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SAPT2002 User Guide - University of Delaware Dept. of Physics

1. Compall gt amp compall log amp e K Shell users Compall gt compall log 2 gt 1 and compilation should begin Check compall log to see if all is well The Compal1 script will create a file SAPT2002 stamp intf containing a summary of the settings you have used in the compilation A subsequent invocation of Compall will detect any changes made to these settings since stamp intf was last created and only those parts of the code will be rebuilt which were affected by these changes Running the script SAPT2002 Cleandirs will restore the SAPT2002 directory to its distribution state i e all object files and executables except shell scripts will be deleted and invocation of Compall will start the compilation from scratch One more customization step may be required before SAPT2002 is run with GAMESS as the SCF fron end the SAPT2002 bin runGAMESS script must be modified by setting the TARGET variable which depends on the platform and on the way GAMESS has been compiled In most cases the default TARGET sockets will be appropriate although on SGI machines TARGET sgi mpi is also popular Consult your local GAMESS installation Further customization of runGAMESS will be needed for other targets if you need to do such a customization see examples given in both runGAMESS and the standard rungms for the GAMESS distribution 13 7 2 Compall_asymp installation script If you have downloaded the asymp_SAPT package
2. int int elst resp exch disp exch disp where the notation e k es E3 has been used e is the part of Ee not included in Ea es and PC a is the estimated exchange counterpart of tpe tp 22 tp 22 pe Eg ee ae Ta Eoxch indresp n0 5 ind resp The highest routinely used level of SAPT approximately equivalent to the fourth order of supermolecular MBPT theory is defined by ESAPT _ gSAPT2 0 4 E int int elst resp exch COSD amp 2 22 6 exch where e CCSD is the part of 1 co with intramonomer excitations at the CCSD level only exch exch The SAPT2 level of theory takes much less time than the full SAPT calculations and therefore it is recommended for large systems If still faster calculations are required the corrections ge and ER disp an be omitted as these are usually fairly small The corrections P o ae sos eee and E can also be computed in non response versions but these forms are not recommended The corrections listed above constitute the current set typically used in SAPT calculations A few other corrections have been developed by the authors of SAPT but these are either not working in the current version of the program or for some other reasons are not recommended to be computed These corrections include E 14 pe 14 higher order approximations to the electrostatic interaction 15 the dispersion energy at the CCD level 16 and some corrections of third order
3. On IBM SP3 brainerd at ARL the command grd_poe also works For TARGETs other than SP ignore this variable 8 SCLPCK specify how the SCALAPACK and BLACS libraries are to be linked If this is set to NO then the sequential CHF procedure will be used will spoil scaling of psapt for large systems and the pcksdisp code for susceptibility functions will not be built at all 9 LPCKLIB specify how the LAPACK library is to be linked This library is needed to build the program tdenfit fitting the densities and propagators in terms of auxiliary bases If LPCKLIB is set to NO the tdenfit will not be built On SP machines LAPACK is a part of ESSL library and hence LPCKLIB does not have to be given at all just set it to YES Once all the variable mentioned above are set simply type e C Shell users compall gt amp compall log amp e K Shell users compall gt compall log 2 gt 1 and compilation should begin Check compall 1log to see if all is well The compall script works by invoking the make command with platform specific makefiles Thus any subsequent invocation of compall will detect changes made to the sources and only those parts of the code will be rebuilt which were affected by these changes Running the script psapt2K2 cleandirs will restore the psapt2K2 directory to its distribution state i e all object files and executables except shell scripts will be deleted and invocation of com
4. out_test NODT 2 gt amp 1 Copy output file back to HOME cp JOB out_test NODT CURDIR The first few lines starting with are options passed on to the queuing system in this case GRD specifying things like the name of the job what machine it should be run on in what queue and on how many processors The syntax of these options depends of the queuing system at hand and so these few lines must be adjusted accordingly The script is submitted typically using a command qsub ARL_script After the script enters execution it first creates the scratch directory named after the name of the job then copies the input files from the home subdirectory CURDIR to the scratch directory and runs the pSAPT o2k script SAPTSCRIPT Upon completion of the psapt2K2 calculation the output file is copied back to the home subdirectory CURDIR Note that after the job is finished the scratch directory will contain all kinds of temporary files which are kept there in case a restart is needed These files should be manually cleaned up 13 4 2 Running psapt2K2 on an SP3 SP4 The job submission technique here is very similar to the one used on an SGI platform except that interactive submissions are generally not possible and everything must be handled by a queuing system Consult the ARL_script and NAVO_script in the psapt2K2 examples SP directories for examples of the GRD and Load Leveler submission scripts 13 4 3 Running psapt2K2 on a
5. which indicate that standard error messages will be written to the same file as standard output and that the process will be run in the background 21 9 1 Calculations of integrals and SCF energies A SAPT2002 run starts with calculations of atomic integrals i e integrals between one electron basis functions and the SCF orbitals and orbital energies for monomers Optionally if the opt1 keyword is set to scfcp a counterpoise CP corrected supermolecular calculation of the HF SCF interaction energy are also performed The number and type of SCF calculations depend on the chosen approach to the basis set construction and on the selection of the supermolecular calculation For a description of possible choices of basis sets see the following subsections and Ref 22 For information on input to the integral SCF programs please refer to the original documen tation for those codes Some remarks on this subject can also be found in Sec 8 For an ATMOL manual see http www theochem kun nl pwormer Please note that symmetry considerations are not built into the SAPT2002 codes so the SCF packages should be asked to output the integrals with no symmetry assumptions The SAPT2002 codes make an implicit assumption that for each monomer the number of occupied orbitals is smaller or equal to the number of virtual orbitals and a crash will occur if this condition is not met It is thus not recommended to run SAPT2002 calculations in m
6. 2002 Vol 3 Part 2 Chap 8 p 37 B Jeziorski R Moszynski A Ratkiewicz S Rybak K Szalewicz and H L Williams SAPT a A Program for Many Body Symmetry Adapted Perturbation Theory Calculations of Inter molecular Interaction Energies in Methods and Techniques in Computational Chemistry METECC 94 edited by E Clementi STEF Cagliari 1993 Vol B p 79 6 During work on SAPT2002 a small error was detected in the ccsdt module of SAPT96 which slightly affected the correction e CCSD especially in calculations for small systems in large basis set In all tested cases the magnitude of this error was small enough not to change the published results 7 V F Lotrich and K Szalewicz J Chem Phys 106 9668 1997 8 R Moszy ski P E S Wormer B Jeziorski and A van der Avoird J Chem Phys 103 8058 1995 Erratum 107 672 1997 9 V F Lotrich and K Szalewicz J Chem Phys 112 112 2000 10 M W Schmidt K K Baldridge J A Boatz S T Elbert M S Gordon J H Jensen S Koseki N Matsunaga K A Nguyen S J Su T L Windus M Dupuis and J A Montgomery J Comput Chem 14 1347 1363 1993 11 V R Saunders and M F Guest ATMOL Program Package SERC Daresbury Laboratory Daresbury Great Britain 12 P E S Wormer and H Hettema POLCOR package University of Nijmegen The Netherlands 1992 P E S Wormer and H Hettema J Chem Phys 97 5592 1992 13 M Jeziorska B
7. Comments e2ex f e2ex aoe and EO aes driver e2ex f exia Pieces of above e2ex f jexi x e2ex f e2iba gt e2ex f exib x e2ex f e2iab 2 e2ex f ex2d e2ex f jex2d z e2ex f exd2 de e2ex f jexd2 7 e2ex f je2iex 7 edab f e220d0 Driver routine for ES a e4ab f srt220 Sorting routine for above e4ab f e220rl Ring ladder piece edab f e220ts Triples contribution e4ab f e220dr Ring diagrams in core e4ab f e220ds Single excitation diagrams e4ab f 1220da Factorizes two Brandow diagrams e4ab f e220da Sums two non triple diagrams e4ab f e220db Sums four Goldstone diagrams eded f e202d0 Same as 220 counterparts e4cd f srt202 gt eded f e202rl a eded f e202ts g e4cd f e202dr dd e4cd f e202ds i eded f 1202da 7 e4cd f e202da gt eded f e202db Se e3 srt3d0 Driver routine for EX e3 sort3d Sorting routine for above e3 e3dsp Calculate above e3 srtind Sorting routine for E disp e3 dspin0 Driver routine for above e3 dspin1 Sums eight diagrams for above e3 dspin2 Compute another part e3 eind3 Driver for W309 e3 e3ind1 Pieces of above e3 e3ind2 z If a subroutine appears in TRAN and has the same function it is not mentioned here 82 C Appendix Input Output files for the example BER Bez e ATMOL1024 file BER intinp TITLE BER2 test run GEOMETRY 0 0 0 0 0 0 4 0 Beri 0 0 7 0 0 0 4 0 Ber2 END GTOS S Berl 0 1 0 0 198210 S Berl 0 1 0 1 767558 P Beri 0 1 0 0 201 S Ber2 0 1 0 0 1
8. The onela data and onelb data files contain the one electron integrals of site A and B respectively The file inta data contains the two electron integrals in some cases the original two electron package from a given set is used The infoa data and infob data files contain some general information about the system being computed like the number of occupied orbitals the geometry and charges of each of the monomers These files vecta data vectb data onela data onelb data infoa data infob data and inta data serve as input files to the four index transformation program This program transforms the one and two electron atomic integrals into molecular integrals and produces the file final2e as output Next the MBPT CC program is run which generates the cluster amplitudes necessary for the sapt perturbation program and puts them into the file interm This file is moved to the file interma for site A or intermb for site B The input files here are the two electron inte grals final2e the eigenvalues and eigenvectors vecta data or vectb data the site A or B info data file and the site data file This last file simply holds a flag to indicate whether at a given moment the calculations are performed for site A or site B The last step of the process is the calculation of the SAPT corrections The input files neces sary are vecta data vectb data onela data onelb data infoa data infob data interma intermb and final2e These files contain
9. delta HF _ int are also given The CORRELATION part of Summary Table contains all the computed SAPT corrections of or 33 der higher than 0 in the intramonomer correlation operator and the dispersion energy as defined in Sec 2 Two partial sums are also provided SAPT_ corr resp and SAPT_ corr The first of these quantities is the sum of eps 1 _ elst r k eps 1 _fexch k or if available eps 1 _fexch CCSD tE 22 _find tE 22 _ ex ind E 2 _ disp k and E 20 _ fexch disp The definition of the second partial sum is completely analogous except that eps 1 _ elst k is used Note that if any of the corrections appearing in the definition of a partial sum is not computed for example because it has not been requested in the namelist INPUTCOR this partial sum will not contain this correction For example if only SAPT T is re quested in the INPUTCOR namelist the non responsed electrostatic corrections will not be computed and the quantity SAPT_ corr will not contain any correlation contribution to electrostatics Finally the last two entries in the Summary Table give the hybrid interaction energies i e the sums of the supermolecular SCF and the correlation parts represented by SAPT_ corr resp or SAPT_ corr If all the relevant corrections have been computed such as when one of the SAPTx variables is set to true in INPUTCOR the quantity SCF SAPT_ corr resp should be considered th
10. no input 9 2 3 Namelist INPUTCOR This namelist tells the SAPT program which of the perturbation theory corrections are to be computed The list of variables and of the associated currently available corrections is as follows 1 E1TOT ECO and ECO elst exch 30 2 E2IND ECO in 3 EZINDR Ela esp 20 20 4 EEX2 dp and Bich sua 20 20 5 EEX2R Dect iets and Se See eer 6 E12 B92 12 7 E12R Bitre 13 8 E13PL ES 9 E13PLR EU elst resp 10 E122 pR currently not used 11 E11 BOY exch 12 E111 Be 13 E12x BO 4 p2 14 E2DSP ERO 15 E21D ERP 16 E22D BY 17 EMP2 0 MBPT2 correction to monomer s correlation energy for tests only 18 E221 tE see Ref 2 12 Notice that the electrostatic energies E are sometimes denoted as a as these result from the ol Rayleigh Schr dinger perturbation theory that in this context is often called polarization theory The acronym pol in several places in the program as well as the letters PL in E13PL are resulting from this terminology If tpe is requested its exchange counterpart will be estimated from the formula of Eq 5 The triple superscripts appearing for example in the correction E a denote the order with respect to the operators V W4 and Wp respectively The following corrections either have not been tested enough do not work or should not be used withou
11. x13 f parta ue x13 f ringla x13 f frho2a 7 x13 f ravv ik x13 f raoo x13 f sla 4 x13 f rhob Driver routine for ring ladder diagrams for monomer B x13 f frho2b Pieces of EGOS x13 f rbvv i x13 f rboo a x13 f ringlb gt x13 f slb l x13 f partb p x13 f frho3b 4 x13 f part2a z x13 f part2b els f el2ex EC EGO driver routine els f sel2ex Sorting for above elx ellex EG driver elx jellex Alternative method for above not used elx je110 Alternative for e110 elx jel01 Alternative for e101 elx e110 Eo mem partitioning and driver elx e101 Bo mem partitioning and driver elx ellle ES driver elx elllex Calculate BGM elx jelllex Alternative for above jkua jkllua Alternative Ki A component jkua pooa Forms Po matrix for monomer A jkua pvva Forms Pv matrix for monomer B jkua jrtla Alternative pieces of ED ER jkua jrt2a Monomer A jkua jrt3a 7 jkua jrt4a A jkua jrt a 2 79 Table 6 Comments on selected subroutines SAPT continued 3 Module Subroutine Comments jkub jkllub Alternative Ky B component jkub jrtlb Alternative pieces of EY Bo jkub jrt2b Monomer B jkub jrt3b de jkub jrt4b i jkub jrt5b A jkub poob Forms Po matrix for monomer B jkub pvvb Forms Pv matrix for monomer B kua f k11u Ky A and B driver kua f kllua Kii A component kua f rt3a Terms of E BE kua f rt4a Monomer A kua f rt a us
12. AAA AA Bs a e 13 4 1 Running psapt2K2 on SGl e 13 4 2 Running psapt2K2 on an SP3 SP4 0 o o 13 4 3 Running psapt2K2 on a Beowulf cluster o Input tlesta aloe ps da eek a e a ide e tada do d Memory and disk requirements e Electrostatics dispersion and induction EDI from monomer properties 13 7 1 The pEDE SCTID S eo ru eG a Bem a da sohbet 13 7 2 Calculating electrostatics induction and dispersion from fitted monomer electron densities and susceptibility functions Appendix Integral SCF interfacing Appendix List of subroutines Appendix Input Output files for the example BER Bez Appendix Capabilities of pcksdisp program Appendix Generation of auxiliary basis 39 41 42 42 44 73 73 83 88 91 1 Introduction SAPT2002 is a computer code implementing the many body version of Symmetry Adapted Per turbation Theory SAPT SAPT is designed to calculate the interaction energy of a dimer i e a system consisting of two arbitrary closed shell monomers Each monomer can be an atom or a molecule The many body phrase used in the title refers to electrons as bodies like in the name Many Body Perturbation Theory MBPT In SAPT the interaction energy is ex pressed as a sum of perturbative corrections each correction resulting from a different physi cal effect This decomposition of the interaction ener
13. B NH3 is constructed from the whole DCTBS set by deleting the last two s the last p and the last d functions of F and the last s and p functions of HF s hydrogen see the file HF_NH3MB inp 26 Note that the sequence of basis functions in the input files is determined by the sequence of atomic centers and the sequence of functions within each center Thus simply deleting a contraction does not change the relative sequence in the remaining set as required The part of the TRN namelist corresponding to this setup is BLKMB F SPHG F basis ssssspppddsssppsspssssspppddsssppsssppssspp tags mmmaammamammamammmmmmbbmmbmbmmbmbmmbmbmmbmb Note that the variable SPHG has been set to FALSE since GAMESS always generates integrals in Cartesian basis even if the SCF calculations are performed in variational space spanned by only pure spherical components as it is done with the option ISPHER 1 in GAMESS input files inp If the tags method is used with some other SCF program make sure that the value of SPHG matches the actual type of basis set for which the atomic integrals are generated Other examples of MC BS input files using the basis and tags options with GAMESS can be found in directories SAPT2002 examples GAMESS MCBS and for ATMOL1024 in SAPT2002 examples ATMOL1024 ArHF_MCBS 27 9 2 Input for post Hartree Fock part The input for the transformation tran the MBPT CC code cc and the proper SAPT prog
14. Beowulf cluster Configurations of Linux based Beowulf clusters may vary between installations Presented below are techniques of running psapt2K2 on our local cluster samson at University of Delaware and on the huinalu cluster at Maui supercomputer center samson The machine consists of 132 compute nodes equipped with 1GHz AMD Athlon processors and connected by ethernet Each node is equipped with a local scratch filesystem not accessible from 54 other nodes On each node this filesystem is mounted as tmp In addition there is a login node which hosts home directories of the users and some shared resources like the MPI implementation mpich The home and shared directories are NFS mounted on all compute nodes Commands and programs can be executed on compute nodes from the login node through the rsh utility It is also possible to rlogin to the compute nodes although it is not necessary for running psapt2K2 The consecutive modules of psapt2K2 are launched from within the script pSAPT mpich using the mpirun command while GAMESS is started using the ddikick x utility of the ddi package It is a good rule on samson that jobs are to be run on compute nodes only and not on the login node For any MPI application this may be accomplished by executing the mpirun command on the login node with the option nolocal supported by mpich Unfortunately this option or a similar one is not available in the ddi package which is the GAMESS paralleliza
15. ICUT 30 MAXIT 50 END SYSTEM TIMLIM 1 MEMORY 100000 END GUESS GUESS HCORE END DATA Beryl Dimer RHF C1 Bert 4 0 0 0 0 0 0 0 S 1 1 0 198210 1 0 S 1 1 1 767558 1 0 P 1 1 0 201 1 0 Ber2 4 0 0 0 7 0 0 0 S 1 1 0 198210 1 0 S 1 1 1 767558 1 0 P 1 1 0 201 1 0 END SCF NCONV 9 END INTGRL NOPK 1 NINTMX 2048 END MOROKM MOROKM FALSE END e GAMESS file BERA inp 85 CONTRL SCFTYP RHF RUNTYP ENERGY COORD UNIQUE UNITS BOHR NPRINT 5 NOSYM 1 INTTYP HONDO ITOL 30 ICUT 30 MAXIT 50 END SYSTEM TIMLIM 1 MEMORY 100000 END GUESS GUESS HCORE END DATA Beryl2 test run C1 Bert 4 0 0 0 0 0 0 0 S 1 1 0 198210 1 0 S 1 1 1 767558 1 0 P 1 1 0 201 1 0 Ber2 0 0 0 0 7 0 0 0 S 1 1 0 198210 1 0 S 1 1 1 767558 1 0 P 1 1 0 201 1 0 END SCF NCONV 9 END INTGRL NOPK 1 NINTMX 2048 END MOROKM MOROKM FALSE END e Perturbation input file BERP data Ber 2 run in 3s1p basis set For testing only amp TRN ISITALCH F ISITG88 F ISITG90 F ISITHNDO F ISITMICR F ISITANEW F ISITGAMS T OUT F TOLER 15 DIMER T MEMTRAN 10000 amp END amp CCINP CCPRINT F VCRIT 1 0D 10 TOLITER 1 0D 5 amp END amp INPUTCOR SAPT T E12 T E13PL T E2IND T CONVAMP T PRINT F TIMEREP F MEMSAPT 100000 amp END e Beg Results 86 Mono A 2 occupied 8 virtual 10 total Mono B 2 occupied 8 virtual 10 total Molecule A 4 Electron s ATOM XX YY ZZ Charge 2 0 000000000 0 000000000 0 000000000 4 0 OA Mol
16. Ok Ok Ok Ok gT Linux and Ok GAMESS does Ok Ok PGF77 not work 3 3 2 Alpha Doesn t work Ok Ok Not checked under Compaq compiler but works under g77 RS 6000 Ok Ok Not checked Not checked SUN Ok Ok Not checked Not checked 7 Installing SAPT2002 Installation of SAPT2002 is controlled by a universal script Compall a small portion of which has to be customized by the user The Compal1 script sets the compilation options appropriate for the hardware platform and for the integral SCF interfaces chosen It then compiles and links all the pieces of the code which sometimes requires access to the I O libraries of the integral SCF packages If ATMOL1024 has been downloaded and the SAPT2002 atmo11024 directory is present this package is also built Finally Compall updates the scripts used to run SAPT2002 10 SAPT Runlot by inserting updated paths to executables The asymp SAPT package is installed by a separate script 7 1 Compall installation script The following adjustments must be made by the user to the Compal1 script 1 Execution shell Change the first line of the script to one of the following e bin bash The BASH shell on a LINUX box or e bin ksh The Korn shell on all other platforms 2 Integral SCF program Declare the SCF packages you wish SAPT2002 to be inter faced with In addition to the SCF front ends listed in Compall we know that other use
17. coefficients from files created by these packages and transform them into a standard form readable by the transformation code two electron integrals are read by transformation directly without such preprocessing Other programs present in misc include int and sort interfacing the transformation to coupled cluster code memory estimator memcalc and a set of geometry converters which can be used with the bin Runlot scripts for automatic generation of potential energy surfaces see Sec 9 for details e bin utility scripts for running SAPT After compilation this directory will also contain the executables used in a SAPT run e doc documentation for SAPT2002 contains this document and the METECC paper 5 in the postscript form Documentation for asymp SAPT can be found in that package in the directory asymp_SAPT doc e examples input and output files for a set of systems and a variety of integral SCF packages p p P y y g P g This is a good source of templates for your runs 6 SAPT installations at a glance Table 1 presents a summary of hardware configurations compilers and integral SCF packages with which SAPT has been tested This list is meant to be used as a guide only Table 1 Grid of systems and front end programs with which SAP T2002 has been tested machine ATMOL1024 GAMESS US CADPAC GAUSSIAN98 SGI OnK Ok although AT Ok Ok Ok MOL properties have some problems Linux and
18. extensively tested while other targets may require some additional customization to make GAMESS run These additional changes are independent of SAPT2002 related portions of runGAMESS and if needed can be introduced with the help of the standard GAMESS documentation If you rather prefer your own GAMESS script instead of runGAMESS you can easily adapt it for use with SAP T2002 by following these steps e Copy your script into the SAPT2002 bin directory In the SAPT script change the name of runGAMESS to that of your own script e The SAPT script communicates with runGAMESS or your custom made script through the syntax of the type runGAMESS JOB VERNO NNODES SCR PUNCHDIR GMSPATH where JOB is the name of the input file like xxx inp give only the xxx part VERNO is the version number of the executable usually the name of the executable is something like gamess VERNO x NNODES is the number of compute processes to be run only 1 can be used with sequential SAPT2002 and that s what the SAPT script is requesting SCR is the scratch directory for GAMESS PUNCHDIR is the punch directory for GAMESS GMSPATH is the path to GAMESS executable All the parameters in the invocation of runGAMESS are set automatically in the SAPT script upon compilation of SAPT2002 or at run time Your custom made replacement of runGAMESS 18 should recognize these command line parameters instead of having them
19. files are created by setting the charge to zero on the proper site For example in the case of monomer A the charges on site B should be set to zero The perturbation program should produce the results given below in Appendix C These results can be found in a Summary Table at the end of an output HF2_DCBS the HF basis set 4s2p1d 2s1p is taken from Ref 17 and a 2s1p set of midbond functions is added Needs about 1 Mword of memory and takes 2 3 minutes to complete In GAMESS input files the option ISPHER 1 is used so that the results of this test performed with GAMESS should agree with those from an ATMOL1024 run HF2_MCBS the MC BS version of the above monomer basis set files HF2MA and HF2MB obtained be removing the d and p orbitals of F and H respectively of the ghost molecule In the GAMESS version of this test the tags technique is used to enforce MC BS whereas in the ATMOL1024 version the basis functions are arranged in blocks pol A isoA mid isoB polB as described in Sec 9 1 2 As in the DC BS variant the space spanned by the basis functions is always restricted to spherical Gaussians even in GAMESS version ArHF_DCBS the basis set 8s5p2d1 f1g 6s3p2d1 f 3s2p1d has been taken from Ref 23 No midbond functions are present here Will need about 5 Mwords of memory and about 1 hour to complete on an Origin2000 platform ArHF_MCBS an MC BS version of the above Monomer basis sets in files ArHF
20. for close configurations While providing an accurate estimate of the required disk space is not possible some guidance can be obtained by considering the upper limits on sizes of different scratch files involved and their scaling with the system and basis sizes With the dimension of the atomic basis DCTBS equal to n the size of the raw integral file produced by an SCF run scales as n 8 This should be multiplied by 12 to 16 bytes each integral is represented by a 8 byte real number plus 4 to 8 bytes for index storage to give an upper bound in bytes to the file size In practice with usual integral thresholds this maximum size is often reduced by about 50 In the transformation step of the calculation the atomic integral file has to coexist with files produced by the transformation it is deleted after the tran program completes During the most demanding four virtual transformations performed in the beginning the upper bound on the disk space becomes roughly 3n 8 v n 4 v 8 x 13 bytes Once the four virtual transformations are completed the files including raw integrals will take at most about n4 8 v4 4 x 13 bytes which will have to coexist with new incoming integrals being generated subsequently At the end of typical transformation for a dimer consisting of identical monomers the disk space taken up by the raw and transformed integrals will scale approximately as 2 504 803v 807v 2 50u 0 250 which shoul
21. g symmetry and higher This is necessary if CADPAC is used to obtain integrals b The large exponents particularly of high symmetries can generally be removed The criterion for this removal is best found by trial and error and by monitoring the con straint conditions We have found useful values of used in the pruning process to be between 0 3 and 0 5 This procedure typically results in an auxiliary basis Y that is 2 to 3 times larger than the basis used to obtain molecular orbitals and eigenvalues While the auxiliary basis for a molecule should be centered on sites between pairs of atoms in addition to atomic sites it is our experience that for sufficiently good auxiliary bases atomic centers are adequate 92
22. hardcoded as it is usually the case with the standard rungms e In your script after the SCF calculation is done but before file cleanup some GAMESS files should be saved with appropriate names SCR JOB FO5 as SCR JOB INP SCR JOB FO8 as SCR inttw data and SCR JOB F10 as SCR JOB DAF where SCR denotes GAMESS scratch directory and JOB is a script variable which will be set by the SAPT script on each call to GAMESS 8 4 4 Interface The sources of GAMESS SAPT2002 interface are located in the SAPT2002 misc gamint subdirectory The interface consists of the Fortran program gamsintf f which extracts one electron integrals and SCF vectors from the dictionary file of GAMESS and two simple awk scripts gms_awk1 and gms_awk2 which scan the GAMESS standard output for the number of basis functions occupied orbitals and system geometry During the integral SCF calculation the standard output from GAMESS is first redirected to a file ooo which is appended to the overall output from the SAPT script after the SCF calculation finishes Output from the interface program gamsintf where some messages from the GAMESS output are repeated has been redirected to ino files to shorten the main output from the SAPT run 8 5 Hondo 8 The SAPT 4 index transformation program expects the integrals in the format that Hondo 8 uses for an SCF only run If post SCF calculations are requested Hondo 8 switches to a differ
23. in V 17 At intermonomer separations R large enough for the exchange effects to be negligible the SAPT results become identical to those of the regular Rayleigh Schr dinger perturbation the ory The calculation of the interaction energies in this region can be substantially simplified by neglecting the overlap effects and expanding V in the multipole series The long range part of the interaction energy becomes then expressed as a power series in R with coefficients that can be obtained using only monomer properties viz multipole moments and polarizabilities These monomer properties can be calculated ab initio at the correlation level consistent with finite R SAPT calculations 18 19 using the monomer parts of the basis set and the POLCOR suite of codes developed by Wormer and Hettema 12 and distributed as a part of the package asymp_SAPT 3 Downloading SAPT2002 The SAPT20020 distribution the parallel version psapt2K2 the asymp_SAPT asymptotic package and theATMOL1024 SCF code can be obtained from the web page http www physics udel edu szalewic SAPT SAPT html All these codes are distributed free of charge but we require users to sign a license agreement which can be downloaded from this web site and mailed or faxed to us as described there We will then email to the interested party the password needed to complete the download The users who download the aaymp_SAPT and ATMOL1024 modules will be also asked to notify t
24. keyword be name Then as the script is running it will look for the nameP data file which contains the input data to the programs tran ccsdt and sapt Similarly the SAPT script will look for input files to the integral SCF parts of a calculation starting with name The number and full names of such files depend on the type of basis set used in calculations and on the choice of the integral SCF code For all SCF front ends except GAMESS the keyword opt2 can be skipped and opt1 is op tional Using the string scfcp for opt1 will request in addition to the standard SAPT calculation also the CP corrected supermolecular SCF interaction energy in the dimer centered basis set If such a calculation is not required leave opt1 blank or better yet use noscfcp instead Using the keyword gototran as opti will result in restarting a SAPT run from the transformation step i e from the program tran Both parameters opti and opt2 are required when GAMESS is used as the SCF program opt1 can assume one of the values listed above but noscfcp must now be used instead of blank while opt2 must be the full path of the scratch directory in which the whole calculation is taking place The output from all programs executed by SAPT is written to a file output file this name can be set by the user to an arbitrary string usually connected with the system being computed and its geometry The last two elements in the command line given above are Unix ksh constructs
25. kua f rtla de kua f rt2a m kub f kllub Kii B component kub f rt3b Terms of E ES kub f rt4b Monomer B kub f rt5b de kub f rtlb kub f rt2b id k2fu k2f1 K3 component k2fu k2fa 2 k2fu k2f2 7 k2fu k2fb 2 k2fu jk2f1 Alternative Ky k2fu jk2fa k2fu jk2f2 k2fu jk2fb 2 k2fu k2u X k2fu jk2u k2fu rtau p 80 Table 6 Comments on selected subroutines SAPT continued 4 Module Subroutine Comments el4f el4 EG resp driver el4 f mp4 MPA energy el4 f tmp4 Triples contribution to MP4 el4 f el4t Pis mem partitioning el4 f el4a Monomer A el4 f el4b Monomer B el4 f sel4pl Sorting for above el4 f mlam Mem partitioning for routine el4 f lambda Calculate A matrix el4 f rho4 Mem partitioning for o and v routines following el4 f rhodo Da term el4 f rho4v Dr term x14 x14 Mem partitioning for Ea routines following x14 x14a Pieces of Po x14 x14b a x14 x14c i x14 x14d i x14 x14e ds x14 x14f x t14 f trho4o l t14 f trho4v 2 t14 f t14e g t14 f t14f e2 f e02 MBPT2 calculation e2 f e200d EGO driver e2 f eind Ee driver e2 f eindab Calculate above e2 f e21 BEV driver Calls next two routines e2 f e210 ase e2 f e201 TER e2 f e211d0 E e2 f srt211 Sorting routine for above e2 f e21la Monomer A e2 f e211b Monomer B 81 Table 6 Comments on selected subroutines SAPT continued 5 Module Subroutine
26. scheme to reference the needed input files For example let the keyword be name Then as the script is running it will look for the nameP data file which contains the input data to the programs ptran pcc and psapt Similarly the pSAPT 02k script will look for GAMESS input files to the integral SCF parts of a calculation starting with name The number and full names of such files depend on the type of basis set used in calculations See Sec 9 for details on how to prepare GAMESS input files for different types of runs Using the string scfcp for opt1 will request in addition to the standard SAPT calculation also the CP corrected supermolecular SCF interaction energy in the dimer centered basis set If such a calculation is not required use noscfcp instead Using the keyword gototran as opt1 will result in restarting a pSAPT o2k run from the transformation step i e from the program ptran The parameter nproc is the number of processors to launch the job on The parameter opt2 must be the full path of the scratch directory in which the whole calculation is taking place The output from all programs executed by pSAPT 02k is written to a file output file located in the scratch directory this name can be set by the user to an arbitrary string usually connected with the system being considered and its geometry The last two elements in the command line given above are Unix ksh constructs which indicate that standard error messages will be writte
27. the number of occupied orbitals of the bigger monomer For the pcc and psapt parts memory requirements can be roughly estimated as 3024 words on each processor where v is the number of virtual orbitals for the larger monomer More precise calculation of the memory required for a psapt2K2 run can be done using the program memcalc built automatically during installation In order to use this program prepare the regular nameP data file with the first title line containing in this order the total number of DC BS basis functions the total number of functions for monomer A will be different than the previous one in a MC BS type run the number of occupied orbitals for monomer A and then the same information for monomer B followed by the number of processors Then run the program by typing memcalc lt nameP data gt memcalc out The file memcalc out will contain detailed information about memory requirements of different parts of the code The variables MEMTRAN from namelist TRN and MEMSAPT from namelist INPUTCOR should then be adjusted accordingly The memory needed to run the pcc program is calculated there explicitly so that no separate namelist variable is needed The memory requirements of the SCF programs are much smaller than those of psapt2K2 For specific information consult the manuals distributed with these programs An estimate of the total disk space requirement can be obtained as presented in Sec 9 5 for a sequential pr
28. the output from each of the previous steps The pertur bation program uses some temporary files and prints to output file the values of the corrections as well as time needed to compute them Near the end of the output file is a table collecting all the corrections expressed in various energy units Each of the direct access files after the integral SCF step have a logical record length of 2728 For each integral or amplitude 5 bytes one 8 bytes are reserved for the packed indices and the value respectively At the beginning of each record there is also one 1 4 for pointing to the previous 39 record using the so called back chaining methodology On most computers computers a single record is 32768 bytes in length This value is controlled by the variable lorec in all programs If the user wishes to change this also note calls to the routine daopen which sets the physical size of the record 40 11 Performance of SAPT2002 SAPT2002 as any molecular structure program requires significant computational resources To help user with estimating resources needed for a run times of several calculations are listed in Table 2 whereas the memory and disk resources needed are given in Table 3 At the moment of this writing the tables are taken unchanged from the SAPT96 manual Timings of SAPT2002 are significantly better Please consult Sec 12 for more up to date estimates Table 2 Timings in seconds on RS6000 950 All calcul
29. the variable GAMESS in Compal1 is to pass the path and name of GAMESS executable to the SAPT execution script No access is needed to any GAMESS files at the compilation time Thus compilation will proceed even if GAMESS is not installed on your system beforehand e CADPAC This package does not need any interface programs since the files created by it can be read directly by SAPT2002 codes Also SAPT2002 does not need acess to any CADPAC libraries so that the compilation will proceed even if CADPAC is not installed on your system e ACES This interface has not been tested recently but should work e ALCHEMY HONDO MICROMOL These packages have not been in use for a long long time and the interfaces to them may be not working Should you choose one of these we would be interested in knowing if it works It is also possible to build the SAPT2002 package for use with the older version of ATMOL such a version limited to 255 basis functions is included in the asymp SAPT distribution This can be accomplished by setting the variable ATMOL in Compall equal to the path of the main ATMOL directory change the line ATMOL NO and removing or renaming the directory SAPT2002 atmo11024 if present The ATMOL package has to be compiled prior to the compilation of SAPT2002 SAPT2002 cannot be interfaced with ATMOL1024 and ATMOL simultaneously 3 PLATFORM Two variables need to be set e TARGET is the system on which SAPT2002 will be compiled
30. to executables and should run properly on any installation without changes If the paths need to be changed for some reasons the script SAPT should be edited and the variable MAIN_SAPT DIR and the SCF_HOME DIRECTORIES changed to reflect user s directory structure if GAMESS is used it concerns also additional directories relevant for this program These variables are set about 500 lines down in the script 20 Also note that the large core memory requested typically by the SAPT2002 programs re quires on some systems the use of the ulimit command to change the default user resources This command built into the SAPT script is currently commented out but it may be reactivated and adjusted as needed The SAPT script is written in ksh although on Linux platforms some of which are not equipped in ksh it is actually executed under bash We recommend that invocations of SAPT are also executed from within ksh or bash although running from within csh or tcsh is also possible A SAPT2002 calculation is launched by typing SAPT with appropriate options Typing SAPT without any options will produce a brief description of the necessary input A typical run statement might be something like in Unix ksh SAPT jobname opti opt2 gt output file 2 gt 1 The keyword jobname has to be the same as the beginning of the name of the input files for the system considered we use a naming scheme to reference the needed input files For example let the
31. tr3 1 6 w Third step out of core trnnw f tr4 1 9 a b w Forth step out of core 74 Table 5 List of subroutines cc Module Subroutine Comments mcc f mcecsd MAIN DRIVER mcc f ienter Start timer mcc f iexit Stop timer mcc f report Write out timing reports ccio f getamp Get amplitudes from disk ccio f putamp Put amplitudes to disk ccio f azero Put dummy amplitude record ccio f moovv Desymmetrize lt oo vv gt array ccio f moooo Desymmetrize lt oo oo gt array ccio f mooov Desymmetrize lt oo ov gt array ccio f imove Move two electron integrals ccio f icopy Copy sorted 2el integrals ccio f wamp Write intermediate amplitudes ccio f alarm Abnormal termination ccio f readbf Read 2el integrals not vvvv ccio f getbuf Read one packet of vvvv ints ccio f getbuf2 As previous transposed storage ccio f readen Read orbital energies ccio f wrtbu Write buffer of integrals ccio f lrecl Calculation for mem partitioning ccio f rbfaa Read integrals with energy denoms ccio f save Kick out small values from int list ccio f rwrite Write amplitude onto disk ccml f xdata Zero some arrays ccm2 f rinfo Restore info from disk ccm2 f rread Read info record from disk ccm2 f show Printing of selected arrays ccm2 f fdump Save info record back to disk ccm2 f fuwik Dump info table for SAPT program ccm2 f result Print final energies mem f ccmem Memory partitioning data f zdata G
32. with respect to the operator W i e PONS E e ne ae PERO A Be 7 elst ind resp exch ind resp disp exch disp This level is recommended for calculations for very large systems when a higher level of theory would be too time consuming One can expect that this level of theory may introduce about 20 30 errors with respect to the exact interaction energies but such an accuracy can be acceptable for large systems Also the errors due to the basis set truncation will most likely be of the same order of magnitude For increased accuracy we recommend to add the ERE resp term The SAPTx variable takes precedence over the settings of individual corrections in this sense that a correction included in a given level will be computed even if it is is explicitly set to false However a correction not included will be computed if it is explicitly set to true The namelist includes also variables LEVELn which however turned out to be not very useful and are rarely applied To ignore the LEVELn settings either omit these variable from the namelist or set them to LEVEL1 0 LEVEL2 0 LEVEL3 0 Each of the three LEVELn n 1 2 3 vari ables can be set to either 0 1 2 or 3 Using the value of 0 the default is equivalent to no action The value of 1 indicates that the nonresponse unrelaxed corrections should be calculated in general nonresponse versions are not recommended The value of 2 tells the program that the response version of the co
33. 0 172 3426 tE 22 _ ind 1 081861739 0 67887906 237 4412 tE 22 _ ex ind 0 945961757 0 59360046 207 6146 E 20 _ disp 1 195076005 0 74992214 262 2889 E 21 _ disp 0 203325820 0 12758899 44 6249 E 22 _ disp 0 473822197 0 29732817 103 9920 eps 2 _ disp k 0 270496377 0 16973918 59 3671 E 2 _ disp k 0 924579628 0 58018296 202 9218 E 20 _ exch disp 0 069731392 0 04375715 15 3043 SAPT_ corr 0 075995167 0 04768773 16 6790 SAPT_ corr resp 0 009656676 0 00605966 2 1194 TOTAL hybrid SCF SAPT_ corr 3 377133735 2 11918519 741 1952 SCF SAPT_ corr resp 3 291481892 2 06543780 722 3968 Conversion Factors 1 0 627 51 219474 63 denotes ESTIMATED corrections a SAPT_ SCF E 10 _ elst E 10 _fexch E 20 _ ind E 20 _ exch ind b SAPT_ SCF resp E 10 _felst E 10 _fexch E 20 _ ind resp E 20 _ exch ind resp e Gaussian92 file g92 inp INT int RWF rwf HP CCSD FULL GEN TEST INT NOSYMM MASSAGE UNITS AU ExtraLinks 1316 BERYLLIUM DIMER W 2S 1P BASIS SET o 1 BEL 0 0 0 0 0 0 BE2 0 0 0 0 7 0 BE 0 s 11 00 0 198210 1 0 s 11 00 1 767558 1 0 P 1 1 00 0 201 1 0 OK 20 0 0 D Appendix Capabilities of pcksdisp program This Appendix contains a more detailed description of the program pcksdisp In the pEDI X scripts this program is used to calculate the CHF static and dynamic susceptibility functions of the monomer
34. 98210 S Ber2 0 1 0 1 767558 P Ber2 0 1 0 0 201 END SAFETY 0 MAINFILE MT3 DUMPFILE ED3 ACCURACY 22 24 16 MULTIPOLE O BYPASS PROPERTY IBLOCK 1 ENTER 1 SEND e ATMOL1024 file BER scfinp SCF 10 4 O 1 ED3 TITLE BER test MFILE MT3 1 0 FPRINT NVCT NEIG NFTE NITE NPOP START DIIS 10 1 0 AUTO 0 0000001 MAXCYC 60 ACCURACY 1 9 ENTER 1 83 e ATMOL1024 file BERA intinp TITLE BER2 test run GEOMETRY 0 0 0 0 0 0 4 0 Beri 0 0 7 0 0 0 0 0 Ber2 END GTOS S Berl O 1 0 0 198210 S Berl O 1 0 1 767558 P Beri 0 1 0 0 201 S Ber2 0 1 0 0 198210 S Ber2 0 1 0 1 767558 P Ber2 0 1 0 0 201 END SAFETY 0 MAINFILE MT3 DUMPFILE ED3 ACCURACY 22 24 16 MULTIPOLE 0O BYPASS TWO BYPASS PROPERTY IBLOCK 1 ENTER 1 e ATMOL1024 file BERA scfinp SCF 10 2 0 1 ED3 TITLE BER test MFILE MT3 1 0 FPRINT NVCT NEIG NFTE NITE NPOP START DIIS 10 1 0 AUTO 0 0000001 MAXCYC 60 ACCURACY 1 9 ENTER 1 e perturbation file BERP data 84 Ber 2 run in 3s1p basis set For testing only amp TRN ISITALCH F ISITG88 F ISITG90 F ISITHNDO F ISITMICR F ISITANEW T OUT F TOLER 15 DIMER T MEMTRAN 10000 amp END amp CCINP CCPRINT F VCRIT 1 0D 10 TOLITER 1 0D 5 amp END amp INPUTCOR SAPT T E12 T E13PL T E2IND T CONVAMP T PRINT F TIMEREP F MEMSAPT 100000 amp END e GAMESS file BER inp CONTRL SCFTYP RHF RUNTYP ENERGY COORD UNIQUE UNITS BOHR NPRINT 5 NOSYM 1 INTTYP HONDO ITOL 30
35. Description Be 2 HF 2 Ar HF M 10 M 40 M 95 inta data SCF 2el file 0 01 1 81 29 25 final2e Transformed 2el 2 06 8 0 58 95 interma CCA amplitudes 9 21 31 0 15 07 intermb CCB amplitudes 9 21 32 4 5 57 ccsort Intermediate CC file 0 52 3 14 27 49 tmp Intermediate SAPT file 2 1 15 5 29 25 a Only the largest intermediate files are shown here Other files which are created but do not use large amounts of disk space are vecta data vectb data infoa data infob data onela data onelb data site data file5 dat and output files depending on the SCF program bM is the size of the basis CONVAMP T for Be 2 and HF 2 calculations and CONVAMP F for Ar HF calculations 12 Tests and example input and output files A set of test and example runs are provided in the distribution of SAPT2002 These include several very small cases which should finish in seconds or minutes and which can be used to check the correctness of the SAPT2002 installation In each case both the complete set of input files and the output files at least from one platform are provided With the large number of front end SCF programs interfaced with SAPT2002 and with large number of hardware platforms on which it can be run it is not practical to provide examples for all possible cases The mix of combination of various factors chosen should be sufficient to establish the correctness of installation and help in preparation of user s production runs In some cases th
36. HHEHHHHEEHHEHHHHAAEHHHAHEHAHEHHEE HERRERA E RR RH ES Create all the needed PROC files based on calcnodes PTRAN SAPTDIR ptran PCC SAPTDIR pec PSAPT SAPTDIR psapt INT SAPTDIR int SORT SAPTDIR sort EVEN SAPTDIR even FRSTNODE head 1 calcnodes echo FRSTNODE O gt PROC echo FRSTNODE O gt PROCc echo FRSTNODE O gt PROCe echo FRSTNODE O gt PROCi echo FRSTNODE O gt PROCs echo FRSTNODE O gt PROCso for i in tail 2 calcnodes do echo i 1 PTRAN gt gt PROC echo i 1 PCC gt gt PROCc echo i 1 EVEN gt gt PROCe 56 echo i 1 INT gt gt PROCi echo i 1 PSAPT gt gt PROCs echo i 1 SORT gt gt PROCso done HHHHHHHHHHH PROCs file ready run the job now HHHHHHHHHHHHHHHHHHHHHHH JOB 1 job name copy all SAPT input files and the PROC file onto the scratch dir on every node specified in PROC file for i in awk print 1 PROC do echo Copying input to i rcp inp i SCRDIR rcp JOB P data i SCRDIR rcp PROC i SCRDIR rcp PROCs i SCRDIR rcp PROCi i SCRDIR rcp PROCc i SCRDIR rcp PROCso i SCRDIR rcp PROCe i SCRDIR done Set the number of nodes NPROC wc PROC awk print 1 Determine the master node the first one in PROC MASTER head 1 PROC awk print 1 echo Submitting job on MASTER Submit the job on master node Make sure that master knows what 57 LOGNAME is me
37. Jeziorski and J Cizek Int J Quantum Chem 32 149 1987 14 R Moszynski B Jeziorski A Ratkiewicz and S Rybak J Chem Phys 99 8856 1993 71 15 16 17 18 19 20 21 22 23 24 25 26 T Korona R Moszynski and B Jeziorski Mol Phys 100 1723 2002 H L Williams K Szalewicz B Jeziorski and R Moszynski J Chem Phys 103 4586 1995 S Rybak B Jeziorski and K Szalewicz J Chem Phys 95 6576 1991 E M Mas K Szalewicz R Bukowski and B Jeziorski J Chem Phys 107 4207 1997 R Bukowski J Sadlej B Jeziorski P Jankowski K Szalewicz S A Kucharski H L Williams and B M Rice J Chem Phys 110 3785 1999 H L Williams and C F Chabalowski J Phys Chem A 105 646 2001 A J Misquitta and K Szalewicz Chem Phys Lett 357 301 2002 H L Williams E M Mas K Szalewicz B Jeziorski J Chem Phys 103 7374 1995 V F Lotrich H L Williams K Szalewicz B Jeziorski R Moszynski P E S Wormer and A van der Avoird J Chem Phys 103 6076 1995 B I Dunlap Phys Chem Chem Phys 2 2113 2000 H L Wiliams K Szalewicz R Moszynski and B Jeziorski J Chem Phys 103 4586 1995 A J Misquitta PhD Thesis University of Delaware 2004 72 A Appendix Integral SCF interfacing A the SAPT group of codes can be interfaced with virtually any integral SCF program A short description of the eleme
38. LSE The dimer type transformation is chosen for DCBS DCTBS cal culations and the monomer type for MCTBS calculations If monomer type of transformation is set several other options become available These are BLKMB BASIS TAGS and SPHG variables connected with the tags system The use of these variables was described in Sec 9 1 2 Also a description is provided in comments of the subroutine mkoffset of the module trans F in subdirectory SAPT2002 tran If the SCF program used is ATMOL1024 and if the two electron integrals produced by this program are stored in more than one file the number of such files has to be given in TRN as the variable NMFILES For example NMFILES 3 will tell the transformation to look for ATMOL1024 integrals in the files MT3 MT4 and MT5 The most likely use of this option is on Linux platforms with the g77 compiler which usually does not support files larger than 2 Gbytes and so the integrals have to distributed over several smaller files This restriction is or will probably be lifted in the upcoming versions of Linux g77 Finally the MEMTRAN variable can be used to dynamically allocate memory for the transforma tion section tran of SAPT2002 As a default the memory for the tran program is set to 40 M words 320 Mbytes If possible the memory should be set large enough so that the transformation program uses the faster in core path The amount of memory needed for the in core path can be calculat
39. MA x and ArHFMB x obtained by deleting the polarization functions d and f on F and Ar and p and d on H of the ghost molecule The tags technique used for MC BS for both GAMESS and ATMOL1024 examples CO2D_MCBS an MC BS run for CO dimer in the 200 term basis of Ref 19 MC BS size 149 This example is larger than the previous ones it requires about 40 Mwords of memory and takes bout 17 hours to complete on our SunFire 6800 machine Some additional examples are also included namely e GAMESS HF NH3 MCBS an example illustrating the use of the MCTBS technique with GAMESS with the tags and basis options as described in Sec 9 1 2 About 40 minutes on Ori gin2000 43 e ATMOL1024 ArH20 MCBS an example of using the RunlotATMOL script as described in Sec 9 4 Consists of two jobs each taking slightly more than 1 hour on an Origin2000 machine In addition to the tests examples described above a set of older examples taken from the SAPT96 distribution is provided in the directory SAPT2002 examples old_SAPT96 These should also work sometimes with minor modifications of the input files e g remember to replace ISITATM with ISITANEW in the P data files when running the old examples with ATMOL1024 12 2 Running tests jobs The simplest way to run an example is to copy all files from the corresponding directory e g SAPT2002 examples ATMOL1024 BER to a scratch directory then cd to this scrat
40. SAPT2002 An Ab Initio Program for Many Body Symmetry Adapted Perturbation Theory Calculations of Intermolecular Interaction Energies Sequential and parallel versions User s Guide Last updated May 25 2004 Robert Bukowski Wojciech Cencek Piotr Jankowski Bogumit Jeziorski Malgorzata Jeziorska Stanistaw A Kucharski Alston J Misquitta Robert Moszynski Konrad Patkowski Stanistaw Rybak Krzysztof Szalewicz Hayes L Williams and Paul E S Wormer Department of Physics and Astronomy University of Delaware Newark Delaware 19716 Department of Chemistry University of Warsaw ul Pasteura 1 02 093 Warsaw Poland May 26 2004 Contents 1 Introduction 2 Short overview of theory 3 Downloading SAPT2002 4 Packages included in the distribution 5 Structure of SAPT2002 directory 6 SAPT installations at a glance 7 Installing SAPT2002 7 1 Compall installation script s oo e 7 2 Compall_asymp installation script 2 2 0 0 0 000 000 0220 0008 7 3 Testing SAPT2002 installation 0 0 0 000000000002 eee 8 Using SAPT2002 with different front end packages 81 ATMOLTO24 ic suey A ee oR e ke d or a a de ii de aussie he 8 2 CADPAG tau ode ee A OVA RRS YEE Ee es 8 9 E AUSSTAN Ss he cece dy A Mute gous Se a ts Malte e os Sid GAMESS oii SE Ae SB A dee dee A Bota ds Matis ees A 8 4 1 8 4 2 8 4 3 8 4 4 Optional modification of GAMESS source Required and recomme
41. Solver IMSL chf f ludatn Decompose matrix chf f luelmn Forward and backward substitutions el f first EGO and EEN driver el f inv Calculate inverse matrix el f pmat Construct P matrix 77 Table 6 Comments on selected subroutines SAPT continued 1 Module Subroutine Comments el2 f srt12 Bay and BOSD driver routine el2 f sort12 Presort of 2el integrals el2 f e120pl pO driver e12 f e102pl EL driver e122 f e122pl ES2 driver e122 sel22 Sorting routine for ERD e122 tabvv Pieces of E e122 tavv E e122 tbvv X e122 svv a e122 taboo ie e122 taoo ki el22 tboo ii e122 Soo 2 e122 tabxx ds el22 svo je el22 sov Ed el22 tdd dd el22 sdd x e122 txx el22 tdv E e122 tvd i e122 tdo i e122 tod a el3 f e13 EQ driver e13 f sel3pl Sorting routine for above el3 f stra Calculate singles mem partitioning el3 f sta Calculate singles el3 f dtra Calculate double commutator mem partioning el3 f dtal One part of commutator el3 f dta3 Another part el3 f strb As stra only monomer b el3 f stb As sta only monomer b el3 f dtrb As dtra only monomer b el3 f dtb1 As dtal only monomer b el3 f dtb3 As dta3 only monomer b 78 Table 6 Comments on selected subroutines SAPT continued 2 Module Subroutine Comments x13 f rhoa Driver routine for ring ladder diagrams for monomer A x13 f frho3a Pieces of aad
42. T in runGAMESS is set auto matically by the compall script so no additional action is needed here e A separate version of the runGAMESS script called runGMS mpich has been created for sam son our Beowulf cluster here at UD The GAMESS submission instruction present in this script were causing syntax errors on other platforms hence the need to create a separate script for mpich implementation of MPI runGMS mpich will be called automatically from within the pSAPT mpich driver script so the user does not have to worry about these details e A separate version of the runGAMESS script called runGMS mpich maui has been created for huinalu a Beowulf cluster at Maui supercomputer center runGMS mpich maui differs from runGMS mpich slightly in details of how the HOSTLIST is constructed and by the usage of ssh instead of rsh for interhost communication runGMS mpich maui will be called automatically from within the pSAPT mpich maui and pSAPT mpich maui sep driver scripts so the user does not have to worry about these details e Should you prefer to use your own script as a driver for GAMESS adapt it for psapt2K2 following the instructions of Sec 8 with one exception the integral file generated by process 0 JOB FO8 has to be renamed into inta 0 while the integral files from the other pro cesses JOB F08 X into inta X This can be accomplished in C shell using the following syntax mv JOB FO8 inta 0 set m 1 fo
43. This can be one of all lower case sgi ibm32 ibm64 alpha g77 pgf77 or sunf90 sgi stands 12 for the Silicon Graphics ORIGIN or POWER CHALLENGE series computers with the MIPSPRO 7 3 or higher compiler ibm32 for the IBM RS6000 or SP machines on 64 bit IBM platforms ibm64 can be also tried but sometimes it causes problems with dynamic memory allocation alpha for the formerly DEC ALPHA platform g77 and pgf77 for a LINUX box with the G77 or PGF77 compilers respectively sunf90 for the Sun SPARC machine equipped with the FORTRAN90 compiler e BLAS points to the Basic Linear Algebra Subroutine library that is to be used The BLAS library is installed on most Unix computers On SGI IBM RS6000 and LINUX machines set BLAS lblas On an ALPHA set BLAS 1dxml on IBM SP BLAS lessl and on SPARC BLAS xlic_lib sunperf If you have com piled yourself a self optimizing BLAS library like ATLAS set BLAS L lt Full Path to Library gt latlas 4 64 bit GAMESS if you intend to use GAMESS compiled with a 64 bit integer this happens by default on the ALPHA platform but may also happen on SGI when sgi64 is specified during compilation of GAMESS replace the line GAMSI8 NO with GAMSI8 YES SAPT2002 compiled in this way may not work correctly with other SCF front ends in particular with GAUSSIAN Once all the variable mentioned above are set simply type e C Shell users
44. a version of the suite of codes implementing the ideas discussed above The codes allow the generation of monomer charge densities currently at the SCF MBPT2 and MBPT3 levels with and without orbital relaxation and susceptibility functions currently and the CHF level generation of an auxiliary basis and the fitting of the monomer properties in terms of this basis The charge densities susceptibility functions and SCF vectors are then used as input to a program which calculates the electrostatic induction and dispersion energies for an arbitrary set of dimer geometries Two versions of this code exist one utilizing the exact representation of monomer properties i e in terms of the original AO basis called caldisp_gms and the other working with the fitted monomer properties called caldisp_fit Since the techniques of generating effective auxiliary bases are still under development the first of these methods should be preferred as it ensures the accuracy of the results The subsections below describe the details of the EDI runs 13 7 1 The pEDI scripts Most of the the tasks mentioned above are accomplished with the help of the script pEDI X where X stands for the platform at hand This script works very much like the script pSAPT X used in regular psapt2K2 calculations Thus the SCF runs for the two monomers are performed first followed by the integral transformation the CCSD MBPT and psapt runs A new thing is that the
45. actual psapt2K2 run is started using the driver pSAPT mpich maui sep adapted to make use of the local scratch environment Replacing this driver with pSAPT mpich maui changing the scratch directory to the global one say scratch huinalu bukowski and replacing the loop structure with scp by a set of simple cp commands would result in a psapt2K2 calculation utilizing the common scratch directory instead of the local ones Since psapt2K2 jobs are crucially dependent on the efficiency of I O opera tions the local scratch option should be preferred as it allows to avoid competition for bandwidth between the processes 13 5 Input files The input files for GAMESS and the SAPT suite of codes are constructed in essentially the same way as in the case of the sequential version of the program SAPT2002 as described in detail in Sec 9 The only difference is that options SAPTO SAPT2 and SAPT are currently not supported in namelist INPUTCOR The theory levels corresponding to these options may of course be recovered by requesting the appropriate SAPT corrections individually 62 13 6 Memory and disk requirements Memory requirements of psapt2K2 can be estimated based on the total number of basis functions the numbers of occupied and virtual orbitals and the number of processors involved The trans formation code ptran requires slightly more than on3 P 8 byte words on each of the P processors where n is the dimension of the basis set and o is
46. addition to the ones mentioned above The variable PRINT is used to print more information about intermediate results and memory partitioning Finally the variable MEMSAPT can be used to dynamically allocate memory for per turbation theory section sapt of SAPT2002 As a default the memory for the sapt program is set to 20 Mwords The amount of memory required by the sapt program may be computed using the memcalc utility as described in Sec 9 5 9 3 How to read the output The values of all the calculated SAPT corrections are summarized at the end of the output file in the section entitled Summary Table An example of a Summary Table can be found in Ap pendix C The first part of the table lists the numbers of orbitals Cartesian geometry of the dimer and SCF energies of the monomers and the dimer if computed obtained in the full DCtTBS What follows is a set of low order SAPT corrections which when summed up ap proximate the supermolecular SCF interaction energy also printed as E HF _ int if the key word scfcp was used on submission The quantity SAPT SCF_ resp is equal to the sum of E 10 _felst E 10 _ exch E 20 _find resp and E 20 _fex ind r i e the first 4 terms on the rhs of Eq 3 The quantity delta HF _ int r represents the last term in this equation If the non responsed induction correction E 20 _ ind has been computed the corresponding approximation to the SCF interaction energy SAPT SCF and
47. are updated by inserting the current paths to executables 13 2 1 compall installation script The following environment variables must be adjusted by the user in the top section of the compa11 script 1 Execution shell Change the first line of the script to one of the following e bin bash The BASH shell on a LINUX box or e bin ksh The Korn shell on all other platforms 2 TARGET the machine the program is being compiled on Choose one from 02k will work for O3K also sp will work for SP3 and SP4 or mpich on Beowulf clusters 3 BLAS if TARGET mpich specify how you want the BLAS library to be linked usually this is just 1blas but Beowulf configurations differ so beware For other TARGETs ignore this option 4 GAMESS path containing the GAMESS exec you will be using 5 VERNO GAMESS version number compall assumes that the name of GAMESS executable is gamess VERNO x 6 TRGT_GMS if TARGET 02k specify how GAMESS should be run pick from sockets and sgi mpi consistently with your GAMESS installation For other TARGETs this will be set automatically 7 POE_COM if TARGET sp specify which poe command poe grd poe or sge mpirun will be used to run parallel codes Usually an MPI code on an SP machine is launched by the Load Leveler queuing system using the poe command At ARL a wrapper sge_mpirun is 48 used instead which works with the GRD queuing system or grid engine
48. at SAPT has been tested with Whereas extensive tests of SAPT have been performed there may appear unforeseen difficulties with the installation and running of the codes As SAPT2002 and psapt2K are products of a research project no resources are available to provide support for users The authors of the code will try to provide a limited help within the restrictions of their schedules 2 Short overview of theory In SAPT the total Hamiltonian for the dimer is partitioned as H F W V where F F4 F is the sum of the Fock operators for monomers A and B V is the intermolecular interaction operator and W W4 W is the sum of the Mgller Plesset fluctuation operators The latter operators are defined as Wx Hx Fx where Hx is the total Hamiltonian of monomer X The interaction energy Eint is expanded as a perturbative series co oO 4 Fig gt gt ERP BE 1 n 1 j 0 with the indices n and 7 denoting the orders in the operators V and W respectively The polar nj pol are identical to the corrections obtained in a regular Rayleigh Schr dinger ization energies E perturbation theory The exchange corrections E n exe Arise from the use of a global antisymmetrizer to force the correct permutational symmetry of the dimer wave function in each order hence the name symmetry adaptation The polarization corrections of the first order in V EC describe the classical electrostatic pol gt interaction and ar
49. ated by ATMOL1024 exceeds this size it has to be split into several pieces each 2 Gbytes or less For example if the integrals are anticipated to take 5 Gbytes of disk space one should have them distributed over at least three files This can be done by specifying MAINFILE MT3 MT4 MT5 MAXBLOCK 499999 in the intinp files somewhere below the basis set specification but before the ENTER directive The first of the lines above means that the files called MT3 MT4 MT5 will be used to store the integrals and that the size of each will not exceed MAXBLOCK 511 8 bytes which in this case amounts to somewhat less than 2 Gbytes the number 511 comes from some internal data structures of ATMOL1024 Now we have to tell the transformation module of SAPT2002 how many files ATMOL1024 produced by including NMFILES 3 in the TRN namelist in the P data input file see Secs 9 and 9 2 for description of this file Of course the number 3 would have to by changed if some other number of MTx files were used ATMOL1024 and SAPT2002 support up to 18 such files MT3 through MT20 8 2 CADPAC First notice that CADPAC can use only Cartesian basis functions Also currently only angular functions up to f are allowed The input file used for CADPAC runs must include the SAPT keyword This keyword makes CADPAC write out to a file the SCF vectors and other information in the format required by the SAPT2002 transformation code tran Thus there is no interface pr
50. ations are performed in the dimer s basis set System Scaling Be a HP Ar HF Basis 10 40 95 Core Size Mbytes SCFA 137 23 23 745 73 SCF 121 22 86 708 64 SCFg 118 23 01 725 03 MBPT44 g MBPTA MBPT4 Transformation N5 7 66 221 10 3152 99 Coupled Cluster A B n N 2 84f 2894 0f 531 38 SAPT Level 1 n N 0 0 11 7 200 95 BE n N4 0 1 26 26 2120 40 Eto Ha nin 0 0 1 42 20 30 EO n N 0 0 6 29 518 09 BO paz n N 0 2 19 73 343 72 EG nN 0 0 3 99 599 05 EG nN 0 0 12 17 1013 73 ES n gt N4 0 2 127 11 6416 43 Only the transformation part of the SAPT codes depends critically on the size of the core The perturbation part shows no speed up if memory is increased above the indicated core size The core shown is of sufficient size but not necessarily minimum size Not needed for the SAPT calculation Should be performed only if supermolecular energies are of interest Only the non response versions are included in the timings the response versions are about the same a converged amplitudes run PScaling with the number of occupied n and virtual N orbitals JThe scaling of the Coupled Cluster program varies depending on the correction to be computed Generally for LEVEL1 corrections the program scales with the calculation of singles amplitudes and for other corrections with the calculation of doubles amplitudes 41 a Table 3 Disk space requirements Mbytes File
51. be reused for B The eigenvalues and eigenvectors from these two runs are saved whereas both one and two electron integrals are discarded The script will next look for an input file nameA to calculate one and two electron integrals for monomer A in the DCTBS equivalent of the MC BS used this basis is identical to the one described in the previous subsection but in some cases the functions have to be ordered in a special way or the proper tag parameters have to be specified in the file nameP data as discussed below No SCF calculations are needed if performed the results will be discarded This step is needed to produce the integrals for the SAPT calculations Next the script will look for a file nameB to calculate one electron integrals only for the monomer B in the DC basis set the two electron integrals need not be calculated since these are identical as for monomer A Again no SCF step is needed Thus if for example ATMOL1024 is used as the integral SCF program the needed input files are nameMA intinp nameMA scfinp nameMB intinp nameMB scfinp nameA intinp nameB intinp and nameP data In the last of these files the variable DIMER in namelist TRN should be set to F or FALSE If MC BS calculations are performed and the supermolecular HF SCF interaction energy is requested the scfcp option is used the script will as in the previous case first look for input files nameMA and nameMB to perform integral SCF runs for
52. ccurs in the SCF input group NCONV 9 e Werecommend using the option ISPHER 1 in the CONTRL input group which forces GAMESS to do SCF calculations in the basis set of spherical Gaussians instead of the default Cartesian ones and thus reduces the risk of linear dependencies Unfortunately although using this option reduces the dimension of the variational space available to the system the atomic integral file produced by GAMESS remains Cartesian and thus its size is not reduced e In the MCTBS type run see Sec 9 for explanation the variable SPHG in the namelist TRN in the P data file see Secs 9 and 9 2for detailed description of this file must be set to F 17 or FALSE even if GAMESS was run with ISPHER 1 This is because of the Cartesian character of the integrals file as mentioned above The variable SPHG which defaults to TRUE i e spherical basis is assumed is only important for MC BS and MCBS runs and has no effect in the DCBS case 8 4 3 runGAMESS script Whereas most other integral SCF packages are invoked in the SAPT script by just executing a given program GAMESS needs its own script SAPT2002 bin runGAMESS called from the SAPT script runGAMESS is a slightly modified version of the standard script rungms distributed with GAMESS As already pointed out in Sec 7 the user must edit this script and supply the appropriate value of the TARGET variable The targets sockets and sgi mpi have been
53. ch directory and submit the job using the submit line described in Sec 9 for example in ksh SAPT BER scfcp gt BER out 2 gt 1 Recall that the string BER is the same as the initial part of the name of all input files If the SAPT2002 bin directory is not in your PATH you may need to supply the full path to the SAPT script To simplify the process of running multiple tests two simple ksh scripts runtstGAMESS and runtstATMOL are provided in the directories examples GAMES and examples ATMOL1024 respectively The scripts execute loops over the subdirectories selected in the for statement running the SAPT script inside these directories and cleaning up after each such run To select the jobs to be executed adjust the for statement in the runtstGAMESS and runtstATMOL1024 The names of output files from the tests can be given an ending see the variable MACHINE which can be use e g to distinguish between the runs performed on different platforms Under Unix the output file can be viewed as the program is run This allows to check how far the program has advanced Note however the Unix first writes the data to fairly large buffers and only when the buffers are filled to the output file It is important to remember about it when debugging the program some info may not appear in the output after a crash although it may come from a successful part of the run SAPT uses instructions flushing buffers in several places but more su
54. ch statements may have to be added for debugging Also for larger runs one should monitor the disk use by just doing 1s 1t or du k in the working directory The memory actually used by the program can be checked by using the top command called prstat or monitor on some systems When the program crashes our practice shows that in most cases it is due to errors in the integral SCF parts of the code Thus make first sure that these stages have finished successfully When there is an error there consecutive stages of the code do start and immediately fail creating an impression that the code crashed in a later stage than it was the case 44 Once the test runs are completed the results especially the Summary Table at the end of ecah output file should be compared to the reference ones provided in each test directory for at least one platform One can notice slight differences between the results obtained with different front ends and or on different platforms In any case reproducibility of at least 5 significant digits should be expected The main differences come in the corrections using the converged CCSD amplitudes The CC convergence threshold has sometimes to be adjusted to obtain several digit agreement Notice also that in different versions of SAPT the threshold was changing between relative and absolute which of course makes a significant difference 45 13 Parallel SAPT psapt2K2 The parallel version of SAPT2002 called
55. cts the MOLECULE ALCHEMY programs e ISITHNDO selects HONDO 8 e ISITMICR selects MICROMOL e ISITACES selects ACES e ISITG88 selects GAUSSIAN 88 e ISITATM selects the older version of ATMOL 28 Of course selecting a given SCF package in amp TRN namelist will work only if SAPT2002 has been compiled for use with this package see Sec 7 Setting the OUT variable to TRUE will give more extensive printing from tran showing mainly memory partitioning and the input vectors The variable TOLER sets the threshold for writing the transformed integrals to disk The input is an integer n which is then used to discard all integrals which are less than 107 in absolute value An input of 1 gives a threshold of identically 0 We recommend values slightly tighter than normally used for similar purposes in isolated molecules calculations of about 1071 around the van der Waals minimum and progressively smaller as one proceeds farther away from the minimum Note that the usual default thresholds in most integral SCF programs will be larger than this value and must usually be lowered so that the atomic integrals files which are the input to the transformation contain enough of small integrals It is also advisable to tighten the threshold for convergence on the density matrices in order to increase the accuracy of the SCF eigenvectors The variable DIMER is used to determine whether the transformation type is dimer default or monomer DIMER FA
56. d be multiplied by 13 to give the maximum number of bytes Again due to nonzero thresholds this has a good chance to be reduced by about 50 37 In the subsequent stages of the calculation the ccsdt and sapt codes will generate additional scratch files of the order of 07v ov and smaller which will have to share disk space with the transformed integrals However the original file of raw atomic integrals n 8 will be removed beforehand 38 10 Description of some internal data sets We present here a short schematic of the program run sequence with emphasis on description of various files used First the integral SCF program performs the appropriate calculations for the dimer monomer A and monomer B depending on the type of basis set used and on the choice to calculate or not the supermolecular SCF interaction energy The output of the integral SCF calculations is included in the file output file with the name selected on the command submitting the SAPT script In the later stages output from other programs as well as output of some system commands will be added to this file Next with the aid of an interface program written specifically for that integral SCF package several new files are created by extracting information from the data sets of the integral SCF program just run The vecta data and vectb data files contain the eigenvalues orbital energies and eigenvectors molecular orbital coefficients produced by the SCF step
57. d most natural method is to use in SAPT the monomer centered basis set MCBS i e a basis that includes only functions that one would have used if the calculations involved only the energies and properties of a given monomer calculations for monomer X involve only basis orbitals centered on this monomer In the limit of infinite orbital basis set the MCBS approach converges to the exact values for each SAPT correction However for several reasons this convergence is slow for some corrections 22 The simplest cure for this problem is to use the DCBS or even better the DC BS approach The advantage of such a method is a close relation to the supermolecular approach with the CP correction The disadvantage is that the basis set is increased by a factor of two between MCBS nad DCBS methods for identical monomers Reference 22 has shown that many of the functions used in DCBS DCTBS are not needed for the SAPT convergence If a DCBS DC BS is reduced to some intermediate size it is called an MC BS It has been recommended in Ref 22 that MC BS s are constructed from an MCBS by adding all the midbond functions and only a part of the basis set on the interacting 23 monomer so called farbond functions The simplest choice for the farbond part is the isotropic part of the basis set i e orbitals with symmetries appearing in the occupied orbitals of constituent atoms i e s part of the basis for H and He and sp part of the bas
58. e denoted by El oig The second order corrections can be decomposed into the induction and dispersion parts 2j 2j 2j 2j 2j 2j E a AS E and EON ET a B d 2 The induction component is the energy of interaction of the permanent multipole moments of one monomer and the induced multipole moments on the other whereas the dispersion part comes from the correlations of electron motions on one monomer with those on the other monomer The SAPT interaction energy can be computed at different levels of intramonomer correlation and an approximate correspondence can be made between these levels and the correlation levels of the supermolecular methods It can be shown 13 for example that the sum of the polarization and exchange corrections of the zeroth order in W provides a good approximation to the supermolecular Hartree Fock interaction energy EPF BBP p09 4 00 y pO p20 6BBE 3 int elst exc ind resp exch ind resp int resp where EHF defined by the equation above collects all the third and higher order induction and exchange induction terms The subscript resp means that the coupled Hartree Fock type response of a perturbed system is incorporated in the calculation of this correction Including the intramonomer correlation up to a level roughly equivalent to the supermolecular second order MBPT calculation we obtain the interaction energy referred to as SAPT2 ESAPT2 _ PHF ppll2 7D 2 ge de Pe at ECO pO 4
59. e libraries are missing To date the program has been tested on the SGI Origin2000 and Origin3800 shared memory machines the SP3 and SP4 platforms shared distributed memory as well on a Beowulf cluster running Linux operating system From the standpoint of that latter machine it is important that psapt2K2 is able to distribute its temporary files over filesystems local to the nodes so that the scratch filesystems do not have to be NFS mounted across the whole cluster Novel algorithms have also been developed for efficient calculation of the electrostatic in duction and dispersion energies The idea behind these algorithms is that all these interaction components are expressible through monomer charge densities and dynamic susceptibility func tions These monomer properties can be calculated just once for each monomer at a high level of correlation then simplified stored and reused many times for different dimer geometries Scalable beta versions of these new algorithms are also included in this distribution As mentioned before the induction dispersion module requires the SCALAPACK BLACS libraries to be installed The file psapt2K2 tar gz size of about 7 Mbyte containing the parallel version of the SAPT codes psapt2K2 is available for download on the SAPT web page http www physics udel edu szalewic SAPT SAPT html 46 13 1 Structure of psapt2K2 directory After unpacking the psapt2K2 main directory will contain the followin
60. e recommended SAPT interaction energy 9 4 Submitting a sequence of SAPT2002 jobs The directory SAPT2002 bin contains two utility scripts RunlotATMOL and RunlotCADPAC which allow automatic calculations for multiple points on a potential energy surface in a single submission of a computer task Some members of our group found it also convenient to utilize RunlotATMOL2 a more elaborate and flexible version of RunlotATMOL Currently available only for ATMOL1024 and CADPAC these scripts can be fairly easily extended to other integral SCF programs An example of using RunlotATMOL can be found in the directory SAPT2002 examples ATMOL1024 ArH20 MCBS The idea behind the Runlot scripts is to construct the input files appropriate for a given SCF front end by combining universal geometry independent templates containing basis set and all the necessary integral SCF options with Cartesian geometries calculated from a minimal set geometric data Once all the input files are generated the SAPT script is invoked to calculate the interaction energy for a given dimer geometry and the results are recorded in a file with a name unique for this geometry Then the input files are prepared and the calculation performed for the next geometry from the set and the process continues until the set of geometries is exhausted Below using the ArH20_MCBS example we describe steps needed to set up a RunlotATMOL job 1 Prepare the files containing the basis sets i
61. e test files compute all currently available SAPT corrections This is not needed for calculations of interaction potentials In such calculations use one of the SAPTn control variables to select the minimal needed set of corrections This will reduce the time of calculations 12 1 The examples directory The directory SAPT2002 examples is divided into subdirectories corresponding to different SCF front end programs e g GAMESS or ATMOL1024 Each of those subdirectories contains the following test job directories named the same for all SCF programs e BER a very small test calculation for beryllium dimer in a DCBS consisting of a 2s1p set on each atom Will complete in seconds using 0 1 Mwords of memory and should be tried first We note again the naming convention for clarity for ATMOL1024 the dimer files are called BER intinp and BER scfinp the monomer A files are called BERA intinp and BERA scfinp the monomer B files are called BERB intinp and BERB scfinp and the perturbation file input is given by BERP data The SCF input files for dimer and monomer A as well as 42 the perturbation input file are listed in Appendix C The input files necessary when using GAMESS are called BER inp BERA inp and BERB inp integral SCF input files and BERP data perturbation input file and again the integral SCF input files for dimer and monomer A as well as the perturbation input file are listed in Appendix C Monomer A and monomer B input
62. ecule B 4 Electron s 0 0 000000000 7 000000000 0 000000000 4 0 E HF _ AB 21 5579794623086020 hartrees E HF _ A 10 7773391618701010 hartrees E HF _ B 10 7773391618701010 hartrees Correction mHartree Kcal mol 1 cm SCF SAPT_super E HF _ int 3 301138568 2 07149746 724 5162 E 10 _ elst 3 687513414 2 31395154 809 3156 E7 1 10 _fexch 3 149525961 1 97635904 691 2410 E7 10 _ exch S 2 3 135991890 1 96786627 688 2707 E 10 _ exch S 2 0 013534072 0 00849277 2 9704 E 20 _ ind 4 659057543 2 92360520 1022 5449 E 20 _ ind resp 6 900439671 4 33009490 1514 4714 E 20 _ ex ind 4 109230712 2 57858336 901 8719 E 1 20 _fex ind r 6 033628695 3 78616234 1324 2284 SAPT SCF a 1 087814283 0 68261434 238 7476 SAPT SCF_ resp b 1 404798429 0 88152506 308 3176 delta HF _ int 2 213324286 1 38888312 485 7685 delta HF _ int r 1 896340139 1 18997240 416 1986 CORRELATION E 12 _felst 0 616739823 0 38701041 135 3587 E71 13 _1elst 0 811463862 0 50920169 178 0957 eps 1 _felst k 1 428203685 0 89621209 313 4545 E7 12 _ elst resp 0 748858177 0 46991599 164 3554 E7 13 _ elst resp 0 764997351 0 48004349 167 8975 eps 1 _felst r k 1 513855528 0 94995948 332 2529 E 11 _f exch 0 640864839 0 40214910 140 6536 E 12 _ exch 0 125792342 0 07893595 27 6082 eps 1 _fexch k 0 515072498 0 32321314 113 0453 eps 1 _fexch CCSD 0 785250599 0 4927526
63. ed beforehand using the program memcalc in SAPT2002 bin see Sec 9 5 Declaring more than this amount makes no difference for the performance of transformation and may in crease the probability of crashing due to requesting more memory than available on a system at a given time The transformation will work in smaller memory except that the slower out of core pathway will be chosen see the source module memory F for more details One can read from 29 the transformation output of a test run whether the out of core or in core faster pathway has been chosen and what was the largest size of memory used This method can also be used to adjust the MEMTRAN variable appropriately look for lines containing phrases similar to Mem 8182228 CPU 463 7 or AABBOVVV Integrals Out of core 2 passes Mem 29848693 The only information absolutely necessary for namelist TRN is given by amp TRN ISITx T amp END where x is one of the symbols denoting the integral SCF program listed above 9 2 2 Namelist CCINP The purpose of this namelist is to pass information to the MBPT CC program which generates the required cluster amplitudes for the intermolecular perturbation theory program sapt The namelist variable CCPRINT tells the program whether or not to do extra printing This printing involves information about the memory partitioning and the integral class which is currently being read in The namelist variable VCRIT gives the tol
64. eded for psapt rsh MASTER LOGNAME bukowski export LOGNAME echo LOGNAME cd SCRDIR SAPT_SCRIPT JOB scfcp NPROC SCRDIR gt OUT 2 gt 1 amp exit The variables SCRDIR scratch directory the name of which is assumed to be the same on each node SAPT_SCRIPT full path to the driver script and SAPTDIR location of psapt2K2 executables have to be customized by the user Using the node information from calcnodes the script first creates the files PROC PROCc PROCe PROCi PROCs and PROCso which will be used by mpich to run the consecutive modules of psapt2K2 The input files and the PROC files are then copied from the home subdirectory to the scratch directory on each node Based on analyzing the PROC file the script detects the number of processors and the master node on which pSAPT mpich will be submitted this is the first node listed in calcnodes Finally having set up some environment parameters it launches pSAPT mpich on the master node The temporary files produced by GAMESS and psapt2K2 will be created and stored in local directories tmp bukowski The output from the run will be written to the file OUT in the scratch directory tmp bukowski of the master node in this case sam2 only It will have to be copied by rcp for example back to the home subdirectory huinalu The machine consists of 256 batch nodes and 4 interactive or login nodes each equipped with two 933MHz Pentium III proces
65. endix as a whole has been borrowed directly from the Thesis by Alston Misquitta 26 The following procedure can be applied to construct an auxiliary basis for each atom in the dimer under consideration Denote by M the decontracted basis set used in obtaining the molecular orbitals and eigenvalues The auxiliary basis denoted by Y is developed as follows 1 Construct an auxiliary basis as the tensor product of M with itself That is x M8M 10 If GM 1 a and GM lj aj are two basis functions of M centered at the same point where l and lj are the angular quantum numbers and a and a are the exponents then the product is a basis function belonging to centered at the same point and given by G l ax where ly li lj and a a a The resulting basis Y is a large basis including high symmetry functions compared to the original basis 2 Within each symmetry of Y a reduction is performed in the number of basis functions as follows Given an e if there are n basis functions for which log a log ax log Ax are 91 in an neighbourhood then these n functions are replaced by one function with exponent B Op Az A Perform this reduction for all basis functions 3 If necessary the resulting basis can be reduced even further with the previous step repeated on the reduced basis with a different value of e 4 Further pruning of the reduced basis Y can be done as follows a Reject all functions of
66. ent format Therefore such calculations cannot be done in the same run as SAPT The Hondo 8 interface program hndintf f produces an execution error message associated with a direct access file This message is ignorable 19 9 How to run SAPT2002 To perform a SAPT2002 calculation for one dimer geometry one has to run a dozen or so pro grams integral SCF calculations for the monomers and possibly for the dimer interface programs in most cases rewriting integral SCF files into different forms 2 and 4 electron integral transfor mations MBPT CCSD calculations for monomers and finally the proper SAPT calculations All of this is performed automatically using the script SAPT from SAPT2002 bin directory note however that a special script doSAPT_CADPAC has to be used if CADPAC is the front end SCF program This script calls other executables and scripts which can be found in the same place Calculation of the interaction potential energy surface of a dimer involves multiple invocations of the SAPT script for different dimer geometries This process can be simplified and automated with the help of the Runlot utility scripts described in Sec 9 4 One of the scripts called by SAPT is the script bin Clean that cleans up unnecessary files after a SAPT run it will erase the SAPT related files from the directory in which it is run The files are not automatically erased at the end of of each run in order to enable restarts which has t
67. eometries supplied in dimer cnf of the monomers the z y z Euler angles 64 and ya of monomer A and the z y z Euler angles ag 3g and yg of monomer B These angles to be supplied in degrees are measured with respect to the coordinate system in which the z axis points from A to B The Euler angle a is not needed since the intermolecular potential depends only on the difference ag aa so that aa may be assumed zero without loss of generality At the end of each line of geoparm d there is also a string DOIT including apostrophes If for some reason you do not need the calculation for a given geometry but still want to keep it in the geoparm d file put DONE instead The file geoparm d may contain any number of lines Once all these files are prepared copy them along with the RunlotATMOL script itself to your scratch directory where the whole calculation is to take place Then start the job with a command nohup time RunlotATMOL name gt name con 2 gt amp 1 amp in ksh or time RunlotATMOL name gt amp name con amp in csh where as usual name is how the job is called and how the names of all input files start The calculation will then proceed as follows First the program getgeoATMOL is invoked by RunlotATMOL this program is automatically compiled during the installation of SAPT2002 and 35 the path to it is inserted into RunlotATMOL which analyzes the geoparm d file looking for the first line contain
68. er can be divided into two arbitrary subsets Examples of MC BS input files set up using this strategy can be found in the directo ries SAPT2002 examples ATMOL1024 HF2 MCBS SAPT2002 examples ATMOL1024 CO2D MCBS and also SAPT2002 examples ATMOL1024 ArH20_MCBS A more general method that works for all integral SCF front ends is the tags method In this method chosen by BLKMB F the ordering of functions is arbitrary except that it has to be the same in all input files Of course the MCBS files nameMA and nameMB will contain only subsets of the whole basis It is however required that the basis specifications in these files are related to the specification in the name nameA and nameB by only the deletion of functions which belong exclusively to the other monomer i e the sequence of functions in the subset remaining after such deletion is not altered with respect to the whole DC BS set The role of a given function is specified by tagging it in the TRN namelist read from the file nameP data This is achieved by first setting the variable basis to a string containing letters spdf one letter for each orbital in the DC BS type basis thus for a part of the basis with 3s2pd the string should be sssppd Since the program expands each symbol into a number of orbitals one has to provide information on the type of basis set spherical or Cartesian which is done by setting the variable SPHG to true and false respec
69. er of processors on which the pEDI X script was run It is however important 69 that all the files used with an exception of input edi are obtained in a single pEDI X run For example using vecta data vectb data obtained on a different number of processors or different machine than than used to get denaMO data denbMO data or propa data propb data may result in nonsense if orbital degeneracies are present for one or both monomers as it is the case e g for atoms and linear molecules In such cases GAMESS can perform arbitrary rotations within the degenerate subspaces These rotations are dependent on the number of processors and even on the platform where the calculation is run so it is imperative that all the files are obtained consistently It is therefore recommended that the monomer properties are always moved around in the form of the compressed files name prop tar gz rather than separately 70 References 1 B Jeziorski R Moszynski and K Szalewicz Chem Rev 94 1887 1994 2 K Szalewicz and B Jeziorski in Molecular Interactions from van der Waals to strongly bound complexes edited by S Scheiner Wiley New York 1997 p 3 3 B Jeziorski and K Szalewicz in Encyclopedia of Computational Chemistry edited by P von Ragu Schleyer et al Wiley New York 1998 vol 2 p 1376 4 B Jeziorski and K Szalewicz in Handbook of Molecular Physics and Quantum Chemistry edited by S Wilson Wiley
70. erance for retaining cluster amplitudes Here we recommend a tolerance of 1 x 10 again with progressively tighter limits the further away from the van der Waals minimum The last namelist variable for this section is TOLITER This variable is to be used in conjunction with the variable CONVAMP of the next input namelist INPUTCOR When performing an Eo CCSD calculation the CC program will continue iterations until one of two exch conditions is met The first is that 39 iterations have been completed and the second condition is that the relative CCSD correlation energy change in a given iterative step is less than TOLITER We set the default for this variable to be 1075 The variables RPA CCD CCSD and several other can be set to true or false to chose one of possible forms of CC theory At this moment only CCSD T is guaranteed to work and only this option and low order MBPT amplitudes are needed for the current set of SAPT corrections Since CCSD T and all other variables of this type are false by default these keywords can be omitted from the namelist if CC iterations are not needed The variables SITEA and SITEB allow to perform MBPT CC calculations for one of the monomers only for testing purposes The default values are true and therefore these variables can be omitted from the list The defaults should be sufficient for this namelist so all that is absolutely necessary would be a statement of the form amp CCINP amp END e g
71. ess printing of the groups or ordered GTOs Adding the word BASI to the list will also suppress the ba sis set outprint To avoid calculation of the multipole integrals not needed in a SAPT calcu lation include the directive BYPASS PROPERTY this may be important especially on SGI ma chines where the absence of such directive may cause a run time error Inclusion of a line FPRINT NVCT NEIG NFTE NITE NPOP in the scfinp input files will ask the scf program to skip the outprint of the vectors eigenvalues Fock trial matrix iterations and populations for that run When the supermolecular SCF interaction energy is calculated during a SAPT run i e when the scfcp option is in effect most runs are like this the files nameA intinp and nameB intinp shouldcontain the directive BYPASS TWO to avoid recalculation of two electron integrals This di rective should not be present in the file name intinp or in the case of a MCTBS calculation in 14 nameMA intinp and nameMB intinp name denotes here the name of the job If the supermolecu lar SCF calculations are not performed i e if the scfcp option is not in effect then the directive BYPASS TWO must be also removed from the file nameA intinp See Sec 1 9 for further explanation On Linux platforms with g77 compiler except possibly for its latest verisons there is a restriction on the size of the file which cannot exceed 2 Gbytes In such a case if the two electron integral file gener
72. et to T or TRUE If DCBS or DCTBS is used and a supermolecular SCF interaction energy calculation is re quested the scfcp option is set the script will additionally look for a dimer input file or files name notice the convention nameA nameB and name for the monomers A B and for the dimer respectively Thus for example for ATMOL1024 the complete set of input files necessary for this type of run are name intinp name scfinp nameA intinp nameA scfinp nameB intinp nameB scfinp and nameP data In the DCBS or DC BS approach the basis set specifications for all integral SCF calculations are identical except for different charges set to zero in different files and for different numbers of electrons in each run If the scfcp option is used the file of two electron integrals can be computed only once during the dimer run and the subsequent SCF calculations for monomers A and B can then use this file most integral SCF programs are flexible enough to allow such a route Note however that the one electron integrals must be computed separately for monomers A and B If the scfcp option is not used only the monomer A calculation need to compute the two electron integrals 9 1 2 MCBS and MC BS approaches An alternative and strongly recommended way of performing SAPT calculations is to use the so called monomer centered plus basis set MC BS 22 To understand this approach first notice that the conceptually simplest an
73. et user input data data f howmany Choose number of iterations 75 Table 5 List of subroutines CC continued Module Subroutine Comments int 1 2 f iq 0 9 a Calculate x amplitudes intl f fi 0 2 3 a Calculate f intermediates double f d 0 1 2 a Calculates t2 amplitude CCSD double f vda Calculate single excitation for t2 double f energy Calculate CC energy after each iteration single f sda Calculate CC single amplitude in CCD approx single f vsta More singles for CCSD single f ssa Calculate single amplitude in CCSD approx triple f iql0a Calculate t3 amplitudes triple f t2atot More 3 amplitudes triple f totsamp Sum single amplitudes triple f totamp Sum double amplitudes triple f triple Calculate triples triple f edt Calculate MP4 sort f asort Presort integrals A good reference for this program is the paper by M Urban I Cernus k V Kell and J Noga in Methods in Computational Chemistry edited by S Wilson Plenum Press 1987 page 117 bIf a subroutine appears in TRAN and has the same function it is not mentioned here 76 Table 6 Comments on selected subroutines SAPT Module Subroutine Comments m f driver MAIN SAPT DRIVER m f theta Calculate O intermediate for monomer A m f thetb Same as theta for monomer B m f veta Calculate v intermediate for monomer A m f vetb Same as veta for monomer B m f omaov Calcula
74. euing system a command similar to mpirun np 8 caldisp_gms gt dimers out 2 gt amp 1 modifying of course the number of processing nodes paths and output file name appropriately As usual the executable caldisp_gms can be found in psapt2K2 bin directory 13 7 2 Calculating electrostatics induction and dispersion from fitted monomer electron densities and susceptibility functions A promising alternative route of EDI calculation utilizes the approximate representations of monomer properties in terms of the auxiliary basis sets The accuracy of this method strongly depends on the quality of these sets which are still under development At this point the auxiliary basis sets 68 can be obtained using the utility program make_aux and the property fitting can be accomplished with the help of the program tdenfit the relevant lines in the compa11 script must be commented out if these two programs are to be built during installation The driver scripts pEDI X can be easily adapted to perform the property fitting by uncomment ing the Generate auxiliary basis and Fit propagators and densities using auxiliary basis sections The invocation of the tar command should also be changed so that the fitted representations of monomer properties are included in the name prop tar file The pEDI X script modified in this way will ask for two additional input files input aux A and input aux B spec ifying parameters needed for the construction of auxi
75. g files and subdirectories e bin utility scripts for running SAPT After compilation this directory will also contain the executables used in a SAPT run e pcksdisp contains sources and detailed documentation for the code generating the static and dynamic susceptibility functions currently at the CHF level e cleandirs use this script to clean the entire psapt2K2 directory tree before recompiling from scratch e compall script used to build the package see Sec 13 2 e doc documentation for SAPT2002 contains this document and the METECC paper 5 in the postscript form e edi notran contains sources of the code implementing the new transformationless algo rithms for calculations of electrostatic dispersion and induction energies using the precom puted densities susceptibility functions and the Casimir Polder formula e examples input and output files for a set of systems and platforms This is a good source of templates for your runs e misc contains various interface and utility programs Most integral SCF packages need an interface program to extract one electron integrals and SCF orbital energies and coefficients from files created by these packages and transform them into a standard form readable by the transformation code two electron integrals are read by transformation directly without such preprocessing Other programs present in misc include int sort and even interfacing the transformation
76. gy into distinct physical components is a unique feature of SAPT which distinguishes this method from the popular supermolecular ap proach The SAPT methodology and its applications are discussed in several review papers 1 2 3 4 where complete references to the original developments can be found The set of formulas programmed in SAPT2002 is included in the paper published in the book accompany ing the METECC collection of computer codes 5 The METECC paper is available on the SAPT web page http www physics udel edu szalewic SAPT SAPT html and can be also found in the SAPT2002 distribution SAPT2002 doc METTEC ps The METECC project 5 was the first distribution of the SAPT codes The next version of SAPT called SAPT96 6 was available since 1996 Compared to SAPT96 the current version SAPT2002 is about a factor of two faster in medium size about 200 functions bases It also allows calculations with up to 1023 basis functions SAPT96 was restricted to 255 is interfaced with a larger number of front end SCF packages and runs on a larger number of platforms A parallel version of SAPT2002 has also been developed which will be referred to as psapt2K2 This version runs on SGI Origin IBM SP and on Linux clusters and scales well up to about 32 processors See Sec 13 for detailed description of this version A version of SAPT has also been developed 7 8 9 which allows calculations of the nonaddi tive portion of the interactio
77. he authors of ATMOL and POLCOR suites of the intended use of their codes 4 Packages included in the distribution Currently there are five options for downloading SAPT2002 and the accompanying programs 1 SAPT2002 size of about 2 1 Mbyte This file contains only the SAPT2002 codes You will have to obtain some integral SCF package like GAMESS CADPAC GAUSSIAN etc or download the ATMOL1024 code see below before running SAPT2002 On decompression this file expands into SAPT2002 ATMOL1024 size of about 0 14 Mbyte This file contains the ATMOL1024 package This package is a subset of the ATMOL code 11 modified by us to handle basis sets of up to 1023 orbitals On decompression this file expands into SAPT2002 atmo11024 so please decompress it in the root directory that SAPT2002 is in asymp_SAPT size of about 2 4 Mbyte Contains the POLCOR suite 12 and the ac companying programs necessary for computation of asymptotic coefficients Also included is the potential energy fitting program genfit_v1 developed in our group On decompres sion this file expands into asymp_SAPT Documentation for this package is located in asymp_SAPT doc COMPLETE SET OF SEQUENTIAL CODES size of about 4 8 Mbyte This file contains all the above modules On decompression it expands into SAPT2002 and asymp_SAPT psapt2K2 size of about 7 Mbyte Contains the parallel version of the SAPT codes psapt2K2 To make
78. i JOB out_tst NPROC copy all SAPT input files onto the scratch dir on every node assigned by scheduler With common filesystem use just a simple copy cd CURDIR Create the list of nodes rm f calcnodes for node in echo MAUI_JOB_NODES sed e s g do echo node gt gt calcnodes done cp calcnodes PROC Copy input files and lists of nodes to each local scratch directory for i in awk print 1 calcnodes do echo Copying input to i ssh i mkdir SCRDIR scp inp i SCRDIR scp JOB P data i SCRDIR scp PROC i SCRDIR scp calcnodes i SCRDIR 61 done Submit the job in scratch directory cd SCRDIR SAPT_SCRIPT JOB nocp NPROC SCRDIR gt OUTFILE 2 gt amp 1 for i in awk print 1 calcnodes do echo Cleaning up on i ssh i rm SCRDIR done The script sub_s_sep launches the psapt2K2 calculation using the local scratch filesystems scratch local where all the necessary data files including input are copied using the scp com mand The number and the list of nodes are retrieved from the environment variables MAUI _TASK_COUNT and MAUI_JOB_NODES supplied from within the scheduler environment Due to some file man agement issues still to be resolved it is necessary that only one process is launched on each compute node i e the parameter TaskPerNode in MAUI_script must be set to 1 This lim itation will be removed in the future The
79. id input edi file containing 4 geometries The first of these geometries is exactly the same as the one for which the interaction energies are computed during the pEDI X run 4 Run the EDI job the same way a regular psapt2K2 job would be run For example on 02K 03K platform without a queueing system to run in scratch mydir on 8 processors one would type pEDI o2k name nocp 8 scratch mydir gt name out 2 gt amp 1 amp Note that the nocp keyword has been used since the supermolecular SCF interaction energy is of no interest here A result of running the pEDI X script will be the file name out containing standard output from the whole run In this file the SAPT corrections requested in the nameP data file will be reported in the Summary Table section as well as the dispersion and induction energies cal culated by the propagator code pcksdisp for one specific dimer configuration described earlier The last part of name out will be the output from the caldisp_gms code i e the electrostatic induction and dispersion energies for all geometries specified in input edi Specifically the fol 10 pD pD pas pO pe pe peo lowing corrections will be calculated Fast gt elst gt elst resp elst gt elst resp ind gt ind resp gt disp and roe RPA The last of the corrections mentioned above is calculated from the dynamic susceptibility functions at the CHF level equivalent to RPA and currently doe
80. ing DOIT directive When such a line is found getgeoATMOL reads the COM separation and Euler angles and uses them along with the data of dimer cnf to produce a set of files geo d containing Cartesians of all atoms comprising the given dimer configuration with appropriately set charges A ghost i e zero charge site called Mb is also inserted half way between the COMs of the monomers A copy of geomparm d is also produced fort 7 in which the just processed input line is given a label DONE The RunlotATMOL script then proceeds to overwrite the old geoparm d with this modified copy and create all the needed intinp files out of the previously prepared pieces header d end d iso d polA d polB d and the Cartesian geometry files geo d generated by getgeoATMOL Once all the intinp files are created the SAPT script is called the path pointing to this script is automatically set up during installation to do the proper SAPT2002 calculation for this geometry The output is written to the file name1 out After the SAPT script completes its task the whole cycle is repeated i e geoparm d is searched for the new geometry labeled DOIT the input files for are generated and the SAPT script invoked The process continues automatically until all the geometries in geoparm d are taken care of Consecutive output files are named name1 out name2 out name3 out in accordance with the position of geometries in geoparm d In this way us
81. ing the Runlot utility the whole surface or a significant portion of it can be filled up with data points with minimum interference on the user s part The philosophy behind the script RunlotCADPAC and the related getgeoCADPAC geometry conversion program is very similar please consult the script itself for details The structure of both scripts is simple enough to allow relatively easy modifications 9 5 Memory and disk requirements When setting up a SAPT2002 computational project it is imperative to know how much com putational resources this project will consume and whether or not it will fit into the memory and disk of the machine at hand Memory requirements of SAPT2002 can be estimated based on the total number of basis functions and the numbers of occupied and virtual orbitals The transformation code tran should work even with small memory although it may then choose the out of core path which signifi cantly increases the time of this step To allow the transformation to work entirely in core except maybe for the four virtual transformations the amount of available memory should be slightly more than on 2 8 byte words where n is the dimension of the basis set and o is the number of occupied orbitals of the bigger monomer For the cc part memory requirements can be roughly estimated as 30 4 words where v is the number of virtual orbitals for the larger monomer The sapt code will ask for about 507v or v 30 4 word
82. ing the mpirun command on SP systems poe grd_poe or sge_mpirun is used for this purpose The details of the calculation flowchart input files and the use of various types of basis sets are presented in Sec 9 Here we only expose the features characteristic of the parallel version of the code The executables invoked by the pSAPT X script communicate with one another through various usually large temporary files Most of these files are written and read by only one process and do not need to be accessed directly by other processes This means that such files can be stored locally in some scratch directory accessible only to one process This is indeed the case on a Beowulf cluster where scratch filesystems are usually local to the nodes Another class of smaller temporary and input files have to be accessed from all processes On a Beowulf cluster such files have to be replicated in each processes local scratch area This problem does not exist on most other multiprocessor platforms like the SGIs and SPs in DoD centers where all temporary files are stored in a common large filesystem accessible to all processes All the details of how the files are handled are taken care of by the pSAPT X scripts and the MPI executables themselves and are completely transparent to the user with an exception of the input files vide infra During the compilation the script compall adapts the appropriate pSAPT X script by insert ing the proper globa
83. inimal basis sets 9 1 1 DCBS and DC BS approaches If a dimer centered basis set DCBS possibly including the bond functions denoted then by DC BS is used and the supermolecular SCF interaction energy is not needed then only two inte gral SCF calculations for monomer A and for monomer B will be performed The DCBS DCTBS approach means that the calculations for monomer X are performed using the orbital basis set con sisting of all functions those belonging to monomer X i e centered on the nuclei of monomer X those of the interacting partner i e centered at the positions where the partner s nuclei are in the dimer and the bond functions In the inputs the bond functions and the functions of the in teracting partner are typically connected with zero charge centers and are sometimes called ghost orbitals The script will then look for files nameA and nameB for the respective monomers The number and full names of the files depend on the integral SCF code used Here is a list of files needed for some of the front end codes ATMOL1024 nameA intinp nameA scfinp nameB intinp and nameB scfinp GAMESS nameA inp and nameB inp GAUSSIAN nameA data and nameB data 22 HONDO 8 nameA hnd nameB hnd In each case the file nameP data will also be needed containing input for the post SCF part of the calculation tran cc and sapt stages In a DC BS run the variable DIMER in the namelist TRN in this file must be s
84. is centered on the first and second row atoms In practice MCT basis sets match the accuracies of DC bases and at the same time reduce several times the costs of SAPT calculations If the MC BS approach is used SAPT calculations need significantly less computer time than supermolecular calculations of equivalent accuracy An MC BS approach requires a little more work with setting up the basis sets than a DCTBS calculation The reason is that in the former approach the basis functions appear in three different roles a given basis function can belong only to monomer A only to monomer B or to both monomers A calculation of the integrals in a set with repeated functions would be unnecessarily time and disk space consuming but a method has been developed to avoid this problem Below the individual files needed for an MCTBS calculation are listed first and then the dependence between the structure of these files and control parameters in the file nameP data is described If MC BS calculations are performed and the supermolecular SCF interaction energy is not requested scfcp keyword not present the SAPT script will look for input files nameMA nameMB to perform integral SCF calculations for monomers A and B respectively The input files for these runs should contain the basis of a given monomer plus the midbond and farbond functions on ghost centers Since the basis sets are different for A and B the two electron integrals from A cannot
85. it will expand into asymp_SAPT directory Change to this directory and use Compall_asymp script to build all programs in this package The subdirectory doc contains the user s manual for these programs The asymptotics calculations are presently limited to 255 orbitals and the relevant codes are interfaced only with the older version of ATMOL included in asymp_SAPT package 7 3 Testing SAPT2002 installation Once the compilation has been completed successfully if unsure just grep the compall log file for the word error we strongly recommend that you perform as many tests as is possible before starting to use SAPT2002 for production runs A suite of test jobs of varying size and for various SCF front ends has been provided for this purpose in sub directory examples Sample outputs from different platforms can be also found there For more information on running the test jobs see Sec 12 8 Using SAPT2002 with different front end packages 8 1 ATMOL1024 A good place to look for the description of input to ATMOL1024 is Paul Wormer s web page http www theochem kun nl pwormer strictly speaking this is a description of the older ver sion of ATMOL but the input options are the same as for ATMOL1024 Below we discuss several options relevant for a SAPT2002 run It is convenient to reduce outprints from the integral integw module of ATMOL1024 by adding the directive NOPRINT GROU GTOS to the intinp files This will suppr
86. l paths to executables and should run properly on any installation without changes Currently this feature is not functional in the case of scripts used on huinalu namely pSAPT mpich maui and pSAPT mpich maui sep The paths in these scripts need to be changed manually so that the variables MAIN_SAPT_DIR and the SCF HOME_DIRECTORIES reflect user s di rectory structure if GAMESS is used it concerns also additional directories relevant for this program These variables are set about 500 lines down in the pSAPT X script The pSAPT X script is written in ksh although on Linux platforms some of which are not equipped in ksh it is actually 51 executed under bash 13 4 1 Running psapt2K2 on SGI We first consider a situation where there is no queuing system installed and a psapt2K2 job can be submitted interactively from a command line Before launching a psapt2K2 run the scratch directory should be created and all the input files should be copied to this directory The psapt2K2 calculation is then launched in this scratch directory by typing pSAPT o2k with appropriate options If ksh is used as the login shell and an SGI machine is the platform one would type pSAPT o2k jobname opti nproc opt2 gt output file 2 gt 1 amp if psapt2K2 bin is not in your PATH then the full path to pSAPT 02k will have to be given The keyword jobname has to be the same as the beginning of the name of the input files for the system considered we use a naming
87. liary basis These involve the number of pruning cycles and the e parameter for each of these cycles for each atom For example in the case of molecule A consisting of 2 atoms and with 3 pruning cycles required for each of them the file input aux A could look like 3 0 8 0 o o WwW 00 9 1 0 Details of the method currently used to generate the auxiliary basis sets are presented in Ap pendix E After the run finishes the auxiliary bases generated by make_aux will be placed in files auxa data and auxb data similar to infoa data and infob data whereas the fitted properties will be placed in unformatted sequential files auxdena data auxdenb data auxprop0a data auxprop0b data auxpropa data and auxpropb data To perform the interaction energy cal culation using the fitted monomer properties collect all these files along with input edi in a scratch directory e g by uncompressing the name prop tar gz file resulting from the modified pEDI X script and then run the caldisp_fit executable by typing a command similar to mpirun np 8 caldisp_fit gt dimers out 2 gt amp 1 possibly modifying the number of processing nodes paths and output file name The output file in this case dimers out will contain for each dimer geometry the following corrections 10 12 12 13 13 20 2 E E EA Eno E eg Es and Eo RPA Important note The number of processors to run caldisp_gms and caldisp _fit has nothing to do with the numb
88. mation used in the Gauss Legendre quadrature schemes involves a constant wo The namelist variable OMEGAO allows you to set this constant It is typically between 0 3 and 0 5 The Gauss Laguarre quadrature scheme involves the constant a For the integrals encountered here we should set ALPHA 0 0 90 e Debugging levels There are many debugging levels built into the code These can be activated by setting the relevant combination of debugging flags to T Nota Bene large matrices may be printed out at certain levels Here is a list of current debugging levels DEBUG1 T F Test the quadrature grid DEBUG2 T F Use the un coupled propagator in the coupled propagator route This is very useful when testing the code as the dispersion energy obtained this way should be the same as the value of B obtained from the SOS formula DEBUG3 T F Print out all matrices in the construction of the coupled propagator DEBUG4 T F Print out all 2 e integrals read in DEBUG5 T F Print out information in the N summation algorithm subroutine SUMN6 DEBUG6 T F Print out information in the PROPERTIES and C6DISP routines DEBUG7 T F Print out integrals etc used in making the H and H matrices in the CHF approximation DEBUG8 T F Print out information in the induction module Integrals and interme diates printed Can be a lot E Appendix Generation of auxiliary basis This App
89. monomers A and B in an appropriate MCTBS Next the script will look for the file s name to perform integral SCF 24 calculations for the dimer in the DC BS equivalent of the MCTBS used In the next two steps the files nameA and nameB containing the same DC basis set will be used as in the calculations described in the previous paragraph However now neither the monomer A nor B calculation need to compute the two electron integrals since these are already available from the dimer calculation Also in contrast to the case of the previous paragraph the SCF calculations are performed for each monomer since the total SCF energies are needed to compute the supermolecular HF SCF interaction energy The SCF orbital energies and coefficients from these runs are discarded Thus if for example ATMOL1024 is used as the integral SCF program the following input files needed nameMA intinp nameMA scfinp nameMB intinp nameMB scfinp name intinp name scfinp nameA intinp nameA scfinp nameB intinp nameB scfinp and nameP data If GAUSSIAN is used as the integral SCF program the input files needed are nameMA data nameMB data name data nameA data nameB data and nameP data The possibility of skipping parts of integral SCF calculations varies between programs In the case of ATMOL1024 the calculations of two electron integrals are omitted by simply including the BYPASS TWO statement in the proper intinp file and an SCF calculation is omitted b
90. n to the same file as standard output and that the processes will be run in the background A more common situation occurs when jobs have to be submitted through some sort of a queuing system such as GRD or more recently the grid engine at ARL HPC MIL In this case all the operations described above should be performed by a script submitted to the queue A sample script ARL_script could look like bin ksh S bin ksh 52 N ArHF_Tc 1 03k pe pe_4hr 8 HHHHHHHRHHHHHHHERAEHAA AHHH HHA RAR RRR Set the these parameters HHEFHHHHHHHEEHEHHHAHEHHEHHHAAEHHAEHEHRHERRRHR RHEE NODT 8 number of processors to run everything CURDIR home bukowski ArHF_Tc Starting directory WRKROOT usr var tmp bukowski root of the scratch directory SAPTSCRIPT home bukowski psapt2K2 bin pSAPT o2k driver script JOB ArHF Core of the job name HHHHHHHHHHHHHHHERAEHAA EHH HHHR RHA A RRR RRA RARA No need to modify anything below this line HHEHHHHHHHHHEHHHHHHHHEHEHHEAHEHHAEHHAEHHREEEHRHR RHEE WRKDIR WRKROOT JOB scratch directory where the calculation will take place cd CURDIR Create the job specific scratch directory if d WRKDIR then mkdir WRKDIR fi Copy the input files from HOME to scratch cp JOB inp WRKDIR cp JOB A inp WRKDIR cp JOB B inp WRKDIR cp JOB P data WRKDIR 53 Run the job in scratch cd WRKDIR SAPTSCRIPT JOB scfcp NODT WRKDIR gt gt JOB
91. n ATMOL1024 format e iso d isotropic part of the whole DCBS basis i e the functions which will be used in SCF calculations for both monomers the sequence should be A midbond if 34 present and B e polA d and polB d polarization functions for A and B respectively functions for polA d will not be used in expansion of molecular orbitals of B and vice versa e head d a simple file containing a header common to all intinp files e end d endA d endB d endMA d and endMB d end parts of inintp files specific for a given system e g end d corresponds to the dimer endMA d to monomer A in its MC BS endA d to monomer A in DC BS and so on note that in this example the files endA d and endB d contain the directive BYPASS TWO which allows to avoid recalculation of two electron integrals generated during the dimer SCF run e scfinp files needed for SCF calculations on all subsystems 2 Prepare the file dimer cnf which specifies the Cartesian geometry in bohr of monomers A and B in their initial configurations i e for all Euler angles equal to zero The charge atomic mass and an up to two character symbol are also given for each atom 3 Prepare the file geoparm d which specifies dimer geometries for which the SAPT calculations are to be performed Each such geometry is specified by a single line containing the separation in A between the centers of mass as defined by the masses and g
92. n energy for an arbitrary trimer consisting of closed shell monomers Thus SAPT can now be used to calculate the two leading terms in the many body expansion of the interaction energy of a cluster where bodies here are monomers The programs implementing the three body SAPT can be obtained by a special request The calculation of the interaction energy of a dimer using SAPT2002 involves four steps In the first step one and two electron integrals are computed in a chosen orbital basis set and then SCF calculations are performed on both monomers The SCF calculation for the dimer can be also performed at this stage Several integral SCF packages are interfaced to SAPT and can be used including free packages such as GAMESS 10 see http www msg ameslab gov GAMESS GAMESS htm1 and ATMOL 11 a modified version of the latter package ATMOL1024 is included in SAPT2002 distribution and can be down loaded from SAPT web page After the SCF calculations are completed the atomic integrals i e integrals between functions of the basis set are transformed into molecular integrals using scalable the 4 index transformation program tran In the third step the Coupled Cluster CC program cesdt is invoked to calculate the MBPT and or CC amplitudes for monomers A and B Finally the sapt program is run to compute the interaction energy components Several short interface programs are also invoked between calls to tran and ccsdt The computa
93. nctions have to be performed only once for each monomer and not at each and every dimer geometry In particular costly four index transformations usually needed in highly correlated methods are done only in a single point monomer calculations and avoided during the actual interaction energy calculations These latter calculations are thus transformationless The electron density of monomer can be expressed as a combination of products of n n 1 2 atomic orbitals AOs where n denotes the number of these orbitals in the basis set used Thus a calculation of electrostatic energy from two precomputed monomer densities requires of the order of n 2 electron integrals for similar size monomers so that n is approximately the same for both of them The monomer susceptibility functions both static and dynamic are given as combinations of ov x ov 1 2 terms products of four molecular orbitals two depending on coordinates of electron 1 and the other two on coordinates of electron 2 The time cost of obtaining induction and dispersion components is again dominated by the need to compute n 2 electron integrals This unfavorable scaling can be greatly reduced if both the electron densities and the susceptibility functions are fitted in terms of a suitably chosen auxiliary basis In most cases the size of this basis m can be assumed to proportional to the size of the original AO basis several times larger The electron density can now be expre
94. nded input options 0 FUNGAMESS SCD aia SS GSE eS eres Be Wiel enna a INLerrace apli te tee fas hy ang Nd oo ead ash ast ee aay gay eri a o 0 Hondo S aar aa a A AS cas Way aa aa aa eas Peed Se 9 How to run SAPT2002 9 1 Calculations of integrals and SCF energies 2 000 9 1 1 DCBS and DC BS approaches 2 20 00 0000 00 eee eee 9 1 2 MCBS and MO BS approaches 9 2 Input for post Hartree Fock part e 9 214 NamelistiTRN x m oee ea a A ee ee E 972 2 Namelist CCINP ers ra a E AA AAA ti 9 2 3 Name list ENPUTCOR ua a tt tata ee a 9 3 How to read the output 0 ee ee 9 4 Submitting a sequence of SAPT2002 jobs o o e 10 10 11 14 14 14 14 15 15 16 16 17 18 19 19 9 5 Memory and disk requirements 2 2 0 0 eee 10 Description of some internal data sets 11 Performance of SAPT2002 12 Tests and example input and output files 12 1 12 2 The examples directory o ee Running tests Jobs t di a eR iaa 13 Parallel SAPT psapt2K2 13 1 13 2 13 3 13 4 13 5 13 6 13 7 Structure of psapt2K2 directory o o a Installing psapt2 K2 is bei di a eee 13 2 1 compall installation script o s a daa aiae 0 002 002 0000 13 2 2 Testing psapt2K2 installation 2 0 2 oo e Using psapt2K2 with GAMESS as a front end 0 Howto run psapt2K2 vts ia pd A A
95. nts of the interfacing process is presented here The existing interfaces can be used as a template for the creation of new interfaces A short listing of what the tran program needs follows e One Electron Integrals 1 Overlap 2 Hamiltonian 3 Kinetic 4 Potential e Two Electron Integrals SCF Eigenvalues SCF Eigenvectors Information about the run 1 Basis set size 2 Number of occupied orbitals 3 Number of virtual orbitals 4 Charge on each atom 5 Geometry of the monomers Most of the information is read by a small interface program from the integral SCF program files and then rewritten into a simple form that the next stages of the process can easily understand Modifications to the transformation program must be made to read in the two electron integrals in trans f atmtr f and trnn f modules Notice also the common block SCFPACK which contains logical variables indicating which integral SCF program is used This common must be changed throughout the program to include a logical variable for any new integral SCF program Finally in the driver subroutine trans F make sure that there is a similar setting of the logical input record length for the new integral SCF program B Appendix List of subroutines This appendix contains the list of subroutines with a short description of the their functions 73 Table 4 List of subroutines TRAN Module Subroutine Comments main f timit Read ela
96. o be done on a case by case basis by modifying the SAPT script except for starting from the transformation step However bin Clean is called at the beginning of the SAPT script so that a consecutive calculation can be performed in the same directory do not forget to change the name of the output file This is necessary since several temporary files are named with no reference to the jobname Thus two simultaneous calculations cannot be done in the same directory but can be run of course in separate directories It is also prudent to run bin Clean itself just by executing SAPT2002 bin Clean to release unnecessary disk space after finishing calculations in a given working directory The actual running of the program when using the SAPT script is very simple On most installations runs are performed in a working or scratch directory designed to hold large temporary files We find it simplest to make a subdirectory there copy the input files created by the user or taken from the SAPT2002 examples to this subdirectory and either execute the SAPT script in this directory using the full path e g home local SAPT2002 bin SAPT or simply copy the SAPT script to the working directory several other possibilities exist for example users can add the SAPT2002 bin directory to their PATH environment variable During the compilation the script Compall adapts the SAPT script and other scripts by in serting the proper global paths
97. ode pcksdisp is generated automatically by pEDI X script and appended to file5 dat so the user does not have to worry about it For the sake of completeness we state here that this namelist currently contains the following ISITCASPOL T ISITINDUCT T ISITSOSDISP F ISITPROP F ISITCKS T ISITUCKS F ISITPOL F ISITC6DISP F USESUMN6 T MAKEH1H2 T IQUADTYP 1 NQUAD 16 OMEGAO 0 5 The meaning of these parameters is described in Appendix D In particular the user may want 66 to alter the length NQUAD of the quadrature employed in calculation of the Casimir Polder integral 3 Prepare the file input edi specifying the dimer geometries for which the interaction energies are to be calculated by caldisp_gms out of the precomputed monomer properties input edi consists of lines one for each dimer geometry containing in this order the COM COM separation in A the 3 and y Euler angles in degrees for monomer A a is assumed as zero followed by the a 8 and y Euler angles of monomer B It is assumed that the COM of monomer A coincides with the origin of the coordinate system and that monomer B is shifted in the positive direction of the z axis For example 5 29177249 0 O O O O 2 38521611 86 80692336 90 00000000 180 00000000 93 37890335 360 00000000 2 63658901 87 13779711 90 00000000 180 00000000 81 94039222 360 00000000 2 89422970 87 42491802 90 00000000 180 00000000 75 80434134 359 99999915 would be a val
98. ogram It should be noted here that most of the large scratch files are distributed between the processes The amount of disk space needed on a single processor is thus only a fraction 1 P of the total disk requirement This feature becomes important on Beowulf clusters where typically only a relatively small scratch area is available on each node 13 7 Electrostatics dispersion and induction EDI from monomer prop erties It is well known that the electrostatic component of the interaction energy can be calculated from monomer charge densities which are purely monomer properties Similarly the second order in duction energy may be expressed in terms of monomer charge densities and the static susceptibility functions The same holds also for the dispersion energy which is given by an integral of the prod uct of two monomer dynamics susceptibility functions over imaginary frequency the so called 63 Casimir Polder integral Thus with an exception of the exchange energies all the components of the interaction are in fact determined by purely monomer properties These properties can be calculated only once for each monomer at a high level of intramonomer correlation and then used after rotating and translating to the new monomer positions to obtain the three interaction components for any dimer configuration The point is that the expensive parts of the calculation those of the correlated charge density and susceptibility fu
99. ogram required for CADPAC Due to the large number of density functional theory DFT eXchange Correlation XC functionals implemented in CADPAC this is a good program to use if the SAPT method based on Kohn Sham orbitals and orbital energies SAPT KS 20 21 is to be applied To run SAPT2002 with CADPAC as a front end a special script SAPT2002 bin SAPT_CADPAC should be used instead of SAPT used for all other SCF programs 83 GAUSSIAN When using GAUSSIAN with SAPT2002 a symbolic link in the compilation script Compall is made to point to the util a file in the GAUSSIAN directory structure The transformation 15 module tran of SAPT2002 links to this library to be able to read the rwf and two electron integral files If for some reason GAUSSIAN92 were to be used the GAUSSIAN94 interface can be easily modified for this purpose The only parameter that has to be changed is the number of words read from disk in the program misc g94intf f Specifically line 243 which currently looks like CALL FILEIO 2 501 1000 T 0 has to be changed to CALL FILEIO 2 501 32 T 0 so that the read does not go past the end of the file In GAUSSIAN94 and in higher versions of this code the default method of SCF calculation was changed to direct two electron integrals calculated in core and not stored to disk Since SAPT2002 always needs the two electron integrals the command SCF CONV which stands for do conventional SCF must be used
100. pall will start the compilation from the beginning 13 2 2 Testing psapt2K2 installation Once the compilation has been completed successfully if unsure just grep the compall log file for the word error we recommend that you perform as many tests as is possible before starting to use psapt2K2 for production runs A suite of test jobs of varying size and for different parallel platforms has been provided for this purpose in sub directory examples Sample outputs from different machines out_ref and queuing system submission scripts can be also found there Examples of using the new monomer property based algorithms for electrostatics induction and dispersion can be found in directories psapt2K2 examples PLATFORM EDI where PLATFORM is one of 03K SP3 SP4 and BEOWULF 13 3 Using psapt2K2 with GAMESS as a front end GAMESS US is currently the only parallel SCF package psapt2K2 is interfaced with See Sec 8 for information about setting up the GAMESS input files for psapt2K2 runs and about 49 the structure of the GAMESS driver script runGAMESS and of the GAMESS ptran interface program gamsintf There are a few minor differences between the runGAMESS script used with the sequential program SAPT2002 described in Sec 8 and the one used with psapt2K2 Although these differences are completely transparent to the user we list them here for the sake of completeness e Unlike in the sequential version of the code the variable TARGE
101. psapt module now calculates the MBPT2 and MBPT3 densities and stores them on disk and the pcksdisp program is called to produce the susceptibility functions currently at the CHF or RPA level In addition to generating the monomer properties the regular psapt2K2 calculation is also performed for one dimer geometry obtained by shifting the position of monomer B by 10 bohr along the positive z axis with respect to the position specified in the nameB file The CHF dispersion energy is also computed for this geometry by the program pcksdisp the same one that generates the susceptibility functions The results for this one geometry reported in the output from the pEDI X run may then be compared to their counterparts obtained using the transforma tionless codes to assess the correctness and accuracy of the latter The transformationless code itself caldisp_gms is invoked at the end of pEDI X to compute the electrostatics induction and dispersion for specified dimer geometries The detailed instructions for running pEDI X are as follows 65 1 Assuming that the name of your job is name prepare the files nameA and nameB containing the specifications of the geometries and basis sets of monomers A and B in GAMESS US format Remember to put blank lines after basis set of each atom including the blank at the end of the file Out of these files the pEDI X script will construct GAMESS input files needed to calculate the SCF vectors and generate integ
102. psapt2K2 has essentially the same functionality as the sequential version Slight differences exist in user interface related areas such as compilation more libraries are needed in psapt2K2 input options SAPT2002 is more user friendly when it comes to input defaults or output presentation In particular since psapt2K2 is still under development its output contains a lot of debugging and profiling information SAPT2002 has been tested with a large number of sequential SCF front end programs while in the case of psapt2K2 the parallel GAMESS US is effectively the only SCF code which can be used psapt2K2 should also work with the sequential SCF codes like ATMOL1024 although quite often the time cost of such a calculation would be dominated by the SCF step All modules of the psapt2K2 code have been parallelized using only MPI library and thus the suite is very portable and should run on any parallel architecture It is also recommended that the program is linked with the SCALAPACK BLACS libraries as these are needed for the CHF routine to run in parallel In the case these libraries are not available the CHF routines will run in sequential mode which may have substantial impact on the timings especially for larger numbers of occupied orbitals The SCALAPACK BLACS libraries are also necessary to build the code generating the static and dynamic CHF propagators also referred to as susceptibility functions This code will not be built if th
103. psed time main f prsq Print square main f rdvc Read eigenvectors main f ifa Initialize table lookup values main f copy Copy vector A to B main f flagl Choose either eigenvectors main f flag2 of monomer A or B main f alarm Abnormal ending io f daopen Open direct access files io f dawrit Write to direct access files io f daread Read from direct access files io f daclos Close direct access files io f r8zero Zero a R 8 array io f i4zero Zero an I 4 array io f putrec Put a record on disk io f ropen Open input file io f seopen Open other sequential files memory f memory Partition core memory tonel f onel One electron transformation tonel f trle routines tonel f mult Matrix vector multiplication tran f tran Calling for in core transformation trans f trans MAIN DRIVER routine trans f whichint Flag integral types needed tranw f tranw Calling for out of core trans trnn f inread G88 two electron reading trnn f labscf Unpack G88 record label trnn f packg Repack indicies trnn f unpackg Unpack indicies G88 trnn f unpackm Unpack indicies Molecule trnn f packm Pack indicies Molecule trnn f search Find beginning of record Molecule trnn f tr1 1 2 3 4 First step in core transformation trnn f tr2 1 2 3 4 5 6 Second step in core transformation trnn f tr3 1 9 a b Third step in core transformation trnnw f tr1 1 2 3 4 w First step out of core trnnw f tr2 1 6 w Second step out of core trnnw f
104. rals A spherical basis set will be assumed i e ISPHER 1 and the name of the job will be used as comment line Geometries of the monomers specified in nameA and nameB should correspond to whatever you consider to be the initial configuration of the given monomer i e the COM or other characteristic point around which rotations will be performed should coincide with the origin of the coordinate system and all Euler angles describing the orientation of the monomer will be assumed zero at this geometry 2 Prepare the file nameP data as for the regular pure MCBS SAPT calculation note that in namelist TRN the variables basis and tags have to be specified for such a calculation In the namelist INPUTCOR the variables CHFDISP T CHFIND T E12 T E12R T E13PL T E13PLR T have to be specified in order for the MBPT2 and MBPTS3 densities to be dumped on disk Failure to specify any of these corrections will result in the corresponding density missing in the dump files denaMO data and denbMO dat it does not hurt the subsequent calculations except that the quantities requiring the missing densities will be reported as zero Also some other corrections may be specified so that the results from Summary Table may be later compared to what comes out of the transformationless algorithms for the geometry considered in the pEDI X run These may include E1TOT T E2IND T E2INDR T and E2DSP T The namelist INPUT controlling the behavior of the propagator c
105. ram sapt is supplied in the file nameP data This input consists of a title line and three namelist sets On card one there are 80 characters reserved for the titling of the run The three namelists that follow are TRN which is for input to the transformation program CCINP which passes information to the MBPT CC program and INPUTCOR which informs the perturbation program which corrections are to be run It should be noted that the exact syntax of a namelist statement depends on the platform For example on SGI and Linux platforms each namelist should start with the name preceded by Y e g amp TRN and end with END On the other hand IBM compilers prefer to treat a forward slash as the namelist end marker In the following examples the former convention will be followed 9 2 1 Namelist TRN The major function of this namelist is to tell the tran program which integral SCF package is in use Currently supported codes are listed in Table 1 In addition a number of legacy codes should still work although several of them have not been used for years Out of the 10 possible integral SCF selections the user should select only one by setting the corresponding variable equal to TRUE and all the other variables equal to FALSE The selection variables are given by e ISITANEW selects ATMOL1024 e ISITGAMS selects GAMESS e ISITG9O selects GAUSSIAN 92 or GAUSSIAN 94 e ISITG98 selects GAUSSIAN 98 e ISITCADP selects CADPAC e ISITALCH sele
106. reach fle ls 1 JOB FO8 mv fle inta m O m end e On some BEOWULF clusters such as huianlu at Maui center the communication between the nodes is furnished in terms of ssh rather than rsh In such cases GAMESS s parallel launcher ddikick x must be modified to use ssh instead of rsh and recompiled as suggested in the source ddikick c 50 13 4 How to run psapt2K2 To perform a psapt2K2 calculation for one dimer geometry one has to run a dozen or so pro grams integral SCF calculations for the monomers and possibly for the dimer interface programs in most cases rewriting integral SCF files into different forms 1 and 2 electron integral transfor mations MBPT CCSD calculations for monomers and finally the proper SAPT calculations All of this is performed automatically using the script pSAPT X from psapt2K2 bin directory where X denoting a platform is one of 02k sp mpich mpich maui and mpich maui sep The last two cases pertain to the huinalu cluster at Maui center While pSAPT mpich maui con trols a calculation utilizing the common scratch filesystem scrtach huinalu the other script pSAPT mpich maui sep makes use of local scratch disk scratch local on every node The pSAPT X script is executed on one master processor which in turn calls other executables and scripts also found in the psapt2K2 bin directory The MPI executables such as ptran pcc psapt are launched by the master us
107. rrection should be calculated where possible The value of 3 indi cates that both types of corrections should be computed this is usually needed only to evaluate 32 the size of response effects The LEVEL1 variable asks the program to calculate E1TOT E2IND E2DSP EEX2 and E12 LEVEL2 asks for all LEVEL1 corrections plus E21D E211D E22D without the contribution from triple excitations E13PL E13PLR and E11 LEVEL3 adds to LEVEL2 the contri bution from triple excitations in E22D as well as the E122 E111 and E12X corrections Selecting LEVEL2 to be greater than zero and LEVEL3 0 indicates to the program that E22D triples is not to be calculated whether or not that correction is specifically set to TRUE The LEVELn variables only switch the corrections on Thus any corrections requested explicitly will be computed in addition to the corrections selected by LEVELn Usually only one of the LEVELn variable is set to a nonzero value although setting more than one may switch on additional corrections The set ting LEVEL1 2 LEVEL2 0 LEVEL3 0 E22I T is equivalent to SAPT2 T The setting LEVEL1 0 LEVEL2 0 LEVEL3 3 E22I T will compute all currently available and recommended to be used corrections plus E122 The variable CONVAMP selects the use of the converged CCSD amplitudes in the expressions analogous to the corrections BOU ney and E Setting this variable to TRUE results in 1 the calculation of the ebken CCSD correction in
108. rs have interfaced SAPT with DALTON and MOLPRO but these interfaces are not yet available in SAPT2002 An integral SCF package is activated by simply setting the cor responding variable in the script to the complete path to the directory where the libraries or executables depending on the SCF package of a given package are located for example GAMESS home local gamess Otherwise set the variable to NO note the capitals In addition for GAMESS the so called version number VERNO XX needs to be specified SAPT2002 assumes that the name of the GAMESS executable is gamess VERNO x The list of SCF codes included in Compall does not include ATMOL1024 This latter option is activated automatically if ATMOL1024 has been downloaded and is present in the SAPT2002 atmo11024 directory Thus you may set all the integral SCF variables to NO provided that ATMOL1024 has been downloaded Otherwise at least one inte gral SCF variable must be set by specifying the path If ATMOL1024 is present and in addition one or more integral SCF packages are selected both ATMOL1024 and the ex plicitly selected interfaces should work with the created SAPT2002 executables In most cases the SAPT2002 codes use I O libraries of the integral SCF packages in order to read the data created by these packages Therefore a given SCF package has to be installed before SAP T2002 and its libraries must be accessible Two exceptions are CADPAC and GAMESS bo
109. s In addition both these objects can also be calculated at the UCHF level The CHF and UCHF induction and dispersion energies are also reported The uncoupled UCHF dispersion and induction energies are equivalent to E 20 and Be SAPT corrections respectively At the disp El CHF level the induction energy is equal to id resp The CHF dispersion is equivalent to the so called RPA dispersion see Ref 25 for examples PRA dispersion is currently not computed by regular SAPT algorithms Two other quantities that can be obtained using pcksdisp are the static dynamic dynamic dipole dipole polarizability tensor and the isotropic Cg dispersion asymptotic coefficient for the interaction of identical monomers both at the UCHF or CHF level 88 pcksdisp uses the transformed in the MO representation intra and intermonomer integrals as generated by the ptran module Therefore within a script like pEDI X it should be run after the SCF and transformation Note that currently pcksdisp assumes that all integrals are located in a single file 2e 000 001 Thus all such files have to be properly merged after the parallel ptran run This task is accomplished with the help of the program tmerge To ensure that ptran generates all the integrals necessary for pcksdisp the namelist INPUTCOR in the nameP data file should contain the directives CHFDISP T CHFIND T The actual control parameters for pcksdisp are collected in namelist INPUT which sho
110. s whichever is greater P 8 36 More precise calculation of the memory required for an efficient run can be done using the program memcalc built automatically during installation In order to use this program prepare the regular nameP data file with the first title line containing in this order the total number of DCTBS basis functions the total number of functions for monomer A will be different than the previous one in a MC BS type run the number of occupied orbitals for monomer A and then the same information for monomer B Then run the program by typing memcalc lt nameP data gt memcalc out The file memcalc out will contain detailed information about memory requirements of different parts of the code The variables MEMTRAN from namelist TRN and MEMSAPT from namelist INPUTCOR should then be adjusted accordingly The memory needed to run the cc program is calculated there explicitly so that no separate namelist variable is needed The memory requirements of the SCF programs are much smaller than those of SAPT2002 For specific information consult the manuals distributed with these programs Disk requirements of SAPT2002 are more difficult to estimate as these depend not only on the size of the monomers and basis set dimensions but also on the assumed integral thresholds and the dimer configuration For larger intermonomer separations more two electron integrals will be neglected and the integral files will be smaller than
111. s not have its counterpart among the corrections calculated in a regular psapt2K2 run It is more accurate in 67 terms of theory level than ES In the future the CHF dynamic susceptibility functions will be replaced by a still more accurate approximation e g resulting from a DFT calculation which will lead to even more accurate dispersion interaction The calculated monomer properties will be packed for further use e g a standalone invocation of caldisp_gms into a file name prop tar gz which after running gzip d name prop tar tar xvf name prop tar will decompress info the following files 1 vecta data and vectb data unformatted sequential files with orbital energies and SCF vectors 2 unformatted sequential files denaMO data and denbMO data containing MBPT2 and MBPT3 densities relaxed and non relaxed 3 propa data and propb data dynamic susceptibility functions currently at the CHF level unformatted sequential files 4 prop0a data prop0b data static susceptibility functions currently at the CHF level un formatted sequential files 5 geometry and basis set info of the monomers will be recorded in formatted files infoa data and infob data in the format readable by the subsequent transformationless codes After collecting these files and input edi in one scratch directory one can run the caldisp_gms program independently of the pEDI X script by typing or submitting through the qu
112. sors and 1 GB of memory The nodes are connected via a 200 MB s Myrinet Switch and also via 100 Mbit ethernet Each node is equipped with a local scratch filesystem not accessible from other nodes On each node this filesystem is mounted as scratch local In addition to local scratch all nodes have access to a shared scratch area mounted as scratch huinalu with the capacity of 239 GB All nodes have also access to users home directories and other shared resources The machine features the mpich implementation of MPI and a variety of Fortran compilers g77 Intel and Portland all capable of using both the Myrinet and the ethernet connectivity Special care must be taken at the time of compilation and execution so that the PATH variable points to the proper libraries and mpirun command appro priate for a given connection compiler combination Commands and programs can be executed on compute nodes from the login node through the ssh utility It is also possible to ssh login to the compute nodes although it is not necessary for running psapt2K2 The consecutive modules of psapt2K2 are launched from within the script pSAPT mpich maui or pSAPT mpich maui sep 58 described in the following using the appropriate mpirun command while GAMESS is started using the ddikick x utility of the ddi package The default source of ddikick x ddikick c has to be be modified to use ssh instead of rsh In the debugging stage psapt2K2 jobs may be submitted on
113. ssed as a combination of m terms while the susceptibility functions consist of m m 1 2 terms products of the auxiliary basis functions The cost of the calculation of electrostatics induction and dispersion dominated by 2 electron integrals between the auxiliary functions is now proportional to just m instead of n The disadvantage of this approach is the necessity of constructing a compact auxiliary basis capable of reproducing both densities and susceptibility functions not always an easy task The electron densities and susceptibility functions are fitted by minimizing functionals of the type A flor ar 10 r2 flora 7ra dridra 8 subject to a constraint f Penan 0 9 The quantity p denotes here either one of the MBPT contributions to electron density or a transition density a product of an occupied and a virtual orbital The quantity p is an approximation to p in the form of linear expansion in terms auxiliary basis functions The choice of 1 r12 as the 64 weight in the functional A has been suggested by Dunlap 24 Minimization of the functional A reduces then to solving a system of linear equations for the expansion coefficients Only one such equation system needs to be solved for each of the MBPT components of density whereas fitting of the susceptibility function for each imaginary frequency requires solving ov such systems one for each pair of the occupied and virtual orbitals Presented here is the bet
114. stem called Maui Scheduler The scheduler requires the user to prepare two scripts The first is the scheduler command script which in turn calls the second script which performs the file management tasks and invokes the psapt2K2 driver script The format of the scheduler commands script MAUI_script is as follows Initial working directory and wallclock time 59 IWD u bukowski tests ArHF_Tc Job wall time limit in seconds WCLimit 1800 Task geometry Tasks 8 Nodes 8 TaskPerNode 1 Feature requests Arch x86 OS Linux Account Account AFPRD 0102 001 MPI ethernet job for Myrinet use gm instead of p4 JobType mpi ch_p4 Execute a script file managing files and submitting the SAPT job Exec u bukowski tests ArHF_Tc sub_s_sep Optional arguments to the Exec script Args mn Where scheduler output will end up Output u bukowski LOGS MAUI_JOB_ID out Error u bukowski LOGS MAUI_JOB_ID err Log u bukowski LOGS MAUI_JOB_ID log Input Input dev null The launch script sub_s_sep should be similar to bin sh 60 JOB ArHF job name CURDIR u bukowski tests ArHF_Tc SCRDIR scratch local bukowski local scratch directory SAPT_SCRIPT u bukowski psapt2K2 bin pSAPT mpich maui sep SAPT driver script Set the number of nodes as assigned by the scheduler NPROC MAUI_TASK_COUNT OUTFILE scratch huinalu bukowsk
115. t their exchange counterparts which are currently not available Therefore calcula tions of these corrections are not recommended should be always set to FALSE 1 E14PLR E040 4 0 without triples elst resp elst resp 2 E1CC calculates electrostatic energy at the CCSD level new and not fully tested yet 31 3 TE14 Triples for E 4 elst resp 4 E300D EY 5 E3IND EG 6 DSPIND BOY ain All the variables are by default set to FALSE so only those that one wants to be computed have to appear on the namelist Three variables are provided to select groups of corrections SAPTO SAPT2 and SAPT and only one of them should be set to TRUE The settings SAPT2 T and SAPT T select the groups of corrections defined by Eqs 4 and 6 respectively The latter choice is approximately equivalent in accuracy of predictions to using supermolecular MBPT at the fourth order It has been used for most published recent SAPT calculations for small and medium size systems The former choice equivalent to MBPT2 requires significantly less computer time and can be recommended for larger dimers if time of calculations at the SAPT T level becomes an issue In both cases we recommend that the Et resp term defined by Eq 3 is included as implied by Eqs 4 and 6 This requires the scfcp keyword in the line submitting the SAPT script The choice SAPTO T selects all available SAPT corrections of zeroth order
116. te Q intermediate for monomer A m f ombov Same as omaov for monomer B m f tsa Evaluate singles amplitudes for monomer A m f tsb As tsa for monomer B m f copy Copy vector A to vector B m f rbfov Read into core lel integrals of occ vir type m f omaoo Computes 2 A occ occ intermediate for A m f omavv vir vir for monomer A m f omboo occ occ for monomer B m f ombvv vir vir for monomer B m f rbfoo Read into core 1 el integrals and store occ occ m f rbfvv and store vir vir b readin Read 2el ints in old version b readon Read lel integrals store only occ occ b readov Read lel integrals of a given type b readbf Read 2el integrals b readvv Read lel integrals dived by number of electrons b getbuf Get sorted 2el integral buffer from disk b getfct As above b wrtbu Write sorted 2el buffer b pour Write buffer to intermediate file b getpur Get buffer back from intermediate file b rbfab Read first order CC amplitudes b pourx Slightly different version of pour above b gtpurx Slightly different version of getpur above b getamp Reads from disk nonsorted CC amplitudes chf f setchf Coupled Hartree Fock routine driver chf f solvea Linear eq solver for monomer A chf f solveb Linear eq solver for monomer B chf f quit Exit routine if no convergence chf f putchf Write computed CHF coefficients onto disk chf f getchf Get computed CHF coefficients back chf f leqt1f Linear Equation
117. th of which generate data read by SAPT2002 using its own subroutines The possible SCF programs that can be used to generate atomic integrals and SCF vectors for SAPT2002 are e ATMOL1024 This is the current and maintained version of ATMOL 11 extended to handle up to 1023 basis functions ATMOL1024 is the default integral SCF pack age The Compal script checks if ATMOL1024 source is present in SAPT2002 atmo11024 subdirectory and compiles it automatically If for some reasons ATMOL1024 has to 11 be kept in another location and compiled separately it can still be used by SAP T2002 if the line ATMOL1024 NO in Compall is changed to reflect the current location of the ATMOL1024 main directory ATMOL1024 code has been tested with SAPT2002 more extensively than any other package and is the recommended choice Another package with which SAPT has been extensively tested is GAMESS US which also is currently the only parallel front end for parallel version of SAPT e GAUSSIAN GAUSSIAN94 G94 and GAUSSIAN98 iG98 Set at least one of these variables to NO as these packages are mutually exclusive The path specified here should contain the GAUSSIAN s library util a usually it is main directory of the GAUSSIAN distribution e GAMESS If used set the path to wherever the GAMESS executable is located Also set the variable VERNO which is the middle part of the name ofthis executable e g for gamess 01 x VERNO 01 The sole purpose of
118. the four interactive nodes hnfe01 hnf04 i e on up to 8 processors using a technique similar to that described above for samson The only practical difference is that the invocation of the mpirun command utilizes the machinefile option which for some reason is not working on samson Consequently the PROC file is only needed by GAMESS while the psapt2K2 modules use a file called calcnodes in the format similar to hnfe01 2 hnfe02 2 hnfe03 2 where 2 means that two processes will be run on each of the three interactive 2 processor nodes a total of 6 processes A PROC file consistent with calcnodes needed to inform GAMESS where to run will in this case have the form hnfe01 hnfe01 hnfe02 hnfe02 hnfe03 hnfe03 The driver script to be called by submit is now pSAPT mpich maui which differs from samson s pSAPT mpich in the syntax of mpirun command as well as in some file management portions it is assumed here that the scratch directory is set to the common filesystem scratch huinalu In order to run GAMESS pSAPT mpich maui calls a custom script runGMS mpich maui which differs from runGMS mpich in details of how the ddi s HOSTLIST is constructed and in the use of ssh instead of rsh for internode communication Jobs on interactive nodes can only be run using the ethernet network interface In the production stage psapt2K2 jobs have to be run on compute nodes The legal way to accomplish this is to use the huinalu s queuing sy
119. the isotropic dispersion coefficient that is computed USESUMN6 T F Sets the o v summation algorithm in a Casimir Polder dispersion calcu lation Set this to T unless you want to use the old 0 v summation algorithm MAKEH1H2 T F Set to enable construction of the Electric and Magnetic Hessians the HOW and H matrices in the CHF approximation Transformed integrals of certain types described bellow are required for this option If this option is set to F then the H and HC matrices must be read in from file in either the CHF or CKS approximation See bellow for details NUMFREQ and FREQ1 FREQ2 FREQ8 NUMFREQ is the number of frequencies at which a frequency dependent polarization calculation is to be made This should be less than or equal to 8 The variables FREQ1 FREQ2 FREQ8 contain the frequencies If complex frequencies are required set a negative frequency IQUADTYP and NQUAD The type of quadrature scheme to be used in performing the w integral in the Casimir Polder dispersion calculation and the calculation of the Ce dispersion coefficient IQUADTYP 1 sets the Gauss Legendre quadrature with the transformation w wo at IQUADTYP 2 sets the Gauss Legendre quadrature with the transformation w wotan t IQUADTYP 3 sets the Gauss Laguarre quadrature scheme The variable NQUAD sets the number of quadrature points to be used for the integration e OMEGAO and ALPHA The transfor
120. the most of this version you will have to obtain and install GAMESS US as the integral SCF package See Sec 13 for detailed description of psapt2K2 The instructions on unpacking these files can be found on the SAPT web page in the Download Area 5 Structure of SAPT2002 directory After unpacking the SAPT2002 main directory will contain the following files and subdirectories e Cleandirs use this script to clean the entire SAPT2002 directory tree before recompiling from scratch e Compall script used to build the package see Sec 7 e Makefile a generic makefile used by Compal1 e UPDATES 1log log of the history of changes and updates e atmol1024 present if ATMOL1024 file has been downloaded this directory contains the sources of the ATMOL1024 SCF code e tran program performing the one and two electron integral transformation e cc program performing the coupled cluster singles and doubles calculations for the monomers The first few iterations are performed perturbatively in this way producing MBPT order by order amplitudes needed in SAPT Both CCSD and MBPT amplitudes are later used by sapt module to compute intramonomer correlation contributions to various interaction energy components e sapt program computing the SAPT corrections e misc contains various interface and utility programs Most integral SCF packages need an interface program to extract one electron integrals and SCF orbital energies and
121. tion tool This creates a problem if an MPI application depends on files generated by GAMESS and both are to be run from the same driver script such as pSAPT mpich This means that pSAPT mpich has to be submitted directly on one of the compute nodes rather than on the login node and that the MPI programs should be launched without the nonlocal option The process of submitting a psapt2K2 on samson consists of the following steps 1 In your HOME create a subdirectory for the job and copy the input files job inp jobP data to this subdirectory 2 Create file calcnodes listing the nodes about to be used in the calculation for example sam2 sam4 samb sam6 Make sure there are no blank lines in this file 3 Make sure that the appropriate scratch directory we will use tmp bukowski as an example is present on each of the compute nodes listed in files calcnodes 4 Submit the job using a command submit JOB where JOB is the job name the core of the input file name and submit is a script similar to the following bin bash HHHHHHHHHH Customize scratch directory on compute nodes HHHHHHHHHH and the directory where the driver script resides 55 SCRDIR tmp bukowski scratch directory SAPT_SCRIPT home bukowski psapt2K2 bin pSAPT mpich SAPT driver script HHHHHHH Paths to the SAPT executable directory SAPTDIR home bukowski psapt2K2 bin HHHHHHHHHH End of customized part HH RARA HHEFHHHHHHHHAHHHEEHEHHAE
122. tional cost of the SAPT corrections scales as a product of some powers of the number of occupied orbitals and of the virtual orbitals Therefore with a given basis set size calculations for larger systems will take longer At the present time beginning of the year 2003 the largest runs performed included about 500 300 virtual orbitals for systems with monomers containing about 10 20 occupied orbitals Routine runs typically use basis set of about 200 functions In the asymptotic region i e for large intermonomer separations SAPT calculations may be significantly simplified by means of the multipole expansion which allows to express the interaction energy as a series of inverse powers of intermonomer separation Coefficients of this series the so called van der Waals constants depend only on monomer multipole moments and polarizabilities static and dynamic and can be computed using the POLCOR suite of codes by Wormer and Hettema 12 The POLCOR suite as well as a fitting program developed in our group and utilizing the ab initio asymptotic information comprise the independent package asymp_SAPT distributed optionally with SAPT2002 This document is intended to provide a basic introduction to the SAPT method and the instructions on how to download compile and run the SAPT2002 and psapt2K2 codes Also included are some details on the types of computers compilers and integral plus Hartree Fock self consistent field SCF packages th
123. tively Note that when running SAPT2002 with GAMESS as a front end SPHG must always be set to FALSE even if the ISPHER 1 option was applied during the SCF calculations to enforce removal of spurious spherical components from the Cartesian basis used by GAMESS The other string variable to be specified is tags It has to contain exactly the same number of characters as the basis variable The allowed characters are a b and m denoting basis functions appearing only in the MC BS of monomer A which can be the same as in pol a part of the basis discussed above only in MCTBS of B like polg and in MCTBS sets of both monomers respectively Each of the variables basis and tags should end with a sign denoting the end of a string For an example of using tags with GAMESS see the files in the directory SAPT2002 examples GAMESS HF _NH3_MCBS Here in the HF_NH3 inp HF_NH3A inp and HF NH3B inp files the DCTBS basis functions are input in the order F 5s3p2d H of HF 3s2p midbond 2s1p N 5s3p2d H1 of NH 3s2p H2 of NH 3s2p and H3 of NH 3s2p Now in this example the MCTBS for monomer A HF is constructed by deleting the last two s the last p and the last d functions of N as well as the last s and p function on each H of NH3 see the file HF_NH3MA inp The functions deleted here happen to be the most diffuse ones for each symmetry although in principle other choices could have been made as well Similarly the MC BC for monomer
124. to coupled cluster code memory estimator memcalc and a utility program tmerge which can be used to merge the transformed integral files if these are to be used further by sequential codes e pcc program performing the coupled cluster singles and doubles calculations for the monomers The first few iterations are performed perturbatively in this way producing MBPT order by order amplitudes needed in SAPT Both CCSD and MBPT amplitudes are later used by the psapt module to compute intramonomer correlation contributions to various interaction energy components as well as electron densities at various MBPT levels e psapt program computing the SAPT corrections e ptran parallel program performing the one and two electron integral transformation 47 e updates log log of the history of changes and updates 13 2 Installing psapt2K2 Installation of psapt2K2 is controlled by a ksh script compal11 a small portion of which has to be customized by the user The compall script sets the compilation options appropriate for a given hardware platform It is assumed that the integral SCF code used is GAMESS US No other SCF programs are currently supported by the compall script The use of other SCF packages is still possible although it would require some hand tuning of the compilation process After the compilation options have been set the compall script compiles and links all the pieces of the code Finally the scripts used to run psapt2K2
125. to force the two electron integrals to be written to disk We recommend SCF TIGHT CONV command to be used to tighten the SCF iterations convergence criteria On IBM RS 6000 and SP type computers under various versions of the operating system GAUSSIAN is apparently using two different strategies to equivalence integer and real numbers for the purpose of packing the integrals These two possibilities can be accounted for by setting the intpwp variable in the file tran intpwp f to 1 or 2 This variable stands for the number of integers per working precision word On older systems the working precision word was 4 byte long 32 bit architecture and for newer ones it is 8 byte long 64 bit architecture GAUSSIAN choices for what constitutes a working precision word on IBM computers seem to be sometimes not related to hardware architecture Note that for unknown reasons when using the GAUSSIAN series of codes at least MBPT2 MP2 level of theory must be requested to correctly close the files Also we remind the user that the MASSAGE keyword should be used in GAUSSIAN when setting the charges to zero e g to perform an SCF run for a monomer in a dimer centered basis set 8 4 GAMESS 8 4 1 Optional modification of GAMESS source In order to ensure that the SCF energies from GAMESS are printed with a sufficient number of decimals we recommend one FORMAT change in the rhfuhf src module prior to compilation of 16 GAMESS In the s
126. ubroutine RHFCL the statement 8000 FORMAT CLOSED SHELL ORBITALS GENERATED AT 3A8 10A8 EC A F20 10 ECNUC F16 10 15 ITERS should be replaced by 8000 FORMAT CLOSED SHELL ORBITALS GENERATED AT 3A8 10A8 EC A F24 16 ECNUC F16 10 15 ITERS 8 4 2 Required and recommended input options Please note that standard non direct SCF calculations must be performed and some options in the GAMESS input must have specific values e In the CONTRL input group NOSYM 1 option must be present i e no symmetry must be requested e Inthe INTGRL input group NOPK 1 integrals must not be in supermatrix form and NINTMX 2048 options must be present Maximum number of integrals in a record block NINTMX must be the same as linrec variable in the SAPT2002 module trans f which is set in the IF isitgams THEN block The linrec is currently set to 2048 but can be changed to a different value e We recommend that the following thresholds for the two electron integrals linear dependence and SCF convergence are set instead of the GAMESS default values in the CONTRL input group ICUT 24 ITOL 26 in the CONTRL input group QMTTOL 1 0E 30 this will prevent GAMESS from un expectedly removing quasi linearly dependent combinations of basis functions from the variational space at this point SAPT2002 does not work well if such a removal o
127. uld be appended to nameP data the scripts pEDI X do this automatically and look similar to INPUT ISITCASPOL T ISITINDUCI T ISITSOSDISP T ISITPROP F ISITCKS F ISITUCKS T ISITPOL F ISITC6DISP F USESUMN6 T MAKEH1H2 T IQUADTYP 1 NQUAD 10 OMEGAO 0 5 DEBUG1 T DEBUG2 F DEBUG3 F DEBUG4 F DEBUG5 F DEBUG6 F DEBUG7 F DEBUG8 F amp END The meaning of the options is as follows e Main Control flags ISITCASPOL T F Set if this is a Casimir Polder dispersion calculation ISITINDUCT T F Set if this is an Induction calculation ISITPROP T F Set if a Properties calculation needs to be performed 20 disp calculation ISITSOSDISP T F Set to perform a regular Sum Over States E e Propagator Type only one can be selected ISITCKS T F Set to T if the propagator is to be computed in the CHF approximation otherwise set to F 89 ISITUCKS T F Set to T if the UCHF approximation is to be used otherwise set to F e Properties calculation options ISITPOL T F Set if the Frequency dependent dipole polarizability tensor az y w is to be computed The frequencies at which the computation will be made are set by input keywords NUMFREQ and FREQ lt gt see bellow The dipole integrals are needed for this calculation See bellow for Integral Requirements ISITC6DISP T F Set is the Ce dispersion coefficient is to be computed At the moment it is
128. y not executing the corresponding binary scf The two electron files from a previous ATMOL1024 run will be recognized by a subsequent SCF run due to the naming convention It appears that some integral SCF programs e g GAMESS do not have a working option to skip the calculation of two electron integrals There are two ways of arranging basis functions in an MCTBS run The first way currently works only with ATMOL1024 but can possibly be tried with other packages This method is chosen by specifying the keyword BLKMB T in the TRN namelist read from the file nameP data this is also the default and therefore this keyword can be omitted If this path is used the basis functions in the DC BS type input files specified above name nameA and nameB x have to be ordered as follows pola isoa mid isog polg where isox is the isotropic part of the basis set of monomer X as defined above pol x are the polarization functions on monomer X orbitals with symmetries p and higher for H and He and d and higher for the first and second row atoms and mid are midbond functions optional In the calculations producing the orbital energies and coefficients for monomers A and B files nameMA and nameMB the basis set should be ordered as pola isoa mid isop and iso mid isog polp 25 respectively The method is in fact more general than the names isox and polx indicate As it should be clear from the above the basis set for each monom

SAPT2002 User Guide - University of Delaware Dept. of Physics

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