells the programs which derivatives to calculate This is only necessary for special purposes and you should better not change default options option status description crt l T CARTESIAN ist derivatives sec l T CARTESIAN 2nd derivatives bas F energy derivatives with respect to BASIS SET exponents scaling factors l contraction coefficients glb F energy derivative with respect to a GLOBAL scaling factor dip T cartesian 1st derivatives of DIPOLE MOMENT pol T nuclear contribution to POLARIZABILITY fa l F SPECTROSCOPIC ANALYSIS only tol 0 100D 06 derivative integral cutoff use lt opt gt for enabling lt opt gt for disabling of logical switches lt amp gt will bring you back to GENERAL MENU without more changes lt RETURN gt OR OR q uit WILL TERMINATE THIS MENU 82 CHAPTER 4 PREPARING YOUR INPUT FILE WITH DEFINE The handling of these options is very simple With the exception of tol all are logical switches which are either true or on active or false or off inactive You can switch between the two states if you enter for example crt to switch calculation of Cartesian first derivatives on or crt to switch it off The options crt sec and
322. i level rirpa 221 map 201 362 sys data 54 2e ints shell_statistics 374 2e ints_shell_statistics 374 D2 diagnostic 338 TURBODIR uff parms in 279 actual step 234 alpha shells 139 158 275 297 anadens 200 atoms 65 145 148 273 274 299 316 325 barrier 366 basis 65 104 108 272 347 beta shells 139 158 275 297 boys 351 clalgorithm 325 cabs 170 184 cbas 169 170 183 184 208 219 221 325 326 339 cbasopt 325 cc2_natocc 338 cdspectrum 160 320 326 cgrad 338 339 closed shells 67 68 139 274 289 296 297 collinear 304 constraints 367 coord 53 55 104 107 109 142 144 147 227 238 272 277 279 347 coordinateupdate 104 340 dqmax 340 interpolate 340 statistics 340 corrgrad 346 cosmo 307 311 allocate_nps 308 ampran 308 cavity 308 closed 308 open 308 disex 308 epsilon 308 nppa 308 nspa 308 phsran 308 refind 308 routf 308 rsolv 308 use_contcav 308 use_old_amat 308 cosmo_atoms 307 309 cosmo_isodens 310 cosmo_isorad 310 cosmo_out file 309 csconv 371 422 INDEX csconvaton 371 csmp2 233 371 current 364 curswitchdisengage 160 dcosmo_rs 311 potential file definition 311 denconv 36 156 169 170 172 180 183 184 208 215 283 318 326 denconv 1d 7 222 dfdxi textout 231 317 dft 35 156 222 225 258 283 298 301 304 313 317 batchsize 286 function
323. ick Balzerowski Raffael Schwan Christof Hattig J Chem Phys 136 174106 2012 1 3 HOW TO QUOTE USAGE OF TURBOMOLE Basis sets 19 The following tables can be used to find the proper citations of the standard orbital and auxiliary basis sets in the TURBOMOLE basis set library Orbital basis sets elements H Kr H He Li Be B Ne Na Mg Al Ar K Ca Sc Zn Ga Kr SVP SV P q ala a a a ala a a TZVP q b b b b b b b b b TZVPP q f f f f f f f f f QZVP QZVPP i def2 SV P q j a a j a j a a a def2 SVP q j a a j a j a j a def2 TZVP q f j f j j j f j f def2 TZVPP q j j f j j j f j f Note For H Kr def SV P def SVP are identical with the basis sets without def prefix def2 QZVPP and def2 QZVP are identical with QZVPP and QZVP Orbital basis sets elements Rb Rn Rb Sr Y Cd In Cs Ba La Hg Tl At Rn def SVP def SV P de TZVP d d d d d d d j def TZVPP f d f f d f d j def2 SV P j d d j d d j j def2 SVP j d j j d j j j def2 TZVP def2 TZVPP j def2 QZVP def2 QZVP j Auxiliary basis sets for RI DFT Coulomb fitting H Kr Rb At Rn def SVP def SV P 6 d l def TZVP d d l def2 universal j 20 CHAPTER 1 PREFACE AND GENERAL INFORMATION Auxiliary basis sets for RI MP2 and RI CC2 elements H Ar
324. iefly sy desy susy ai Definition of the Sch nflies symbol of the molecular point group sym metry If you enter only sy define will ask you to enter the symbol but you may also directly enter sy c3v define will symmetrize the geometry according to the new Sch nflies symbol and will create new nuclei if necessary You therefore have to take care that you enter the correct symbol and that your molecule is properly oriented All TURBOMOLE programs require the molecule to be in a standard orien tation depending on its point group For the groups Cy Cnv Cnh Dn Dna and Dna the z axis has to be the main rotational axis secondary twofold rotational axis is always the x axis dy is always the xz plane and cp the xy plane Op is oriented as D4p For Ty the threefold rota tional axis points in direction 1 1 1 and the z axis is one of the twofold axes bisecting one vertex of the tetrahedron desy allows you to determine the molecular symmetry automatically The geometry does not need to be perfectly symmetric for this command to work If there are small deviations from some point group symmetry as they occur in experimentally determined structures desy will rec ognize the higher symmetry and symmetrize the molecule properly If symmetry is lower than expected use a larger threshold lt eps gt up to 1 0 is possible susy leads you through the complete subgroup structure if you want to lower symmetry e g to investigate Jahn
325. ies are generated by following com binable settings to be written in the same line as statement pointval pot fld leads to calculation of electrostatic potential arising from electron den sities nuclei and if present constant electric fields and point charges The densities used for calculation of potentials are the same as above the respective filenames are generated from those of densities by replacement of the d for density by a p for potential By pot eonly only the electronic contribution to the electrostatic potential is calculated calculation of electric field Note that for 3D default output format plt see below only norm is displayed Densities used are the same as above filenames are generated from those of densities by replacement of d for density by f for field mo list of MO numbers calculation of amplitudes of MOs specified by numbers referring to the numbering obtained e g from the tool eiger in the same format The respective filenames are self explanatory and displayed in the output Note that also in MP2 and excited state calculations the HF DFT ground state orbitals are plotted and not natural MP2 excited orbitals Two component cases The density of the spinors specified by numbers referring to the numbering obtained e g from the file EIGS are visualized By setting the keyword minco also the amplitudes of the spinor parts are calculated whose weights the probability of fi
326. ies obtained with TURBOMOLe will deviate from those obtained with other coupled cluster programs by a small RI error This error is usually in the same order or smaller the RI error for a RI MP2 calculation for the same system and basis sets The RI approximation is also used to evaluate the 4 index integrals in the MO basis needed for the perturbative triples corrections Disc space requirements In difference to CC2 and MP2 the CCSD model does no longer allow to avoid the storage of double excitation amplitudes tgip and intermediates of with a similar size Thus also the disc space requirements for the CCSD calculation are larger than for RI MP2 and RI CC2 calculation for the same system For a closed shell CCSD ground state energy calculations the amount of disc space needed can be estimated roughly as Noisk an p mpi1s O N 128 x 1024 MBytes 11 24 where N is the number of basis functions O the number of occupied orbitals and mprrs the number of vectors used in the DIIS procedure by default 10 see Sec 20 2 17 for details For closed shell CCSD T calculations the required disc space is with New 57 50 N oN 128 x 1024 MBytes 11 25 somewhat larger For calculations with an open shell UHF or ROHF reference wavefunctions the above estimates should be multiplied by factor of 4 Memory requirements The CCSD and CCSD T implementation in Turbomole uses multi pass algorithms to avoid strictly the nee
327. ift 14 25 34 37 38 232 234 372 multi core 44 NAO 241 nao 241 natural orbitals atomic 241 transition 242 no weight derivatives 231 317 nohxx 219 222 not converged 98 118 NTO 242 nto 242 NumForce 25 38 39 184 185 198 199 217 221 227 311 Numforce 24 25 27 152 161 162 184 224 225 311 313 INDEX NumForce d 0 02 rirpa 221 odft 256 260 261 263 OMP_NUM_THREADS 44 OpenMP 44 outp 27 PARA ARCH 44 parallelization multi core 44 OpenMP 44 SMP 44 threads 44 parms in 279 PARNODES 44 past 27 PEECM keywords 305 Plane averaged 363 plot coefficient 260 plotting data keywords 354 population analysis 356 properties excited states 196 ground state 194 q 47 quasi Newton 102 Raman 25 38 227 raman 27 Raman spectra 227 RDGRAD keywords 313 Rdgrad 299 rdgrad 23 24 35 37 39 42 44 46 77 98 104 107 117 123 125 12 central ri level 433 141 149 161 196 268 305 307 311 313 373 375 reference potential 260 RELAX keywords 339 relax 14 24 26 38 51 56 83 85 97 98 102 104 106 107 109 111 116 119 339 340 343 345 347 348 restart cc 328 RI ADC 2 23 325 RI CC2 23 325 keywords 325 RI CCS 325 RI CIS 23 325 RI CIS D 23 325 RI MP2 325 RI MP2 F12 45 Ricc2 keywords 325 ricc2 13 14 23 26 36 42 44 45 62 63 80 166 175 179 182 186 188 193 196 198 202 204 205 207 209
328. il it reaches the value tmend default 300 K Note that the default values lead to occupation numbers calculated at a constant T 300K Current occupation numbers are frozen if the energy change drops below the value given by stop default 1 1072 This prevents oscillations at the end of the SCF procedure Calculation of fractional occupation numbers often requires much higher damp ing and orbital shifting Please adjust the values for scfdamp and scforbit alshift if you encounter convergence problems In UHF runs this option can be used to automatically locate the lowest spin state In order to obtain integer occupation numbers tmend should be set to relatively low value e g 50K Calculation of fractional occupation numbers should be used only for single point calculations When used during structure optimizations it may lead to energy oscillations The optional nue value number of unpaired electrons can be used to force a certain multiplicity in case of an unrestricted calculation nue 0 is for singlet nue 1 for dublet etc firstorder Perform first order SCF calculation i e perform only one SCF iteration with the start MOs which should be the orthogonalized MOs of two independent subsystems as is explained in detail in Chapter 16 fldopt options Specification of options related with external electrostatic fields The following options are available 1st derivative on off Calculate numerical 1st derivative of SC
329. ile before invoking the ired option Important options are iprint n print parameter for debug output The larger n is the more output is printed n gt 0 n lt 5 default 0 metric n method for generating and processing of redundant internal coordinates n gt 3 n lt 3 n 0 default 3 Values for the metric option n 1 Delocalized Coordinates The BmBt matrix is diagonalized for the complete set of redundant internal coordinates matrix m is a unit matrix n 3 Delocalized Coordinates obtained with a modified matrix m the val ues of m can be defined by user input see below 276 CHAPTER 20 KEYWORDS IN THE CONTROL FILE 1 Hybrid Coordinates Natural internal coordinates are defined as in the old iaut option If a cage remains delocalized coordinates as for n 1 are defined for the cage B ll n 2 Very simular to the n 1 option but for the remaining cage delocal ized coordinates with modified matrix m are defined as for n 3 n 2_ Decoupled coordinates The redundant coordinates are divided into a sequence of blocks These are expected to have decreasing average force constants i e stretches angle coordinates torsions and weak coordinates The BB matrix is diagonalized for each block separately after the columns of B were orthogonalized against the columns of B of the the preceding blocks n 3 Generalized natural coordinates Natural internal coordinates are defi
330. ill be calculated econv gconv convergence criteria for energy and gradient qtot total charge of the molecule dfac distance parameter to calculate the topology If the distance between the atoms I and J is less than the sum of the covalent radii of the the atoms multiplied with dfac then there is a bond between J and J epssteep if the norm of the gradient is greater than epssteep a deepest descent step will be done epssearch if the norm of the gradient is smaller than epssearch no line search step will be done after the Newton step dqmax max displacement in a u for a coordinate in a relax step mxls dhls ahls parameters of linesearch ahls start value dhis increment mxls number of energy calculations alpha beta gamma modification parameter for the eigenvalues of the Hessian see below f x x alpha beta exp gamma x x transform a switch for the transformation in the principal axis system lnumhess a switch for the numerical Hessian lmd a switch for a MD calculation Input Data Blocks Needed by UFF coord cartesian coordinates of the atoms default coord file coord 20 2 FORMAT OF KEYWORDS AND COMMENTS 279 ufftopology contains a list of the next neigbours of each atom see Section 20 2 4 Some times it is useful to enter the connectivity in the input block nxtnei12 in the file ufftopology by hand not always necessary default ufftopology file ufftopology Beyond th
331. ill be described in the following section 3 1 2 Energy and Gradient Calculations Energy calculations may be carried out at different levels of theory Hartree Fock SCF use modules dscf and grad or ridft and rdgrad to obtain the energy and gradient The energy can be calculated after a define run without any previous runs dscf and grad need no further keywords ridft and rdgrad only need the keyword rij The gradient calculation however requires a converged dscf or ridft run Density functional theory DFT calculations are carried out in exactly the same way as Hartree Fock calculations except for the additional keyword dft For DFT calculations with the fast Coulomb approximation you have to use the modules ridft and rdgrad instead of dscf and grad Be careful dscf and grad ignore RI K flags and will try to do a normal calculation but they will not ignore RI J flags rij and stop with an error message To obtain correct derivatives of the DFT energy expression in grad or rdgrad the program also has to consider derivatives of the quadrature weights this option can be enabled by adding the keyword weight derivatives to the data group dft For a semi direct dscf calculation Hartree Fock or DFT you first have to perform a statistics run If you type 36 MP2 CHAPTER 3 HOW TO RUN TURBOMOLE stati dscf nohup dscf gt dscf stat amp the disk space requirement MB of your current thime and thize combina tion will be c
332. in and opposite spin con tributions to the correlation energy most second order methods can be modified to achieve a hopefully better performance SCS MP2 has first been proposed by S Grimme and SOS MP2 by Y Jung et al see below The generalization of SCS and SOS to CC2 and ADC 2 for ground and excited states is described in 16 It uses the same scaling factors as proposed for the original SCS and SOS MP2 ap proaches see below In the ricc2 program we have also implemented SCS and SOS variants of CIS D for excitation energies and of CIS D for excitation energies and gradients which are derived from SCS CC2 and SOS CC2 in exactly the same man ner as the unmodified methods can be derived as approximations to CC2 see Sec 10 2 and ref 131 Please note that the SCS CIS D and SOS CIS D approxima tions obtained in this way and implemented in ricc2 differ from the spin component scaled SCS and SOS CIS D methods proposed by respectively S Grimme and E I Ugorodina in 132 and Y M Rhee and M Head Gordon in 133 A line with scaling factors has to be added in the ricc2 data group ricc2 scs cos 1 2d0 css 0 3333d0 cos denotes the scaling factor for the opposite spin component css the same spin 206 CHAPTER 10 RI CC2 component As an abbreviation scs can be inserted in ricc2 In this case the SCS parameters cos 6 5 and css 1 3 proposed S Grimme S Grimme J Chem Phys 118 2003 9095 are used These
333. ine else the input is same as for the calculation of excitation energies and first order properties ricc2 cc2 excitations irrep al nexc 2 irrep a2 nexc 2 tmexc istates al 1 fstates all operators diplen 10 5 Ground State Second order Properties with MP2 and CC2 For closed shell restricted Hartree Fock reference states second order properties for one electron perturbation can be computed at the MP2 and the CC2 level For 204 CHAPTER 10 RI CC2 MP2 second order properties are computed as derivatives of the SCF MP2 total energy This approach include the relaxation of the SCF orbitals in the presence of the perturbation and is restricted to the static i e frequency independent limit For coupled cluster model CC2 second order properties can similar as the first order properties calculated in orbital unrelaxed or orbital relaxed approach as derivatives of the of the Lagrange functions in Eqs 10 12 and 10 15 As for MP2 the orbital relaxed calculations are restricted to the static limit Frequency dependent second order properties as e g dipole polarizabilities can be computed with the orbital unrelaxed approach Note that second order properties are currently not yet available in the MPI parallel version or for spin component scaled variants of MP2 and CC2 Furthermore non Abelian point groups are not implemented for second order properties In addition to the standard input second order properties require that the d
334. ing MD the temperature of a run is lowered so as to find minimum energy structures Temperature may be lowered gradually by a small factor each step anneal default factor 0 905 over 100 steps or lowered rapidly by reversing all uphill motion quench default factor 0 8 each step The cooling factors may be changed from the default using x Another option allows the quenching part of the run to be logged to a separate file Alterna tively a standard non dynamical geometry optimization can be carried out in a subdirectory relax md_action free from t lt real gt Finally this instruction turns off any previous action and resumes free dynam ics This is the default status of an MD run surface_hopping This keyword allows to carry out Tully type fewest switches surface hopping SH 196 This option is only available in combination with TDDFT For the TDDFT surface hopping see Tapavicza et al 2007 197 for the current implementation see Tapavicza et al 2011 198 In the current implementation the surface hopping algorithm only allows switches between the first excited singlet state and the ground state However total energies of higher excited 370 CHAPTER 20 KEYWORDS IN THE CONTROL FILE states can be computed during the MD simulation The proper functioning of SH has only been tested for the option md_action fix total energy from t 0 00000000000 To carry out SH dynamics simulations the keyword surface_h
335. ion cycles by the various gradient programs for coordinate and gradient 110 CHAPTER 5 STRUCTURE OPTIMIZATIONS hessian Analytical force constant matrix as provided by the force constant pro gram aoforce only if option hessian is specified The data group hessian projected may be used alternatively for this purpose All output will be written to the screen except for option hessian output to data group forceapprox 5 3 12 The m Matrix The m matrix serves to fix position and orientation of your molecule during geometry optimizations It cannot be used to fix internal coordinates The m matrix is a diagonal matrix of dimension 3n where n is the number of atoms Normally m will be initialized as a unit matrix by relax As an example consider you want to restrict an atom to the xy plane You then set the m z matrix element for this atom to zero You can use at most six zero m matrix diagonals for linear molecules only five corresponding to translational and rotational degrees of freedom Note that the condition of the BmB matrix can get worse if positional restrictions are applied to the m matrix m matrix elements violating the molecular point group symmetry will be reset to one Non default settings for m matrix diagonals of selected atoms have to be specified within data group m matrix as m matrix 1 0 0 0 0 0 0 10 1 0 0 0 0 0 11 1 0 1 0 0 0 5 3 13 Initialization of Force Constant Matrices The most simple initial
336. ion to 107 default n 5 Additionally the following keywords control the accuracy of PEECM calculation 1lmaxmom Maximum order of the multipole expansions in periodic fast multipole method PFMM Default value is 25 potval Electrostatic potential at the lattice points resulting from periodic point charges field will be output if this keyword is present Default is not to output 20 2 FORMAT OF KEYWORDS AND COMMENTS 307 wsicl Well separateness criterion for PFMM Default is 3 0 epsilon Minimum accuracy for lattice sums in PFMM Default is 1 0d 8 20 2 8 Keywords for COSMO The Conductor like Screening Model COSMO is a continuum solvation model where the solute molecule forms a cavity within the dielectric continuum of permittivity ep silon that represents the solvent A brief description of the method is given in chapter 19 The model is currently implemented for SCF energy and gradient calculations dscf ridft and grad rdgrad MP2 energy calculations RIMP2 and mpgrad and MP2 gradients RIMP2 and response calculations with escf The ricc2 implemen tation is described in section 19 For simple HF or DFT single point calculations or optimizations with standard set tings we recommend to add the cosmo keyword to the control file and to skip the rest of this section Please note due to improvements in the A matrix and cavity setup the COSMO ener gies and gradients may differ from older versions 5 7 and older T
337. ions for the iterative conversion procedure internal cartesian coordinates default 25 qconv convergence criterion for the coordinate conversion default 1 d 10 on off options this switch activates special tasks transform coordinates gradients hes sians between spaces of internal cartesian coordinates using the defini tions of internal coordinates given in intdef available suboptions are cartesian gt internal coordinate gradient hessian cartesian lt internal coordinatethe direction of the transformation is indicated by the direction of the arrow Note specification of interconversion on will override optimize forceupdate method options this data group defines both the method for updating the approximate force constant matrix and some control variables needed for the force constant up date Options for method none no update steepest descent ms suboptions Murtagh Sargent update dfp suboptions Davidon Fletcher Powell update bfgs suboptions Broyden Fletcher Goldfarb Shanno update dfp bfgs suboptions combined bfgs dfp update schlegel suboptions Schlegel update ahlrichs suboptions Ahlrichs update macro option suboptions if method ms dfp bfgs schlegel ahlrichs numgeo integer number of structures used maxgeo integer maximum number of geometries rank of the update procedure for ahlrichs only 342 CHAPTER 20 KEYWORDS IN THE CONTROL FILE ingeo integer
338. irections e switch on utilization of localized orbitals for population analysis and or prepa ration of plot data within the same moloch run e set the maximum number of sweeps in the localization procedure e specify a file where localized orbitals shall be written to Option population analyses When activating this option you first have to specify whether the population analysis PA should be performed in the CAO default or AO basis Afterwards define will ask you whether you want to perform a Mulliken population analysis In this case the following submenu will be displayed add or delete one or more special options for a mulliken population analysis option status description spdf F compute MO contributions to atomic brutto populations molap F compute MO contributions to atomic overlap populations netto F compute atomic netto populations l l l l l l l l l l irpspd F compute IRREP contributions to atomic brutto populations l l l l l l l l irpmol F compute IRREP contributions to atomic overlap populations mommul F print electrostatic moments resulting from atomic charges dinean eee se Se Se See E N AE EEE E ET lt option gt switch off lt option gt or q uit leave this menu Here you can activate several optional quantities to be computed along with the Mul liken PA To switch on one or more of these options you must enter the corresponding option keywords e g spdf netto for comput
339. irst described in ref 10 188 CHAPTER 10 RI CC2 Advantages of the RI approximation For RI CC2 calculations the oper ation count and thereby the CPU and the wall time increases as for RI MP2 calculations approximately with O O V N where O is the number of occupied and V the number of virtual orbitals and N the dimension of the auxiliary ba sis set for the resolution of the identity Since RI CC2 calculations require the iterative solution of the cluster equations 10 5 and 10 6 they are about 10 20 times more expensive than MP2 calculations The disk space requirements are approximately O 2V N N N double precision words The details of the algo rithms are described in ref 10 for the error introduced by the RI approximation see refs 107 126 Required input data In addition to the above mentioned prerequisites ground state energy calculations with the ricc2 module require only the data group ricc2 see Section 20 2 17 which defines the methods convergence thresholds and limits for the number of iterations etc If this data group is not set the program will carry out a CC2 calculation With the input ricc2 mp2 cc2 conv 6 the ricc2 program will calculate the MP2 and CC2 ground state energies the latter converged to approximately 1076 a u The solution for the single substitution cluster amplitudes is saved in the file CCRO 1 1 0 which can be kept for a later restart Ground State calculations
340. is evaluated using the periodic fast multipole method PFMM 82 which unlike the Ewald method 83 defines the lattice sums entirely in the direct space In general PFMM yields a different electrostatic potential then the Ewald method but the difference is merely a constant shift which depends on the shape of external infinite surface of the solid i e on the way in which the lattice sum converges toward the infinite limit However this constant does not influence relative energies which are the same as obtained using the Ewald method provided that the total charge of the cluster remains constant Additionally since the electrostatic potential within a solid is not a well defined 142 CHAPTER 6 HARTREE FOCK AND DFT CALCULATIONS quantity both the absolute total energies and orbital energies have no meaning i e you cannot compare energies of neutral and charged clusters 6 5 3 Calculation Setup There are three key steps in setting up a PEECM calculation In the first step the periodic field of point charges has to be defined by specifying the point charges unit cell Next step is the definition of the part infinite of point charges field that will be replaced by the explicit quantum mechanical cluster Finally the quantum mechanical cluster together with surrounding ECPs representing cationic sites as well as point charges representing anions is defined and put in place of the point charges The input preparation steps can be summariz
341. is example would perform only a basis set optimization without accompanying geometry optimization It is possible of course to optimize both simultaneously Just leave out the last line of the example internal off Input data groups are egrad basis Basis set exponents contraction coefficients scaling factors and their re spective gradients as provided and accumulated in subsequent optimiza tion cycles by one of the programs grad or mpgrad if drvopt basis on has been set Description of basis sets used see Section 4 2 Output will be the updated basis on basis and the updated force constant matrix on forceapprox For an example see Section 21 5 5 3 8 Simultaneous Optimization of Basis Set and Structure The optimization of geometry and basis set may be performed simultaneously and requires the specification of optimize internal on or basis on cartesian on and needs as input data groups grad and egrad Output will be on coord basis also on forceapprox updated 5 3 PROGRAM RELAX 109 5 3 9 Optimization of Structure and a Global Scaling Factor Optimization of a global scaling factor is usually not performed in geometry opti mizations It is a special feature for special applications by even more special users As reference see 38 To optimize the structure and a global scaling factor specify optimize internal on or cartesian on global on You need as input data groups
342. is faster and smaller files will be written The external program atbandbta can be used to transform existing mos alpha and beta files from ASCII to binary format and vice versa eht eht performs an extended Hiickel calculation for your molecule The orbital energies available from this calculation are then used to provide occupation numbers for your calculation and the H ckel MOs will be projected onto the space that is spanned by your basis set This start vectors are not as good as the ones which may be obtained by projection of an old SCF vector but they are still better than the core Hamilto nian guess that is used if no start vectors are available When using this command you will be asked if you want to accept the standard Hiickel parameters and to enter the molecular charge Afterwards you will nor mally get a list of the few highest occupied and lowest unoccupied MOs 4 3 GENERATING MO START VECTORS 67 use file man hcore their energies and their default occupation If you don t want to accept the default occupation you will enter the occupation number assignment menu which is described in Section 4 3 2 Note that the occupation based on the H ckel calculation may be unreliable if the difference of the energies of the HOMO and the LUMO is less than 0 05a u you will get a warning You will also have to enter this menu for all open shell cases other than doublets With command use you are able to use information abo
343. is iterative so that the reaction field reflects the density of the first order wave function In contrast to the PTE approach the reaction field i e the screening charges change during the iterations until self consistency is reached Gradients are available on the formally consistent PTE level only 187 Vertical excitations and Polarizabilities for TDDFT TDA and RPA The escf program accounts for the COSMO contribution to the excitation energies and polarizabilities The COSMO settings have to be defined for the underlying COSMO dscf or ridft calculation In case of the excitation energies the solvent response will be divided into the so called slow and fast term 183 188 The screening function of the fast term depends on the refractive index of the solvent which can be defined in the input If only the COSMO influence on the ground state should be taken into account we recommend to perform a normal Cosmo calculation dscf or ridft and to switch off Cosmo i e deactivate cosmo before the escf calculation The Direct COSMO RS method DCOSMO RS In order to go beyond the pure electrostatic model a self consistent implementation of the COSMO RS model the so called Direct COSMO RS DCOSMO RS 189 has been implemented in ridft and dscf COSMO RS COSMO for Real Solvents 190 191 is a predictive method for the calculation of thermodynamic properties of fluids that uses a statistical thermody namics approach based on the results of COSM
344. is switched off the Fock matrix is constructed from scratch in each iteration scfdiis options Control block for convergence acceleration via Pulay s DIIS Options are errvec charspecifies the kind of error vector to be used two different kind of DUS algorithms char FDS or SDF or FDS SDF uses FDS SDF as error vector char none no DIIS char sFDs use S 2FDS1 2 transposed Further suboptions maxiter integer maximum number of iterations used for extrapolation debug integer debug level default 0 integer 1 print applied DIS coefficients integer 2 print DIIS matrix and eigenvalues too qscal real scaling factor in DIIS procedure qscal gt 1 implies some damping qscal 1 0 straight DHS thrd real directs the reduction of qscal to qgscal 1 0 no damping in DIIS done if errvec lt thrd P Pulay Chem Phys Lett 73 393 1980 P Pulay J Comput Chem 4 556 1982 20 2 FORMAT OF KEYWORDS AND COMMENTS 293 Defaults for prediag see above and scfdiis errvec FDS SDF maxiter 5 qscal 1 2 thrd 0 0 this implies DIIS damp ing in all iterations prediag is switched of Recommended errvec sFDs leads to the following defaults qscal 1 2 for SCF runs maxiter 6 and thrd 0 3 prediag is off for DFT runs maxiter 5 and thrd 0 1 prediag is on If you want to switch off prediag put prediag none scfdump Dump SCF restart information onto data group restartd an
345. is uff reads the force field parameters for the atoms from the file parms in If this file exists in the directory from which one starts an uff calculation the program will use this file if not the program reads the data from the file TURBODIR uff parms i If one wants own atom types one has to add these atoms types in the file parms in For each new atom type one has to specify the natural bond distance the natural bond angle the natural non bond distance the well depth of the Lennard Jones po tential the scaling factor the effective charge torsional barriers invoking a pair of sp atoms torsional barriers involving a pair of sp atoms generalized Mulliken Pauling electronegativities the idem potentials characteristic atomic size lower bound of the partial charge upper bound of the partial charge Distances ener gies and charges are in atomic units and angles are in rad UFF Output Data Blocks coord contains the updated cartesian coordinates of the atoms default coord file coord ufftopology contains the full information of the topology of the molecule and the whole force field terms see below default ufftopology file ufftopology uff gradient contains the accumulated cartesian analytical gradients default uffgradient file uffgradient uffhessian contains the cartesian analytical Hessian default uffhessian file uffhessian0 0 The file ufftopology The topology file ufftopology contains t
346. ith the program ridft Optimization to minima and transition structures using STATPT Structure optimizations can be carried out by the program statpt For minimiza tions no additional keywords are required The default values are assumed which work in most of the cases Structure optimization is performed in internal coordi nates if they have been set Otherwise Cartesian coordinates are used One can switch the optimization in internal coordinates on or off respectively in internal redundant or cartesian coordinates For transition structure optimizations the in dex of transition vector has to be set to an integer value gt 0 0 means structure minimization The value of the index specifies transition vector to follow during the saddle point search Note that Hessian eigenpairs are stored in ascending or der of the eigenvalues i e the eigenpair with the smallest eigenvector has the index 1 The command stp gives CONVERGENCE CRITERIA thre 1 000000E 06 thre threshold for ENERGY CHANGE thrd 1 000000E 03 thrd threshold for MAX DISPL ELEMENT thrg 1 000000E 03 thrg threshold for MAX GRAD ELEMENT rmsd 5 000000E 04 rmsd threshold for RMS OF DISPL rmsg 5 000000E 04 rmsg threshold for RMS OF GRAD 4 4 THE GENERAL OPTIONS MENU 79 defl set default values OPTIMIZATION refers to int off int INTERNAL coordinates rdn off rdn REDUNDANT INTERNAL coordinates crt on crt CARTESIAN coordinates NOTE options int an
347. ively Using pot file load the Slater potential is not calculated but read from slater pot the cor rection potential is instead recalculated For spin unrestricted calcula tions the corresponding files are sLaterA pot slaterB pot corrctA pot and correctB pot homo allows the user to specify which occupied orbital will not be included in the calculation of correction potential by default the highest occupied orbital is selected This option is useful for those systems where the HOMO of the starting orbitals e g EHT HF is different from the final LHF HOMO homob is for the beta spin 18 4 HOW TO PLOT THE EXCHANGE POTENTIAL 263 correlation func functional a correlation functional can be added to the LHF potential use func lyp for LYP or func vwn for VWN5 correlation For other options see 18 4 How to plot the exchange potential It is recommended to check plots of the exchange potential for both OEP EXX and LHF potential to avoid spurious numerical oscillations which usually originates from too small or too large basis set To plot the LHF potential over a line add to the control file e g for a 2000 points along the z axis pointval xc geo line gridi vector 0 0 1 range 10 10 points 2000 origin 0 0 0 and run odft proper The plotting subroutine reads the file Lhfcg contaning the matrix elements of the Correation potential is already generated by a previous run The file tx vec will be generated with four co
348. ix element The matrix elements are stored in the AO basis in blocks ordered as 1 Nao 1 Nao 2 matrix elements 2 cartesian component x y z 3 atom number Optional dfdxi textout can be used to generate text output of the matrix elements For bigger systems this can however generate very large output files Chapter 15 Calculation of NMR Shieldings The program mpshift calculates nuclear magnetic shielding constants using the GIAO Gauge Including Atomic Orbital method At present the following methods are implemented HF SCF the coupled perturbed Hartree Fock CPHF equations in the AO basis are solved using a semi direct iterative algorithm 152 similar to dscf DFT using either non hybrid functionals where no iterations are needed 1583 or hybrid functionals where the same algorithm as at the HF SCF level is used MP2 semi direct method see ref 21 15 1 Prerequisites 1 mpshift needs converged MO vectors from a SCF or DFT run dscf or ridft 2 for SCF or DFT calculations no specifications have to be made in the control file but currently only closed shell cases are implemented in mpshift 3 to perform an MP2 calculation of the NMR shieldings you have to prepare the input with mp2prep c 15 2 How to Perform a SCF of DFT Calculation All you have to do for running mpshift is typing mpshift at the shell level 232 15 3 HOW TO PERFORM A MP2 CALCULATION 233 The results of a SCF or DFT calculation
349. ixed internal coordinates and their current values and you will be able to enter a new value for each of them if you like Default lt enter gt keeps the value shown Be aware that all distances are given in atomic units 1 a u 52 9 pm This option allows you to change the status of a coordinate e g from active to display or every other combination The syntax is ic 5 d if coordinate no 5 is to be set to display or ic k d if all active coordinates are to be set to display This option allows you to delete definitions of internal coordinates from your list The indices of the internal coordinates always refer to the full list of coordinates including display and ignore coordinates To make sure you delete the right ones use disi Also the indices will imme diately change if you delete coordinates If you want to delete several coordinates this is therefore done most easily if you delete them in order of descending indices because deletion of a coordinate has only an effect on the coordinates with higher indices After choosing the coordinates 58 CHAPTER 4 PREPARING YOUR INPUT FILE WITH DEFINE to be deleted a list of all coordinates involved will be displayed and you will be asked to confirm deletion The syntax is simply irem 5 to delete internal coordinate no 5 or irem d to remove all display coordinates Hitting lt return gt will bring you back to the geometry main menu Interactive Definition of Internal Coor
350. ized on one or both subsystems To localize the charge on a given subsystem chargeA integer must be used for the subsystem A and chargeB integer for the B one Here integer denotes the charge added to the neutral subsystem For example the command FDE p 3 chargeA 2 performs a FDE calculation for a negative charged closed shell system for example Zn H2O 3 whose subsystem B has charge 2 Note that in this case the starting control file must have a charge 2 fde input option chargeA integer chargeB integer FDE with subsystem B taken frozen FDE can perform embedding calculations where the subsystem B is taken frozen i e without scf calculation on it using an embedding potential Therefore only one step will be performed if the flag frozen will be used FDE p 3 frozen The frozen embedding calculation is store in the subdirectory STEP1 SUBSYSTEM_A The control file is modified with the following keywords 17 2 FROZEN DENSITY EMBEDDING CALCULATIONS USING THE FDE SCRIPT251 fde read fde input zj file fde_ZJ mat fde input kxc file fde_KXC mat The program dscf will read the submatrices fde_ZJ mat and fde_KXC mat and add them to the Hamiltonian fde input option frozen 1 Parallel calculations If PARA_ARCH SMP and OMP calculation will be performed The flag nth nthreads can be used to specify the number of threads For example with the following command FDE p 3 nth 4 will use 4 threads Equiva
351. k and DFT Calculations Energy and gradient calculations at the Hartree Fock HF and DFT level can be carried out in two ways dscf and grad perform conventional calculations based on four center two electron repulsion integrals ERI s ridft and rdgrad employ the RI J approximation as detailed below dscf and grad are modules for energy and gradient calculations at the HF and DFT level which use an efficient semi direct SCF algorithm Calculation of the Coulomb and HF exchange terms is based on the conventional method employing four center two electron repulsion integrals ERI s These modules should be used for HF and DFT calculations with exchange correlation functionals including HF exchange contribution e g B3 LYP if further approximations RI J are to be avoided All functionalities are implemented for closed shell RHF and open shell UHF reference wavefunctions Restricted open shell treatments ROHF are supported on the HF level only i e not for DFT The most important special features of the dscf and grad modules are e Selective storage of the most time consuming and frequently used integrals The integral storage is controlled by two threshold parameters thize and thime related to integral size and computational cost e Efficient convergence acceleration techniques for energy calculations They in clude standard methods for convergence acceleration DHS which reduce the number of SCF iterations needed as well
352. l as these orbitals are necessarily in Cy sym metry Instead you will have to enter the index of the orbital to be plotted and for option mao the index of the atom at which it is situated In all cases you will additionally have to specify the plane in which the amplitudes or densities will be monitored To do this you have to declare two vectors which span that plane and the origin of this new coordinate system relative to the one in which the atomic coordinates are given Furthermore you will have to create a grid of points on this plane The orbital amplitude or electron density will then be calculated for every point in this grid The grid is created by telling define the range to be included along both vectors spanning the plane where the unit in each direction is the length of the corresponding basis vector and the number of points to be calculated in this range It is advantageous to use a wide grid while you test the ranges or planes which give the best results and then to switch to a finer grid for the final calculation Finally input MO vector and output plot data files can be specified In case you do not want to add a new data group as described above but to change 96 CHAPTER 4 PREPARING YOUR INPUT FILE WITH DEFINE an existing one you will be asked which one of the specifications you want to modify Chapter 5 Calculation of Molecular Structure and Ab Initio Molecular Dynamics 5 1 Structure Optimizations using the JOBE
353. l on does not need to be specified You need as input the data groups 5 3 PROGRAM RELAX 107 grad cartesian coordinates and gradients as provided and accumulated in subsequent optimization cycles by the programs grad or rdgrad etc intdef definitions of internal coordinates redundant definitions of redundant coordinates Output will be the updated coordinates on coord and the updated force constant matrix on forceapprox If any non default force constant update option has been chosen relax increments its counting variables lt numgeo gt lt numpul gt within com mand keyword forceupdate If the approximate force constant has been initialized forceinit on relax switches the initialization flag to forceinit off Re fer also to the general documentation of TURBOMOLE It is recommended to check correctness of your definition of internal coordinates 1 Calculate their values for your cartesian start coordinates using the relax program see Section 5 3 11 or within a define session 2 Have a look at the eigenvectors of the BmBt matrix Set some behind keyword intdef if there are any eigenvalues close to zero lt 107 is to be considered bad for small molecules but there is no general rule check those in ternal coordinates for consistency which contribute to the corresponding eigen vector s 5 3 6 Structure Optimization in Cartesian Coordinates For this task you have to specify optimize cartesian on
354. lace transformed implementation of SOS MP2 in the ricc2 module if the sos option has been specified in ricc2 and it provides the options to specify the technical details for the numerical Laplace transformation conv Threshold for the numerical integration used for the Laplace transforma tion of orbital energy denominators The grid points for the numerical integration are determined such that is the remaining root mean squared error RMSE of the Laplace transformation is lt 10 Y By default the threshold is set to the value of conv given in ricc2 see below ricc2 ccs cis mp2 didiag cis d energy only cis dinf adc 2 cc2 ccsd mp3 mp4 ccsd t restart norestart hard_restart nohard_restart conv 8 oconv 7 lindep 15 maxiter 25 mxdiis 10 maxred 100 iprint 1 fmtprop f15 8 geoopt model cc2 state a 2 scs cos 1 2d0 css 0 3333d0 sos 328 CHAPTER 20 KEYWORDS IN THE CONTROL FILE gsonly didiag intcorr specifies the ab initio models methods for ground and excited states and the most important parameters and thresholds for the solution of the cluster equations linear response equations or eigenvalue problems If more than one model is given the corresponding calculations are performed successively Note The CCS ground state energy is identical with the SCF reference energy CCS excitation energies are identical to CIS excitation energies The MP2 results is equivalen
355. last step relax 272 1cg 170 184 208 209 332 les 101 225 316 all 316 lesiterlimit 316 lhf 262 302 localize 236 359 361 mo 359 sweeps 309 thrcont 359 lock off 272 loewdin 351 log 365 log_history 366 368 425 m matrix 110 345 mao 352 mao selection 358 marij 125 300 extmax 300 lmaxmom 300 nbinmax 300 precision 300 thrmom 300 wsindex 300 maxcor 45 80 169 170 183 184 208 214 215 219 225 314 322 326 maximum norm of basis set gradient 348 cartesian gradient 348 internal gradient 348 md_action 368 369 md_status 365 368 mo output format 289 294 mo diagram 289 mointunit 169 172 233 324 371 moments 350 355 moprint 289 mp2energy 36 169 323 325 mp2energy SCS 323 mp2energy SCS pt vall ps val2 323 mp2occ 174 325 mp2pair 324 mulliken 351 mvd 236 355 nac 370 nac_matrix 370 nacme 322 natoms 364 natural orbital occupation 273 natural orbital occupation file natural 361 426 natural orbitals 273 289 occupation 289 natural orbitals file natural 361 newcoord 224 nmr 233 dft 233 mp2 233 rhf 233 shielding constants 233 nomw 101 315 noproj 315 nosalc 231 315 nprhessian 315 nprvibrational normal modes 315 nprvibrational spectrum 315 nsteps 364 oep 259 oldgrad 348 open shells 67 68 274 296 operating system 272 optimize 102 103 226 339 341 basis 103 339
356. lations Stability Dynamic Response Properties and Excited States 145 Vl Punetionalities of Esef and Herad ios s lt 6 64 ee eae ee et 145 f2 Theoretical Background iaoe e ie a wa ca ark bk oe Pe 146 To Implementations 2 2 eek on A ek he te Ee Baek he hee he 149 TA How te Perot 0 4644 bb oie e a oi e a a e e e 150 TAT Preliminaries lt s ostera acc ee hee ee Ee a 150 7 4 2 Polarizabilities and Optical Rotations 151 Talo Dtability Anglysis 4 2 aoe G aaa wae Ee Ee ee EES 152 7 4 4 Vertical Excitation and CD Spectra 152 7 4 5 Excited State Geometry Optimizations ooa 155 7 4 6 Excited State Force Constant Calculations a 155 7 4 7 Polarizability Derivatives and Raman Spectra a 156 Many body perturbation theory in the GW approximation 157 8 amp 1 Theoretical backeround lt eoe s scios 44 ace u Bee Be g 157 Bel GW ealureS e anida Ro De ee ea ek ee Phe E 158 8 3 General recipe for GoWo calculations 00 159 CONTENTS 7 9 Second order Mgller Plesset Perturbation Theory 160 9 1 Functionalities of Mpgrad Rimp2 Ricc2 160 JLL How ROU ee co a e ee ee i Sh e E i 161 92 Some Theory sty ow eS ew Ge A ee eee ee a d 162 9 3 How to Prepare and Perform MP2 Calculations 163 9 4 General Comments on MP2 Calculations Practical Hints 167 95 REMF F12 Caleulations 2 445 286 44 844444 2464 a 169 9 6 LT SOS RI MP2 with O N scaling cost
357. lculations on these fragments 2 jobbsse cycles over the supermolecular complex and the fragments and com putes the energies and if requested gradients for them Then the counterpoise corrected results are evaluated and written to the standard data groups en ergy and grad 3 For geometry optimizations one of the structure relaxation codes statpt or relax is invoked to update the coordinates and check for convergence If the structure optimization is not converged jobbsse continues with the previous step Note that counterpoise corrected calculations with jobbsse are NOT as black box as ordinary geometry optimizations with jobex The input generated for the fragments are based on the default occupation numbers obtained from the EHT guess default assignments for the frozen orbitals memory etc Since this might be different from what is needed or even fail it is recommended to let jobbsse stop after the initial setup step using the flag setup and to check carefully the assigned basis sets 5 6 COUNTERPOISE CORRECTIONS USING THE JOBBSSE SCRIPT 117 occupations number and subsystem symmetries In particular for MP2 or CC2 calculations with molecules containing not only the atoms H Ar also the number of frozen orbitals should be checked and if neccessary corrected 5 6 1 Options Given a shell the usage is nohup jobbsse amp This command invokes cp correction and if needed structure optimization using the default prog
358. ld be intact and you can simply restart it Restart more details If the files are not intact one can still use the optimized coordinates in one way or the other There are basically three phases which are explicitely indicated by the number of iterations riter 0 woelfling reads control coords to generate an initial guess path xyz 1 woelfling reads control gradients to compute an optimized path xyz Hes sian are initialized and written to hessians new gt l woelfling reads control gradients oldgradients and hessians to update hessians and compute an optimized path xyz Hessian are updated and written to hessians new Therefore repeated execution of woelfling will yield the same output unless new energies gradients are computed The woelfling job script takes care of the file handling and should enable restart at any time If files are damaged it will be hard to gather gradients and corresponding hessian and oldgradient information If you have an intact gradients or oldgradients file necessary condition number of lines 3 2 x natoms xnumber of structures name it gradients set riter in the 122 CHAPTER 5 STRUCTURE OPTIMIZATIONS control file to 1 and restart If those file are not intact you can extract whatever structure information you have obtained and use it to provide a better initial guess Modify file coords and ncoord in the control file accordingly set riter to 0 and restart Chapter 6 Hartree Foc
359. ld set to denconv 1 d 7 or less e the maximum core memory the program is allowed to allocate should be defined in the data group maxcor in MB the recommended value is ca 3 4 of the available physical core memory at most e orbitals to be excluded from the correlation treatment have to be specified in data group freeze e the calculation of MP2 gradients is omitted by adding the flag mp2energy to the control file in this case only MP2 energy is calculated Calculations with rimp2 and ricc2 moreover require e an auxiliary basis defined in the data group cbas This is not needed for mpgrad but here one needs e a specification for scratch files and their size in data group mointunit see Section 20 2 16 e and the number of passes for integral evaluations and transformations in data group traloop 170 CHAPTER 9 2ND ORDER M OLLER PLESSET PERTURB THEORY For explicitly correlated MP2 F12 calculations one needs depending the details of the applied approximations additionally a so called complementary auxiliary basis set CABS defined in cabs and a RI SCF auxiliary basis set defined in jkbas Calculations with rimp2 and ricc2 1 RI MP2 calculations require the specification of auxiliary basis sets cbas and a converged SCF calculation with the one electron density convergence thres hold set to denconv 1 d 7 or less In addition the options freeze frozen core approximation and maxcor maximum core memory usage
360. le_65 tar gz and unpacked tar xvf turbomole_65 tar to produce the whole directory structure Note Do not install or run TURBOMOLE as root or with root permissions 2 1 1 Settings for each user The environmental variable TURBODIR must be set to the directory where TURBOMOLE has been unpacked for example TURBODIR my_disk my_name TURBOMOLE Then the most convenient way to extend your path to the TURBOMOLE scripts and binaries is to source the file Config turbo_ env source TURBODIR Config_turbo_env If you have a csh or tcsh as default login shell use source TURBODIR Config_turbo_env tcsh instead It is recommended to add the two lines given above to your bashrc or profile or wherever you prefer to add your local settings 29 30 CHAPTER 2 INSTALLATION OF TURBOMOLE 2 1 2 Setting system type and PATH by hand Check that the Sysname tool works on your computer TURBODIR scripts sysname should return the name of your system and this should match a bin arch subdirec tory If Sysname does not print out a single string matching a directory name in TURBODIR bin and if one of the existing binary versions does work you can force sysname to print out whatever is set in the environment variable TURBOMOLE_SYSNAME TURBOMOLE_SYSNAME em64t unknown 1linux gnu Please make sure not to append _mpi or _smp to the string when setting TURBOMOLE_SYSNAME even if you intend to run parallel calculations sysname will ap
361. lent command nthreads integer fde input option nthreads integer Monomolecular and supermolecular basis set approach The p4 and ppg densities can be expanded using the supermolecular or monomolec ular basis set In a supermolecular basis set expansion the basis functions x of both subsystems are employed to expand the subsystem electron densities In a monomolecular basis set expansion instead only basis functions x centered on the atoms in the th subsystem are used to expand the corresponding density Both monomolecular and supermolecular basis set expansion of the electron densities are implemented in FDE with the flag m a monomolecular expansion is performed while for a supermolecular one s is used In the absence of both flags a monomolec ular expansion is performed by default For an accurate calculation of binding energies of weakly interacting molecular sys tems a supermolecular basis set is required to avoid the basis set superposition error Otherwise a very large monomolecular basis set is necessary NOTE The FDE script supports only basis set in the TURBOMOLE library Equivalent command mono or super fde input option method mono or method super Convergence of the freeze and thaw cycles The script FDE runs a self consistent calculation when a convergence criterion is fulfilled The convergence criterion is the change in the total dipole moment This 252 CHAPTER 17 FROZEN DENSITY EMBEDDING CALCULA
362. lgorithms Comput J 13 3 317 322 1970 H B Schlegel Optimization of equilibrium geometries and transition struc tures J Comput Chem 3 2 214 218 1982 H B Schlegel Estimating the hessian for gradient type geometry optimiza tions Theor Chim Acta 66 5 333 340 1984 M Ehrig Diplomarbeit Master s thesis Universit t Karlsruhe 1990 T Koga H Kobayashi Exponent optimization by uniform scaling technique J Chem Phys 82 3 1437 1439 1985 A K Rapp W A Goddard II Charge equilibration for molecular dynamics simulations J Phys Chem 95 8 3358 3363 1991 C G Broyden The convergence of a class of double rank minimization algo rithms 1 General considerations J Inst Math Appl 6 1 76 90 1970 D Goldfarb A family of variable metric methods derived by variational means Math Comput 24 109 23 26 1970 D F Shanno Conditioning of quasi newton methods for function minimiza tion Math Comput 24 111 647 656 1970 P Pulay Convergence acceleration of iterative sequences the case of SCF iteration Chem Phys Lett 73 2 393 398 1980 M P Allen D J Tildesley Computer Simulation of Liquids Oxford Univer sity Press Oxford 1987 T Halgren W Lipscomb Synchronous transit method for determining re action pathways and locating molecular transition states Chem Phys Lett 49 2 225 232 1977 R Elber M Karplus A method for d
363. limited to values lt 16Gb to avoid integer overflow errors Settings obtained by mp2prep may be changed manually You may change the num ber of passes in traloop by editing the control file e g if the originally intended disc space is not available To adapt the size of scratch files add statistics mpgrad to control file and start an mpgrad statistics run with the command mpgrad 4 Start a single mpgrad calculation with the command mpgrad 5 For optimisation of structure parameters at the non RI MP2 level use the command jobex level mp2 Note that the frozen core approximation is ignored in this case 9 4 General Comments on MP2 Calculations Practical Hints Recommendations e It is well known that perturbation theory yields reliable results only if the perturbation is small This is also valid for MP2 which means that MP2 improves HF results only if HF already provides a fairly good solution to the 9 4 GENERAL COMMENTS 173 problem If HF fails e g in case of partially filled d shells MP2 usually will also fail and should not be used in this case e MP2 results are known to converge very slowly with increasing basis sets in particular slowly with increasing l quantum number of the basis set expansion Thus for reliable results the use of TZVPP basis sets or higher is recom mended When using SVP basis sets a qualitative trend can be expected at the most Basis sets much larger than TZVPP usually do not signific
364. ling LT SOS MP2 calculations Scaled opposite spin CC2 for ground and excited states with fourth order scal ing computational costs Nina O C Winter Christof Hattig J Chem Phys 134 184101 2011 and Scaled opposite spin second order Mgller Plesset corre lation energy An economical electronic structure method Y Jung R C Lochan A D Dutoi and M Head Gordon J Chem Phys 121 9793 2004 e for SCS MP2 calculations S Grimme J Chem Phys 118 2003 9095 e for RI MP2 polarizabilities Large scale polarizability calculations using the approximate coupled cluster model CC2 and MP2 combined with the resolution of the identity approxi mation Daniel H Friese Nina O C Winter Patrick Balzerowski Raffael Schwan Christof Hattig J Chem Phys 136 174106 2012 9 2 Some Theory Second order Mogller Plesset Perturbation Theory MP2 corrects errors introduced by the mean field ansatz of the Hartree Fock HF theory the perturbation operator is just the difference of the exact and the HF Hamiltonian One straightforward obtains the MP2 energy ab Bup2 gt P E ij ab 9 1 iajb with the t amplitudes ab __ _ tj ab 9 2 Ei j Ea p i and j denote occupied a and b virtual orbitals p are the corresponding orbital energies ij ab ij ab ij ba are four center two electron integrals in a com monly used notation 9 3 HOW TO PREPARE AND PERFORM MP2 CALCULATIONS 169
365. llected within the file job lt cycle gt where lt cycle gt is the index of the cycle The convergence criteria and their current values are written out at the bottom of the job last file 5 2 PROGRAM STATPT 99 5 2 Program STATPT 5 2 1 General Information Stationary points are places on the potential energy surface PES with a zero gradi ent i e zero first derivatives of the energy with respect to atomic coordinates Two types of stationary points are of special importance to chemists These are minima reactants products intermediates and first order saddle points transition states The two types of stationary points can be characterized by the curvature of the PES at these points At a minimum the Hessian matrix second derivatives of energy with respect to atomic coordinates is positive definite that is the curvature is positive in all directions If there is one and only one negative curvature the stationary point is a transition state TS Because vibrational frequencies are basically the square roots of the curvatures a minimum has all real frequencies and a saddle point has one imaginary vibrational frequency Structure optimizations are most effectively done by so called quasi Newton Raph son methods They require the exact gradient vector and an approximation to the Hessian matrix The rate of convergence of the structure optimization depends on anharmonicity of the PES and of the quality of the approxima
366. localization including all occupied MOs is carried out i e the squared distance of charge centers of different LMOs is maximized As output one gets localized MOs written to files 1mos or lalp lbet in UHF cases informations about dominant contributions of canonical MOs to LMOs and about location of LMOs from Mulliken PA are written to standard output 16 1 WAVEFUNCTION ANALYSIS AND MOLECULAR PROPERTIES 237 Natural transition orbitals For excited states calculated at the CIS or CCS level the transition density between the ground and an excited state Eig Wen a dal Ver 16 1 can be brought to a diagonal form through a singular value decomposition SVD of the excitation amplitudes Fia OEV 5 5 Vi 16 2 The columns of the matrices O and V belonging to a certain singular value A can be interpreted as pairs of occupied and virtual natural transition orbitals 156 157 and the singular values A are the weights with which this occupied virtual pair con tributes to the excitation Usually electronic excitations are dominated by one or at least just a few NTO transitions and often the NTOs provide an easier understanding of transition than the excitation amplitudes Ej in the canonical molecular orbital basis From excitation amplitudes computed with the ricc2 program NTOs and their weights the singular values can be calculated with ricctools E g using the right eigenvectors for the second singlett excited state in irrep
367. lots of useless output 4 4 THE GENERAL OPTIONS MENU 83 disple F display 1e contributions to desired derivatives onlyle F calculate 1e contributions to desired derivatives only debugte F display 1e shell contributions to desired derivatives WARNING this produces large outputs debug2e F display 2e shell contributions to desired derivatives WARNING this produces VERY large outputs debug switch for vibrational analysis force only disable transfer relations gradient only disable virial scaling invariance in basis set optimizations gradient only debugvib F notrans F novirial F use lt opt gt for enabling lt opt gt for disabling option lt opt gt lt amp gt will bring you back to GENERAL MENU without more changes lt RETURN gt OR OR q uit WILL TERMINATE THIS MENU As there is no need to use these options normally and the menu text is self explaining no further description will be given Note that all options are logical switches and may be enabled and disabled the same way as shown for the last menu Entering will bring you to the last derivative submenu 4 4 3 Relax Options Program relax has a huge variety of options to control its actions which in program define are grouped together in eight consecutive menus These are only briefly described in the following sections for a more detailed discussion of the underlying algorithms refer to the documentation of program relax see Section
368. lumns distance LHF potential Slater potential Correction potential The procedure to plot the OEP EXX potential is the same In this case the expansion coefficients see Eq 18 6 are read from the file oepcVx dat cartesian format The file tx vec will be generated with four columns distance EXX potential EXX potential zero 18 5 How to quote e For LHF calculations with odft Efficient localized Hartree Fock methods as effective exact exchange Kohn Sham methods for molecules Fabio Della Sala and Andreas Gorling J Chem Phys 115 5718 2001 and The asymptotic region of the Kohn Sham exchange potential in molecules Fabio Della Sala and Andreas Gorling J Chem Phys 116 5374 2002 e For OEP EXX calculations with odft Numerically stable optimized effective potential method with balanced Gaus sian basis sets Andreas Hefelmann Andreas W G tz Fabio Della Sala and Andreas Gilling J Chem Phys 127 054102 2007 Chapter 19 Treatment of Solvation Effects with COSMO The Conductor like Screening Model 181 Cosmo is a continuum solvation model CSM where the solute molecule forms a cavity within the dielectric continuum of permittivity that represents the solvent The charge distribution of the solute polarizes the dielectric medium The response of the medium is described by the generation of screening charges on the cavity surface CSMs usually require the solution of the rather complicated boundary conditio
369. m Phys 128 8 084102 2008 W Klopper C C M Samson Explicitly correlated second order M ller Plesset methods with auxiliary basis sets J Chem Phys 116 15 6397 6410 2002 W Klopper W Kutzelnigg Moller Plesset calculations taking care of the correlation cusp Chem Phys Lett 134 1 17 22 1987 S Ten no Explicitly correlated second order perturbation theory Introduction of a rational generator and numerical quadratures J Chem Phys 121 1 117 129 2004 D P Tew W Klopper Open shell explicitly correlated f12 methods Mol Phys 108 315 325 2010 S F Boys Localized orbitals and localized adjustment functions In P O L wdin Ed Quantum Theory of Atoms Molecules and the Solid State Page 253 Academic Press New York 1966 J Pipek P G Mezey A fast intrinsic localization procedure applicable for ab initio and semiempirical linear combination of atomic orbital wave functions J Chem Phys 90 9 4916 4926 1989 D P Tew W Klopper New correlation factors for explicitly correlated elec tronic wave functions J Chem Phys 123 7 074101 2005 W Klopper B Ruscic D P Tew F A Bischoff S Wolfsegger Atomization energies from coupled cluster calculations augmented with explicitly correlated perturbation theory Chem Phys 356 1 3 14 24 2009 F A Bischoff S H fener A Glos W Klopper Explicitly correlated second order perturbation theory c
370. m to restart mpshift number add trast 1 and trand num ber_of_traloops to the control file and start mpshift 20 2 24 Keywords for Parallel Runs On all systems the parallel input preparation is done automatically Details for the parallel installation are given in Section 3 2 1 The following keywords are necessary for all parallel runs parallel_platform architecture Currently the following parallel platforms are supported 20 2 FORMAT OF KEYWORDS AND COMMENTS 373 SMP MPP cluster SGI for systems with very fast communication all CPUs are used for the linear algebra part Synonyms for SMP are HP V Class SP3 SMP and HP S X Class for systems with fast communication like Fast Ethernet the number of CPUs that will be taken for linear algebra part depends on the size of the matrices Synonyms for MPP are SP3 and linuxcluster for systems with slow communication the linear algebra part will be done on one single node Synonyms for cluster are HP Cluster and every platform that is not known by TURBOMOLE similar to SMP but here the server task is treated differently the MPI implementation on the SGIs would cause this task to request too much CPU time otherwise If you want to run mpgrad traloop has to be equal to or a multiple of the number of parallel workers For very large parallel runs it may be impossible to allocate the scratch files in the working directory In this case the scratc
371. mbers of the next neighbours block nxtneil2 in the file ufftopology the program tries to determine the UFF type of an atom The following rules are implemented If the atom has three next neighbours and it is in the nitrogen group then it has a hybridization three If it is not in the nitrogen group it has hybridization two If the atom has four next neighbours and it is in the carbon group it has hybridization three If it is not in the carbon group it becomes hybridization four If the number of next neighbours is six then it gets the hybridization six Since the smallest eigenvalues A of the Hessian has the greatest influence on the convergence of the geometry optimization one can shift these values with Mi Ai a Be and calculates a new Hessian with these modified eigenvalues 282 CHAPTER 20 KEYWORDS IN THE CONTROL FILE 20 2 5 Keywords for WOELFLING Module WOELFLING reads options from data group woelfling The below values of the options are default values with the following meaning ninter 14 Number of interpolated structures for optimization ncoord 2 Number of input structures provided by user align 0 Align input structures by translation rotation 0 yes 1 no maxit 40 Maximum number of iterations dlst 3 00000000000000 Threshold for accuracy of LST interpolation thr 1 000000000000000E 004 Threshold for mean of norms of projected gradients method q Use standard optimization from initial LST path met
372. me based on perturbation theory Phys Rev A 50 196 1994 M K Armbruster F Weigend C van Wiillen W Klopper Self consistent treatment of spin orbit interactions with efficient hartree fock and density func tional methods Phys Chem Chem Phys 10 1748 1756 2008 BIBLIOGRAPHY 411 74 75 76 77 78 79 80 81 82 83 84 85 86 D Peng M Reiher Exact decoupling of the relativistic fock operator Theor Chem Acc 131 1081 2012 D Peng M Reiher Local relativistic exact decoupling J Chem Phys 136 244108 2012 D Peng N Middendorf F Weigend M Reiher An efficient implementation of two component relativistic exact decoupling methods for large molecules J Chem Phys 138 184105 2013 M K Armbruster W Klopper F Weigend Basis set extensions for two component spin orbit treatments of heavy elements Phys Chem Chem Phys 8 4862 4865 2006 M Reiher A Wolf Exact decoupling of the Dirac Hamiltonian I General theory J Chem Phys 121 2037 2047 2004 M Reiher A Wolf Exact decoupling of the Dirac Hamiltonian II The gen eralized Douglas Kroll Hess transformation up to arbitrary order J Chem Phys 121 10945 10956 2004 M Reiher Douglas Kroll Hess Theory a relativistic electrons only theory for chemistry Theor Chem Acc 116 241 252 2006 M Sierka A Burow J Dobler J Sauer Point defe
373. ments are similar to the those for two or three iterations of the eigenvalue problem which reduces the total CPU and wall time for the calculation of a spectrum i e excitation energies and transition moments by almost a factor of three 10 4 2 Transition moments between excited states For the calculation of transition moments between excited states a set of Lagrangian multipliers N py has to be determined instead of the M u for the ground state transition moments From these Lagrangian multipliers and the left and right eigenvectors one obtaines the right transition moment between two excited states i and f as v ae Foye yes Mfi gt Ds N DAE BE Var 10 22 pq where V are the matrix elements of the perturbing operator A similar expression is obtained for the left transition moments The left and right transition moments are then combined to yield the transition strength ie fo fri te fo fei 1 x Sin 5 Mi Mh Me M 10 23 As for the ground state transitions only the transition strengths go y are a well defined observables but not the transition moments My f and MY The single substitution parts of the transition Lagrangian multipliers N y are saved in files named CCNEO s m 2zxrz To obtain the transition strengths for excitations between excited states the keyword tmexc must be added to the data group excitations Additionally the initial and final states must be given in the same l
374. menu see Chapter 4 define will automatically provide most of the keywords discussed below A large number of not necessarily realistic sample inputs is contained in the escf and egrad subdirectories of the test suite TURBOTEST directory 7 4 1 Preliminaries All response calculations require a complete set of converged occupied and virtual SCF MOs It is strongly recommended to use well converged MOs since the error in the ground state wavefunction enters linearly in all response properties Thus before starting escf or egrad specify the keywords scfconv 7 denconv id 7 in control perform a dscf statistics run if semi direct integral processing is to be used see Chapter 3 1 and re run dscf or ridft 7 4 HOW TO PERFORM 157 dscf gt dscf out amp or ridft gt ridft out amp in case of RI J The above tight convergence criteria are also recommended for excited state ge ometry optimizations To perform a two component TDDFT calculation the two component version of ridft has to be run before see Chapter 6 4 using the keywords soghf and kramers 7 4 2 Polarizabilities and Optical Rotations The calculation of dynamic polarizabilities is controlled by the keyword scfinstab dynpol unit list of frequencies unit specifies the unit of the following frequencies and may be ev nm 1 cm or a u default The frequencies may be either purely real or purely imaginary For exam ple to calculate dynamic pola
375. minimum number of geometries needed to start update if method ms dfp bfgs maxgeo 2 mingeo 1 as default additional suboptions if method ahlrichs modus char fmode for an explanation see suboptions pulay gi ven below e g ahlrichs numgeo 7 mingeo 3 maxgeo 4 modus lt g dg gt dynamic NOTES if the macro option ahlrichs has been chosen and n numgeo ncycl number of geometries available e if ncycl lt n geometry update by inter extrapo lation using the last two geometries e if ncycl gt n diagonal update for the hessian by least mean squares fit pulay update for the ge ometry using specified modus fmode see pulay below e if ncycl gt max 5 n 3 and max g lt 0 01 and g lt 0 001 or Hj 4 OVi j diagonal update is replaced by multidimensional BFGS rank n update for the hessian pulay suboptions try to find an optimal linear combination of the coordinates of the numpul previous optimization cycles as specified by modus see below Available suboptions are numpul integer number of geometries to be utilized maxpul znteger maximum number of geometries minpul nteger minimum number of geometries needed to start update modus char fmode char lt g g gt or lt g dq gt or lt dq dq gt defines the quantity to be minimized 20 2 FORMAT OF KEYWORDS AND COMMENTS 343 dq internal coordinate change fmode specifies the force constants to be used only i
376. mmetry c2v coord file coord intdef file coord atoms n 1 basis n def SVP o 2 3 basis o def SVP pople AO basis file basis rundimensions dim fock dens 1098 natoms 3 nshell 18 nbf CAQ 45 nbf A0 42 dim trafo SA0 lt gt A0 CAO 85 rhfshells 2 uhfmo_alpha none file alpha uhfmo_beta none file beta none hamilton core guess will be made files alpha and beta will be generated by the program uhf alpha shells al 1 6 1 a2 1 1 bi 1 4 1 b2 1 1 beta shells al 1 5 1 a2 1 1 bi 1 4 CLD b2 1 1 scfiterlimit 30 scfconv 7 thize LOOOOO00E 04 21 3 NO INPUT FOR AN UNRESTRICTED DFT CALCULATION 383 thime 5 scfdamp start 1 500 step 050 min 100 scfdump scfintunit unit 30 size 2 file work user twoint scfdiis start 0 5 scforbitalshift closedshell 3 drvopt cartesian on basis off global off hessian on dipole on nuclear polarizability interconversion off qconv 1 d 10 maxiter 25 optimize internal on cartesian off global off basis off logarithm coordinateupdate dqmax 0 3 interpolate on statistics 5 forceupdate ahlrichs numgeo 0 mingeo 3 maxgeo 4 modus lt g dq gt dynamic fail 0 1 threig 0 005 reseig 0 005 thrbig 3 0 scale 1 00 damping 0 0 forceinit on diag default energy file energy grad file grad forceapprox file force lock off dft functional b p gridsize m3 last step define end 384 File coord coord 000000000000
377. mp2 program needs many passes for the integral evaluation All what is needed for a RI MP2 gradient calculation with the ricc2 program is a ricc2 data group with the entry geoopt model mp2 If you want only the RI MP2 energy for a single point use as option just mp2 To activate in MP2 energy calculations the evaluation of the D diagnostic for details see Sec 10 1 use instead mp2 didiag Note that the calculation of the D diagnostic increases the costs compared to a MP2 energy evaluation by about a factor of three Comments on the Output e Most important output for ricc2 rimp2 and mpgrad are of course MP2 HF energies written standard output and additionally to file energy and MP2 HF gradients written to file gradient 174 CHAPTER 9 2ND ORDER M OLLER PLESSET PERTURB THEORY e Incase of MP2 gradient calculations the modules also calculate the MP2 dipole moment from the MP2 density matrix note that in case of mpgrad frozen core orbital specification is ignored for gradient calculations and thus for MP2 dipole moments Further output contains indications of the suitability of the HF MP2 treatment e As discussed above reliable HF MP2 results are in line with small MP2 cor rections The size of the MP2 correction is characterised by the t amplitudes as evident from the above equations mpgrad by default plots the five largest t amplitudes as well as the five largest norms of t amplitudes for fixed 7 and j
378. mplementation 2 106 5 5 Molecular Dynamics Calculations 0 108 5 6 Counterpoise Corrections using the JOBBSSE Script 110 561 Opioms scp oreve dosari srini nitran et 111 562 Output eos e woe ale ek eee oe eee ea S a 112 5 7 Reaction Path Optimization e sios osa ni eg ee ee 113 5 7 1 Background and Program structure 113 Da lapat Suee o e aoaaa ua a ek oa a ee ae 113 ara How M WOEKS Go Ae ek a eae a a aa oe aea 114 6 Hartree Fock and DFT Calculations 117 6 1 Backeround Theory gt secs we ee ek a ee e T e 119 CONTENTS 6 2 Exchange Correlation Functionals Available 2 120 6 3 Restricted Open Shell Hartree Fock 124 634A Briel Description 2 4 6444 8 ee Le eS Eee ee 124 632 One Open Shell iis esi ee eS ae ae Bae eee es 124 6 3 3 More Than One Open Shell 0 127 6 34 Miscellaneous oe oac sacs Fee ew ee ee ee es 129 64 Relativistic effects 00464444 S445 2 be bbe he a ee bs 131 6 4 1 One and two component relativistic methods 131 Gale How tous r ke a ek oR ee ae be eo e SE ae kG 133 6 5 Periodic Electrostatic Embedded Cluster Method 135 6 5 1 General Information s se sos sonsos ba w ea pai e t 135 6 5 2 Theoretical Background aa aaa 135 65 3 Caleulation Setup ios aie Soe bE a E e ee e a 136 6 6 Dispersion Correction for DFT Calculations 143 Hartree Fock and DFT Response Calcu
379. n En En n Gxs En g Vcn 8 2 163 164 CHAPTER 8 MBPT CALCULATIONS An approximation to the solution of this equation can be obtained by linearizing it En En Zn n E en Vac n 8 3 here Zn is given by d3 E Zn OE 1 n 1 m 8 4 E en reducing the computational effort to a single iteration The self energy appearing in Eqn 8 2 is calculated in the GW approximation from the KS Green s function and screening This is the so called GoWo approxi mation The Self energy splits in an energy independent exchange part and a correlation part that does depend on energy Their matrix elements are given by n n nilin 8 5 and nl Ben In SO lene __ 8 6 Se ee mSgn En H Where Zm Qm in are the excitation energies shifted infinitesimally into the complex plane The pm are the corresponding excitation densities More details tests and benchmark calculations are can be found in Ref 105 8 2 GW features GoWo is implemented in TURBOMOLE in the escf module supporting the following features e LDA GGA and Hybrid functionals can be used for the underlying DFT cal culation e RI approximation e In GoWo the linearized Eqn 8 3 and solved Eqn 8 2 quasi particle equa tion e Both RPA and TDDFT response functions can be used to screen the coulomb interaction in constructing W e Closed shell systems with rpas exci
380. n 2 a 0 b Nir Nir Nir T 2 2n 2 e n Nir 2 a ir A b Nir Nir 3 nir 1 This covers the 1S states of p pt d d8 etc Average of high spin states n electrons in MO with degenerate Nir nin 4h k 1 1 1 L 1 a Nir 1 n i Qnip Qk k 1 1 11 1 E Nir 1 n where k max 0 n nir l n 2k 2S spin This covers most of the cases given above A CSF results only if n 1 nir 1 Nir Nir 1 2nri 1 since there is a single high spin CSF in these cases The last equations for a and b can be rewritten in many ways the probably most concise form is n n 2 4 28 n 2f n Bo n n 2 28 n 2f n This applies to shells with one electron one hole the high spin couplings of half filled shells and those with one electron more ore less For d d d and d it represents the weighted average of high spin cases 3F P for d d 4F 4P for d d 6 4 RELATIVISTIC EFFECTS 137 6 4 Relativistic effects TURBOMOLE provides two different possibilities for the treatment of relativistic ef fects Via effective core potentials ECPs or via all electron approaches X2C DKH BSS Both techniques can be employed in an one component scalar relativistic or two component including spin orbit coupling framework The latter is only avail able in the module RIDFT 6 4 1 One and two component relativistic methods Incopora
381. n ROHF calculations e g with more than one open shell see the sample input in Section 21 6 and the tables of Roothaan param eters in Section 6 3 Note that this keyword toggles the ROHF mode also for more than one open shell If it is not given the open shell electrons are simply ignored UHF alpha shells and beta shells these two data groups specify the occupation of alpha and beta spin UHF MOs syntax as any data group related with orbital occupation information e g closed shells Example alpha shells a 1 8 1 b 1 2 1 beta shells a 1 7 1 b 1 3 1 C C J Roothaan Rev Mod Phys 32 1960 179 298 CHAPTER 20 KEYWORDS IN THE CONTROL FILE uhf directs the program to carry out a UHF run uhf overwrites closed shell occupation specification uhfmo_alpha and uhfmo_beta These two data groups contain the UHF MO vectors for alpha and beta spin respectively same syntax as scfmo uhfmo_beta see uhfmo_alpha DFT dft functional b p gridsize m3 for DFT calculations one has to specify the functional and the grid for the quadra ture of the exchange correlation part The settings above are default both lines can be left out if the B P86 functional and grid m3 are required Other useful functionals supported are b lyp b3 lyp b3 lyp_Gaussian equivalent to the Gaussian98 keyword B3LYP with VWNIID bh lyp s vwn s vwn_Gaussian equivalent to the Gaussian98 keyword SVWN with VWNII
382. n as 168 occ Tay D aN OST K ty 18 8 ate p Here the vector y r contains the basis functions S stands for the corresponding overlap matrix the vector Ua Collects the coefficients representing orbital a and the matrix K represents the non local exchange operator 6N in the basis set While the numerical Slater is quite expensive but exact the basis set method is very fast but its accuracy depends on the completeness of the basis set Concerning the correction term Eq 18 3 shows that it depends on the exchange potential itself Thus an iterative procedure is required in each self consistent step this is done using the conjugate gradient method Concerning conditions 18 4 and 18 5 both are satisfied in the present implemen tation KS occupied orbitals are asymptotically continued 176 on the asymptotic grid point r according to 7 MAA aie hie eo EL e PiUFI Yo 5 18 9 where ro is the reference point not in the asymptotic region 8 2e and Q is the molecular charge A surface around the molecule is used to defined the points ro 18 3 How to Perform OEP EXX To run OEP EXX calculations select dft functional oep As the computation of the OEP functional is completely analytic and grid free any selection of a grid type or size will not influence the OEP calculation in contrast to other density functionals Particular care is instead required to orbital and auxiliary basis set
383. n each step help list all commands proximation to hybrid or orbital dependent exchange correlation potentials in Vemb r All LDA GGA functionals in TURBOMOLE can be considered as approximations For example the command FDE p 3 f b lyp can be used to approximate bh lyp or b3 lyp hybrid non additive potentials while the command FDE p 3 f pbe approximates the pbeO hybrid non additive potentials Other combinations of func tionals are not recommended meta GGA are not supported Finally also calculations with the Local Hartree Fock LHF potential can be per formed In this case the command FDE p 3 f becke exchange can be used to approximate the LHF non additive potential 164 Equivalent command func string fde input option func string Chapter 18 Orbital Dependent Kohn Sham Density Functional Theory 18 1 Theoretical Background Approximations to the exchange correlation XC functional of the Kohn Sham KS Density Functional Theory DFT can be classified by the so called Jacob s ladder The ground on which the ladder lies is the Hartree approximation XC energy is zero and the first rung is the local density approximation LDA in which the XC energy density is a simple local function of the density The second rung of the Jacob s ladder is the generalized gradient approximation GGA in this case the XC energy density depends also on the gradient of the density In the third rung meta
384. n models see chapter 10 6 38 CHAPTER 3 HOW TO RUN TURBOMOLE USER INPUT coordinates input generator From TURBOMOLE library define basis sets ground state energy vib frequencies dscf thermodynamics erate aoforce Freeh NumForce TDDFT excited states response properties HF DFT TDDFT MP2 CC2 escf egrad gradient energy gradient grad ricc2 2 NMR shieldings rdgrad rimp2 mpshift Raman spectrum geometry changes Raman molecular dynamics CC excited states and response properties ricc2 Figure 3 1 The modules of TURBOMOLE and the main data flow between them 3 2 PARALLEL RUNS 39 e mpgrad parallel conventional i e non RI MP2 energy and gradient cal culations Please note that RI MP2 is one to two orders of magnitude faster than conventional MP2 so even serial RI MP2 will be faster than parallel MP2 calculations e aoforce parallel Hartree Fock and DFT analytic 2nd derivatives for vi brational frequencies IR spectra generation of Hessian for transition state searches and check for minimum structures SMP only e escf parallel TDDFT RPA CIS excited state calculations UV Vis and CD spectra polarizabilities SMP only e egrad parallel TDDFT RPA CIS excited state analytic gradients including polarizability derivatives for RAMAN spectra SMP only e NumForce this script can used for a trivial parallelization of the numerical displa
385. n of expectation values for S to not yet use OpenMP paralleliza tion If the OpenMP parallelization is switched on by setting OMP_NUM_THREADS these parts will still be executed sequentially e In the dscf program the DFT part will only be executed sequentially by a single thread and the incore option will be ignored if more than one thread is used Semi direct dscf calculations i e if a size larger than 0 is given two electron integral scratch file in scfintunit can not be combined with the 46 CHAPTER 3 HOW TO RUN TURBOMOLE OpenMP parallel runs The program will than stop with error message in the first Fock matrix construction Multi thread parallelization of aoforce escf and egrad The parallelization of those modules is described in 22 and is based on fork and Unix sockets Except setting PARNODES which triggers the environment variable SMPCPUS nothing has to be set in addition Alternatively the binaries can be called with smpcpus lt N gt command line option or with the keyword smp_cpus in the control file Global Arrays parallelization of ridft and rdgrad ridft and rdgrad are parallelized with MPI using the Global Arrays toolkit Those versions are automatically used when setting PARA_ARCH SMP Due to the explicit usage of shared memory on an SMP system user has to be allowed to use sufficient shared memory e In addition to the usual stack size limit problem make sure that your maximum shared memory you
386. n shell UHF reference wavefunctions with the exception of second order propeties which are only available for a closed shell RHF reference Ground state energies for MP2 MP2 F12 and CC2 and excited state energies for CC2 are also implemented for single determinant restricted open shell Hartree Fock ROHF ref erence wavefunctions cmp Sec 9 3 Note that no gradients are available for MP2 and CC2 with ROHF reference wavefunctions The second order models MP2 CIS D CIS Dx ADC 2 and CC2 can be com bined with a spin component scaling SCS or SOS Not yet available for second order properties For the SOS variants one can switch to an implementation with O N scaling costs by setting the keyworkd for the numerical Laplace transforma tion LT laplace For calculations with CCSD CCSD T and other higher order models beyond CC2 see Chapter 11 Prerequisites Calculations with the ricc2 module require almost the same prerequisites as RI MP2 calculations 1 a converged SCF calculation with the one electron density convergence thres hold set to denconv 1 d 5 or less 2 if non standard basis sets used an auxiliary basis defined in the data group cbas for standard basis sets where a corresponding auxiliary basis set is found in the basis set library the program will automatically use this if cbas is not set 3 if orbitals should be excluded from the correlation treatment and excitation processes the data gr
387. nal orbital dependent diagonal ijij method of Ref 115 with amplitudes c ij not recommended unless in combination with localised orbitals fixed is the diagonal and orbital invariant rational generator approach of Ref 116 where the F12 ampli tudes are not optimised but predetermined using the coalescence conditions default An additional keyword noflip suppresses the use of spin flipped geminals in open shell calculations by default spin flipped geminals are used as described in Ref 117 controls which orbitals are used in the F12 energy contribution hf means that semi canonical Hartree Fock orbitals are used default rohf means that ROHF orbitals are used any frozen orbitals will then also implicitly be ROHF For calculations on closed shell systems localised orbitals may be used Both the Boys 118 and Pipek Mezey 119 methods are available for lo calisation of the orbitals corresponds to the choice of correlation factor f 2 in the geminal basis functions R12 results in a calculation using linear rj2 and LCG results in a calculation using the Slater type correlation factor with exponent 1 4 ag 1 represented as a linear combination of six Gaussians see Ref 120 Note that the exponents 0 9 1 0 and 1 1 ap 1 are recommended for use with the cc pVXZ F12 basis sets 113 switches on off the calculation of a second order correction to the Hartree Fock energy by accounting for single excitations into the c
388. nding the electron in this part lie above the threshold lmo list of LMO numbers calculation of amplitudes of LMOs previously generated by localize ordered by the corresponding diagonal element of the Fock matrix in the LMO basis nmo list of NMO numbers calculation of amplitudes of NMOs previously generated by natural orbitals file natural and natural orbital occupation file natural dens has to be set if additionally to one of the above quantities also the density is to be computed 362 XC CHAPTER 20 KEYWORDS IN THE CONTROL FILE calculation of the Kohn Sham exchange correlation potential It is only valid for DFT calculations and it works for all exchange correlation func tionals including LHF Note that for hybrid functionals only the Kohn Sham part of the potential will be computed the HF part is a non local operator and can t be plotted For GGA functional the full potential will be computed local and non local terms For line plots the output file is tx vec For UHF calculations the output files are tx vec alpha spin potential and sx vec beta spin potential For a line plot the file has three columns 1 total potential 2 local term or Slater potential for LHF 3 non local terms or Correction term for LHF Output formats may be specified by e g fmt xyz if written to the same line as pointval Supported are xyz plt map txt vec cub in case of scalars density L
389. ndividual defined force constant diagonals for e internal coordinates supplied in intdef fdiag e a global scale factor global fdiag This does not work for basis set optimization For the correct syntax of fdiag see descriptions of intdef global 20 2 FORMAT OF KEYWORDS AND COMMENTS 345 carthess read a cartesian e g analytical hessian from hessian and use it as a start force constant matrix if optimize internal has been set use its transform in internal coordinate space If large molecules are to be optimized it may be necessary large core memory requirements to deactivate the numerical evaluation of the derivative of the B matrix with respect to cartesian coordi nates which is needed to transform H cart H int exactly by specifying no dbdx last SCF energy change real last MP2 energy change real These keywords depend on the optimization task to be processed and are updated by the corresponding program i g SCF energy m matrix options This data block contains non default specifications for the m matrix diagonals This is of use if some cartesian atomic coordinates shall be kept fixed during optimization Available options are integer real real real atomic index followed by diagonal elements of the m matrix for this atom scratch files The scratch file ftmp allocated by relax can be placed anywhere in your file systems instead of the working directory by referencing
390. ned first for the remaining cage decoupled coordinates are defined type r a positive real number which is an approximate force constant can be read in for each type of coordinate see below The force constants are used for the definition of the matrix m in BmBt Types of internal coordinates for the definition of m The matrix m is assumed to be a diagonal matrix For each type of coordinate a different value for the force constants m can be read in Types of coordinates are stre invr bend outp tors linc linp wstr winv bond stretch default 0 5 inverse bond stretch default 0 5 bond angle default 0 2 Out of plane angle default 0 2 dihedral or torsional angle default 0 2 Special angle coordinate for collinear chains bending of the chain a b c in the plane of b c d default 0 2 bending of the chain a b c perpendicular to the plane of b c d default 0 2 stretch of a weak bond i e the bond is assumed to have a very low force constant e g a hydrogen bond or a van der Waals bond default 0 05 inverse stretch of a weak bond default 0 05 20 2 FORMAT OF KEYWORDS AND COMMENTS 277 wbnd bond angle involving at least one weak bond default 0 02 wout Out of plane angle for weak bonds default 0 02 wtor dihedral angle for weak bonds default 0 02 wlnc linc coordinate for weak bonds default 0 02 wlnp linp coordinate for weak bonds
391. nergies are given in a u cdspectrum unit The calculated excitation energies and corresponding rotatory strengths are appended to a file named cdspectrum unit can have the same values as in spectrum start vector generation e Flag for generation of UHF start MOs in a triplet instability calculation The option will become effective only if there are triplet instabilities in the totally symmetric IRREP The optional real number e specifies the approximate second order energy change in a u default 0 1 velocity gauge Enables calculation of dipole polarizability rotatory dispersion in the velocity gauge Active only for pure DFT no HF exchange sum rules unit list of frequencies Enable calculation of oscillator and rotatory strength sum rules at frequencies specified by list of frequencies in unit unit see scfinstab dynpol Note that the sums will be taken only over the states specified in soes rpaconv n the vectors are considered as converged if the Euclidean residual norm is less than 107 Larger values of n lead to higher accuracy The default is a residual norm less than 107 escfiterlimit n Sets the upper limit for the number of Davidson Iterations to n Default is nm 25 20 2 13 GW Keywords gw The main keyword that switches on a GW calculation Provided that the response function is calculated setting this keyword will perform a standard GoW calulation with default values for the
392. nergy EH and a correlation energy piece EC RPA rirpa computes Eq 12 1 non selfconsistently from a given set of converged input orbitals The correlation energy EC RPA _ S gpk Paes 12 2 n is expressed in terms of RPA excitation energies at full coupling QRPA and within the Tamm Dancoff approximation QTPARPA The further discussion is restricted to the one component nonrelativistic treatment for the sake of convenience For the derivation of the two component RPA theory see ref 147 The excitation energies are obtained from time dependent DFT response theory and are eigenvalues of the symplectic eigenvalue problem 148 149 K Oa Aan O 12 3 The super vectors Xon and Yon are defined on the product space Loce X Lyvirt and Doce X Lyirt respectively where Doce and Lyirt denote the one particle Hilbert spaces spanned by occupied and virtual static KS molecular orbitals MOs The super operator A B A amp N 12 4 contains the so called orbital rotation Hessians A F Bagh a T Ei ij ab 2 ia jb 12 5 A B iajb a Ei ij ab 12 6 ci and a denote the energy eigenvalues of canonical occupied and virtual KS MOs rirpa computes so called direct RPA energies only i e no exchange terms are included in Eqs 12 5 and 12 6 In RIRPA the two electron integrals in Eqs 12 5 are approximated by the resolution of the identity approximation In conjunction with a frequency integration this
393. next submenu which deals with the specification of these data groups there are 1 data groups points manipulate data group s points a add another data group m lt integer gt modify lt integer gt th data group m all modify all data groups d lt integer gt delete lt integer gt th data group d all delete all data groups off lt integer gt switch off lt integer gt th data group off all switch off all data groups on lt integer gt switch on lt integer gt th data group on all switch on all data groups s scan through data groups quit The first line informs you how many of these data groups already exist in your control file Each of these data groups may consist of several points at which the properties will be calculated You may now create new data groups delete old 4 4 THE GENERAL OPTIONS MENU 91 ones or simply switch on or off individual data groups without deleting them from control The number of different data groups points as well as the number of points in each of them are not limited However if you use many points you should consider specifying them in a separate file This is most easily done using option file in the potential menu This option will create a file for your data groups points and will write a reference of this file to file control Option cowan griffin This option activates the computation of the first order relativistic correction to the energy as given by the expe
394. ng tetrahedron grid in A default 0 3A all_dens real use one isodensity value for all atom types value in a u The outlying charge correction will be performed with a radii based outer cavity Therfore and for the smoothing of the density changes in the intersection areas of the scaled density method radii are needed as for the standard COSMO cavity Please note The isodensity cavity will be constructed only once at the beginning of the SCF calculation The density constructed from the initial mos will be used file mos or alpha beta in case of unrestricted calculations Because the mos of an initial guess do not provide a good density for the cavity construction it is necessary to provide mos of a converged SCF calculation e g a Cosmo calculation with standard cavity We recommend the following three steps perform a standard Cosmo calculation add the isodensity options afterwards and start the calculation a second time Radii based Isosurface Cavity The cosmo_isorad section defines the radii defined isosurface cavity construction The option uses the algorithm of the isoden sity cavity construction but the objective function used depends on the cosmo radii instead of the electron density The default values of nspa and nsph are changed to 162 and 92 respectively This values are superseded by the user defined nspa value of the cosmo section The resulting surface exhibits smoother intersection seams and the segment areas are
395. ngle as defined in Bend evalgrad 1 2 3 4 prints the torsional angle as defined in Tors drives the Frozen Density Embedding calculations prepares the control file for a Hamilton core guess usage see Section 5 1 is the TURBOMOLE driver for all kinds of optimizations example kdg scfdiis kills a data group here scfdiis in the control file 1 5 TOOLS lhfprep log2x log2egy log2rog mdprep MECPprep MECPopt mp2prep Numforce outp past raman screwer scanprep vibration 27 prepares for Localized Hartree Fock calculations by adjusting param eters of the control file converts the file logging an MD trajectory into coordinates in frames appropriate for jmol animation program extracts the energy data KE total energy PE from an MD log file computes the radius of gyration geometric radius and diameter from an MD log file interactive program to prepare for an MD run checking in particular the mdmaster file mdprep is actually a FORTRAN program prepares the input for minimum energy crossing point calculations The subdirectories state1 and state2 will be created Multiplicity and charge for the two states can be set For further details call MECPprep h driver for geometry optimizations of minimum energy crossing points The electronic structure calculations are carried out in the subdirec tories state1 and state2 and the optimizer step is performed in the starting directory
396. no first order properties are implemented for CIS in the ricc2 program Orbital unrelaxed first order properties The unrelaxed first order properties are calculated from the variational excited states Lagrangian 129 which for the calculation of unrelaxed properties is composed of the unrelaxed ground state Lagrangian Eq 10 12 and the expression for the excitation energy L CC ex Et p FIECO Y B Ay t B E 10 18 pV Y EA al H THF M1 SH ug H Fo BV T HF H2 where it is assumed that the left and right eigenvectors are normalized such that oy E ult Ey 1 and H Ho BV The first order properties are calculated as first derivatives of L CO amp E E t plex B with respect to the field strength 6 and are evaluated via a density formalism ur ex OLU E t plen p ur ex Vj r 3B 5 D Vog 1019 0 Pq 10 3 FIRST ORDER PROPERTIES AND GRADIENTS 197 Again R indicates that the real part is taken The unrelaxed excited state proper ties obtained thereby are related in the same way to the total energy of the excited states as the unrelaxed ground state properties to the energy of the ground state and the differences between excited and ground state unrelaxed properties are identical to those identified from the second residues of the quadratic response function For a detailed description of the theory see refs 128 129 the algorithms for the RI CC2 implementation are d
397. ns and only minor extra disk space The implementation of the excited state gradients for the RI CC2 approach is described in detail in Ref 14 There one can also find some information about the performance of CC2 for structures and vibrational frequencies of excited states For the calculation of an excited state gradient with CC2 at a single point without geometry optimization and if it is not a calculation with NumForce one can use the input ricc2 cc2 excitations irrep al nexc 2 xgrad states al 2 Note that presently it is not possible to compute gradients for more than one excited state in one ricc2 calculation For geometry optimizations or a numerical calculation of the Hessian with NumForce the wavefunction model and the excited state for which the geometry should be optimized have to be specified in the data group ricc2 with the keyword geoopt ricc2 geoopt model cc2 state al 2 10 3 FIRST ORDER PROPERTIES AND GRADIENTS 199 excitations irrep al nexc 2 If the geometry optimization should carried out for the lowest excited state of those for which an excitation energy is requested in excitation one can use alternatively state s1 Since the calculation of unrelaxed and relaxed first order properties can be combined gradient calculations without significant extra costs a request for excited state gra dients will automatically enforce the calculation of the relaxed and unrelaxed dipole moments If
398. ns for a dielectric in order to obtain the screening charges COSMO instead uses the much simpler boundary condition of vanishing electrostatic potential for a conductor g 0 This represents an electrostatically ideal solvent with oo The vector of the total electrostatic potential on the cavity surface segments is determined by the solute potential which consist of the electronic and the nuclear part and the vector of the screening charges q pict ps as Aq 0 A is the Coulomb matrix of the screening charge interactions For a conductor the boundary condition amp 0 defines the screening charges as q A l sel To take into account the finite permittivity of real solvents the screening charges are scaled by a factor e 1l f e pl q f e jq 264 265 The deviation between the COSMO approximation and the exact solution is rather small For strong dielectrics like water it is less than 1 while for non polar sol vents with 2 it may reach 10 of the total screening effects However for weak dielectrics screening effects are small and the absolute error therefore typically amounts to less than one kcal mol The dielectric energy i e the free electrostatic energy gained by the solvation process is half of the solute solvent interaction energy 1 Ediel LOI ee The total free energy of the solvated molecule is the sum of the energy of the isolated system calculated with the sol
399. nternal coordinates from your list their status is changed from k or f to d If B is only near singular a warning is issued and the lowest eigenvalue s as well as the corresponding eigenvector s are displayed In this case you should try to find better internal coordinates although this may not always be possible After the command imet there may be too few active plus fixed internal coordinates but certainly not too many because linear dependencies have been eliminated Perhaps you will have to add new ones or better try command iaut or ired in the preceding menu Command imet should be used always after creating internal coordinates with iaut or idef especially after iaut because this command creates usually an overcomplete set of internal coordinates idef idef unfolds a little submenu where you can define internal coordinates manually The exact procedure of the definition will be described below in a separate section 4 1 THE GEOMETRY MAIN MENU 57 ideg a jaut iman a icir irem i This command gives you the number of symmetry restricted degrees of freedom for the atomic set specified by a Without symmetry this is just 3N 6 where N is the number of atoms but if there is symmetry some of these degrees of freedom will violate symmetry and therefore are not valid For geometry optimizations only the symmetry allowed degrees of freedom are needed because the symmetry requirements are imposed anyw
400. nts globgrad global scale factor and its gradient hessian the force constant matrix in the space of cartesian coordinates 3 Output data from program relax coord cartesian atomic coordinates basis exponents and scale factors global global scale factor For structure optimizations the use of redundant internal coordinates is recom mended see Section 4 0 6 Normally internal coordinates are not used for input or output by the electronic structure programs dscf mpgrad etc Instead the coor dinates gradients etc are automatically converted to internal coordinates by relax on input and the updated positions of the nuclei are written in cartesians coordinates to the data group coord Details are explained in the following sections 5 3 3 Force Constant Update Algorithms In a Newton type geometry update procedure often only a crude approximation to the force constant matrix H is available What can be done then is to update F H in each iteration using information about previous coordinates and gradients This constitutes the quasi Newton or variable metric methods of which there are a few variants 5 3 PROGRAM RELAX 105 1 Murtagh Sargent MS es Ages k _ pk 1 F F 5 Zk 1 tdGk l 2 Broyden Fletcher Goldfarb Shanno BFGS S dq 1 idg 1 dq 1 dG A pk 1_ pk ldGk l dq INi S1 PR pki 3 Davidon Fletcher Powell DFP dq tdqk 1 FR ldaGk gt dGr A pk 1 FE pk
401. nts the explicitely correlated double excita tions are neglected for the calculation of the triples corrections 207 208 CHAPTER 11 CCSD CCSD F12 AND CCSD T Prerequisites MP3 MP4 CCSD and CCSD T calculations with the ricc2 module require the same prerequisites as RI CC2 calculations ale 5 a converged SCF calculation with the one electron density threshold set to denconv 1 d 5 or less an auxiliary basis defined in the data group cbas if orbitals should be excluded from the correlation treatment the data group freeze has to be set the maximum core memory which the program is allowed to allocate should be defined in the data group maxcor the recommended value is 66 75 of the available physical core memory the data group ricc2 with a specification of the coupled cluster model Calculations with the CCSD F12 and CCSD F12 methods require in addition e the data group rir12 with the definition of the standard approximations for the explicitly correlated contributions see Sec 9 5 for details e the data group 1cg which define the correlation function here it is in par ticular important to choose for F12 calculations the exponent recommended values are 0 9 for cc pVDZ F12 1 0 for cc pVTZ F12 and 1 1 for cc pVQZ F12 basis sets e a complementary auxiliary CABS basis set Furthermore it is recommeded to select in addition an auxiliary JK basis set for the evaluation of the Fock
402. number of loops or passes over occupied orbitals n performed in the mpgrad run the more passes the smaller file space requirements but CPU time will go up mointunit type intermed unit 61 type 1111 type 1112 type 1122 type 1212 type 1212a type gamma 1 type gamma 2 type 1212u type 1112u unit 62 unit 63 unit 64 unit 65 unit 70 unit 71 unit 72 unit 73 unit 74 type gamma iu unit 75 size 0 size 0 size 0 size 0 size 0 size 0 size 0 size 0 size 0 size 0 size 0 The data group mointunit specifies e which scratch files are needed e where they are located path name and file halfint file moint 0 file moint 1 file moint file moint k file moint a file gamma 1 file gamma 2 file moint u file moint v file gamma iu e after a statistics run see below an estimated file size statistics mpgrad statistics run estimation of disc space needed for the adjustment of the file sizes will be performed MPGRAD Optional Keywords mp2pair calculation of MP2 pair correlation energies 20 2 FORMAT OF KEYWORDS AND COMMENTS 325 Rimp2 Essential Keywords Apart from keywords maxcor mp2energy and freeze see above rimp2 also needs cbas file auxbasis cross reference for the file specifying the auxiliary basis as referenced in atoms We strongly recommend using auxbasis sets optimized for the corresponding MO basis sets Reasonable settings for these keywords may be
403. o achieve better convergence of the geometry optimization The use of linear com binations rather than primitive coordinates is especially recommended for rings and cages see ref 24 Command iaut uses linear combina tions in most cases After you entered k comp n where n is the number of primitive internal coordinates to be combined you will be asked to enter the type of the coordinate stre bend Then you will have to enter the weight the coefficient of this primitive coordinate in the linear combination and the atomic indices which define each coordinate The definition of the prim itive coordinates is the same as described above for the corresponding coordinate types It is not possible to combine internal coordinates of different types This type helps you to define special ring coordinates You only have to enter k ring n where n is the ring size Then you will be asked for the atomic indices of all atoms which constitute the ring and which must be entered in the same order as they appear in the ring The maximum number of atoms in the ring is 69 but in most cases the ring size will be limited by the maximum number of atoms which is allowed for define Hitting lt return gt will bring you back to the internal coordinate menu where you can see the new number of internal coordinates in the headline 60 CHAPTER 4 PREPARING YOUR INPUT FILE WITH DEFINE 4 1 3 Manipulating the Geometry Note that the molecular geometry can
404. o be called with the cosmo option If no solvent refractive index refind REAL is given in the cosmo section of the control file the program uses the default 1 3 Cosmo in vertical excitations and polarizabilities COSMO is implemented in escf and will be switched on automatically by the COsMo keywords of the underlying SCF calculation The refractive index used for the fast term screening of the vertical excitations needs to be defined in the cosmo section of control file refind REAL DCCOSMO RS The DCOSMO RS model see chapter 19 has been implemented for restricted and unrestricted DFT and HF energy calculations and gradients pro grams dscf ridft and grad rdgrad In addition to the COSMO settings defined at the beginning of this section the dcosmo_rs keyword has to be set 312 CHAPTER 20 KEYWORDS IN THE CONTROL FILE dcosmo_rs file filename pot activates the DCOSMO RS method The file defined in this option con tains the DCOSMO RS o potential and related data examples can be found in the defaut potentials in the TURBODIR parameter directory If the potential file cannot be found in the local directory of the calculation it will be searched in the TURBODIR parameter directory The following o potential files for pure solvents at 25 C are implemented in the current TURBOMOLE distribution see parameter subdirectory Water h20_25 pot Ethanol ethanol_25 pot Methanol methanol_25 pot Tetrahydrofurane thf_25 po
405. o get more accurate re sults Default is that the derivatives of quadrature weights will be not considered see section 20 2 9 on page 307 gridordering Grid points are ordered into batches of neighbouring points This in creases efficiency since now zeros can be skipped for entire batches gridordering is default for serial version not for the parallel one You cannot use weight derivatives and gridordering together Example for switching off gridordering dft gridordering 0 electrostatic field Specification of external electrostatic field s The specification may take place either by Ex Ey Ez or by x y z E See also fldopt Example electrostatic field 0 1000E 03 0 000 0 000 fermi tmstrt lt 300 0 gt tmend lt 100 0 gt tmfac lt 0 9 gt hlcrt lt 1 0E 01 gt stop lt 1 0E 03 gt nue lt N gt Requests calculation of occupation numbers at a finite temperature T For an orbital with the energy the occupation number n 0 1 is calculated as nj 2e A 2 fT where u is the Fermi level The factor f 4k 7 is chosen to yield the same slope at the Fermi level as the Fermi distribution Calculation of the fractional occupation numbers starts when the current HOMO LUMO gap drops below the value given by hlcrit default 0 1 The initial 288 CHAPTER 20 KEYWORDS IN THE CONTROL FILE temperature given by tmstrt default 300K is reduced at each SCF cycle by the factor tmfac default 1 0 unt
406. o molecular dynamics MD can be carried out on the ground and excited state Born Oppenheimer potential hypersurface In addition non adiabatic Tully type Surface Hopping MD can be performed using TDDFT At the start of an MD run the user must specify the initial atomic positions and velocities and give some 5 5 MOLECULAR DYNAMICS CALCULATIONS 115 general instructions for the run This is managed by running the interactive pro gram Mdprep and generating the command file mdmaster If this is successful the MD run itself may be started jobex md Time is then advanced in steps The electronic potential energy and its gradients are calculated quantum mechanically at the required coordinates each timestep as detailed above e g dscf and grad The MD program frog uses the Leapfrog Verlet algorithm 44 to turn the gradients into new atomic positions and velocities The atoms thus undergo classical Newtonian dynamics on the ab initio potential hypersurface Trajectory information is recorded in a log file mdlog It is possible to instruct frog to heat or cool the system use a thermostat for canonical dynamics conserve total energy or read in new positions or velocities the appropriate keywords are described in Section 20 2 22 below 116 CHAPTER 5 STRUCTURE OPTIMIZATIONS 5 6 Counterpoise Corrections using the JOBBSSE Script The shell script jobbsse controls and executes the automatic calculation of the counterpoise correction as it has been
407. occupation numbers menu but will terminate the whole occupation number and start vector section and will bring you to the last main menu which is described in Section 4 4 If you want to leave this menu without assigning all electrons in your molecule to shells define will issue a warning and suggest to continue defining occupation numbers You can ignore this warning if you do not want to assign all electrons e Calculates and displays the extended Hiickel total energy of your molecule f f will give you some information about the commands in this menu You may overwrite occupation numbers once given by just redefining the correspond ing shell For example if you choose shells 1 10 as closed shells and afterwards shell no 9 as open shell with any occupation number the open shell will be correctly assigned 4 3 3 Orbital Specification Menu define provides the possibility to assign the occupation numbers of the MOs man ually if you like To do that use the command man in the occupation number main menu and you will arrive at the following submenu lt label gt lt list gt select orbitals within lt list gt lt label gt lt list gt skip orbitals within lt list gt amp ignore input for last label clear clear all assignments p rint print actual orbital selection for help type or help for quit type or q uit Depending on whether you are in the closed or in the open shell section the com mands of t
408. of these keywords see Section 20 2 6 cbas file auxbasis Auxiliary basis set for RI approximation For details Section 20 2 16 freeze Freeze orbitals in the calculation of correlation and excitation energies For details see Section 20 2 16 printlevel 1 Print level The default value is 1 tmpdir work thisjob Specify a directory for large intermediate files typically three index coulomb integrals and similar intermediates which is different from the directory where the ricc2 program is started maxcor 20 The data group maxcor adjusts the maximum size of core memory in MB which will be allocated during the RI CC2 run This keyword can be set in define or with the Rimp2prep tool the default is 20 MB maxcor has a large influence on computation times for RI CC2 runs It is recommended to set maxcor to ca 75 85 of the available physical core memory spectrum unit The calculated excitation energies and corresponding oscillator strengths are appended to a file named spectrum Possible values of unit are eV nm and 1 cm or rem If no unit is specified excitation energies are given in a u cdspectrum unit The calculated excitation energies and corresponding rotatory strengths are appended to a file named cdspectrum unit can have the same values as in spectrum laplace conv 5 20 2 FORMAT OF KEYWORDS AND COMMENTS 327 The purpose of this data group is twofold It activates the Lap
409. of the cluster equations As mentioned above it has some impact on the amount of disc space used by a CCSD calculation Unless disc space becomes a bottleneck it is not recommended to change the default value With maxiter one defines the maximum number of iterations for the solution of the cluster equations If convergence is not reached within this limit the calculation is stopped Usually 25 iterations should be sufficient for convergence Only in difficult cases with strong correlation effects more iterations are needed It is recommended to increase this limit only if the reason for the strong correlation effects is known Since one reason could also be an input error as e g unreasonable geometries or orbital occupations as a wrong basis set assignment The two parameters conv and oconv define the convergence thresholds for the iter ative solution of the cluster equations Convergence is assumed if the change in the energy with respect to the previous iteration has is smaller than 10 Y and the euclidian norm of the residual the so called vector function is smaller than 107 If conv is not given in the data group ricc2 the threshold for changes in the energy is set to value given in denconv by default 1077 If oconv is not given in the data group ricc2 the threshold for the residual norm is by default set to 10 times the threshold changes in the energy With the default settings for these thresholds the energy will thu
410. off optimize molecular structures in redundant internal coordinates using definitions of redundant internal coordinates given in redundant For an optimization in redundant internal coordinates option internal has to be switched on too and option cartesian has to be switched off default on cartesian on off optimize molecular structures in the space of symmetry distinct carte sian coordinates default off basis on off suboptions optimize basis set exponents default of f Available suboptions are logarithm exponents of uncontracted basis functions will be optimized after conversion into their logarithms this improves the condition of the approximate force constant matrix obtained by variable metric methods and the behavior of the optimization procedure scale factors of contracted basis functions will not be affected by the logarithm suboption scale ALL basis set exponents will be optimized as scale factors i e contracted blocks and single functions will be treated in the same 340 CHAPTER 20 KEYWORDS IN THE CONTROL FILE way if both suboptions scale and logarithm are given the loga rithms of the scale factors will be optimized global on off optimize a global scaling factor for all basis set exponents default off NOTES basis and global have to be used exclusively e if optimize has been specified but forceapprox is absent the option forceinit on is switched on by default e specifi
411. ol file Note that unlike in the TURBOMOLE definition of internal coordinates the apex atom is the second optimize auxiliary basis sets for RI MP2 and RI CC2 calculations Uses ricc2 to calculate the error functional and its gradient and relax as optimization module For further details call cbasopt h manages macro iterations for RI MP2 RI CC2 or RI ADC 2 calcula tions in an equilibriated solvent environment described by cosmo see Chapter 19 plots energies as a function of SCF iteration number gnuplot re quired sets up control file for a cosmo run see Chapter 19 example dist 1 2 calculates atomic distances from TURBOMOLE input files dist 1 4 gives all interatomic distances to 4 a u 5 a u is the default automates dynamic reaction coordinate calculations forward and back ward along the imaginary vibrational mode of a transition state struc ture A transition state optimization with a subsequent frequency calculation is prerequisite For further details call DRC h displays orbital eigenvalues obtained from data group scfmo Shows HOMO LUMO gap occupation checks if there are holes in the occu pation and much more reads the gradient file and prints the energies of each cycle versus bond lengths or angles Five operational modes are possible evalgrad prints the energy evalgrad 1 prints the coordinate of atom 1 evalgrad 1 2 prints the distance between atoms 1 and 2 evalgrad 1 2 3 prints the bending a
412. ol file the old control file will be saved in control hf and the molecular orbitals in mos hf or in alpha hf and beta hf for the spin unrestricted case See lhfprep help for options Actually LHF can be started from any guessed orbitals but if HF orbitals are used a much faster convergence is expected By default the script lhfprep will add modify the control file with dft functional lhf gridtype 6 gridsize 3 radsize 3 lhf off diag on num slater off asymptotic dynamic 1 d 3 conj grad conv 1 d 6 maxit 20 output 1 asy 1 slater dtresh 1 d 9 slater region 7 0 0 5 10 0 0 5 corrct region 10 0 0 5 scfdump scfiterlimit 30 scfconv 6 scfdamp start 0 000 step 0 500 min 0 50 scforbitalshift noautomatic correction matrix elements file lhfcg correction alpha matrix elements file lhfcg_alpha correction beta matrix elements file lhfcg_beta 3 Run odft With the LHF potential Rydberg series of virtual orbitals can be obtained To that end diffuse orbital basis sets have to be used and special grids are required gridtype 4 is the most diffuse with special radial scaling gridtype 5 is for very good Rydberg orbitals gridtype 6 default in Lhfprep is the least diffuse only for the first Rydberg orbitals Only gridsize 3 5 can be used no modified grids Use test integ to check if the selected grid is accurate enough for the employed basis set see page 295 262 CHAPTER 18 ORBITAL DEPENDENT DFT The options in
413. ollowed by a comma seperated pair of operators If more pairs are needed they have to be given with additional sop commands Default is to compute all symmetry allowed elements of the dipole dipole polarizability With the freq flag on can specify a frequency default is to compute static po larizabilities The relaxed flag switched from the unrelaxed approach which is used by default to the orbital relaxed approach Note that the orbital relaxed approach can not only be used in the static limit freq 0 0d0 For further restrictions for the computation of second order properties check Chapter 10 5 ent require calculation of geometric gradients In difference to the geoopt 336 conv ZConv CHAPTER 20 KEYWORDS IN THE CONTROL FILE keyword in the data group ricc2 this can be used to compute gradients for several methods within a loop over models but gradients and energies will not be written to the data groups grad and energy as needed for geometry optimizations Note that in the present version gradients are only available for MP2 and CC2 and only for a closed shell RHF reference convergence threshold for norm of residual vectors in linear response equations is set to 107 If not given in the response data group a default value is used which is chosen as max 10 107 2 1076 where conv and oconv refer to the values given in the data group ricc2 convergence threshold for the norm of th
414. ometry opti mization is intended For this model the gradient will be calculated and the energy and gradient will be written onto the data groups energy and grad Required for geometry optimizations using the jobex script Note that in the present version gradients are only available for ground states at the MP2 and CC2 and for excited states at the CC2 level and not for ROHF based open shell calculations Not set by default The default model is CC2 the default electronic state the ground state To obtain gradients for the lowest excited state of those included in the 330 CHAPTER 20 KEYWORDS IN THE CONTROL FILE excitation energy calculation but else of arbitrary multiplicity and sym metry the short cut s1 can be used x is treated as synonym for the ground state scs the opposite spin scaling factor cos and the same spin scaling factor css can be chosen If scs is set without further input the SCS parameters cos 6 5 and css 1 3 are applied This keyword can presently only be used in connection with MP2 sos the SOS parameters cos 1 3 and css 0 0 are applied This keyword can presently only be used in connection with MP2 didiag request the calculation of the D diagnostic for the ground state wave function Only needed for MP2 see above for the alternative input option mp2 didiag For all other correlated methods the D diagnostic is evaluated by default without significant extra costs intcorr calculates the second order c
415. omparison with the reference For every output file used for testing the validate option produces a copy with an additional val extension The match strings evaluated for test criteria are highlighted in the output by lt and gt gt gt marks There is a lot of options controlling the behavior of TTESTTesting specific versions of TTURBOMOLE modules is provided by loading path options 1 for binaries 1s for scripts and x for a specific executable For benchmarking you need the timings option to produce the timing summaries and the newref option to save the current program timings as the new reference The module specifications and short long and r options can be used for selecting the test examples The more specialized options are summarized in the following table Note that most of these options can also be set in the DEFCRIT file see below Operation modes help h list clean realclean check dir validate dir val dir 22 4 MODES AND OPTIONS OF THE TTEST SCRIPT 403 Prints out the help message and exits Lists the available test examples Deletes the test directories and summary files for the current architecture given by SYSNAME see Chapter 1 5 Deletes all test directories and protocols Checks the correctness of an existing program test in the directory dir default TESTDIR sysname Useful if new criteria or new references are established Examines the output files in t
416. omplementary auxiliary basis set CABS The single excitations into the CABS basis can be computed without extra costs if the CABS Fock matrix elements are required anyway for the F12 cal culation i e for ansatz 2 approximation B or comaprox F K The computation of CABS singles cannot be switched off if it is free of costs 178 CHAPTER 9 2ND ORDER M OLLER PLESSET PERTURB THEORY pairenergy controls whether or not the F12 contribution to the MP2 pair energies appear in the output default off Further options corrfac LCG refers to a further data group for the definition of the correlation factor When define is used the default is 1lcg nlcg 6 slater 1 4000 The nature of the LCG correlation factor may be changed by editing this data group in the control file For example to use a Slater type correlation factor with exponent 1 0 ag 1 represented as a linear combination of three Gaussians use 1lcg nlcg 3 slater 1 0000 Alternatively the exponents and coefficients of the fit may be given explicitly 1lcg nlcg 3 expol coefl expo2 coef2 expo3 coef3 MP2 F12 calculations may be combined with Grimme s SCS approach S Grimme J Chem Phys 118 2003 9095 by inserting scs in ricc2 ricc2 mp2 energy only SCS In this case the SCS parameters cos 6 5 and css 1 3 are used Also individual scaling factors for the same spin and opposite spin contributions may be defined see Section 10 7 For open shell c
417. omplete diagrammatic equations J Chem Phys 129 071101 2008 A K hn G W Richings D P Tew Implementation of the full explicitly correlated coupled cluster singles and doubles model CCSD F 12 with optimally reduced auxiliary basis dependence J Chem Phys 129 201103 2008 C Hattig D P Tew A K hn Accurate and efficient approximations to explicitly correlated coupled cluster singles and doubles CCSD F12 J Chem Phys 132 231102 2010 T B Adler G Knizia H J Werner J Chem Phys 127 221106 2007 G Knizia T B Adler H J Werner J Chem Phys 130 054104 2009 M Torheyden E F Valeev Phys Chem Chem Phys 10 3410 2008 E F Valeev D Crawford J Chem Phys 128 244113 2008 K D Vogiatzis E C Barnes W Klopper Interference corrected explicitly correlated second order perturbation theory Chem Phys Lett 503 1 3 157 161 2011 H Eshuis J Yarkony F Furche Fast computation of molecular random phase approximation correlation energies using resolution of the identity and imaginary frequency integration J Chem Phys 132 234114 2010 H Eshuis J E Bates F Furche Electron correlation methods based on the random phase approximation Theor Chem Acc 131 1084 2012 A M Burow J E Bates F Furche H Eshuis Analytical first order molecular properties and forces within the adiabatic connection random phase approxi mation J Chem
418. ompleted so far To get a display of energies and gradients use the UNIX command grep cycle gradient which yields e g H20 cycle 1 SCF energy 76 3432480651 dE dxyz 0 124274 cycle 2 SCF energy 76 3575482860 dE dxyz 0 082663 cycle 3 SCF energy 76 3626983371 dE dxyz 0 033998 cycle 4 SCF energy 76 3633251080 dE dxyz 0 016404 cycle 5 SCF energy 76 3634291559 dE dxyz 0 010640 cycle 6 SCF energy 76 3634910117 dE dxyz 0 000730 This should be self evident To see the current or if the optimization is con verged the final atomic distances use the tool dist Bond angles torsional an gles etc are obtained with the tools bend tors outp etc In the file gradient are the collected cartesian coordinates and corresponding gradients of all cycles The values of the general coordinates and corresponding gradients are an output of relax written to job lt cycle gt of job last within jobex To look at this search for Optimization statistics in job last or job lt cycle gt 5 4 Force Field Calculations 5 4 1 Purpose uff preoptimizes a structure and calculates an analytical Hessian which can be used as a start Hessian in a geometry optimization This will accelerate the convergence 112 CHAPTER 5 STRUCTURE OPTIMIZATIONS of an optimizations For optimizations in cartesian space this will be faster by a factor of two for any molecule 5 4 2 How to Perform a UFF Calculation You have
419. omputed and written to the data group scfintunit size integer see Section 20 2 6 The requirement of other combinations will be computed as well and be written to the output file dscf stat The size of the integral file can be set by the user to an arbitrary but reasonable number The file will be written until it reaches the given size and dscf_ will continue in direct mode for the remaining integrals Note that TURBOMOLE has no 2GB file size limit MP2 calculations need well converged SCF runs the SCF run has to be done with at least the density convergence denconv 1 d 7 and scfconv 7 as described in Section 20 This applies also to CC2 the spin component scaled variants of MP2 and CC2 and other post HF methods For MP2 calculations in the RI approximation use the ricc2 module The input can be prepared with the cc2 menu in define Alternatively the older rimp2 module and for preparation of its input the tool rimp2prep maybe used The module mpgrad calculates the canonical non RI MP2 energy as well as the energy gradient If only the energy is desired use the keyword mp2energy For all further preparations run the tool mp2prep Excited states with CIS TDHF and TDDFT escf Single point excited state energies for CIS TDHF and TDDFT methods can be calculated using escf Excited state energies gradients and other first order properties are provided by egrad Both modules require well converged ground state orbitals Excited s
420. oms pople char RHF This data group specifies the number of Cartesian components of basis func tions i e 5d and 7f in AO Basis 6d and 10f in CAO Basis for which the SCF calculation should be performed Possible values for char are AO default or CAO If CAO is used which is not recommended a core guess must be used instead of a Hiickel guess see scfmo closed shells Specification of MO occupation for RHF e g alg 1 4 2 a2g 1 2 open shells type 1 MO occupation of open shells and number of open shells type 1 here means that there is only a single open shell consisting e g of two MOs b2g 1 1 b3g 1 1 roothaan 1 a 1 b i N 20 2 FORMAT OF KEYWORDS AND COMMENTS 275 roothaan Roothaan parameters for the open shell here a triplet case define recognizes most cases and suggests good Roothaan parameters For further information on ROHF calculations see the sample input in Sec tion 21 6 and the tables of Roothaan parameters in Section 6 3 UHF uhf directs the program to carry out a UHF run e g alpha shells alg 1 4 1 a2g 1 1 beta shells aig 1 4 1 a2g 1 1 The specification of MO occupation for UHF uhf overwrites closed shell oc cupation specification 20 2 3 Keywords for redundant internal coordinates in redund_inp With the parameters in redund_inp the generation of redundant internal coordi nates can be modified All entries have to be made in the control f
421. on interaction singles CIS excitation energies are identical to the CCS excitation energies The operation count for a RI CIS calculation is O ON N per iteration and transformed trial vector The second order perturbative correction CIS D to the CIS excitation energies is calculated from the expression wS p CIS 4 y BOIS Aeff MP1 CIS ACIS 10 11 Note that t are the first order double substitution amplitudes from which also the MP2 ground state energy is calculated the first order single substitution am plitudes vanish for a Hartree Fock reference due to the Brillouin theorem The operation count for a RI CIS D calculation is similar to that of a single iteration for the CC2 eigenvalue problem Also disk space requirements are similar 10 2 CALCULATION OF EXCITATION ENERGIES 191 Running excitation energy calculations The calculation of excitation ener gies is initiated by the data group excitations in which at least the symmetries irreducible representations and the number of the excited states must be given for other options see Section 20 2 17 With the following input the ricc2 program will calculate the lowest two roots states for the symmetries A and B of singlet mul tiplicity at the CIS CIS D and CC2 level with default convergence thresholds Ground state calculations will be carried out for MP2 needed for the CIS D model and used as start guess for CC2 and CC2 ricc2 cis cis d cc2 excit
422. onal Spectra Calculation of second derivatives of total energies leads to the molecular Hessian which enables prediction of vibrational frequencies and infrared spectra within the harmonic approximation as well as the application of improved algorithms for ge ometry optimization and transition state search The aoforce module calculates analytically harmonic vibrational frequencies with in the HF or RI DFT methods for closed shell and spin unrestricted open shell systems Broken occupation numbers would lead to results without any physical meaning Note that RI is only used partially which means that the resulting Hessian is only a very good approximation to exact second derivatives of the RIDFT energy expression Apart from a standard force constant calculation which predicts all symmetry allowed and forbidden vibrational transitions it is also possible to specify certain irreps for which the calculation has to be done exclusively or to select only a small number of lowest eigenvalues and eigenvectors that are generated at reduced computational cost Furthermore the Numforce script allows the calculation of second derivatives for all methods for which a program for analytic gradients is available in TURBOMOLE i e the main use of this script is the prediction of vibrational spectra at the MP2 level and for excited states using RI CC2 or TDDFT If force constant calculations result in imaginary frequencies molecular distorti
423. ons along these normal modes should lower the energy To distort the molecule use the interactive module vibration output of the new coordinates is done to the general input file on newcoord Vibrational frequencies also enable calculation of the molecular partition function and thus prediction of thermodynamic functions at temperatures other than 0 K 224 225 and finite pressure within the assumption of an ideal gas and no coupling between degrees of freedom These functions can be obtained with the interactive module Freeh results are printed to standard I O Prerequisites 1 Both aoforce and even more Numforce require well converged SCF DFT calculations e g scfconv 8 and jobex ri gcart 4 2 The maximum core memory the program aoforce is allowed to allocate should be defined in the data group maxcor the recommended value is about 50 of the available physical core memory in case of RI calculations subtract the memory specified in ricore 3 To start aoforce in the lowest eigenvalue search mode use the keyword 1les For its use as well as other keywords dealing with the calculation of only some irreps see the Referenceguide part of this manual 4 Numforce additionally requires the file gradient and will not work if the calculation is not done at a stationary point of the molecular total energy For reliable results always use Numforce with the option central i e central differences and be aware of eff
424. ons is given at the end of the 270 CHAPTER 19 TREATMENT OF SOLVATION EFFECTS WITH COSMO ricc2 output Chapter 20 Keywords in the control file 20 1 Introduction The file control is the input file for TURBOMOLE which directly or by cross references provides the information necessary for all kinds of runs and tasks control is usu ally generated by define the input generator This chapter provides a short hand documentation a list of the most important key words the possible parameters for each keyword default values and a brief explanation 20 2 Format of Keywords and Comments TURBOMOLE input is keyword directed Keywords start with a e g title Com ments may be given after dummy or by a line starting with these lines are ignored by TURBOMOLE Blank lines are also ignored Keywords may be in any order unless stated otherwise below The sample inputs given below should help to give an idea how the keywords are to be used They are sorted according to program Complete control files are provided in Chapter 21 An alphabetical list of all keywords is given in the index 20 2 1 General Keywords operating system unix path lock off suspend off 271 272 CHAPTER 20 KEYWORDS IN THE CONTROL FILE The four keywords above are set by define but are not necessary statistics dscf or statistics mpgrad Only a statistics run will be performed to determine file space requirements as specified for dscf o
425. op states all operators qudlen xgrad states ag 3 1 conv 6 thrdiis 2 preopt 3 leftopt bothsides oldnorm In this data group you have to give additional input for calculations on excited states irrep the irreducible representation multiplicity spin multiplicity 1 for singlet 3 for triplet default singlet not needed for UHF nexc the number of excited states to be calculated within this irrep and for this multiplicity npre the number of roots used in preoptimization steps default npre nexc nstart the number of start vectors generated or read from file default nstart npre spectrum This flag switches on the calculation of oscillator strengths for excited state ground state transitions Setting the parameter states all is mandatory for the calculation of transition properties in the present ver sion The operators flag can be followed by a list of operators see below for which the transition properties will be calculated Default is to compute the oscillator strengths for all components of the dipole operator 334 CHAPTER 20 KEYWORDS IN THE CONTROL FILE tmexc This flag switches on the calculation of oscillator strengths for excited state excited state transitions Specifying the initial and final states via istates all and fstates all is mandatory for the calculation of transition properties in the present version The operators flag can be followed by a list of operators see below fo
426. opping has to be added to the control and mdmaster file In addition several keywords are required in the control file nacme needed to compute non adiabatic couplings this keyword requires the use of weight derivatives in section dft nac keyword needed to collect Cartesian non adiabatic coupling vectors along the trajectory exopt 1 keyword needed to ensure dynamics starting in S ex_energies file ex_energies collects excitation energies along the trajectory integral_ex file integral_ex collects time integration of excitation energies along the trajectory sh_coeffs file sh_coeffs collects amplitudes of the adiabatic states along the trajectory nac_matrix file nac_matrix collects NAC elements along the trajectory Special caution has to be taken to control problems related to conical intersec tions 199 200 At geometries where conical intersections between the ground and excited state are present DFT often exhibits singlet instabilities which leads to imaginary excitation energies in linear response TDDF T in this case the MD run is terminated This problem can be circumvented by the use of the Tamm Dancoff approximation TDA to TDDFT see 7 In addition an optional keyword for the md_ master file can be used gap_threshold lt real gt enforces a switch to the ground state in case the 5 Sg energy gap drops below lt real gt eV As default a switch to Sg is enforced if the S TDDFT TDA exci
427. or RIDFT method is chosen according to the dft or ridft keywords specified above It is recommended to use well converged orbitals specifying scfconv 7 and denconv id 7 for the ground state 318 CHAPTER 20 KEYWORDS IN THE CONTROL FILE calculation The input for an escf calculation can be conveniently generated using the ex menu in define see Section 4 In an escf run one of the following properties can be calculated please note the or in the text do only one thing at a time 1 RPA and time dependent DFT singlet or triplet or spin unrestricted excitation energies HF RI DFT scfinstab rpas or scfinstab rpat or scfinstab urpa 2 TDA for HF CI singles singlet or triplet or spin unrestricted or spin flip exci tation energies HF RI DFT scfinstab ciss or scfinstab cist or scfinstab ucis or scfinstab spinflip 3 Two component TDDFT excitation energies of Kramers restricted closed shell systems scfinstab soghf 4 Eigenvalues of singlet or triplet or non real stability matrices HF RI DFT RHE scfinstab singlet or scfinstab triplet or scfinstab non real 5 Static polarizability and rotatory dispersion tensors HF RI DFT RHF UHF scfinstab polly 20 2 FORMAT OF KEYWORDS AND COMMENTS 319 6 Dynamic polarizability and rotatory dispersion tensors HF RI DFT RHF UHF scfinstab dynpol unit list of frequencies where unit can be eV nm rcm default is a u Hart
428. or reasons of economy a pre optimization by a pure non hybrid DFT functional is reasonable Important For the converged wave function one should check whether the resulting state is really the desired one This can quite reliably be done by a Mulliken popu lation analysis For this purpose add pop to the control file type ridft proper or dscf proper respectively and check the signs of the calculated numbers of unpaired electrons in the output 00 00 74 CHAPTER 4 PREPARING YOUR INPUT FILE WITH DEFINE 4 4 The General Options Menu After you specified all data concerning the molecule you want to examine you are on your way to the last of the four main menus Before reaching it you will perhaps get a message like the following DO YOU WANT TO DELETE DATA GROUPS LIKE energy grad hessian hessian projected last energy change maximum norm of internal gradient dipgrad vibrational normal modes vibrational spectrum cartesianforce interspace LEFT OVER FROM PREVIOUS CALCULATIONS DEFAULT n define has scanned your input file for this session and found some data groups which might have become obsolete If they are still acceptable depends on the changes you made during your present define session They are obviously incorrect if you changed the molecule under consideration but any change in the basis sets or the occupation numbers will make them dangerous too because you might not know some day if they really re
429. orrections to the CCSD T energy from the interference corrected MP2 F12 INT MP2 F12 if rir12 is switched on It can be combined either with the mp2 or the ccsd t meth ods In the latter case the CCSD T INT F12 energy is printed The intcorr all keyword writes on the output all pair energies rir12 ansatz r1i2model comaprox cabs examp ri2orb pairenergy corrfac cabsingles ansatz char char 1 2 or 2 20 2 FORMAT OF KEYWORDS AND COMMENTS 331 The ansatz flag determines which ansatz is used to calculate the RI MP2 F12 ground state energy Ansatz 2 is used if ansatz is absent ri2model char char A A or B The ri2model flag determines which approximation model is used to calculate the RI MP2 F12 ground state energy Ansatz B is used if r12model is absent comaprox char cabs char F K or T V The comaprox flag determines the method used to approximate the com mutator integrals T fi2 Approximation T V is used if comaprox is absent char val char svd or cho The cabs flag determines the method used to orthogonalize the orbitals of the CABS basis val is the threshold below which CABS orbitals are removed from the calculation svd 1 0d 08 is used if cabs is absent examp char char noinv fixed or inv with flip or noflip The examp flag determines which methods are used to determine the F12 amplitudes For inv the amplitudes are optimized using the orbital invariant method For fixed and
430. ory in the GW approximation 8 1 Theoretical background A method to systematically improve upon DFT estimates of single particle excita tion spectra i e ionization potentials and electron affinities is the GW method Its central object is the single particle Green s function G its poles describe single par ticle excitation energies and lifetimes In particular the poles up to the Fermi level correspond to the primary vertical ionization energies The GW approach is based on an exact representation of G in terms of a power series of the screened Coulomb interaction W which is called the Hedin equations The GW equations are obtained as an approximation to the Hedin equations in which the screened Coulomb interac tion W is calculated neglecting so called vertex corrections In this approximation the self energy X which connects the fully interacting Green s function G to a reference non interacting Green s function Go is given by X GW This approach can be used to perturbatively calculate corrections to the Kohn Sham spectrum To this end the Green s function is expressed in a spectral representation as a sum of quasi particle states Gers gt n W t 2 U a r z z En z insgn en u 8 1 Under the approximation that the KS states are already a good approximation to these quasi particle states Y n the leading order correction can be calculated by solving the zeroth order quasi particle equatio
431. ostatic Embedded Cluster Method The Periodic Electrostatic Embedded Cluster Method PEECM functionality pro vides electronic embedding of a finite quantum mechanical cluster in a periodic infinite array of point charges It is implemented within HF and DFT energy and gradient TURBOMOLE modules dscf grad ridft rdgrad and escf Unlike embed ding within a finite set of point charges the PEEC method always yields the correct electrostatic Madelung potential independent of the electrostatic moments of the point charges field It is also significantly faster than the traditional finite point charges embedding The basic PEECM settings are defined in the embed block It can be redirected to an external file using embed file lt file_name gt Following keywords are used for the PEECM calculation setup periodic Specifies the number of periodic directions Allowed values for number are 3 for a bulk three dimensional system 2 for a two dimensional surface slab and 1 for a one dimensional system Default value is 3 cell Unit cell parameters in a form of six real values a b c a 6 y where al b c are lengths of the appropriate cell vectors a is the angle between vectors b and c 6 is the angle between vectors a and c and y is the angle between vectors a and b Default are atomic units and degrees You can specify unit cell parameters in A and degrees using cell ang content label x y z end 306 CHAPTER 20 KEY
432. ou finished the closed shell occupations hcore tells programs dscf and ridft to run without a start vector it writes the data group scfmo none to file control dscf or ridft will then start from the core Hamiltonian start vector which is the vector obtained by diagonalizing the one electron Hamiltonian Note that you still have to specify the occupation numbers This concerns only the first SCF run however as for the following calculations the converged 68 flip CHAPTER 4 PREPARING YOUR INPUT FILE WITH DEFINE vector of the previous iteration will be taken A SCF calculation with a core Hamiltonian start vector typically will take 2 3 iterations more than a calculation with an extended Hiickel start vector a calculation with the converged SCF vector of a previous calculation will need even less iterations depending on how large the difference in the geometry between the two calculations is flipping of spins at a selected atom Requirements converged UHF molecular orbitals and no symmetry C1 definewill localize the or bitals assign them to the atoms and give the user the possibility to choose atoms at which alpha orbitals are moved to beta orbitals or vice versa This is useful for spin broken start orbitals but not for spatial symmetry breaking This command as well as use and eht terminates this menu but with out providing a start vector If the keyword scfmo exists in your input file it will be kept unchanged
433. oup freeze has to be set 4 the maximum core memory which the program is allowed to allocate should be defined in the data group maxcor the recommended value is 66 75 of the available physical core memory 184 CHAPTER 10 RI CC2 5 depending on the type of calculations that should be carried out additionally the data groups ricc2 excitations response laplace rir12 and 1cg have to be set see below and Section 20 2 17 For calculations with the ricc2 program it is recommended to use the cc2 submenu of the define program to set the data groups denconv freeze cbas maxcor MP2 F12 calculations require in addition the data groups rir12 cabs jkbas and lcg The exponent of the Slater function in the interelectronic distance r12 which appears in the geminals used MP2 F 12 is defined in the data group 1cg and should be adapted to the one electron basis set which is used Note that the implementation of non Abelian point groups in ricc2 is limited to the electronic ground state but comprises all of the RI MP2 functionality included in ricc2 In the present version ricc2 can for excited states only deal with real Abelian point groups C1 Cs C2 Ci Can Cay D2 Don The F12 correction can only be calculated in the C4 point group How To Perform a Calculation Single point calculations Call the ricc2 program after a converged SCF calculation which can be carried either with the dscf or the ridft program Geom
434. oups d lt integer gt delete lt integer gt th data group d all delete all data groups off lt integer gt switch off lt integer gt th data group off all switch off all data groups on lt integer gt switch on lt integer gt th data group on all switch on all data groups s scan through data groups quit The commands in this menu serve for the manipulation of data groups grid in an analogous way as described for points in the potential section above grid data groups contain the input information necessary to create the plot data by moloch one data group for each plot If you want to add a new data group you will enter this submenu specify the input orbital input density mo lt label gt use occupied molecular orbital lt label gt mo density use one electron density built from the occupied molecular orbitals lmo lt i gt use localized molecular orbital no lt lmo gt mao lt i gt lt k gt use modified atomic orbital no lt i gt centered on atom no lt k gt help explanation of the syntax for lt label gt quit Here you may specify the orbital to be plotted To plot the amplitude of the fifth orbital in irrep a1 e g you would enter mo 5a1 Equivalently you can use localized orbitals from a Boys localization procedure or modified atomic orbitals as obtained in a Roby Davidson Ahlrichs Heinzmann population analysis In the latter cases you will not have to enter an irrep labe
435. out re calculation of integrals As a rule of thumb m should be ca 90 of the available main memory If RI J is used ridft it is recommended to set ricore to a small value and rpacor to a large value if the number of states is large and vice versa if it is small Since two component calculations are more demanding concerning computation time and required memory it is strongly recommended to increase rpacor By specifying spectrum unit and or cdspectrum unit a list of excitation energies and oscillator and or rotatory strengths of the optically allowed transitions is written onto file spectrum and or cdspectrum As above unit specifies the energy unit and may be ev nm 1 cm or a u default The files spectrum and cdspectrum may conveniently be used for further processing e g using a plotting program such as Gnuplot By specifying curswitchdisengage inclusion of the current density response for MGGA calculations is disabled Note that the results of calculations using this flag will no longer be gauge invariant and will differ from results obtained with the standard gauge invariant implementation 7 4 HOW TO PERFORM 161 7 4 5 Excited State Geometry Optimizations The input for computing excited state gradients and properties using egrad is exactly the same as for an excited state calculation using escf see the previous section Gradients and properties are calculated only for one state at a time By default this i
436. output for the HF dimer FDE Version 1 02 Frozen Density Embedding Main Driver Scf like procedure for closed shell interacting systems dimers program development Savio Laricchia Eduardo Fabiano Fabio Della Sala S Laricchia E Fabiano L A Constantin F Della Sala J Chem Theory Comp 2011 S Laricchia E Fabiano F Della Sala J Chem Phys 133 164111 2010 L A Constantin E Fabiano S Laricchia F Della Sala Phys Rev Lett 106 186406 2011 S Laricchia E Fabiano F Della Sala Chem Phys Lett 518 114 2011 Sun Mar 25 23 00 01 CEST 2012 Monomolecular basis set approach Serial calculation will be performed 17 2 FROZEN DENSITY EMBEDDING CALCULATIONS USING THE FDE SCRIPT247 running home fabiods REDO branch64 TURBOMOLE bin em64t unknown 1linux gnu dscf b lyp exchange correlation potential in KS supermolecular calculation revapbek kinetic energy approximation will be used Default convergence criterion on the system dipole 0 005 Default value of starting damping parameter is 0 45 Default value of step damping parameter is 0 10 Default value of maximum damping parameter is 0 90 Default value of maximum fde iterations is 20 Saving options in fde input Subsystem A atomic coordinates and basis set information x y Zz atom basis set ecp Specie EES RS NO eS fe ee ee ele eke 2 5015 0 1705 0 0000 f def2 TZVP none 3 2889 1 3859 0 0000 h def2 TZVP none ise are
437. parated by at least one blank For a description of the internal coordinate definitions refer to 4 1 2 Entering as first character of file will tell define to take file from the structure library The name following the actually does not need to be a filename in this case but rather a search string referenced in the structure library contents file see Section 4 1 same as a but assumes the atomic coordinates to be in A rather than a u This command allows you to replace one atom in your molecule by an other molecule For example if you have methane and you want to create ethane you could just substitute one hydrogen atom by another methane molecule The only requirement to be met by the substituted atom is that it must have exactly one bond partner The substituting molecule must have an atom at the substituting site in the example above it would not be appropriate to use CH3 instead of CH for substitution Upon substitution two atoms will be deleted and the two ones forming the new bond will be put to a standard distance define will then ask you to specify a dihedral angle between the old and the new unit It is also possible to use a part of your molecule as substituting unit e g if you have some methyl groups in your molecule you can create further ones by substitution Some attention is required for the specification of this substituting unit because you have to specify the atom which will be deleted upon bond
438. pecified coordinate transformation and write the transformed coordinates to file control To achieve this enter on to switch to the transformation only mode and one of the last four options e g crtint to specify the desired transformation Updating the Hessian relax provides a variety of methods to generate an updated Hessian every cycle This includes the well known methods such as BFGS DFP or MS update methods as well as some less common procedures option status description none l F NO UPDATE STEEPEST DESCENT bfgs l F BROYDEN FLETCHER GOLDFARB SHANNO UPDATE dfp l F DAVIDON FLETCHER POWELL UPDATE bfgs dfp F COMBINED BFGS DFP UPDATE ms l F MURTAGH SARGENT UPDATE schlegel F SCHLEGEL UPDATE diagup F DIAGONAL UPDATE AHLRICHS EHRIG multidim F RANK gt 2 BFGS TYPE UPDATE ahlrichs T MACRO AHLRICHS UPDATE DEFAULT USE lt opt gt FOR ENABLING OPTION lt opt gt AND THUS DISABLING ALL OTHER OPTIONS lt RETURN gt OR OR q uit WILL TERMINATE THIS MENU We recommend to use the default method ahlrichs which provides excellent con 86 CHAPTER 4 PREPARING YOUR INPUT FILE WITH DEFINE vergency in most cases General Boundary Conditions for Update The force constant matrix will only be updated if least mingeo cycles exist The maximum number of cycles used for the update is specified by the parameter maxgeo Normally the default values provided by define need not be changed DEFINE BOUNDARY C
439. pectively In the expressions above T p is the unknown non interacting kinetic energy density functional and F p is the exchange correlation 243 244 CHAPTER 17 FROZEN DENSITY EMBEDDING CALCULATIONS energy functional Note that while the first two terms in Eq 17 1 refer to classical electrostatics and could be described by e g external point charges the last two terms are related to quantum mechanical effects Using freeze and thaw 162 cycles the role of the frozen and the embedded subsys tem is iteratively exchanged till convergence If expressions 17 2 and 17 3 are computed exactly then the density p4 pg will coincide with the exact density of the total system Because the FDE KSCED was originally developed in the Kohn Sham framework using standard GGA approximations for F p the non additive exchange correlation potential 5 224 5p r can be computed exactly as a functional of the density leaving the expression of the non additive kinetic energy term as the only approxima tion with respect the corresponding GGA calculation of the total system because the exact explicit density dependence of T from the density is not known Using GGA approximations for the kinetic energy functional T TECA we have qadding pp TCin pp TO p4 TOCA pp 17 4 and ae ST Tea PB pCa dpa r where 24 r TSSA 5p r The FDE total energy of total system is pa pal r F pa x
440. pend this string au tomatically to the system name if PARA_ARCH is set to MPI or SMP see chapter 3 2 1 how to set up parallel environment You can call TURBOMOLE executables and tools easily from anywhere if you add the corresponding directories to your path kornshell or bash syntax PATH PATH TURBODIR scripts PATH PATH TURBODIR bin sysname Note that sysname is set in back quotes which tells the shell to substitute the entry by the output of sysname Now the TURBOMOLE executables can be called from a directory with the required input files For example to call dscf and save the output TURBODIR bin sysname dscf gt dscf out or if the path is OK simply dscf gt dscf out Executable modules are in the bin arch directory for example Linux modules are in bin em64t unknown linux gnu Tools including jobex are in scripts and auxiliary basis sets are kept in the directories basen jbasen jkbasen cbasen xbasen and cabasen Coordinates for some common chemical fragments are supplied in structures The documentation and a tutorial can be found in the folder DOC 2 1 3 Testing the installation In addition some sample calculations are supplied in Turbotest so that the modules can be tested Just run TTEST from this directory to run all tests or TTEST help to get help on how this works 2 2 INSTALLATION PROBLEMS HOW TO SOLVE 31 cd TURBODIR TURBOTEST TTEST 2 2 Installation problems How to solve
441. pical for d metal compounds somewhat higher values are tolerable A similar idea is pursued by the D and D diagnostics 108 109 which is implemented in ricc2 D is a diagnostic for strong interactions of the HF reference state with doubly excited determinants while D is a diagnostic for strong interactions with singly excited determinants 9 5 RI MP2 F12 Calculations To obtain the F12 correction to the MP2 energy the data group rir12 must be added to the control file A typical run will include the input ricc2 9 5 RI MP2 F12 CALCULATIONS 175 mp2 energy only rir12 The MP2 F12 ground state energy is Eyyp2 ri2 EMP2 EFia 9 3 where Eyyp2 is the conventional MP2 energy and Ep12 the correction from explicitly correlated theory The second term contains contributions from explicitly correlated geminal basis functions of the form Qiz fizlij 9 4 where i7 is a two electron determinant of occupied semi canonical Hartree Fock spin orbitals f 2 is a correlation factor which can be either linear r12 in this case the approach is denoted MP2 R12 instead of MP2 F12 or a function of rj2 and Qi defines the doubles excitation space covered by the geminals it also ensures strong orthogonality to the occupied orbitals Usually Ore is chosen to be O12 1 O1 1 O2 Vi V2 where O 37 yx 14 lpr lu is the projection operator onto the space spanned by the occupied spin orbitals yy and V Vo
442. plt sf plt etc For non default grid types and outputs that allow also for displaying of components of electric fields see Section 20 2 21 Exchange correlation potentials Only for DFT Computation of the Kohn Sham exchange correlation potential on a grid pointval xc Canonical molecular orbitals Visualization of molecular orbitals i e genera tion of plt files containing amplitudes of MOs i Rp civdr Rp 16 5 or in the two component case Al Rp dG b Rp 16 6 with T as a part of the coefficient matrix Re a Im a Re G Im 8 is achieved e g by pointval mo 10 12 15 This yields amplitudes for MOs spinors 10 12 and 15 on the default grid The numbering of MOs refers to that you get from the first column of the output of the tool Eiger the one for spinors refers to the file EIGS The filenames contain the type of the irreducible representation irrep of the MO the current number within this irrep and in case of UHF calculations also the spin e g 2aig_a plt contains amplitudes for the second alpha spin MO of aj type For more dimensional irreps columns are written to separate files e g 1t2g1_a plt 1t2g2_a plt and 1t2g3_a plt contain the amplitutes of the three columns of the first irrep alpha spin of type tag 16 2 INTERFACES TO VISUALIZATION TOOLS 241 Two component wavefunctions only module ridft and only if soghf is set By default only the density of the chosen spinors is written in files n
443. ponse calculations For the calculation of vertical excitation energies it is recommended to use the mos of a DCOSMO RS calculation in a COSMO response calculation see above Solvation effects on excited states using COSMO in ricc2 The COSMO approach has been recently implemented into the ricc2 module of TURBOMOLE It is now possible to equilibrate the solvent charges for any excited state or the ground state as mentioned in the MP2 section above Using the methods CCS CIS or ADC 2 the implementation is complete for CC2 or higher methods however it still has to be proven if there are terms missing The recent implementation contains con tributions to the off diagonal elements of the one electron density Furthermore the 269 energy contributions for non equilibrated states can be calculated Non equilibrated means in this sense that the slow part of the solvent charges described by f e are still equilibrated with a given initial state while the fast electronic part of the solvent charges described by f n are in equilibrium with the target state To handle this one has to do a macro iteration like in MP2 This macro iteration can be managed with the script cc2cosmo which is the same as mp2cosmo but using ricc2 instead of rimp2 or mpgrad To set up the basic settings one can reuse the cosmoprep module note that one has to specify the refractive index refind when observing excited states To specify the state to which th
444. ptimizations can be computed within the random phase approximation RPA using the rirpa module Theory and development of the rirpa module is published in references 144 145 for the energy and reference 146 for the first order properties In case of two component relativistic RPA energy calculations see reference 147 For energy and gradients the resolution of the identity RI approximation is used to approximate the two electron repulsion integrals in the correlation treatment and is combined with an imaginary frequency integration The RI approximation is also employed by default for the computation of the Coulomb integrals for the HF en ergy For the energy it is optional to use RI for the Fock exchange integrals RI K while RI K for the gradients is not available yet Open shell systems and the frozen core approximation may be used in RPA energy calculations but are not presently available in gradient calculations Two component RPA energy calculations are only possible for Kramers restricted closed shell systems ECPs are presently not compat ible with RIRPA gradients Neither RPA energy nor gradients support symmetry at the moment The gradients may be used together with the scripts jobex for struc ture optimizations and NumForce for numerical harmonic vibrational frequencies 12 1 Ground State Energy Theory The RPA energy 217 218 CHAPTER 12 RANDOM PHASE APPROXIMATION consists of the Hartree Fock exact exchange e
445. puted after the RIRPA correlation energy Tight SCF scfconv 7 and one electron density matrix denconv 1d 7 convergence criteria large basis sets QZVP and large frequency grids which ensure a sensitivity measure of no more than 1d 4 should be used in combina tion with rpagrad for accurate results 12 4 Comments on the Output e The most important output for rirpa are the Hartree Fock HXX energy and the RIRPA correlation energy which are written to the standard output 12 4 COMMENTS ON THE OUTPUT 223 e The optimal scaling parameter for the quadrature grid is printed together with a sensitivity parameter The sensitivity parameter provides a numerical es timate for the error in the numerical integration used to evaluate EC RIRPA Experience demonstrates that the sensitivity parameter correlates well with the condition number of the matrix Q Small gap systems have large condi tion numbers and therefore require large grids An estimate of the number of eigenvalues smaller than 0 05 H is given and if necessary a warning to increase the grid size is printed to standard output e The molecular dipole and quadrupole moments are written to the standard output whenever a gradient calculation is carried out e Rotational constants are provided in the rirpa output below the coodinates section e Enabling the option rpaprof will output additional timings information Chapter 13 Calculation of Vibrational Frequencies and Vibrati
446. quality for H to Rn Design an assessment of accuracy F Weigend and R Ahlrichs Phys Chem Chem Phys 7 3297 2005 k Optimization of auxiliary basis sets for RI MP2 and RI CC2 calculation Core valence and quintuple basis sets for H to Ar and QZVPP basis sets for Li to Kr C Hattig Phys Chem Chem Phys 7 59 2005 l Accurate Coulomb fitting basis sets for H to Rn F Weigend Phys Chem Chem Phys 8 1057 2006 m Optimized accurate auxiliary basis sets for RI MP2 and RI CC2 calculations for the atoms Rb to Rn A Hellweg C Hattig S Hofener and W Klopper Theor Chem Acc 117 587 2007 n Property optimized Gaussian basis sets for molecular response calculations D Rappoport and F Furche J Chem Phys 133 134105 2010 o Segmented contracted basis sets for one and two component Dirac Fock effective core potentials F Weigend and A Baldes J Chem Phys 133 174102 2010 22 CHAPTER 1 PREFACE AND GENERAL INFORMATION Auxiliary basis sets for density fitted correlated wavefunction calculations Weight ed core valence and ECP basis sets for post d elements C Hattig G Schmitz J Kofmann Phys Chem Chem Phys 14 6549 2012 unpublished 1 4 MODULES AND THEIR FUNCTIONALITY 23 1 4 Modules and Their Functionality For references see Bibliography define uff dscf grad ridft and rdgrad mpgrad rimp2 ricc2 interactive input generator which create
447. r mpgrad On return the statistics option will be changed to statistics off actual step dscf means current step Keyword and data group as e g dscf is set by every program and removed on successful completion last step relax Keyword and data group as e g relax set by every program on successful comple tion General file cross references coord file coord intdef file coord user defined bonds file coord basis file basis ecp file basis jbas file auxbasis scfmo file mos uhfmo_alpha file alpha uhfmo_beta file beta natural orbitals file natural natural orbital occupation file natural energy file energy grad file gradient forceapprox file forceapprox It is convenient not to include all input in the control file directly and to refer instead to other files providing the corresponding information The above cross references are default settings from define you may use other file names define will create most of these files Examples of these files are given below in the samples coord and intdef and userdefined bonds contains atom specification type and location and the bonds and internal coordinates convenient for geometry optimizations basis specification of basis sets 20 2 FORMAT OF KEYWORDS AND COMMENTS 273 ecp specification of effective core potentials jbas auxiliary fitting basis for the Coulomb terms in ridft scfmo uhfmo_alpha uhfmo_beta MO vectors of S
448. r which the transition prop erties will be calculated Default is to compute the oscillator strengths for all components of the dipole operator exprop require calculation of first order properties for excited states For the states option see spectrum option above for details for the operators input see below xgrad request calculation of the gradient for the total energy of an excited state If no state is specified the gradient will be calculated for the low est excited state included in the calculation of excitation energies Note that only a single state should be specified simultaneous calculation of gradients for several states is in the present version not possible conv convergence threshold for norm of residual vectors in eigen value problems is set to 107 If not given a default value is used which is chosen as max 10 10 10 where conv refers to the values given in the data group ricc2 preopt convergence threshold used for preoptimization of CC2 eigenvectors is set to 10 Pre P default 3 thrdiis threshold 10 4445 for residual norm below which DHS extrapolation is switched on in the modified Davidson algorithm for the non linear CC2 eigenvalue problem default 2 leftopt If the flag leftopt is set the left eigenvectors are computed default is to compute the right eigenvectors for test purposes only bothsides The bothsides flag enforces the calculation of both the left and the ri
449. ram statpt Note that the program needs to know which calculation is being done Structure optimizations using program relax can be performed using relax flag nohup jobbsse opt relax amp nohup means that the command is immune to hangups logouts and quits amp runs a background command jobbsse accepts the following arguments controlling the level of calculation convergence criteria and many more for example nohup jobex gcart 4 amp energy integer converge total energy up to 10 lt integer gt Hartree default 6 gcart integer converge maximum norm of cartesian gradient up to 10 lt integer gt atomic units default 3 c integer perform up to integer cycles default 100 gradient calculate the gradient as well opt optimise the structure relax use the relax program for force relaxation level level define the optimization level level scf dft mp2 or cc2 default is scf Note that the program needs this input If the level is DFT the grid will be automatically set to m4 ri use RI modules ridft and rdgrad fast Coulomb approxi mation instead of dscf and grad as well as rimp2 instead of mpgrad 1 lt path gt employ programs from directory lt path gt mem integer Is able to control the memory from outside define Note that if you did not define any memory it is automatically set to 1 GB 118 CHAPTER 5 STRUCTURE OPTIMIZATIONS trimer calculates in case we have a trimer Energy ABC
450. ratch scratch files 371 373 scratch files 295 345 373 seed 365 senex 300 sh_coeffs 370 sijuai_out 231 317 soes 156 159 161 319 320 322 soghf 138 139 157 159 219 237 304 305 spectrum 160 320 326 spinor 139 start vector generation 158 320 statistics 293 296 dscf 125 272 296 dscf parallel 296 374 grad parallel 374 kora 296 mpgrad 172 272 296 324 mpshift 233 off 272 296 polly 296 statpt 99 101 349 bfgs 101 hssfreq 349 hssidiag 349 itrvec 100 349 keeptmode 349 INDEX powell 101 radmax 349 radmin 349 threchange 100 thrmax displ 100 thrmaxgrad 100 thrrmsdispl 100 thrrmsgrad 100 tradius 99 349 update 349 sum rules 320 surface_hopping 369 suspend off 272 symmetry 156 273 thime 123 125 156 296 326 371 thize 123 125 156 233 289 296 326 371 title 273 366 tmpdir 205 325 326 tplot 174 325 traloop 169 172 233 324 371 373 trand 372 trast 372 turbomole 365 uff 112 277 maxcycle 112 uffgradient 277 279 uffhessian 277 279 ufftopology 277 279 uhf 275 298 uhfmo_alpha 158 273 294 298 uhfmo_beta 158 273 294 298 userdefined bonds 272 vdw_fit 354 velocity gauge 320 amp 47 plt 360 429 NUMFORCE frznuclei 227 frznuclei NUMFORCE 227 1d 4 222 actual 25 actual step dscf 272 ADC 2 RL 325 analysis of normal modes internal coordinate 226 AOFORCE key
451. rd disp is found For the usage of DFT D3 just add keyword disp3 to the control file Only one of the three keywords is expected to be present If DFT D3 is used the total energy is given by Eprr p3 Exs prr Edisp 6 8 where Exs prrt is the usual self consistent Kohn Sham energy as obtained from the chosen functional and Egjsp is a dispersion correction given by the sum of two and three body energies Edisp Ee T B 6 9 with the dominating two body term CAB EO X X sn fanlraB 6 10 AB n 6 8 10 AB The first sum runs over all atom pair CA denotes the nth order dispersion coef ficient for atom pair AB rap is their interatomic distance and fg is a damping function Becke Johnson BJ damping can be invoked by adding the option bj or bj to the disp3 keyword disp bj If you use this damping option please also cite 89 Please have look at DFT D3 homepage Grimme group Bonn for more detailed infor mation Density based dispersion corrections of non local vdaW DF type A non local electron density dependent dispersion correction which is based on Vy drov and Van Voorhis VV10 90 has been implemented by the Grimme group 91 and is available for ridft and rdgrad This correction can either be applied in a post SCF and non self consistent way for energy calculations or self consistently which is required to compute the gradients 150 CHAPTER 6 HARTREE FOCK AND DFT CALCULATIONS To switch on DFT
452. rected results are to be expected if doing gradient calcula tions for elements heavier than Kr using all electron basis sets and very small grids To use the weight derivatives option add weight derivatives in dft The option 314 CHAPTER 20 KEYWORDS IN THE CONTROL FILE point charges in drvopt switches on the evaluation of derivatives with respect to coordinates of point charges The gradients are written to the file p0int_charge_gradients old gradients will be overwritten 20 2 10 Keywords for Module AOFORCE This module calculates analytically harmonic vibrational frequencies within the HF or RI DFT methods for closed shell and spin unrestricted open shell systems Bro ken occupation numbers would lead to results without any physical meaning Note that RI is only used partially which means that the resulting Hessian is only a very good approximation to exact second derivatives of the RIDFT energy expression Apart from a standard force constant calculation which predicts all allowed and for bidden vibrational transitions it is also possible to specify certain irreps for which the calculation has to be done exclusively or to select only a small number of lowest eigenvalues and eigenvectors that are generated at reduced computational cost General keywords drvopt is the keyword for non default options of gradient and second derivative cal culations Possibilities in case of the module aoforce are frequency
453. ree For example to calculate dynamic polarizabilities at 590 nm and 400 i nm i is the imaginary unit scfinstab dynpol nm 590 400 i The number and symmetry labels of the excited states to be calculated is controlled by the data group soes Example soes big 17 eu 23 t2g all will yield the 17 lowest excitations in IRREP b1g the 23 lowest excitations in IRREP eu and all excitations in IRREP t2g Specify soes alln to calculate the n first excitations in all IRREPS If n is not specified all excitations in all IRREPS will be obtained During an escf run a system independent formatted logfile will be constructed for each IRREP It can be re used in subsequent calculations restart or extension of eigenspace or of rpaconv An escf run can be interrupted by typing touch stop in the working directory general keywords rpacor n The maximum amount of core memory to be allocated for the storage of trial vectors is restricted to n MB If the memory needed exceeds the threshold given by rpacor a multiple pass algorithm will be used However especially for large cases this will increase computation time significantly The default is 200 MB 320 CHAPTER 20 KEYWORDS IN THE CONTROL FILE spectrum unit The calculated excitation energies and corresponding oscillator strengths are appended to a file named spectrum Possible values of unit are eV nm and 1 cm or rem If no unit is specified excitation e
454. rfaces to Visualization Tools Visualization of Molecular Geometry The tool t2x can be used to convert the atomic coordinates stored in the grad and coord data groups into the xyz format which is supported by most viewers e g jmol http jmol sourceforge net Typing t2x gt opt xyz in a directory containing the control file generates a series of frames using the information of grad Note t2x writes to standard output which here is redirected to a file If you are only interested in the most recent structure type t2x c gt str xyz which only extracts the information on coord Visualization of Densities MOs Electrostatic Potentials and Fields There are several possibilities to visualize molecular orbitals or densities tm2molden simply converts MO and geometry information to molden format The conversion program is interactive and self explanatory The generated file can be visualized using either molden http www cmbi ru nl molden molden htm1 or molekel http www cscs ch molekel1 For larger systems this may become very time consuming as plotting data values on grids are calculated by the respective programs molden molekel It is more ef ficient to calculate the data for plots MO amplitudes densities etc by TURBOMOLE modules and to use a visualization tool afterwards a way that is described in the following Calculation of data on grids to be used for plots with visualization tools e g gOpen
455. rizabilities at 590nm and 400i nm i is the imaginary unit specify scfinstab dynpol nm 590 400 i and run escf escf gt escf out amp The resulting polarizabilities and rotatory dispersions are given in a u in the program output escf out in the above example The conversion of the optical rotation in a u to the specific rotation a in deg dm g cc is given in Eq 15 of ref 97 aly C d w 7 16 where C 1 343 10 4w M with M being the the molar mass in g mol w the frequency in cm 1 and 6 w is 1 3 trace of the electronic rotatory dispersion tensor given in atomic units Please note that 6 w has the wrong sign in older TURBOMOLE versions It has been corrected in version 6 2 Note that convergence problems may occur if a frequency is close to an electronic excitation energy This is a consequence of the physical fact that the response diverges at the excitation energies and not a problem of the algorithm Static polarizabilities are calculated most efficiently by specifying scfinstab polly before starting escf 158 CHAPTER 7 HF AND DFT RESPONSE CALCULATIONS 7 4 3 Stability Analysis Stability analysis of spin restricted closed shell ground states is enabled by scfinstab singlet for singlet instabilities scfinstab triplet for triplet instabilities most common and scfinstab non real for non real instabilities After that it is necessary to specify the IRREPs of the elect
456. rograms also permit to approximate HF ex change within the RI K approximation The exchange correlation func tionals supported are specified in define requires a well converged SCF run by dscf see keywords and per forms closed shell RHF or UHF calculations yielding single point MP2 energies and if desired the corresponding gradient calculates MP2 energies and gradients for RHF and UHF wavefunctions significantly more efficient than mpgrad by using the RI technique 8 9 calculates electronic excitation energies transition moments and prop erties of excited states at the CIS CIS D ADC 2 and CC2 level using either a closed shell RHF or a UHF SCF reference function Calculates R12 basis set limit correction for MP2 energies Employs the RI tech nique to approximate two electron integrals Includes as a subset also the functionalities of the rimp2 program 10 17 24 relax statpt frog aoforce escf egrad CHAPTER 1 PREFACE AND GENERAL INFORMATION requires a gradient run by grad rdgrad rimp2 or mpgrad and pro poses a new structure based on the gradient and the approximated force constants The approximated force constants will be updated performs structure optimization using the Trust Radius Image Mini mization algorithm It can be used to find minima or transition struc tures first order saddle points Transition structure searches usually require initial Hessian matrix calculated analytically
457. ronic Hessian eigenvectors orbital rotations to be considered Without additional knowledge of the system one usually needs to calculate the lowest eigenvalue within every IRREP soes all 1 Positivity of the lowest eigenvalues in all IRREPs is sufficient for stability of the ground state solution If one is interested in say the lowest eigenvalues in IRREPs eg and t2g only one may specify soes eg 1 t2g 1 Triplet instabilities in the totally symmetric IRREP indicate open shell diradical states singlet or triplet In this case start MOs for spin symmetry broken UHF or UKS ground state calculation can be generated by specifying start vector generation escf will provide the start MOs uhfmo_alpha uhfmo_beta as well as occupa tion numbers gt alpha shells beta shells for a spin unrestricted calculation with equal numbers of a and electrons pseudo singlet occupation 7 4 4 Vertical Excitation and CD Spectra The calculation of excited states within the TDHF RPA TDDFT approach is en abled by scfinstab rpas for closed shell singlet excitations scfinstab rpat for closed shell triplet excitations and 7 4 HOW TO PERFORM 159 scfinstab urpa for excitations out of spin unrestricted reference states If it is intended to use the TDA instead specify scfinstab ciss for closed shell singlet excitations scfinstab cist for closed shell triplet excitations scfinstab ucis for exci
458. roperties and gradients ricc2 mp2 cc2 response static relaxed operators diplen qudlen gradient A different input is required for geometry optimizations in this case the model for which the geometry should be optimized must be specified in the data group ricc2 by the keyword geoopt ricc2 mp2 196 CHAPTER 10 RI CC2 cc2 geoopt model cc2 For CC2 calculations the single substitution part of the Lagrangian multipliers t are saved in the file CCLO 1 1 0 and can be kept for a restart for MP2 and CCS the single substitution part t vanishes For MP2 only relaxed first order properties and gradients are implemented unre laxed MP2 properties are defined differently than in CC response theory and are not implemented For MP2 only the CPHF like Z vector equations for Kuo need to be solved no equations have to be solved for the Lagrangian multipliers CPU time and disk space requirements are thus somewhat smaller than for CC2 properties or gradients For SCF CIS CCS it is recommended to use the modules grad and rdgrad for the calculation of ground state gradients and first order properties 10 3 2 Excited State Properties Gradients and Geometries Also for excited states presently unrelaxed and relaxed first order properties are available in the ricc2 program These are implemented for CCS and CC2 Note that in the unrelaxed case CIS and CCS are not equivalent for excited states first order properties and
459. rovides step by step the control file Coordinates atomic attributes e g basis sets MO start vectors and keywords specific for the desired method of calculation We recommend generating a set of Cartesian coordinates for the desired molecule using special molecular design software and converting this set into TURBOMOLE format see Section 21 2 as input for define Alternatively the graphical user interface TmoleX can be used to import and or build molecules A straightforward way to perform a TURBOMOLE calculation from scratch is as follows e generate your atomic coordinates by any tool or program you are familiar with e save it as an xyz file which is a standard output format of all programs or use a conversion tool like babel e use the TURBOMOLE script x2t to convert your xyz file to the TURBOMOLE coord file x2t xyzinputfile gt coord e since input files for TURBOMOLE are always called control each input has to be placed in a different directory Create a new directory and copy the coord file there e call define after specifying the title you get the coord menu just enter a coord to read in the coordinates Use desy to let define determine the point group automatically 33 34 CHAPTER 3 HOW TO RUN TURBOMOLE If you want to do geometry optimizations we recommend to use generalized internal coordinates ired generates them automatically you may then go through the menus without doing anything just press l
460. s 173 10 Second Order Approximate Coupled Cluster CC2 Calculations 176 11 12 10 1 CC2 Ground State Energy Calculations 181 10 2 Calculation of Excitation Energies 2 183 10 3 First Order Properties and Gradients 187 10 3 1 Ground State Properties Gradients and Geometries 188 10 3 2 Excited State Properties Gradients and Geometries 190 10 3 3 Visualization of densities and Density analysis 193 10 3 4 Fast geometry optimizations with RI SCF based gradients 195 10 4 Transition Moments cue ace ee et ee he ee ee ak ae we a E 195 10 4 1 Ground to excited state transition moments 195 10 4 2 Transition moments between excited states 197 10 5 Ground State Second order Properties with MP2 and CC2 197 10 6 Parallel RI MP2 and RI CC2 Calculations 2 198 10 7 Spin component scaling approaches SCS SOS 199 CCSD CCSD F12 and CCSD T calculations 201 11 1 Characteristics of the Implementation and Computational Demands 203 Random Phase Approximation Calculations Energy and First Order Properties 211 12 1 Ground State Energy Theory 2 2208 211 122 Gradients Theory sos e sensei ee pee Ee ee e E e we we 213 12 3 Further Recommendations 0 22 00008 215 12 4 Comments on the Output sos r osobe ee be ee ee ee ed 216 13 Calculation of Vibrational Frequencies and
461. s R Bauernschmitt M H ser O Treut ler and R Ahlrichs Chem Phys Letters 264 573 1997 RI MP2 first derivatives and global consistency F Weigend and M H ser Theor Chem Acc 97 331 1997 A direct implementation of the GIAO MBPT 2 method for calculating NMR chemical shifts Application to the naphthalenium and anthracenium ions M Kollwitz and J Gauss Chem Phys Letters 260 639 1996 Parallelization of Density Functional and RI Coulomb Approximation in TUR BOMOLE M v Arnim and R Ahlrichs J Comp Chem 19 1746 1998 Geometry optimization in generalized natural internal Coordinates M v Arnim and R Ahlrichs J Chem Phys 111 9183 1999 CC2 excitation energy calculations on large molecules using the resolution of the identity approximation C Hattig and F Weigend J Chem Phys 113 5154 2000 Implementation of RI CC2 for triplet excitation energies with an application to trans azobenzene C Hattig and Kasper Hald Phys Chem Chem Phys 4 2111 2002 First order properties for triplet excited states in the approximated Coupled Cluster model CC2 using an explicitly spin coupled basis C Hattig A K hn and Kasper Hald J Chem Phys 116 5401 2002 and Vir J Nano Sci Tech 5 2002 Transition moments and excited state first order properties in the coupled cluster model CC2 using the resolution of the identity approximation C Hattig and A Kohn J Chem Phys 117
462. s and compute the energy at each point The maximum energy structure is usually a good guess for the true TS After obtaining a reasonable initial guess for the TS structure you have to perform a vibrational analysis or LES calculation for a large molecule and to identify the index of the transition vector to follow during the optimization Ideally this is a vector with a negative eigenvalue or imaginary frequency The best way to find the right vector is to use some graphical interface to visualize vibrations For a reasonable guess structure there should be one vibration that resembles the reaction under study Remember that statpt uses a different ordering of eigenvalues as compared to the aoforce output six five zero eigenvalues are shifted to the end 102 CHAPTER 5 STRUCTURE OPTIMIZATIONS There is an important thing to remember at this point Even such sophisticated optimization methods like TRIM will not replace your own chemical intuition about where transition states may be located If you need to restart your run do so with the coordinates which have the smallest RMS gradient Note that the energy does not have necessarily to decrease in a transition state search as opposed to minimizations It is sometimes necessary to do restart several times including a recomputation of the Hessian before the saddle point can be located Assuming you do find the TS it is always a good idea to recompute the Hessian at this structure It
463. s also included in the Fock operator pr 002 ex F Bt 2 8 HF H CC Y BA wlt B E 10 20 pv Y 6 ui H H To HF p S37 A wolff F T HE Y RE Fg H2 Lo Compared to unrelaxed properties the calculation of relaxed properties needs in addition for each excited state the solution of a CPHF equations for the Lagrangian 198 CHAPTER 10 RI CC2 multipliers RED for which the computational costs are similar to those of a Hartree Fock calculation Orbital relaxed properties are requested by adding the flag relaxed to the input line for the exprop option The following is an example for a CC2 single point calculation for orbital relaxed excited state properties ricc2 cc2 excitations irrep al nexc 2 exprop states all relaxed operators diplen qudlen Note that during the calculation of orbital relaxed excited state properties the corre sponding unrelaxed properties are also automatically evaluated at essentially no ad ditional costs Therefore the calculation of unrelaxed properties can not be switched off when relaxed properties have been requested Again the construction of gradients requires the same variational densities as needed for relaxed one electron properties and the solution of the same equations The construction of the gradient contributions from one and two electron densities and derivative integrals takes approximately the same time as for ground states gradients approx 3 4 SCF iteratio
464. s be converged until changes drop below 1077 Hartree which typi cally ensures an accuracy of about 1 uH These setting are thus rather tight and conservative even for the calculation of highly accurate reaction energies If for your application larger uncertainites for the energy are tolerable it is recommended to use less tight thresholds e g conv 6 or conv 5 for an accuracy of respectively at least 0 01 mH 0 03 kJ mol or 0 1 mH 0 3 kJ mol The settings for conv and oconv have not only an impact on the number of iterations for the solution of the 216 CHAPTER 11 CCSD CCSD F12 AND CCSD T cluster equations but as they determine the thresholds for integral screening also to some extend on the costs for the individual iterations CCSD T energy with a second order correction from the interference corrected MP2 F12 The error introduced from a CCSD T calculation with a finite basis set can be corrected from second order corrections of the the interference corrected MP2 F12 INT MP2 F12 Ref 143 The approximate CCSD T INT F12 at the basis set limit is given from Ecesp ty ces Eceso X FY leg Fe ef 11 26 i lt j From define in the submenu ricc2 select the ccsd t method and add the key word intcorr ricc2 ccsd t intcorr Then switch on the 12 method approximation A or B inv or fixed The cor rected CCSD T INT F12 energy will be printed in the end of the calculation It is highly recommended
465. s in this menu are selected by entering their number as indicated in the first column For example to switch on option trace enter 1 The flag off will then change to active To switch off an option enter its negative number e g 1 for trace Most of the options require additional input and will therefore lead you to further submenus These are briefly described below Option trace trace will calculate the trace of density times overlap matrix N tr DS If the orbitals are orthonormal N should yield the total number of electrons in your molecule If this is not true your MO vector will most probably be erroneous For example the vector might belong to another geometry or basis set As this is a very sensitive test for errors like these and the calculation requires almost no time you should always switch on this option Option moments This option leads you to the following submenu add change options for data group moments option status description E E N AS S General a a T a e point lt x gt lt y gt lt z gt T reference point x y z atom lt i gt F reference point atom no lt i gt Oth T compute Oth moment 1st F compute 1st moment 2nd F compute 2nd moment 3rd F compute 3rd moment sald il Sy Rte ib et at AETI eraled sy at Sle EEE Sabet lt moment gt skip computation of lt moment gt or q uit terminate input 90 CHAPTER 4 PREPARING YOUR INPUT FILE WITH DEFINE This menu
466. s of Mulliken overlap ma trix are calculated mosum list of MOs Summed Mulliken contributions for a group of molecular orbitals defined by numbers referring to the numbering obtained e g from the tool eiger Note that occupancy of MOs is ignored i e all orbitals are treated as occupied mo list of MOs Mulliken contributions for single MOs defined by numbers independent of whether they are occupied or not If this option is valid one may additionally set dos width real points integer to calculate a simulated density of states by broadening the dis crete energy levels with Gaussians and superimposing them The width of each Gaussian may be set by input default 0 01 a u The resolution number of points may be chosen automatically default values are usually sufficient to generate a satisfactory plot or specified by hand The output files dos in case of RHF wave functions and dos_atb dos_a b dos_alpha dos_beta for UHF cases contain energies first column resulting DOS for the re spective energy second column as well as s p d contributions for the respective energy following columns Example pop mo 23 33 dos atoms 2 3 7 8 20 2 FORMAT OF KEYWORDS AND COMMENTS 307 leads to Mulliken PA CAO basis for each of the eleven MOs 23 33 regarding only contributions from atoms 2 3 and 7 8 results are written to standard output and generation of file s with the respective simulated density of states
467. s present conv The conv parameter gives the convergence threshold for the CC2 ground 20 2 FORMAT OF KEYWORDS AND COMMENTS 329 state energy as 10 The default value is taken from the data group deneps oconv The oconv parameter gives an additional threshold for the residual of the cluster equations vector function If this parameter is given the iterations for the cluster equations are not stopped before the norm of the residual is lt 107 By default the threshold is set to oconv conv 1l or 10x deneps if no input for conv is given lindep If the norm of a vector is smaller than 10 4 P the vector is assumed to be zero This threshold is also used to test if a set of vectors is linear dependent The default threshold is 10715 maxiter gives the maximum number of iterations for the solution of the cluster equations eigenvalue problems or response equations default 25 mxdiis is the maximum number of vectors used in the DIIS procedures for CC2 ground state or excitation energies default 10 maxred the maximum dimension of the reduced space in the solution of linear equations default 100 iprint print level by default set to 1 or if given the the value of the printlevel data group fmtprop Fortran print format used to print several results in particular one electron properties and transition moments to standard output geoopt specify wavefunction and electronic state for which a ge
468. s the highest excitation specified by soes only one IRREP is allowed Sometimes e g close to excited state intersections it may be necessary to include higher excited states in the initial excitation vector calculation to prevent root flipping This is accomplished using exopt n which explicitly enforces treatment of the n th state n must be less or equal the number of states specified in soes After the input for the ground and excited state calculations has been set up an excited state geometry optimization can be started by issuing the command nohup jobex ex amp The option ex forces jobex to call egrad instead of grad or rdgrad if ri is also specified In each geometry step the excitation energy is written on the fourth column in energy and the data group last excitation energy change is up dated Otherwise the excited state optimization proceeds in exactly the same way as a ground state optimization see Chapter 3 1 7 4 6 Excited State Force Constant Calculations Excited state vibrational frequencies can be calculated by numerical differentiation of analytic gradients using Numforce see Chapter 13 A Numforce calculation for an excited state may be started by the command nohup NumForce ex n gt force out amp where n is the number of the excited state in C1 symmetry In order to determine n it is recommended to perform an escf calculation in C1 symmetry Note that numerical calculation of excited state
469. s the input file control define supports most basis sets in use especially the only fully atom optimized consistent basis sets of SVP and TZV quality 2 6 available for the atoms H Rn excluding lanthanides define determines the molecular symmetry and internal coordinates allowing efficient geometry optimiza tion define allows to perform a geometry optimization at a force field level to preoptimize the geometry and to calculate a Cartesian Hessian matrix define sets the keywords necessary for single point calculations and geometry optimizations within a variety of methods There are also many features to manipulate geometries of molecules just try and see how it works performs a geometry optimization at a force field level The Universal Force Field UFF 7 is implemented Beyond this it calculates an analytical Hessian Cartesian which will be used as a start Hessian for an ab initio geometry optimization for semi direct SCF HF and DFT calculations see keywords for func tionals supported dscf supports restricted closed shell RHF spin restricted ROHF as well as UHF runs dscf includes an in core version for small molecules requires a successful dscf run and calculates the gradient of the energy with respect to nuclear coordinates for all cases treated by dscf perform direct SCF HF and DFT calculations as dscf and grad within the very efficient RI J approximation for the interelectronic Coulomb term These p
470. sary for geometries or energies ECPs are not supported in mpshift 21 calculates thermodynamic functions from molecular data in a control file an aoforce or a NumForce run is a necessary prerequisite calculates Raman scattering cross sections from molecular data in a control file an aoforce and an egrad run are a necessary prerequisite Please use the Raman script to run these three steps in an automated way computes a finite number of structures along reaction paths within dif ferent interpolation algorithms It provides an initial path using a mod ified Linear Synchronous Transit See Section 5 7 for details Please use the woelfling job script to run optimizations with it 1 5 Tools Note these tools are very helpful and meaningful for many features of TURBOMOLE This is a brief description of additional TURBOMOLE tools Further information will be available by running the programs with the argument help actual please use actual help aoforce2g98 usage aoforce2g98 aoforce out gt g98 out converts output from the aoforce program to Gaussian 98 style which can be interpreted by some molecular viewer e g jmol to animate the normal coordinates 26 bend cbasopt cc2cosmo cgnce cosmoprep dist DRC eiger evalgrad FDE hcore jobex kdg CHAPTER 1 PREFACE AND GENERAL INFORMATION example bend 1 2 3 displays the bending angle of three atoms specified by their number from the contr
471. scf ridft mpgrad rimp2 and egrad In case of spin unrestricted calculations results are given for total densities D D and spin densities D D If not explicitly noted otherwise in the following D is the SCF density D SCF in case of dscf and ridft the MP2 corrected density 20 2 FORMAT OF KEYWORDS AND COMMENTS 355 D SCF D MP2 for mpgrad and rimp2 and the entire density of the excited state in case of egrad For modules dscf and ridft the analysis of properties may be directly started by calling dscf proper or ridft proper In case of mpgrad and rimp2 this is possible only if the MP2 density has already been generated i e after a complete run of mpgrad or rimp2 Functionalities of analyses are driven by the following keywords mvd leads to calculation of relativistic corrections for the SCF total density in case of dscf and ridft for the SCF MP2 density in case of rimp2 and mpgrad and for that of the calculated excited state in case of egrad Quantities calculated are expectation values lt p gt lt pt gt and the Darwin term gt 1 Z4 p Ra moments pop yields calculation of electrostatic moments arising from nuclear charges and total electron densities Also without setting this keyword moments up to quadrupole are calculated with respect to reference point 0 0 0 Supported extensions moments lt i gt x y1 z1 x2 y2 z2 By integer i the maximum order of momen
472. scripts Tbtim and Tblist help to convert this data to a more readable form and produce summaries as IATFX tables The Tbtim script creates a summary of benchmark results for a given computer platform from the original timings file Tblist produces benchmark comparisons of different platforms The corresponding timings files must be provided as arguments to the Tblist script For more details and options see TBTIM help and TBLIST help 402 CHAPTER 22 PERL BASED TEST SUITE 22 4 Modes and options of the TTEST script The TTEST script knows several operation modes run check list clean realclean and validate controlled by its options The run mode is default and means that the test calculations are performed and the results are written to the TESTPROTOKOLL file The check mode differs only in that the programs are not executed but the existing program output is checked against the reference The results of the check are written to the CHECKPROTOKOLL file Calling the test script in the list mode simply lists the test examples that are currently available This allows the user to save the full list to file edit and re use it with the r option The clean and realclean options are for cleaning up the test directories and protocols Finally the validate mode is mainly of use for writing the CRIT files It helps to verify the match patterns provided in the test criteria and shows if it extracts the expected data for c
473. ser defined bonds file coord pople AO basis file basis rundimensions dim fock dens 141 natoms 1 nshel1 6 nbf CAO 15 nbf AQ 14 dim trafo SA0 lt gt AQ CAO 17 rhfshells 2 scfmo none file mos roothaan 1 a i b 2 scfiterlimit 60 scfconv 10 thize 0 10000000E 04 thime 5 scfdamp start 1 500 step 0 050 min 0 100 scfdump scfintunit unit 30 size 90 file twoint scfdiis start 0 5 scforbitalshift closedshell 4 drvopt cartesian off optimize basis gt basis on basis on global off hessian on dipole on nuclear polarizability 394 CHAPTER 21 interconversion off qconv 1 d 7 maxiter 25 optimize internal off cartesian off global off optimize basis gt basis on logarithm basis on logarithm coordinateupdate dqmax 0 3 interpolate on statistics 5 forceupdate SAMPLE CONTROL FILES ahlrichs numgeo 0 mingeo 3 maxgeo 4 modus lt g dq gt dynamic fail 0 6 threig 0 005 forceinit on reseig 0 005 thrbig 3 0 diag default energy file energy grad file gradient optimize basis gt egrad file egradient egrad file egradient forceapprox file forceapprox lock off atoms n 1 basis n def SV P closed shells scale 1 00 damping 0 0 alg 1 2 2 open shells type 1 tiu 1 Ct end File coord coord 0 00000000000000 0 00000000000000 O 00000000000000 n user defined bonds end File basis 21 5 BASISSET OPTIMIZATION FOR NITROGEN
474. set to zero while the diagonale ele ments for the frozen coordinates will be set to an arbitrarly chosen large value This feature is mainly intended to allow for a vibrational analysis in embbeded cluster calculations e g for defects in ionic crystals The vibrational analysis uses a kind of frozen phonon approximation which corresponds to setting the masses of the fixed atoms to infinity i e decoupling the fixed atoms mechanically from the mechani cally active subsystem The resulting vibrational frequencies will thus only provide 228 CHAPTER 13 VIBRATIONAL FREQUENCIES good approximations to the true harmonic frequencies for such modes for which the mechanical coupling to the embedding environment is negligible In particular the frequencies of stretch modes which involve bonds between the mechanically ac tive subsystem and atoms with frozen coordinates will be strongly affected by this approximation Note e The frznuclei is not compatible with the polyhedral difference algorithm It can only be used with central differences which should be enforced with the central option e If the option frznuclei is switched on the program assumes that the con straints enforced by fixing coordinates remove the six external degrees of free dom for on overall rotation or translation of the system and therefore the hessian matrix is not projected onto the subspace of internal coordinates Fix ing the coordinates of only on
475. should be set All these settings can be done during the input generation with the pro gram define under the entry mp2 cc2 of last main menu 2 Alternatively the interactive program Rimp2prep can be used This program sets default values for auxiliary basis sets data group cbas for frozen core orbitals data group freeze all orbitals with energies below 3a u are sug gested to be frozen and for the amount of memory to be allocated maxcor These defaults can be confirmed with return or modified if desired Note the amount of memory to be allocated determines the number of multiple passes and thus the efficiency of rimp2 It is also possible to run Rimp2prep directly after define 3 The ricc2 program requires the data group ricc2 mp2 geoopt model mp2 Where the last line should only be included if the calculation of gradients is needed e g in geometry optimizations This can be prepared with define in the menus mp2 or cc2 4 For explicitly correlated MP2 F12 calculations with ricc2 also the data groups rir12 and lcg is needed 5 Start a single rimp2 calculation with the command ricc2 or rimp2 6 For optimisation of structure parameters at the RI MP2 level use the command jobex level cc2 or jobex ri level mp2 For geometry optimizations with RI JK SCF as reference for RI MP2 with the ridft and ricc2 binaries the additional option rijk has to be given 7 The combination of RI MP2 with RI JK SCF can lead to signi
476. signment of auxiliary basis sets mandatory for ricc2 the specification of frozen orbitals and the definition of a scratch directory and of the maximum core memory usage 2nd analytical derivatives The program aoforce computes force constants and IR and Raman Spectra on SCF and DFT level Analytical second derivative calculations can directly be started from converged SCF or DFT calculations Note that the basis is restricted to d functions and ROHF as well as broken occupation numbers are not allowed For better efficiency in case of larger systems use the keyword maxcor as described in Chapter 13 to reduce computational cost RI will be used if the RI option for DFT has been specified 4 4 THE GENERAL OPTIONS MENU 81 4 4 2 Special adjustments Adjustments described by the following menus are often better done directly in the control file have a look at the keywords in Chapter 20 For common calculations just start with the defaults and change keywords directly in control if you encounter problems with your calculation SCF options ENTER SCF OPTION TO BE MODIFIED conv ACCURACY OF SCF ENERGY scfconv thi INTEGRAL STORAGE CRITERIA thize thime ints INTEGRAL STORAGE ALLOCATION scfintunit iter MAXIMUM NUMBER OF ITERATIONS scfiterlimit diis DIIS CONVERGENCE ACCELERATION scfdiis damp OPTIONS FOR DAMPING scfdamp shift SHIFTING OF ORBITALS scforbitalshift order ORDERING OF ORBITALS scforbitalorder ferm
477. sitions of nuclei may be used as an efficient tool to distinguish atoms of similiar atomic numbers thus providing a complement to X Ray Structure Analysis details see ref 158 Chapter 17 Frozen Density Embedding calculations 17 1 Background Theory In the subsystem formulation of the density functional theory a large system is de composed into several constituting fragments that are treated individually This approach offers the advantage of focusing the attention and computational cost on a limited portion of the whole system while including all the remaining enviromen tal effects through an effective embedding potential Here we refer in particular to the fully variational Frozen Density Embedding FDE 159 with the Kohn Sham Constrained Electron Density KSCED equations 160 161 In the FDE KSCED method the embedding potential required by an embedded subsystem with density p4 to account for the presence of another frozen subsystem with density pp is OTS paipa _ SEze pa pB B Vemb L Vaxt r V r 17 1 b t sipB dpa r dpa r where v8 r and vz pg r are the electrostatic potentials generated by the nuclei and electron density of the subsystem B respectively and T3 pa pB Tslea pB Telpa Tolon 17 2 Epad oa pB Exclpa pB Exclpa EzcleB 17 3 are the non additive non interacting kinetic energy and exchange correlation energy functionals res
478. ssful Optimization If there is no reasonable TS guess or a frequency calculation does not give the correct number of imaginary frequencies you can 5 7 REACTION PATH OPTIMIZATION 121 1 Check if have used the best structure as TS guess maybe the structure with the highest energy is not the best 2 Check if the RP has a reasonable amount of structures if they are far apart it is unlikely that a structure is close to the TS ne 3 Check if the RP is reasonably converged mean of rms g in output lt 1 0d 3 path is continuous in terms of energy and structure a If it is not yet converged converge it b Ifit is not going to converge provide useful structures for the initial guess or maybe use more structures for the path Restart 1 If you have stopped the calculation adding a stop file you can just run woelfling job again 2 If you have run the maximum number of cycles just increase maxit and run woelfling job again It will then run from the old maxit to the new maxit If the calculation crashed on its own it is likely that the SCF failed to converge improve the corresponding options If the optimization crashed in the middle of the run it is most likely that it crashed during a SCF or gradient step since basically all cpu time is spent there In that case remove at least the folder where the SCF and gradient program had been running when the program crashed The files necessary for woelfling shou
479. st order properties ricc2 cc2 excitations irrep al nexc 2 spectrum states all operators diplen qudlen For the ADC 2 model which is derived by a perturbation expansion of the expres sions for exact states the calculation of transition moments for excitations from the ground to an excited state would require the second order double excitation am plitudes for the ground state wavefunction which would lead to operation counts scaling as O N if no further approximations are introduced On the other hand the second order contributions to the transition moments are usually not expected to be important Therefore the implementation in the ricc2 program neglects in the calculation of the ground to excited state transition moments the contributions which are second order in ground state amplitudes i e contain second order ampli tudes or products of first order amplitudes With this approximation the ADC 2 transition moments are only correct to first order i e to the same order to which also the CC2 transition moments are correct and are typically similar to the CC2 results The computational costs for the ADC 2 transition moments are within this approximation much lower than for CC2 since the left and right eigenvectors 10 5 GROUND STATE SECOND ORDER PROPERTIES WITH MP2 AND CC2203 are identical and no lagrangian multipliers need to be determined The extra costs i e CPU and wall time for the calculations of the transitions mo
480. standard RI DFT input nohup jobex ri amp many features such as NMR chemical shifts on SCF and DFT level do not require further modifications of the input just call e g mpshift after the ap propriate energy calculation mpshift runs with SCF or DFT using a hybrid functional need a file size of the semi direct file twoint that is non zero 3 1 A QUICK AND DIRTY TUTORIAL 35 e other features such as post SCF methods need further action on the input using either the last menu of define where one can activate all settings needed for DFT TDDFT MP2 CC2 etc calculations this is the recommended way or tools like Mp2prep or Rimp2prep Please refer to the following pages of this documentation 3 1 1 Single Point Calculations Running TURBOMOLE Modules All calculations are carried out in a similar way First you have to run define to obtain the control file or to add change the keywords you need for your pur pose This can also be done manually with an editor Given a bash and a path to TURBODIR bin arch see installation Chapter 2 you call the appropriate module in the following way e g module dscf nohup dscf gt dscf out amp nohup means that the command is immune to hangups logouts and quits amp runs a background command The output will be written to the file dscf out Several modules write some additional output to the control file For the required keywords see Section 20 The features of TURBOMOLE w
481. statistical with charges from an ESP fit It is the default choice c for additional information about MAOs info Eigenvalues and occupations for each MAO are written to output 20 2 FORMAT OF KEYWORDS AND COMMENTS 309 dump Entire information about each MAO is written to output Lengthy Further for each atom the number of MAOs and the sorting mode can be specified individually in lines below this keyword Example atom 1 3 4 eig 7 leads to choice of the 7 MAOs with largest eigenvalue at atoms 1 3 4 localize enables the generation of localized molecular orbitals LMOs using Boys lo calization By default all occupied orbitals are included localized orbitals are written by default in the AO basis to file s 1mo in case of RHF and lalp and lbet in case of UHF orbitals Note that LMOs usually break the molecular symmetry so even for symmetric cases the AO not the SAO basis is used for the output The localized orbitals are sorted with respect to the corresponding diagonal element of the Fock matrix in the LMO basis In order to character ize these orbitals dominant contributions of canonical MOs are written to standard output as well as results of a Mulliken PA for each LMO for plotting of LMOs see option pointval The keyword allows for following options to be written in the same line mo list of MOs Include only selected MOs e g valence MOs in localization procedure numbering as available from Eiger
482. sums 176 CHAPTER 9 2ND ORDER M OLLER PLESSET PERTURB THEORY of products of 2 electron integrals intrinsic to the F12 method the complementary auxiliary basis CABS approach is used 111 If define is used to set up the cabs basis the library cabasen is searched This library contains the optimised cabs basis sets 112 for the cc pVXZ F12 basis sets of Peterson et al 113 For other basis sets the auxilliary basis in the library cabasen is identical with the auxilliary basis in the library cbas The rir12 data group may be set by choosing the 12 option in the cc menu when running define This command activates the 12 menu where the default options may be changed if desired Orbital basis cc pVTZ F12 Cardinal number ar Recommended exponent 1 0000 Actual exponent 1 0000 INPUT MENU FOR MP2 F12 CALCULATIONS ansatz ri2model comaprox cabs examp ri2orb corrfac cabsingles pairenergy slater end amp ansatz ri2model CHOOSE ANSATZ CHOOSE MODEL COMMUTATOR APPROXIMATION CABS ORTHOGONALIZATION CHOOSE FORMULATION CHOOSE GEMINAL ORBITALS CHOOSE CORRELATION FACTOR CABS SINGLE EXCITATIONS PRINT OUT PAIRENERGIES SLATER EXPONENT 2 1 2 2 B A B F K F K T V svd 1 0D 08 cho svd fixed noflip inv fixed noinv flip noflip hf hf rohf boys pipek LCG R12 LCG on on off off on off 1 0000 write rir12 to file and leave the menu go back
483. t Acetone propanone_25 pot Chloroform chc13_25 pot Tetrachloromethane ccl4_25 pot Acetonitrile acetonitrile_25 pot Nitromethane nitromethane_25 pot Dimethylsulfoxide dimethylsulfoxide_25 pot Diethylether diethylether_25 pot Hexane hexane_25 pot Cyclohexane cyclohexane_25 pot Benzene benzene_25 pot Toluene toluene_25 pot Aniline aniline_25 pot The DCOSMO RS energies and total charges are listed in the COSMO section of the output SCREENING CHARGE cosmo 0 012321 correction 0 011808 total 0 000513 correction on the COSMO level ENERGIES a u Total energy 76 4841708454 COSMO 0 0006542315 DCOSMO RS 0 0011042856 Combinatorial contribution of the solute 0 0017627889 at inf dil in the mixture pure solvent Not included in the total energy above Outlying charge corr Outlying charge corr 20 2 FORMAT OF KEYWORDS AND COMMENTS 313 The outlying charge correction cannot be defined straight forward like in the normal CosMo model Therefore the output shows two corrections that can be added to the Total energy The first one is the correction on the Cosmo level COSMO and the second is the difference of the DCOSMO RS dielectric energy calculated form the corrected and the uncorrected CosMo charges respectively DCOSMO RS The charges are corrected on the Cosmo level only The Total energy includes the Ediel rzs defined in section 19 Additionally the combinatorial contribution at infinute
484. t Enter gt or qg whatever ends the menu or by confirming the proposed decision of define again by just pressing lt Enter gt This way you get the necessary specifications for a SCF based run with SV P as the default basis set which is roughly 6 31G for more accurate SCF or DFT calculations choose larger basis sets e g TZVP by entering b all def TZVP or b all def2 TZVP in the basis set menu ECPs which include scalar relativistic corrections are automatically used be yond Kr an initial guess for MOs and occupation numbers is provided by eht for DFT you have to enter dft in the last menu and then enter on for efficient DFT calculations you best choose the RI approximation by entering ri and providing roughly 3 4 of the memory with m number number in MB your computer has available Auxiliary basis sets are provided automatically In the printout of an ridft run you can check how much is really needed a top statement will tell you if you overplayed your cards B P86 is the default functional It has a good and stable performance through out the periodic system for an HF or DFT run without RI you simply enter nohup dscf gt dscf out amp or for a RI DFT run nohup ridft gt ridft out amp for a gradient run you simply enter nohup grad gt grad out amp or nohup rdgrad gt rdgrad out amp for a geometry optimization simply call jobex for a standard SCF input nohup jobex amp for a
485. t a states no 1 3 4 5 and the singlet biu states no 1 2 3 and the singlet which is default if no is found bg state no 4 istates all fstates all The specification of initial and final states for transition properties between excited states is mandatory The syntax is analog to the states option i e either all or a list of of states is required D2 diagnostic Calculate the double substitution based diagnostics D cc2_natocc Write MP2 CC2 natural occupation numbers and natural orbitals to a file cgrad 1000 Calculate the error functional dp for the RI approximation of ai bj integrals ae 1 abl 7 exact ab i3 Rx RI Ea Ei amp Ej 20 2 FORMAT OF KEYWORDS AND COMMENTS 339 and its gradients with respect to exponents and coefficients of the auxiliary basis set as specified in the data group cbas The results are written to egrad scaled by the factor given with the keyword cgrad and can be used to optimize auxiliary basis sets for RI MP2 and RI CC2 calculations see Section 1 5 20 2 18 Keywords for Module RELAX optimize options define what kind of nonlinear parameters are to be optimized by relax and specify some control variables for parameter update Available options are internal on off optimize molecular structures in the space of internal coordinates us ing definitions of internal coordinates given in intdef as described in Section 4 1 default on redundant on
486. t to the result from the rimp2 module cis dinf denotes the iterative CIS D variant CIS D The option ccsd t request a CCSD calculation with the perturbative triples correction CCSD T and as a side result also the CCSD T energy will be printed mp2 didiag Request the calculation of the D diagnostic in MP2 energy calculations ignored in MP2 gradient calculations Note that the evaluation of the D diagnostic increases the computational costs of the RI MP2 energy calculation roughly by a factor of 3 cis d energy only If the energy only flag is given after the cis d keyword it is assumed that only excitation energies are requested This switches on some short cuts to avoid the computation of intermediates needed e g for the gen eration of improved start vectors for CC2 no restart If the restart flag is set the program will try to restart the CC2 cal culations from previous solution vectors on file If the norestart flag is set no restart will be done Default is to do a restart for CC2 if and only if the file CCRO 1 1 0 exists Note There is no restart possibility for CCS CIS or MP2 CIS D no hard_restart If the hard_restart flag is set the program will try to reuse integrals and intermediates from a previous calculation This requires that the restart cc file has been kept which contains check sums and some other informations needed The hard_restart flag is switched on by default if the restart cc file i
487. tals that can be obtained from a singular value de composition of the excitation amplitudes See Sec 16 1 for further details Another but computational more involved possibility is plot the difference density between the ground and the respective excited state This requires however a first order property or gradient calculation for the excited state to obtain the difference density For further details see Sec 10 3 3 194 CHAPTER 10 RI CC2 10 3 First Order Properties and Gradients For the ground state first order properties expectation values are implemented at the SCF MP2 and CC2 level Note that for the ground state CCS and CIS are equivalent to SCF For excited states first order properties are implemented only at the CCS and CC2 level Gradients are presently only available for the ground state at the MP2 and the CC2 and for excited states only at the CC2 level 10 3 1 Ground State Properties Gradients and Geometries For CC2 one distinguishes between orbital relaxed and unrelaxed properties Both are calculated as first derivatives of the respective energy with respect to an external field corresponding to the calculated property They differ in the treatment of the SCF orbitals In the orbital relaxed case the external field is formally already included at the SCF stage and the orbitals are allowed to relax in the external field in the orbital unrelaxed case the external field is first applied after the SCF calculation an
488. tates with second order wavefunction methods ricc2 The module ricc2 calculates MP2 and CC2 ground state energies and CIS identical to CCS CIS D CIS Dx ADC 2 or CC2 excitation energies using the resolution of the identity RI approximation Also available are spin component scaled SCS and SOS variants of the second order methods CIS D CIS Dx ADC 2 or CC2 Excited state gradients are available at the CCS CIS D ADC 2 and CC2 levels and the spin component scaled variants of the latter three methods In addition transition moments and first order properties are available for some of the methods For more details see Section 10 The input can be prepared using the cc2 menu of define CCSD F12 ricc22 Presently also implemented in the ricc22 module are CCSD and CCSD T and explicitly correlated F12 variants thereof The latter have much faster basis set convergence are therefore more efficients We recommend in particular CCSD F12 and CCSD F12 T Excitation energies are only available for conventional CCSD 3 2 PARALLEL RUNS 37 3 1 3 Calculation of Molecular Properties See Section 1 4 for the functionality and Section 20 for the required keywords of the modules dscf ridft mpshift escf and ricc2 3 1 4 Modules and Data Flow See Figure 3 1 3 2 Parallel Runs Some of the TURBOMOLE modules are parallelized using the message passing inter face MPI for distributed and shared memory machines or with Op
489. tation energy becomes negative 20 2 FORMAT OF KEYWORDS AND COMMENTS 371 Often times if a switch is enforced due to a negative TDA excitation energy the potential energy surface is discontinuous and limited numerical precision of the nuclear forces may lead to a loss of total energy conservation In this case the nuclear velocities are rescaled to obtain a conserved total energy 20 2 23 Keywords for Module MPSHIFT In order to control the program execution you can use the following keywords within the control file csmp2 Switches on the calculation of the MP2 NMR shieldings The required SCF shielding step will be performed in the same run This flag will be set by the script mp2prep traloop n specifies the number of loops or passes over occupied orbitals n when doing an MP2 calculation the more passes the smaller file space requirements but CPU time will go up This flag will be set by the script mp2prep mointunit Scratch file settings for an MP2 calculation Please refer to Section 20 2 16 for a description of the syntax This flag will be set by the script mp2prep csconv real Sets the convergence threshold for the shielding constant of succeeding CPHF iterations The unit is ppm and the default value is 0 01 csconvatom integer This selects the atom number for convergence check after each cphf iteration After this convergence is reached all other atoms are checked too default 1 thime thiz
490. tational costs Large values of D indicate a multireference character of the ground state introduced by strong orbital relaxation effects In difference to the T and S2 diagnostics proposed earlier by Lee and coworkers the D4 diagnostic is strictly size intensive and can thus be used also for large systems and to compare results for molecules of different size MP2 and CC2 results for geometries and vibrational frequencies are in general in excellent agreement with those of higher order correlation methods if respectively D MP2 lt 0 015 and D CC2 lt 0 030 13 108 For D MP2 lt 0 040 and D CC2 lt 0 050 MP2 and or CC2 usually still perform well but results should be carefully checked Larger values of D indicate that MP2 and CC2 are inadequate to describe the ground state of the system correctly The D diagnostic proposed by Nielsen and Janssen 109 can also be evaluated This analysis can be triggered whenever a response property is calculated e g dipole moment with the keyword D2 diagnostic Note that the calculation of Do requires an additional O N step D2 MP2 CC2 lt 0 15 are in excellent agreement with those of higher order correlation methods for D2 MP2 CC2 gt 0 18 the results should be carefully checked 10 2 Calculation of Excitation Energies With the ricc2 program excitation energies can presently be calculated with the RI variants of the methods CCS CIS CIS D CIS Dx ADC 2 and CC2 The CC2
491. tations and open shell systems with urpa excitations 8 3 GENERAL RECIPE FOR GoWo CALCULATIONS 165 8 3 General recipe for GoW calculations The general recipe for a GgWo calculation is as follows 1 define session 2 Provide additional GW control flags 3 dscf or ridft calculation 4 escf calculation Ad 1 Symmetry has not yet been implemented for GW sensible calculations can only be done in C1 The def2 TZVPP basis seems to be the most useful it comes for all tested systems within 0 1 eV of the def2 QZVP result with about half the number of basis functions In the define session the calculation of the response function needs to be defined In the final define menu select the ex menu and select the calculation of RPA singlet excitations or urpa in case of open shell Select all all to get all excitations For systems and basis set having less than 4000 rpas excitations just set for all excitations For large systems start to run GoWo with 4000 rpas excitations In subsequent runs add more excitations until a converged result is reached escf will keep the converged roots so not much time is lost using this restart approach Ad 2 If gw is set in the control file the quasi particle energies will be evaluated according to equation 8 3 Additional options are described in the keyword section section 20 2 13 Ad 4 In the escf run the response function is calculated which is needed to determine the screened coulomb interaction At t
492. tations out of spin unrestricted reference states and scfinstab spinflip for spin flip z component of the total spin changes by 1 excitations out of spin unrestricted reference states For details concerning the theory see ref 103 In practice this functionality can be used for the calculation of triplet singlet quartet doublet excitations see ref 104 also for further information about the implementation It is only available within the TDA in combination with LDA functionals and the HF exchange It is strongly recommended to increase escfiterlimit In the two component case specify scfinstab soghf for two component excitation energy calculations on Kramers restricted closed shell systems 99 The keywords soghf and kramers also have to be set The implementation is only available in combination with LDA and GGA functionals Next the IRREPs of the excitations need to be defined which is again accomplished using soes For example to calculate the 17 lowest excitations in IRREP big the 23 lowest excitations in IRREP eu and all excitations in IRREP t2g use soes big 17 eu 23 t2g all and run escf Since point group symmetry cannot be exploited in two component calculations there is only the totally symmetric IRREP a Note that soes specifies the IRREP of the excitation vector which is not necessarily identical to the IRREP of the excited state s involved In general the IRREP s of the excitation s
493. te s from the energy difference s one may calculate approximate values for the spin spin coupling parameters as described by e g the above authors Access to broken symmetry states usually is possible by the choice of appropriate start MOs followed by an SCF procedure Start MOs may be obtained by first applying a localization procedure to the MOs of the high spin state and then by moving localized alpha orbitals to the beta subset The preparation of broken symmetry start MOs can be done with define semi automatically Prerequisite is a converged wave function for the high spin state in Ci symmetry that fulfills the aufbau principle If in this case one enters flip in the orbital definition menu define selects the occupied valence orbitals of the system by an orbital energy criterion which one can usually accept unless the system is highly charged and the orbital energies are shifted Next a Boys orbital localization procedure is carried out which depending on the size of the problem may take some time Then the user is asked ENTER INDICES OF ATOMS OR ELEMENT TO BE MANIPULATED example 1 2 3 or mn In case of our above example one may enter cu which immediately leads to the following output a def SV P basis and the B P functional were used for the high spin state RELEVANT LMOS FOR ATOM 1 cu ALPHA index occupation energy s p d f daxx dyy dzz dxy dxz dyz 15 1 000 0 357 0 01 0 00 0 98 0 20 0 27 0 01 0 50
494. ted either within the full time dependent HF TDHF or time dependent DFT TDDFT formalisms or within the Tamm Dancoff approximation TDA 151 152 CHAPTER 7 HF AND DFT RESPONSE CALCULATIONS Furthermore two component relativistic Kramers restricted closed shell ground states are supported vertical electronic excitation energies as well as transition moments oscillator and rotatory strengths LDA and GGA functionals are implemented in combination with the RI J approximation Excited state first order properties can be evaluated analytically using egrad They include e Gradients of the excited state energy with respect to nuclear positions Excited state equilibrium structures jobex adiabatic excitation energies emission spectra e Exited state densities Charge moments population analysis e Excited state force constants by numerical differentiation of gradients using the script Numforce Moreover analytical gradients of static and frequency dependent polarizabilities are available from egrad Together with vibrational normal modes from the aoforce or Numforce they are used to calculate vibrational Raman intensities Excited state gradients for MGGA functionals are presently unavailable Again ground states may be spin restricted closed shell or spin unrestricted RI J is available and either full TDDFT TDHF or the TDA can be used For further details we refer to a recent review 92 7 2 Theoretical Background
495. teger cycles default 100 begin with a direct SCF step begin with a gradient step begin with a force relaxation step use the relax program for force relaxation perform transition state search define the optimization level level scf mp2 cc2 uff or rirpa default is scf use RI modules ridft and rdgrad fast Coulomb approxi mation instead of dscf and grad as well as rimp2 instead of mpgrad obligatory option if level rirpa in connection with level cc2 the RI JK versions of HF and CPHF are switched on perform excited state geometry optimization using egrad employ programs from directory lt path gt load scripts from directory lt path gt a molecular dynamics MD run using frog instead of relax commands for MD run are contained in this file default mdmaster option to execute a shell script before the frog step keep program output from all optimization steps shows a short description of the commands above There will be an output written to file job start which informs you about the current options The convergence is signalled by the file converged otherwise you should find the file not converged within your working directory If jobex finds a file named stop or STOP in the working directory jobex will stop after the present step has terminated You can create stop by the command touch stop The output of the last complete cycle is written to file job last while the output of the running cycle is co
496. ter response theory according to Eq 10 21 have the same symmetry with respect to an interchange of the operators Vj and V2 and with respect to complex conjugation as the exact transition moments In difference to SCF RPA TD DFT or FCI transition strengths calculated by the coupled cluster response models CCS CC2 etc do not become gauge independent in the limit of a complete basis set i e for example the dipole oscillator strength calculated in the length velocity or acceleration gauge remain different until also the full coupled cluster equivalent to the full CI limit is reached For a description of the implementation in the ricc2 program see refs 13 126 The calculation of transition moments for excitations out of the ground state resembles the calculation of first order properties for excited states In addition to the left and right eigenvectors a set of transition Lagrangian multipliers M y has to be deter mined and some transition density matrices have to be constructed Disk space core memory and CPU time requirements are thus also similar The single substitution parts of the transition Lagrangian multipliers N u are saved in files named CCMEO s m sxaz To obtain the transition strengths for excitations out of the ground state the key word spectrum must be added with appropriate options see Section 20 2 17 to the data group excitations else the input is same as for the calculation of excitation energies and fir
497. than half filled shells of degenerate orbitals the calculations half to be done in a point group that lifts the degeneracy such that it 172 CHAPTER 9 2ND ORDER M OLLER PLESSET PERTURB THEORY becomes possible to assign integer occupation numbers A symmetry breaking of the orbitals can be avoided by doing the Hartree Fock calculation in the full point group The input and MO coefficients can then be transformed to a lower point group using define only for the ricc2 calculation Calculations with mpgrad 1 Add denconv 1 d 7 to the control file and perform a dscf run 2 If any orbitals are decided to be excluded from MP2 treatment add data group freeze manually to the control file see also Section 20 2 16 3 For preparation of an mpgrad run use the script Mp2prep mp2prep e g m memory p discspace scratch file directory As an example with the command mp2prep e m 100 p 1000 work an MP2 energy calculation is prepared the amount of available core memory is restricted to 100 MB the MOs are blocked so that integral scratch files located in the directory work do not need more than 1000 Mb The number of blocks i e the number of passes with repeated integral evaluations is writ ten to the control file traloop as well as the specification of scratch files mointunit see Section 20 2 16 Note less disc space means more passes and thus lower efficiency of mpgrad but due the technical limitations discspace should be
498. than the traditional finite point charges embedding 6 5 2 Theoretical Background Generally the PEEC method divides the entire periodic and infinite system into two parts the inner I part or so called cluster and the outer O part which describes its environment Thus unlike true periodic quantum mechanical meth ods PEECM primarily aims at calculations of structure and properties of localized defects in dominantly ionic crystals The innermost part of the cluster is treated quantum mechanically QM whereas in the remaining cluster part cations are re placed by effective core potentials ECPs and anions by ECPs or by simply point charges Such an isolating outer ECP shell surrounding the actual QM part is necessary in order to prevent artificial polarization of the electron density by cations which would otherwise be in a direct contact with the QM boundary The outer part or the environment of the cluster is described by a periodic array of point charges representing cationic and anionic sites of a perfect ionic crystal The electronic Coulomb energy term arising from the periodic field of point charges surrounding the cluster has the following form NEUC u v 7 F p n gt D S Dwa f ET heat LEO where UC denotes the unit cell of point charges Dy are elements of the density matrix u v are basis functions qk Ry denote charges and positions of point charges and L denote direct lattice vectors of the outer part O It
499. the initial state while the latter file contains the same data but associated with the keywords for the final state In order to run a hotFCHT calculation you need to optimize the structures of two electronic states usually the electronic ground state and an excited or ionized state and obtain the harmonic force fields for both using either aoforce or NumForce In order to generate the hotFCHT input just concatenate the hotfcht_header inp file from any of the two calculations and the hotfcht_data_i inp file from the calculation that refers to 13 4 INTERFACE TO HOTFCHT 229 the initial state e g the ground state in case of an absorption spectrum and the hotfcht_data_f inp file from the calcuation of the final state the excited state in case of an absorption spectrum Carefully edit the keywords in the header of the resultant file and run hotFCHT please refer to the hotFCHT documentation for further information Chapter 14 First order electron vibration coupling 14 1 Theoretical background At the effective single particle level the Hamiltonian of the coupled system of elec trons and vibrations is given by H H H H 14 1 where the first term H describes the electronic system and the second term HY the vibrational degree of freedom respectively The last term in the Hamiltonian HY X X df Aad bh ba 14 2 pv a describes the first order EV interaction The EV coupling constants are given as ee dH
500. the keyword geoopt is used the relaxed dipole moment for the specified excited state and wavefunction model will be written to the control file and used in calculations with NumForce for the evaluation of the IR intensities 10 3 3 Visualization of densities and Density analysis As most other programs which allow for the calculation of wavefunctions and densi ties also the ricc2 module is interfaced to wavefunction analysis and visualization toolbox described in chapter 16 From ricc2 module this interface can used in two different ways 1 If through the geoopt keyword in ricc2 a unique method and state has been specified for which the density gradient and properties are evaluated the density analysis and visualization routines will called by default with the orbital relaxed density for this state and method similar as in dscf ridft mpgrad etc 2 The ricc2 program can be called in a special analysis mode which allows to analyse densities and combination e g differences of densities evaluated in preceeding ricc2 calculations Default density analysis and visualization As in a single calculations with the ricc2 program one electron densities can be calculated for more than one method and or electronic state the interface to the analysis and visualization routines require the specification of a unique level of cal culation and a unique state This is presently done through the geoopt flag which determines the method state for whic
501. the numerical integration in Eq 9 8 and can be understood and estimated from the following considerations e The computational costs for the most expensive step in canonical RI MP2 energy calculations for large molecules requires 50 V Nz floating point mul tiplications where O and V are respectively the number occupied and virtual orbitals and Ny is the number of auxiliary functions for the RI approxima tion For the LT SOS RI MP2 implementation the most expensive step in volves npOV N2 floating point multiplications where nz is the number of grid points for the numerical integration Thus the ratio of the computational costs is approximately 50 V Nz OV npOVN2 2niNz where for the last step Ny 3V has been assumed Thus the Laplace transformed implementation will be faster than the conventional implemen tation if O gt nz conv LT x x O 6nr The number of grid points nz depends on the requested accuracy and the spread of the orbital energy denominators in Eq 9 8 The efficiency of Laplace transformed SOS RI MP2 calculations can therefore in difference to conventional RI MP2 cal culations be enhanced significantly by a carefull choice of the thresholds the basis set and the orbitals included in the correlation treatment e The threshold conv for the numerical integration is by default set to the value of conv specified for the ground state energy in the data group ricc2 see Sec 20 2 17 which is initi
502. the submenu rijk choose on and select your auxiliary basis set Then run the jobex script the additional rijk flag gt jobex level cc2 rijk 10 4 Transition Moments Transition moments are presently implemented for excitations out of the ground state and for excitations between excited states for the coupled cluster models CCS and CC2 Transition moments for excitations from the ground to an excited state are also available for ADC 2 but use an additional approximation see below Note that for transition moments as for excited state first order properties CCS is not equivalent to CIS and CIS transition moments are not implemented in the ricc2 program 10 4 1 Ground to excited state transition moments In response theory transition strengths and moments for transitions from the ground to excited state are identified from the first residues of the response func tions Due to the non variational structure of coupled cluster different expressions are obtained for the CCS and CC2 left and right transitions moments M f and M i The transition strengths ce y are obtained as a symmetrized combinations of both 130 1 y of V V V V Sth 5 M M o ME M o 10 21 202 CHAPTER 10 RI CC2 Note that only the transition strengths gy w are a well defined observables but not the transition moments My f and MY o For a review of the theory see refs 128 130 The transition strengths calculated by coupled clus
503. the total distance correction to be applied on each constraint iteration type X A const rmax commands frog to find the closest A atom to each atom X that is closer than rmax and apply const The first type line above examines each H 368 CHAPTER 20 KEYWORDS IN THE CONTROL FILE atom and looks for any 0 atoms within 1 2 A The shortest distance if any is then fixed at 0 9A Similarly the second type line binds each F to the closest C within 1 7 but since const 0 0 that distance is fixed at the current value The third type line attaches H atoms to the appropriate nearby C but at the current average H C distance multiplied by the absolute value of const Explicitly specified constraints are listed by atom index and supercede auto generated constraints A positive third number fixes the constraint at that value while zero fixes the constraint at the current distance and a negative number unsets the constraint The output of frog contains the full list of constrained atom pairs and their current constraints in explicit format User defined instructions allow the user to tell frog to change some aspect of the MD run at some point in time t real number The same format is used for md_status above Here is an example md_action fix total energy from t 2000 0 anneal from t 2500 0 free from t 3000 0 In this example starting from the time 2000 0a u velocities are to be scaled every step to keep average total energy
504. tic energy by Lembarki and Chermette 167 LC94 e string t f gradient expansion truncated at the zeroth order GEAQO corre sponding to the Thomas Fermi functional For example the command FDE p 3 k 1c94 approximates the non additive kinetic contribution to the embedding potential through the functional derivative of LC94 kinetic energy functional 250 CHAPTER 17 FROZEN DENSITY EMBEDDING CALCULATIONS A pure electrostatic embedding can be also performed with FDE script where the embedding potential required by a subsystem A to account for the presence of the B one will be merely Vemb P Vex t vy pa r 17 9 with v8 r and vy pg r the electrostatic potentials generated respectively by the nuclei and electron density of the subsystem B To perform an electrostatic embed ding calculation use FDE p 3 k electro and can be performed for both Kohn Sham only for LDA GGA exchange correlation functionals and Hartree Fock methods The electrostatic embedding is implemented only for testing purpose It resembles an electrostatic embedding with external point charges and or point dipoles but it is exact as it is based on the whole densities i e it considers all multipole moments of the density and the polarizabilies at all orders Equivalent command kin string fde input option kin string FDE charged subsystems FDE can perform calculations for charged closed shell systems whose charge is lo cal
505. ting up the parallel environment as described in the previous section parallel jobs can be started just like the serial ones If the input is a serial one it will be prepared automatically for the parallel run The parallel versions of the programs dscf and grad need an integral statistics file as input which is generated by a parallel statistics run This preparation step is done automatically by the scripts dscf and grad that are called in the parallel version In this preparing step the size of the file that holds the 2e integrals for semi direct calculations twoint is recalculated and reset It is highly recommended to set the path of this twoint file to a local scratch directory of each node by changing the line unit 30 size 7 7 file twoint to unit 30 size 7 7 file local_scratchdir twoint For the additional mandatory or optional input for parallel runs with the ricc2 program see Section 10 6 Running calculations on different nodes If TURBOMOLE is supposed to run on a cluster we highly recommed the usage of a queuing system like PBS The parallel version of TURBOMOLE will automatically recognise that it is started from within the PBS environment and the binaries will run on the machines PBS provides for each job Important Make sure that the input files are located on a network directory like an NFS disk which can be accessed on all nodes that participate at the calculation A file that contains a list of machines has to be
506. tion of scalar relativistic effects leads to additional contributions to the one electron integrals either from ECP or all electron approach The program structure is the same as in non relativistic theory all quantities are real Two component treatments allow for self consistent calculations including spin orbit interactions These may be particularly important for compounds containing heavy elements ad ditionally to scalar relativistic effects Two component treatments require the use of complex two component orbitals stay 6 wv r instead of real non complex one component orbitals needed for non relativistic or scalar relativistic treatments The Hartree Fock and Kohn Sham equations are now spinor equations with a complex Fock operator foa fob YN We psa pee ya T wre The wavefunction is no longer eigenfunction of the spin operator the spin vector is no longer an observable In case of DFT for open shell systems rotational invariance of the exchange correlation energy was ensured by the non collinear approach In this approach the exchange correlation energy is a functional of the particle density and the absolute value of the spin vector density m r are the Pauli matrices mle v avl This quantity replaces the spin density difference between density of alpha and beta electrons of non or scalar relativistic treatments For closed shell species the Kramers restricted scheme a generalization of t
507. tion to the Hessian matrix The optimization procedure implemented in statpt belongs to the family of quasi Newton Raphsod methods 30 It is based on the restricted second order method which employes Hessian shift parameter in order to control the step length and direction This shift parameter is determined by the requirement that the step size should be equal to the actual value of the trust radius tradius and ensures that the shifted Hessian has the correct eigenvalue structure all positive for a minimum search and one negative eigenvalue for a TS search For TS optimization there is another way of describing the same algorithm namely as a minimization on the image potential The latter is known as TRIM Trust Radius Image Minimization 31 For TS optimizations the TRIM method implemented in statpt tries to maximize the energy along one of the Hessian eigenvectors while minimizing it in all other directions Thus one follows one particular eigenvector hereafter called the tran sition vector After computing the Hessian for your guess structure you have to identify which vector to follow For a good TS guess this is the eigenvector with negative eigenvalue or imaginary frequency A good comparison of different TS optimization methods is given in 32 Structure optimizations using statpt are controlled by the keyword statpt to be present in the control file It can be set either manually or by using the stp menu of
508. tions can be done employing the X2C the BSS or the DKH Hamiltonian Implemented for modules dscf and ridft rx2c switches on X2C calculation rbss switches on BSS calculation rdkh integer switches on DKH calculation of order integer dkhparam integer selects parameterization of the DKH Hamiltonian Valid values are 1 de fault 2 3 4 and 5 dkhparam 1 Optimum parametrization OPT dkhparam 2 Exponential parametrization EXP dkhparam 3 Square root parametrization SQR dkhparam 4 McWeeny parametrization MCW dkhparam 5 Cayley parametrization CAY Note in particular that the parametrization does not affect the Hamiltonian up to fourth order Therefore as long as you run calculations with DKH Hamil tonians below 5th order you may use any symbol for the parametrization as they would all yield the same results Higher order DKH Hamiltonians depend slightly on the chosen paramterization of the unitary transformations applied 20 2 FORMAT OF KEYWORDS AND COMMENTS 305 in order to decouple the Dirac Hamiltonian but this effect can be neglected For details on the different parametrizations of the unitary transformations see 194 rlocal switches on local DLU approach rlocpara integer selects parameterization of the local approximation Valid values are 0 or 1 For details on the different parametrizations see 75 All of these keywords are combinable with soghf 20 2 7 Keywords for Periodic Electr
509. tions rohf orbitals can be used which also implies that the freeze data group options refer to ROHF rather than semi canonical orbitals For closed shell species lo calised orbitals can be used with either the Boys or Pipek Mezey method For the non semi canonical options the r12orb noinv F12 energy cor rection is evaluated using active occupied orbitals transformed to the same basis as the orbitals in the geminal function ccsdapprox label defines the approximation to CCSD F12 which will be used if the MP2 F12 calculation is followed by a CCSD or CCSD T calculation The available approximation and corresponding labels are CCSD F12 ccsd 12 CCSD F12 ccsd 12 CCSD F12 ccsd 12 CCSD F12b ccsd f12b CCSD 2 a5 ccsd 2 _ f12 CCSD 2 Fp ccsd 2 _ f12 It is recommended that these approximations are only used in combina tion with ansatz 2 and the SP approach i e geminal coefficients fixed by the cusp conditions For CCSD F12b calculations also the CCSD F12a energies are calculated as a byproduct By default a CCSD F12 calcu lation is carried out but it is recommended that whenever appropriate the computationally more efficient CCSD F12 approximation is used 20 2 FORMAT OF KEYWORDS AND COMMENTS 333 excitations irrep au multiplicity 1 nexc 4 npre 6 nstart 8 irrep bg multiplicity 3 nexc 2 npre 4 nstart 5 spectrum states all operators diplen dipvel tmexc istates all fstates all operators diplen dipvel expr
510. tive Effective core potentials ECPs are not presently compatible with the HF energy at the KS reference as computed in rirpa The nohxx option must therefore be included for systems where ECPs were used to obtain the reference KS orbitals in order to skip the HF energy calculation and compute solely the correlation energy To perform a two component relativistic RIRPA calculation 147 on Kramers restricted closed shell systems taking into account spin orbit coupling the two component version of ridft has to be run before see Chapter 6 4 using the keywords soghf and kramers The implementation is currently only available in combina tion with the nohxx option 12 2 Gradients Theory All details on the theory and results are published in 146 The RI RPA energy is a function of the MO coefficients C and the Lagrange multipliers and depends parametrically i on the interacting Hamiltonian H ii on the AO basis functions and the auxiliary basis functions All parameters may be gathered in a supervector X and thus en C eX 12 9 C and e in turn depend parametrically on X the exchange correlation matrix V and the overlap matrix S through the KS equations and the orbital orthonormality 220 CHAPTER 12 RANDOM PHASE APPROXIMATION constraint First order properties may be defined in a rigorous and general fashion as total derivatives of the energy with respect to a perturbation parameter However the RI RP
511. to a non local exchange contribution as in conventional hybrid GGAs also a non local perturbation correction for the correlation part In the following options restrictions of this method are given single point calculations only computed with the DSCF RIDFT and RIMP2 RICC2 modules UKS treatment for open shell cases can be combined with resolution of identity approximation for the SCF step RI JK or RI J option can be combined with the dispersion correction DFT D method sg B2 PLYP 0 55 The non local perturbation correction to the correlation contribution is given by second order perturbation theory The idea is rooted in the ab initio Kohn Sham perturbation theory KS PT2 by Gorling and Levy 71 72 The mixing is described by two empirical parameters a and ae in the following manner Exc DHDF 1 az Ex GGA a Ex HF 6 6 1 a Ec GGA acEc KS PT2 where Ey GGA is the energy of a conventional exchange functional and Ec GGA is the energy of a correlation functional x HF is the Hartree Fock exchange of the occupied Kohn Sham orbitals and Ec AS PT2 is a M ller Plesset like perturbation correction term based on the KS orbitals Ec KS PT2 ald ia jb iblja 6 7 ea The method is self consistent only with respect to the first three terms in Eq 6 6 i e first a SCF using a conventional hybrid GGA is performed first Based on these orbitals Ec AS
512. to configuration interaction including all single excitations from the HF reference CIS The TDA is 154 CHAPTER 7 HF AND DFT RESPONSE CALCULATIONS not gauge invariant and does not satisfy the usual sum rules 93 but it is somewhat less affected by stability problems see below For MGGA functionals the response of the paramagnetic current density is required to ensure gauge invariance and is included by default Stability analysis of closed shell electronic wavefunctions amounts to computing the lowest eigenvalues of the electric orbital rotation Hessian A B which decom poses into a singlet and a triplet part and of the magnetic orbital rotation Hessian A B Note that A B is diagonal for non hybrid and non MGGA DFT while A B generally is not See refs 19 96 98 for further details The two component relativistic TDDFT eigenvalue problem for excitations of Kramers restricted closed shell systems taking approximately into account the effect of spin orbit coupling is M X Y 2 X Y 7 11 M is a Hermitian complex matrix containing spinor energy differences Coulomb matrix elements as well as matrix elements of the two component noncollinear exchange correlation kernel An explicit expression for M can be found in ref 99 X Y are complex two component excitation vectors Properties of excited states are defined as derivatives of the excited state energy with respect to an external perturbation It is
513. to start the CCSD T INT F12 calculation from a converged SCF calculation with symmetry which is transfromed to C4 It is furthermore rec ommended to use Boys localized orbitals in the rir12 submenu A table with the corrected second order pair electron energies and the corresponding interference fac tors can also be printed in the output by using the keyword intcorr all instead of intcorr Excitation energies with CCSD Since release V6 5 electronic excitation ener gies can also be computed at the conventional CCSD level For this the data group excitations has be added the same keyword as for CC2 apply The implemen tation is currently restricted to vertical excitation energies no transition moments or properties available and in the closed shell case to singlett excited states Note that for single excitation dominated transitions CCSD is as CC2 correct through second order in H and does not neccessarily more accurate than CC2 It is however for double excitations still correct through first order while CC2 describes double excitations only in a zero order approximation Therefore CCSD results are more robust with respect to double excitation contributions to transitions and are thus usefull to check if CC2 is suitable for a certain problem Chapter 12 Random Phase Approximation Calculations Energy and First Order Properties Ground state energies and analytic first order properties e g gradients for struc ture o
514. tomic orbitals momao print MO contributions to occupation numbers of modified atomic orbitals MAOs maodump print all MAOs on standard output maofile mao all print all MAOs to file mao This kind of population analysis basically aims at so called shared electron numbers SEN between two or more atoms By default 2 3 and 4 center contributions to the total density are plotted if they are larger than 0 01 elec trons Thresholds may be individually chosen as well as the possibility to compute SENs for molecular orbitals shared electron numbers orbitals 2 center threshold real 3 center threshold real 4 center threshold real Results of this kind of PA depend on the choice of MAOs By default all MAOs with eigenvalues of the atomic density matrices larger than 0 1 will be taken into account This is a reasonable minimal basis set for most molecules If modified atomic orbitals shall not be selected according to this criterion the data group mao selection has to be specified mao selection threshold real The default criterion for the selection of MAOs is the occupation number for which a global threshold can be specified within the same line as the keyword maoselection If the global criterion or threshold is not desirable for some atoms lines of the following syntax have to be added for each atom type of these atom symb list nmao i method meth threshold r 20 2 plot FORMAT OF KEYWORDS AND COMMENTS 3
515. tropic part and the anisotropy of the differ entiated polarizability tensor respectively The coefficients c and Ca depend on the scattering geometry and the polarization of the incident and scattered radiation The factor w ww go om 4rekc Quy includes the frequency w and the degeneracy g of the vibration c is speed of light and o stands for the dielectric constant of vacuum Computation of Raman spectra with TURBOMOLE is a three step procedure First vibrational frequencies and normal modes are calculated by aoforce Cartesian polarizability derivatives are computed in the second step by egrad see Section 7 4 7 Finally the program intense is used to project the polarizability derivatives onto vibrational normal modes and to compute Raman scattering cross sections which are written out along with vibrational frequencies and normal modes The script Raman can be used to perform all these steps automatically 13 3 Vibrational frequencies with fixed atoms using NumForce The NumForce script provides with the option frznuclei a possibility to do a vi brational analysis with fixed atoms The atoms for which the cartesian coordinates should frozen have to be marked in coord with a f behind the atom type The frozen coordinates will be skipped during the numerical evaluation of the force con stant matrix instead all off diagonal elements of the force constant matrix which refer to one or two frozen coordinates will be
516. ts scaling factors global on off Optimization of global scaling factor for all basis set expo nents Note All options except internal are switched off by default unless they have been activated explicitly by specifying on Some of the options may be used simultaneously e g e internal basis e internal global e cartesian basis Other options have to be used exclusively e g e internal cartesian e basis global 104 CHAPTER 5 STRUCTURE OPTIMIZATIONS The update of the coordinates may be controlled by special options provided in data group coordinateupdate which takes as options dqmax real Maximum total coordinate change default 0 3 interpolate on off Calculate coordinate update by inter extrapolation us ing coordinates and gradients of the last two optimiza tion cycles default interpolate on if possible statistics integer off Display optimization statistics for the integer previous optimization cycles Without integer all available in formation will be displayed off suppresses optimiza tion statistics The following data blocks are used by program relax 1 Input data from gradient programs grad rdgrad egrad rimp2 mpgrad etc grad cartesian atomic coordinates and their gradients egrad exponents and scale factors and their gradients globgrad global scale factor and its gradient 2 Input data from force constant program aoforce grad cartesian atomic coordinates and their gradie
517. ts for interpolation between the two isotopes compared by the isosub option to six Default value is 21 Keywords for the treatment of only selected nuclear displacement vectors ironly CPHF iteration is done only for distortions that are IR active ramanonly les CPHF iteration is done only for distortions that are Raman active This causes a lowest Hessian eigenvalue search to be performed instead of a complete force constant calculation The lowest eigenvalue search consists of the calculation of a guess Hessian and macro iterations to find the solution vector s for the lowest eigenvalue s In each macro iteration the CPHF equations are solved for the present search vector s les all 1 means that one lowest eigenvalue for each irrep will be determined other numbers of lowest eigenvalues per irrep are admissible too Different numbers of lowest eigenvalues for different irreps are requested by e g les al 3 a2 all b2 1 The convergence criterion of the Davidson iterations for the solution of the CPHF equations as well as the maximal residual norm for the lowest Hessian eigenvalue in the macro iteration are specified by forceconv as explained above The maximum number of macro iterations is specified by lesiterlimit x with the default x 25 The maximum number of iterations for each solution of the CPHF equations is again determined by forceiterlimit as shown above 20 2 FORMAT OF KEYWORDS AND COMME
518. ts is specified maximum and default is i 3 octopole moments real numbers x y z allow for the specification of one or more reference points drives the options for population analyses By default a Mulliken PA in the basis of cartesian atomic orbitals CAQOs is performed for the total density D D leading to Mulliken brutto charges and in case of spin unrestricted calculations also for the spin density D D leading to Mulliken brutto numbers for unpaired electrons Besides total numbers also contributions from s p functions are listed separately Two component wavefunctions only module ridft and only if soghf is set In two component calculations instead of S Sz Sy Sz is written to the out put Additionally a vector file named spinvec txt is written which includes the resulting spinvector for each atom in the system also the direction 356 CHAPTER 20 KEYWORDS IN THE CONTROL FILE The following modifications and extensions are supported if the respective commands are written in the same line as pop lall Additional information about pz Py pz and analogous for d and f func tions is displayed lengthy output atoms list of atoms Contributions are plotted only if arising from atoms selected by list thrpl real Contributions smaller than thrpl are not displayed default 0 01 overlapMulliken atomic overlap matrix is displayed nettoMulliken netto populations diagonal element
519. ual approximate force constant matrix from forceapprox if this energy change will be exceeded the force constants will be scaled appropriately The default 0 0 means NO action scale real scaling factor for the input hessian default 1 0 344 CHAPTER 20 KEYWORDS IN THE CONTROL FILE threig real lower bound for eigenvalues of the approximate hessian default 0 005 if any eigenvalue drops below threig it will be shifted to a reasonable value defined by reseig realdefault texttt0 005 thrbig real upper bound for eigenvalues of the hessian if any eigenvalue exceeds thrbig it will limited to this value default 1000 0 damping real damp the variable metric update for the hessian by 1 1 real default 0 0 forceinit option specify initialization of the approximate force constant matrix Available options are on off this activates or deactivates initialization if on has been set relax will provide an initial force constant matrix as specified by one of the possible initialization options as described below and will store this matrix in data group forceapprox after initialization relax resets forceinit to off diag suboptions provide a diagonal force constant matrix with available suboptions are real this will lead to an assignment of diagonal elements default 1 0 default this will lead to an assignment of initial force constant diagonals depending on the coordinate type individual Provide i
520. uantitative DFT TZVP HF TZVPP MP2 QZVPP basis set limit DFT QZVP HF QZVP If you want a better basis than SV P assigned automatically use b all def2 TZVP or another basis The assignment can be checked by b1 Diffuse functions should only be added if really necessary E g for small anions or treatment of excited states use TZVP instead of SVP diffuse This is more accurate and usually faster Only for excited states of small molecules or excited states with a partial Rydberg character add additional diffuse functions e g by using the aug cc pVTZ basis as well as the keyword diffuse for more information see page 279 in the keyword section Old basis sets def XYZ For standard correlated calculations MP2 RI MP2 RI CC2 use the doubly polarized TZVPP or def TZVPP basis Correlation Consistent Dunning Basis Sets Dunning basis sets like cc pVDZ cc pVTZ cc pVQZ are also supported e g by b all cc pVTZ But these basis sets employ generalized contractions for which TURBOMOLE 4 2 THE ATOMIC ATTRIBUTES MENU 63 is not optimized This has in particular strong effects on the performance of all pro grams which use 4 index electron repulsion integrals for RI MP2 and RI CC2 this is partially compensated by the RI approximation The following correlation consistent basis sets are available in the TURBOMOLE basis set library cc pVXZ standard valence X tuple zeta basis sets X D T Q 5 6 available for H
521. ue difference integer plot Two molecular orbitals are considered as degenerated due to symmetry or incidentally if the difference between them is smaller then 107 9 The variable integer must have an integer value The default value is 6 coefficient string The expansion coefficients for the auxiliary basis functions which build the local exact exchange potential are written to the file oepcVx dat or in case of a spin unrestricted calculation to the files oepcVxa dat and oepcVxb dat If string is cartesian the expansion coefficients are given for a cartesian atomic orbital auxiliary basis if string equals spherical the expansion coefficients are given for a spherical atomic orbital auxiliary basis In any case the expansion coefficients are given for the single atomic orbital auxiliary basis function and contain no information about the symmetry of the system cl case The default value is cartesian reference potential Use the reference potential constructed by the applied conditions to the OEP calculation as exchange potential The solution of the OEP equa tion is skipped The default value is false To run a LHF calculations select dft functional lhf gridsize 3 This can be done using define modified grid are not supported and then run odft A more suitable procedure is the following 18 3 HOW TO PERFORM 261 1 Do a Hartree Fock calculation using dscf 2 Use the script lhfprep to prepare the contr
522. ue is 75 85 of the available physical core memory 3 Calculations using MARI J method require the keyword marij 4 For RI HF calculations auxiliary bases defined in the data group jkbas are needed This group is created by the rijk menu in define How to Perform a Calculation Single point calculations Call the dscf or ridft program after running define Geometry optimizations and molecular dynamics For HF or DFT calculations using dscf and grad simply invoke jobex For DFT calculations using ridft and rdgrad type jobex ri see Sec tion 5 1 for additional options and parameters for geometry optimizations and ab initio molecular dynamics calculations 6 1 Background Theory In Hartree Fock theory the energy has the form Egyr h J K Vnue 6 1 where h is the one electron kinetic plus potential energy J is the classical Coulomb repulsion of the electrons K is the exchange energy resulting from the quantum fermion nature of electrons and Vnuc is the nuclear repulsion energy 126 CHAPTER 6 HARTREE FOCK AND DFT CALCULATIONS In density functional theory the exact Hartree Fock exchange for a single determi nant is replaced by a more general expression the exchange correlation functional which can include terms accounting for both exchange energy and the electron cor relation which is omitted from Hartree Fock theory The DFT energy is expressed as a functional of the molecular electron density p r Eprr p
523. ular it is possible to calculate the xy Singlet case As a guide for expert users complete ROHF TURBOMOLE input for O for various CSFs configuration state function is given in Section 21 6 Further examples are collected below The ROHF ansatz for the energy expectation value has a term for interactions of closed shells with closed shells indices k l a term for purely open shell interactions indices m n and a coupling term k m E 2 p hkk 5 QJ Ky k k l m n k m where f is the fractional occupation number of the open shell part 0 lt f lt 1 and a and b are the Roothaan parameters numerical constants which depend on the particular configuration of interest 6 3 2 One Open Shell Given are term symbols up to indices depending on actual case and group and a and b coefficients n is the number of electrons in an irrep with degeneracy nir Note that not all cases are Roothaan cases All single electron cases are described by a b 0 6 3 RESTRICTED OPEN SHELL HARTREE FOCK Table 6 1 Roothaan coefficients a and b for cases with de generate orbitals 131 Nip 2 e div groups 7 6 Coov Dooh n f e mh 6 a b 3A oy 35 1 2 2 1 2 1B 1A IT 1 2 0 TA 5 D 0 2 3 3 4 2E 21 2A 8 9 8 9 1 nip 3 p O 3 t T O D n f p a b 3P 3 4 3 2 2 1 3 Ip 9 20 3 10 Is 0 3 1S 1 2
524. ulation with a larger grid i e gridsize 7 The test suite example TURBODIR TURBOTEST dscf short H3P04 DSCF DIFFUSE provides an example of usage this also gives reasonable values for damp ing and orbitalshift to reach convergence in this and similar cases see scfdamp and scforbitalshift p 285 and p 288 Example Recommendation dft gridsize m4 diffuse 2 rhostart integer howtos titaet for developers only Radial grid points have a linear scaling parameter see Eq 16 19 and Table 1 in Ref 192 With the following input dft rhostart 50 rhostop 200 286 CHAPTER 20 KEYWORDS IN THE CONTROL FILE one performs a numerical integration for the density and the exchange correlation term for 0 5 0 01 2 0 for given MOs and functional NOTE only molecules with a single atom type can be used The results serve to establish stable optimal values see Figure 1 in Ref 192 Program stops after this testing reference Usage of the reference grid which is a very fine grid with very tight thresholds The default values for the different variables are gridsize 7 radsize 14 fullshell 1 dgrenze 16 fgrenze 16 qgrenze 16 fcut 16 Please refer to the corresponding sub keywords for explanation If you want to use the reference grid you have to skip the keyword gridsize and type instead reference Example dft functional b p reference test integ Check if the selected grid is a
525. ulations of NMR shielding constants using the localized Hartree Fock method Chem Phys Lett 383 1 2 115 121 2004 E Fabiano M Piacenza S D Agostino F Della Sala Towards an accurate description of the electronic properties of the biphenylthiol gold interface The role of exact exchange J Chem Phys 131 23 234101 2009 F Della Sala E Fabiano Accurate singlet and triplet excitation energies using the Localized Hartree Fock Kohn Sham potential Chem Phys 391 1 19 26 2011 A Klamt G Schiitirmann COSMO A new approach to dielectric screening in solvents with explicit expressions for the screening energy and its gradient J Chem Soc Perkin Trans 2 5 799 805 1993 420 182 183 184 185 186 187 188 189 190 191 192 193 BIBLIOGRAPHY A Klamt V Jonas Treatment of the outlying charge in continuum solvation models J Chem Phys 105 22 9972 9981 1996 A Klamt Calculation of UV Vis spectra in solution J Phys Chem 100 9 3349 3353 1996 F J Olivares del Valle J Tomasi Electron correlation and solvation effects I Basic formulation and preliminary attempt to include the electron correla tion in the quantum mechanical polarizable continuum model so as to study solvation phenomena Chem Phys 150 2 139 150 1991 J G Angyan Rayleigh Schr dinger perturbation theory for nonlinear Schr dinger equations
526. ult the positions of point charges are specified in atomic units as Cartesian coordinates You can change this by specifying cluster frac for fractional crystal coordinates or cluster ang for Cartesian coordinates in Finally you have to specify the coordinates of the QM cluster along with the sur rounding ECPs representing cationic sites and explicit point charges representing anions This is done in the usual way using the coord keyword coord O 00000000000000 0 00000000000000 O 00000000000000 f 2 86167504097169 2 86167504097169 2 86167504097169 ca 2 86167504097169 2 86167504097169 2 86167504097169 ca 2 86167504097169 2 86167504097169 2 86167504097169 ca 2 86167504097169 2 86167504097169 2 86167504097169 ca O 00000000000000 5 24009410923923 O 00000000000000 f 5 24009410923923 0 00000000000000 O 00000000000000 f O 00000000000000 5 24009410923923 O 00000000000000 f O 00000000000000 0 00000000000000 5 24009410923923 f 5 24009410923923 0 00000000000000 O 00000000000000 f O 00000000000000 0 00000000000000 5 24009410923923 f O 00000000000000 5 24009410923923 5 24009410923923 f 5 24009410923923 5 24009410923923 O 00000000000000 f 5 24009410923923 5 24009410923923 O 00000000000000 f O 00000000000000 5 24009410923923 5 24009410923923 f O 00000000000000 5 24009410923923 5 24009410923923 f repeated for Caz16 F389 end 6 5 PERIODIC ELECTROSTATIC EMBEDDED CLUSTER METHOD 145 This is the standard
527. ultipliers t are solved which requires similar resources CPU disk space and memory as the calculation of a single excitation energy For orbital relaxed properties also a CPHF like linear equation for the Lagrangian multipliers K needs to be solved and the two electron density has to be build since it is needed to set up the inhomogeneity right hand side The calculation of relaxed properties is therefore somewhat more expensive the operation count for solving the so called Z vector equations is similar to what is needed for an SCF calculation and requires also more disk space to keep intermediates for the two electron density about O 2V 2N N N2 in addition to what is needed for the solution of the cluster equations For ground states orbital relaxed first order properties are standard in the literature The calculation of the gradient implies the calculation of the same variational den sities as needed for relaxed one electron properties and the solution of the same equations The construction of the gradient contributions from the densities and derivative integrals takes about the same CPU time as 3 4 SCF iterations and only minor extra disk space For details of the implementation of CC2 relaxed first order properties and gradients and a discussion of applicability and trends of CC2 ground state equilibrium geometries see ref 13 The following is in example input for a MP2 and CC2 single point calculation of first order p
528. using the stp menu of define The necessary keywords are described in Section 20 2 19 below For structure optimization of minima with statpt as relaxation program just use jobex amp TS optimizations are performed by the jobex invokation jobex trans amp 5 2 2 Hessian matrix The choice of the initial Hessian matrix has a great effect on the convergence of the structure optimization At present there are three choices for the Hessian matrix in statpt For minimization a diagonal matrix or approximate Hessian matrix from a forcefield calculation using uff see Section 5 4 can be used For transition state optimizations you have to provide either the exact Hessian or results from the low est eigenvalue search LES see Section 13 Note also that you can calculate the Hessian with a smaller basis set and or at a lower wavefunction level and use it for higher level structure optimization Usually a Hessian matrix calcu lated in a minimal basis using RI DFT is good enough for all methods implemented in TURBOMOLE 5 2 PROGRAM STATPT 101 statpt automatically takes the best choice of the Hessian from the control file For minimizations it first looks for the exact Hessian and then for the UFF Hes sian If none of them is found it takes the scaled unit matrix For transition state optimization the exact Hessian has a higher priority than the results of LES The results of LES can be used to obtain an initial Hessian matrix for tr
529. ussian LDA S VWN III 1 3 pwlda LDA IS PW 1 2 4 becke exchange GGA S B88 1 2 5 b lyp GGA S B88 LYP 1 2 6 b vwn GGA S B88 VWNCV 1 3 5 lyp GGA LYP 6 b p GGA S B88 VWNC V P86 1 3 5 7 pbe GGA S PBE X PW PBE C 1 2 4 8 tpss MGGA S TPSS X PW TPSS C 1 2 4 14 bh lyp HYB 0 5 S B88 LYP 1 2 5 6 9 l 0 5HF b3 lyp HYB 0 8S 0 72B88 0 19VWN CV 1 3 5 6 10 l 0 2HF 0 81LYP b3 lyp_Gaussian HYB 0 8S 0 72B88 0 19VWNCIII 1 3 5 6 10 l 0 2HF 0 81LYP pbe0 HYB 0 75 S PBE X PW PBE C 1 2 4 8 11 l 0 25HF tpssh HYB 0 9 S TPSS X PW TPSS C 1 2 4 14 15 0 1HF 1hf EXX EXX 12 13 b97 d GGA B97 refit B97 refit 16 b2 plyp DHYB 0 47 SB88 0 53HF 0 73LYP 0 27PT2 17 Default is b p i e B P86 which is probably best for the whole of Chemistry 27 For main group compounds we recommend b3 lyp note that GAUSSIAN uses partly different implementations 27 The programs dscf and grad are used to carry out conventional DFT treatments i e J and K are evaluated without approximations RI J calculations For non hybrid functionals we strongly recommend the RI J procedure which speeds up calculations by a factor 10 at least as compared to conventional treatments without sacrificing accuracy Command ri gives STATUS OF RI OPTIONS RI IS NOT USED Memory for RI 200 MB Filename for auxbasis a
530. ut occupied MOs and start vectors from a former calculation on the same molecule file should be the path and name of the control file of this former calcula tion of which all data groups related to occupation numbers and vectors will be read As the new generated data will overwrite the existing data if both resist in the same directory it is best and in some cases necessary to have the data of the former calculation in another directory than the one you started the define session in Then just type use lt path gt control to construct a new SCF vector from the data of the old calculation with out changing the old data The data groups closed shells and open shells will be taken for your new calculation and the SCF vector from the old calculation will be projected onto the space which is spanned by your present basis set These start vectors are usually better than the ones you could obtain by an extended Htickel calculation man allows you to declare occupation numbers or change a previous dec laration manually After selecting this command you will get a short information about the current occupation numbers actual closed shell orbital selection range al 1 18 a2 1 1 e 1 13 any further closed shell orbitals to declare DEFAULT y If you answer this question with y you enter the orbital specification menu which will be described in Section 4 3 3 The same procedure applies to the open shell occupation numbers after y
531. uxbasis ENTER RI OPTION TO BE MODIFIED m CHANGE MEMORY FOR RI 4 4 THE GENERAL OPTIONS MENU TT f CHANGE FILENAME jbas ASSIGN AUXILIARY RI J BASIS SETS on TO SWITCH ON RI Use lt ENTER gt q end or to leave this menu Activate RI J with on and choose with m the memory you can dedicate to store three center integrals Keyword ricore default is 200 MB The more memory the faster the calculation A rough guide put ricore to about 2 3 of the memory of the computer Use OS specific commands top on most UNIX systems during an ridft run to find the actual memory usage and then adjust ricore the keyword in control specifying memory If the option jbas is selected define enters a submenu which allows the assignment of auxiliary basis sets for an explanation of the menu items see Section 4 2 Where available the program will select by default the auxiliary basis sets optimized for the orbital basis used Please note that treatment of systems with diffuse wavefunctions may also require an extension of the auxiliary basis For this cases enlarge the sets of s and p functions with diffuse functions The RI J option is only supported by programs ridft and rdgrad if you use jobex to optimize molecular geometry put nohup jobex ri MARI J option RI J calculations can be done even more efficiently with the Multipole Accelerated RI J MARI J option especially for larger molecules where almost linear scaling is achieved 2
532. vated wave function and the dielectric energy E E W Euiet A CosMoO energy calculation starts with the construction of the cavity surface grid Within the SCF procedure the screening charges are calculated in every cycle and the potential generated by these charges is included into the Hamiltonian This ensures a variational optimization of both the molecular orbitals and the screening charges and allows for the evaluation of analytic gradients Radii based Cavity Construction In order to ensure a sufficiently accurate and efficient segmentation of the molecular shaped cavity the COSMO implementation uses a double grid approach and segments of hexagonal pentagonal and triangular shape The cavity construction starts with a union of spheres of radii R RSOLV for all atoms 7 In order to avoid problems with symmetric species the cavity con struction uses de symmetrized coordinates The coordinates are slightly distorted with a co sinus function of amplitude AMPRAN and a phase shift PHSRAN Ini tially a basis grid with NPPA segments per atom is projected onto atomic spheres of radii Ri RSOLV In order to avoid the generation of points in the problematic intersections all remaining points which are not in the interior of another sphere are projected downwards onto the radius R In the next step a segment grid of NSPH segments per H atom and NSPA segments for the other atoms is projected onto the surface defined by R The basis grid
533. w Nnb xyz TIJN D TT Nnb TS qr 4s Er The Fourier coefficients Ca Ce Ce of the general angle terms are evaluated as a function of the natural angle Oo 1 C 5 2 2 Asin 09 22 Ce 4 Of cos Op ci c 2 cos 0o 1 5 4 The expressions in the energy term are Ng Na NT Ni Nna the numbers of the bond angle torsion inversion and the non bonded terms Kij Kijk forceconstants of the bond and angle terms r TIJ bond distance and natural bond distance of the two atoms I and J 0 0o angle and natural angle for three atoms I J K Ce Ce Ge Fourier coefficients of the general angle terms Q do torsion angle and natural torison angle of the atoms J J K L Vo height of the torsion barrier n periodicity of the torsion potential w inversion or out of plane angle at atom I 114 CHAPTER 5 STRUCTURE OPTIMIZATIONS Va height of the inversion barrier Ci Ct Oi Fourier coefficients of the inversions terms T LIJ distance and natural distance of two non bonded atoms I and J Dij depth of the Lennard Jones potential qI partial charge of atoms J and dielectric constant One major difference in this implementation concerns the atom types The atom types in Rapp s paper have an underscore _ In the present implementation an sp C atom has the name C 3 instead of C_ 3 Particularly the bond terms are described with the harmonic potential and the non bonded van der W
534. w transition elements J Chem Phys 86 2 866 872 1986 C C J Roothaan Self consistent field theory for open shells of electronic systems Rev Mod Phys 32 2 179 185 1960 R Ahlrichs F Furche S Grimme Comment on Assessment of exchange correlation functionals Chem Phys Lett 325 1 3 317 321 2000 M Sierka A Hogekamp R Ahlrichs Fast evaluation of the Coulomb po tential for electron densities using multipole accelerated resolution of identity approximation J Chem Phys 118 20 9136 9148 2003 F Weigend A fully direct RI HF algorithm Implementation optimised aux iliary basis sets demonstration of accuracy and efficiency Phys Chem Chem Phys 4 18 4285 4291 2002 R Fletcher Practical Methods of Optimization Unconstrained Optimization Band 1 Wiley New York 1980 T Helgaker Transition state optimizations by trust region image minimiza tion Chem Phys Lett 182 5 503 510 1991 F Jensen Locating transition structures by mode following A comparison of six methods on the Arg Lennard Jones potential J Chem Phys 102 17 6706 6718 1995 408 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 BIBLIOGRAPHY P Cs sz r P Pulay Geometry optimization by direct inversion in the iterative subspace J Mol Struct 114 31 34 1984 R Fletcher A new approach to variable metric a
535. words 314 aoforce 14 24 25 38 39 44 46 80 82 87 101 104 110 152 224 228 230 231 314 346 347 aoforce2g98 25 B matrix 55 56 babel 33 Bend 26 bend 26 Boys localization 359 Broken symmetry 71 bsse_out 118 bsseenergy 116 cbasopt 26 ccisd 200 ccitd 200 ccitd cc2 gs 1ai1 001 200 ccitd cc2 xs 3a2 001 200 CC2 23 RI 325 cc2cosmo 26 CCLO m ss xxx 196 CCLEO s m xxx 191 CCMEO s m xxx 202 430 CCNEO s m xxx 203 CCNLO s m xxx 197 CCREO s m xxx 191 CCS RI 325 CCSD 325 CCSD T 325 CCSD T 325 cgnce 26 charge vector 259 CIS 23 RI 325 CIS D 23 RI 325 condition 259 conjugate gradients 102 control 23 25 33 35 47 49 64 67 74 100 174 199 205 222 235 converged 98 coord 33 coordinates frozen 227 core memory 260 cos 205 330 COSMO keywords 307 cosmo 26 183 cosmoprep 26 309 counterpoise calculation 64 CP corrections 116 CPHF 232 css 205 330 debug 260 Define 173 222 define 23 28 33 36 38 47 49 51 56 59 64 68 70 72 74 77 83 86 88 91 92 94 95 99 100 106 107 109 116 117 125 139 156 INDEX 160 165 170 175 176 178 184 201 208 216 226 235 241 259 260 271 272 275 294 297 299 301 318 326 340 377 degrees of freedom 55 dens 200 DIS 102 340 dist 26 dos_atb 356 dos_a b 356 dos_alpha 356 dos_beta 356 DRC 26 DSscF keywords 283 Dscf 299
536. xchange can also be calculated seminumerically 54 The calculation of 4c 2e Integrals is split into an analytical and a numerical part The latter is evaluated on a dft type integration grid The seminumerical calculation scales better with system size than RIK and is suitable for large molecules and large basis sets 6 1 BACKGROUND THEORY 125 Prerequisites Both dscf and ridft require the control file and starting orbitals obtained from the extended Hiickel guess using define Energy calculations using dscf can be performed in a direct or semi direct mode In the direct mode all four center ERI s are recalculated at each SCF iteration The semi direct mode uses a selective storage of the most time consuming and frequently used integrals The amount of integrals stored is controlled by the keywords thize and thime related to integral size and computational cost The semi direct mode requires a separate dscf statistics run to estimate the disk space needed for integral storage The statistics run requires the keyword statistics dscf to be present in the control file It can be set either manually or using the tool Stati For ridft and rdgrad following additional prerequisites are required 1 An auxiliary basis defined in the data group jbas This group is created automatically when using ri menu of define 2 The maximum core memory the program is allowed to allocate should be de fined in the data group ricore the recommended val
537. y all the parallel keywords needed for the different parts of the geometry optimization i e those for dscf and grad or those for ridft and rdgrad or those for dscf and mpgrad 376 CHAPTER 20 KEYWORDS IN THE CONTROL FILE Chapter 21 Sample control files 21 1 Introduction The file control is the input file for TURBOMOLE which directly or by cross references provides the information necessary for all kinds of runs and tasks control is usu ally generated by define the input generator The following sample control files cover a variety of methods and systems The keywords themselves are explained in Chapter 20 377 378 CHAPTER 21 SAMPLE CONTROL FILES 21 2 NH Input for a RHF Calculation Main File control title NH3 c3v SVP operating system unix symmetry c3v coord file coord intdef atoms file coord n 1 basis n def SVP h 2 4 basis h def SVP pople AO basis file basis rundimensions dim fock dens 495 natoms 4 nshell 15 nbf CAQ 30 nbf A0 29 dim trafo SA0 lt gt AQ CAO 69 rhfshells 1 scfmo file mos closed shells al 1 3 e 1 scfiterlimit 30 scfconv 7 thize LOOOOO00E 04 thime 5 scfdamp start 500 step 050 min 100 scfdump scfintunit unit 30 size 0 file twoint scfdiis start 0 5 drvopt cartesian on basis off global off hessian on 2 2 21 2 NH3 INPUT FOR A RHF CALCULATION 379 dipole on nuclear polarizability interconversion off q
538. y interacting systems e full or pure electrostatic embedding e LDA GGA hybrid or orbital dependent exchange correlation potentials e multilevel FDE calculation e energy decompostion e FDE calculation with subsystem B taken frozen In order to perform a FDE calculation the files coord and control for the total system are necessary to take informations on atomic coordinates and basis sets The input file for the total system can be generated as usual with define but no calculation on the total system is required denconv 1 d 7 option should be defined 246 CHAPTER 17 FROZEN DENSITY EMBEDDING CALCULATIONS in file control in order to better converge the embedded densities and better describe the dipole moment Given a closed shell supramolecular system with a GGA LDA exchange correlation functional the command FDE p 3 invokes an iterative resolution of the KSCED equations with revAPBEk 165 166 as approximation of the non additive kinetic potential see Eq 17 5 in the monomolec ular basis set approach The two subsystems are defined via an integer m 3 in the example above which identifies the first atom of the subsystem B in the file coord of the supramolecular system with n atoms where the atoms 1 m 1 belong to the subsystem A while the atoms m n to the B one Thus the file coord must contains first all the atoms of the system A and then all the atoms of the system B As an example we report here the FDE p 3
539. ybrid functionals are available a mixture of Hartree Fock exchange with DFT exchange correlation functionals e The BH LYP exchange correlation functional Becke s half and half exchange in a combination with the LYP correlation functional 57 58 61 62 66 e The B3 LYP exchange correlation functional Becke s three parameter functional with the form 0 85 0 72B88 0 2HF 0 19VWN V 0 81LY P 6 3 where HF denotes the Hartree Fock exchange 57 58 61 62 67 e The B3 LYP exchange correlation functional with VWN functional V in the paper This is the same functional form as available in the Gaussian program e The 1996 hybrid functional of Perdew Burke and Ernzerhof with the form 0 75 S PBE X 0 25HF PW PBE C 6 4 where PBE X and PBE C are the Perdew Burke Ernzerhof exchange and correlation functionals and PW is the Perdew Wang correlation functional 57 58 60 64 68 128 CHAPTER 6 HARTREE FOCK AND DFT CALCULATIONS The TPSSH exchange correlation functional of Staroverov Scuseria Tao and Perdew with the form 0 915 TPSS X 0 1HF PW TPSS C 6 5 where HF denotes the Hartree Fock exchange 57 58 60 65 69 The Double Hydbrid Functional B2 PLYP can be used for single point energy cal culations Note that one has to run a MP2 calculation after the DFT step to get the correct B2 PLYP energy B2 PLYP is a so called double hybrid density functional DHDF 70 that uses in addition
540. ynamic_fraction 0 300000 and for a grad statistics run statistics grad parallel 2e ints _shell_statistics file GRAD par stat parallel_parameters maxtask 400 maxtask is the maximum number of two electron integral tasks maxdisk defines the maximum task size with respect to mass storage MBytes and dynamic_fraction is the fraction of two electron integral tasks which will be allo cated dynamically For parallel grad and rdgrad runs one can also specify grad_send_dens This means that the density matrix is computed by one node and distributed to the other nodes rather than computed by every slave 20 2 FORMAT OF KEYWORDS AND COMMENTS 375 In the parallel version of ridft the first client reads in the keyword ricore from the control file and uses the given memory for the additional RI matrices and for RI integral storage All other clients use the same amount of memory as the first client does although they do not need to store any of those matrices This leads to a better usage of the available memory per node But in the case of a big number of auxiliary basis functions the RI matrices may become bigger than the specified ricore and all clients will use as much memory as those matrices would allocate even if that amount is much larger than the given memory To omit this behavior one can use ricore_slave integer specifying the number of MBs that shall be used on each client For parallel jobex runs one has to specif
541. ysis J Chem Phys 83 2 735 746 1985 C Ehrhardt R Ahlrichs Population Analysis Based on Occupation Numbers II Relationship between Shared Electron Numbers and Bond Energies and Characterization of Hypervalent Contributions Theor Chim Acta 68 3 231 245 1985 A V Luzanov A A Sukhorukov V E Umanskii Application of transition density matrix for analysis of excited states Theor Exp Chem 10 354 1976 R L Martin Natural transition orbitals J Chem Phys 118 4775 2003 F Weigend C Schrodt Atom type assignment in molecule and clusters by pertubation theory A complement to X ray structure analysis Chem Eur J 11 12 3559 3564 2005 418 159 160 161 162 163 164 165 166 167 168 169 170 BIBLIOGRAPHY P Cortona Self consistently determined properties of solids without band structure calculations Phys Rev B 44 8454 1991 T A Wesolowski A Warshel Frozen density functional approach for ab initio calculations of solvated molecules J Phys Chem 97 8050 1993 T A Wesolowski In J Leszczynski Ed Chemistry Reviews of Current Trends Band 10 Page 1 World Scientific Singapore 2006 Singapore 2006 T A Wesolowski A Warshel Kohn Sham equations with constrained elec tron density an iterative evaluation of the ground state electron density of interacting molecules Chem Phys Lett 248 71 19
542. zation of the Hessian Default values stretches 0 5 angles 0 2 4 4 4 Definition of External Electrostatic Fields This submenu allows you to calculate first and second numerical derivatives of the energy with respect to an external electric field The first three options should be clear 1st and 2nd are logical switches which are turned on and off the usual way 1st or 1st and delta is the increment for the numerical differentiation that is the finite value of the external field which replaces the ideally differential field 88 CHAPTER 4 PREPARING YOUR INPUT FILE WITH DEFINE option status description 1st F numerical 1st derivative dE dField 2nd F numerical 2nd derivative d2E dField2 delta lt real gt increment for numerical differentiation l DEFAULT 5000E 02 geofield F geometry optimization with external field man F explicit definition of electrostatic field s geofield gives the possibility to perform a whole geometry optimization under the influence of a finite external field and thus to obtain the distorted minimum geom etry in this field To do this an external electrostatic field must be defined explicitly which can be done using command man Note that geofield must also be switched on if any properties are to be evaluated in the presence of an electric field The most prominent example is the calculation of hyperpolarizabilies Take Care due to some inconsistencies in define it is always
543. ze and interconversion and the corresponding options which will be described in the following sections 5 3 PROGRAM RELAX 103 5 3 2 Optimization of General Coordinates After gradients G have been calculated for coordinates q in optimization cycle k new coordinates or basis set exponents q 1 can be obtained from the quasi Newton update ght gt FFG where F is the inverse of an approximate force constant matrix H This method would immediately converge to the equilibrium geometry if F would be the inverse of the exact force constant matrix and the force field would be quadratic In real applications usually none of these requirements is fulfilled Often only a crude ap proximation to the force constant matrix H is known Sometimes a unit matrix is employed which means coordinate update along the negative gradient with all coordinates treated on an equal footing The optimization of nuclear coordinates in the space of internal coordinates is the default task performed by relax and does not need to be enabled Any other opti mization task requires explicit specifications in data group optimize which takes several possible options optimize options internal on off Structure optimization in internal coordinates redundant on off Structure optimization in redundant coordinates cartesian on off Structure optimization in cartesian coordinates basis on off Optimization of basis set exponents contraction coefficien

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