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Turbomole USER`S MANUAL

1. 81 82 83 84 BIBLIOGRAPHY C Hattig A K hn Transition moments and excited state first order proper ties in the second order coupled cluster model CC2 using the resolution of the identity approximation J Chem Phys 117 15 6939 6951 2002 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 1998 T Helgaker P J rgensen J Olsen Molecular Electronic Structure Theory Wiley New York 2000 O Christiansen P Jorgensen C H ttig Response functions from Fourier com ponent variational perturbation theory applied to a time averaged quasienergy Int J Quantum Chem 68 1 1 52 1998 C Hattig P Jorgensen Derivation of coupled cluster excited states response functions and multiphoton transition moments between two excited states as derivatives of variational functionals J Chem Phys 109 21 9219 9236 1998 A Kohn 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 O Christiansen P Jorgensen 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 W Klopper C C M Samson Explicitly correlated second order Mg
2. an initial guess for MOs and occupation numbers is provided by eht e for DFT you have to enter dft in the last menu and then enter on for non hybrid functionals you best choose the efficient RI approximation by entering ri and providing roughly 3 4 of the memory with m number number 1 7 HOW TO RUN TURBOMOLE A QUICK AND DIRTY TUTORIAL 27 in MB your computer has available Auxilliary basis sets are provided auto matically 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 e By the way we strongly recommend B P86 with RI or B3 LYP as non hybrid and hybrid functionals e for an SCF or hybrid functional DFT run 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 e for a geometry optimization simply call JOBEX for a standard SCF input nohup jobex amp for a 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 appropriate energy calculation mpshift runs with SCF or DFT using a hybrid functional need a filesize of the semi direct file twoint that is non zero other features such as MP2 need further action on the inpu
3. end 3s2p1d 511 31 1 53934125305E 02 40221581118E 01 17931144990 46376317823 44171422662 1 0000000000 1 0000000000 40072398852E 01 21807045028 51294466049 1 0000000000 1 0000000000 3s2p1d 511 31 1 53431809926E 02 39890039230E 01 17853911985 46427684959 44309745172 1 0000000000 1 0000000000 43394573193E 01 23094120765 51375311064 1 0000000000 1 0000000000 253 254 CHAPTER 13 SAMPLE CONTROL FILES 13 4 TaCl Input for an RI DFT Calculation with ECPs 13 4 1 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 CAD 122 nbf A0 115 dim trafo SAO 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 10000000E 04 thime 5 sc damp 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 hessian on dipole on nuclear polarizability interconversion off qconv 1 d 10 maxiter 25 optimize internal on 13 4 TACLs INPUT FOR AN REDFT CALCULATION WITH ECPS 255 cartesian off
4. 2 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 2 0 2 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 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 bb bl bm bp ecp ecpb ecpi ecpl CHAPTER 2 PREPARING YOUR INPUT FILE WITH DEFINE 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 cal culations 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 app
5. CONTENTS 14 8 Bending potential for Ags 15 The Perl based Test Suite Structure 15 1 General 15 2 Running the tests 15 3 Taking the timings and benchmarking 15 4 Modes and options of the TTEST script Bibliography 270 271 271 271 273 273 277 283 10 CONTENTS Chapter 1 Preface 1 1 Contributions and Acknowledgements TURBOMOLE has been designed by the Quantum Chemistry Group University of Karlsruhe Germany since 1988 The following members of the group have made contributions Reinhart Ahlrichs Michael Bar Hans Peter Baron R diger Bauern schmitt Stephan B cker Nathan Crawford Peter Deglmann Michael Ehrig Karin Eichkorn Simon Elliott Filipp Furche Frank Haase Marco H ser Christof H ttig Arnim Hellweg Hans Horn Christian Hu ber Uwe Huniar Marco Kattannek Andreas K hn Christoph K lmel Markus Kollwitz Klaus May Paola Nava Christian Ochsenfeld Hol ger Ohm Holger Patzelt Dmitrij Rappoport Oliver Rubner Ansgar Schafer Uwe Schneider Marek Sierka Oliver Treutler Barbara Unter reiner Malte von Arnim Florian Weigend Patrick Weis Horst Weiss Contact address Lehrstuhl fiir Theoretische Chemie Institut fir Physikalische Chemie Universitat Karlsruhe Kaiserstr 12 D 76128 Karlsruhe E mail reinhart ahlrichs chemie uni karlsruhe de or helpdesk turbomole com 11 12 CHAPTER 1 PREFACE We acknowledge help from
6. add change options for data group moments option status description Sister A A a e da 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 capai seee Exe oS oa E ee ee lt moment gt skip computation of lt moment gt or q uit terminate input This menu 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 moments are zero The default for the reference point is the origin 1 e the coor dinate 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 electrosta
7. prepares the control file for a Hamilton core guess RHF only displays the highest occupied and the lowest unoccupied orbital usage see Section 3 1 is the TURBOMOLE driver for all kinds of optimizations example kdg scfdiis kills a data group here scfdiis in the control file interface between MOLOCH grid output and gle graphics perl is re quired please adjust the path at the top of the script prepares lhf calculations by adjusting parameters of the control file converts the file logging an MD trajectory into coordinates in frames appropriate for XMOL animation program extracts the energy data KE total energy PE from an MD log file interactive program to prepare for an MD run checking inparticular the mdmaster file mdprep is actually a FORTRAN program population analysis for UHF input Obsolete since properties can be computed with most modules directly Please refer to chapter 10 prepares MP2 calculations interactively by adjusting parameters of the control file according to your system resources calculates numerically force constants vibrational frequencies IR and Raman cross sections the latter only for closed shell molecules Open shell molecules have to be calculated in point group C1 Note that the name of the kornshell script is NumForce with capital F displays out of plan angles interactive tool for preparing the control file for RIMP2calculations by adjusting the required paramet
8. 0 1 is calculated as i ni gente gt 184 CHAPTER 12 KEYWORDS IN THE CONTROL FILE where 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 temperature given by tmstrt default 300 K is reduced at each SCF cycle by the factor tmfac default 1 0 until it reaches the value tmend default 300K 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 1073 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 firstorder Perform first order SCF calculation i e perform only one SCF iteration with the s
9. 87 88 gcart integer c integer dscf grad relax statpt trans level level ex 1 lt path gt ls lt path gt md mdfile file mdscript file keep help 3 1 2 Output CHAPTER 3 STRUCTURE OPTIMIZATIONS converge maximum norm of cartesian gradient up to 10 lt integer gt atomic units default 3 perform up to integer cycles default 20 begin with a direct SCF step begin with a gradient step begin with a force relaxation step use the STATPT program for force relaxation perform transition state search using program STATPT im plies statpt define the optimization level level scf mp2 cc2 or uff 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 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 RE LAX 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 director
10. 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 2 2 THE ATOMIC ATTRIBUTES MENU 55 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 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 numbe
11. 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 X YZ MP2 implies RI MP2 and RICC2 exploratory MP2 SVP almost quantitative DFT SV P HF SVP MP2 TZVPP properties HF and DFT TZVPP quantitative 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 181 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 2 2 THE ATOMIC ATTRIBUTES MENU 57 Correla
12. global off basis off logarithm coordinateupdate dqmax 0 3 interpolate on statistics 5 forceupdate ahlrichs numgeo 0 mingeo 3 maxgeo 4 modus lt gl 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 2 e 1 10 2 a2 1 8 2 e 1 4 2 end 13 4 2 File coord coord 00000000000000 00000000000000 00000000000000 ta 2 19392179448315 3 79998401587749 00000000000000 cl 2 19392179448315 3 79998401587749 00000000000000 cl 4 38784358896629 00000000000000 00000000000000 cl 00000000000000 00000000000000 4 46615918865523 cl 00000000000000 00000000000000 4 46615918865523 cl intdef definitions of internal coordinates 1 k 1 0000000000000 stre 1 2 val 4 38784 2 k 1 0000000000000 stre 1 5 val 4 46616 end 13 4 3 File basis basis 256 ta def SVP ta 2 s 14 400000000 12 000000000 1 s 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 61042908544 24216276510 1 d 87909318337E 01 cl def SVP cl 5 s
13. gradients for auxiliary basis sets for RI MP2 CC2 etc calculations based on the RI MP2 error functional R12 corrections to RI MP2 MP2 ground state energies can be computed in C symmetry using explicitly correlated two electron basis functions in the framework of the MP2 R12 model 70 All functionalities are implemented for closed shell RHF and open shell UHF refer ence wavefunctions 136 137 Prerequisites Calculations with R1CC2 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 7 or less 2 an auxiliary basis defined in the data group cbas 3 if orbitals should be excluded from the correlation treatment and excitation processes the data group 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 75 85 of the available physical core memory 5 depending on the type of calculations that should be carried out in addition the data groups ricc2 excitations response and rir12 have to be set see below and Section 12 2 12 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 and maxcor Note that the implementation of non abelian point groups in RICcC2 is limited to the el
14. 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 TTEST dscf called in the TURBOTEST directory performs only the tests for DSCF module TTEST called in the 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 15 3 TAKING THE TIMINGS AND BENCHMARKING 273 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
15. 2002 2111 C H ttig A Kohn and K Hald J Chem Phys 116 2002 5401 e for geometry optimizations include C Hattig J Chem Phys 118 2003 7751 7 1 CC2 GROUND STATE ENERGY CALCULATIONS 139 e for geometry optimizations for excited states include A K hn and C Hattig J Chem Phys 119 2003 5021 for calculations with RI ADC 2 RI CIS D RI CIS D include C Hattig Adv Quant Chem 50 2005 37 for calculations with RI MP2 R12 include C Villani and W Klopper J Phys B 38 2005 2555 2567 e if the parallel version of RICC2 is used include a reference to C H ttig A Hellweg A K hn Phys Chem Chem Phys 8 2006 1159 Appropiate 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 pV XZ cc pV X d Z aug cc pVXZ 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
16. Chem Phys 4 18 4285 4291 2002 BIBLIOGRAPHY 279 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 R Fletcher Practical Methods of Optimization Unconstrained Optimization Band 1 Wiley New York 1980 T Helgaker Transition state optimizations by trust region image minimization 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 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 algorithms 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 Universitat 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 III 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
17. Chem Phys 105 22 9982 9985 1996 V N Staroverov G E Scuseria J Tao J P Perdew Comparative assess ment of a new nonempirical density functional Molecules and hydrogen bonded complexes J Chem Phys 119 23 12129 12137 2003 F D Sala A Gorling Efficient localized Hartree Fock methods as effective exact exchange Kohn Sham methods for molecules J Chem Phys 115 13 5718 5732 2001 BIBLIOGRAPHY 281 58 59 60 61 62 63 64 67 68 69 70 F D Sala A G rling The asymptotic region of the Kohn Sham exchange potential in molecules J Chem Phys 116 13 5374 5388 2002 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 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 qu
18. Dscr GRADand RIDFT RDGRAD pardft can be specified pardft 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 mem div 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 dynamic_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 246 CHAPTER 12 KEYWORDS IN THE CONTROL FILE This means that the density matrix is computed by one node and distributed to the other nodes rather than computed by every slave In the paral
19. Initially 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 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 A Matrix Setup The A matrix elements are calculated as the sum of the con tributions of the associated basis grid points of the segments k and l if their distance is below a certain threshold the centers of the segments are used otherwise For all segments that do not have associated basis grid points i e intersection seam segments the segment centers are used The diagonal elements Akk that represent the self energy of the segment are calculated via the basis grid points contrib
20. 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 A E Reed R B Weinstock F Weinhold Natural population analysis J Chem Phys 83 2 735 746 1985 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 Preu Energy adjusted ab initio pseudopo tentials for the first row 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 potential for electron densities using multipole accelerated resolution of identity approx imation 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
21. ORDER MOLLER PLESSET PERTURB THEORY 5 2 Some Theory Second order Mgller 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 3 5 Ex ij ab 5 1 iajb with the t amplitudes lab ata a 0 i and j denote occupied a and b virtual orbitals ey are the corresponding orbital energies ij ab ij ab ij ba are four center two electron integrals in a com monly used notation 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 saving
22. in for each type of coordinate see below The force constants are used for the definition of the matrix m in BmB 174 CHAPTER 12 KEYWORDS IN THE CONTROL FILE 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 bond stretch default 0 5 invr inverse bond stretch default 0 5 bend bond angle default 0 2 outp Out of plane angle default 0 2 tors dihedral or torsional angle default 0 2 linc Special angle coordinate for collinear chains bending of the chain a b c in the plane of b c d default 0 2 linp bending of the chain a b c perpendicular to the plane of b c d default 0 2 wstr 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 winv inverse stretch of a weak bond default 0 05 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 default 0 02 12 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 grou
23. 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 coefficients 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 94 CHAPTER 3 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 previ ous optimization cycles Without integer all available information will be displayed off suppresses opti mization statistics The following data blocks are used by program RELAX 1 Input data from gr
24. written to file gradient e In case of MP2 gradient calculations both 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 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 but comparison of values for several similar calulations will yield some information 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 d8s bad MP2 case is ca 0 14 e A more descriptive criterion may be derived from the MP2 density matrix The eigenvalues
25. 1 54 4 1 1 0 Od o 1 constraints specifies and or automatically generates atomic distance constraints The optional flag angstroms can be used to indicate that data will be entered in Angstroms 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 12 2 FORMAT OF KEYWORDS AND COMMENTS 241 adjpercyc is the fraction of the total distance correction to be applied on each constraint iteration type X A normalfont const rmaz 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 atom and looks for any O 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 A 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
26. 10449 827566 1571 7365221 357 12065523 100 25185935 30 812727554 3 s 51 923789434 5 7045760975 2 3508376809 1 s 44605124672 1 s 16848856190 5 P 307 66790569 7s5p 6s2p 7s6p5d 6s3p2d 99343296745 1 6510077975 1 0000000000 1 0000000000 1 0000000000 1 0000000000 1 0000000000 26979695152 46968874449 50905100155 52298161137 1 0000000000 1 0000000000 52799310714 18558319471 42959071631 43497228232 1 0000000000 211 CHAPTER 13 SAMPLE CONTROL FILES 211111 411 41 E 01 111 41 19708362484E 02 14754727977 66679112875 17228924084 15883786100 10009298909 60841752753 54352153355 1 0000000000 1 0000000000 87801484118 E 01 E 01 E 02 13 4 TACLs INPUT FOR AN REDFT CALCULATION WITH ECPS 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 s f 1345 8806470 36 7668062 12 0179609 378 4253015 22 2930909 12 0179609 104 8839557 8 7558481 12 0179609 end 63563355471E 01 24016428276 47798866557 38515850005 1 0000000000 1 0000000000 1 0000000000 13 4 4 File auxbasis jbas ta def SVP 3 s 15 521335 7 555743 3 699576 1 s 1 820141 1 s 0 898838 1 s 0 445062 1 s lmax 3 r n exponent 2 2 0178811 2 14 5464077 2 7 2732038 2 2 0178811 2 9
27. 125 211 mp2pair 210 mulliken 229 mvd 161 232 natoms 238 natural orbital occupation 171 natural orbitals 171 186 occupation 186 newcoord 154 nmr 158 dft 158 mp2 158 rhf 158 shielding constants 158 nomw 91 204 noproj 203 nosalc 203 nprhessian 204 nprvibrational normal modes 204 nprvibrational spectrum 204 nsteps 238 numprocs 244 oldgrad 226 open shells 61 62 172 193 operating system 169 optimize 92 93 156 218 220 basis 93 219 logarithm 219 scale 219 cartesian 93 219 global 93 219 internal 93 96 218 223 redundant 93 218 paboon 229 parallel parameters 245 INDEX parallel_platform 244 pardft 245 path 169 point_charges 130 186 points 81 85 228 pointval 150 162 235 dens 236 fld 163 236 fmt 236 map 237 plt 237 vec 237 xyz 237 geo 164 237 line 237 plane 237 point 237 integrate 235 Imo 164 236 mo 164 236 nao 164 pot 163 236 pop 161 232 233 atoms 233 dos 233 lall 233 mo 233 netto 233 overlap 233 thrpl 233 pop nbo 234 pople 172 prediag 187 189 printlevel 211 213 properties 79 228 ramanonly 204 redund_inp 173 redundant 97 156 218 224 response 216 conv 216 fop 216 gradient 216 nosemicano 216 semicano 216 thrsemi 216 zconv 216 287 response 137 147 216 217 restart 189 restartd 187 189 ricc2 137 138 140 143 147 211 212 216 217
28. 5 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 Rb Rn Rb Sr Y Cd In Cs Ba La Hg TI At def SVP def SV P f def2 SVP def2 SV P H f A def TZVP def TZVPP f def2 TZVP def2 TZVPP def2 QZVP def2 QZVP EIEI 1 3 HOW TO QUOTE USAGE OF TURBOMOLE 19 a Fully Optimized Contracted Gaussian Basis Sets for Atoms Li to Kr A Sch fer 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 Treutler H Ohm M Haser and R Ahlrichs Chem Phys Let ters 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 bas
29. 65 64 TS 15 16 5 8 9 9 10 D H 80 81 80 81 except cases e g Dog or Day where e irreps which are not Roothaan cases t only p given the state for groups Ty etc follows from S A T 0 I P gt T T 0 I D gt H J E T 7 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 gives only one dimensional Example The 4d 5s 2D state of Ag in symmetry I closed shells a 1 5 2 t1 1 3 2 h 1 2 open shells type 1 h 2 9 5 roothaan 1 a 80 81 b 80 81 4 3 3 Maore Than One Open Shell A Half filled shell and all spins parallel All open shells are collected in a single open shell and a 1 b 2 4 3 RESTRICTED OPEN SHELL HARTREE FOCK 117 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 4 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 Ba state from 3a 1b2 molecule in x z plane closed shells al 1 2 b1 1 open shells type 1 al 3 b2 1 roothaan 1 rohf 3al 3al a 0 b 0 1b2 1b2 3al 1b2 a 1 b 2 Pa E m N N U vu F
30. 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 4 3 4 Miscellaneous Valence states Valence states are defined as the weighted average of all CSFs arising from an electronic configuration occupation MO This is identical to the average energy of all Slater determinants _ 2nir n 1 2nir 1 n This covers e g the cases n 1 and n 2n 1 p p d d etc since there is only a single CSF which is identical to the average of configurations a b Totally symmetric singlets for 2 or 2n 2 electrons n 2 a 0 b Nir Nir Nir ny 2 2nj 2 gt n 2 2 a e 17 b Nir Nir 3 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 nir 4k k 1 1 I l 1 nip 1 n ie 2nir 2k k 1 1 1 1 1 Nir 1 n a 120 CHAPTER 4 HARTREE FOCK AND DFT CALCULATIONS where k max 0 n mr 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 2Nir 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 b n n 2 285 n 2f n This applies to shells with one electron one hole the high spin couplings
31. DEFINE may be enabled and disabled the same way as shown for the last menu Entering will bring you to the last derivative submenu 2 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 8 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 per formed option status description optimization refers to 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 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
32. 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 12 2 FORMAT OF KEYWORDS AND COMMENTS 205 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 The convergence of the macro iterations is strongly influenced by the size of th
33. Egs denotes the ground state energy F and S are the Fock and overlap matrices 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 Lagrange 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 6 3 IMPLEMENTATION 129 requires the solution of a single static TDHF TDKS response equation 6 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 derivative 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 6 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 67 Simultaneous vector iteration The solutions of Eqs and are ex panded in a subspace of L which is iteratively expanded Davidson method 68 The iteration is stopped when the Euclidean norm of the residual vector is smaller than 10 The default for k is 5 which usually gives exc
34. Essential Keywords All essential data groups for MPGRAD may be generated by the preparation tool mp2prep apart from maxcor see above these are the following traloop n specifies the 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 file halfint file moint 0 file moint 1 file moint j file moint k file moint a file gamma 1i file gamma 2 file moint u file moint v file gamma iu 210 CHAPTER 12 KEYWORDS IN THE CONTROL FILE The data group mointunit specifies e which scratch files are needed e where they are located path name and 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 RimpP2 Essential Keywords Apart from keywords maxcor mp2energy and freeze see above RIMP2 also needs cbas file auxbasis cross reference for the file specifying
35. H ser H Horn C K lmel Electronic structure calculations on workstation computers The program system Turbomole Chem Phys Lett 162 3 165 169 1989 A Schafer H Horn R Ahlrichs Fully optimized contracted gaussian basis sets for atoms Li to Kr J Chem Phys 97 4 2571 2577 1992 A Schafer 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 va lence and quadruple zeta valence quality for H to Rn Design an assessment of accuracy Phys Chem Chem Phys 7 18 3297 3305 2005 A K Rapp C J Casewit K S Colwell W A Goddard II 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 H ser RI MP2 first derivatives and global consistency Theor Chem Acc 97 1 4 331 340 1997 F Weigend M H ser H Patzelt R Ahlrichs RI MP2 Optimi
36. 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 label as these orbitals are necessarily in C symmetry 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 86 CHAPTER 2 PREPARING YOUR INPUT FILE WITH DEFINE the origin of this new coordinate system relative to the one in which the atomic coor dinates 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 calculat
37. INDEX start vector generation 132 207 statistics 189 192 dscf 110 169 192 dscf parallel 192 245 grad parallel 245 kora 192 mpgrad 124 169 192 210 mpshift 158 off 170 192 polly 192 statpt 89 91 227 bfgs 91 hessfreq 227 hssidiag 227 itrvec 90 227 keeptmode 227 powell 91 radmax 227 radmin 227 threchange 90 thrmax displ 90 thrmaxgrad 90 thrrmsdispl 90 thrrmsgrad 90 tradius 89 227 update 227 sum rules 207 suspend off 169 symmetry 129 171 thime 109 110 129 192 211 243 thize 109 110 129 158 185 192 211 243 title 171 239 tmpdir 153 210 211 tplot 125 211 traloop 123 124 158 209 242 244 trand 243 trast 243 turbomole 238 twoint 157 uff 102 174 maxcycle 102 uffgradient 174 177 uffhessian 174 177 INDEX ufftopology 174 176 uhf 172 194 uhfmo_alpha 132 170 190 194 uhfmo_beta 132 170 190 194 userdefined bonds 170 vdw_fit 231 velocity gauge 207 Zadd_control_commands 39 charge 39 coord 38 method 34 basis set choice 35 ENRGY 34 FORCE 34 GEOMY 34 GRADI 34 level of calculation 34 properties 34 run options 35 general 35 SCF 36 structure optimization 37 scan 39 title 39 Al plt 235 ACTUAL 22 actual step dscf 170 ADC 2 RL 211 analysis of normal modes internal coordinate 155 AOFORCE 13 21 23 29 30 38 71 73 78 91 94 100 154 156 203 224 225 keyword
38. In general the IRREP s of the excitation s from the ground to an excited state is given by the direct product of the IRREPs of the tow states For example to calculate the first Ag state in a Cay symmetric molecule with a Bz open shell ground state it is necessary to specify soes bi 1 The number of excitations that have to be calculated in order to cover a certain spectral range is often difficult to determine in advance The total number of exci tations 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 without
39. Lee and coworkers the D 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 respec tively D MP2 lt 0 015 and D CC2 lt 0 030 72 13 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 142 CHAPTER 7 RI CC2 7 2 Calculation of Excitation Energies With the Ricc2 program excitation energies can at present be calculated with the RI variants of the methods CCS CIS CIS D CIS D ADC 2 and CC2 The CC2 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 7 8 aco We _ 1114 LH Ta 71H mll 7 HF we dt uall Tu HF H2 F Tu HF Since the CC2 Jacobian is a non symmetric matrix left and right eigenvectors are different and the right left eigenvectors E are not orthogonal among them selves but form a biorthonormal basis if properly normalized EE Ef El EE by 7 9 To obtain excitation energies only the ri
40. MPGRAD the population analysis can be carried out after the corresponding calculation in a short additional run by the command lt program gt proper provided the necessary keywords in the control file have been set Generation of localized MOs localize enables calculation of localized molec ular orbitals Per default a Boys 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 1bet 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 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 For this purpose the real elec trostatic potential is calculated at spherical shells of grid points around the atoms By default Bragg Slater radii rgs are taken as shell radii 10 2 Interfaces 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 162 CHAPTER 10 PROPERTIES AND ANALYSIS AND GRAPHICS t2x gt opt xyz
41. QUOTE USAGE OF TURBOMOLE 17 Basis sets 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 Be B Ne SVP SV P m al la TZVP b fb TZVPP f QZVP QZVPP def2 SV P al al al a def2 SVP al Ta i al def2 TZVP a f j f def2 TZVPP 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 In Cs y v La Hg TI At deFSVP deFSV P def TZVP def TZVPP def2 SV P def2 SVP def2 TZVP def2 TZVPP def2 QZVP def2 QZVP afpepfpel o Auxiliary basis sets for RI DFT Coulomb fitting H Kr Rb At Rn def SVP def SV P def TZVP def2 universal 18 CHAPTER 1 PREFACE Auxiliary basis sets for RI MP2 and RI CC2 elements H Kr H He Li Be B F Ne Na Mg Ar K Ga Br r SVP SV P TZVP TZVPP k k f k f k QZVP QZVPP JSV 7 MI def2 SVP f ii ii def2 TZVP def2 TZVPP ffl j aug cc pVXZ X D Q aug cc pV5Z cc pWXZ X D
42. a separate section 2 1 THE GEOMETRY MAIN MENU 51 ideg a iaut iman a icizx irem 2 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 anyway 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 com mand 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 happen 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 a
43. 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 XV 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 6939 2002 XVI 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 XVII Efficient characterization of stationary points on potential energy surfaces P Deglmann and F Furche J Chem Phys 117 9535 2002 XVIII 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 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 em
44. 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 intsdebug cao Output of one electron matrices expressed in cao basis This works only prop erly if the molecule is in C symmetry Note that the output gives one triangle of the one electron matrices Thus the entries are The order of the basis functions is such that all s orbitals are given first then all p orbitals all d orbitals and so on So we have 1 atom 1s 2s 3s 2 atom 1s 2s 3s 1 atom 1px 1py 1pz 2px 2py 2pz 2 atom 1px 1py 1pz 2px 2py 2pz estimates mo diagram 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 186 CHAPTER 12 KEYWORDS IN THE CONTROL FILE 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 u
45. 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 maxcor 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 12 2 FORMAT OF KEYWORDS AND COMMENTS mp2energy SCS pt vall ps val2 freeze alg 1 2 tiu 1 209 The data group freeze specifies frozen orbitals in the above syntax by The symmetry independent and for standard applications recommended syntax is irreducible representations 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 MPGRAD
46. 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 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 correction potential is instead recalculated For spin unrestricted calculations 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 12 2 FORMAT OF KEYWORDS AND COMMENTS 199 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 maxium number of iteration maxit 20 output level output 0 3 asymptotic continuatio
47. 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 12 2 FORMAT OF KEYWORDS AND COMMENTS 243 mointunit Scratch file settings for an MP2 calculation Please refer to Section 12 2 11 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 thize scftol scfintunit scfmo have the save meaning as in DSCF see Section 12 2 5 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 scratch files mpshift csssmat path1 filel mpshift cshsmat path2 file2 mpshift csdgsmat path3 file3 mpshift csusmat path4 file4 mpshift dens path5 file5 mpshift fock path6 file6 mpshift dfock path7 file7 mpshift idvds1 path8
48. 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 Oryg is the angle value of I J K and j xK1 is the cwone for J K L The hybridizations of J and K determine ttyp 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 wa 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 Lis O ityp 11 like ityp 10 but L is any atom ityp 2 Iis 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 J 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 12 2 FORMAT OF KEYWORDS AND COMMENTS 179 Based on the numbers 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
49. calculations yielding single point MP2 energies and if desired the corresponding gradient calculates MP2 energies and gradients for RHF and UHF wavefunctions siginificantly more efficient than MPGRAD by using the RI technique 89 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 Employs the RI technique to approximate two electron integrals Includes as a subset also the functionalities of the RIMP2 program offs 1 4 MODULES AND THEIR FUNCTIONALITY 21 RELAX STATPT FROG AOFORCE ESCF EGRAD requires a gradient run by GRAD RDGRAD RIMP2 or MPGRAD and proposes 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 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 s
50. change due to the displacements available in the numforce KraftWerk log files is reasonably small For a NUMFORCE run the convergence criteria should be tightened It is recom mended to use at least 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 Chapter 7 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 69 All calculations employ the resolution of the identity RI approximation for the electron repulsion integrals needed for the correlation treat ment and and the description of excitation processes At present the following functionalities are implemented ground state energies for MP2 and CC2 the MP2 results are identical with those obtained with Rimp2 but usually the calculations are somewhat faster excitation energies for the models CIS CCS CIS D CIS D ADC 2 and CC2 transition moments for ground state excited state transition and the models CCS and CC2 first order properties for the ground state SCF CCS MP2 and CC2 and ex cited states CCS and CC2 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
51. 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 4 3 RESTRICTED OPEN SHELL HARTREE FOCK Table 4 1 Roothaan coefficients a and b for cases with de generate orbitals Nir 2 e div groups 7 Cow Doon n f e T 6 a b 3A oy 233 1 2 2 1 2 Th TA IT 1 2 0 TA D 5 0 2 3 3 4 E 211 2A 8 9 8 9 1 njp 3 p O 3 t T O D n f p a b 3P 3 4 3 2 2 1 3 a 9 20 3 10 tS 0 3 IS 1 2 3 1 2 pe 4 5 4 5 ZP 2 3 0 3P 15 16 9 8 4 2 3 ip 69 80 27 40 TS 3 4 0 5 5 6 p 24 25 24 25 only irrep g 1 mainly high spin available n f g a b 1 1 8 2G 0 0 2 1 4 T 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 l 26 27 28 27 TA 8 9 4 9 7 7 8 2G 48 49 48 49 continues on next page 115 116 CHAPTER 4 HARTREE FOCK AND DFT CALCULATIONS Table 4 1 Roothaan coefficients a and b for cases with de generate orbitals continued d 03 h 1 mainly high spin cases work n f d a b 1 1 10 2D 0 0 2 1 5 Sp49p tt 5 8 5 4 18 0 5 3 3 10 F44p wm 5 6 5 3 4 2 5 5D oH 15 16 15 8 5 1 2 65 5A 1 2 6 3 5 9D H 35 36 25 18 7 7 10 44 4Pit 95 98 55 49 8 4 5 3p 3pit 125 128
52. determined 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 are saved in files named CCME0 s m IXL To obtain the transition strengths for excitations out of the ground state the keyword spectrum must be added with appropriate options see Section 12 2 12 to the data group excitations else the input is same as for the calculation of excitation energies and first order properties ricc2 cc2 excitations irrep al nexc 2 spectrum states all operators diplen qudlen 7 5 RI MP2 R12 Calculations To obtain the R12 correction to the MP2 energy the keyword rir12 must be added to the control file A typical run will include the keywords ricc2 mp2 rir12 The MP2 R12 ground state energy is Eyp2 ri2 mp2 Frio 7 24 where Eupa is the conventional MP2 energy and ERj2 the correction from explicitly correlated theory The R12 correction is obtained by minimizing the functional Fr12 y cf Bijcij 2c Vi 7 25 i lt j 152 CHAPTER 7 RI CC2 with respect to the amplitudes collected in the vector c The vectors v and the matrices B are defined as vi kl kl r2 izr lij 7 26 B kl mn kllri2Qral fo e ej Q12r12 mn 7 27 in the spin orbital formalism m n denote spin orbitals and mn is a two electron de terminant fu is the Fo
53. disk space requirements are approximately O 2V N N N2 double precision words The details of the algorithms see ref 10 for the error introduced by the RI approximation see refs 601 71 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 12 2 12 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 107 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 for other methods than CC2 The MP2 equa tions and the energy are obtained by restricting in the CC2 equations the single substitution amplitudes ta to zero For CCS CIS the double substitution ampli tudes are excluded from the cluster expansion and in this case the single substitution amplitudes for the ground state become zero and the energy is identical to the SCF energy For the Methods CIS D CIS D and ADC 2 the ground state is identi fied with the MP2 ground state 7 1 CC2 GROUND STATE ENERGY CALCULATIONS 141 Fast RI MP2 calculations with the Ricc2 program The Ricc2 pro
54. 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 Berlin e Stefan Brode BASF AG Ludwigshafen e Heinz Schiffer HOECHST AG Frankfurt and financial support by the University of Karlsruhe BASF AG BAYER AG HOECHST AG the DFG and the Fonds der Chemischen Industrie 1 2 Features of TURBOMOLE TURBOMOLE has been specially designed for UNIX workstations and PCs and effi ciently 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 Scientific publications require proper citation of methods and 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 subse quent list For module R1CC2 see also Section 7 Additionally but not alternatively the version employed should be indicated e g TURBOMOLE V5 9 e Programs and methods 1 3 HOW TO QUOTE USAGE OF TURBOMOLE 13 general program structure and
55. 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 aes a eo E ee ee se eee eee 2c lt r gt T compute 2 center SEN and print if ISEN gt lt r gt DEFAULT 1000E 01 3c lt r gt T compute 3 center SEN and print if ISEN 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 See S AA a ee tes A nosym F switch off use of symmetry orbs F compute orbital contributions to SEN irreps F compute irrep contributions to SEN eee ee eee E A 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 2 4 THE GENERAL OPTIONS MENU 85 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 orbi
56. excited states Well converged orbitals are required The following methods are available for spin restricted closed shell or spin unrestricted open shell reference states 22 MPSHIFT MOLOCH CHAPTER 1 PREFACE 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 3 1 and in finite difference force constant calculations using NUMFORCE Details see 16 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 necessary for geometries or energies ECPs are not supported in MPSHIFT 17 computes a variety of first order properties and analyses of the wave function as can be seen from the keywords Also atomic point charges can be fitted to the electrostatic potential of a a molecule Please note that MOLOCHis not longer supported and obsolete Prop erties are included in most of the modules please see chapter for details 1 5 Tools Note these tools are very helpful a
57. expected if doing gradient calculations 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 point charges in drvopt switches on the evaluation of derivatives with respect to coordinates of point charges The gradients are written to the file point_charge_gradients old gradients will be overwritten 12 2 8 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 12 2 FORMAT OF KEYWORDS AND COMMENTS 203 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 analysis only analysis only to r
58. for substi tution 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 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 P 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 2 1 2 48 frag w file name del banal CHAPTER 2 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 2 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
59. for the global protocol file default TESTPROTOKOLL sysname checkfile file errfile file probfile file timfile file valfile file Execution options short long restart file r file newref string fileref batchmode errorstop noerrorstop timings notimings runopts 0 15 4 MODES AND OPTIONS OF THE TTEST SCRIPT 275 Name for the check protocol file default CHECKPROTOKOLL Name for the local error output file default output err Name for the failed tests list default PROBLEMS sysname Name for the timings file default TIMINGS sysname Name for the validation file for run criteria default RUNCRIT val Only short long subdirectories of the test suite will be tested default long short The list of test examples for execution will be read in from file default PROBLEMS sysname Produces new reference timings and writes them to the CRIT file A short description of the refer ence platform is provided by string Produces new reference files Running in batch mode no screen output Stops Does not stop after the first error default noerrorstop Writes Does not write the timings on file for further processing default notimings Sets the conditions under which the test is run default sequential parallel 276 CHAPTER 15 PERL BASED TEST SUITE Bibliography 1 10 11 R Ahlrichs M Bar M
60. 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 0 a u velocities are to be scaled every step to keep average total energy constant Then from 2500 0 a u gradual cooling at the default rate annealing is to occur until the time 3000 0a 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 ki netic energy i e quasi temperature or the average total energy approximately constant This is only possible once enough information about run history is available to give reliable statistics Keywords log history ke_control md_action 242 CHAPTER 12 KEYWORDS IN THE CONTROL FILE 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
61. 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 2 1 tors linc linp comp ring THE GEOMETRY MAIN MENU 53 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 H3CCO 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 angle of the C C
62. 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 has been chosen See 3 3 13 and 12 2 13 226 CHAPTER 12 KEYWORDS IN THE CONTROL FILE forcestatic a static i e never updated approximate force constant matrix to be used in DIIS 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 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 dat
63. help for options 3 Run again Dscr 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 1hf off diag on numerical slater off pot file save asymptotic dynamic 1 d 3 homo 1b1u homob 1b1u ONLY UNRESTRICTED 198 CHAPTER 12 KEYWORDS IN THE CONTROL FILE 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 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 can be used only for the density matrix convergence or if Rydberg virtual orbitals
64. le eed eee e 134 6 4 6 Excited State Force Constant Calculations 134 136 ee i eee eee ees 139 er ee ree re 142 Renee oe eee ET 145 eee 145 Sade 147 7 3 3 Visualization of densities 2 2208 149 7 4 Transition Moments e 150 15 REMP2 R12 Calculations 2 2 2 a 151 7 6 Parallel REMP2 and RI CC2 Calculations 152 8 Calculation of Vibrational Frequencies and Infrared Spectra 154 8 1 Analysis of Normal Modes in Terms of Internal Coordinates 155 9 Calculation of NMR Shieldings 157 Pade a seed on dad a eee tea aed a A 157 9 2 How to Perform a SCF of DFT Calculation 157 9 3 How to Perform a MP2 calculation 00 158 9 4 Chemical Shifts 0 0 0 0 0 0 000000 0000000084 158 CONTENTS 7 9 5 Other Features and Known Limitations 159 10 Molecular Properties Wavefunction Analysis and Interfaces to Vi 160 rer 160 10 2 Interfaces to Visualization Tools 4 161 165 169 Lida ae ee ee de dae lak Be 4A De eG ee 169 bP he ek WS SS eee es 169 NN 169 EE hE Re ew aS 171 173 dE buh HA A Ee ge 174 errr eee 179 o ab ce Ee ate Ao eee we ee Be 199 Soo enone 202 apie oped ae pes a See He 202 oY wade hohe fee be eo 205 LGR poh b Ao ob Be ae eS 208 oa neers 208 Ge Bl RA aS aE a Gis 211 ae uate e cee oe ar 218 A GN a wo ee tee eet 226 ied Medes EA a ice ea 228 NE E eee a ee Or ae
65. 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 e specify other localization directions 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 2 4 THE GENERAL OPTIONS MENU 83 add or delete one or more special options for a mulliken population analysis option status description pas A A ea spdf F compute MO contributions to atomic brutto populations molap F compute MO contributions to atomic overlap populations netto F compute atomic netto populations irpspd F compute IRREP contributions to atomic brutt
66. 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 2 4 THE GENERAL OPTIONS MENU 75 dqmax lt real gt coordinates are allowed to change by at most lt real gt DEFAULT 0 3000 a u polish perform 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 option description on switch on interconversion DEFAULT off qconv lt r gt set convergence threshold for interconversion 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 grdi
67. population analyses By default a Mulliken PA in the 12 2 FORMAT OF KEYWORDS AND COMMENTS 233 basis of cartesian atomic orbitals CAOs is performed for the total den sity D DP leading to Mulliken brutto charges and in case of spin unrestricted calculations also for the spin density D D leading to Mul liken brutto numbers for unpaired electrons Besides total numbers also contributions from s p functions are listed separately The following modifications and extensions are supported if the respective commands are written in the same line as pop lall Additional information about pyr 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 thrpl1 are not displayed default 0 01 overlapMulliken atomic overlap matrix is displayed nettoMulliken netto populations diagonal elements 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 r
68. see Section 2 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 polly off STATIC POLARIZABILITY dynpol off DYNAMIC POLARIZABILITY single off SINGLET STABILITY ANALYSIS triple off TRIPLET STABILITY ANALYSIS nonrel off NON REAL STABILITY ANALYSIS ENTER lt OPTION gt TO SWITCH ON OFF OPTION OR q TO QUIT 2 4 THE GENERAL OPTIONS MENU 71 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 RiImp2 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 assign auxiliary basis sets for RI MP2 calculations etc 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
69. should choose o n where n is the index of the p shell and an occupation of 5 3 per MO You may enter the occupation 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 With this command you can remove an orbital occupation if you spec ified a wrong one list is again a list of shell indices in usual syntax 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 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 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 64 CHAPTER 2 PREPARING YOUR INPUT FILE WITH DEFINE 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 op
70. 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 cur rent combination 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 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 12 2 FORMAT OF KEYWORDS AND COMMENTS 193 RHF ROHF closed shells Specification of MO occupation for RHF e g alg 1 4 a2g a NN wv w 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 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 pa
71. 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 suite is that only the specific information about an individual test example is included in its local directory along with the in put and reference files This information is stored in the criteria file CRIT which con tains 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 pro tocol file TESTPROTOKOLL 15 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
72. 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 generated by the tool RIMP2PREP Moreover you may specify by hand tmpdirworkthisjob 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 C symmetry rather for debugging cbasopt enforces calculation of lt jllab gt exact lt ij ab gt RI E eli e 5 ela e b necessary for characterisation of auxiliary basis set quality and for auxiliary basis optimizations works only for C symmetry Note all integrals are kept in memory so this is for atoms and small molecules only 12 2 FORMAT OF KEYWORDS AND COMMENTS 211 tplot Enforces plotting of five largest t amplitudes as well es five largest norms of t amplitudes for fixed pair of occupied orbitals ij By additional integer this number may be changed mp20cc Enforces plotting of all eigenvalues of the MP2 density matrix 12 2 12 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 denconv scfconv scftol and for the solution of Z vector equation with 4 index in
73. 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 coordinates and TURBOMOLE offers the following choices internals based on bond distances and angles see Section 2 1 2 44 CHAPTER 2 PREPARING YOUR INPUT FILE WITH DEFINE redundant internals defined as linearly independent combinations of internals see ref 19 provided automatically by the command ired in the geometry main menu in Section 2 I 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 assigned as default if one leaves the main geometry menu and no other internals have been defined 2 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 ON
74. the default parameter are used recommended For the generation of the cavity COSMO also requires the definition of atomic radii which must 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 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 SCREENING CHARGE cosmo 0 003925 correction 0 003644 total 0 000282 ENERGIES a u Total energy 76 0296831863 76 0297567835 0 0118029468 0 0118765440 The following value is included for downward compatibility Total energy corrected 76 0297199849 Total energy OC corr Dielectric energy Diel energy OC corr 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 outlying charge corrected energy in the old definition used in TURBOMOLE 5 7 and older versions Cosmo in MP2 Calculations The iterative Cosmo PTED scheme see chapter 111 can be used with the mp2cosmo script Options are explained 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 inpu
75. the identity RI ap proximation Gradients are available for ground states the MP2 and CC2 and for excited states at the CC2 level In addition transition moments and first order properties for ground and excited states are available for some of the methods For more details see Section 7 The Ricc2 module requires are well converged SCF moleculare orbitals The input can be prepared using the cc2 menu of DEFINE For a semi direct DscF calculation Hartree Fock or DFT you first have to perform a statistics run If you type 1 8 PARALLEL RUNS 29 stati dscf nohup dscf gt dscf stat amp the disk space requirement MB of your current thime and thize combination will be computed and written to the data group scfintunit size integer see Section 12 2 5 The requirement of other combinations will be computed as well and be written to the output file dscf stat 1 7 3 Calculation of Molecular Properties See Section 1 4 for the functionality and Section 12 for the required keywords of the modules AOFORCE ESCF MPSHIFT and MOLOCH 1 7 4 Modules and Data Flow See Figure above 1 8 Parallel Runs The additional keywords neccessary for parallel runs are described in Chapter 12 1 8 1 Running Parallel Jobs The parallel version of TTURBOMOLE runs on all supported systems e workstation cluster with Ethernet or other connection e SMP systems DEC IBM HP SGI SUN e or combinations of SMP and cluster like IBM
76. 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 12 2 FORMAT OF KEYWORDS AND COMMENTS 213 other informations needed The hard_restart flag is switched on by default if the restart cc file is present conv The conv parameter gives the convergence threshold for the CC2 ground state energy as 107 Y 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 Y By default the threshold is set to oconv conv 1 or 10x deneps if no input for conv is given lindep If the norm of a vector is smaller than 10 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
77. the same keywords are used to control these steps as in semi direct SCF namely thime thize scfintunit see Chapter 4 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 response and eigenvalue problems 6 4 and 6 7 decompose into separate problems 130 CHAPTER 6 HF AND DFT RESPONSE CALCULATIONS 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 Cy 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 Other features Escr and EGRAD fully support external fields using the key word electrostatic field specify geofield on in fldopt point charges us ing the keyword point_charges and effective core potentials using ecp In EscF calculations occupied and virtual MOs can be frozen using freeze 6 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
78. 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 CAD 108 nbf A0 98 dim trafo SA0 lt gt A0 CAO 256 rhfshells 1 scfconv integer SCF convergency criterion will be 10 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 Damping parameters for SCF iterations in order to reduce oscillations The 188 CHAPTER 12 KEYWORDS IN THE CONTROL FILE old Fock operator is added to the current one with weight 0 5 as start if convergence 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 vectors integer Output level concerning molecular orbitals integer 0 default means minimal output gt 1 will output all start MOs and all MOs in each iteration density integer Output level concerning difference density matrices debug integer integer gt 0 will dump a lot of information be careful scfdenappro
79. times are achieved with the RI technique for both Coulomb J and exchange K terms in SCF calculations the RI JK method 25 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 RI JK calculations can be carried out with 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 sm
80. to 9 5 OTHER FEATURES AND KNOWN LIMITATIONS 159 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 12 2 18 9 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 molecular point groups that contain reducible e representations are not sup ported Cn Cna with n gt 2 e as in MPGRAD basis sets with a contraction that is greater than 10 are cur rently not supported e PBE and PBEO DFT functionals are not implemented in MPSHIFT Chapter 10 Molecular Properties Wavefunction Analysis and Interfaces to Visualization Tools 10 1 Wavefunction analysis and Molecular Properties Molecular properties electrostatic moments relativistic corrections population anal yses for densities and MOs construction of localized MO
81. to control all pos sible actions of program MOLOCH 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 options 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 80 CHAPTER 2 PREPARING YOUR INPUT FILE WITH DEFINE 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
82. 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 VWNIII bh lyp s vwn s vwn_Gaussian equivalent to the Gaussian98 keyword SVWN with VWNIITI tpss tpssh 12 2 FORMAT OF KEYWORDS AND COMMENTS 195 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 m3m5 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 RI Dscr 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 ridft Obsolete keyword use rij instead For c
83. 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 the RI MP2 R12 energy W Klopper and W Kutzelnigg Chem Phys Lett 134 1987 17 22 W Klopper Chem Phys Lett 186 1991 583 585 W Klopper and C C M Samson J Chem Phys 116 2002 6397 6410 F R Manby J Chem Phys 119 2003 4607 4613 Implementation e please include always are reference to the publication reporting the im plemenation of the core part of the RICC2 program C H ttig and F Weigend J Chem Phys 113 2000 5154 e for transition moments and excited state first order properties C H ttig and A K hn J Chem Phys 117 2002 6939 e for triplett excited states include C H ttig and K Hald Phys Chem Chem Phys 4
84. used to set the keywords needed for RIMP2 calculations Conventional MP2 calculations with MPGRAD require a number of additional set tings for which it is recommended to invoke the interactive tool mp2prep For ge ometry 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 assignment of auxiliary basis sets mandatory for R1CC2 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 8 to reduce computational cost RI will be used if the RI option for DFT has been specified 2 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 For common calcula tions just start with the defaults and change keywords directly in control if you encounter problems with your calcul
85. usly and that for programs Dscr 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 p Ep Y Dindv Rp ou Rp 10 1 vu 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 12 2 16 10 2 INTERFACES TO VISUALIZATION TOOLS 163 Names of output files are td plt total density UHF a density plus 8 density sd plt spin density a density minus density mp2d plt 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 plt 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 programs if pointval is set in the contro1 file Electrostatic potentials In an analogous way electrostatic potentials can be calculated on grids pointval pot leads to calculation of the electrostatic potential of electrons and nuclei and external constant electric fields and point charge
86. 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 24 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 2 4 THE GENERAL OPTIONS MENU 69 Note trunc is presently not compatible with marij RI in SCF calculations Considerable savings in CPU
87. 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 refer 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 66 CHAPTER 2 PREPARING YOUR INPUT FILE WITH DEFINE GENERAL MENU SELECT YOUR TOPIC scf SELECT NON DEFAULT SCF PARAMET
88. 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 lots of useless output disple F display 1e contributions to desired derivatives onlyle F calculate le contributions to desired derivatives only debugle 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 74 CHAPTER 2 PREPARING YOUR INPUT FILE WITH
89. 00000000 00000000000000 00000000000000 fend 14 4 DFT calculation of Benzene ri mp2 TZVP for_nfre 1 gen_symm c2v 68300008773804 74300003051758 34150004386902 37150001525879 34150004386902 37150001525879 34150004386902 37150001525879 34150004386902 37150001525879 68300008773804 00000000000000 00000000000000 32354623433702 10755851657859 32354623433702 10755851657859 32354623433702 10755851657859 32354623433702 10755851657859 00000000000000 OPoOpyOo po E o A A o Energy calculation of Benzene at DFT B P86 level using SVP basis set Integration grid is set to m4 scf_grid m4 A title is specified title A statistics run is performed before the energy calculation gen stat 1 The options are continued in the next line at the end of the line 268 CHAPTER 14 SAMPLES FOR TURBO IN FILES title DFT calculation of Benzol method ENRGY b p SVP gen_stat 1 scf_msil 99 amp scf_grid m4 charge 0 coord 00000000000000 2 68300008773804 00000000000000 c 00000000000000 4 74300003051758 00000000000000 h 00000000000000 1 34150004386902 2 32354623433702 c 00000000000000 2 37150001525879 4 10755851657859 h 00000000000000 1 34150004386902 2 32354623433702 c 00000000000000 2 37150001525879 4 10755851657859 h 00000000000000 1 34150004386902 2 32354623433702 c 00000000000000 2 37150001525879 4 10755851657859 h 00000000000000 1 3
90. 0000000000 stre 4 1 val 1 90084 2 k 1 0000000000000 bend 4 3 val 106 27756 1 0000000000000 bend 3 2 1 0000000000000 bend 2 4 end 13 2 3 File basis basis n def SVP Hon 7s4pid 3s2p1d 511 31 1 5 s 1712 8415853 257 64812677 58 458245853 16 198367905 5 0052600809 1 s 58731856571 1 s 18764592253 53934125305E 02 40221581118E 01 17931144990 46376317823 44171422662 1 0000000000 1 0000000000 250 CHAPTER 13 SAMPLE CONTROL FILES 3 p 13 571470233 40072398852E 01 2 9257372874 21807045028 79927750754 51294466049 1 p 21954348034 1 0000000000 1d 1 0000000000 1 0000000000 h def SVP h 7s 3s 511 3 s 13 010701000 19682158000E 01 1 9622572000 13796524000 44453796000 47831935000 1 s 12194962000 1 0000000000 1 p 80000000000 1 0000000000 end 13 2 4 File mos scfmo expanded format 4d20 14 1 al eigenvalue 15633041862301D 02 nsaos 10 98699003163455D 00 47221435341751D 01 55873125006179D 02 48016374887169D 02 26746008768233D 02 20823779196149D 03 14270460008808D 01 90849517503597D 02 58676121352806D 03 29091871198884D 03 2 al eigenvalue 99896275238736D 00 nsaos 10 26412162337482D 00 51846472345768D 00 37623729061179D 00 77139882704089D 02 47252329287316D 02 21494050853221D 02 11795673774658D 00 83316086019184D 01 11229203933488D 01 27038186251429D 02 3 al eigenvalue 57101279949392D 00 nsaos 10 35584199011701D 01 96938258881594D 0
91. 1 cos 40 quadratic planar case KIJK 1 cos 40 octahedral case Kirk C Cf cos 0 C cos 20 general case Nr 1 gt q Vg 1 cos noo cos n Nr X Vo C8 C cosw C cos 2w Nnb LIJN ay 2 5 Da 2 2 wt arg POT D2 ET The Fourier coefficients Er Ge Ge of the general angle terms are evaluated as a function of the natural angle 6o 1 C 32 2 Asin Oo 22 Cf 4 CF cos bo 3 3 ci c 2 cos 0o 1 3 4 The expressions in the engery term are Ng Na Nr Ni Nap 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 00 angle and natural angle for three atoms J J K CH Ce Ce Fourier coefficients of the general angle terms bo 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 104 CHAPTER 3 STRUCTURE OPTIMIZATIONS Vo height of the inversion barrier C C4 C4 Fourier coefficients of the inversions terms L EIJ 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 type
92. 1 88 94 107 121 123 125 136 141 160 162 209 210 212 224 231 232 keywords 208 rimp2 out dimer 107 RIMP2PREP 23 27 28 123 124 210 211 Roothaan parameters 64 292 SCHAKAL 24 SCREWER 24 92 SDG 24 Simulated Annealing 242 STATI 24 110 STATPT 21 30 35 69 87 91 106 107 keywords 226 statpt out x 107 steepest descent 92 STOP 88 108 stop 38 108 structure library 47 structure optimization 87 substitution 47 SYSNAME 24 25 271 273 SYSNAME 25 T2S 24 T2x 24 161 162 TBLIST 24 273 TBTIM 24 273 temperature 241 time 105 238 timestep 238 TM2MOLDEN 24 162 TMOLE 33 38 266 input 33 Tors 24 TTEST 271 274 turbo in 33 38 TURBOMOLE installation 24 modules 20 quotation of 12 tools 22 TURBOTEST 25 twoint 27 31 UFF 20 38 90 91 101 102 174 176 269 keywords 174 uffgradient 102 uffhessian0 0 102 ufftopology 102 176 179 nxtn12 176 UHFUSE 24 INDEX vector function 140 velocity 241 VIBRATION 154 Vibrational Frequencies 154 wave function analysis keywords 232 x2T 24 26 43 XMOL 23
93. 1 70254605702716D 01 65569041318341D 00 44746149963029D 00 40094287741992D 03 51691151834284D 01 47722350097160D 01 19189122068531D 02 56638497851180D 03 1 e eigenvalue 64374209294851D 00 nsaos 9 49313475446075D 00 33757893447603D 00 76142296567409D 04 74524664248740D 04 26407572210452D 00 22619038902975D 00 50035170531670D 05 12199166245418D 03 63021657663245D 04 end 13 3 NO2 INPUT FOR AN UNRESTRICTED DFT CALCULATION 251 13 3 NO input for an unrestricted DFT calculation 13 3 1 Main File control title NO2 c2v UKS SVP operating system unix symmetry 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 nshel1 18 nbf CA0 45 nbf AQ 42 dim trafo SAD 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 b1 1 4 1 b2 1 1 beta shells al 1 5 1 a2 1 1 b1 1 4 1 b2 1 1 scfiterlimit 30 scfconv 7 thize 10000000E 04 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 252 CHAPTER 13 SAMPLE CONTROL FILES cartesian on basis off global off hessian on di
94. 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 minimization 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 University Press Oxford 1987 K Eichkorn O Treutler H Ohm M H ser R Ahlrichs Auxiliary basis sets to approximate coulomb potentials erratum 1995 242 283 Chem Phys Lett 242 6 652 660 1995 J A Pople R K Nesbet Self consistent orbitals for radicals J Chem Phys 22 3 571 572 1954 280 43 44 45 46 47 48 49 50 ol 52 53 54 55 56 57 BIBLIOGRAPHY J i ek 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 P A M Dirac Quantum mechanics of many electron systems Proc Royal Soc London A 123 792 714 733 1929 J C Slater A simplification of the Hartree Fock method Phys Rev 81 3 385 390 1951 S Vosko L Wilk M Nusair Accurate spin dependent electron li
95. 1 56 1995 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 polyatomic molecules J Chem Phys 88 4 2547 2551 1988 Index non append mode 58 41 fanal 150 relax 106 statpt 87 map 150 236 sys data 48 2e ints _ shell statistics 245 2e ints_shell_statistics 245 TURBODIR uff parms in 176 actual step 159 alpha shells 132 172 194 anadens 150 atoms 59 171 172 195 196 204 210 barrier 240 basis 59 94 98 170 225 beta shells 132 172 194 boys 229 clalgorithm 210 cbas 123 137 210 211 218 cbasopt 210 cdspectrum 133 207 cgrad 218 closed shells 61 62 172 186 193 194 constraints 240 coord 47 49 94 97 99 161 170 174 176 225 coordinateupdate 94 219 dqmax 219 interpolate 219 statistics 220 corrgrad 224 cosmo 199 202 allocate_nps 200 ampran 200 cavity 200 closed 200 open 200 disex 200 epsilon 200 nppa 200 nspa 200 phsran 200 routf 200 rsolv 200 use_o1d_amat 200 cosmo_atoms 199 201 csconv 243 csconvatom 243 csmp2 158 242 current 238 denconv 28 122 123 130 137 179 205 211 dft 28 129 155 179 194 197 202 205 batchsize 182 functional 179 debug 180 dgrenze 183 diffuse 181 fgrenze 183 fullshell 182 functional 194 gridordering 183 gridsize
96. 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 geometry optimiza tion 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 excitation energy calculation but else of arbitrary multiplicity and symmetry the short cut s1 can be used x is treated as synonym for the ground state 214 CHAPTER 12 KEYWORDS IN THE CONTROL FILE rir12 ri2model noinv local pairenergy ri2model char char A or A The ri2model flag determines which approximation model is used to calculate the REMP2 R12 ground state energy Approximation A is used if ri2model is absent noinv Calculates only the orbital dependent RI MP2 R12 ground state energy It reduces the computational cost for the last step of the energy calcu lation from O O N to O
97. 11 gdiishistory 220 global 94 99 223 225 globgrad 94 99 224 grad 94 97 99 161 171 213 216 224 226 forceapprox 96 100 171 219 222 223 grad_send_dens 246 225 format 225 forceconv 203 205 forceinit 45 223 225 grid 85 231 hOhessian 91 hessian 73 94 100 101 203 204 223 hessian projected 73 225 286 incore 185 intdef 47 49 96 97 156 170 218 220 223 224 interconversion 92 220 maxiter 220 on 96 219 220 qconv 220 intsdebug 185 ironly 204 isopts 204 isosub 204 jbas 110 170 195 jkbas 111 196 ke_control 239 241 last MP2 energy change 223 last SCF energy change 223 last excitation energy change 134 last step relax 170 les 91 155 204 all 204 lesiterlimit 205 lhf 198 localize 161 234 236 mo 235 sweeps 235 thrcont 235 lock off 169 loewdin 229 log 238 log history 239 241 m matrix 100 224 mao 230 marij 111 196 extmax 196 lmaxmom 196 nbinmax 196 precision 196 thrmom 196 wsindex 196 maxcor 71 122 123 137 155 203 208 211 maximum norm of basis set gradient 226 cartesian gradient 226 internal gradient 226 INDEX md_action 241 242 md_status 239 241 mo output format 186 190 mo diagram 185 mointunit 123 124 158 210 243 moments 228 232 moprint 185 mp2energy 28 123 208 210 mp2energy SCS 208 mp2energy SCS pt vall ps val2 209 mp2occ
98. 179 194 gridtype 179 nkk 180 nphi 180 ntheta 180 old_RbCs_xi 180 qgrenze 183 radsize 180 reference 182 rhostart 182 rhostop 182 284 INDEX sgrenze 183 symblock1 183 symblock2 183 test integ 182 197 weight derivatives 183 drvopt 72 202 203 basis on 98 drvopts 156 drvtol 72 ecp 130 170 egrad 94 98 218 224 226 electrostatic field 130 183 184 end 47 171 energy 134 171 213 216 escfiterlimit 208 esp_ fit 235 excitations 137 138 143 148 151 214 217 bothsides 214 conv 214 exprop 148 214 irrep 214 leftopt 214 preopt 214 spectrum 151 214 thrdiis 214 xgrad 214 exopt 134 208 fermi 72 183 hicrt 183 stop 183 tmend 183 tm ac 183 tmstrt 183 firstorder 184 fldopt 130 183 184 1st derivative 185 2nd derivative 185 edelt 185 fields 185 geofield 185 285 diag 223 carthess 223 default 223 individual 223 off 97 223 on 45 97 100 219 223 225 carthess 45 101 225 diag 100 forceiterlimit 203 205 forcestatic 226 forceupdate 97 220 225 ahlrichs 221 indgeo 221 maxgeo 221 numgeo 221 allow 222 bfgs 220 damping 223 dfp 220 dfp bfgs 220 diagonal 222 ms 220 offdamp 222 offreset 222 pulay 221 226 fail 222 maxpul 221 minpul 221 modus 222 numpul 221 reseig 222 scale 222 schlegel 220 thrbig 223 threig 222 freeze 123 130 137 209 2
99. 3 scf_popu options scf_popu nbo Natural population analyses scf_popu mulli Mulliken population analyses Available run options for structure optimizations geo_nasp option starting program geo_nasp en energy step default geo nasp gd_ gradient step geo_nasp rx relax or statpt step 38 CHAPTER 1 PREFACE geo_nrgc integer number of optimization cycles default 20 geo_suff option switch for UFF start Hessian geo suff 0 no UFF Hessian is used geo suff 1 UFF Hessian is used default geo_dqmax real maximum allowed atom displacement in a u default 0 3 see coordinateupdate geo_ecoc integer SCF convergence critertia will be 107 default integer 6 integer au for the energy geo_gcoc integer gradient convergence criteria in 10797 a u default integer 3 Miscellaneous run options for_maxc integer memory flag in MB maxcor in case of AOFORCE calculations default 200 MB for_nfre option switch for frequency calculation for_nfre 0 calculation of analytical frequencies default for_nfre 1 calculation of frequencies by numerical differentiation of gradi ents Section coord This section defines the molecular structure If the coord file does not exist TMOLE will read in the cartesian coordinates from turbo in and will write them to the newly generated coord file syntax coord options coordinates Available options tmxyz TURBOMOLE format in a u default XYZ xyz format in Angs
100. 30 CHAPTER 12 KEYWORDS IN THE CONTROL FILE 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 electrons 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 The parameters in this definition have the following meaning symb atom symbol list list of all atoms for whi
101. 4150004386902 2 32354623433702 c 00000000000000 2 37150001525879 4 10755851657859 h 00000000000000 2 68300008773804 00000000000000 c 00000000000000 4 74300003051758 00000000000000 h Zend 14 5 AOFORCE calculation of Benzene Analytical for nfre 0 default calculation of the vibrational spectrum at DFT B 3LYP level using the RI approximation Number of SCF cycles ist set to 99 scf_msil 99 title Force calculation of Benzol method FORCE ri b p SVP scf_msil 99 charge 0 coord 00000000000000 2 68300008773804 00000000000000 c 00000000000000 4 74300003051758 00000000000000 h 00000000000000 1 34150004386902 2 32354623433702 c 00000000000000 2 37150001525879 4 10755851657859 h 00000000000000 1 34150004386902 2 32354623433702 c 00000000000000 2 37150001525879 4 10755851657859 h 00000000000000 1 34150004386902 2 32354623433702 c 00000000000000 2 37150001525879 4 10755851657859 h 00000000000000 1 34150004386902 2 32354623433702 c 00000000000000 2 37150001525879 4 10755851657859 h 00000000000000 2 68300008773804 00000000000000 c 00000000000000 4 74300003051758 00000000000000 h hend 14 6 UFF CALCULATION OF WATER 269 14 6 UFF calculation of Water Geometry optimization with max 99 cycles geo_nrgc 99 of water at UFF level The coordinates are in the general xyz format coord xyz The symmetry is de termined automatically gen_symm auto method GEOMY uff geo_nrgc
102. 56 The localized Hartree Fock method LHF to obtain an effective exact ex change Kohn Sham potential module DscrFonly 114 CHAPTER 4 HARTREE FOCK AND DFT CALCULATIONS 4 3 Restricted Open Shell Hartree Fock 4 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 es are open shells type 1 eg i 1 roothaan 1 a 1 b 2 It can also treat more complicated open shell cases as indicated in the tables below In particular it is possible to calculate the xy Singlet case As a guide for expert users complete ROHF TURBOMOLE input for Og for various CSFs configuration state function is given in Section 13 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 1 a term for purely open shell interactions indices m n and a coupling term k m E 2 hir 241 Kr k k l 12 hmm 2aJmn bKmn 29 2 4km Krm 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 4 3 2 One Open Shell Given are term symbols up to indices depending on actual case and group and a and b
103. 59621171D 000 10794148212163D 01 end 13 6 ROHF OF TWO OPEN SHELLS 263 13 6 ROHF of Two Open Shells 13 6 1 Extracts from control for O 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 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 13 6 2 Extracts from control for O in D Symmetry HF SCF SVP Triplet sigma in D2h 264 CHAPTER 13 SAMPLE CONTROL FILES 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 085973
104. 7713 1 68855816889786 1 31008893646566 3 07002878668872 1 68840815751978 1 31008893646566 3 07002878668872 1 68840815751978 4 12184425921830 2 06288409251899 O 00000000000000 end 3 5 Molecular Dynamics Calculations Ab initio molecular dynamics MD can be carried out on the ground state Born Oppenheimer potential hypersurface At the start of an MD run the user must specify the initial atomic positions and velocities and give some general instructions for the run This is managed by running the interactive program MDPREP and rrpyppyppyraoeda 3 5 MOLECULAR DYNAMICS CALCULATIONS 105 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 coor dinates each timestep as detailed above e g DSCF and GRAD The MD program FROG uses the Leapfrog Verlet algorithm 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 12 2 17 below 106 CHAPTER 3 STRUCTURE OPTIMIZATIONS 3 6 Counterpoise
105. 893646566 3 07002878668872 1 68840815751978 4 12184425921830 2 06288409251899 O 00000000000000 end 3 3 7 Optimization of Basis Sets SCF only For this task you have to specify optimize basis on internal off This 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 set exponents contraction coefficients scaling factors and their respective gradients as provided and accumulated in subsequent opti mization cycles by one of the programs GRAD or MPGRAD if drvopt basis on has been set basis Description of basis sets used see Section 2 2 Output will be the updated basis on basis and the updated force constant matrix on forceapprox For an example see Section 13 5 1 3 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 cartesian on basis on and needs as input data groups grad and egrad Output will be on coord basis also on forceapprox updated rrpypppyoaoedqaa 3 3 PROGRAM RELAX 99 3 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 fe
106. 9355653 2 4 9677824 2 2 0178811 2 6 3473769 2 3 1736885 2 2 0178811 493702989D 00 259256574D 01 523168657D 01 262393615D 01 157711902D 01 200789711D 00 257 258 CHAPTER 13 SAMPLE CONTROL FILES 0 220729 185974307D 00 1 s 0 109530 765184411D 01 1 p 1 5024958 1 0 1 p 0 5629855 1 0 1 p 0 2281880 1 0 1 p 0 09507835 1 0 2d 1 337006 190072032D 01 0 599535 155214344D 01 1 d 0 280427 138946250D 01 1 d 0 133078 895263676D 02 1 f 1 1428211 1 0 1 f 0 4395465 1 0 1 f 0 1758186 1 0 3 g 1 630421 100251139D 00 0 747093 737448223D 01 0 349040 276219913D 01 1 g 0 164143 546316580D 02 cl def SVP 8 s 4097 080409 198054511D 01 1203 083193 530973450D 01 386 280948 132352655D 02 135 337690 107149960D 02 51 567046 132565114D 01 21 261034 271180364D 01 9 420135 754640511D 01 4 445228 173603618D 01 1 s 2 209399 140197496D 01 1 s 1 141575 982719736D 00 1 s 0 604182 464178589D 00 1 s 0 322378 369336889D 00 4 p 13 4 TACLs INPUT FOR AN REDFT CALCULATION WITH ECPS 51 8499902611 17 5847835188 6 49227239618 2 55889114714 1 p 1 05118767781 1 p 437994865757 4 d 34 705550 10 704427 3 568067 1 249848 1 d 0 445360 1 f 1 1872146118 1 g 1 30000000 end 359335506D 01 869599318D 01 721211200D 01 634201864D 01 264152293D 01 197670692D 01 548703710D 01 619019402D 02 337450480D 01 905232209D 01 418680075D 01 0000000 0000000 260 C
107. 97921317 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 2 rohf 1b2g 1b3g a b 2 1b2g 1b2g a 1 b 0 1b3g 1b3g a 1 b 0 energy SCF SCFKIN SCFPOT 1 149 4297623516 149 4298351805 298 8595975321 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 13 6 ROHF OF TWO OPEN SHELLS 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 2 rohf 1b2g 1b3g8 a 1 b 2 1b2g 1b2g a 0 b 0 1b3g 1b3g8 a 0 b 0 energy SCF SCFKIN 1 149 4297623501 149 4298391833 SCFPOT 298 8596015334 265 Chapter 14 Samples for turbo in files 14 1 turbo in is a GAUSSIAN type input file from which the script TMOLE generates the TURBOMOLE input and executes the necessary TURBOMOLE modules and or tools The following sample inputs demonstrate typical usage of TMOLE The syntax of Introduction the file turbo in is explained in Section 14 2 RI MP2 calculation of Phenyl Geometry optimization at MP2 level using the RI approximation Number of max SCF iterations is set to 99 scf_msil 99 The number of ge
108. 99 gen_symm auto charge 0 coord xyz 3 Energy 76 46516801323 0 0 0000000 0 0000000 0 0668805 H 0 7658756 0 0000000 0 5307937 H 0 7658756 0 0000000 0 5307937 end 14 7 Potential curve for the O H bond in HO Calculation of the potential curve for stretching one O H bond in H20 The bond will be stretched from 0 95 Angstrom to 1 35 Angstrom in steps of 0 10 Angstrom The geometry is specified in Z matric format see Section coord gauzmat method GEOMY ri b p SVP gen_symm c1 charge 0 coord gauzmat o h 1 bi h 1b2 2al bi 0 95 b2 0 95 al 109 scan bi 0 95 0 1 1 35 Zend 270 CHAPTER 14 SAMPLES FOR TURBO IN FILES 14 8 Bending potential for Ag Calculation of the potential curve of Ags for bending in the range from 62 to 142 in 4 steps For each step an optimization of remaining geometry parameters here Ag Ag distance will be done The symmetry C is preserved during the calcula tion The MO occupation will be overwritten with Section add_control_commands method GEOMY b3 lyp SVP geo_nrgc 99 gen_stpt 0 gen_crds ired gen_symm auto gen_blow 1 4 scf_msil 99 charge 0 coord gauzmat ag ag 1 bi ag 1b2 2al bi 2 70 b2 2 70 al 62 scan al 62 4 140 fadd_control_commands alpha shells al 1 11 1 a2 1 4 1 bi 1 9 1 b2 1 5 1 beta shells al 1 11 1 a2 1 4 1 b1 1 8 1 b2 1 5 1 ADD END fend Chapter 15 The Perl based Test Suite Structure 15 1 General Testing
109. AO 232 12 2 17 Keywords for Module Frog 2 238 Sirk ok Bede ae ike wee Beg a S 242 ef eaten Gata oid aan Gees 244 13 Sample control files 247 8 CONTENTS ae dynes ape e a e ay ge e a ees Gat ae ia go a 247 Seg ite ete Gt ge Berm Sea go aaa 248 13 2 1 Main File control 0 020020 0004 248 13 22 Filecord a isk a Rak me Gk Sk eg ee 249 oe ae Aa A hd Ge eee GE Bah a wow G 249 Syke AR Pe Ra ee A E 250 pppoe eas 251 13 3 1 Main File comtroll o e 251 133 2 File coord as ic a Ra Rw a ee 252 of We ke ae OS A a ee Bee Se wk a 252 baie ea bee 254 13 4 1 Main File control 02020004 254 13 42 File ord nys sse eg ge a Bk ed Gah a a 255 he Ye Bed Be EAS eh eae BES 255 a a E de ee ree gs eee ee 257 A 260 13 5 1 Main File control o e 260 13 52 File EPA oi o ee A a 261 Ea A A A a a 261 La a e a a e A ee 262 aa e ooh Go dd 2 263 13 6 1 Extracts from control for O2 in D3g Symmetry 263 13 6 2 Extracts from control for Og in Doa Symmetry 263 266 a Gk ee e Sele eg gs ee ae ee eee a es 266 14 2 RI MP2 calculation of Phenyl 0 266 14 3 Vibrational Spectrum of Phenyl 0 267 Dai be ea ge be a D A G 267 14 5 AOFORCE calculation of Benzenel o 268 14 6 UFF calculation of Water 2 2 ee ee 269 14 7 Potential curve for the O H bond in H20l 269
110. BOMOLE keywords grad etc 12 2 FORMAT OF KEYWORDS AND COMMENTS 239 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 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 title Arbitrary title log_history 100 71 mdlog P mdlog Q ke_control length 50 response 1 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 speci
111. CALCULATIONS RIDFTand RDGRAD RIDFTwill use techniques that reduce the scaling behaviour of the exchange evaluation This reduces the computational cost of such calculations especially for large systems significantly 4 2 Exchange Correlation Functionals Available The following exchange correlation functionals are available for all four modules Dscr GRAD RIDFT and RDGRAD The Slater Dirac exchange functional only S 441 45 The 1980 correlation functional functional V in the paper of Vosko Wilk and Nusair only VWN 46 A combination of the Slater Dirac exchange and Vosko Wilk and Nusair 1980 functional V correlation functionals S VWN 44 45 46 The S VWN functional with VWN functional III in the paper This is the same functional form as available in the Gaussian program 14 45 46 A combination of the Slater Dirac exchange and Perdew Wang 1992 corre lation functionals A combination of the Slater Dirac exchange and Becke s 1988 exchange func tionals B88 441 45 48 Lee Yang and Parr s correlation functional LYP 49 The B LYP exchange correlation functional B88 exchange and LYP correla tion functionals asjas The B VWN exchange correlation functional B88 exchange and VWN V correlation functionals 44 45 48 46 The B P86 exchange correlation functional B88 exchange VWN V and Perdew s 1986 correlation functionals 44 45 48 46 50 The Perd
112. Calculations e e o 101 9 4 1 PUrpOSE 2 cane ne eR Raw ea A we ee 101 ps be Go eee ee G 102 ioe Gruss Gabe se A 102 sn ies ee ee ge SO ee ee 8 104 3 6 Counterpoise Corrections using the JOBBSSE Script 106 3 Os OPUIOMS e ao mosa a e Re ee RS 106 3 6 2 Output saad s 688442 bo ead eee Ree ee EE KS 107 109 4 1 Background Theory a 111 de bee tee A ee 112 4 3 Restricted Open Shell Hartree Fock 2 0 114 4 3 1 Brief Description 2 20200 114 4 3 2 One Open Shell 2 0 20 20 2 02 202 00 114 4 3 3 More Than One Open Shelll 116 4 3 4 MiscellameQus ee 119 5 Second order Mgller Plesset Perturbation Theory 121 5 1 Functionalities of MPGRAD and RIMP2 121 5 2 Some Theory mms ee a Ree eae RE wR a E 122 5 3 How to Prepare and Perform MP2 Calculations 122 6 CONTENTS 5 4 General Comments on MP2 Calculations Practical Hints 124 6 Hartree Fock and DFT Response Calculations Stability Dynamic Response Properties and Excited States 126 Rok Woe eS ek Ae oe ee amp s 126 6 2 Theoretical Background 2 22 20 2004 127 cote bad dow A bia bh b OR AE OO SESS 129 bs Gini Ah Ebene O ae oe Ge weigher E 130 6 4 1 Preliminaries 2 2 0 0 0 e 130 ot ates yy at rene gs 130 Mood ee ee oe ak ke eed oe oe ee ee 131 oh bbe ES et eed es 132 El agoi Bote
113. Corrections using the JobBSSE Script The shell script JOBBSSE controls and executes the automatic calculation of the counterpoise correction as it has been formulated by Boys and Bernadi S F Boys and F Bernardi Mol Phys 19 553 1970 to estimate the Basis Set Superposi tion Error BSSE Note that you need to set up the fragments and possibly their symmetries using DEFINE in the geometry menu beforehand For a dimer the cp correction takes the form for the monomers A and B Energy corrected AB A B A B A A while parentheses denote ghost atoms on molecule A or B respectively It basically does the same as the JOBEX script cycling through the direct SCF and if needed 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 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 To the inner works of the program Unlike jobex it calls the program BSSEENERGY which does the operations via system calls JOBBSSE is just there to provide the setup like directories creating of files which are read in by BSSEENERGY and cleaning up 3 6 1 Options Given a Korn shell the usage is nohup jobbsse amp This command invokes cp cor
114. DEFINE menu see Chapter 2 DEFINE will automati cally 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 6 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 1d 7 in control perform a DSCF statistics run if semi direct integral processing is to be used see Chapter 1 7 and re run Dscr or RIDFT 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 geom etry optimizations 6 4 2 Polarizabilities and Optical Rotations The calculation of dynamic polarizabilities is controlled by the keyword 6 4 HOW TO PERFORM 131 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 example to calculate dynamic polarizabilities 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
115. E 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 1 INTERNAL COORDINATE MENU ired REDUNDANT INTERNAL COORDINATES red_info DISPLAY REDUNDANT INTERNAL COORDINATES 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 2 1 THE GEOMETRY MAIN MENU 45 structure can be manipulated by the commands sub m name and del The com mand sy allows you to define th
116. EFINE Note that if you did not define any memory it is automatically set to 1 GB keep program output from all optimization steps keep all directories debug mode calculates in case we have a trimer Energy ABC 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 In case we have a complicated molecular structure occupation or non default freezing in case of MPGRAD or R1CC2 of the orbitals in DEFINE this will cycle through DEFINE several times Note that frag should not be called in DEFINE as this overwrites some of the setup After this jobbsse should be called without the define flag shows a short description of the commands above 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 bsse_out initial grad_out initial control initial and coord initial are the files from the first iteration of the tentative geometry optimization Otherwise you will find all the last full output files like dscf out dimer rimp2 out dimer dscf out A ghostB and so on in the main directory these should be self explanatory The program also keeps all outputs from STATPT or RELAX in the files statpt out x 108 CHAPTER 3 STRUCTURE OPTIMIZATIO
117. ENT OF SOLVATION EFFECTS WITH COSMO Chapter 12 Keywords in the control file 12 1 Introduction The file control is the input file for TURBOMOLE which directly or by cross refer ences provides the information necessary for all kinds of runs and tasks control is usually 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 12 2 Format of Keywords and Comments TURBOMOLE input is keyword directed Keywords start with a e g title Comments may be given after dummy or by a line starting with t 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 13 An alphabetical list of all keywords is given in the index 12 2 1 General Keywords operating system unix path lock off suspend off The four keywords above are set by DEFINE but are not necessary statistics dscf or statistics mpgrad 169 170 CHAPTER 12 KEYWORDS IN THE CONTROL FILE Only a statistics run will be performed to determine file space requirements as specified for DSCF or MPGRAD On return the statistics option will be changed to statisti
118. ER mp2 cc2 OPTIONS AND DATA GROUPS FOR MP2 CC2 ETC 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 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 END 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 2 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 sp
119. HAPTER 13 SAMPLE CONTROL FILES 13 5 Basisset optimization for Nitrogen 13 5 1 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 user defined bonds file coord pople A0 basis file basis rundimensions dim fock dens 141 natoms 1 nshell 6 nbf CAO 15 nbf AD 14 dim trafo SA0 lt gt AO CAO 17 rhfshells 2 scfmo none file mos roothaan 1 a 1 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 interconversion off qconv 1 d 7 maxiter 25 optimize internal off cartesian off global off optimize basis gt basis on logarithm 13 5 BASISSET OPTIMIZATION FOR NITROGEN 261 basis on 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 6 threig 0 005 reseig 0 005 thrbig 3 0 scale 1 00 damping 0 0 forceinit on diag default energy file energy grad file gradient optimize basis gt egrad file egradient egrad file egradient for
120. 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 a coord desy CHAPTER 2 PREPARING YOUR INPUT FILE WITH DEFINE read coord determine symmetry quit main geometry menu 2 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 PH3 as example The commands in this menu will now be described briefly 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 ori entation depending on its point group For the groups Cn Cnv Cnh Dn Dnp and Dna the z axis has to be the main rotational axis secondary twofold rotational axis is always the x axis 0 is always the xz plane and cp the xy plane O is oriented as D4 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 al
121. MOLE_SYSNAME em64t unknown 1inux gnu Please make sure not to append _mpi to the string when setting TURBOMOLE_SYSNAME even if you intend to run parallel calculations SYSNAME will append this string au tomatically to the system name if PARA_ARCH is set to MPI see chapter 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 PATH PATH TURBODIR scripts PATH PATH TURBODIR bin 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 In addition some sample calculations are supplied in TURBOTEST so that the mod ules can be tested Just run TTEST from this directory to get help on how this works 26 CHAPTER 1 PREFACE 1 7 How to Run Turbomole A Quick and Dirty Tu torial 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 12 DEFINE step by step provides 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 molecu
122. NS or relax out x The convergence is signalled by the file converged otherwise you should find the file not converged within your working directory If JOBBSSE finds a file named stop or STOP in the working directory JOBBSSE will stop after the present step has terminated You can create stop by the command touch stop The convergence criteria and their current values are written out at the not converged file Chapter 4 Hartree Fock and DFT Calculations DscF and GRAD are modules for energy and gradient calculations at the Hartree Fock HF and density functional theory DFT levels 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 All func tionalities are implemented for closed shell RHF and open shell UHF reference wave functions 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 accelerati
123. O N by sacrificing the orbital invariance Default Both the orbital dependent and invariant energies are com puted local char char boys or pipek The active occupied molecular orbitals are localized by Boys or Pipek Mezey method Currently the local flag is restricted to closed shell cases within approximation A pairenergy In addition to the RI MP2 R12 summary the R12 pair energies are printed out 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 exprop states all operators qudlen xgrad states ag 3 1 conv 6 thrdiis 2 preopt 3 leftopt bothsides In this data group you have to give additional input for calculations on excited states irrep the irreducible representation 12 2 FORMAT OF KEYWORDS AND COMMENTS 215 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 vers
124. ORDS AND COMMENTS 191 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 shift may help to get better convergence Options are 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 closedshe11 0 4 Note Normally this will disable the automatic shift of energies of vir tual 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
125. PERTURB THEORY 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 TJ Note less disc space means more passes and thus lower efficiency of MPGRAD Settings obtained by MP2PREP may be changed manually You may change the number of passes in traloop by editing the control file e g if the originally intended disc space is not avail able To adapt the size of scratch files add statistics mpgrad to control file and start an MPGRAD statistics run with the command mpgrad Start a single MPGRAD calculation with the command mpgrad 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 5 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 val
126. REQUENCIES 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 cre ating them manually via idef We recommend to use the irem command first to delete all previous definitions of internal coordinates See Section 2 for further de tails If the molecule s point group is not C1 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 drvopts 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 paren thesis e diagonal elements of the Hessian in internal coordinates force constants of bonds angles etc print level 0 e comple
127. 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 eigenvalues too DIIS too default 10 energies scfdump Dump SCF restart information onto data group restartd and 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 a statistics 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 190 CHAPTER 12 KEYWORDS IN THE CONTROL FILE Thus your data group scfintunit may look like this scfintunit unit 30 size 35 file
128. SP3 Setting up the parallel environment In addition to the installation steps described in Section 1 6 see page 24 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 or MPGRAD from your command line without their explicit path expand your PATH environment variable to export PATH TURBODIR bin sysname PATH 30 CHAPTER 1 PREFACE Input data DEFINE AOFORCE ESCF GRAD RDGRAD EGRAD MPSHIFT MOLOCH RELAX STATPT Ricc2 Figure 1 1 The modules of TURBOMOLE and the main data flow between them 1 8 PARALLEL RUNS 31 The usual binaries are replaced now by scripts that prepare the input for a parallel run and start mpiexec or poe on IBM SP3 automatically The number of CPUs that shall be used can be chosen by setting the environment variable PARNODES export PARNODES 8 On all systems TURBOMOLE is using the MPI library that has been shipped with your operating system On Linux the freely available portable implementation of MPI MPICH2 http www unix mcs anl gov mpi mpich is used The scripts that initialize the MPD ring mpdboot and start the parallel binaries mpiexec are located in the TURBODIR mpirun_scripts MPICH2
129. TER 12 KEYWORDS IN THE CONTROL FILE bothsides response The bothsides flag enforces the calculation of both the left and the right eigenvectors for test purposes only fop unrelaxed_only operators diplen gradient conv 6 zconv 6 semicano nosemicano thrsemi 3 In this data group you have to give additional input for the calculation of ground state properties and the solution of response equations fop 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 gradient conv require calculation of geometric gradients In difference to the geoopt 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 tha
130. TION TOOLS 161 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 gt 31 ZaA p Ra Note that at least the Darwin term requires an accurate description of the cusp in the wave function thus the use of basis sets with uncontracted steep basis functions is recommended Moreover note that when using of ECPs these quantities are not too reasonable a respective warning is written to the output Population analyses pop enforces a Mulliken population analysis MPA or a natural population analysis NPA with pop nbo 18 for all densities present in the respective 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 Sub options see Section also allow for calculation of Mulliken contributions of selectable atoms to selectable MOs including provision of data for graphical output simulated density of states Till now only the Natural Population Analysis NPA is implemented Note that all of the following quantities may be calculated simulta neusly For treatments of type Dscr RIDFT RIMP2 and
131. TURBOMOLE Program Package for ab initio Electronic Structure Calculations USER S MANUAL TURBOMOLE Version 5 9 17th February 2008 Contents 1 1 Contributions and Acknowledgements 1 2 Features of TURBOMOLE o 4 PG a AA ea ds 1 4 Modules and Their Functionality Lib Fools i e Qe ee Ree ARR ae REP ee a hee ee oe GS a ahaa aa aoe ek pert ative GP oes ee at ea E 1 7 How to Run TURBOMOLE A Quick and Dirty Tutorial 1 7 1 Single Point Calculations Running TURBOMOLE Modules te Re a A ee ae ee 1 7 3 Calculation of Molecular Properties 1 7 4 Modules and Data Flow 2 1 8 Parallel Runs 2 20 02 2000 00 a 1 8 1 Running Parallel Jobs o 1 9 Running TURBOMOLE using the script TMOLE 1 9 1 ImplementatioM o e 19 2 The file turbo idl 2 Preparing your input file with DEFINE 2 0 1 Universally Available Display Commands in DEFINE 2 0 2 Specifying Atomic Sets o o 2 0 3 control as Input and Output File 2 0 4 Be Prepared 2 0 0022 eee eee ee 2 1 The Geometry Main Menu 202005 11 11 12 12 20 22 24 26 28 29 29 29 29 33 33 33 4 CONTENTS 2 1 1 Description of commands o 46 e de ds co ee ie amp 49 2 1 3 Manipul
132. U without more changes lt RETURN gt OR OR q uit WILL TERMINATE THIS MENU 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 bas should provide no problems glb refers to a global scaling factor for all 2 4 THE GENERAL OPTIONS MENU 73 basis set exponents Imagine that you would like to replace your basis set which contains basis functions Xp x zo y yo z 20 exp nulr ro by another basis set which contains basis functions Xp x zo y yo z 20 exp any r ro 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 polarizabil ity 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
133. UHF WITH lt int gt UNPAIRED ELECTRONS 1 lt list gt PRINT MO S FROM EHT IN lt list gt DEFAULT ALL p lt index gt PRINT MO COEFFICIENTS OF SHELL lt index gt c lt list gt CHOOSE SHELLS IN lt list gt TO BECOME CLOSED SHELLS o lt index gt CHOOSE SHELL lt index gt TO BECOME AN RHF OPEN SHELL a lt list gt CHOOSE SHELLS IN lt list gt TO BECOME UHF ALPHA SHELLS b lt list gt CHOOSE SHELLS IN lt list gt TO BECOME UHF BETA SHELLS v lt list gt CHOOSE SHELLS IN lt list gt TO BECOME EMPTY SHELLS amp REPEAT THE EXTENDED HUECKEL CALCULATION SAVE OCCUPATION NUMBERS amp GO TO NEXT ITEM dis GEOMETRY DISPLAY COMMANDS e CALCULATE EHT ENERGY f FURTHER ADVICE lt int gt INTEGER lt index gt INDEX OF MO SHELL ACCORDING TO COMMAND s lt list gt LIST OF MO SHELL INDICES LIKE 1 5 7 8 11 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 onl
134. UNDANT 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 INTERNAL 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 fixed internal coordinates specified These coordinates will be included in the B matrix see command imet but their v
135. UPDATE TO DIAGONAL ELEMENTS IF METHOD IS BFGS DFP OR MS DEFAULT n DISCARD OFF DIAGONAL ELEMENTS DEFAULT n 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 SCALE INPUT HESSIAN BY lt real gt DE IF DE THE OBSERVED ABSOLUTE CHANGE IN ENERGY IS OBEYING THE CONDITION DE gt lt real gt gt 0 DEFAULT NO SCALING 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 diagonal offreset offdamp lt r gt damp lt real gt scale lt real gt allow lt real gt min lt real gt 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 78 CHAPTER 2 PREPARING YOUR INPUT FILE WITH DEFINE OPTION DESCRIPTION off switch off initialization DEFAULT on cart use analytical cartesian hessian provided by a 2nd derivatives calculation DEFAULT n diag use diagonal matrix with diagonal elements set individually within data gr
136. a from data blocks grad egrad as accumulated by the GRAD program degrees 12 2 14 Keywords for Module STATPT statpt itrvec 0 update bfgs hssfreq 0 keeptmode hssidiag O radmax O radmin 1 0d 4 O Wow Ya tradius threchange 1 0d 5 thrmaxdispl 1 0d 3 12 2 FORMAT OF KEYWORDS AND COMMENTS 227 thrmaxgrad 1 0d 3 thrrmsdispl 5 0d 4 thrrmsgrad 5 0d 4 Only non default values are written in the control file except statpt 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 hessfreq Frequency of hessian calculation 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 5 thrmaxdispl threshold for maximal dis
137. ab rpas or 206 CHAPTER 12 KEYWORDS IN THE CONTROL FILE scfinstab rpat or scfinstab urpa 2 CI singles singlet or triplet or spin unrestricted excitation energies HF scfinstab ciss or scfinstab cist or scfinstab ucis 3 Eigenvalues of singlet or triplet or non real stability matrices HF RI DFT RHF scfinstab singlet or scfinstab triplet or scfinstab non real 4 Static polarizability and rotatory dispersion tensors HF RDDFT RHF UHF scfinstab polly 5 Dynamic polarizability and rotatory dispersion tensors HF RI DFT RHF UHE scfinstab dynpol unit list of frequencies where unit can be eV nm rcm default is a u Hartree 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 12 2 FORMAT OF KEYWORDS AND COMMENTS 207 will yield the 17 lowest excitations in IRREP b1g the 23 lowest excitations in IRREP eu and all excitations in IRREP t2g Specify soes all textitn 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
138. adc 2 212 cc2 212 ccs 212 cis 212 cis d 212 cisdinf 212 conv 212 fmtprop 212 geoopt 147 212 hard_restart 212 iprint 212 lindep 212 maxiter 212 maxred 212 mp2 212 mxdiis 212 nohard_restart 212 norestart 212 oconv 212 restart 212 ricore 68 110 111 129 133 155 195 196 246 ricore_slave 246 ridft 129 133 195 196 rij 195 rik 110 195 196 ripop 195 rir12 137 151 214 local 152 214 noinv 152 214 pairenergy 214 ri2model 152 214 rohf 193 roothaan 172 193 rpaconv 129 207 rpacor 133 207 rundimensions 187 scfconv 28 70 130 187 191 205 211 settings for AOFORCE 155 NUMFORCE 155 288 scfdenapproxl 185 188 scfdiis 187 189 scfdump 185 187 189 scfinstab 110 129 207 ciss 206 cist 206 dynpol 206 non real 206 polly 206 rpas 206 rpat 206 singlet 206 triplet 206 ucis 206 urpa 206 scfintunit 129 187 189 190 192 211 243 file 190 size 190 unit 190 scfiterinfo 189 scfiterlimit 190 scfmo 61 62 170 172 186 187 189 190 194 243 expanded 190 file 190 format 190 none 61 190 scfconv 190 scfdump 190 scfmo none 61 scforbitalorder 191 scforbitalshift 191 automatic 191 closedshell 191 individual 191 noautomatic 191 scftol 191 211 243 scratch scratch files 243 245 scratch files 191 224 244 seed 239 sharedtmpdir 153 soes 130 133 134 206 208 spectrum 133 207
139. adient programs GRAD RDGRAD EGRAD RIMP2 MP GRAD 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 gradients 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 Normally internal coordinates are not used for input or output by the electronic structure programs Dscr MPGRAD etc Instead the coordinates gradients etc are automatically converted to internal coordinates by RELAX on input and the updated positions of the nuclei are written in carte sians coordinates to the data group coord Details are explained in the following sections 3 3 PROGRAM RELAX 95 3 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 t
140. al 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 forceapprox approximate force constant for geometry optimizations The control file must end with this keyword end 12 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 Sch nflies 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 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 specify the basis set and the auxiliary fitting basis for RIDFT calculations the ECP if this is used 7 172 CHAPTER 12 KEYWORDS IN THE CONTROL FILE The files basis ecp and jbas must provide the necessary information under the labels specified in atoms pople char This data group specifies the number of cartesi
141. allest 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 70 CHAPTER 2 PREPARING YOUR INPUT FILE WITH DEFINE 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 and 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
142. alues will not be changed during geometry optimization 50 CHAPTER 2 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 DEFINE 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 respect to Cartesian coordinates This matrix is used in program RELAX for the
143. ameter 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 type r 1 Delocalized Coordinates The BmBt matrix is diagonalized for the complete set of redundant internal coordinates matrix m is a unit matrix Delocalized Coordinates obtained with a modified matrix m the val ues of m can be defined by user input see below 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 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 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 coordi nates 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 Generalized natural coordinates Natural internal coordinates are defined first for the remaining cage decoupled coordinates are defined a positive real number which is an approximate force constant can be read
144. an 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 RHE closed shells Specification of MO occupation for RHF e g alg 1 4 a2g OS N N U a 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 Ci b3g 1 Ci roothaan 1 a 1 b 2 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 and the tables of Roothaan parameters in Section 4 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 alg 1 4 1 a2g 1 1 The specification of MO occupation for UHF uhf overwrites closed shell occupation specification 12 2 FORMAT OF KEYWORDS AND COMMENTS 173 12 2 3 Keywords for redundant internal coordinates in redund_inp With the parameters in redund_inp the generation of redundant internal coor dinates can be modified All entries have to be made in the control file before invoking the ired option Important options are iprint n print par
145. and internal coordinates allowing efficient geome try optimization 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 sin gle 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 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 and DFT calculations see keywords for function als supported DscF supports restricted closed shell RHF spin restricted ROHF as well as UHF runs DscrF 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 DFT calculations as Dscr and GRAD within the RI J ap proximation i e the total density is approximated by a sum of atom centered s p d functions the auxiliary or fitting basis This allows for a very efficient treatment of Coulomb interactions The functionals supported are specified in DEFINE requires a well converged SCF run by Dscr see keywords and per forms closed shell RHF or UHF
146. 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 92 The first approach often referred to as PT E performs a normal MP2 energy calculation on the solvated HF 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 93 94 In the so called PTD approach the vacuum MP2 density is used to calculate the reaction field The third approach often called PTED 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 168 CHAPTER 11 TREATM
147. antum chemistry Annual Reports in Computational Chemistry 1 19 30 2005 D Rappoport F F 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 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 H ser A direct algorithm for self consistent field linear response theory and application to Cgp Excitation energies oscillator strengths and frequency dependent polarizabilities J Chem Phys 99 2 1262 1270 1993 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 O Christiansen H Koch P Jorgensen 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 282 71 72 73 74 75 78 79 80
148. ar dynamics calculations 4 1 Background Theory In Hartree Fock theory the energy has the form Eyr h J K Vuc 4 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 Vauc is the nuclear repulsion energy 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 Eprrle Tle Vrelo Jle Erlo Eclpl Vines 4 2 where Tp is the kinetic energy Vre 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 With TURBOMOLEversion 5 9 the exact non RI exchange for DFT hybrid func tionals and Hartree Fock can be used in combination with RI J using the modules 112 CHAPTER 4 HARTREE FOCK AND DFT
149. ar momentum 4 L2 v all three components individual components can be specified with the labels xangmom yangmom zangmon nef electronic force on nuclei WZ v where Zy is the charge of the nucleus J and r is the position vector of the electron rela tive 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 proper ties 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 calcu lated Alternatively one can select a subset of these listed in parentheses e g states ag 3 1 3 5 biu 1 1 3 b2u4 This will select the triplet ay states no 1 3 4 5 and the singlet bj states no 1 2 3 and the singlet which is default if no is found ba state no 4 cgrad 1000 Calculate the error functional dpy for the RI approximation of ai bj integrals jara 1 ab 27 exact abl ij ral R Ea Ei b Ej 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 Sec tion L 5 12 2 13 Keywords
150. arefully optimized for all atoms individ ually 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 gridsize is given as number of radial grid points ioffrad radsize 1 5 12 2 FORMAT OF KEYWORDS AND COMMENTS 181 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 gridsize 1 2 3 4 5 6 7 8 radsize 1 2 3 6 8 10 14 9 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 gt 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 scali
151. 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 com mands and results of all test criteria are found in the TESTPROTOKOLL file in the test subdirectory 271 272 CHAPTER 15 PERL BASED TEST SUITE 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 1s usr local TURBOMOLE scripts A specific executable 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
152. asisform 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 14 CHAPTER 1 PREFACE auxiliary basis sets for RI DFT d el auxiliary basis sets for RI MP2 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 II HI IV VI VII VIII IX XI Electronic Structure Calculations on Workstation Computers The Program System TURBOMOLE R Ahlrichs M Bar M H ser H Horn and C K lmel Chem Phys Letters 162 165 1989 Improvements on the Direct SCF Method M H ser and R Ahlrichs J Com put Chem 10 104 1989 Semi direct MP2 Gradient Evaluation on Workstation Computers The MP GRAD Program F Haase and R Ahlrichs J Comp Chem 14 907 1993 Efficient Molecular Numerical Integration Schemes O Treutler and R Ahlrichs J Chem Phys 102 346 1995 Stability Analysis for Solutions of the Closed Shell Kohn Sham Equation R Bauernschmitt and R Ahlrichs J Chem Phys 104 9047 1996 Treatment of Electronic Excita
153. ating the Geometry o 54 o AS 54 a Ba kG g ii Be he a eo 57 Lor a Ria age a lee a e 59 i fie be kee ee Sha 59 Sie eRe amp a ene E 62 Gosh ad rok holy teen ak ds ade e amp 64 2 3 4 Roothaan Parameters 0202 0200 64 ore ek eae a a T E 65 2 4 1 Important commands 2 2200 66 Hae abe we Ae ck Sere Bodog Mp eg Be 71 Pe WR dee ie ae ae Be GAN a te a 74 2 4 4 Definition of External Electrostatic Fields 78 SG i de Ae eo a th a A ee a r 79 87 3 1 Structure Optimizations using the JOBEX Script 87 i fe ey eh had ee hae Shwe ee ae 87 331 2 OUTPUT aus a Mask ees walk ats oe bane oa eo 88 bode Geeks bag Roe ee Ea ke e reis we hn RE dae 89 3 2 1 General Information o oa aa 89 Sf GER A eee AA Ea eee Be Boe es 90 deine Bae Mag dh ak Ae BO ge Ad ee 91 Sogo eh BA eee areca woe Shee ee E 91 Su SON pre Gee ee ee A ek a aa 92 3 d 1 Purpose s s oe ad ba ga a eG eG we Ak ee 92 bead age ee Rae a 93 Leh bbe Saeed a bes 95 3 3 4 Definition of Internal Coordinates 96 CONTENTS 5 TERN 97 bal 97 3 3 7 Optimization of Basis Sets SCF only 98 er 99 3 3 10 Conversion from Internal to Cartesian Coordinates 99 Constants to Internals o 99 Era ee 100 3 3 13 Initialization of Force Constant Matrices 100 3 3 14 Look at Results o o 0008 101 3 4 Force Field
154. ation 72 CHAPTER 2 PREPARING YOUR INPUT FILE WITH DEFINE 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 fermi 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 T CARTESIAN 1st derivatives sec T CARTESIAN 2nd derivatives bas F energy derivatives with respect to BASIS SET exponents scaling factors 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 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 MEN
155. atural 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 1 o s 2 p 1 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 localize enables the generation of localized molecular orbitals LMOs using Boys lo calization By default all occupied orbitals are included localised 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 characterize 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 normalfontlist of MOs Include only selected MOs e g valence MOs in localization procedure numbering as available from EIGER 12 2 FORMAT OF KEYWORDS AND COMMENTS 235 sweeps integer maximum number of orbital rotations to get LMOs default va
156. ature for special applications by even more special users As reference see 84 To optimize the structure and a global scaling factor specify optimize internal on or cartesian on global on You need as input data groups 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 3 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 3 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 n
157. be considered bad for small molecules but there is no general rule check those internal coordinates for consistency which contribute to the correspond ing eigenvector s 3 3 6 Structure Optimization in Cartesian Coordinates For this task you have to specify optimize cartesian on 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 pro grams 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 98 CHAPTER 3 STRUCTURE OPTIMIZATIONS coord 2 02693271108611 2 03672551266230 0 00000000000000 1 08247228252865 0 68857387733323 0 00000000000000 2 53154870318830 2 48171472134488 0 00000000000000 1 78063790034738 1 04586399389434 0 00000000000000 2 64348282517094 0 13141435997713 1 68855816889786 2 23779643042546 3 09026673535431 O 00000000000000 2 64348282517094 0 13141435997713 1 68855816889786 1 31008893646566 3 07002878668872 1 68840815751978 1 31008
158. bond out of the CHH plane But then two degrees of freedom still remain which cannot be specified using these normal coordinate 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 carbon 3 carbon 4 hydrogen would solve the problem The type comp describes a compound coordinate i e a linear combi nation of primitive internal coordinates This is often used to prevent strong coupling between primitive internal coordinates and to 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 20 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 co ordinate 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 primitive coordinates is the same as described above for the correspond ing 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 th
159. c2 mp2 cc2 response static relaxed operators diplen qudlen gradient 7 3 FIRST ORDER PROPERTIES AND GRADIENTS 147 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 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 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 Ko need to be solved no equations have to be solved for the Lagrangian multipliers t CPU time and disk space requirements are does somewhat smaller than for CC2 properties or gradients For SCF CIS CCS it is recommended to use the modules GRAD and MOLOCH for the calculation of respectively ground state gradients and first order properties 7 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 no fi
160. cases necessary to have the data of the former calculation in another di rectory 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 without changing the old data The data groups closed shells and open shells will be taken for your new calcula tion and the SCF vector from the old calculation will be projected onto the space which is spanned by your present basis set These start vec tors are usually better than the ones you could obtain by an extended Hiickel calculation man allows you to declare occupation numbers or change a previous declaration 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 2 3 3 The same procedure applies to the open shell occupation numbers after you 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 n
161. ceapprox file forceapprox lock off atoms n 1 basis n def SV P closed shells alg 1 2 2 open shells type 1 tiu 1 1 end 13 5 2 File coord coord 0 00000000000000 0 00000000000000 0 00000000000000 n user defined bonds end 13 5 3 File basis sis n def SV P Hon 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 262 CHAPTER 13 SAMPLE CONTROL FILES 3 p expopt contopt 13 571470233 0 40072398852E 01 2 9257372874 0 21807045028 0 79927750754 0 51294466049 1 p expopt 0 21954348034 1 0000000000 1 d 1 0000000000 1 0000000000 13 5 4 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 30506869715453D 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 956756
162. cf_grid m4 Available Properties GEOMY optimization of all structure parameters for ground states default geo_nrgc 20 ENRGY single point energy calculation default gen_spca 1 GRADI calculation of the gradient default gen_spca 1 FORCE calculation of the vibrational spectrum First the energy will be calcu lated Possible levels of calculation UFF universal force field see Section 3 4p HF Hartree Fock see Chapter 4 DFT switch to choose the exchange correlational functional e g ENRGY s vwn SVP The functionals available and their abbreviations are listed in Menu 2 4 1 and are described in Section MP2 second order Mgller Plesset Pertubation Theory see Chapter 5 RI DFT and RI MP2 to use the RI approximation type ri before the description of the level This is possible for all non hybrid and hybrid functionals see Section 4 2 and for MP2 e g ENRGY ri s vwn SVP 1 9 RUNNING TURBOMOLE USING THE SCRIPT TMOLE 35 UHF and UKS the molecule will be calculated in unrestricted formalism if the first letter of the level ist an u e g ENRGY uhf TZVP Basis set choice the available basis sets are the standard basis sets of TURBOMOLE see Section 2 2 Default basis set is def SV P If the level of calculation is UFF there is no need to specify the basis set Available general run options gen_crds options choose coordinate system see optimize ired redundant internal coordinates
163. ch 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 Kp 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 properties and gradients ric
164. ch this definition should apply The syntax for this list is as usual in TURBOMOLE e g 2 3 8 10 12 nmao 1 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 nick name 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 12 2 plot fit FORMAT OF KEYWORDS AND COMMENTS 231 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 Dscr RIDFT RIMP2 or EGRAD as described below If nevertheless plot is active you need grid 1 mo 4alg origin 000000 000000 000000 vectorl 1 000000 000000 000000 vector2 000000 1 000000 000000 grid1 range 5 000000 5 000000 points 100 grid2 range 5 000000 5 000000 points 100 outfile 4alg to obtain two dimensional plot data of mo 4alg
165. ck operator for electron js and ex is a canonical Hartree Fock orbital energy Q12 1 O1 1 O2 is the strong orthogonality projection oper ator with O gt gt er p 0x 1 the projection operator onto the space spanned by the occupied spin orbitals pz The present implementation of the MP2 R12 method computes the vectors vj and matrices B in the following manner e It uses either approximation A default or approximation A to compute the vectors vj and the matrices B These approximations are described in de tail in Ref 78 It is recommended to use approximation A The keyword ri2model must be used for calculations in the framework of approximation A e The calculation is based on the orbital invariant ijkl Ansatz of Ref 79 The keyword noinv must be used if only the original orbital dependent diagonal ijij Ansatz of Ref shall be applied not recommended e It uses either canonical or localized Hartree Fock orbitals Both the Boys and Pipek Mezey methods can be used to localize the orbitals keyword local The diagonal ijij Ansatz can be used in conjunction with localized orbitals but be aware of the dependence of the results on the orbitals For 99399 example spin adapted singlet and triplet pairs ij are taken for RHF cases 995599 while aa af Ba and 88 pairs ij are taken for UHF cases yielding different results even for identical RHF and UHF determinants
166. columns of the first irrep alpha spin of type tag 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 Furthermore 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 P type orbitals then if you are interested in plotting the G type LMOs only you have to type pointval lmo 6 8 Non default grids are decribed in detail in Sections 12 2 16 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 positions 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 88 Chapter 11 Treatment of Solvation Effects with C
167. 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 coordinates run into linear dependency during their optimization imet checks the B matrix and removes linear dependent internal 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
168. cs 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 com pletion 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 ecp specification of effective core potentials jbas auxiliary fitting basis for the Coulomb terms in RIDFT scfmo uhfmo_alpha uhfmo_beta MO vectors of SCF or DFT calculations for RHF or UHF runs 12 2 FORMAT OF KEYWORDS AND COMMENTS 171 natural orbitals natur
169. date schlegel suboptions Schlegel update 12 2 FORMAT OF KEYWORDS AND COMMENTS 221 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 ingeo integer 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 extra polation 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 y 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 integer ma
170. default intern internal coordinates cart cartesian coordinates gen_symm options assign symmetry of the molecule Sch nflies symbol auto DEFINE assigns point group default any any Schonflies symbol e g gen_symm c2v gen_sthr real threshold for symmetry determination default 1d 3 gen_prep options switch for a preparation run gen_prep 0 a calculation is done default gen prep 1 only input files such as control etc are generated gen_stpt options switch for using RELAX or STATPT gen_stpt 0 using RELAX default gen_stpt 1 using STATPT gen_spca options switch for single point calculation gen_spca 0 structure optimization default gen spca 1 single point calculation 36 CHAPTER 1 PREFACE gen_stat options switch for statistics run see statistics gen stat 0 no statistics run default gen stat 1 statistics run will be performed gen blow nteger add dummy orbitals per irrep default 0 Needed for non default occupation if one chages the occupation with add_control_commands gen_basl lt path gt path for basis sets default TURBODIR basen gen_jbas lt path gt path for auxiliar basis sets default TURBODIR jbasen gen scrd lt path gt path for scripts default TURBODIR scripts gen_bind lt path gt path for binaries default TURBODIR bin sysname gen_mult nteger multiplicity of molecule default 1 gen _ncpu integer number of CPUs only necessary fo
171. diates will be placed under the path specified in the control file with tmpdir see Section 12 2 12 which should point to a directory in a file system with a good performance The parallel version of the Ricc2 program can presently account for the following two situations Clusters with single processor nodes and local disks Specify in tmpdir a directory in the file system on the local disk All large files will be places on the nodes in these file systems The local file system must have the same name on all nodes Clusters with multiple e g dual processor nodes and local disks Set in addition to tmpdir the keyword sharedtmpdir to indicate that several pro cesses might share the same local disk The program will than create in s the directory given in tmpdir subdirectories with node specific names 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 R1icc2 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 m
172. directory These scripts require Python version 2 2 or later which should be available in any reasonable Linux distribution Note the parallel TURBOMOLE modules except R1ICC2 need an extra server run ning in addition to the clients This server is included in the parallel binaries and it will be started automatically but this results in one additional task that does not need any CPU time So if you are setting PARNODES to N N 1 tasks will be started If a queueing system is used check that N 1 processes will be provided Starting parallel jobs After setting up the parallel environment as described in Chapter 1 8 1 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 This is not true for the program MPGRAD To prepare the parallel input for this program call turbo_preproc in the directory where your serial input lies and follow the instructions 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 l
173. e It uses the robust fitting techniques of Ref 83 e The approximate completeness relations of R12 theory that avoid four and three electron integrals are inserted in terms of the same orbital basis that is used to expand the wave function This implies that the basis set must be chosen with special care 7 6 Parallel RI MP2 and RI CC2 Calculations The Ricc2 program is partially parallized for distributed memory archtectures 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 7 6 PARALLEL RI MP2 AND RI CC2 CALCULATIONS 153 While in general the parallel execution of RIcc2 works similar to that of other parallized 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 the program is started in a directory which is readable and writeable on all compute nodes under the same path e g a NFS directory 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 interme
174. e between the atoms J 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 linesearch step will be done after the Newton atep dqmax max displacement in a u for a coordinate in a relax step mxls dhls ahls parameters of linesearch 176 CHAPTER 12 KEYWORDS IN THE CONTROL FILE 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 ufftopology contains a list of the next neigbours of each atom see Section 12 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 this 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 pro gram will use th
175. e control title NH3 c3v SVP operating system unix symmetry c3v coord file coord intdef file coord atoms n i 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 CAD 30 nbf A0 29 dim trafo SAO lt gt A0 CAD 69 rhfshells 1 scfmo file mos closed shells al 1 3 e 1 scfiterlimit 30 scfconv 7 thize 10000000E 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 dipole on nuclear polarizability interconversion off qconv 1 d 10 maxiter 25 optimize internal on cartesian off IN mS N N NED 13 2 NH INPUT FOR A RHF CALCULATION 249 global off basis off logarithm coordinateupdate dqmax 0 3 interpolate on statistics 5 forceupdate ahlrichs numgeo 0 mingeo 3 maxgeo 4 modus lt gl 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 13 2 2 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 1 000
176. e cou pled cluster models different expressions are obtained for left and right transi tions moments Mj s and Mio and the transition strengths Se y are obtained as a symmetrized combinations of both 1 Of _ V V V V Sty 5 mgt ME 4 M M o 7 23 Note that only the transition strengths ote y are a well defined observables but not For a review of the theory see refs 1741177 0 the transition moments MY_ sand MY 7 5 REMP2 R12 CALCULATIONS 151 The transition strengths calculated by coupled cluster response theory according to Eq have the same symmetry with respect to interchange of the operators Vi 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 71113 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 has to be
177. e eigenvalue or imaginary frequency A good comparison of different TS optimization methods is given in 28 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 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 90 CHAPTER 3 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 1076 a u e the maximum displacement element drops below the value given by thrmaxX displ default 107 a u e the maximum gradient element drops below the value given by thrmaxgrad default 107 a u e the root mean sq
178. e 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 Therefore the Universal Force Field UFF developed from Rapp et al in 1992 is implemented see also Section 3 4 Beyond this one can calculate a Cartesian analytical Hessian If one does so the start Hessian for the ab ini tio 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
179. e 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 only with functional 1hf Checking if the selected grid is accurate enough for the employed basis set by performing a numerical integration of the norm of all orbitals For more detailed information about LHF please refer to page 197 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 fullshell 12 2 FORMAT OF KEYWORDS AND COMMENTS 183 dft functional b p gridsize m4 fullshell symblocki1 real dl i symblock2 real or developers only Values of real effects efficiency of the quadrature default is symblock1 0 001 and symblock2 0 001 one can try higher or small
180. e 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 54 CHAPTER 2 PREPARING YOUR INPUT FILE WITH DEFINE 2 1 3 Manipulating the Geometry Note that the molecular geometry can 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
181. e starting search subspace Generally all guess Hessian eigenvectors cor responding 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 Force constant calculations on the DF T 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 12 2 9 Keywords for Module EscrF ESCF calculations to perform an ESCF calculation converged molecular orbitals from a HF DFT or RIDFT calculation are needed The HF DFT 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 1d 7 for the ground state calculation The input for an EscF calculation can be conveniently generated using the ex menu in DEFINE see Section 2 In an Escr 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 scfinst
182. e the external field is first applied after the SCF calculation and 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 L CC2 3 HF H CC tp ulf H T2 HF 7 12 p X Ey Hel Fo BV To HF H2 with H Ho PV where V is the one electron operator describing the external field 8 the field strength and Hop and Fo are the Hamiltonian and Fock operators of the unperturbed system by the expression VS ze JS ee es 7 13 0 pq ero Dial VE 724 pi Patol ne H2 146 CHAPTER 7 RI CC2 where indicates that the real part is taken Relaxed 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 PO HF H CC a 441 H H To HF 7 15 pi fpa ual F To HE Fo Fo H2 Ho where F is the Fock operator corresponding to the Hamiltonian of the perturbed system H Hj GV One electron properties are then obtained as vye 002 9 caro Y Bal V TIHE 7 16 p Y fa ual V T HE Y Bro Vio Lo H2 ID Vo 7 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 multipliers t are solved whi
183. ead 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 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 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 01cm 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 functions and 100 atoms noproj forces the program not to project out translations and rotat
184. eal 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_a b 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 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 234 CHAPTER 12 KEYWORDS IN THE CONTROL FILE pop nbo to perform a natural population analyses 18 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 n
185. ecify 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 2 4 THE GENERAL OPTIONS MENU 67 The functionals supported are obtained with the command func SURVEY OF AVAILABLE EXCHANGE CORRELATION ENERGY FUNCTIONALS FUNCTIONAL TYPE EXCHANGE CORRELATION REFERENCES slater dirac LDA S 1 2 exchange s vwn LDA IS VWNCV 1 3 vwn LDA VWNCV 3 s vwn_Gaussian LDA S VWNCIII 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 VWN V P86 1 3 5 7 pbe GGA S PBE X PW PBE C 1 2 4 8 tpss HGGA S TPSS X PW TPSS C 1 2 4 14 bh lyp HYB 0 5 S B88 LYP 1 2 5 6 9 0 5HF l l b3 lyp HYB 0 88 0 72B88 0 19VWN CV 1 3 5 6 10 0 2HF 0 81LYP b3 lyp_Gaussian HYB 0 8S 0 72B88 0 19VWNCIII 1 3 5 6 10 0 2HF 0 81LYP pbe0 HYB 0 75 S PBE X PW PBE C 1 2 4 8 11 0 25HF l tpssh HYB 0 9 S TPSS X PW TPSS C 1 2 4 14 15 0 1HF l l 1hf EXX EXX 12 13 Default is b p i e B P86 which is probably best
186. ection 12 2 5 on page 194 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 1hf see page L97 For the definition of gridtype 1 3 please refer to Eq 16 17 and 19 in Ref 95 Example default value 180 CHAPTER 12 KEYWORDS IN THE CONTROL FILE dft gridtype 3 debug integer Flag for debugging debug 0 means no debug 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 96 default is nkk 3 The usage of nkk makes sense only in the range 1 lt nkk lt 6 Example dft nkk 3 ntheta integer e not recommended for use nphi integer Only for user specified Lobatto grids i e gridsize 9 ntheta specifies the number of 9 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 c
187. ectronic 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 abelian point groups C1 Cs C2 Ci Con Cov Da Dan The R12 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 Geometry optimizations and molecular dynamics Invoke jobex with the level CC2 option see Section 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 on the gradients Invoke for this NumForce with the level CC2 option see Chapter 8 for details about NUMFORCE The usage of the NUMFORCE interface for excited states is restricted to C1 symmetry 138 CHAPTER 7 RI CC2 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 interfaces is specified in the option geoopt see Section in datagroup ricc2 see Section 12 2 12 For calculations on excited states this state has in addition to be included in the input for excitation energies in datagroup excitations How to quote If results obtained with the RICC2 program are
188. ee keywords and performs an analytic calculation of force constants vi brational frequencies and IR intensities AOFORCE is also able to calcu late only the lowest Hessian eigenvalues with the corresponding eigen vectors 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 approxima tion poles of the frequency dependent polarizibility 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 is of non hybrid type we recommend B P86 but slightly better results are obtained for the hybrid functional B3 LYP 14 stability analysis of single determinant closed shell wave functions second derivative of energy with respect to orbital rotations computes gradients and first order properties of
189. eed 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 optimization cycles by the various gradient programs for coordinate and gradient 100 CHAPTER 3 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 3 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 set
190. efined in the cosmo and the cosmo_atoms block Example with default values 200 CHAPTER 12 KEYWORDS IN THE CONTROL FILE 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 the following options are not used by default allocate_nps 140 use_old_amat epsilon real defines a finite permittivity used for scaling the screening charges allocate_nps integer skips the COSMO segment statistics run and allocates memory for the given number of segments 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 k 10 x 3 x n 2 12 32 42 92 nspa integer number of segments per atom allowed values k 10 x 3 x n 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 fill in seams between atoms with points cavity open leave untidy seams between atoms ampran real amplitude of the cavity de symmetrization 12 2 FORMAT OF KEYWORDS AND COMMENTS 201 phsran real phase of the cavity de symmetrization use_old amat uses A matrix setup of TURBOMOLE 5 7 If the cosmo keyword is given without further specifications
191. en shell will be correctly assigned 2 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 this 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 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 2 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
192. ence 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 maxiter n maximum number of iterations 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 hessians between spaces of internal cartesian coordinates using the def initions of internal coordinates given in intdef available suboptions are cartesian gt internal coordinate gradient hessian cartesian lt internal coordinatethe direction of the transforma tion 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 up
193. end 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 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 Ca
194. er 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 on page 187 weight derivatives Includes the derivatives of quadrature weights to get more accurate re sults Default is that the derivatives of quadrature weights will be not considered see section 12 2 7 on page 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 orby x y z lEl 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 Requests calculation of occupation numbers at a finite temperature T For an orbital with the energy e the occupation number n
195. ers according to your system re sources and by specifying auxiliary basis sets and frozen core shells This can also be done in DEFINE 24 SCREWER SDG SYSNAME STATI T2S T2X TM2MOLDEN TORS TBTIM TBLIST UHFUSE X2T CHAPTER 1 PREFACE distorts a molecule along a vibrational mode 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 SCHAKAL format converts TURBOMOLE coordinates to xyz format 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 WT Xtables for options please type TBLIST help is used to produce summaries of timings from TURBOBENCH calcula tions to ATEX format for options please type TBLIST help transforms the UHF MOs from a given symmetry to another symme try which is C4 by default just enter uhfuse but can be specified e g as C2y by entering uh
196. es 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 4 1 BACKGROUND THEORY 111 2 The maximum core memory the program is allowed to allocate should be defined in the data group ricore the recommended value 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 Section 3 1 for additional options and parameters for geometry optimiza tions and ab initio molecul
197. es can be applied steepest descent Pulay s DIIS quasi Newton conjugate gradients as well as com binations of them RELAX carries out e update of general coordinates e update of approximate hessians if needed e conversion of coordinates internal cartesian The mode of operation is chosen by the keywords optimize and interconversion and the corresponding options which will be described in the following sections 3 3 PROGRAM RELAX 93 3 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 g can be obtained from the quasi Newton update ght gt FRG 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 approximation 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 optimization task requires explicit specifications in data group optimize which
198. es 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 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 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 MP GRAD RIMP2 Ricc2 EGRAD etc egrad Basis set exponents scale factors and their gradients as calculated in subse quent 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 ob tained from treatments e g correlation or relativistic on higher level See the exam
199. ew Burke and Ernzerhof PBE exchange correlation functional al The Tao Perdew Staroverov and Scuseria functional Slater Dirac TPSS exchange and Perdew Wang 1992 and TPSS correlation functionals EBA Additionally for all four modules DscF GRAD RIDFT and RDGRAD following hybrid functionals are available a mixture of Hartree Fock exchange with DFT exchange correlation functionals 4 2 EXCHANGE CORRELATION FUNCTIONALS AVAILABLE 113 The BH LYP exchange correlation functional Becke s half and half exchange in a combination with the LYP correlation functional 441 45 48 49 53 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 4 3 where HF denotes the Hartree Fock exchange 44 45 48 49 54 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 The 1996 hybrid functional of Perdew Burke and Ernzerhof with the form 0 75 S PBE X 0 25HF PW PBE C 4 4 where PBE X and PBE C are the Perdew Burke Ernzerhof exchange and correlation functionals and PW is the Perdew Wang correlation functional ala The TPSSH exchange correlation functional of Staroverov Scuseria Tao and Perdew with the form 0 S TPSS X 0 1HF PW TPSS C 4 5 where HF denotes the Hartree Fock exchange 44 45 47 521
200. features HF SCF Dscr DFT quadrature Dscr RIDFT Escr AOFORCE Ev a m grids RI DFT Riprt Aororce Escr e d XXIIT marij VI Escr XXIV AOFORCE MP2 MPGRAD II REMP2 Rimp2 VI ff stability analysis ESCF electronic excitations by CIS RPA TD DFT EscF VI VIT XV TT XX VIT excited state structures and properties with CIS RPA TD DFT EGRAD XTX XXVI XXVII RL CC2 Ricc2 triplet excitations XTV properties for triplet states XV transition moments and properties of excited states ground state geometry optimizations X XT excited state geometry op timizations and orbital relaxed properties XXVIII parallelization analytical second derivatives force fields AOFORCE REJK Riprt XX NMR chemical shifts MPsHIFT X MP2 parallel DFT RFT X geometry optimization in redundant internal coordinates RELAX RI integral evaluation e Orbital and auxiliary basis sets basis sets SV SV P SVP DZ a TZV TZVP TZVPP b TZVPP Rb Hg 1 QZV QZVP QZVPP new balanced basis sets with smaller ECPs i e the def2 basis sets j x allelectron basis sets for Rb to Xe SVPall SVPPall TZVPall TZVPPall x references for the correlation consistent basis sets cc pVXZ etc can be found e g at http tyr0 chem wsu edu kipeters Pages cc_append html or http www ems1 pnl gov forms b
201. fied in ke_control barrier angstroms type elps limits 5 0 10 0 7 5 constant 2 0 thickness 1 0 temperature 300 0 240 CHAPTER 12 KEYWORDS IN THE CONTROL FILE 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 ngstroms 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 axis of 20 A along y semi major of 15 on z and minor of 10 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 thickness 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 00 2 type F C O T type H C 1 0 1 2 210 0 31
202. 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 244 CHAPTER 12 KEYWORDS IN THE CONTROL FILE steps and to do the remaining work copy all restart files to one directory and rename them to restart mpshift number add trast 1and trand num ber_of_traloops to the control file and start MPSHIFT 12 2 19 Keywords for Parallel Runs On all systems the parallel input preparation is done automatically Details for the parallel installation are given in Section The following keywords are necessary for all parallel runs parallel_platform architecture numprocs number CPUs Currently the following parallel platforms are supported SMP 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 MPP for systems with fast communicat
203. 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 default on redundant on 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 12 2 FORMAT OF KEYWORDS AND COMMENTS 219 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 0ff 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 way if both subo
204. for the whole of Chemistry 23 For main group compounds we recommend b3 1yp note that GAUSSIAN uses partly different implementations 23 The programs DscrF 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 Filename for auxbasis 200 MB auxbasis ENTER RI OPTION TO BE MODIFIED m CHANGE MEMORY FOR RI 68 CHAPTER 2 PREPARING YOUR INPUT FILE WITH DEFINE 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 2 2 Where available the program
205. form a whole geometry optimization under the influence of a finite external field and thus to obtain the distorted minimum geometry 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 2 4 THE GENERAL OPTIONS MENU 79 Take Care due to some inconsistencies in DEFINE it is always 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 2 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
206. fuse s c2v Now this functionality is included in the MO definition menu of DEFINE program see Sec tion 2 3 1 converts standard xyz files into TURBOMOLE coordinates 1 6 Installation of TURBOMOLE Installation requires familiarity with some simple UNIX commands The TURBO MOLE package is generally shipped as one tar file This has to be uncompressed and unpacked gunzip turbomole tar gz tar xvf turbomole tar 1 6 INSTALLATION OF TURBOMOLE 25 to produce the whole directory structure Note Do not install or run TURBOMOLE as root or with root permissions Executable modules are in the bin arch directory for example IBM modules are in bin rs6000 ibm aix 5 2 Tools including JOBEX are in scripts and auxiliary basis sets are kept in the directories basen jbasen jkbasen and cbasen Coordinates for some common chemical fragments are supplied in structures The environmental variable TURBODIR must be set to the directory where TURBO MOLE has been unpacked for example TURBODIR my_disk my_name TURBOMOLE 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 subdi rectory 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 TURBO
207. ght 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 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 or other reviews The Ricc2 program exploits that the doubles doubles block of the CC2 Jacobian is diagonal 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 ASIT t w ACC t ACC t An w ASL t Ads Go Pua E uE This allows to avoid the storage of the double substitution part of the eigen or excitation vectors Ey Evs The algorithms are described in refs 10 11 about the RI error see ref 71 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 previ ous CC2 excitation energy calculation The operat
208. gram includes as a subset also the functionalities of the RI MP2 program Because of refined batching algorithms screening and symmetry treatment the RICC2 program is usually somewhat faster than the RIMP2 program This is in particular the cases in the following situations e when the molecular point group is Da or one of its subgroups and a significant number of atoms is positioned on symmetry elements e g planar molecules e when because of memory restrictions the RIMP2 program needs many passes of the integral evaluation All what is needed for a RI MP2 gradient calculation with the RICC2 program is ricc2 geoopt model mp2 If you want only the RI MP2 energy for a single point use as input ricc2 mp2 energy only The supplement energy only disables the calculation of intermediates for the re siduum or vector function which are not needed to evaluate only the energy But note that it will also disable the calculation of the D diagnostic see below Diagnostics Together with the MP2 and or CC2 ground state energy the pro gramm evaluates the D diagnostic proposed by Janssen and Nielsen 72 which is defined as Di qua mos 2 taati Amax 5 taitaj 7 7 where Amax M is the largest eigenvalue of a positive definite matrix M 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
209. gy 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 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 3 3 Program Relax 3 3 1 Purpose RELAX drives and controls a non linear optimization procedure to locate the min imum 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 current and if available previous iterations Various procedur
210. her non hybrid functionals where no iterations are needed or hybrid functionals where the same algorithm as at the HF SCF level is used MP2 semi direct method see ref 17 9 1 Prerequisites 1 MPSHIFT needs converged MO vectors from a SCF or DFT run DscrF or RIDFT 2 for SCF or DFT calculations no specifications have to be made in the control file 3 it is not possible to run the program in the fully direct mode when doing an SCF MP2 or a DFT using hybrid functionals run so you will have to perform a statistics run of DSCF before calling MPSHIFT or just set the size of the twoint file to a non zero value 4 to perform an MP2 calculation of the NMR shieldings you have to prepare the input with mp2prep c 9 2 How to Perform a SCF of DFT Calculation All you have to do for running MPSHIFT is typing mpshift at the shell level 157 158 CHAPTER 9 SHIELDINGS The results of a SCF or DFT calculation 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 rendering 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
211. here are a few variants 1 Murtagh Sargent MS pe pela Aani Ad EDF 2 Broyden Fletcher Goldfarb Shanno BFGS S dq tdg 1 e dat dG Fe 1 a FR 14G Udgk My FE pr S1 3 Davidon Fletcher Powell DFP a aga pk ldaGk der Ly tp 1 St SD FE pol de 4 combined method BFGS DFP If S1 lt S 1 S1 and S1 gt 0 perform DFP update otherwise BFGS The meaning of the symbols above is as follows F ANA 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 dg 7 gk qt dgk 1 gk gk 1 Zk dq 1 Fk 1qdGF 1 S1 dg dg S 1 dg 1 tF 1dG 1 S1 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 96 CHAPTER 3 STRUCTURE OPTIMIZATIONS with the new estimate h for the diagonal elements obtained by y Er dGtdqt yon day and the error d obtained by the regression Lin dgh h2 da y t k 2 Another alternative is to use DIIS like methods structure optimization by direct inversion in the iterative subspace See ref for the description of the algorithm The DIIS procedure can often be applied with good success using static or updated force constant matrices di Any of the algorithms mentioned above may be chosen Recommended is the
212. ibution to the electrostatic potential is calcu lated fld 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 normalfontlist 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 Imo 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 dens has to be set if additionally to one of the above quantities also the density is to be computed Output formats may be specified by e g fmt xyz if written to the same line as pointval Supported are xyz in case of scalars density L 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
213. ickname 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 2 3 Generating MO Start Vectors 2 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 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 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 60 CHAPTER 2 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 l
214. id for MP2 which means that MP2 improves HF results only if HF already provides a fairly good solution to the 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 MP2 results are known to converge very slowly with increasing basis sets in particular slowly with increasing quantum number of the basis set expansion Thus for reliable results the use of TZVPP basis sets or comparable is rec ommended when using SV P basis sets a qualitative trend can be expected at the most Basis sets much larger than TZVPP or cc pVTZ usually do not significantly improve results moreover in this case the errors of the method and those of the basis sets are no longer balanced It is recommended to exclude all non valence orbitals from MP2 calculations as neither TURBOMOLE standard basis sets nor cc pVXZ X T Q 5 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 RIMP2PREP orbitals below 3 a u are frozen provides a reasonable guess 5 4 GENERAL COMMENTS 125 e RimP2 We strongly recommend the use of auxiliary basis sets optimized for the corresponding MO basis sets Comments on Output e Most important output for RIMP2 and MPGRAD are of course MP2 HF ener gies written standard output and additionally to file energy and MP2 HF gradients
215. ied 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 208 CHAPTER 12 KEYWORDS IN THE CONTROL FILE 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 n 25 12 2 10 Keywords for Module EGRAD EGRAD uses the same general keywords as ESCF and GRAD see Sections 12 2 7 and 12 2 9 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 12 2 11 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 Keywords Valid for Both MPGRAD
216. 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 hybridiza tion 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 Ni Ai a Be and calculates a new Hessian with these modified eigenvalues 12 2 5 Keywords for Modules Dscr 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 194 and for definition of the functionals the section 4 2 on page 112 Example default input dft functional b p gridsize integer or minteger Specification of the spherical grid see s
217. 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 molekel For larger systems this may become very time consuming as plotting data values on grids are calculated by the respective pro grams molden molekel It is more efficient 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 gOpenMol available via http www csc fi gopenmol is driven by the keyword pointval This keyword is evaluated by all density matrix generating TURBO MOLE modules i e by Dscr RIDFT RIMP2 MPGRAD RICC2 see Section 7 3 3 and EGRAD Note that all of the following quantities may be calculated simultane
218. 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 Escr 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 8 electrons pseudo singlet occupation 6 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 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 and scfinstab ucis for excitations out of spin unrestricted reference states 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 blg the 23 lowest excitations in IRREP eu and all excitations in IRREP t2g use 6 4 HOW TO PERFORM 133 soes big 17 eu 23 t2g all and run ESCF Note that soes specifies the IRREP of the excitation vector which is not necessarily identical to the IRREP of the excited state s involved
219. ine unit 30 size 777 file twoint to unit 30 size file local_scratchdir twoint For the additional mandatory or optional input for parallel runs with the Ricc2 program see Section 32 CHAPTER 1 PREFACE Testing the parallel binaries The binaries RIDFT RDGRAD DscF GRAD and RIcc2 can be tested by the usual testsuite go to TURBODIR TURBOTEST and call TTEST 1 9 RUNNING TURBOMOLE USING THE SCRIPT TMOLE 33 1 9 Running TURBOMOLE using the script TMOLE The Perl script TMOLE drives the required TURBOMOLE modules on the basis of a GAUSSIAN style input file turbo in This facilitates the use of TURBOMOLE for users familiar with GAUSSIAN which we assumed to be the case TMOLE allows e g to calculate the potential curve for stretch bending and dihedral modes a feature not automatically available in TURBOMOLE TMOLE does not support yet the whole functionality of TURBOMOLE and GAUSSIAN To give an idea here a simple example for using TMOLE If you want to perform a geometry optimization of water at DFT level with the B P86 correlation exchange functional and a basis set of SVP quality you have to create the following file turbo in title geometry optimization for water method GEOMY b p SVP charge 0 coord 0 00000000000000 0 00000000000000 0 69098999073900 o 1 46580510295113 O 00000000000000 0 34549499536950 h 1 46580510295113 O 00000000000000 0 34549499536950 h end Then start TMOLE to perform the calc
220. ion 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 an existing one you will be asked which one of the specifications you want to modify Chapter 3 Calculation of Molecular Structure and Ab Initio Molecular Dynamics 3 1 Structure Optimizations using the Jobex 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 3 1 1 Options Given a Korn shell the usage is nohup jobex amp This command invokes structure optimization using the default program RELAX Structure optimizations using program STATPT can be performed using statpt flag nohup jobex statpt amp nohup means that the command is immune to hangups logouts and quits amp runs a background command JOBEX accepts the following arguments control ling 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
221. ion 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 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 lowest 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 10 If not given a default value is used which is chosen as max 107 Y 107 1076 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 P Pt default 3 thrdiis threshold 107 rdiis for residual norm below which DIIS 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 216 CHAP
222. ion 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 7 2 CALCULATION OF EXCITATION ENERGIES 143 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 CCS Aw Zz ae E mal LH Tv HF gt 7 10 is a symmetric matrix and left and right eigenvectors are identical and form an orthonormal basis The configuration 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 WIS CIS 4 YP gOS Aef MP1 CIS CIS 7 11 Note that MP1 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 Bril
223. ion 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 cluster 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 SGI 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 numprocs is the number of slaves i e the number of nodes doing the parallel work If you want to run MPGRAD traloop has to be equal to or a multiple of numprocs For very large parallel runs it may be impossible to allocate the scratch files in the working directory In this case the scratch 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 dens home dfs cd00 cd03_dens dscf fock home dfs cd00 cd03_fock dscf dfock home dfs cd00 cd03_dfock dscf ddens home dfs cd00 cd03_ddens dscf xsv home dfs cd00 cd03_xsv dscf pulay home dfs cd00 cd03_pulay dscf statistics home dfs cd00 cd03_statistics 12 2 FORMAT OF KEYWORDS AND COMMENTS 245 dscf errvec home dfs cd00 cd03_errvec dscf oldfock home dfs cd00 cd03_oldfock dscf oneint home dfs cd00 cd03_oneint For all programs employing density functional theory DFT i e
224. ions when form ing a basis of symmetry adapted molecular displacements This option may 204 CHAPTER 12 KEYWORDS IN THE CONTROL FILE 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 Out put 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 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 points for interpolation between the two isotopes compared by the isosub option to six
225. is file if not the program reads the data from the file TURBODIR uff parms in 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 potential 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 energies 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 12 2 FORMAT OF KEYWORDS AND COMMENTS 177 uffgradient 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 the blocks nxtneil2 nxteneil3 nxtneil4 connectivity angle torsion inversion nonbond and qpartial It starts with uff topology and e
226. is 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 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 unpublished n to be published 20 CHAPTER 1 PREFACE 1 4 Modules and Their Functionality For references see Bibliography DEFINE UFF DSCF GRAD RIDFT and RDGRAD MPGRAD RIMP2 Ricc2 interactive input generator which creates the input file control DE FINE supports most basis sets in use especially the only fully atom opti mized consistent basis sets of SVP and TZV quality 21181411516 available for the atoms H Rn excluding lanthanides DEFINE determines the molecular symmetry
227. 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 D 18 which have different values of a and b For the definition of these parameters and their use refer to Roothaan s original paper 22 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 2 4 THE GENERAL OPTIONS MENU 65 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 OCCUPATION 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 7 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 2 4 The General Options Menu After you specified all data concerning the molecule you want to examine
228. itation energies accurate to 8 10 digits and properties accurate to 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 calculation of whole excita tion 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 IR REP 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 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
229. ivatives for all methods that have an analytical gradient program i e the main use of this script is the prediction of vibrational spectra on the MP2 level as well as for excited states using RI CC2 or TDDFT If force constant calculations result in imaginary frequencies molecular distortions 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 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 154 8 1 ANALYSIS OF NORMAL MODES IN TERMS OF INTERNAL COORDINATES155 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 sub tract the memory specified in ricore 3 To start AOFORCE in the lowest eigenvalue search mode use the keyword les For its use as well as other keywords dea
230. l 65 66 geometry main 44 geometry menu 46 internal coordinate 49 50 occupation number assignment 62 63 start vectors 59 60 molecular dynamics 104 238 MOLOCH 22 23 29 30 79 82 83 85 147 160 228 keywords 228 MOLOCH2 23 MP2 RI 211 MP2PREP 23 27 28 124 MPGRAD 13 20 21 28 31 71 88 94 98 107 121 125 159 162 170 179 192 199 201 209 224 232 244 246 turbo_preproc 31 keywords 208 MPSHIFT 13 22 27 29 30 157 159 244 keywords 242 no weight derivatives 205 not converged 88 108 NUMFORCE 202 NUMFORCE 21 23 127 134 135 137 138 154 155 202 OUTP 23 291 parms in 176 plotting data keywords 232 population analysis 233 properties excited states 147 ground state 145 q 41 quasi Newton 92 RDGRAD 20 21 28 30 32 68 88 94 97 107 109 112 134 195 199 202 245 246 keywords 202 RELAX 13 21 23 30 35 45 50 74 75 87 88 92 94 96 97 99 101 106 107 218 220 222 224 226 keywords 218 relax out x 108 restart cc 212 RI ADC 2 211 RI CC2 20 211 keywords 211 RI CCS 211 RLCIS 20 211 RI CIS D 20 211 RI MP2 211 Ricc2 12 13 20 22 28 30 32 56 57 71 107 136 145 147 149 153 160 162 163 211 224 keywords 211 RIDFT 13 20 21 27 30 32 33 61 68 69 88 107 109 112 130 157 160 162 170 171 191 192 195 196 199 202 231 232 245 246 keywords 179 RIMP2 13 20 21 23 28 30 56 57 7
231. l ground state MOs yi x y 2 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 z where y is the electric dipole operator vector Next we define the 2 x 2 super matrices mS ee 63 where the four index quantities A and B are the so called orbital rotation Hessians Explicit expressions for A and B can be found e g in ref 16 The vector X Y is determined as the solution of the TDHF TDDFT response problem A wA X Y P Q 6 4 If X Ya arises from an electric dipole perturbation Ha the electronic dipole polarizability at frequency w is aaplw Xa Yal up 6 5 a b x y z Similarly if ma is a component of the magnetic dipole moment operator the optical rotation is dap w 3 Im Xoa Yalmg 6 6 128 CHAPTER 6 HF AND DFT RESPONSE CALCULATIONS where c is the light velocity Excitation energies Q are the poles of the frequency dependent density matrix response They are thus the zeros of the operator on the left hand side of Eq 6 4 OS Da 0 6 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
232. le using special molecular design software and converting this set into TURBOMOLE format see Section as input for DEFINE The main problem in using TURBOMOLE appears to be the definition of the molecule atoms coordinates etc The easiest way around is as follows 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 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 If you want to do geometry optimizations we recommend to use generalized internal coordinates ired generates them automatically e you may then go through the menus without doing anything just press lt Enter gt or q 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 e 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 e ECPs which include scalar relativistic corrections are automatically used beyond Kr
233. lel 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 behaviour 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 specify 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 Chapter 13 Sample control files 13 1 Introduction The file control is the input file for TURBOMOLE which directly or by cross refer ences provides the information necessary for all kinds of runs and tasks control is usually 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 247 248 CHAPTER 13 SAMPLE CONTROL FILES 13 2 NH Input for a RHF Calculation 13 2 1 Main Fil
234. ling 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 effects due to the step length option d 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 12 2 7 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 cal culations 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 To select the correct option s use the explana tions you get by calling NumForce h For a review of theory and implementation see refs 841 85 Limitations AOFORCE can handle only up to g functions the functionals TPSS and TPSSh are not yet implemented 8 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 you keep a copy of the file hessian 156 CHAPTER 8 VIBRATIONAL F
235. lization 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 lmo At the most sweeps 10000 orbital rotations are performed Non defaults may be specified using the following suboptions lmofile 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 population analysis is based on decomposing VSDyYS 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 atomic orbitals momao print MO contributions to occupation numbers of modified atomic orbitals MAOs 2
236. ller Plesset methods with auxiliary basis sets J Chem Phys 116 15 6397 6410 2002 W Klopper Orbital invariant formulation of the MP2 R12 method Chem Phys Lett 186 6 583 585 1991 W Klopper W Kutzelnigg Moller Plesset calculations taking care of the correlation cusp Chem Phys Lett 134 1 17 22 1987 S F Boys Localized orbitals and localized adjustment functions In P O L wdin Ed Quantum Theory of Atoms Molecules and the Solid State Seite 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 F R Manby Density fitting in second order linear r 2 Mgller Plesset pertur bation theory J Chem Phys 119 9 4607 4613 2003 P Deglmann F Furche R Ahlrichs An efficient implementation of second analytical derivatives for density functional methods Chem Phys Lett 362 5 6 511 518 2002 BIBLIOGRAPHY 283 85 86 90 91 92 94 95 96 P Deglmann F Furche Efficient characterization of stationary points on po tential 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 clu
237. loit symmetry group Dn to create an n membered planar ring by putting an atom on the X axis You may also read atomic coordinates and possibly internal coordi nates 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 separated by at least one blank For a description of the internal coordinate definitions refer to 2 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 2 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
238. loser 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 products 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 92 CHAPTER 3 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 ener
239. louin 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 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 12 2 12 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 excitations irrep al nexc 2 irrep b1 nexc 2 The single substitution parts of the right eigenvectors are stored in files named CCREO s m xzxx where s is the number of the symmetry class irreducible repre sentation 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 2zaz These files can be kept for later restarts Provided that it is not an unrestricted open shell run In this case the wavefunctions will not be spin eigenfunctions and multiplicities are not well defined 144 CHAPTER 7 RI CC2 Tro
240. lows 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 Teller distortions The molecule is automatically reoriented if necessary Example Ty Dag gt Coy 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 2 1 THE GEOMETRY MAIN MENU 47 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 exp
241. lue 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 esp_fit fits point charges at the positions of nuclei to electrostatic potential arising from electric charge distribution for 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 ree 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 21 s1 shell 22 s2 Integer numbers 7 define the number of points for the respective shell real numbers s the scaling of radii default corresponds to one shell with s 1 0 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 pl1t for UHF dscf
242. m DEFINE within the geometry specification menu fdiag serves for the input of diagonal force constants for the individual in ternal coordinates to initialize forceapprox 3 3 PROGRAM RELAX 97 3 3 5 Structure Optimizations Using Internal Coordinates This is the default task of RELAX optimize internal on does not need to be specified You need as input the data groups 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 3 3 11 or within a DEFINE session 2 Have a look at the eigenvectors of the BmB matrix Set some behind keyword intdef if there are any eigenvalues close to zero lt 107 is to
243. m 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 transition 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 positive definite The powell update is the default for transition state optimizations since the Hessian can develop a negative curvature as the search progresses 3 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 3 2 4 Finding transition states Locating minima on a PES is straightforward In contrast transition state opti mization 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 c
244. 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 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 3 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 def initions have to be provided on data block intdef The types available and their definitions are described in Section 2 1 2 For recommendations about the choice of internal coordinates consult ref 20 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 2 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 cartesian coordinates it will be read in by RE LAX if the flag for interconversion of coordinates has been activated interconversion on or by the interactive input progra
245. mation 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 Excited states Single point excited state energies for CIS TDHF and TDDFT methods can be calculated using Escr Excited state energies gradients and other first order properties are provided by EGRAD Both modules require well converged ground state orbitals MP2 the module MPGRAD calculates the MP2 energy as well as the energy gradient If only the energy is desired use the keyword mp2energy 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 6 as described in Section 12 For all further preparations run the tool MP2PREP 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 CC2 the moldule Ricc2 calculates MP2 and CC2 ground state energies and CIS CCS CIS D or CC2 excitation energies using the resolution of
246. me 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 example 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 2 0 4 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 13 Sample control files for an example Recommendation We strongly recommend to create
247. n E n e e NY Ns w ll ej ll o Two open shells This becomes tricky in general and we give only the most important case shell 1 is a Roothaan case see 4 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 s 3P states or the d s D states of atoms The coupling information is given following the keyword rohf The a b within a shell are taken 118 CHAPTER 4 HARTREE FOCK AND DFT CALCULATIONS from above 4 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 closed shells a 1 4 2 t1 1 3 C2 h 1 2 open shells type 1 a 5 1 h 2 4 5 roothaan 1 rohf 5a ba a 0 b 0 5a 2h a 1 b 2 2h 2h a 15 16 b 15 8 Example 2 The 4d 5s 7S state of Mo symmetry I see Section 4 3 3 can also be done as follows roothaan 1 rohf 5a ba a 0 b 0 5a 2h a 1 b 2 2h 2h 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 The shells 5s and 4d have now been made inequivalent Result is identical to which is also more efficient Example 3 The 4d 5s 3D state of Ni symmetry I 4 3 RESTRICTED OPEN SHELL HARTREE FOCK 119 closed shells a 1 3 2 t1 1 2 2 open shells type 1 a 4 1 h 1 9 5 roothaan 1 rohf 4a 4a a 0 b 0 1h 1h a 80 81 b 80
248. n 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 Rp Ap 0 Rp Ap basis set correction potential Rp Ar Rp Ar smooth region Rr Ar 00 asymptotic correction Defaults Rp 10 Ap 0 5 slater region Ry Ay Rp Ap 0 Ry Ay basis set Slater potential Ry Any Ry Ayn smoothing region Ry Avn Rp A numerical Slater Ep Ap Rp Alp smoothing region r A 00 asymptotic Slater Note Rp Ap lt Rr AF Defaults Ry 7 Ay 0 5 Rp 10 Ap 0 5 Use correct b region and slater b region for the beta spin 12 2 6 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 per mittivity epsilon that represents the solvent A brief description of the method is given in chapter The model is currently implemented for SCF energy and gradi ent calculations DscF RIDFT and GRAD RDGRAD and MP2 energy calculations RIMP2 and MPGRAD Please note due to improvements in the A matrix and cavity setup the COSMO energies and gradients may differ from older versions The use_old_amat option can be used to calculate energies not gradients using the old cavity algorithm The basic COSMO settings are d
249. n 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 2 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 file sys data The file has the following simple format c h 2 2 h h 2 0 2 1 THE GEOMETRY MAIN MENU 49 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 2 1 2 Internal Coordinate Menu INTERNAL COORDINATE MENU ttideg 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 RED
250. nce for the file specifying the JK auxiliary basis as referenced in atoms This group is created by the rijk menu in DEFINE 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 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 1 107 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 10724 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
251. nd 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 Prints out the help message and exits h list Lists the available test examples clean Deletes the test directories and summary files for the current architecture given by SYSNAME see Chapter 1 5 realclean Deletes all test directories and protocols check dir 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 the directory dir default TESTDIR sysname and highlights the positions of the retrieved matches validate dir val dir Loading path and naming options loaddir dir Loading path for the TURBOMOLE binaries 1 dir default TURBODIR bin sysname scriptdir dir Loading path for the TURBOMOLE scripts ls dir testprog prog X prog dir dir critfile file defcritfile file protfile file output file gprotfile file 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
252. nd 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 BEND CBASOPT CGNCE CONVGREP please use actual help example bend 1 2 3 displays the bending angle of three atoms specified by their number from the control 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 plots energies as a function of SCF iteration number gnuplot re quired greps lines for convergence check out of control file COSMOPREP sets up control file for a COSMO run see Chapter 11 1 5 TOOLS DIST EIGER FINIT FREEH HCORE HOLUMO JOBEX KDG KONTO LHFPREP LoG2x LOG2EGY MDPREP MOLOCH2 MP2PREP NUMFORCE OUTP RIMP2PREP 23 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 displays orbital eigenvalues obtained from data group scfmo initialises the force constant matrix for the next RELAX step calculates thermodynamic functions from molecular data in a control file an AOFORCE run is a necessary prerequisite
253. nds 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 Here are I 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 mr JI NTIK 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 nry and nrg are the number of the bonds between J and I and the bond between J and K The hybridization of atom J determines wtyp g Then the torsion terms follow starting with the number of the torsion terms Each line contains one torsion term I J K L nrk ttyp OK OJKL Here are J J K and L the atom numbers nr yx is the number of the bond between J and K ttyp is the torsion type 178 CHAPTER 12 KEYWORDS IN THE CONTROL FILE ttyp 1 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
254. ng indices because deletion of a coordinate has only an effect on the coordinates with higher indices After choosing the coordinates 52 CHAPTER 2 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 Coordinates 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 3627 f bend 345 i outp 347 9 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
255. ng parameter see Eq 16 19 and Table 1 in Ref 95 In addition the reduction of spherical grid points near nuclei is su pressed i e fullshell on is set see page 182 Note the keyword radsize integer overrules the setting of incr for more information see p 180 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 calculation with a larger grid i e gridsize 7 The test suite example TURBOTEST dscf short P0 0H 3 DIFFUSE pro vides 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 and p 191 Example Recommendation dft gridsize m4 diffuse 2 182 CHAPTER 12 KEYWORDS IN THE CONTROL FILE rhostart integer hostop Mice for developers only Radial grid points have a linear scaling parameter see Eq 16 19 and Table 1 in Ref 95 With the following input dft rhostart 50 rhostop 200 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 95 Program stops after this testing reference Usage of th
256. ns 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 approximation to the Hessian matrix The optimization procedure implemented in STATPT belongs to the family of quasi Newton Raphsod methods 26 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 For TS optimizations the TRIM method implemented in STATPT tries to maxi mize the energy along one of the Hessian eigenvectors while minimizing it in all other directions Thus one follows one particular eigenvector hereafter called the transition 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 negativ
257. ns 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 DIIS 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 neccessary to increase the limit for the number of iterations maxiter In rare cases complex roots might persist even with tight 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 7 3 FIRST ORDER PROPERTIES AND GRADIENTS 145 Large contributions from double excitations can not be monitored in the output of the quasy linear solver But it is possible to do in advance a CIS D calculation The CIS D results fo
258. nt 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 characteristics 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 specified coordinate transformation and write the transformed co ordinates 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 76 CHAPTER 2 PREPARING YOUR INPUT FILE WITH DEFINE as well as some less common procedures option status description none F NO UPDATE STEEPEST DESCENT bfgs F BROYDEN FLETCHER GOLDFARB SHANNO UPDATE dfp F DAVIDON FLETCHER POWELL UPDATE bfgs dfp F COMBINED BFGS DFP UPDATE ms 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 l
259. nt 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 convergence 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 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 keyword 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
260. o populations irpmol F compute IRREP contributions to atomic overlap populations mommul F print electrostatic moments resulting from atomic charges DIETEN PA A A e E ee 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 Mulliken PA To switch on one or more of these options you must enter the cor responding option keywords e g spdf netto for computation of atomic neto pop ulations 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 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 MAD occupation numbers maodump E dump all MAOs onto standard output write MAOs onto a separate file select F write only those MAQs which have been empl
261. ode where the communication of integral intermediates is replaced by a reevaluation of the intermediates at the expense of a larger operation count whereever this is feasible Add for this in the control the following data group mpi_param min_comm Chapter 8 Calculation of Vibrational Frequencies and Infrared 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 der
262. 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 F 3P for d d 4F P for ae d Chapter 5 Second order Moller Plesset Perturbation Theory 5 1 Functionalities of MPGRAD and RIMP2 TURBOMOLE offers two possibilities for the calculation of MP2 data A conven tional implementation 59 MPGRAD based on the calculation of four center inte grals not further developed for several years and a treatment within the resolution of the identity RI approximation 8 Rimp2 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 Functionality of RIMP2 e Calculation of MP2 energies and or gradients for RHF and UHF wave func tions within the efficient RI approximation e The frozen core approximation is implemented for both RI MP2 energies and gradients e RIMP2 needs optimised auxiliary basis sets which are available for all TUR BOMOLE 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 e Exploitation of symmetry of all point groups 121 122 CHAPTER 5 2ND
263. of this matrix reflect the changes in occupation numbers re sulting from the MP2 treatment compared to the SCF density matrix where occupation 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 oc cupation 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 typical for d metal compounds somewhat higher values are tolerable Chapter 6 Hartree Fock and DFT Response Calculations Stability Dynamic Response Properties and Excited States 6 1 Functionalities of ESCF and EGRAD Escr and EGRAD are designed as efficient tools for response and excited state cal culations 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 stability analysis are supported The RI J approximation in conjunction wi
264. 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 actual 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 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 12 2 FORMAT OF KEYWORDS AND COMMENTS 223 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 reset
265. ometry cycles is set to 40 geo _nrgc 40 The program will determine the symmetry of the molecule gen_symm auto default The coordinates are in TURBOMOLE format there is no need for specifying a coordinate format method GEOMY charge 0 coord hend 00000000000000 00000000000000 00000000000000 00000000000000 00000000000000 00000000000000 00000000000000 00000000000000 00000000000000 00000000000000 00000000000000 DYNEN 68300008773804 74300003051758 34150004386902 37150001525879 34150004386902 37150001525879 34150004386902 37150001525879 34150004386902 37150001525879 68300008773804 266 ri mp2 TZVP geo_nrgc 40 scf_msil 99 gen_symm auto 00000000000000 00000000000000 32354623433702 10755851657859 32354623433702 10755851657859 32354623433702 10755851657859 32354623433702 10755851657859 00000000000000 QOpyPOpyOopOopgOobpOoa 14 3 VIBRATIONAL SPECTRUM OF PHENYL 14 3 Vibrational Spectrum of Phenyl 267 Calculation of the vibrational spectrum of Phenyl at MP2 level Analytical second derivatives are not implemented in TURBOMOLE so they are calculated numerically for nfre 1 Symmetry is set explicitly to Co gen_symm c2v metho FORCE charg 0 coord d e 00000000000000 00000000000000 00000000000000 00000000000000 00000000000000 00000000000000 00000000000000 00000000000000 000000
266. ompatibility reasones ridft will still be accounted for Enforces a ridft calculation if module RIDFT is used rij Enforces a 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 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 the less memory you give the more integrals are treated directly i e recomputed on the fly in every iteration jbas file aurbasis Cross reference for the file specifying the auxiliary basis as referenced in atoms We strongly recommend using auxbasis sets optimized for the respec tive 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 representation of the density 196 CHAPTER 12 KEYWORDS IN THE CONTROL FILE RI JK If the keyword rik is found in the control file RIDFT performs a Hartree Fock SCF calculation using the Rl approximation for both Coulomb and HF exchange efficient for large basis sets For this purpose needed apart from ricore jkbas file auxbasis Cross refere
267. on DIIS which reduce the number of SCF iterations needed as well 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 gradi ent at the DFT level using pure functionals i e without the HF exchange term 41 Both programs employ the Resolution of the Identity approach for computing the electronic Coulomb interaction RI J This approach expands the molecular elec tron density in a set of atom centered auxiliary functions leading to expressions in volving three center ERI s only This usually leads to a more than a tenfold speedup compared to the conventional method based on four center ERI s for example the DscF module The most important special features of the RIDFT and RDGRAD modules are 109 110 CHAPTER 4 HARTREE FOCK AND DFT CALCULATIONS 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 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 N method for large molecules It significantly reduces calculation times for molecules with more than 1000 2000 basis func
268. on in cartesian space and for the optimization of basis set parameters carthess Data group hessian projected is used 3 3 14 Look at Results The energy file includes the total energy of all cycles of a structure optimization completed 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 converged the final atomic distances use the tool dist Bond angles torsional angles 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 3 4 Force Field Calculations 3 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 accele
269. ontrols 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 optimization 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 be fully specified 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 automati cally as default as well as ECPs small core beyond Kr 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 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 41 42 CHAPTER 2 PREPARING YOUR INPUT FILE WITH DEFINE 2 0 1 Universally Available Dis
270. orithm will become numerical unstable 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 uv diplen dipole operator in length gauge yu r v with i z y z the index O indicates dependency on the origin for expectation val ues 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 j1 V v all three components individual components can be specified with the labels xdipvel ydipvel zdipvel 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 Mj the isotropic second moment a Mr M and the anisotropy pe B 413 X Ma Mirri 3 Maa 1 x 1 2 Furthermore the traceless quadrupole moment 1 Os 3rirj rij 2 218 CHAPTER 12 KEYWORDS IN THE CONTROL FILE including nuclear contributions is given angmom angul
271. osmo The Conductor like Screening Model Cosmo is a continuum solvation model CSM where the solute molecule forms a cavity within the dielectric continuum of permittivity e 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 conditions 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 p 0 This represents an electrostatically ideal solvent with e oo The vector of 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 screening charges q pio pr de Aq 0 A is the Coulomb matrix of the screening charge interactions For a conductor the boundary condition 0 defines the screening charges as q ATs To take into account the finite permittivity of real solvents the screening charges are scaled by a factor e 1 Fe c qt fed The deviations of this COSMO approximation from the exact solution are rather small For strong dielectrics like water they are less than 1 while for non polar 165 166 CHAPTER 11 TREATMENT OF SOLVATION EFFECTS WITH COSMO solvent
272. oups intdef or basis or global DEFAULT n unit lt r gt use multiple of the unit matrix H lt r gt E 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 cal culation 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 initialization of the Hessian Default values stretches 0 5 angles 0 2 2 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 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 DEFAULT 5000E 02 geofield F geometry optimization with external field man F explicit definition of electrostatic field s geofield gives the possibility to per
273. oyed in the population analysis all F write all MAOs maofile F 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 84 CHAPTER 2 PREPARING YOUR INPUT FILE WITH DEFINE global criterion for selection of Modified Atomic Orbitals MAOs 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 MAOs 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 actual settings for data group shared electron numbers 2 center shared electron numbers will be computed values are printed if absolute value
274. perties thus requires also the calculation of the ground state density matrix In addition the left E and right E eigenvectors and the Lagrangian multipliers need to be determined for each excited state The disk space and CPU requirements for solving the equations for E and 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 CCNEO s m tI1 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 Because for calculation of excited states first order properties also the unrelaxed ground state density is evaluated it is recommended to specify also ground state first order properties in the input since they are obtained without extra costs To obtain orbital relaxed first order properties or analytic derivatives gradients the Lagrange functional for the excited state in Eq is analogously to the treatment of ground states augmented by the equa
275. placement element default 1 0d 3 thrmaxgrad threshold for maximal gradient element default 1 0d 3 228 CHAPTER 12 KEYWORDS IN THE CONTROL FILE 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 12 2 15 Keywords for Module MOLOCH properties specifies the global tasks for program MOLOCH by virtue of the fol lowing 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 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 reference point 0 0 0 12 2 FORMAT OF KEYWORDS AND COMMENTS 229 localization if loca
276. play 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 INTERNAL 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 2 0 2 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 ho
277. ple below 12 2 FORMAT OF KEYWORDS AND COMMENTS 225 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 default format is format 8f10 5 but other 10 digit f10 x for mats e g x 4 6 are possible and will be used after being manually specified 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 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
278. ploy ing the resolution of the identity approximation A Kohn 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 9136 2003 16 CHAPTER 1 PREFACE 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 III of Computational Pho tochemistry Ed by M Olivucci Vol 16 of Computational and Theoretical Chemistry Elsevier Amsterdam 2005 XXVIII Distributed memory parallel implementation of energies and gradients for second order Mgller Plesset perturbation theory with the resolution of the identity ap proximation Christof Hattig Arnim Hellweg Andreas Kohn Phys Chem Chem Phys 8 1159 1169 2006 1 3 HOW TO
279. plt 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 map 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 12 2 FORMAT OF KEYWORDS AND COMMENTS 237 vec for planes and lines default in these cases In case of a line speci fied by a Y see below output is a f x y z for scalars for vectors components and norm are displayed vectors Analogously in case of planes it is a B f x y z The output file suffix vec may be visual ized by plotting programs suited for two dimensional plots A command file termed gnuset to get a contour plot by gnuplot is automatically generated For 3D grids non default boundarys basis vector directions origin and reso lutions 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 O range 1 1 points 300 origin 1 1 1 Grid vectors automatically normalised 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 dimensionalit
280. pole 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 13 3 2 File coord coord 00000000000000 00000000000000 1 00494155217173 n 1 85766051386774 00000000000000 50247077608587 o 1 85766051386774 00000000000000 50247077608587 o intdef definitions of internal coordinates 1 k 1 0000000000000 stre 2 1 val 2 39232 2 d 1 0000000000000 stre 3 1 val 2 39232 3 k 1 0000000000000 bend 2 3 1 val 101 88429 end 13 3 3 File basis basis 13 3 NO2 INPUT FOR AN UNRESTRICTED DFT CALCULATION n def SVP O 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 o 7s4p1d 5 s 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
281. program 9 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 10000000E 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 mointita type gamma 1 unit 71 size 0 file gamma 1 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 detected 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 9 4 Chemical Shifts NMR shifts are obtained by comparing nuclear shieldings of your test compound with a reference molecule dsubst Sref Gref Tsubst Therefore you have
282. ps 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 12 2 FORMAT OF KEYWORDS AND COMMENTS 175 25 0 10 0 00 mxls dhls 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 000100 inversion terms will be calculated 000010 non bonded van der Waals terms will be calculated 000001 non bonded electrostatic terms will 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 distanc
283. ptions scale and logarithm are given the log arithms of the scale factors will be optimized global on off optimize a global scaling factor for all basis set exponents default off NOTES e 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 specification 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 dgmaz 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 cho sen i e forceupdate method none otherwise it will only be activated if the DIIS update for the geometry is expected to fail 220 CHAPTER 12 KEYWORDS IN THE CONTROL FILE 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 pres
284. quid corre lation energies for local spin density calculations a critical analysis Can J Phys 58 8 1200 1211 1980 J P Perdew Y Wang Accurate and simple analytic representation of the electron gas correlation energy Phys Rev B 45 23 13244 13249 1992 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 Perdew 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
285. r 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 in spect to see which other basis sets are supported automatically The corresponding publications can be found here 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 Quality 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 QZV1f for basis set limit SCF or DFT quadruple zeta 3d1f or A4d1f for atoms beyond Ne 3p1d for H QZVP and QZVPP for highly correlated treatments quadruple zeta 3d2flg or 4d2flg beyond Ne 3p2d1f for H 56 CHAPTER 2 PREPARING YOUR INPUT FILE WITH DEFINE 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 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 X YZ 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
286. r parallel runs default 1 gen mpil lt path gt path for MPI only necessary for parallel runs default usr app 1ib mpich bin Available SCF run options scf_grid gridsize definition of the gridsize necessary for DFT Possible values are 1 5 and m1 m5 default m3 see dft scf_mrij options switch for MARI J details see marij scfmrij 0 no MARLJ default scf mrij 1 MARI J is enabled scf_msil maximum numbers of SCF cycles default 30 see scfiterlimit scf_conv integer SCF convergency criterion will be 107 for the energy default for SCF 7 for DFT 6 see scfconv 1 9 RUNNING TURBOMOLE USING THE SCRIPT TMOLE 37 scf_rico integer memory core for RI calculation in MB default 200 MB see ricore scf_dsta real start value for SCF damping default 1 000 see scfdamp scf_dink real increment for SCF damping default 0 050 see scfdamp scf_dste real minimum for SCF damping default 0 050 see scfdamp scf_ferm options switch for fracctional occupation FON numbers see fermi scf_ferm 0 no fracctional occupation numbers default scf_ferm 1 fracctional occupation numbers enabled scf_fets real starting temperature for FON default 300 K scf_fete real end temperature for FON default 300K scf_fetf real temperature factor for FON default 1 0 scf_fehl real hicrt parameter for FON default 0 1 scf_fest real energy convergence parameter for FON default 1d
287. r the T2 diagnostic correlate usually well with the CC2 results for this diagnostic Else the DIIS solver will print the T2 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 partitioned formula tion used in the RICC2 program However the results obtained with second order methods for double excited states will anyway be poor It is strongly recommended to use in such situations a higher level method 7 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 7 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 cas
288. raloop Rimp2 Calculations 1 RI MP2 calculations require the specification of auxiliary basis sets cbas and a converged SCF calculation with the one electron density convergence threshold set to denconv 1 d 7 or less In addition the options freeze frozen core approximation and maxcor maximum core memory usage should be set All these settings can be done during the input generation with the program DEFINE under the entry mp2 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 Start a single RIMP2 calculation with the command rimp2 4 For optimisation of structure parameters at the RI MP2 level use the command jobex ri level mp2 Mpgrad Calculations 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 12 2 11 124 CHAPTER 5 2ND ORDER MOLLER PLESSET
289. rameter has no meaning in this case For more details see Section roothaan For ROHF calculations with only one open shell the Roothaan parameterg 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 on ROHF calculations e g with more than one open shell see the sample input in Section and the tables of Roothaan pa rameters in Section 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 TC C J Roothaan Rev Mod Phys 32 1960 179 194 CHAPTER 12 KEYWORDS IN THE CONTROL FILE 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 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
290. rate the convergence 102 CHAPTER 3 STRUCTURE OPTIMIZATIONS of an optimizations For optimizations in cartesian space this will be faster by a factor of two for any molecule 3 4 2 How to Perform a UFF Calculation You have 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 con nectivity in the file ufftopology The program will calculate the bond angle tor sion inverison and non bonded terms force field terms based on the connectivity specified in the topology file 3 4 3 The UFF implementation The UFF implementation follows the paper by Rapp 7 The energy expression in UFF is as follows 3 4 FORCE FIELD CALCULATIONS 103 NB y Burr 9 Ku ru on Erik 1 cos 20 linear case Na Er 1 cos 30 trigonal planar case de 5 Kik
291. 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 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 134 CHAPTER 6 HF AND DFT RESPONSE CALCULATIONS 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 6 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 is the highest excitation specified by soes only one IRREP is al lowed 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 Af
292. re 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 comparison 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 lt lt lt lt and gt gt gt gt gt marks 274 CHAPTER 15 PERL BASED TEST SUITE There is a lot of options controlling the behavior of TTESTTesting specific versions of TURBOMOLE 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 cur rent program timings as the new reference The module specifications and short long a
293. rection and if needed structure optimization using the default program 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 jobex 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 con trolling 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 3 6 COUNTERPOISE CORRECTIONS USING THE JOBBSSE SCRIPT 107 gradient opt relax level level 1 lt path gt mem integer keep trimer define help 3 6 2 Output calculate the gradient as well optimise the structure use the RELAX program for force relaxation 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 use RI modules RIDFT and RDGRAD fast Coulomb approxi mation instead of DSCF and GRAD as well as RIMP2 instead of MPGRAD employ programs from directory lt path gt Is able to control the memory from outside D
294. resulting polarizabilities and rotatory dispersions are given in a u in the pro gram output escf out in the above example For conversion of the optical rotation in a u to the specific rotation in deg dm g cc see Eq 15 of ref 65 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 6 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 electronic Hessian eigen vectors orbital rotations to be considered Without additional knowledge of the system one usually needs to calculate the lowest eigenvalue within every IRREP soes all 1 132 CHAPTER 6 HF AND DFT RESPONSE CALCULATIONS 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
295. 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 pl1t and the MP2 contribution on mp2d plt and in the UHF case one obtains the total density D SCF MP2 DP SCF MP2 on td plt the spin density D SCF M P2 DP 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 pointval integrate 2 Y zr eps 236 CHAPTER 12 KEYWORDS IN THE CONTROL FILE 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 densities are generated by following com binable settings to be written in the same line as statement pointval pot 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 replace ment of the d for density by a p for potential By pot eonly only the electronic contr
296. 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 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 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 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 specif
297. rs and cause fluctuations and drift in the total energy Asa 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 momentum 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 natoms 9 Number of atoms in system current file mdlog aa The file containing the current position velocity time and timestep that is the input configuration During an MD run the current information is generally kept at the end of the log file log 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 TUR
298. rst order properties are implemented for CIS in the Ricc2 program The unrelaxed first order properties are calculated from the variational excited states Lagrangian 75 which for the calculation of unrelaxed properties is decomposed into a ground state contribution and Lagrange functional for the excitation energy which leads to expressions for difference densities or changes of the density matrix upon excitations LON E E t t 6 LLO LIN EEC 1118 ESEN E EBGA Y Bidet BBs 7 19 pu No al A Fo BV Ta HF H2 Me A 7 20 Don DO DE ADE Vo 721 pq pq 148 CHAPTER 7 RI CC2 with H Ho BV and R indicating that only the real part is taken D is the unrelaxed ground state density and ADpg the difference density matrix The unrelaxed excited state properties obtained thereby are equivalent to those identified from the second residues of the quadratic response function and 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 For a detailed description of the theory see refs the algorithms for the RI CC2 implementation are described in refs 71 12 ref also contains a discussion of the basis set effects and the errors introduced by the RI approximation In the present implementation the ground state and the difference density matrices are evaluated separately The calculation of excited state first order pro
299. rtesian 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 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 and refer ences therein ecpl gives you a list of all pseudopotentials assigned so far 2 3 GENERATING MO START VECTORS 59 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 n
300. s 202 B matrix 49 50 BABEL 26 BEND 22 Boys localization 235 bsse_out 107 bsse_out initial 107 BSSEENERGY 106 289 CBASOPT 22 ccisd 150 ccitd 149 ccitd cc2 gs 1a1 001 150 ccitd cc2 xs 3a2 001 150 CC2 20 RI 211 CCLO m ss xxx CCLEO s m xxx CCMEO s m xxx CCNEO s m xxx CCREO s m xxx CCS RI 211 CGNCE 22 CIS 20 RI 211 CIS D 20 RI 211 conjugate gradients 92 control 20 26 27 41 43 58 61 65 90 125 151 153 160 control initial 107 converged 88 108 CONVGREP 22 coord 26 coord initial 107 Cosmo 22 165 167 199 202 keywords 199 COSMOPREP 22 201 counterpoise calculation 58 CP corrections 106 CPHF 157 147 143 151 148 143 DEFINE 20 23 24 26 28 30 33 35 41 43 45 50 53 58 61 63 65 68 74 76 79 81 82 85 86 89 90 96 97 99 106 107 110 111 123 130 133 137 156 160 169 170 172 190 193 195 197 205 220 247 degrees of freedom 49 dens 150 DIIS 92 219 DIST 23 dos_atb 233 290 dos_a b 233 dos_alpha 233 dos_beta 233 Dscr 13 20 21 25 27 32 60 61 67 88 94 105 107 109 113 123 130 153 157 160 162 170 171 187 191 192 195 197 199 202 231 232 243 246 keywords 179 dscf out A_ghostB 107 dscf out dimer 107 dummy center 47 edens 150 EGRAD 18 21 22 28 30 88 94 126 129 130 134 160 162 208 224 231 232 keywords 208 EIGER 23 164 234 energ
301. s 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 differences to MPGRAD of RIMP2 in connection with optimised auxliliary basis sets are small and well documented 9 60 The use of the MPGRAD modul is rec ommended rather for reference calculations or if suitable auxiliary basis sets are not available 5 3 How to Prepare and Perform MP2 Calculations Prerequisites Calculations with MPGRAD or RIMP2 require e a converged SCF calculation with the one electron density convergence thres hold set to denconv 1 d 7 or less e the maximum core memory the program is allowed to allocate should be de fined in the data group maxcor in MB the recommended value is ca 3 4 of the available physical core memory at most 5 3 HOW TO PREPARE AND PERFORM MP2 CALCULATIONS 123 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 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 e and the number of passes for integral evaluations and transformations in data group t
302. s 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 ex cited states are not possible For the current version of moloch we refer to the keywords listed in Section 12 2 15 which partly can also be set by DEFINE see also Chapter 2 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 Dscr 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 or density generating step in case of programs Dscr 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 12 2 16 Electrostatic moments up to quadrupole moments are calculated by default for the above modules 160 10 2 INTERFACES TO VISUALIZA
303. s 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 individual 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 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 224 CHAPTER 12 KEYWORDS IN THE CONTROL FILE m matrix options This data block contains non default specifications for the m matrix diagonals This is of use if some cartesian atomic coordinat
304. s Q if present V Rp f eO asra y a BPE 5 Ree 10 2 r A Q In order to prevent the calculation of singularities at the positions of nuclei for gridpoints that are closer to a nucleus than 1074 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 plt sf plt etc For non default grid types and outputs that allow also for displaying of components of electric fields see Section 12 2 16 Molecular orbitals Visualization of molecular orbitals i e generation of plt files containing amplitudes of MOs 2 Alp cindy Rp 10 3 is achieved e g by 164 CHAPTER 10 PROPERTIES AND ANALYSIS AND GRAPHICS pointval mo 10 12 15 This yields amplitudes for MOs 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 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 2a1g_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
305. s 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 equivalent to the result from the RIMP2 module cis dinf denotes the iterative CIS D variant CIS D mp2 energy only If the energy only flag is given after the mp2 keyword it is assumed that only a MP2 ground state energy is requested This switches on some shortcuts to avoid the computation of intermediates needed e g for the calculation of properties gradients the D diagnostic etc or for CIS D and CC2 calculations cis d energy only If the energy only flag is given after the cis d keyword it is as sumed that only excitation energies are requested This switches on some shortcuts to avoid the computation of intermediates needed e g for the generation 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
306. s 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 Waals terms with the Lennard Jones potential The partial charges needed for electrostatic nonbond terms are calculated with the Charge Equilibration Modell QEq from Rapp 35 There is no cutoff for the non bonded terms gt 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 36 37 30 38 Pulay s DIIS procedure is implemented for big molecule to accelarate the optimization 39 29 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 1 08247228252865 0 68857387733323 0 00000000000000 2 53154870318830 2 48171472134488 0 00000000000000 1 78063790034738 1 04586399389434 O 00000000000000 2 64348282517094 0 13141435997713 1 68855816889786 2 23779643042546 3 09026673535431 O 00000000000000 2 64348282517094 0 1314143599
307. s 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 fixed 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 La 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 descendi
308. s 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 expectation value of the Cowan Griffin operator Option localization Specifying option localization will switch on a Boys localization of molecular orbitals 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 82 CHAPTER 2 PREPARING YOUR INPUT FILE WITH DEFINE 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
309. s with e 2 they 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 sf aie The total free energy of the solvated molecule is the sum of the energy of the isolated system calculated with the solvated wave function and the dielectric energy A Cosmo 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 which then also allows the evaluation of analytic gradients 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 In order to avoid problems with symmetric species the cavity construction uses de symmetrized coordinates The coordinates are slightly distorted with a co sinus function of amplitude AMPRAN and a phase shift PHSRAN
310. set 7 1 CC2 Ground State Energy Calculations The CC2 ground state energy is similar as other coupled cluster energies ob tained from the expression Eco HF H CC HF Hexp T HF 7 1 Escp es n aA 2ia jb jalib 7 2 iajb where the cluster operator T is expanded as T Ti To with Ti y bai Tak 7 3 ai 1 R 3 Y ras 7 4 aibj for a closed shell case in an open shell case an additional spin summation has to be included The cluster amplitudes ta and taipj are obtained as solution of the 140 CHAPTER 7 RI CC2 CC2 cluster equations 69 Qa ml H T HF 0 7 5 Qu ue A F T2 HF 0 7 6 with H exp T H exp T The residual of the cluster equations Q tai taibj is the so called vector function The recommended reference for the CC2 model is ref 69 the implementation with the resolution of the identity approximation RI CC2 was first described in ref 10 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 Nz where O is the number of occupied and V the number of virtual orbitals and N the dimension of the auxiliary basis set for the resolution of the identity Since RI CC2 calculations require the iterative solution of the cluster equations and 7 6 they are about 10 20 times more expensive than MP2 calculations The
311. 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 Schonflies symbol After you specified the atomic set to be considered you get the following information INPUT 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 O 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 2 2 The Atomic Attributes Menu
312. sing 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 a 6 1 99949836999366 a 7 1 99687490286069 a 8 1 00000000000000 a 9 00312509713931 a 10 00050163000634 point_charges 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 self energy list 2 5 0 2 5 ONI 2 5 In addition the following optional arguments may be given thrdistance threshold for discarding redundant point charges default value 1076 selfenergyif given the selfenergy of the point charge array will will be in cluded in the energy and the gradient 12 2 FORMAT OF KEYWORDS AND COMMENTS 187 listprint all poi
313. sities D DP and spin densities D DP 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 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 MP GRAD and for that of the calculated excited state in case of EGRAD Quan tities calculated are expectation values lt p gt lt pt gt and the Darwin term 071 Za p Ra moments 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 x1 y1 z1 x2 y2 z2 By integer i the maximum order of moments is specified maximum and de fault is 3 octopole moments real numbers z y z allow for the specification of one or more reference points pop drives the options for
314. sters 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 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 A Klamt G Sch irmann 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 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 correlation in the quantum mechanical polarizable continuum model so as to study solvation phenomena Chem Phys 150 2 139 150 1991 J G ngy n Rayleigh Schr dinger perturbation theory for nonlinear Schr dinger equations with linear perturbation Int J Quantum Chem 47 6 469 483 1993 J G ngy n Choosing between alternative MP2 algorithms in the self consistent reaction field theory of solvent effects Chem Phys Lett 241 1 2 5
315. sum of their extents plus wsindex are considered as far field Default is 0 0 and should be changed only by the experts 12 2 FORMAT OF KEYWORDS AND COMMENTS 197 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 LHF Use the Localized Hartree Fock LHF method to obtain an effective Exact Ex change Kohn Sham potential module Dscr The LHF method is a serial imple mentation for spin restricted closed shell and spin unrestricted ground states dft functional lhf gridsize 6 test integ 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 test integ will check if the selected grid is accurate enough for the employed basis set by performing a numerical integration of the norm of all orbitals How to do LHF runs 1 Do a Hartree Fock calculation using Dscr 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 beta hf for the spin unrestricted case See lhfprep
316. t 202 CHAPTER 12 KEYWORDS IN THE CONTROL FILE Cosmo in Numerical Frequency Calculations NUMFORCE can handle two types of COSMO frequency calculations The first used the normal relaxed COSMO energy and gradient It can be performed with a standard DscrF or RIDFT input without further settings This is the right method to calculate a Hessian for op timizations The second type which uses the approach described in chapter is implemented for RIDFT only The input is the same as in the first case but NUMFORCE has to 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 12 2 7 Keywords for Modules GRAD and RDGRAD Many of the Dscr 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 deriva tives 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 effects 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 uncorrected results are to be
317. t 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 Moloch see Section 10 2 This can be done by calling R1CC2 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 10 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 ccltd cc2 xs 3a2 001 1d0 ccitd cc2 gs 1a1l 001 pointval and invoke gt 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 10 2 7 4 Transition Moments Transition moments are presently only implemented for excitations out of the ground state and only for the coupled cluster models CCS and CC2 Note that for transition moments as excited state first order properties CCS is not equivalent to CCS and CIS transition moments are not implemented in the RICC2 program In response theory transition strengths and moments are identified from the first residues of the response functions Due to the non variational structure of th
318. t using tools like MP2PREP or RIMP2PREP Please refer to the following pages of this documentation 1 7 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 purpose This can also be done manually with an editor Given a kornshell and a path to TURBODIR bin arch see installation Section 1 6 you call the appropriate module in the following way e g module Dscr 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 The features of TURBOMOLE will be described in the following section 28 CHAPTER 1 PREFACE 1 7 2 Energy and Gradient Calculations Energy calculations may be carried out at different levels of theory Hartree Fock SCF use modules DscF and GRAD to obtain the energy and gradient The energy can be calculated after a DEFINE run without any further keywords or previous runs The gradient calculation however requires a converged DSCF 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 approxi
319. t 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 occupation If you accept you are done if not you get the occupation number assignment menu explained in 2 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 SAOs 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 calc
320. t 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 10 If not given in the response data group a default value is used which is chosen as max 107 10 1076 where conv and oconv refer to the values given in the data group ricc2 ZCOnV convergence threshold for the norm of the residual vector in the solution of the Z vector equations will be set to 107797 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 12 2 FORMAT OF KEYWORDS AND COMMENTS 217 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 krsemi If set to tight the semi canonical algorithm will become inefficient if the threshold is to large the alg
321. t 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 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 CONDITIONS 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 dqldq gt IF lt i gt 0 lt gldq gt IF lt i gt 1 2 4 THE GENERAL OPTIONS MENU TT 2 3 lt glg gt IF lt i gt lt dE gt IF lt i gt DEFAULT lt i gt 1 IGNORE GDIIS IF lt gldq gt lt gldq gt LARGER THAN lt r gt DEFAULT lt r gt lt RETURN gt OR OR q uit WILL TERMINATE THIS MENU fail lt r gt Oo Be For detailed description consult Section 3 3 RESTRICT
322. tals are calculated This is described in Chapter 10 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 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 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 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
323. tart MOs which should be the orthogonalized MOs of two independent subsystems as is explained in detail in Chapter 10 fldopt options Specification of options related with external electrostatic fields The following options are available 1st derivative on off Calculate numerical 1st derivative of SCF 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 12 2 FORMAT OF KEYWORDS AND COMMENTS 185 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
324. te force constant matrix in internal coordinates print level 2 e normal modes in terms of internal coordinates print level 1 e Potential energy contributions Ve defined as Vip LPL FR w where L are the elements of the normal coordinate belonging to mode n and Fj 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 Vp print level 1 the off diagonal contributions Vp Vp z IvA print level 2 for up to 10 atoms else print level 10 and the brutto contributions gt gt Va 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 contri butions print level 0 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 Chapter 9 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 similar to DSCF DFT using eit
325. tegrals for relaxed properties and gradients on the settings for integrals storage in semi direct SCF runs i e thime thize scfintunit For the explanation of these keywords see Section 12 2 5 cbas file auxbasis Auxiliary basis set for RI approximation For details Section 12 2 11 freeze Freeze orbitals in the calculation of correlation and excitation energies For details see Section 12 2 11 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 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 ricc2 ccs cis mp2 energy only cis d energy only cis dinf adc 2 212 CHAPTER 12 KEYWORDS IN THE CONTROL FILE cc2 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 specifies the ab initio models methods for ground and excited states and the most important parameter
326. ter 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 updated Otherwise the excited state optimization proceeds in exactly the same way as a ground state optimization see Chapter 1 7p 6 4 6 Excited State Force Constant Calculations Excited state vibrational frequencies can be calculated by numerical differentiation of analytic gradients using NUMFORCE see Chapter 8 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 C symmetry In order to determine n it is recommended to perform and ESCF calculation in C symmetry Note that numerical calculation of excited state 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 6 4 HOW TO PERFORM 135
327. th LDA and GGA functionals is implemented for all properties Excitation energies and transi tion moments can be computed either within the full time dependent HF TDHF or time dependent DFT TDDFT formalisms or within the Tamm Dancoff approx imation TDA 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 126 6 2 THEORETICAL BACKGROUND 127 e Exited state densities Charge moments population analysis e Excited state force constants by numerical differentiation of gradients using the script NUMFORCE 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 61 6 2 Theoretical Background 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 and refs therein The first order frequency dependent response of the density matrix can be expanded as yz a gt Kaupile pala Yaipala oi a 6 1 The real expansion coefficients Xai and Ya are conveniently gathered in a super a 6 2 on L the linear space of products of occupied and virtua
328. 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 a bf number of basisfunc tions scratch files The scratch files allocated by DSCF and RIDFT 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 192 CHAPTER 12 KEYWORDS IN THE CONTROL FILE scratch files dscf dens pathi filet dscf fock path2 file2 dscf dfock path3 file3 dscf ddens path4 file4 dscf XSV path5 file5 dscf pulay path6 file6 dscf statistics path7 file7 dscf errvec path8 file8 dscf oldfock path9 file9 dscf oneint path10 file10 The first column specifies the program type dscf stands for SCF energy cal culations and is valid for both Dscr and RIDFT programs the second column the scratch file needed 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
329. 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 distance 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 232 CHAPTER 12 KEYWORDS IN THE CONTROL FILE One line per element has to be specified it contains the name of the element and the van der Waals radius in Bohr 12 2 16 Keywords for wave function analysis and generation of plot ting data Properties of RHF and UHF wave functions as well as those of SCF MP2 densities or such from excited state DFT calculations can be directly analysed within the respective programs Dscr RIDFT MPGRAD RIMP2 and EGRAD In case of spin unrestricted calculations results are given for total den
330. their symmetry When assigning atom numbers to fragments 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 After 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 ca
331. tic 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 2 4 THE GENERAL OPTIONS MENU 81 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 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 ones or simply switch on or off individual data groups without deleting them from control The number of different data groups points a
332. tings 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 3 3 13 Initialization of Force Constant Matrices The most simple initial 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 82 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 3 4 FORCE FIELD CALCULATIONS 101 internal coordinates stretches 0 50 angles 0 20 scaling factors 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 optimizati
333. tion 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 TUR BOMOLE is not optimized This has in particular strong effects on the performance of all programs which use 4 index electron repulsion integrals for RI MP2 and RI CC2 this is partially compensated by the Rl 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 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 weighted core valence X tuple zeta basis sets X D T Q 5 avail able for H He B Ne Al Ar 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 d Z cc pwCVXZ or cc pV X d Z available for H He B Ne Al Ar with X D 6 and Ga Kr with X D 5 For calculations with the programs RIMP2 and RICC2 optimized auxiliary basis sets are available for the basis set series cc pVXZ cc pV X d Z cc pwCVXZ cc pwCV X d Z aug cc pVXZ aug cc pV X d Z aug cc pwCVXZ and aug cc pwCV X d Z with X D T Q 5 but not for X 6
334. tions All algorithms implemented in Dscr GRAD RIDFT and RDGRAD modules can exploit molecular symmetry for all finite point groups Typically the CPU time is proportional 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 Dscr and RIDFT modules include the following common features e An UHF implementation with automatic generation of optimal start vec tors by solving the HF instability equations in the AO basis see the keyword 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 Prerequisites Both DscrF 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 us
335. tions for the SCF orbitals and external perturbations are formally included in the SCF step i e also in the Fock operator Since relaxed densities or often computed in connection with geometry optimizations for individual states rather than simultaneously for many states a Lagrangian for the total energy of the excited state is used This has the advantage the only one equation for Lagrangian multipliers for cluster amplitudes V needs to be evaluated instead of two one for the ground state and one for the energy 7 3 FIRST ORDER PROPERTIES AND GRADIENTS 149 difference DAX E Et HF H CC y Ey Aw tE 7 22 pu No u2lH F To HE Rug Fug H2 Ho 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 con struction of the gradient contributions from one and two electron densities and derivative integrals takes approximately the same time as for ground states approx 3 4 SCF iterations and only minor extra disk space The implementation of the excited state gradients for the RI CC2 approach is described in detail in Ref 76 There also some information about the performance of CC2 for structures and vi brational frequencies of excited states can found The following is an example for the CC2 single point calculation for an an excited state gradient not that in the present implementation it is not possible
336. tions 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 expansions 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 Haser 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 1 3 HOW TO QUOTE USAGE OF TURBOMOLE 15 XII CC2 excitation energy calculations on large molecules using the resolution of the identity approximation C H ttig and F Weigend J Chem Phys 113 5154 2000 XIII 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 XIV First order properties for triplet excited states in the approximated Coupled Cluster model CC2 using
337. to Xn A Yn 1 6 8 Transition moments are evaluated by taking the trace with one particle operators e g 6 po Xn Yala 6 9 for the electric and m Xn Y m 6 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 to configu ration interaction including all single excitations from the HF reference CIS The TDA is not gauge invariant and does not satisfy the usual sum rules 62 but it is somewhat less affected by stability problems see below Stability analysis of closed shell electronic wavefunctions amounts to computing the lowest eigenvalues of the electric orbital rotation Hessian A B which decomposes 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 DFT while A B generally is not See refs for further details Properties of excited states are defined as derivatives of the excited state energy with respect to an external perturbation It is advantageous to consider a fully variational Lagrangian of the excited state energy 16 ia pq Here
338. to compute gradients for several excited states at the same time ricc2 cc2 excitations irrep al nexc 2 exprop states all operators diplen qudlen xgrad states al 2 A different input is again required for geometry optimizations in this case the model and 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 excitations irrep al nexc 2 exprop states all operators diplen qudlen 7 3 3 Visualization of densities By default Ricc2 saves relaxed densities generated during a calculation 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 150 CHAPTER 7 RI CC2 cc1td cc2 gs 1a1 001 cc1td 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 forma
339. trom gauzmat a Z matrix as in GAUSSIAN is used distances in Angstrom and angles in degree You can generate the Z matrix with Molden For more information about Molden see http www cmbi ru nl molden molden htm1 1 9 RUNNING TURBOMOLE USING THE SCRIPT TMOLE 39 Optional Sections charge title specifies the charge of the molecule in a u title of the calculation fZadd_control_commands scan specifies additional commands which will be added to the generated control file This section has to be the last section except the end section So a TURBOMOLE expert may start only with this section Example fadd_control_commands marij scfiterlimit 300 ADD END specifies a path along which a potential curve is calculated Coords of the starting final and intermediate geometries have to be defined in the Z matrix format see option gauzmat in Section coord If remaining coordinates are to be optimized at every scan point one needs for the present implementation an additional system of internal coordinates which contains the mode in question as a seperate internal syntax scan lt internal coordinate gt lt starting point gt lt increment gt lt end point gt see Sample inputs in Chapter 14 40 CHAPTER 1 PREFACE Chapter 2 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 c
340. twoint1 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 none To perform a calculation without a start vector i e use a core Hamil tonian guess file char 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 appear 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 integer 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 12 2 FORMAT OF KEYW
341. uare of the displacement elements drops below the value given by thrrmsdispl default 5 10 4a u e the root mean square of the gradient elements drops below the value given by thrrmsgrad defaul t 5 1074 a u The default values for the convergence criteria can be changed using the stp menu of DEFINE The necessary keywords are described in Section 12 2 14 below For structure optimization of minima with STATPT as relaxation program use jobex statpt amp TS optimizations are performed by the JOBEX invokation as jobex trans amp which implies use of STATPT for force relaxation 3 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 3 4 can be used For transition state optimizations you have to provide either the exact Hessian or results from the lowest eigenvalue search LES see Section 8 Note also that you can calcu late 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 calculated in a minimal basis using RI DFT is good enough for all methods implemented in TURBOMOLE 3 2 PROGRAM STATPT 91 STATPT automatically takes the best choice of the Hessian fro
342. uble shooting For the iterative second order methods CIS D 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 assumed 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 neccessary to select tighter thresholds In 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 in the neighbour hood of conical intersections e large contributions from double excitations The first two reaso
343. ulation A successful completion is indicated by tmole ended normally at the end of output The output is the same as a JOBEX output Additional examples for turbo in are given in Chapter 1 9 1 Implementation TMOLE first generates from turbo in an input file for DEFINE the general input generator for TURBOMOLE see Section f2 Then DEFINE is executed to generate the input file control specifiying the type of calculation basis set etc TMOLE finally executes the required modules of TURBOMOLE The output of each program will be written to a file with suffix out So the output of RIDFT for example is in the file ridft out If one wants to perform a geometry optimization TMOLE starts the script JOBEX for a description see Section 3 1 1 9 2 The file turbo in The file turbo in is the input file for a TURBOMOLE calculation with TMOLE This file consists of the following sections method coord and the optional ones charge title add_control_commands scan The file has to end with end 34 CHAPTER 1 PREFACE Section method description defines the properties to calculate the level of calculation the basis set used and further options general syntax method PROPERTY level of calculation basis set run options Note the after PROPERTY and the brackets run options If you want to continue on the next line type amp at the end of the line e g ENRGY b p SVP gen_stat 1 scf_msil 99 amp s
344. ulation and the Hiickel 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 normally get a list of the few highest occupied and lowest unoccu pied MOs 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 Note that the occupation based on the Hiickel calculation may be unreliable if the dif ference of the energies of the HOMO and the LUMO is less than 0 05 a u you will get a warning You will also have to enter this menu for all open shell cases other than doublets use file With command use you are able to use information about occupied 2 3 GENERATING MO START VECTORS 61 man hcore 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 cal culation of which all data groups related to occupation numbers and vectors will be read As the new generated data will overwrite the ex isting data if both resist in the same directory it is best and in some
345. umbers This concerns only the first SCF run however as for the following calculations the converged 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 H ckel 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 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 CHAPTER 2 PREPARING YOUR INPUT FILE WITH DEFINE file it will be kept unchanged 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 2 4 2 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 NUMBER ASSIGNMENT MENU e 60 c 0 0 0 s CHOOSE UHF SINGLET OCCUPATION t CHOOSE UHF TRIPLET OCCUPATION u lt int gt CHOOSE
346. utions or by using the segment area Akk 3 8 S if no associated basis grid points exist 167 Outlying charge correction Because the electron density is not zero outside the cavity one makes a mistake which should be corrected 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 which is constructed by an outward projection of the spherical part of the surface onto the radius R ROUTF x RSOLV for the estimation of the energy and charge correction 90 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 the dielectric energy for the disturbed state can be written as Fhe 5f a P P 10 P3 8 P3 Fal PEPS where P denotes the density difference between the distorted state and the initial state with density PY The interaction is composed of three contributions the initial state dielectric energy the interaction of the potential difference with the initial state charges
347. 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 Annealing 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 optimisation 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 12 2 18 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
348. wever 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 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 2 0 3 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 43 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 na
349. 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 15 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 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 15 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 a
350. ximum number of geometries minpul integer minimum number of geometries needed to start update 222 CHAPTER 12 KEYWORDS IN THE CONTROL FILE modus char fmode char lt g g gt or lt g dq gt or lt dq dq gt defines the quantity to be minimized dq internal coordinate change fmode specifies the force constants to be used only if 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 al 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 dq 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 offre set 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
351. xl integer This keyword can be used to reduce the time needed to update the fock matrix in each SCF iteration by exploiting information on previously computed den sities The differential density will be minimized using a linear combination of up to integer previous density matrices If this keyword is absent the default value is 20 scfdiis options Control block for convergence acceleration via Pulay s DIIS Options are errvec char specifies the kind of error vector to be used two different kind of DIS algorithms char FDS or SDF or FDS SDF use the commutator FDS SDF as error vector char none no DIS char sFDs use S71 2F DS 2 transposed char dF not supported anymore Further suboptions maxiter integer maximum number of iterations used for extrapolation P Pulay Chem Phys Lett 73 393 1980 P Pulay J Comput Chem 4 556 1982 12 2 FORMAT OF KEYWORDS AND COMMENTS 189 debug nteger debug level default 0 integer 1 print applied DIIS 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 DIIS thrd real directs the reduction of qscal to qscal 1 0 no damping in DIIS done if errvec lt thrd 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
352. y 101 Escr 13 21 28 30 70 126 129 134 205 207 208 keywords 205 extended Hiickel calculation 60 FINIT 23 FREEH 23 155 FROG 21 30 88 105 238 241 242 keywords 238 geometries excited states 147 ground state 145 geometry manipulation of 54 GRAD 20 21 28 32 67 73 88 94 97 98 105 107 109 112 134 147 153 199 202 208 224 226 245 246 keywords 202 grad_out 107 grad_out initial 107 gradients excited states 147 ground state 145 HCORE 23 INDEX HOLUMO 23 Infrared Spectra 154 internal coordinates linear combination of 53 manual definition of 52 types of 52 intersections conical 142 job lt cycle gt 88 job last 88 job start 88 JOBBSSE 48 106 108 JOBEX 22 23 25 27 33 43 68 71 87 88 90 91 101 106 126 134 137 138 213 226 246 JOBEX 111 jobex c 87 106 define 106 dscf 87 energy 87 106 ex 87 gcart 87 106 grad 87 gradient 106 keep 87 106 1 87 106 level 87 106 1s 87 106 md 87 mdfile 87 mdmaster 87 mem 106 opt 106 relax 87 106 ri 87 106 statpt 87 trans 87 trimer 106 KDG 23 kinetic energy 241 KONTO 23 lalp 234 INDEX lbet 234 Leapfrog Verlet algorithm 105 238 LHFPREP 23 197 LHFPREP 197 Imo 234 LoG2EGY 23 LoG2x 23 mdens 150 mdlog 105 mdmaster 238 mdmaster 105 MDPREP 23 104 238 239 mdprep 238 menu atomic attributes 54 57 genera
353. y 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 collected 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 3 2 PROGRAM STATPT 89 3 2 Program STATPT 3 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 optimizatio
354. y a single open 2 3 GENERATING MO START VECTORS 63 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 v list 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 tal 15 63244 2 2 0 0000 0 0000 2 2al 0 99808 2 4 0 0000 0 0000 3 le 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 0000 6 4al 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
355. y 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 O 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 0 238 CHAPTER 12 KEYWORDS IN THE CONTROL FILE 12 2 17 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 erro
356. zed auxiliary basis sets and demonstration of efficiency Chem Phys Letters 294 1 3 143 152 1998 C Hattig F Weigend CC2 excitation energy calculations on large molecules using the resolution of the identity approximation J Chem Phys 113 13 5154 5161 2000 C Hattig 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 277 278 12 13 15 16 17 18 19 20 21 22 23 24 25 BIBLIOGRAPHY C H ttig A Kohn 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 H ttig Geometry optimizations with the coupled cluster model CC2 using the resolution of the identity approximation J Chem Phys 118 17 7751 7761 2003 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 M Kollwitz

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