The PSI3 User`s Manual - Sherrill Group
Contents
1. For the B state of methylene the electronic configuration is 1a1 2 2a1 2 1b2 2 3a1 1 1b1 1 so the docc and socc arravs are reference rohf or uhf multiplicity 3 docc 20 0 1 socc 1 0 1 0 For the 1B state of methylene however the doce and socc arrays are also reference rohf multiplicity 1 docc 20 0 1 socc 1 0 1 0 Since most of the basis sets are highly contracted in the core regions core electrons are routinely frozen and corresponding virtual orbitals are deleted This is accomplished via the frozen docc and frozen uocc arrays Simply specify the symmetry of the frozen orbital and PSI3 will do the rest To freeze the lowest a orbital and delete the corresponding highest ba orbital they would look like this NA frozen_docc 10 0 0 frozen uocc 0001 NA 4 5 Single Point Energy Computation Along with the wavefunction type the nuclear framework basis set and electronic config uration are sufficient for a single point evaluation of the electronic energy The electronic wavefunction is specified via the wfn keyword The range of allowed wavefunctions is listed in Table 1 4 6 Geometry Optimization optking is the program responsible for orchestrating the process of geometry optimization It can do a number of tasks automatically such as generating internal coordinates produce empirical force constant matrix if necessary update it and check if geometry optimization is over Some or2. OK the calculation did converge in 4 steps What if it didn t Just increasing the number of optimization steps might just do that but might not In general 10 optimization steps should be enough for anyone If it doesn t converge by then your initial guess geometry or initial FC matrix or both were bad Rethink your situation Oops this is supposed to be a howto psi not a QC theology 4 Running PSI3 4 1 Geometry Specification Full molecular geometry has to be specified in form of Cartesian coordinates or a Z matrix Cartesian coordinates of atoms are specified via a keyword geometry which has to be a member of either default or input sections geometry atomnamel xi vi z1 13 atomname2 x2 y2 z2 atomname3 x3 y3 z3 atomnameN xN yN zN where atomname can take the following values e element symbol H He Li Be B etc e full element name hydrogen helium lithium etc e ghost atom symbol G or name ghost Ghost atom is an atom of formal charge 0 0 it can be useful to specify the location of the off nucleus basis functions e dummy atom symbol X Dummy atoms can be useful only to specify Z matrices of proper symmetry not used in PSI3 see below or which contain linear fragments Hence the following two examples are equivalent to one another geometry hydrogen FLUORINE Lithium berillium oO OO Oo oOoooo gt 0970 oooo oooo U MU NN DO Ro The keyword units specifies t
3. be executed The following programs would otherwise be executed cints cscf c4 20 gt As you can see some defaults are chosen We are now doing a RHF SCF Energy Point First the module or program cints will run to calculate the integrals then cscf will run to calculate the RHF SCF energy Should we run this just for the learning experience Sure but first we need to do a couple things Like find out what files and input parameters are needed by cints and cscf c4 20 gt man cints c4 20 gt man cscf cints needs input dat and file30 and will generate file33 file35 file36 and file37 It requires only 2 input parameters and the defaults look ok cscf needs input dat file30 file33 file35 file36 and file37 and a few input parameters which we will come back to So what s this file307 It is the basic binary working file for the PSI3 quantum chemistry package It contains all the juicy details of your job such as geometry basis set occupation scheme etc Since no one likes to write binary files we will create file30 with the program input For more information on this program c4 20 gt man input 3 3 Setting up a Calculation I ve decided that we ll start with STO water for our example and after reading the man pages described above I come up with the following file input dat default label water STO HF energy point memory 8 0 Mbytes win scf reference rhf files default name
4. cial characters e g parentheses asterisks then the string must be enclosed in quo tation marks e g 6 3114 G d p e basis stringi string2 string3 stringN string specifies the basis set for atom 2 Thus the number of strings in the basis vector has to be the same as the number of atoms including ghost atoms but excluding dummy atoms Another restriction is that symmetry equivalent atoms should have same basis sets otherwise input will use the string provided for the so called unique atom out of the set of symmetry equivalent ones e basis elementi string1 element2 string2 elementi stringN string 1 specifies the basis set for chemical element element 4 3 1 Default Basis Sets PSI3 default basis sets are located in pbasis dat which is located in psipath share Table 77 lists basis sets defined in pbasis dat 16 Table 3 Basis sets available in PSI 3 2 Basis Set Atoms Aliases Huzinaga Dunning 45 25 H 9S5P 4S2P B F 11S7P 6S4P ALCI DZ H B F ALCI DZP H B F ALCI DZ DIF H B F ALCI DZP DIF H B F ALCI Wachters WACHTERS K Sc Cu WACHTERS F Sc Cu Pople tvpe STO 3G H Ar 3 21G H Ar 6 31G H Ar K Ca Cu 6 31G H Ar K Ca Cu 6 31G d 6 314 G H Ar 6 31 G d 6 31G H Ar K Ca Cu 6 31G d p 6 311G H Ar 6 311G H Ar 6 311G d 6 311 G H Ne 6 3114 G d 6 311G H Ar 6 311G d
5. force constants or Hessian is critical for optimizing weakly bound struc tures In order to start an optimization one needs the fconst dat file For those of you that can speak Fortran 77 this file is written in 8F10 7 format It is the lower triangle of the force constant matrix in internal coordinates The order of the forces is identical to the order of the SYMM and ASYMM vectors For the methane water dimer an excerpt from a real fconst dat is shown below 5 654908 217027 5 616085 006096 001145 6 078154 055291 026921 023732 317485 004063 155489 003880 170201 873999 146900 285108 001153 023346 196008 605239 001037 001959 002945 024597 014432 005302 388622 Ideallv vour diagonal elements should be the much larger than the non diagonal elements If you need an fconst dat file you have four options 1 Create a diagonal matrix of 1 s 2 Create a diagonal matrix with 5 for stretching coordinates 2 for bending coordinates and 1 for all other coordinates 3 Let optking generate an empirical Hessian for you 4 Run a second derivative to obtain a Cartesian Hessian and transform that to internals fconst dat with intder Clearly the list starts at the most approximate and gets more accurate 4 7 Frequency Analysis Currently analytic second derivatives are avaliable only for closed shell Hartree Fock the preliminary implementation is not yet very efficient For methods with analytic gradi
6. h2osto nvolume 4 volumel tmp1 psiuser volume2 tmp2 psiuser volume3 tmp2 psiuser volume4 tmp2 psiuser file30 nvolume 1 volumel psi check true input note that all atoms are specified now not only the symmetry unique portion basis sto 3g units angstrom zmat o h 1 0 9600 h 1 0 9600 2 104 5 end file input dat You may wonder about the memory flag I ve tucked in the default As far as I know it s un documented but can be set for some PSI modules Acceptable units are REAL INTEGER BYTES KBYTES or MBYTES Generally it is a good practice to keep default memory small and increase program_id memory as necessary The default files section tells PSI3 where to store temporary scratch files Here a user is telling PSI3 to write the scratch files to four different directories where in this case psiuser is used as the user s username The file handling capability of PSI3 is very 10 flexible it is possible for example to tell each module to place files in different locations although this would rarely ever be useful By placing a files section in the default area PSI3 will use this information by default for all of its modules unless overridden by a files section inside a particular module like cscf for example Specifying four volumes such as in this example tells PSI3 to stripe split the files over four different direct
7. of high quality images with a pro gram MegaPov version 0 5 MegaPov is an unofficial patch for a ray tracing code POV Ray Information on MegaPov can be found at http nathan kopp com patched htm Let s look at how to set up input for spin density evaluation on a two dimensional grid An input secion of oeprop might look like this oeprop grid 2 spin_prop true grid origin 0 0 5 0 5 0 grid_unit_x 0 0 1 0 0 0 grid_unit_y 0 0 0 0 1 0 grid_xy0 0 0 0 0 grid_xy1 10 0 10 0 nix 20 niy 20 grid specifies the type of a property and the type of a grid oeprop needs to compute Allowed values are 0 default no property evaluation on a grid 1 electrostatic potential on a 2D grid 2 electron spin density on a 2D grid 3 gradient of electron spin density on 24 a 2D grid 4 Laplacian of electron spin density on a 2D grid 5 molecular orbital values on a 3D grid Since spin prop is set the spin density will be evaluated on a grid Grid specification is a little bit tricky but very flexible grid origin specifies the ori gin of the rectangular coordinate system associated with the grid in the refernence frame grid_unit_x specifies a reference frame vector which designates the direction of the x axis of the grid coordinate system grid unit v is analogously a reference frame vector which along with the grid_unit_x completely specifies the grid coordinate system grid unit x and grid unit v do not have t
8. p 6 311G 2df 2pd H Ne 6 311 G H B Ar 6 311 G d p 6 311G 2d 2p H Ar 6 311 G 2d 2p H Ar 6 311 G 3df 3pd H Ar Triple Zeta TZ2P H B F ALCI TZ2PD H TZ2PF H B F ALCI TZ DIF H B F ALCI TZ2P DIF H B F ALCI TZ2PD DIF H TZ2PF DIF H B F AlCl Correlation Consistent N D T Q 5 6 CC PVNZ H Ar cc pVNZ CC PV N D Z ALAr cc pV N d Z CC PCVNZ B Ne cc pCVNZ AUG CC PVNZ H He B Ne Al Ar aug cc pVNZ AUG CC PV N D Z Al Ar aug cc pCV N d Z AUG CC PCVNZ N lt 6 B F 17 aug cc pCVNZ D AUG CC PVNZ H PV7Z H C ATT I DITAN pV7Z NA UD dw 4 4 3 2 Custom Basis Sets To make a custom basis set enter the information in either of the following four files e pbasis dat only if you think it should be added to PSI3 You also might want to check in your additions and changes so that everyone could benefit from them Refer to the PSI3 Programmer s Manual for information on how to access PSI3 repository e An arbitrary text file To specify the file s location use keyword basisfile input The meaning of this is pretty obvious basisfile home users tool chem h20 mybasis in If the location ends with basis dat is automatically appended Hence this specifies home users tool chem basis dat basisfile home users tool chem Use this option if you want to use the basis set file in a project which involves running more than one computation e File named basis dat which re
9. that guessing algorithms cscf uses are far from perfect Hence you should check guessed occupations every time you let cscf guess them for you To determine the electronic occupations in PSI3 manually first construct symmetry or bitals using group theory and fill them according to regular valence bond arguments To define your occupations in PSI3 use the docc and socc arrays But only docc and socc may not be enough to specify precisely the spin couplings in your system That s where reference and multiplicity keywords come in multiplicity is equal 25 1 where S is the spin quantum number of the system reference can equal e rhf default spin restricted reference for closed shell molecules multiplicity may only equal to 1 in this case e rohf spin restricted reference for open shell molecules If multiplicity 1 and socc has two singly occupied orbitals in different symmetry blocks it s equivalent to the old opentype singlet statement Otherwise it s assumed to be a high spin open shell case equivalent to the old opentype highspin statement e uhf spin unrestricted reference for closed shell or high spin parallel spins open shell system e twocon for two determinantal wavefunctions The largest component should be speci fied by the docc and socc arrays Multiplicity has to be set to 1 19 For A methylene the occupation is 1a1 2 2a1 2 1b2 1 3a1 2 so the doce is reference rhf or uhf multiplicity 1 docc 3 0 0 1
10. variety of jobs First of all let s move on to another basis set The only thing that needs to be changed is the parameter input basis sto 3g to for instance input basis dz But for consistency why not change default label and default files default name c4 20 gt input c4 20 gt psi Whenever you change the basis parameter you must run input so that the change in basis is included into file30 Very important Changing default files default name every time you change the basis parameter is a good habit as it will insure that you run input Do you see why An aside about cscf and guess wavefunctions when you run cscf it by default but can be overridden automatically checks to see if there is an old wavefunction in file30 12 which can be used as a guess wavefunction and if so it uses it Each time cscf completes converged or not it writes the final wavefunction to file30 Each time input is run it overwrites file30 and any wavefunction that might have been in there is lost Nothing tricky about any of this but just something to keep in mind If you want to re use MO s from a previous calculation as a guess you can run input with the chkptmos option This will work even if the previous calculation used a different basis set but the geometry and point group symmetry should be the same Another useful flag is noreorient which prevents the molecule from reorienting after shifting the origin to the center of mass Well en
11. with more advanced aspects of PSI3 calculations including cutomization of basis sets scratch disk space and troubleshooting The appendix includes a description of the input keywords and command line options for each module as well as numerous examples of PSI3 input and basis set files Instructions for obtaining compiling and installing PSI3 on UNIX systems are given in the separate Installation Manual The latest PSI3 documentation can be found at http vergil chemistry gatech edu psi 2 PSI3 Preliminaries 2 1 Capabilities PSI3 can perform ab initio computations employing basis sets of up to 32768 contracted Gaussian type functions of virtually arbitrary orbital quantum number PSI3 can recognize and exploit the largest Abelian subgroup of the point group describing the full symmetry of the molecule Table 1 displays the range of theoretical methods available in PSI3 Geometry optimization currently restricted to true minima on the potential energy surface and vi brational frequency computations can be performed with the methods for which analytic gradients and Hessian respectively are available Methods for which analytic gradients are not yet implemented may still be used for geometry optimization if the gradients are computed numerically from energies this is automated by the optking program Numerical computation of Hessians is being developed PSI3 can also compute an extensive list of one electron properties Finally it shou
12. 2 0 1 1 Note the equivalence of the following three examples with the preceding one scf convergence 12 docc 2 0 1 1 scf convergence 12 docc 2 0 1 1 scf convergence 12 docc 2 0 1 1 A default token can be used as a wild card to fill any initial token field However explicit tokens will always override default tokens if both are present For instance a typical keyword search priority would be First module_id parameter and then default parameter Thus the two following examples will achieve the same effect when the module transqt is run but not when cscf is run default convergence 8 docc 2 0 1 1 scf convergence 12 default convergence 8 docc 2 0 1 1 scf convergence 10 Ok enough of all that you ve got the basics down the rest can be learned by doing The smallest input dat file you would probably ever want to use and this only as a learing experience is file input dat psi check true end file input dat If we run psi now what happens c4 20 gt psi The Psi Execution Driver ERROR a problem arose while reading the required string valued keyword WFN c4 20 gt Obviously we need to add a WFN So file input dat psi check true wfn scf for instance end file input dat c4 20 gt psi The Psi Execution Driver WFN SCF DERTYPE NONE REFERENCE RHF CHECK YES CHECK is YES so nothing will
13. S 0 5800 1 000000 S 0 1923 1 000000 S 0 06742 1 000000 P 35 91 0 016916 8 480 0 102200 2 706 0 338134 0 9921 0 669281 P 0 3727 1 000000 P 0 1346 1 000000 P 0 04959 1 000000 D 1 60 1 000000 D 0 40 1 000000 HVDROGEN t2pd S 33 64 0 025374 5 058 0 189684 1 147 0 852933 S 0 3211 1 0 S 0 1013 1 0 S 0 03016 1 0 P 1 50 1 0 P 0 375 1 0 30
14. The PSI3 User s Manual Jeffrey C Stephens George Vacek C David Sherrill Justin T Fermann Timothy J Van Huis and T Daniel Crawford Revised for PSI3 by Edward F Valeev and C David Sherrill Center for Computational Quantum Chemistry University of Georgia Athens Georgia 30602 Center for Computational Molecular Science and Technology Georgia Institute of Technology Atlanta GA 30382 0400 Department of Chemistry Virginia Tech Blacksburg VA 24061 0212 Version of January 20 2003 Contents 1 Introduction 4 2 PSI3 Preliminaries 4 Xr Capabilities A A Oe ee ZI MTA A 4 2 2 Before You Obtain PSI3 Prerequisites 00000000 4 2 3 Before You Run PSIS ei oh a OM 2S SM DE ZS 5 3 PSI3 Tutorial 6 ol Ata PSS ci Ep chs gs eke ce abt a PAR Se e a he ie es ee 6 32 Format oranput sdat 24 4 i fad i A PRE PS SE ib R a 6 3 3 Setting up a Calculation a alee le 18 alae te HW mew Ne Rare E Wt ese E WH 9 3 4 Carrying Out a Calculation Verla Sleek he ide aiii 12 4 Running PSI3 13 4 1 Geometry Specification aaa a a a 13 4 2 Molecular Symmetry a A A AA A ta 15 AS BARS Sets paren na a A A AA A 16 4 3 1 Default Basisoets lora a td Ye a ta dt 16 4 3 2 Custom Basis els alv ane E a Oe A 18 4 4 Electronic Structure Specification 4 64 aa ke de ad Pa ee eS 19 4 5 Single Point Energy Computation 40d it You Et E ta Yok 20 4 6 Geometry Optimization 2002 A BL sie A AA AA A 20 4 6 1 Internal Coordinates and Structure of intco
15. Vector 21 4 6 2 Force Constant Matrix and Structure of fconst dat 23 A Freguency Analysis Sk A A aaa 23 4 8 Evaluation of one electron properties o 00000 24 4 9 Plotting one electron properties o e ee 24 A TOS hee A oh sake a ea 8 oh eh ot ete A A E O O ae te UM 26 A PEON ceo SN Sh a si 26 5 PSI3 modules 26 5 1 Overview of modules of PSI3 424 54240 54 ts ee hee we 26 pili APUESTA E BSR Meee Rae we 26 S2 O hr B fil 94 SED dota La IT es Loles Ben ig es As RA aid transitare tado actas id sida article resida 3 E O die ti a a a g In SRO CENETA A ia ka u p a e Gow NN o L A TE a ae hes i as ee he Ses b a e ko he ER l Seen JARS o A Ai ta A Bis Pa oe Ms vA Ps ul hs VA ZA al Di APs Pel Tas ve 48 GO CAS aiet e ta el ea el t a a ae ed a ka ek SI 5 1 10 detcasman A AAA AAA A II a eh i A cee ed A PSI3 Reference B Sample input dat file C Sample basis dat file 28 28 30 1 Introduction This manual is intended to provide users with up to date information on running the PSI3suite of ab initio quantum chemical programs In section 2 we provide an overview of some of the features of PSI3 along with the prerequisite steps for running calculations Section 3 provides a brief tutorial to help new users get started Section 4 offers further details into the structure of PSI3 calculations including descriptions of the most important options and modules Later sections deal
16. all of the following files are necessary to perform a geometry optimization with optking 20 e file11 dat contains the cartesian geometry and the nuclear forces produced by cints derivl e fconst dat contains force constants if absent empirical force constants will be generated by optking e intco dat contains internal coordinates in a format readable by a human if absent internal coordinates are generated automatically by optking The procedure for setting up such a calculation is as follows e define internal coordinates if desired or do nothing and optking will do it for you automatically e obtain a set of force constants in an fconst dat file or again optking can do this automatically for you e If analytic gradients are available for your chosen method set dertype first If not set dertype none and also set numerical_dertype first in the default section e Run the optimization by setting the opt flag set to true and nopt to the number of geometry optimization steps say around 5 to 10 If analytic gradients are not avail able then nopt instead gives the number of energy points to compute This should be the desired number of geometry optimization steps multiplied by 2 num_symm coord 1 where num_symm_coord is the number of totally symmetric internal coordinates The precision with which geometry is optimized depends on the residual forces on the nuclei By default optking will terminate the job if
17. chieved like this set psipath put psi installation directory here setenv PATH psipath psipath bin host sh bin PATH setenv MANPATH psipath doc man MANPATH Note that in previous versions of PSI the installation directory was frequently in a subdi rectory of the source distribution directory This is no longer the case Now psipath is commonly something like usr local psi3 while the source directory will be elsewhere 3 PSI3 Tutorial 3 1 Running PSI3 The PSI3 suite of codes is built around a modular design which allows it great power and flexibility Any module can be run independently provided suitable datafiles of course There also exists a master program appropriately called psi which will parse an input file recognize the overall calculation desired and run all the necessary modules in the correct order To begin with c4 20 gt man psi will get the online manual page for the psi master program Other man pages for the psi code can be retrieved likewise The only required file is to run PSI3 is input dat Unfortunately no good and simple description of this file exists It is rather simple though and essentially free format Examples can be found in almost every man page It should be fairly easy to understand all the examples using common sense 3 2 Format of input dat Some keys to remember are the following e Input parsing is case insensitive once parsed everything is treated as upper case e A
18. ents 23 one must carry out finite difference calculations to obtain second derivatives If one has the misfortune of needing frequencies for methods where only energies exist e g FCI or MP2 R12 finite differences with gradients approximated by energy points must be used At present obtaining the Hessian numerically from energies or gradients is not automated by the program There are two types of frequency analysis programs available within PSI3 normco and intder95 For more details regarding these programs see the manual pages for each program respectively 4 8 Evaluation of one electron properties For now take a look at the available documentation for oeprop 4 9 Plotting one electron properties Program oeprop can evaluate certain one electron properties on a grid of points and then print them out in format suitable for image rendering with external programs Currently electron and spin density electron and spin density gradient Laplacian of electron and spin density and electrostatic potential can be evaluated on an arbitrary rectangular two dimensional grid and output in a format suitable for feeding to a interactive visualization program PlotMTV version 1 3 and higher PlotMTV is a freeware code developed by Kenny Toh It can be downloaded off many web sites in source or binary form In addition values of molecular orbitals can be evaluated on an arbitrary rectangular three dimensional grid and output for furher rendering
19. ergy points are well and good but without optimizations we are not going to get very far So we need psi dertype first psi opt true and psi nopt 7 to run up to 7 cycles of geometry optimization Or we could set default dertype first and default opt true or even mix and match Set psi check true and run psi to see what modules will be run Then check the man pages for each module and see what you need for it to run For instance in this case we see that cints derivi will be run man cints shows that us that everything is set OK optking is the last program to be run in each optimization cycle PSI2 users will appreciate the ease with which it can optimize molecules as it can generate internal coordinates for you as well as guess a force constant matrix Hence defaults are sufficient to run this program OK Go ahead and run psi In the 5th cycle optking should return a non zero value and psi will stop the procedure It will indicate that the optimization is over Let s up the ante and go for an optimization with a DZP basis set You know the procedure for improving the basis set Just switch the label the files name and the basis parameter Oh before I forgot you have to remove file named opt aux Then run input and psi The job runs fine Go ahead and look at output dat You may also wish to look at file11 dat fconst dat contains now an improved force constant matrix optking will automatically use this improved FC matrix if it is present
20. gy 5 1 8 detci This module performs many different types of CI computation including CI s truncated according to substitution level e g CISD CISDT CISDTQ etc full CI and any CI which can be formulated as a restricted active space RAS CI including second order configuration interaction SOCI and other types of multi reference CP s It can compute one and two particle density matrices and can obtain CI natural orbitals 5 1 9 detcas This program works together with the detci program to do CASSCF calculations in a two step procedure It obtains the orbital gradient and rotates the orbitals to optimize them 5 1 10 detcasman This is a driver program that controls detci and detcas to perform CASSCF computations 5 1 11 clag This forms the CI lagrangian which is needed for CASSCF and CI gradients 27 A PSI3 Reference T Daniel Crawford C David Sherrill Edward F Valeev Justin T Fermann Matthew L Leininger Rollin A King Shawn T Brown Curtis L Janssen Edward T Seidl Yukio Yamaguchi Wesley D Allen C Brian Kellogg and Henry F Schaefer III PSI 3 2 2002 B Sample input dat file default hhhhhhhhhhhhhhhhhhhhhhhhhhh Test input dat for errors hhhhhhhhhhhhhhhhhhhhhhhhhhh check true check false Ahhhhhhhhhhhhhhhhhhhhhhhhhh System parameters and job title Ahhhhhhhhhhhhhhhhhhhhhhhhhh memory 50 0 MB label CH3 cc pVTZ SCF hhhhhhhhhhhhhhhhhhhhhhhhhhh Choose wavefunctio
21. he units for the coordinates e units bohr atomic units Bohr default e units angstrom angstroms A The zmat keyword can be used to specify a Z matrix for the molecule It also has to be put in either default or input sections The format of this vector is as follows zmat atomnamel atomname2 ref21 bond_dist2 14 atomname3 ref31 bond_dist3 ref32 bond_angle3 atomname4 ref41 bond_dist4 ref42 bond_angle4 ref43 tors_angle4 atomname5 ref51 bond dist5 ref52 bond angle5 ref53 tors_angle5 atomnameN refNi bond distN refN2 bond angleN refN3 tors angleN where e bond disti is the distance in units specified bv kevword units from nucleus number i to nucleus number refil The units e bond angle is the angle formed by nuclei i refil and refi2 e tors angle is the torsion angle formed by nuclei i refil refi2 and refi3 Some care has to be taken when constructing a Z matrix for a molecule which contains linear fragments For example let s construct a Z matrix for a linear conformation of HNCO The first three atoms HNC can be specified as is but the fourth atom O poses a problem the torsional angle cannot be defined with respect to the linear HNC fragment The solution is to add 2 dummy atoms to the definition zmat h n 1 012 1 x 2 1 000 1 90 0 c 2 1 234 3 90 0 1 180 0 x 4 1 000 2 90 0 3 180 0 o 4 1 114 5 90 0 2 180 0 Of course a choice of the method for geometry s
22. ify two diagonally opposite vertices of the grid box via grid_xyz0 and grid xvzi The number of intervals along z is specified via niz The final input may look like this oeprop grid 5 mo_to_plot 10 grid_origin 5 0 5 0 5 0 grid_unit_x 1 0 0 0 0 0 grid_unit_y 0 0 1 0 0 0 grid_xyz0 0 0 0 0 0 0 grid_xyz1 10 0 10 0 10 0 nix 20 niy 20 niz 20 Running oeprop on input like this will produce two files e mo dat MO values tabulated in a column in order where x runs fast 25 e mo pov the MegaPov command file which sets a number of parameters You might have to adjust a number of parameters manually to obtain the best looking output Rendering of an image can be done via megapovplus Imo pov Consult MegaPov docu mentation for more information on how to use it 4 10 Utilities 4 10 1 geom The program geom reads a set of Cartesian coordinates and determines from them the bond distances Bohr and angstrom bond angles torsional angles out of plane angles optional moments of inertia and rotational constants It requires either a file11 dat or geom dat and writes geom out 5 PSI3 modules 5 1 Overview of modules of PSI3 Below is a very brief list of some of the modules available in the PSI3 program For more information consult the individual manual pages 5 1 1 input This program prepares the checkpoint file file30 Errors will result if the psi program is run before input This
23. ld be mentioned that whenever PSI3 is used it should be cited fully see appendix 2 2 Before You Obtain PSI3 Prerequisites The majority of PSI3 was developed on IBM RS 6000 AIX and Intel i386 Linux worksta tions The complete list of tested processor OS combinations to which PSI3 has been ported is shown in Table 2 If you don t find your system in the Table there s a good chance that you will be able to install PSI3 on your system if you have all of the following Table 1 Summary of theoretical methods available in PSI3 Method Energy Gradient Hessian RHF SCF Y Y Y ROHF SCF Y Y N UHF SCF Y N N CIS RPA TDHF Y N N TCSCF Y X N CASSCF Y Y N RAS CI Y N N RHF MP2 Y N N RHF MP2 R12 Y N N RHF CCSD Y Y N ROHF CCSD Y x N VOO CCD Y Y N RHF CCSD T Y N N UHF CCSD T Y N N RHF EOM CCSD Y N N ROHF EOM CCSD Y N N Table 2 Platforms on which PSI3 has been installed successfully Hardware Operating System s Special Notes Compaq Alpha Compaq TrueUNIX64 64 bit mode IBM RS 6000 AIX 3 2 5 ATX 4 1 4 3 0 IBM C C and Fortran compilers IBM PowerPC AIX 4 3 2 IBM C C and Fortran compilers 64 bit mode Intel ix86 Linux 2 2 SGI Origin 2000 IRIX64 6 5 64 bit 2 3 Before You Run PSI3 Every user needs to configure her or his shell environment prior to running PS13 1 add the location of the binaries to PATH 2 add the location of the manpages to MANPATH In C shell it may be a
24. n hhhhhhhhhhhhhhhhhhhhhhhhhhh wfn scf win mp2 win detci win ccsd Ahhhhhhhhhhhhhhhhhhhhhhhhhh Derivative level Ahhhhhhhhhhhhhhhhhhhhhhhhhh dertype none dertype first hhhhhhhhhhhhhhhhhhhhhhhhhhh Electronic structure info hhhhhhhhhhhhhhhhhhhhhhhhhhh reference rhf Pad reference rohf reference uhf reference twocon e SE 28 hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Optimize geometry hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh opt true opt true nopt 10 hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Finite difference hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh disp true ndisp 1 hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Scratch files note you must change psiuser to your username Ahhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh files default name ch3 volumel tmp1 psiuser volume2 tmp2 psiuser volume3 tmp3 psiuser volume4 tmp4 psiuser file30 nvolume 1 volumel Ahhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Section that generate file30 Ahhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh input units angstrom basis ccpvtz zmat x c 1 1 0 h 2 0 97 1 90 0 h 2 0 97 1 90 0 3 120 0 h 2 0 97 1 90 0 3 120 0 29 C Sample basis dat file basis NITROGEN t2pd S 13520 0 000760 1999 0 006076 440 0 0 032847 120 9 0 132396 38 47 0 393261 13 46 0 546339 S 13 46 0 252036 4 993 0 779385 S 1 569 1 000000
25. nds denoted linl and lin2 All of these are defined in Wilson Decius and Cross An example for methane is below intco stre 1 1 2 2 1 3 3 1 4 4 1 5 bend 5 2 1 5 6 3 1 5 741 5 8 2 1 4 931 4 10 2 1 3 After the primitives are defined they are constructed into symmetrized internals with the totally symmetric placed in the SYMM vector and the rest placed in the ASYMM vector For optimizations only the SYMM internals need to be defined Likewise if during an optimization a molecule breaks symmetry the internals have been improperly defined Again methane is done below symm C 1 stretch 1 2 3 4 asymm 2 E bend 10 7 C 3 T2 stretch 1 2 3 4 4 T2 bend 10 7 5 E torsion 8 5 9 6 6 T2 bend 8 6 7 T2 bend 5 9 8 T2 stretch 1 3 2 4 9 T2 stretch 1 4 2 3 The SYMM and ASYMM vectors have two or three components the first is a label enclosed by quotation marks and the second is the list of primitive internals comprising this vector 22 Some internals have been multiplied by 1 to reflect the appropriate symmetries If the internals need to be weighted by some prefactor then a third vector may be used symm generic coord 1 2 3 2 0 1 0 1 0 For more information in defining symmetric internals refer to Cotton s text 4 6 2 Force Constant Matrix and Structure of fconst dat The quality of the
26. nything following a percent mark i e is commented out up until the next carriage return e White space of more than a single space is ignored e Anything between double quotes e g usr c4 sw psi is considered one token there is no change of case and special characters and white space are maintained as part of the token but otherwise ignored e The old Fortran input parser does not like the TAB character Please avoid using Tabs until this goes away There does not appear to be a problem with the C library libipv1 Input data types are the following e String a character sequence e Integer a sizeof integer byte integer datum e Real a sizeof double byte real datum e Boolean yes true 1 these three values are equivalent no false 0 these three values are equivalent Input parameters come in only a few flavors e Keywords value e g convergence 12 e Vectors valuel value2 valuen e g docc 2 0 1 1 e Arrays il i2 in ji j2 jn ni n2 nn Note the proper number of opening and closing parentheses Arrays can conceptually be any depth dimension but in practice never go much beyond level 2 The elements of vectors and arrays need not be of the same data type 99 99 Segmented Keywords are joined by a colon i e scf convergence 12 gugaci convergence 8 Segmented keywords with common initial segments can be joined in vectors scf convergence 12 docc
27. o be normalized neither they need to be orthogonal to ei ther other orthogonalization is done automatically to ensure that unit vectors of the grid coordinate system are normalized in the reference frame too grid_xy0 is a vector in the grid coordinate system that specifies a vertex of the grid rectangle with the most negative coordinates Similarly grid xvi specifies a vertex of the the grid rectangle diagonally op posite to grid_xy0 Finally nix and niy specify the number of intervals into which the x and y sides of the grid rectangle are subdivided To summarize the above input specifies a rectangular in fact square 21 by 21 grid of dimensions 10 0 by 10 0 lying in the yz plane and centered at origin Running oeprop on such input will create a file called sdens dat for file names refer to man page on oeprop which can be fed directly to PlotMTV to plot the data Specification of a three dimensional grid for plotting MO isosurfaces grid 5 is just slightly more complicated The index of the MO which needs to be plotted is specified by keyword mo_to_plot The index is specified in Pitzer order and not according to the orbital energies The reference frame is specified by keywords grid origin grid unit x and grid origin y the third axis of the grid coordinate system is specified by by the vector product of grid unit x and grid unit y Since in this case we are dealing with the three dimensional grid coordinate system one needs to spec
28. ories This can be useful if there are four hard disks all used for scratch data However modern operating systems allow different physical hard drives to be striped automatically by the operating system into a single directory so having nvolume more than 1 is pretty unusual nowadays One downside to listing these specific scratch directories is that if you send your PSI3 input file to a co worker he or she will have to modify the file to use their scratch directories instead of yours assuming you don t all write to the same directory like tmp This problem is solved by the psirc file If this file exists in the user s home directory then it will override the file information in input dat For example with a psirc file containing the following information default files default nvolume 4 volumel tmp1 psiuser volume2 tmp2 psiuser volume3 tmp2 psiuser volume4 tmp2 psiuser file30 nvolume 1 volumel then the relevant section in input dat can be vastly simplified to just files default name h20 Once you have a input dat file prepared the first thing to do is to create the checkpoint file the previously mentioned file30 You can do this by running the program c4 20 gt input You should now have two new files output dat and h2osto 30 The latter file is a binary file it cannot be directly examined The first file should contain text giving the program outp
29. pecification is solely a matter of conve nience 4 2 Molecular Symmetry PSI3 can determine automatically the largest Abelian point group for a valid framework of centers the framework also includes ghost atoms but it does not include dummy atoms It will then use the symmetry porperties of the system in computing energy forces and other properties However in certain instances it is desirable to use a lower than the full symmetry The keyword subgroup is used to specify a subgroup of the full molecular point group The allowed values are c2v c2h d2 c2 cs ci and c1 For certain combinations of a group and its subgroup there is no unique way to determine which subgroup is implied For example D n has 3 non equivalent Coy subgroups e g Cay X consists of symmetry operations Cala Oxy and ozz To specify subgroups precisely one has to use the unique_axis keyword 15 E g the following input will specify the C2 X subgroup of D n to be the computational point group input geometry units angstrom subgroup c2v unique_axis x 4 3 Basis Sets PSI3 uses basis sets comprised of Cartesian puream false default or Spherical Har monic puream true Gaussian basis functions An atomic basis set is normally identified by a string Currently there exist three ways to specify which basis sets to use for which atoms e basis string all atoms use basis set type If the basis string contains any spe
30. program reads the default input and if given basis sections of the input file and places molecule geometry and basis information into the checkpoint file The molecule may be reoriented to a standard reference frame and the molecular point group symmetry is identified It is possible to tell input to re use orbitals from a previous calculation input chkptmos although presently this only works if the point group has not changed 5 1 2 cints This program computes one and two electron integrals and derivative integrals It is multi threaded and has some advanced capabilities related to integrals direct computations 5 1 3 cscf This program carries out the Hartree Fock procedure It can handle RHF ROHF UHF and TCSCF It can also simply re orthogonalize previously existing MO s 26 5 1 4 transqt This module transforms one and two electron integrals from the symmetry adapted atomic orbital SO basis to the molecular orbital MO basis for use in correlated computations by program such as detci or ccenergy It can also back transform one and two particle density matrices to the AO basis for contraction with the derivative integrals to obtain energy gradients 5 1 5 ccsort This module sorts the one and two electron integrals for use bv the PSI3 coupled cluster programs 5 1 6 ccenergv This module computes the CCSD energy 5 1 7 cctriples This module computes the T correction to CCSD to give the CCSD T ener
31. sides in the working directory along with input dat Same use as the previous entry e input dat The order in which input program searches for basis sets is the order in which files appear in our checklist A contracted Cartesian Gaussian Type Orbital caro ry z re exp a x y 27 1 where L l m n 2 is written as basis ATOM_NAME BASIS_SET_LABEL L C1 alphal C2 alpha2 C3 alpha3 Cn alpha4 18 To scale a basis set a scale factor may be added as the last item in the specification of each contracted Gaussian function For example to scale the S functions in a 6 31G basis for hydrogen one would use the following hvdrogen 6 31Gxx C S 18 73113696 0 03349460 2 82539437 0 23472695 0 64012169 0 81375733 1 2 S 0 16127776 1 00000000 1 2 P 1 10000000 1 00000000 In this example both contracted S functions have their exponents scaled by a factor of 1 2 1 44 The output file should show the exponents after scaling 4 4 Electronic Structure Specification The reference electronic configuration of a molecule is specified via a combination of keywords reference and multiplicity and occupation vectors docc and socc However the latter may not be necessary as cscf may guess occupations doce and socc arrays for you had charge multiplicity and reference have been specified It is the easiest way to specify electronic configuration for your system but remember
32. the residual cartesian gradients in file11 dat are less than 1E 5 in atomic units It is probably enough for most tasks Going below this will most likely waste CPU time unless you are doing benchmarks An important aspect of a geometry optimization is the accuracy of the first derivatives of energy that PSI3 computes Depending on how poorly your wavefunction has been con vereged the gradients themselves may not be sufficiently accurate for the requested conver gence criterion After computing first derivatives of the energy cints runs a simple check of the quality of the energy derivative It s a good idea to look at cints output to make sure that the gradients are OK Let us take a look at each step involved in optimizing molecular geometry 4 6 1 Internal Coordinates and Structure of intco Vector This section is largely obsolete now with the addition of the optking program which can generate internal coordinates automatically At present optking cannot handle molecules larger than a few atoms but it should change in the immediate future Hence you may still specify internal coordinates manually as described here but this ability may become obsolete someday 21 PSI3 currently carries out all optimizations in internal coordinates The internals are specified in either input dat or intco dat First the primitive internals are defined These are individual stretches bends torsion out of plane deformations and two different linear be
33. ut Take a look at this file and see what kind of information it gives 11 Going on c4 20 gt psi reminds us that we will be running cints and cscf We have everything we need for the first but how about the second c4 20 gt man cscf Well there are alot of possibilities but the defaults are generally sound so we really only need to add in our occupation scheme for the doubly occupied orbitals Or do we The fact is cscf can guess occupations for you using core Hamiltonian orbital eigenvalues but as with any computer program you have to be cautious Let us be adventurous here and let the program guess In general always make sure you are computing the state you want to and not the state that the program chose Notice at this point that I am leaving out the majority of the file input dat It is getting a little big to repetitiously include it within this document 3 4 Carrying Out a Calculation Assuming you have done everything detailed in the previous section we can run an actual job and get a number out c4 20 gt psi Ahhhh We forgot to change the psi check true flag so nothing was really run Change it to psi check false or simply comment it out since the default value is false by inserting a at the start of that line and run psi again Take a look at the file output dat and become familiar with it We now have the basic input dat file Only minor modifications will allow it to be used to run a great
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