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GAMESS-UK USER'S GUIDE and REFERENCE MANUAL Version

1. k file save file in home directory of job t file save file in temporary directory l file access library file file must be ed0 or table n name provide root part of name for files default is the jobname r jobtype request save of all files required for restart T time time for job queue q none place job into an NQS queue Q queue args place job into an NQS queue non default job settings p nodes specify number of nodes for parallel execution S none Provide listing on stdout i none print information 3 GAMESS UK Pre Directives The program is capable of processing a set of pre directives each such directive extending over one data line and appearing as input before the program specific data These pre directives allow the user to define or modify through data input certain characteristics of the job environment e g time allocations routing of output file allocations memory requirements etc 3 1 The memory Pre directive This pre directive provides a mechanism for specifying the dynamic core to be associated with the present run of the code Memory requirements are in general a function of the RUNTYPE requested in the data input allocation can be modified through MEMORY data specification The pre directive consists of a single data line the first data field being set to the character string memory or core the second to an integer defining the number of words of memory Presenting the data line
2. 14 2 Analytic Force Constants 0000002 eee 15 Use of Bond centred Functions 16 SCF Analytic Force Constants for C2H4 17 MP2 Analytic Force Constants for C2H4 18 MP2 Polarisability for C2H4 19 Direct MP2 Calculation of C H N 20 CASSCF Geometry Optimisations 21 CASSCF 2nd order Cl Calculations on BeO 12 15 17 20 22 24 26 29 30 30 32 34 35 36 37 38 39 41 CONTENTS 22 MCSCF 2nd order CI Calculations on BeO 23 Table Cl calculations on the Ammonia Cation 24 ECP CASSCF and Direct Cl Calculations on NICCH gt 25 Table Cl Calculations of the Electronic Spectra of Pyridine 26 Full CI calculations 44 47 53 61 70 1 INTRODUCTION 2 1 Introduction In the present section we consider execution of GAMESS UK using the UNIX shell script rungamess The jobs perform the same function as those in the previous Chapter and the GAMESS UK directives themselves are identical However the input files contain only GAMESS UK directives all reference to pathnames for executable library and scratch files is handled by the script The principle differences associated with this mode of usage of the program are as follows 1 The users data files do not contain reference to specific pathnames for executables scratch directories etc These are taken from user set environment variables or are supplied by the local support staff 2 The job executes in a specially c
3. c n 1 ren x 2 1 0 1 90 0 c 1 rcc1 2 t1 3 pl c 1 rcc1 2 t1 3 p1 c 4 rcc2 1 t2 2 p2 c 5 rcc2 1 t2 2 p2 c 7 rcc3 5 t3 1 p3 o 2 rnoi 1 t5 3 90 0 o 2 rnol 1 t5 3 90 0 h 4 rchi 1 t6 2 pd h 5 rchi 1 t6 2 pd h 6 rch2 4 t7 11 p6 h 7 rch2 5 t7 12 p6 h 8 rch3 7 t8 14 p7 variables rcn 1 49 rcc1 1 37 rcc2 1 43 rcc3 1 37 rnol 1 21 rchi 1 084 rch2 1 084 rch3 1 084 t1 120 0 6 SCF CALCULATIONS ON C4F4 CeH NO2 AND Ce H NO2 3 CH3 t2 120 t3 120 t5 120 t6 120 t7 120 t8 120 pi 90 0 p2 180 0 p3 0 0 p5 0 0 p6 0 0 p7 0 0 end O O OOOO maxcyc 20 enter to run rungamess nitrobenzene Closed shell SCF Job for CgsH2 NO2 3CHs3 Contents of file tnt in title 2 4 6 tri nitro toluene 3 21g basis noprint distance basis vectors hessian zmat angstrom c 1 ri c 1 r2 2 al c 1 r2 2 al 3 180 c 1 r3 2 a2 3 0 c 1 r3 2 a2 3 180 x 1 d 2 90 3 180 c 1 r4 7 90 2 180 n 3 r5 2 a3 1 180 o 9 r6 3 a4 2 0 o 9 r7 3 a5 2 180 n 4 r5 2 a3 1 180 o 12 r6 4 a4 2 0 o 12 r7 4 a5 2 180 x 8 1 1 90 6 0 n 8 r8 15 90 1 180 o 16 r9 8 a6 5 0 o 16 r9 8 a6 5 180 x 2 1 1 90 4 0 c 2 r10 19 90 1 180 h 20 rii 2 a7 19 90 h 20 r12 2 a8 21 120 h 20 r12 2 a8 21 120 h 5 r13 8 a9 6 180 h 6 r13 8 a9 5 180 variables 7 STO 3G CALCULATIONS ON NA MG 15 to run ri 1 431 r2 1 367 r3 1 397 r4 1 395 al 60 38 a2 120 67 r5 1 521 r8 1 505 r6 1 277 r7 1 278 r9 1 277 a3 123 52 a4 121 19 a5 1
4. memory 8000000 will yield an allocation of 64 MBytes The default allocation of 4 000 000 words will prove adequate for most runs involving both SCF and Cl wavefunctions 3 2 The time Pre directive GAMESS UK monitors the CPU time available at intervals and if it is found that insufficient time remains to usefully continue will send restart control information to the Dumpfile and terminate execution The time pre directive is used to specify the time limit for the job in CPU minutes e g 4 SINGLE POINT SCF CALCULATION 9 time 120 will allocate 2 hours of CPU time to the job In the absence of the time pre directive a default allocation of 600 minutes will be in effect 4 Single Point SCF Calculation Let us consider a simple SCF run for H20 in a 3 21G basis and describe submission using the script rungamess Assume that the following lines reside in the file myjob in title h2o0 3 21g scf zmat angstrom o h 1 roh h 1 roh 2 theta variables roh 0 956 hess 0 7 theta 104 5 hess 0 2 end enter The command rungamess may then be used to run the job in the background rungamess myjob amp If batch submission were required the option q should be added rungamess myjob q gt amp myjob err amp This will result in the files used by GAMESS UK in this case ED2 ED3 and ED7 being created in the scratch directory for the job run and deleted on job termination The output from the job will be routed to the file myjob out Sys
5. diag title pyridine imir ground state dz 3s2p2d rydberg basis extrap 3 natorb civec 1 putq aos 2 enter to run rungamess r mrdci l table n pyridine2 pyridine2_imir 3 6M 1R Table CI Job for the X A State Contents of file pyridine2_6m1r in restart title pyridine dz bond centred functions super off nosym bypass scf zmat angstrom 10 c2c3 1 ccn 2 180 9 c2h6 1 nch2 2 0 0 10 c2h6 1 nch2 2 0 0 11 c3h5 9 c2c3h 1 180 12 c3h5 10 c2c3h 1 180 bq 1 1 39 3 90 2 180 variables c4n 2 7845546 ch4 1 0823078 c2n 1 3372389 c2nz 120 641858 c2c3 1 3944571 ccn 122 662269 c2h6 1 0814291 c3h5 1 0809550 nch2 116 400433 n x 11 0 x 1 1 0 2 90 x 1 1 0 2 90 3 90 c 1 c4n 3 90 2 180 x51 1 90 3 0 0 x 5 1 0 1 90 40 0 h 5 ch4 6 90 1 180 c 1 c2n 2 c2nz 3 180 c 1 c2n 2 c2nz 3 0 0 c 9 c2c3 1 ccn 2 180 c h h h h 25 TABLE CI CALCULATIONS OF THE ELECTRONIC SPECTRA OF PYRIDINE66 c2c3h 120 158516 end basis dz h 1 0 1 0 dz n dz c s bq 1 0 0 021 s bq 1 0 0 008 s bq 1 0 0 0025 p bq 1 0 0 017 p bq 1 0 0 009 d bq 1 0 0 015 d bq 1 0 0 008 end runtype ci mrdci adapt bypass tran freeze discard bypass 6040 1 to 6 1 to 4 8060 38 to 45 23 to 28 select cntrl 22 spin singlet symmetry 1 conf 1 2 3 4 5 32 33 44 45 46 62 1 2 3 4 5 32 38 44 45 46 62 1 2 3 4 5 32 33 44 45 46 65 32 33 38 39 12345 44 45 46 62 32 39 6265 12345 33 44 45 46 33 38 62 65 1
6. n x 11 0 x 1 1 0 2 90 x 1 1 0 2 90 3 90 c 1 c4n 3 90 2 180 x 5 1 0 1 90 30 0 x 5 1 0 1 90 4 0 0 h 5 ch4 6 90 1 180 c 1 c2n 2 c2nz 3 180 c 1 c2n 2 c2nz 3 0 0 c 9 c2 c3 1 cen 2 180 c h h h h basis dz h 1 0 1 0 dz n dz c s bq 1 0 0 021 s bq 1 0 0 008 s bq 1 0 0 0025 p bq 1 0 0 017 p bq 1 0 0 009 d bq 1 0 0 015 d bq 1 0 0 008 end runtype ci mrdci 26 FULL CI CALCULATIONS ad tr apt bypass an freeze discard bypass 6040 1 to 6 1 to 4 8060 38 to 45 23 to 28 select cntrl 22 spin singlet symmetry 4 conf 2 5 65 1 2 3 4 32 33 44 45 46 62 2 33 47 1 2 3 4 5 32 44 45 46 62 2 5 63 1 2 3 4 32 33 44 45 46 62 2 33 48 1 2 3 4 5 32 44 45 46 62 2 8 62 1 2 3 4 5 32 33 44 45 46 2 7 62 1 2 3 4 5 32 33 44 45 46 2 33 50 1 2 3 4 5 32 44 45 46 62 2 5 64 1 2 3 4 32 33 44 45 46 62 2 33 49 1 2 3 4 5 32 44 45 46 62 2 6 62 1 2 3 4 5 32 33 44 45 46 4 5 33 38 65 1 2 3 4 32 44 45 46 62 4 5 33 38 63 1 2 3 4 32 44 45 46 62 4 33 47 62 65 1 2 3 4 5 32 44 45 46 4 5 33 34 65 1 2 3 4 32 44 45 46 62 4 7 33 38 62 1 2 3 4 5 32 44 45 46 4 33 47 62 63 1 2 3 4 5 32 44 45 46 4 8 33 38 62 1 2 3 4 5 32 44 45 46 4 5 33 34 63 1 2 3 4 32 44 45 46 62 4 33 48 62 63 1 2 3 4 5 32 44 45 46 ro ots 10 12345678910 thresh 30 10 ci di ti pyridine 19mi0r 1a2 dz 3s2p2d rydberg basis ex ag tle trap 3 enter to run rungamess r mrdci l table n pyridine2 pyridine2_19m10r 26 Fu
7. na 1 r2 2 90 6 72 na 1 rl 3 90 2 180 variables ri 3 0286740 r2 3 194799 end 8 EXTENDED BASIS SET CALCULATIONS OF NA MG basis s mg 005004 5609 67 037083 841 969 171495 191 263 444597 53 2621 480060 16 6003 s mg 352170 2 97082 692921 1 00728 s mg 1 00000 113641 s mg 1 000000 044678 p mg 039884 50 9665 223321 11 4364 514536 3 21935 P mg 1 00000 0 914433 p mg 1 00000 0 16 d mg 1 00000 0 175 s na 003064 6902 67 022198 1059 04 095576 255 445 280448 77 3172 452587 26 8224 29313 10 0718 s na 1 000000 2 17902 s na 1 000000 689482 s na 1 0 040274 p na 042422 38 9438 229433 8 71012 509774 2 42053 p na 1 00000 661896 p na 1 0 065 end maxcyc 40 vectors getq ed3 1 1 enter to run rungamess t ed2 t ed3 n na7mg na mg_ext Open shell RHF Job 8 EXTENDED BASIS SET CALCULATIONS OF NA MG Contents of file na7mg_ext_orhf in dumpfile ed3 500 restart open shell scf using closed shell vectors from above bypass integral evaluation title na7mg 4s3p 4s3pid triplet rhf energy 1330 766950 super off bypass mult 1 charge 1 zmat angs mg na iri na i r2 2 90 na 1 r2 2 90 3 72 na 1 r2 2 90 4 72 na 1 r2 2 90 5 72 na 1 r2 2 90 6 72 na 1 ri 3 90 2 180 variables ri 3 0286740 r2 3 194799 end basis s mg 005004 5609 67 037083 841 969 171495 191 263 444597 53 2621 480060 16 6003 s mg 352170 2 97082 69292
8. 1 1 39 3 90 2 180 variables c4n 2 7845546 ch4 1 0823078 c2n 1 3372389 c2nz 120 641858 c2c3 1 3944571 ccn 122 662269 c2h6 1 0814291 c3h5 1 0809550 nch2 116 400433 c2c3h 120 158516 end n x 11 0 x 1 1 0 2 90 x 1 1 0 2 90 3 90 c 1 c4n 3 90 2 180 x 5 1 0 1 90 30 0 x 5 1 0 1 90 40 0 h 5 ch4 6 90 1 180 c 1 c2n 2 c2nz 3 180 c 1 c2n 2 c2nz 3 0 0 c 9 c2c3 1 ccn 2 180 c h h h h basis dz h 1 0 1 0 dz n dz c s bq 1 0 0 021 bq 0 0 008 bq 0 0 0025 b 0 0 017 p bq HO RU EF u 25 TABLE CI CALCULATIONS OF THE ELECTRONIC SPECTRA OF PYRIDINE63 1 0 0 009 d bq 1 0 0 015 d bq 1 0 0 008 end enter to run rungamess t ed2 t ed3 n pyridine2 pyridine2_rhf 2 1M 1R Table CI Job for the X A State An examination of the SCF output reveals the following symmetry adapted basis functions given the Co geometry and DZ plus Rydberg basis set IRREP NO OF SYMMETRY ADAPTED BASIS FUNCTIONS Thus the orbital reordering performed by the Table Cl module will yield the sequence numbers 1 45 for the a MOs 46 57 for the b MOs 58 85 for the bo MOs and 86 91 for the ao MOs We are both freezing and discarding orbitals in the subsequent Cl calculations Confining this to both a and bo MOs the first six orbitals of aj symmetry and first four orbitals of bo symmetry are to be frozen and the eight highest energy orbitals of aj symmetry and six highest of bo are to be discarded Thus th
9. 1 2 14 123 12 13 124 12 moment 36 1 36 2 1 enter to run rungamess r mrdci t table n nh3 nh3_analy 24 ECP CASSCF and Direct CI Calculations on NICCH This example illustrates the use of CASSCF and Direct Cl calculations in the framework of ECP studies The molecular system under investigation is NICCHo with a 5 reference direct Cl calculation performed using a CASSCF wavefunction for the lowest triplet state Five data files are presented below 24 ECP CASSCF AND DIRECT CI CALCULATIONS ON NICCHo 54 1 Start up closed shell SCF calculation for the Ay state Note the SUPER directive for compatibility with the subsequent open shell calculation The ECP library file scr1 gamess GAMESS UK libs ecplib on the HP735 at Daresbury is allocated to LFN ed0 with the NIHAY and C non local ECPs requested under control of the PSEUDO directive 2 Restart SCF job with appropriate use of the SWAP directive to converge the closed shell SCF 3 RHF calculation for the 3A state 4 CASSCF calculation for the 3A state 5 5 reference Direct Cl calculation for the 2A state Closed shell SCF Start up Job Contents of file nicch2_rhf in title ni cch2 1a1 rhf hay s ni bar s nm ecp s mult 1 super force zmat angstrom ni c 1 nica x 2 1 0 1 90 0 c 2 cacb 3 90 0 1 180 0 x 41 0 2 90 0 3 0 0 h 4 hcb 2 hcc 5 90 0 h 4 hcb 2 hcc 5 90 0 variables nica 2 0895 cacb 1 3604 hcb 1 1047 hcc 122 646 end basis
10. 1 831 131 ype analyse hics 2d e square 2d grid ni co 4 total density calc type titl ni c sect dens e 0 4 total density ion 151 11 2 PAIR GVB CALCULATION ON CH gt CH 4NHX to run plot type line title ni co 4 total density vectors 1 enter rungamess t ed3 nico4 ed3 nico4_grid The grid data will appear in the punchfile nico4_grid pun 11 2 Pair GVB Calculation on CH CH NH Closed shell SCF Job Contents of file imino_rhf in open shell rhf sto3g check super force title 1 imino 2 4 pentadiene energy 245 073475 super force nosym mult 1 accuracy 20 7 charge 1 zmat angs c c iri c 2 r2 1al c 3 r3 2 a2 1 cx c 4 r4 3 a3 2 c2 n 1 r5 2 a4 3 c2 h 1 r6 2 a5 3 ci h 2 r7 3 a6 7 c2 h 3 r8 4 a7 8 c2 h 4 r9 5 a8 9 c2 h 5 r10 4 a9 10 ci h 5 r11 4 a10 11 c2 h 6 r12 1 a11 7 c1 h 6 r13 1 a12 13 c2 variables r 1 3463261 r2 1 4632685 r3 1 3961480 r4 1 3568062 r5 1 3416773 r6 1 0748794 r7 1 0669518 r8 1 0811641 r9 1 0707072 24 11 2 PAIR GVB CALCULATION ON CH gt CH 4NHX rio 1 0729928 rii 1 0747118 ri2 0 9971261 r13 0 9985437 al 118 2539432 a2 122 8419092 a3 119 3229511 a4 125 9857684 a5 119 9766875 a6 122 1120978 a7 116 3317717 a8 120 9014063 a9 121 5606571 a10 121 8124933 a11 120 9303349 a12 121 8324395 constants c1 0 c2 180 cx 90 end basis sto3g runtype scf scftype rhf open 1 1 1 1 enter to run rungamess t ed2 t ed3
11. 2 23 TABLE CI CALCULATIONS ON THE AMMONIA CATION zmat angstrom n h i roh h 1 roh 2 theta h 1 roh 2 theta 3 theta 1 variables roh 1 03 hessian 0 7 theta 104 2 hessian 0 2 end runtype ci mrdci adapt tran select bypass symmetry 1 spin 2 cntrl 9 conf 14123 12 13124 12 roots 2 thresh 5 5 ci bypass diag bypass extrap 3 dthr 0 0001 0 0001 enter to run rungamess r mrdci t table n nh3 nh3_sa_tran Table CI Job II Configuration Selection Contents of file nh3_select in restart ci title nh3 3 21g mrdci energies ir 55 6393336 2r 55 4116210 bypass scf charge 1 mult 2 zmat angstrom n h 1 roh h 1 roh 2 theta h 1 roh 2 theta 3 theta 1 variables roh 1 03 hessian 0 7 theta 104 2 hessian 0 2 end runtype ci mrdci adapt bypass 50 23 TABLE CI CALCULATIONS ON THE AMMONIA CATION tran bypass select symmetry 1 spin 2 cntrl 9 conf 14123 12 13124 12 roots 2 thresh 5 5 ci bypass diag bypass extrap 3 dthr 0 0001 0 0001 enter to run rungamess r mrdci t table n nh3 nh3_select Table CI Job III CI Hamiltonian Construction Contents of file nh3_hamil in restart ci title nh3 3 21g mrdci energies ir 55 6393336 2r 55 4116210 bypass scf charge 1 mult 2 zmat angstrom n h 1 roh h 1 roh 2 theta h 1 roh 2 theta 3 theta 1 variables roh 1 03 hessian 0 7 theta 104 2 hessian 0 2 end runtype ci mrdci adapt bypass tran bypass
12. BeO MCSCF 2nd order CI calculations of the X D state of BeO Table Cl calculation of the X A4 and 12A states of the ammonia cation NHF cation ECP calculation on NiCCH2 with CASSCF and Direct Cl calculations of the lowest triplet state wavefunction Table Cl calculations typical of those performed in the calculation of electronic spectra In this case we are studying the disposition of the lowest A and 1 Ag states of pyridine The sequence of calculations involve the determination of the lowest 10 states of each category performed in a DZ plus rydberg basis Full Cl calculations of the XTA state of H20 2 USAGE OF THE RUNGAMESS SCRIPT 4 2 Usage of the Rungamess Script 2 1 Installation Please see the README file in the GAMESS UK rungamess directory for the installation and configuration instructions 2 2 Running a Job In its simplest usage the script is invoked by typing rungamess followed by a job name for example rungamess myjob This will cause GAMESS UK to read the file myjob in and generate the listing file myjob out and when appropriate punch file myjob pun in the directory of submission The exact pathnames used for the executable and scratch files are determined from values of environment variables as follows e The executable name is taken from the environment variable GAMESS_EXE e The environment variable GAMESS_SCR must be set to the name of a directory in which the user has permission to
13. all CSFs which can be generated by distributing 6 electrons in 6 MOs i e the CASSCF space This may be achieved in a single run through the following job specification Contents of file beo_mcscf_ci in restart new super off nosym 23 TABLE CI CALCULATIONS ON THE AMMONIA CATION 47 title beo dzp mcscf 2nd order ci 6 electrons in 6 mos zmat angstrom be o 1 beo variables beo 1 300 hessian 0 7 end basis dzp runtype ci active 4 to 31 end core 1 to 3 end scftype mcscf thresh 4 mcscf orbital 3cor1 doc1 doc3 doc2 uoci uoc2 uoc3 end direct 6 6 22 conf 222000 refgen 141516 242526 343536 refgen 141516 242526 343536 refgen 141516 242526 343536 refgen 141516 242526 343536 refgen 141516 242526 343536 refgen 141516 242526 343536 vectors i enter 20 21 to run rungamess t ed3 n beo beo_mcscf_ci Note that the vectors specification is requesting that the closed shell SCF eigenvectors be used to initiate the MCSCF calculation The MCSCF natural orbitals routed to section 20 of the Dumpfile will be used as the orbitals for the Direct Cl calculation 23 Table ClI calculations on the Ammonia Cation We consider below a Table Cl calculation of the X Aq state and 172A state of the ammonia cation In the first instance we consider performing the calculation in two steps initially the open shell SCF calculation followed by the MRD CI 2 reference state calculation We then sub divide the Cl calculation into 5 separa
14. beo 1 300 hessian 0 7 end basis dzp runtype ci active 4 to 31 end core 1 to 3 end scftype casscf thresh 4 config print fzc 1 to 3 doc 4 to 6 uoc 7 to 9 end superci 1 to 8 newton 9 to 20 hessian 9 to 20 simul 9 to 20 direct 6 6 22 conf 222000 refgen 141516 242526 343536 refgen 141516 242526 343536 refgen 141516 242526 343536 refgen 141516 242526 343536 refgen 22 MCSCF 2ND ORDER CI CALCULATIONS ON BEO 44 141516 242526 343536 refgen 141516 242526 343536 enter to run rungamess t ed2 t ed3 n beo beo_casscf_ci If restarts are envisaged the following invocation would be suitable rungamess r ci r casscf n beo beo_casscf_ci 22 MCSCEF 2nd order CI Calculations on BeO First we consider below a MCSCF calculation on the X X state of BeO characterised by the configuration 107207307407 10 2 The initial closed shell SCF using a DZP basis was conducted with the following job Contents of file beo_rhf in super off nosym title beo dzp zmat angstrom be o 1 beo variables beo 1 300 hessian 0 7 end basis dzp enter to run rungamess t ed2 t ed3 n beo beo_rhf An examination of the closed shell SCF output reveals the following symmetry adapted basis information IRREP NO OF SYMMETRY ADAPTED BASIS FUNCTIONS and the SCF MO ordering shown below 22 MCSCF 2ND ORDER CI CALCULATIONS ON BEO 1 1 20 45769692 2 0000000 2 1 4 72825831 2 0000000 3 1 1 15792230 2 000000
15. example is concerned with locating the transition state in the HPSi HSiP isomerisation process and calculating the associated vibrational frequencies We provide sample jobs using both numerical and analytical techniques in the transition state location and subsequent force constant evaluation Note that latter example is computationally the most efficient and should certainly be adopted for small medium sized molecules 14 1 Numerical Force Constants In the first step we perform an initial SCF for subsequent use in the saddle point calculation Closed shell SCF Job Contents of file hsip_scf in title psih saddle point 14 HSIP HPSI TRANSITION STATE LOCATION 31 zmat ang P x 1 1 0 si 1 psi 2 90 0 h 1 ph 2 90 0 3 hpsi variables psi 2 053 type 3 ph 2 44 type 3 hpsi 51 02 type 3 end enter to run rungamess t ed2 t ed3 n hsip hsip_scf In the subsequent location of the transition state note the use of TYPE 3 which causes the program to calculate the complete force constant matrix numerically before commencing the search for the saddle point and the use of XTOL to provide more stringent optimisation criteria in view of the subsequent force constant evaluation LOCK is used to retain the initial SCF configuration throughout the search Transition State Job Contents of file hsip_ts in restart new title psih lt gt hpsi saddle point bypass zmat angs P x 1 1 0 si 1 psi 2 90 0 h 1 ph 2 90 0 3 hps
16. occupied orbital list The NOGEN facility reorders the orbitals so that the GVB pairs occur together Note the ADAPT OFF specification now required when using localised orbitals as the input orbital set Contents of file water_gvb in restart title water gvb calculation using localised orbitals adapt off zmat ang o h 1 oh h 1 oh 2 hoh variables oh 0 956 hoh 104 5 end scftype gvb 2 vectors nogen 5 swap 25 3 4 end enter to run rungamess t ed2 t ed3 n water water_gvb 6 SCF Calculations on C F CsH NO and CgH2 NO2 3CH3 We show below the input files and job submission commands for three straightforward closed shell SCF calculations providing more examples of z matrix specification and reliance on the default options in such calculations In each case the direct access files will be deleted on job completion Closed shell SCF Job for Cy4F4 Contents of file cubane in title kkk c4f4 3 21g zmat angs x c 1 rl EiT F225 90 ci ri 3 90 2 180 6 SCF CALCULATIONS ON C4F4 CeH NO2 AND Cs H NO2 3 CH3 ci r2 4 90 3 180 x21 1 90 3 0 f 2 r3 6 90 3 180 x 4 1 1 90 30 f 4 r3 890 3 180 X 3 d 1 90 40 f 3 r3 10 90 4 180 XD d 1 90 4 0 f5 r3 12 90 4 180 variables ri 1 2 r2 1 3 r3 1 313 end enter to run rungamess cubane Closed shell SCF Job for CGH5NO gt Contents of file nitrobenzene in title c6h5 no2 3 21g accuracy 20 7 noprint zmat angstrom
17. script files for submission to NQS PBS and LoadLeveler are provided as part of the distribution You will need to set the environment GAMESS_SUBMODE to determine which of the submission scripts are chosen See the file README in the rungamess directory for up to date details of the setup required 2 6 Parallel Job Execution The p argument specifies the number of processors to be used to run the job It will only have an effect on a parallel machine and relies on the appropriate environment variables having been made to rungamess to invoke the parallel code Execution scripts for execution using TCGMSG GA IBM SP under POE LAM MPI and the Cray T3E series are included in the distribution You will need to set the environment variable GAMESS_PAREXE to the name of the parallel executable and GAMESS_PARMODE to specify which of the execution scripts to use on the current platform For interactive use on cluster systems GAMESS_HOSTS should be set to a list of hostnames to be use See the file README in the rungamess directory for up to date details of the setup required 2 7 Summary of Command Line Arguments The command line arguments accepted by rungamess are tabulated in Table 2 A listing of this information may be obtained on line by issuing the command rungamess i which will indicate which options are supported on your local installation 3 GAMESS UK PRE DIRECTIVES 8 Table 2 Arguments to rungamess Argument Keyword Function
18. select bypass symmetry 1 spin 2 cntrl 9 conf 14123 12 13124 12 roots 2 thresh 5 5 ci diag bypass 51 23 TABLE CI CALCULATIONS ON THE AMMONIA CATION to run extrap 3 dthr 0 0001 0 0001 enter rungamess r mrdci t table n nh3 nh3_hamil Table CI Job IV Diagonalisation Contents of file nh3_diag in to run restart ci title nh3 3 21g mrdci energies ir 55 6393336 2r 55 4116210 bypass scf charge 1 mult 2 zmat angstrom n h 1 roh h 1 roh 2 theta h 1 roh 2 theta 3 theta 1 variables roh 1 03 hessian 0 7 theta 104 2 hessian 0 2 end runtype ci mrdci adapt bypass tran bypass select bypass symmetry 1 spin 2 cntrl 9 conf 14123 12 13124 12 roots 2 thresh 5 5 ci bypass diag extrap 3 dthr 0 0001 0 0001 enter rungamess r mrdci t table n nh3 nh3_diag Table CI Job V CI Wavefunction Analysis Contents of file nh3_analy in 52 24 ECP CASSCF AND DIRECT CI CALCULATIONS ON NICCH 53 restart ci title nh3 3 21g mrdci energies ir 55 6393336 2r 55 4116210 bypass scf charge 1 mult 2 zmat angstrom n h 1 roh h 1 roh 2 theta h 1 roh 2 theta 3 theta 1 variables roh 1 03 hessian 0 7 theta 104 2 hessian 0 2 end runtype ci mrdci adapt bypass tran bypass select bypass symmetry 1 spin 2 cntrl 9 conf 14123 12 13124 12 roots 2 thresh 5 5 ci bypass diag bypass extrap 3 dthr 0 0001 0 0001 natorb cive 1 2 prop cive
19. t ed3 nico4 ed3 nico4_scf Examination of the output reveals the following symmetry designation sk kk kk k k kk k kkk MOLECULAR SYMMETRY FO k kk k kkk MOLECULAR POINT GROUP TD ORDER OF PRINCIPAL AXIS 0 SYMMETRY POINTS 10 GRAPHICAL ANALYSIS OF NI CO 4 23 POINT 1 0 0000000 0 0000000 0 0000000 POINT 2 0 0000000 0 0000000 1 0000000 POINT 3 0 0000000 1 0000000 0 0000000 and the follow ing atomic coordinates 0000000 0 0000000 0 0000000 NI 9976836 1 9976836 1 9976836 c 9976836 1 9976836 1 9976836 c 9976836 1 9976836 1 9976836 c 9976836 1 9976836 1 9976836 c 2316433 3 2316433 3 2316433 0 2316433 3 2316433 3 2316433 0 2316433 3 2316433 3 2316433 0 2316433 3 2316433 3 2316433 0 The following job may be used to construct a total density plot of the SCF wavefunction in a plane containing the Ni atom and two carbonyl groups with the Ni at the centre of the plot a contour plot will be generated on line printer output Contents of file nico4_grid in rest punc art h grid 151 title ni co 4 3 21g SCF total energy 1947 864822 au zmat ni O KO KK OFM OR 0 a 0 0 oP BP W W NDE EH EF 5 vari nic co 1 end runt grap gdef type titl angstrom nic nic 2 109 471 nic 2 109 471 3 120 0 nic 2 109 471 4 120 0 1 0 1 90 0 3 180 0 co 6 90 0 1 180 0 1 0 1 90 0 2 180 0 co 8 90 0 1 180 0 1 0 1 90 0 5 180 0 co 10 90 0 1 180 0 1 0 1 90 0 4 180 0 co 12 90 0 1 180 0 ables
20. 0 12 3 0 29518660 0 0000000 13 2 0 29518660 0 0000000 14 1 0 57290305 0 0000000 15 4 0 66957865 0 0000000 16 1 0 66957865 0 0000000 17 2 0 84348942 0 0000000 18 3 0 84348942 0 0000000 19 1 1 01733643 0 0000000 20 2 1 05237116 0 0000000 21 3 1 05237116 0 0000000 22 1 1 24301610 0 0000000 21 CASSCF 2ND ORDER CI CALCULATIONS ON BEO 43 23 1 1 45883277 0 0000000 24 1 1 80402496 0 0000000 25 4 2 36534068 0 0000000 26 1 2 36534068 0 0000000 27 2 2 62307878 0 0000000 28 3 2 62307878 0 0000000 29 1 3 16009549 0 0000000 30 1 4 37857805 0 0000000 31 1 45 42979631 0 0000000 We wish to perform a CASSCF calculation in which the inner shell and O2s orbitals the 1o 30 remain doubly occupied with the active space including the formally vacant SCF virtual MOs the 5o and 27 This example utilises the vectors from the closed shell SCF calculation We wish to perform the CASSCF calculation under RUNTYPE Cl specification where having performed the 6 electrons in 6 orbital CASSCF we use the natural orbitals in carrying out a second order Cl using the Direct Cl module Specifically we aim to use a reference space in the Cl consisting of all CSFs which can be generated by distributing 6 electrons in 6 MOs i e the CASSCF space This may be achieved in a single run through the following job specification Contents of file beo_casscf_ci in restart new title beo dzp casscftci 6 electrons in 6 mos bypass zmat angstrom be o 1 beo variables
21. 0 4 1 0 46629250 2 0000000 5 3 0 39257378 2 0000000 6 2 0 39257378 2 0000000 7 1 0 05704423 0 0000000 8 2 0 09936415 0 0000000 9 3 0 09936415 0 0000000 10 1 0 15573442 0 0000000 11 1 0 25156032 0 0000000 12 3 0 29518660 0 0000000 13 2 0 29518660 0 0000000 14 1 0 57290305 0 0000000 15 4 0 66957865 0 0000000 16 1 0 66957865 0 0000000 17 2 0 84348942 0 0000000 18 3 0 84348942 0 0000000 19 1 1 01733643 0 0000000 20 2 1 05237116 0 0000000 21 3 1 05237116 0 0000000 22 1 1 24301610 0 0000000 23 1 1 45883277 0 0000000 24 1 1 80402496 0 0000000 25 4 2 36534068 0 0000000 26 1 2 36534068 0 0000000 27 2 2 62307878 0 0000000 28 3 2 62307878 0 0000000 29 1 3 16009549 0 0000000 30 1 4 37857805 0 0000000 31 1 45 42979631 0 0000000 45 We wish to perform a CASSCF calculation in which the inner shell and O2s orbitals the 10 30 remain doubly occupied with the active space including the the formally vacant SCF virtual MOs the 5c and 27 This example utilises the vectors from the closed shell SCF calculation Contents of file beo_mcscf in to run restart new super off nosym title beo dzp bypass zmat angstrom be o 1 beo variables beo 1 300 hessian 0 7 end basis dzp scftype mcscf thresh 4 mcscf orbital 3cor1 doci doc3 doc2 uoci uoc2 uoc3 end enter 22 MCSCF 2ND ORDER CI CALCULATIONS ON BEO 46 rungamess t ed2 t ed3 n beo beo_mcscf The following points should be noted e The MCSCF Natural orbitals are routed
22. 1 1 00728 s mg 1 00000 113641 s mg 1 000000 044678 p mg 039884 50 9665 223321 11 4364 514536 3 21935 p mg 1 00000 0 914433 P mg 1 00000 0 16 d mg 1 00000 0 175 s na 003064 6902 67 022198 1059 04 095576 255 445 280448 77 3172 9 ECP CALCULATIONS OF NA7 MG P P 1 en 452587 26 8224 29313 na 10 0718 1 000000 2 17902 na 1 000000 689482 na 1 0 na 042422 229433 509774 na 1 00000 na 0 d 040274 38 9438 8 71012 2 42053 661896 065 open 1 1 1 1 ma en to run rungamess t ed2 t ed3 n na7mg na mg_ext_orhf 9 ECP calculations of Na Mgt xcyc 40 ter 20 In this example on Na7Mg we perform a local ECP calculation using the Hay Wadt ECP s together with the associated double zeta basis sets augmented by a d function on Mg Having carried out the closed shell SCF calculation we perform an RHF calculation on the singlet state of NazMg using the integrals calculated in the closed shell case Note that we are overwriting the files from the previous example Closed shell SCF Job Contents of file na7mg_ecp in ti tle na7mg LANL ecp closed shell singlet ch su zm mg na na na na na na na arge 1 per off at angs ri r2 r2 r2 r2 r2 ri PRPrPRPRPR EB W ND ND DD N 90 90 90 90 90 90 3 72 4 72 5 72 6 72 2 180 9 ECP CALCULATIONS OF NA MG to run variables rl 3 0286740 r2 3 1
23. 14 42 7200 1938645 11 7600 4596238 3 8170 5599305 1 1690 ni 0000000 0 2836 end HD O O O O QL HF ED EH O HH pseudo nonlocal nihay ni cc runtype scf maxcyc 40 level 3 0 10 1 0 swap 45 6 8 8 10 10 11 end enter to run rungamess t ed2 t ed3 1 edO n nicch2 nicch2_swap 24 ECP CASSCF AND DIRECT CI CALCULATIONS ON NICCH Open shell SCF Job Contents of file nicch2_orhf in restart new title ni cch2 3a1 rhf hay s ni bar s nm ecp s mult 3 super force bypass zmat angstrom ni c i nica x 21 0 1 90 0 c 2 cacb 3 90 0 1 180 0 x 41 0 2 90 0 3 0 0 h 4 hcb 2 hcc 5 90 0 h 4 hcb 2 hcc 5 90 0 variables nica 2 0895 cacb 1 3604 hcb 1 1047 hcc 122 646 end basis sh 0 032828 13 3615 0 231208 2 0133 0 817238 0 4538 sh 1 000000 0 1233 sc 1 000000 0 4962 sc 1 000000 0 1533 pc 0 018534 18 1557 0 115442 3 9864 0 386206 1 1429 0 640089 0 3594 pec 1 000000 0 1146 s ni 0 4372528 0 6778 1889453 0 1116 ni 0000000 0 0387 ni 0000000 0 0840 ni 0000000 0 0240 ni 0360414 42 7200 1938645 11 7600 4596238 3 8170 OO OAHU EF Hp HH 24 ECP CASSCF AND DIRECT CI CALCULATIONS ON NICCHp2 58 0 5599305 1 1690 d ni 1 0000000 0 2836 end pseudo nonlocal nihay ni cc runtype scf scftype gvb maxcyc 50 level 2 0 3 0 15 1 0 1 0 open 2 2 swap 11 12 14 15 end enter to run rungamess t ed2 t ed3 1 edO n nicch2 nicch2_orhf Eigenvecto
24. 16 17 a6 117 53 r10 1 529 r11 1 087 r12 1 082 a7 110 07 a8 109 7 r13 1 086 a9 121 26 end enter rungamess tnt 7 STO 3G Calculations on Na Mgt In this calculation we perform an STO 3G calculation on Na7Mg followed by an RHF and then UHF calculation on the triplet state Note the use of the SUPER directive to ensure an integral file format compatible with the use of BYPASS in the subsequent RHF and UHF calculations Closed shell SCF Job Contents of file na7mg_rhf in to run title nafmg sto 3g closed shell scf energy 1314 828516 mult 1 super force charge 1 zmat angs mg na 1 ri r2 r2 r2 r2 r2 na iri 90 90 3 72 90 4 72 90 5 72 90 6 72 90 2 180 na na na na HERE RPR HR na WDN ND ND DP N variables ri 3 0286740 r2 3 194799 end basis sto3g level 1 5 10 1 0 maxcyc 40 enter rungamess t ed2 t ed3 n nafmg na 7mg_rhf 7 STO 3G CALCULATIONS ON NA MG Open shell RHF Job Contents of file na7mg_orhf in to run restart title na7mg sto 3g triplet scf super force bypass mult 3 charge 1 zmat angs mg na iri na 1 r2 2 90 na 1 r2 2 90 3 72 na 1 r2 2 90 4 72 na 1 r2 2 90 5 72 na 1 r2 2 90 6 72 na iri 3 90 2 180 variables rl 3 0286740 r2 3 194799 end basis sto3g maxcyc 40 enter energy 1314 900829 rungamess t ed2 t ed3 n na7mg na mg_orhf UHF Job Contents of file na7mg_uhf in restart super fo
25. 2345 32 44 45 46 roots 11 thresh 30 10 ci diag title pyridine 6mir ground state dz 3s2p2d rydberg basis extrap 3 natorb BRR OOO civec 1 putq aos 2 enter to run rungamess r mrdci l table n pyridine2 pyridine2_6mir 25 TABLE CI CALCULATIONS OF THE ELECTRONIC SPECTRA OF PYRIDINE67 4 21M 10R Table CI Job for the A States Contents of file pyridine2_21m10r in restart title pyridine dztrydberg basis super off nosym bypass scf zmat angstrom 10 c2 c3 1 ccn 2 180 9 c2h6 1 nch2 2 0 0 10 c2h6 1 nch2 2 0 0 11 c3h5 9 c2c3h 1 180 12 c3h5 10 c2c3h 1 180 bq 1 1 39 3 90 2 180 variables c4n 2 7845546 ch4 1 0823078 c2n 1 3372389 c2nz 120 641858 c2c3 1 3944571 ccn 122 662269 c2h6 1 0814291 c3h5 1 0809550 nch2 116 400433 c2c3h 120 158516 end n x 11 0 x 1 1 0 2 90 x 1 1 0 2 90 3 90 c 1 c4n 3 90 2 180 x 5 1 0 1 90 30 0 x 5 1 0 1 90 4 0 0 h 5 ch4 6 90 1 180 c 1 c2n 2 c2nz 3 180 c 1 c2n 2 c2nz 3 0 0 c 9 c2c3 1 ccn 2 180 c h h h h basis dz h 1 0 1 0 dz n dz c s bq 0 0 021 bq 0 0 008 bq 0 0 0025 bq 0 0 017 bq 0 0 009 b 0 0 015 pk RQ HO EHO FU PF U 25 TABLE CI CALCULATIONS OF THE ELECTRONIC SPECTRA OF PYRIDINE68 d bq 1 0 0 008 end runtype ci mrdci adapt bypass tran freeze discard bypass 6040 1 to 6 1 to 4 8060 38 to 45 23 to 28 select cntrl 22 spin singlet symmetry 1 conf 62 65 33 34 581 62 63 3
26. 285 3 8664887 8 0 9 4719556 4 5440252 0 5381892 1 0 9 3293820 4 5891096 2 6957586 1 0 9 1872029 6 0381561 0 4734880 1 0 7 5522104 7 5798978 2 5757500 1 0 end basis sto3g scftype direct enter to run rungamess direct_scf Direct SCF Geometry Optimisation of Be CzH5 2 bb bb o o ot O bb Qa O Q b bo O O ba O b ba boo bo ba O bo bb b a B A O 12 DIRECT SCF CALCULATIONS Contents of file berylocene_opt in time 60 title be c5h5 2 sto3g optimised total energy 394 279009 au zmatrix angstrom x x 1 fxa c 2 xc 1 xxc c 2 xc 1 xxc 3 cxc c 2 xc 1 xxc 4 cxc c 2 xc 1 xxc 3 cxc c 2 xc 1 xxc 6 cxc x 2 xx 3 xxc 4 xxc h 2 hx 8 hxx 3 hcx h 2 hx 8 hxx 4 hcx h 2 hx 8 hxx 5 hcx h 2 hx 8 hxx 6 hcx h 2 hx 8 hxx 7 hcx x 2 fxt 3 xxc 4 xxc c 14 xc 1 xxc 3 cxxc c 14 xc 1 xxc 15 cxc c 14 xc 1 xxc 16 cxc c 14 xc 1 xxc 15 cxc c 14 xc 1 xxc 18 cxc x 14 xx 15 xxc 16 xxc h 14 hx 20 hxx 15 hcx h 14 hx 20 hxx 16 hcx h 14 hx 20 hxx 17 hcx h 14 hx 20 hxx 18 hcx h 14 hx 20 hxx 19 hcx be 2 fxa 3 xxc 4 xxc variables fxa 1 47 fxt 3 37 xc 1 22 hx 2 12 hxx 88 4 constants cxc 72 0 cxxc 36 0 xxc 90 0 hex 0 0 xx 1 0 end basis sto3g runtype optimize scftype direct level 2 0 10 1 4 enter to run rungamess berylocene_opt 13 HCN HNC TRANSITION STATE LOCATION 13 HCN HNC Transition State Location 29 Transition state calculation for the HCN HNC isomerisation process The first job uses the default trust r
27. 3 38 33 35 571 33 37 2 4 5 32 33 44 45 46 2 4 5 32 44 45 46 62 2 32 33 44 45 46 62 2 4 5 32 33 44 45 46 2 4 5 32 44 45 46 62 2 4 5 32 44 45 46 62 2 32 33 44 45 46 62 2 4 5 32 44 45 46 62 2591 32 33 44 45 46 62 2 62 64 4 5 32 33 44 45 46 2 33 36 4 5 32 44 45 46 62 2 2 2 2 4 4 4 4 4 4 RE RANE NDNEPEE VDE HE ND NW NW NV PD NN W DB N WUW BW BE W WUW i BE W W 5 11 12 3 4 32 33 44 45 46 62 33 39 1 2 3 4 5 32 44 45 46 62 32 34 1 23 4 5 33 44 45 46 62 32 38 1 23 45 33 44 45 46 62 5 8 33 38 1 2 3 4 32 44 45 46 62 33 38 62 65 1 2 3 4 5 32 44 45 46 32 33 34 38 1 2 3 4 5 44 45 46 62 33 34 62 65 1 2 3 4 5 32 44 45 46 32 38 62 63 1 2 3 4 5 33 44 45 46 57 33 38 1 2 3 4 32 44 45 46 62 roots 10123456789 10 thresh 30 10 ci diag title pyridine 2imiOr ial dz 3s2p2d rydberg basis extrap 3 enter to run rungamess r mrdci l table n pyridine2 pyridine2_21m10r 5 19M 10R Table CI Job for the A gt States Contents of file pyridine2_19m10r in restart 25 TABLE CI CALCULATIONS OF THE ELECTRONIC SPECTRA OF PYRIDINE69 title pyridine dztrydberg basis super off nosym bypass scf zmat angstrom 10 c2c3 1 ccn 2 180 9 c2h6 1 nch2 2 0 0 10 c2h6 1 nch2 2 0 0 11 c3h5 9 c2c3h 1 180 12 c3h5 10 c2c3h 1 180 bq 1 1 39 3 90 2 180 variables c4n 2 7845546 ch4 1 0823078 c2n 1 3372389 c2nz 120 641858 c2c3 1 3944571 ccn 122 662269 c2h6 1 0814291 c3h5 1 0809550 nch2 116 400433 c2c3h 120 158516 end
28. 94799 end basis ecpdz na ecpdz mg d mg 1 0 0 175 end ecp na na mg mg level 1 0 enter rungamess t ed2 t ed3 n na7mg na mg_ecp Open shell RHF Job Contents of file na7mg_ecp_orhf in restart title na mg ecp open shell singlet rhf mult 1 charge 1 super off bypass zmat angs mg na 1 ri r2 r2 r2 r2 r2 na 1 ri variables ri 3 0286740 r2 3 194799 end 90 90 3 72 90 4 72 90 5 72 90 6 72 90 2 180 na na na na PRPRPrRPRP HP na WN DND NV DV ND basis ecpdz na ecpdz mg d mg 1 0 0 175 end ecp na na mg mg runtype scf 21 10 GRAPHICAL ANALYSIS OF NI CO s 22 open 1 1 1 1 level 0 3 1 0 enter to run rungamess t ed2 t ed3 n na7mg na mg_ecp_orhf 10 Graphical analysis of Ni CO The following example illustrates features of the Graphical Analysis module in analysing the ground state SCF wavefunction of Ni CO 4 Let us assume the following job has been used in constructing this wavefunction Contents of file nico4_scf in title ni co 4 3 21g SCF total energy 1947 864822 au zmat angstrom ni c 1 nic c 1 nic 2 109 471 c 1 nic 2 109 471 3 120 0 c 1 nic 2 109 471 4 120 0 x 2 1 0 1 90 0 3 180 0 o 2 co 6 90 0 1 180 0 x 3 1 0 1 90 0 2 180 0 o 3 co 8 90 0 1 180 0 x 4 1 0 1 90 0 5 180 0 o 4 co 10 90 0 1 180 0 x 5 1 0 1 90 0 4 180 0 o 5 co 12 90 0 1 180 0 variables nic 1 831 co 1 131 end level 1 5 enter to run rungamess
29. CONTENTS Computing for Science CFS Ltd CCLRC Daresbury Laboratory Generalised Atomic and Molecular Electronic Structure System GAMESS UK USER S GUIDE and REFERENCE MANUAL Version 8 0 June 2008 PART 13 GAMESS UK under UNIX Rungamess M F Guest J Kendrick J H van Lenthe and P Sherwood Copyright c 1993 2008 Computing for Science Ltd This document may be freely reproduced provided that it is reproduced unaltered and in its entirety Contents 1 Introduction 2 Usage of the Rungamess Script 2 1 Installation o a 2 02 44 ia VA 22 Running Job lt ao cn ss etaa 2 3 Saving Files 2 4 Accessing Library Files 2 5 Batch Job Submission 2 6 Parallel Job Execution 2 7 Summary of Command Line Arguments 3 GAMESS UK Pre Directives IA OTO A A A CONTENTS 3 1 The memory Pre directipe LL oo a a A 1 32 The time Pre directive 4 lt bg ca da WR g wo wo wrak a RUR mik 4 Single Point SCF Calculation 5 Sequence of Calculations on H20 6 SCF Calculations on C4F4 CgH NO2 and CgH2 NO2 3CHs 7 STO 3G Calculations on Na7Mg 8 Extended Basis Set Calculations of Na Mg 9 ECP calculations of Na Mg 10 Graphical analysis of Ni CO 11 2 Pair GVB Calculation on CH gt CH 4NH3 12 Direct SCF Calculations 13 HCN HNC Transition State Location 14 HSiP HPSi Transition State Location 14 1 Numerical Force Constants 0 0 0004 eee
30. CULATIONS direct scf generate zmatrix sto3g basis title test2a energy 1550 28679356 charge 2 geometry distance angles torsions all 2 9512196 0 1547624 2 3287565 8 0 1 0815728 1 9700376 1 5385361 6 0 1 1603816 3 5363478 2 8467927 1 0 1 6367703 0 8475562 1 5624978 6 0 2 1566895 0 4797763 3 4976155 1 0 3 5011251 2 6669663 0 4827273 7 0 2 9474874 3 6433853 1 0782554 1 0 1 7359097 1 7242063 0 1090391 6 0 1 3150929 1 4125382 1 8702785 1 0 4 1957289 2 9182102 0 4054688 8 0 0 3417469 3 5022051 1 1895255 6 0 0 0532604 3 8272799 3 1681491 1 0 0 3292201 5 9011224 0 0783133 8 0 1 4442971 7 1126500 0 6802213 1 0 2 9721287 2 1997957 0 9534701 6 0 3 3279629 1 8049798 1 0197182 1 0 5 1750163 3 9122805 1 8751357 6 0 4 8159917 4 4971112 3 8035825 1 0 6 8815215 2 7942026 1 8646838 1 0 5 4889849 6 1460386 0 3379417 8 0 7 5612331 6 0739323 1 4363625 6 0 7 4278090 4 3945431 2 5896385 1 0 5 7357642 3 1285958 1 6502323 6 0 5 5713092 1 7094915 3 4875662 8 0 7 8017770 5 1679189 1 7463198 6 0 7 0224823 6 8328410 2 6479587 1 0 8 3530583 5 6784964 0 1498644 1 0 5 9321304 2 9668945 1 2970693 6 0 6 7897779 1 7121829 3 0617741 8 0 7 7021385 4 8380024 0 0564767 6 0 7 1302965 6 7576698 0 3499893 1 0 7 6050313 4 5640081 2 0812894 1 0 1 5715523 2 9124352 0 9658559 8 0 3 9184431 4 8124121 0 9101853 15 0 3 1659952 7 1913356 0 3438675 8 0 6 0342521 3 6456571 0 4943459 8 0 4 4900093 5 1460
31. ESS UK 1libs export GAMESS_LIB GAMESS_TMP scr1 xyz export GAMESS_TMP GAMESS_SCR scr1 xyz export GAMESS_SCR 2 3 Saving Files Command line options are used to request that datasets are to be retained beyond the end of the job The option k followed by a GAMESS UK logical filename presented in lowercase will cause the file to be retained in the directory from which the job is run with a suffix derived from the logical filename For example rungamess k ed3 myjob will save the dumpfile with filename myjob ed3 If control of the filename is required it may be provided using the symbol The following will associate the file on LFN ed3 with the file oldjob dump again in the directory of job submission rungamess k ed3 oldjob dump myjob If the filename supplied in this way is a UNIX relative pathname ie it does not start with it is taken to be relative to the current directory at the time the job is submitted Otherwise an absolute pathname is assumed as in the following example rungamess k ed3 scri xyz oldjob dump myjob This provides a completely general way of assigning the GAMESS UK datasets equivalent to the explicit setenv commands in the previous chapter However it becomes cumbersome if many datasets have to be named in this way The remaining file options t r n and l serve to provide a more concise syntax The t option is identical to k except that the default directory is the tem
32. ETRY OPTIMISATIONS to run 20 CASSCF Geometry Optimisations 10 c2c3 1 ccn 2 180 9 c2h6 1 nch2 2 0 0 10 c2h6 1 nch2 2 0 0 11 c3h5 9 c2c3h 1 180 12 c3h5 10 c2c3h 1 180 variables c4n 2 7845546 ch4 1 0823078 c2n 1 3372389 c2nz 120 641858 c2c3 1 3944571 ccn 122 662269 c2h6 1 0814291 c3h5 1 0809550 nch2 116 400433 c2c3h 120 158516 end basis 6 31g scftype direct mp2 enter x110 x 1 1 0 2 90 x 1 1 0 2 90 3 90 c 1 c4n 3 90 2 180 x 5 1 0 1 90 30 0 x 5 1 0 1 90 4 0 0 h 5 ch4 6 90 1 180 c 1 c2n 2 c2nz 3 180 c 1 c2n 2 c2nz 3 0 0 c 9 c2c3 1 ccn 2 180 c h h h h rungamess t ed3 pyridine 39 We consider below a CASSCF calculation on the XA state of H20 using a full valence criterion in specifying the active space so that the formally vacant SCF virtual MOs 4a and 2b2 are permitted variable occupancy This example utilises the vectors from the closed shell SCF calculation of Example 1 Contents of file water_cas in restart new title water at casscf level 3 21g basis set zmat angstrom o h 1 oh h 1 oh 2 hoh variables oh 0 956 20 CASSCF GEOMETRY OPTIMISATIONS to run hoh 104 5 end scftype casscf config print doc 1 to 5 uoc 6 7 end superci 1 to 8 newton 9 to 20 hessian 9 to 20 simul 9 to 20 enter rungamess t ed3 n water water_cas The following points should be noted 40 e It is not possible to use BYPASS in the above given the data for the SC
33. F job of Example 1 This would have resulted in generation of a P supermatrix which is not usable in a CASSCF run see Part 2 Table 1 e CASSCF calculations require two scratch FORTRAN data sets FTO1 and FT02 In the above we have assumed that the CASSCF calculation completes in the time allocated with the associated direct access files allocated in default scratch status The following rungamess invocation is typical of that required if restarts of the CASSCF step are envisaged here we are using the r argument which will cause all datasets required for a casscf scf or optimise restart calculation specifically edl ed2 ed4 ed6 ed9 ed10 and ed11 to be saved rungamess r casscf n water water_cas Assuming the above job terminated prior to convergence the calculation might be restarted as follows Contents of file water_cas_rest in restart scf title water at casscf level 3 21g basis set zmat angstrom o h 1 oh h 1 oh 2 hoh variables oh 0 956 hoh 104 5 end scftype casscf config bypass 21 CASSCF 2ND ORDER CI CALCULATIONS ON BEO Al doc 1 to 5 uoc 6 7 end superci 1 to 2 newton 3 to 20 hessian 3 to 20 simul 3 to 20 vectors 6 7 enter 6 7 to run rungamess r casscf n water water_cas_rest where the default sections housing the CASSCF vectors and ci coefficients sections 6 and 7 respectively created in the startup job are explicitly declared above and CONFIG processing is bypass ed Having c
34. FOrRROR kk R O O OO O ODE HO O O O O O ed3 t ed5 t ed6 l edO n nicch2 nicch2_ci 25 Table CI Calculations of the Electronic Spectra of Pyri dine This example demonstrates the use of the Table Cl module in the calculation of the low lying states of Pyridine Specifically we are involved in determining the disposition of the first ten 1A and A gt states using a common set of orbitals the X A SCF MOs in a DZ plus Rydberg basis set of 91 functions Five job files are presented below 1 Start up closed shell SCF calculation for the X A state Note the SUPER directive for compatibility with the subsequent Cl calculation Note also the particular syntax for siting the DZ basis on H the third and fourth data fields are to provide an unscaled hydrogen basis since the default specification will scale the two components by 1 2 the more contracted and 1 15 the more diffuse component 2 1M IR Table Cl calculation of the X A state 3 6M 1R Table Cl calculation of the X A state 25 TABLE CI CALCULATIONS OF THE ELECTRONIC SPECTRA OF PYRIDINE62 4 21M 10R Table Cl calculation of the ten lowest A states 5 19M 10R Table Cl calculation of the ten lowest LA states 1 Closed shell SCF Job Contents of file pyridine2_rhf in title pyridine dz bond centred functions super off nosym zmat angstrom 10 c2c3 1 ccn 2 180 9 c2h6 1 nch2 2 0 0 10 c2h6 1 nch2 2 0 0 11 c3h5 9 c2c3h 1 180 12 c3h5 10 c2c3h 1 180 bq
35. calculation of the triplet state 1 INTRODUCTION 3 10 11 12 13 14 15 16 17 18 19 20 21 22 23 Extended basis set calculation on Na7Mg with SCF calculation of the singlet state preceding an RHF calculation of the triplet state ECP calculation on Na7Mgtin a double zeta valence basis with SCF calculation of the singlet state preceding an RHF calculation of the triplet state 2 pair GVB calculation on 1 imino 2 4 pentadiene CH CH 4NH3 Graphical analysis of the X Aq state of Ni CO 4 STO 3G direct SCF calculations on C 10 10NPH s and the geometry optimisation of Be C5H5 o Determination of the transition state for the HCN HNC isomerisation reaction This example demonstrates usage of the three saddle point algorithms available the default trust region method plus the synchronous transit and Simons Jorgensen algorithms Location of the transition state for the HPSi HSiP isomerisation and subsequent force constant evaluation Specification of bond centred functions located at the midpoint of the C N bond in the HCN HNC transition state SCF geometry optimisation and analytic force constants of C2H4 MP2 geometry optimisation and analytic force constants of CzH MP2 geometry optimisation and polarisability of C2H4 Direct MP2 calculation of CzH5N in a 6 31G basis CASSCF geometry optimisation of the XA state of H20 CASSCF 2nd order CI calculations of the X X state of
36. create files A directory will be created under this directory for each job that is run and all binary datasets that are not routed elsewhere will be written here for the duration of the job The directory is deleted at the end of the job If GAMESS_SCR does not exist an attempt will be made to create it The environment variable GAMESS_TMP should be set to a directory in which storage of files between jobs is possible see below although it is not used in this simple example e The environment variable GAMESS LIB must be set to the name of a directory containing the GAMESS UK Library files see Accessing Library Files below The values of these variables will usually be set as part of the login procedure On a central computer facility the values should be provided by the support staff in other cases the user should edit values into the appropriate login scripts For users of the C Shell bin csh the entry should be made in the script login The following is appropriate for user xyz on the DEC AXP 433AU at Daresbury setenv GAMESS_EXE scri wab GAMESS UK bin gamess setenv GAMESS_LIB scri wab GAMESS UK libs setenv GAMESS_TMP scri xyz setenv GAMESS_SCR scri xyz Users of the Borne shell bin sh and Korn shell bin ksh should make the corresponding definitions in the file profile in their home directory 2 USAGE OF THE RUNGAMESS SCRIPT 5 GAMESS_EXE scr1 wab GAMESS UK bin gamess export GAMESS_EXE GAMESS_LIB scr1 wab GAM
37. dered canonicalised open shell vectors written on termination of the SCF process Note that the table keyword will activate generation of the Table Cl data base to be used in the subsequent steps below In this case the data base will be written to the file nh3 table in the temporary directory for subsequent use Note that on most installations a copy of the data base will already be available and some time is saved if recomputation is avoided It is accessed with the library or option on the rungamess command line ln this case the table keyword must be removed rungamess t ed2 t ed3 l table n nh3 nh3_mrdci Now let us consider dividing the above CI calculation The following points should be noted in this division e the r mrdci option has been used to save all files that must be retained between separate runs of the program The option t ed2 is now implicit and so may be omitted We assume below that the Table Cl data base is available from the previous job thus omitting the TABLE step e Note the use of the BYPASS keyword on the various steps comprising the Table Cl proce dure Such a keyword is required on both those steps already completed and those steps to be handled in a subsequent run of the program Table CI Data I Symmetry Adaption and Integral Transformation Contents of file nh3_sa_tran in restart title nh3 3 21g mrdci energies ir 55 6393336 2r 55 4116210 bypass scf charge 1 mult
38. e final sequence numbers for the active orbitals in the Cl are 1 31 for the a MOs 32 43 for the bi MOs 44 61 for the b MOs and 62 68 for the aa MOs The CONF data line specifying the reference configuration is based on the associated sequence numbers of these active orbitals Contents of file pyridine2_Im1r in restart title pyridine dz bond centred functions super off nosym bypass scf zmat angstrom 1 0 1 0 2 90 1 0 2 90 3 90 c4n 3 90 2 180 1 0 1 90 3 0 0 1 0 1 90 4 0 0 HH KMK O K K K OB NORE PE HP 25 TABLE CI CALCULATIONS OF THE ELECTRONIC SPECTRA OF PYRIDINE64 ch4 6 90 1 180 c2n 2 c2nz 3 180 c2n 2 c2nz 3 0 0 c2c3 1 cen 2 180 10 c2c3 1 ccn 2 180 9 c2h6 1 nch2 2 0 0 10 c2h6 1 nch2 2 0 0 11 c3h5 9 c2c3h 1 180 12 c3h5 10 c2c3h 1 180 bq 1 1 39 3 90 2 180 variables c4n 2 7845546 ch4 1 0823078 c2n 1 3372389 c2nz 120 641858 c2c3 1 3944571 ccn 122 662269 c2h6 1 0814291 c3h5 1 0809550 nch2 116 400433 c2c3h 120 158516 end Orre bb pb Qa 0 0 a B basis dz h 1 0 1 0 dz n dz c s bq 1 0 0 021 s bq 1 0 0 008 s bq 1 0 0 0025 p bq 1 0 0 017 p bq 1 0 0 009 d bq 1 0 0 015 d bq 1 0 0 008 end runtype ci mrdci adapt tran freeze discard 6040 1 to 6 1 to 4 8060 38 to 45 23 to 28 select cntrl 22 spin singlet symmetry 1 conf 0123 45 32 33 44 45 46 62 25 TABLE CI CALCULATIONS OF THE ELECTRONIC SPECTRA OF PYRIDINE65 roots 1 1 thresh 30 10 ci
39. egion algorithm the second the synchronous transit algorithm and the third the Jorgensen Simons algorithm Contents of file hcn_tr in to run title hcn 4 31G saddle point zmat angs c x 1 1 0 n 1 cn 2 90 0 h 1 ch 2 90 0 3 hen variables cn 1 1484 type 3 ch 1 5960 type 3 hen 90 0 type 3 end basis 4 31g runtype saddle enter rungamess hcn_tr Saddle point for HCN using the synchronous transit algorithm note the definition of the minima required on the variable definition lines and the LSEARCH directive The default saddle point method does nor require minima definition see above Contents of file hcn_st in to run title hcn saddle point synchronous transit zmat angs c x 11 0 n 1 cn 2 90 0 h 1 ch 2 90 0 3 hen variables cn 1 1484 minima 1 1371 1 1597 ch 1 5960 minima 1 0502 2 1429 hen 90 0 minima 180 0 0 0 end basis 4 31g runtype saddle lsearch 0 4 enter rungamess hcn_st 14 HSIP HPSI TRANSITION STATE LOCATION 30 Saddle point for HCN using the Jorgensen Simons algorithm Contents of file hcn_js in title hcn hnc ts search jorgensen simons zmat angs c x 1 1 0 n 1 cn 2 90 0 h 1 ch 2 90 0 3 hen variables cn 1 1484 type 3 ch 1 5960 type 3 hen 90 0 type 3 end basis 4 31g runtype saddle jorgensen powell maxjor 55 recalc off rfo off cutoffs optprint on xtol 0 0018 enter to run rungamess hcn_js 14 HSiP HPSi Transition State Location This
40. er to run rungamess t ed3 ethene ed3 ethene_fcm 17 MP2 Analytic Force Constants for CH We consider below computing the analytic force constants for CoH4 initially optimising the molecule at the MP2 level followed by the force constant calculation Note again the use of the XTOL directive in the optimisation job to ensure a higher degree of optimisation than that derived using the default XTOL MP2 Geometry Optimisation Contents of file ethene_mp2opt in title ethylene 6 31g MP2 optimised total energy 78 3272309 zmatrix angstrom cc ch 2 hcc ch 2 hcc 3 180 0 ch 1 hcc 3 0 0 2 ch 1 hcc 3 180 0 variables cc 1 40 ch 1 10 hcc 118 0 end basis 6 31g runtype optimize scftype mp2 xtol 0 0001 enter bbb ba Qa Ner PR to run rungamess t ed3 ethene ed3 ethene_mp2opt MP2 Analytic Force Constants Contents of file ethene_mp2fem in 18 MP2 POLARISABILITY FOR C2H4 to run restart title ethylene MP2 6 31g ground state vibrational frequencies freq 847 7 941 6 994 1 1091 6 1267 4 1414 5 freq 1525 2 1729 7 3241 3 3259 2 3336 6 3359 8 zmatrix angstrom cc ch 2 hcc ch 2 hcc 3 180 0 ch 1 hcc 3 0 0 2 ch 1 hcc 3 180 0 variables cc 1 40 ch 1 10 hcc 118 0 end basis 6 31g runtype hessian scftype mp2 enter rpprpprppyraa DEEP HP rungamess t ed3 ethene ed3 ethene_mp2fcm 18 MP2 Polarisability for C gt H4 37 We consider below computing the molecular polarisab
41. i variables psi 2 053 type 3 ph 2 44 type 3 hpsi 51 02 type 3 end runtype saddle lock xtol 0 0005 enter 2 to run rungamess t ed2 t ed3 n hsip hsip_ts Finally we present the job for numerical evaluation of the force constants at the optimised ge ometry Note the use of restart in requesting usage of the geometry from the Dumpfile rather 14 HSIP HPSI TRANSITION STATE LOCATION 32 than from the data file Numerical Force Constant Job Contents of file hsip_fc in restart title psih lt gt hpsi saddle point numerical fcm zmat angs P x 11 0 si 1 psi 2 90 0 h 1 ph 2 90 0 3 hpsi variables psi 2 053 type 3 ph 2 44 type 3 hpsi 51 02 type 3 end runtype force vectors 2 lock enter 3 to run rungamess t ed2 t ed3 n hsip hsip_fc 14 2 Analytic Force Constants In the first step we perform the computation of the trial hessian under RUNTYPE HESSIAN control for subsequent use in the saddle point calculation Computing the trial Hessian Contents of file hsip_fcm1 in title psih trial hessian SCF zmat ang P x 11 0 si 1 psi 2 90 0 h 1 ph 2 90 0 3 hpsi variables psi 2 053 ph 2 44 hpsi 51 02 end runtype hessian enter 14 HSIP HPSI TRANSITION STATE LOCATION 33 to run rungamess t ed2 t ed3 n hsip hsip_fcmi In the subsequent location of the transition state note the use of the FCM keyword on the RUNTYPE data line to restore the trial hessian computed in the first
42. ility of C H4 initially optimising the molecule at the MP2 level followed by the property calculation Note again the use of the XTOL directive in the optimisation job to ensure a higher degree of optimisation than that derived using the default XTOL MP2 Geometry Optimisation Contents of file ethene_mp2opt in title ethylene 6 31g MP2 optimised total energy 78 3272309 zmatrix angstrom 1 cc 1 ch 2 hcc 1 ch 2 hcc 3 180 0 2 ch 1 hcc 3 0 0 2 ch 1 hcc 3 180 0 variables cc 1 40 ch 1 10 hcc 118 0 bb bb a Q 19 DIRECT MP2 CALCULATION OF C H N to run end basis 6 31g runtype optimize scftype mp2 xtol 0 0001 enter rungamess t ed3 ethene ed3 ethene_mp2opt MP2 Polarisability Contents of file ethene_mp2pol in to run restart title ethylene MP2 6 31g ground state polarisability zmatrix angstrom cc ch 2 hcc ch 2 hcc 3 180 0 ch 1 hcc 3 0 0 2 ch 1 hcc 3 180 0 variables cc 1 40 ch 1 10 hcc 118 0 end basis 6 31g runtype polarisability scftype mp2 enter bb bb a Q verre rungamess t ed3 ethene ed3 ethene_mp2pol 19 Direct MP2 Calculation of C H N 38 We show below the data for performing a direct MP2 calculation on the CzH5N molecule conducted in a 6 31G basis set Note the use of the MEMORY pre directive in requesting a memory allocation of 4 MWords Contents of file pyridine in title pyridine 6 3ig direct mp2 zmat angstrom n 20 CASSCF GEOM
43. is dunning 9s5p 3s2p bond s p p h zmat angstrom c bq 1 rcn2 x 21 0 1 90 0 n 2 rcn2 3 90 0 1 180 0 x 11 0 2 90 0 3 0 0 h 1 rch 5 90 0 4 phi variables ren2 0 5991 rch 1 2128 phi 71 2 end basis sv h h 0 0 7 bq 0 1 0 bq 0 0 7 svc HO RH U eS sv n end enter rungamess hcn_bf 16 SCF ANALYTIC FORCE CONSTANTS FOR C gt H4 16 SCF Analytic Force Constants for CoH We consider below computing the analytic force constants for CoH4 initially optimising the molecule at the SCF level followed by the force constant calculation XTOL directive in the optimisation job to ensure a higher degree of optimisation than that derived using the default XTOL Geometry Optimisation Contents of file ethene_opt in to run title ethylene 6 31g geometry optimisation zmatrix angstrom cc ch 2 hcc ch 2 hcc 3 180 0 ch 1 hcc 3 0 0 2 ch 1 hcc 3 180 0 variables cc 1 40 ch 1 10 hcc 118 0 end basis 6 31g runtype optimize xtol 0 0001 enter bb bb a Q DEEP HP rungamess t ed3 ethene ed3 ethene_opt Analytic Force Constants Contents of file ethene_fcm in restart title ethylene 6 31g ground state vibrational frequencies zmatrix angstrom cc ch 2 hcc ch 2 hcc 3 180 0 ch 1 hcc 3 0 0 2 ch 1 hcc 3 180 0 variables cc 1 40 ch 1 10 bb bb a Qa DEE HP Note the use of the 17 MP2 ANALYTIC FORCE CONSTANTS FOR C2H4 36 hcc 118 0 end basis 6 31g runtype hessian ent
44. job and the use of XTOL to provide more stringent optimisation criteria in view of the subsequent force constant evalu ation LOCK is used to retain the initial SCF configuration throughout the search Transition State Job Contents of file hsip_tsfcm in restart new title psih lt gt hpsi saddle point location using trial hessian zmat angs P x 1 1 0 si 1 psi 2 90 0 h 1 ph 2 90 0 3 hpsi variables psi 2 053 ph 2 44 hpsi 51 02 end runtype saddle fcm xtol 0 0005 vectors 1 lock enter 2 to run rungamess t ed2 t ed3 n hsip hsip_tsfcm Finally we present the job for analytic computation of the force constants at the optimised geometry under control of runtype hessian Note the use of restart in requesting usage of the geometry from the Dumpfile rather than from the data file Analytic Force Constant Job Contents of file hsip_fcm2 in restart title psih lt gt hpsi saddle point force constants zmat angs P 15 USE OF BOND CENTRED FUNCTIONS to run 15 x 1 1 0 si 1 psi 2 90 0 h 1 ph 2 90 0 3 hpsi variables psi 2 053 ph 2 44 hpsi 51 02 end runtype hessian vectors 2 lock enter 2 rungamess t ed2 t ed3 n hsip hsip_fcm2 Use of Bond centred Functions 34 In this example we demonstrate the use of bond centred functions s p cited at the mid point of the C N bond in the HCN HNC transition state Contents of file hcn_bf in to run title hcn hnc bas
45. ll CI calculations 70 We consider below Full Cl calculations of the X A state of the H2O molecule In the first in stance we consider correlating all electrons We then perform a valence only calculation freezing the Ols orbital through the ACTIVE and CORE directives specifying a total of 8 electrons on the FULLCI data line All electron Job 26 FULL CI CALCULATIONS 71 Contents of file fullci_all in to run core 8000000 title h2o DZ basis full ci super off nosym zmat angstrom o h 1 roh h 1 roh 2 theta variables roh 0 956 hess 0 7 theta 104 5 hess 0 2 end basis dz runtype ci fullci 14 5 5 enter rungamess r fullci n h2o_fullci fullci_all Assuming the above job did not complete in the time allocated and dumped to disk in a controlled fashion the following job would act to continue the processing assuming that the FORTRAN file from stream ftn008 had been saved along with the Mainfile ed2 Dumpfile ed3 and Transformed integral file ed6 All these files should be stored on temporary disk space given the r fullci argument Restarting the Full CI job Contents of file fullci_rest in to run core 8000000 restart ci title h2o DZ basis restart full ci super off nosym zmat angstrom o h 1 roh h 1 roh 2 theta variablesNroh 0 956 hess 0 7 theta 104 5 hess 0 2 end basis dz runtype ci fullci 14 55 enter rungamess r fullci n h2o_fullci fullci_rest Valence electron Job Conte
46. n imino imino_rhf Two Pair GVB Job Contents of file imino_gvb in gvb scf with two pairs bypass integral evaluation restart bypass title 1 imino 2 4 pentadiene energy 245 114661 mult 1 super force nosym accuracy 20 7 charge 1 zmat angs c c iri c 2 r2 1al c 3 r3 2 a2 1 cx c 4 r4 3 a3 2 cz n 1 r5 2 a4 3 c2 h 1 r6 2 a5 3 ci h 2 r7 3 a6 7 c2 12 DIRECT SCF CALCULATIONS h 3 h4 h 5 r10 4 h 5 r11 4 h 6 r12 1 h 6 r13 1 variables r 1 r2 1 r3 1 r4 1 r5 1 r6 1 r7 1 r8 1 r9 1 r10 1 rii 1 r12 0 r13 0 al 118 a2 122 a3 119 a4 125 a5 119 a6 122 a7 116 a8 120 a9 121 a10 121 a11 120 a12 121 constants c1 0 c2 180 cx 90 end r8 4 a7 8 c2 r9 5 a8 9 c2 a9 10 c1 a10 11 c2 ail 7 ci ai2 13 c2 3463261 4632685 3961480 3568062 3416773 0748794 0669518 0811641 0707072 0729928 0747118 9971261 9985437 2539432 8419092 3229511 9857684 9766875 1120978 3317717 9014063 5606571 8124933 9303349 8324395 basis sto3g runtype scf scftype gvb 2 enter to run rungamess t ed2 t ed3 n imino imino_gvb 12 Direct SCF Calculations 26 In the first example below we show a direct SCF calculation in which the input geometry in cartesian coordinates is converted to z matrix representation the second calculation features geometry optimisation of Be C5H5 2 using the direct SCF module Contents of file direct_scf in 12 DIRECT SCF CAL
47. nts of file fullci_val in core 8000000 restart new title h2o DZ basis valence full ci super off nosym 26 FULL CI CALCULATIONS 72 bypass zmat angstrom o h 1 roh h 1 roh 2 theta variables roh 0 956 hess 0 7 theta 104 5 hess 0 2 end basis dz runtype ci active 2 to 14 end core 1 end fullci 13 4 4 enter to run rungamess r fullci n h2o_fullci fullci_val The following points should be noted e the use of r which causes the FORTRAN stream ftn008 to be saved e the use of the core pre directive to specify memory requirements
48. ompleted the single point calculation the following might be used to perform a geometry optimisation at the CASSCF level Contents of file water_cas_opt in restart new title water geometry optimisation at casscf level zmat angstrom o h 1 oh h 1 oh 2 hoh variables oh 0 956 hoh 104 5 end runtype optimise scftype casscf config bypass doc 1 to 5 uoc 6 7 end superci 1 to 5 newton 6 to 20 hessian 6 to 20 simul 6 to 20 enter to run rungamess r casscf n water water_cas_opt 21 CASSCF 2nd order CI Calculations on BeO First we consider below a CASSCF calculation on the X X state of BeO characterised by the configuration 1072073074071 1 21 CASSCF 2ND ORDER CI CALCULATIONS ON BEO 42 The initial closed shell SCF using a DZP basis was conducted with the following job Contents of file beo_rhf in super off nosym title beo dzp zmat angstrom be o 1 beo variables beo 1 300 hessian 0 7 end basis dzp enter to run rungamess t ed2 t ed3 n beo beo_rhf An examination of the closed shell SCF output reveals the following symmetry adapted basis information IRREP NO OF SYMMETRY ADAPTED BASIS FUNCTIONS 1 1 20 45769692 2 0000000 2 1 4 72825831 2 0000000 3 1 1 15792230 2 0000000 4 1 0 46629250 2 0000000 5 3 0 39257378 2 0000000 6 2 0 39257378 2 0000000 7 1 0 05704423 0 0000000 8 2 0 09936415 0 0000000 9 3 0 09936415 0 0000000 10 1 0 15573442 0 0000000 11 1 0 25156032 0 000000
49. ors 5 swap 14 15 end enter to run 24 ECP CASSCF AND DIRECT CI CALCULATIONS ON NICCHp2 rungamess t ed2 t ed3 t ed4 t ed6 l edO n nicch2 nicch2_cas Direct CI Job Contents of file nicch2_ci in restart new title ni cch2 3a1 mrsdci 3 2 2 0 hay s ni bar s nm ecp s mult 3 super off nosym bypass scf zmat angstrom ni c i nica x 2 1 0 1 90 0 c 2 cacb 3 90 0 1 180 0 x 41 0 2 90 0 3 0 0 h 4 hcb 2 hcc 5 90 0 h 4 hcb 2 hcc 5 90 0 variables nica 2 0895 cacb 1 3604 hcb 1 1047 hcc 122 646 end basis sh 0 032828 13 3615 0 231208 2 0133 0 817238 0 4538 sh 1 000000 0 1233 sc 1 000000 0 4962 sc 1 000000 0 1533 pec 0 018534 18 1557 0 115442 3 9864 0 386206 1 1429 0 640089 0 3594 pec 1 000000 0 1146 s ni 0 4372528 0 6778 1889453 0 1116 ni 0000000 0 0387 ni 0000000 0 0840 ni 0000000 0 0240 ni ard EDO FU HH 25 TABLE CI CALCULATIONS OF THE ELECTRONIC SPECTRA OF PYRIDINE61 ni KH O O O end 0000000 0 2836 pseudo nonlocal nihay ni cc runtype ci core end active 1 to 40 end direct 20 14 26 spin triplet conf 2 2 2 2 2 NN NV DP ND 2 vprint 100 0 0 ND NN DV DB N NN NN ND ND ND ND 2 NN NN ND N NN NV DPD ND NN NV DP ND 2 maxcyc 10 ente to run r 2 2 2 2 1 1 1 0360414 42 7200 1938645 11 7600 4596238 3 8170 5599305 1 1690 DN NO kE EH ND HE NE ENDE rungamess t ed2 t
50. porary directory GAMESS_TMP Since GAMESS_TMP will usually refer to a scratch disk this means that large files may be retained beyond the end of the job without being written to the users own filestore where space will usually be limited On most installations the variables GAMESS_TMP and GAMESS_SCR will actually be set to the same directory The distinction is that GAMESS_TMP should point to a directory which will exist beyond the end of the job since it will contain files required to restart calculations whereas that referenced by GAMESS_SCR a subdirectory of GAMESS_SCR named after the job name will be deleted after the program has finished As an example consider an installation where GAMESS_SCR has been set to point to a workdi rectory scr2 xyz and GAMESS_TMP to scrl xyz The rungamess invocation 2 USAGE OF THE RUNGAMESS SCRIPT 6 Table 1 Keywords accepted by the r argument keyword function hf save ed2 and ed3 casscf save edl ed2 ed3 ed4 ed6 ed9 ed10 ed11 mescf save ed2 ed3 ed4 ed6 ed13 ci save ed2 ed3 ed4 ed5 ed6 for direct CI calculations mrdci save ed2 ed3 ftn031 ftn033 ftn034 ftn035 ftn036 fullci save ed2 ed3 ed6 ftn008 rungamess k ed3 t ed2 myjob will cause a temporary directory scr2 xyz myjob to be created and will contain all datasets used by GAMESS UK except that associated with LFN ed3 which will have pathname myjob ed3 and ed2 which will have pathname scr1
51. r utilisation in the above job will drive off the default sections of the Dumpfile with the open shell SCF module using the closed shell SCF vectors from section 1 to initiate the SCF process and writing the SCF open shell orbitals to sections 4 and 5 the energy ordered SCF MOs These latter orbitals will be used below to instigate the CASSCF processing CASSCF Job Contents of file nicch2_cas in restart new title ni cch2 3a1 c2v cas at opt 3 2 2 0 hay s ni bar s nm ecp s mult 3 super off nosym zmat angstrom ni nica 1 0 1 90 0 cacb 3 90 0 1 180 0 1 0 2 90 0 3 0 0 hcb 2 hcc 5 90 0 4 hcb 2 hcc 5 90 0 variables nica 2 0895 cacb 1 3604 hcb 1 1047 hcc 122 646 end 5b KO K Q BB NV NV basis sh 24 ECP CASSCF AND DIRECT CI CALCULATIONS ON NICCHp2 0 032828 13 3615 0 231208 2 0133 0 817238 0 4538 sh 1 000000 0 1233 sc 1 000000 0 4962 sc 1 000000 0 1533 pec 0 018534 18 1557 0 115442 3 9864 0 386206 1 1429 0 640089 0 3594 pec 1 000000 0 1146 s ni 0 4372528 0 6778 1889453 0 1116 ni 0000000 0 0387 ni 0000000 0 0840 ni 0000000 0 0240 ni 0360414 42 7200 1938645 11 7600 4596238 3 8170 5599305 1 1690 ni 0000000 0 2836 end RH O O OO PQ HF END EH U HH pseudo nonlocal nihay ni cc runtype scf scftype casscf config print fzc 1 to 7 doc 8 to 9 alp 10 to 11 uoc 12 to 14 end superci 1 to 12 newton 13 to 20 hessian 13 to 20 simul 15 to 20 vect
52. rce title na mg sto 3g triplet uhf mult 3 charge 1 bypass zmat angs mg na 1 ri na 1 r2 2 90 na 1 r2 2 90 3 72 na 1 r2 2 90 4 72 na 1 r2 2 90 5 72 na 1 r2 2 90 6 72 na 1 ri 3 90 2 180 variables energy 1314 901919 16 8 EXTENDED BASIS SET CALCULATIONS OF NA MG 17 rl 3 0286740 r2 3 194799 end basis sto3g scftype uhf vectors 5 enter to run rungamess t ed2 t ed3 n nafmg na mg_uhf Note that we are using the energy ordered open shell RHF eigenvectors to initiate the UHF calculation as written to the default section 5 by the Open shell RHF Job Had this section not been specified using the VECTORS directive then the closed shell SCF MOs would been used in default 8 Extended Basis Set Calculations of Na Mg In this example we use the STO 3G calculation on Na7Mgt performed above as a starting point for a more extensive basis set calculation In particular the set of closed shell vectors is restored under control of GETQ with the STO 3G Dumpfile used as a foreign Dumpfile We then perform an RHF calculation on the singlet state of Na7Mg using the integrals calculated in the closed shell case Closed shell SCF Job Contents of file na7mg_ext in dumpfile ed3 500 title na7mg 4s3p 4s3pid scf energy 1330 808718 mult 1 charge 1 super off noprint vectors zmat angs mg na 1 ri na 1 r2 2 90 na 1 r2 2 90 3 72 na 1 r2 2 90 4 72 na 1 r2 2 90 5 72
53. reated directory which will usually be on a scratch disk Files are routed back to the directory of submission or to longer term temporary filestore as required 3 A variety of batch queuing systems are provided local configuration is required 4 The decision regarding which files to retain beyond the end of the job may be set auto matically given the type of job 5 The job may execute on a remote networked machine without the need to explicitly move input and output or files binary datasets are retained on the execution machine Note that this documentation describes version 3 x of rungamess these versions differs sub stantially from the earlier versions From a user point of view the main differences are e only the short forms of the arguments are now accepted keep must be replaced by k etc e the job name must be the last argument The next section summarises the syntax and the function of the arguments to the rungamess script and subsequent sections contain the following illustrative examples 1 Single point SCF calculation of water using the default basis 2 Sequence of calculations on water including starting and restarting geometry optimisation of the neutral molecule an RHF calculation on the 2B cation boys localisation and 2 pair GVB calculation of the neutral molecule 3 Closed shell SCF calculations on C4F4 CeHsNOgand CgH2 NO2 3CH3 4 STO 3G calculation of Na7Mg together with an RHF and UHF
54. s h 0 032828 13 3615 0 231208 2 0133 0 817238 0 4538 sh 1 000000 0 1233 sc 1 000000 0 4962 sc 1 000000 0 1533 pec 0 018534 18 1557 0 115442 3 9864 0 386206 1 1429 0 640089 0 3594 pec 24 ECP CASSCF AND DIRECT CI CALCULATIONS ON NICCHp2 to run 1 000000 0 1146 s ni 0 4372528 0 6778 1889453 0 1116 ni 0000000 0 0387 ni 0000000 0 0840 ni 0000000 0 0240 ni 0360414 42 7200 1938645 11 7600 4596238 3 8170 5599305 1 1690 ni 0000000 0 2836 end H A O O OO QH KFT EH 0 HH pseudo nonlocal nihay ni cc runtype scf maxcyc 30 level 2 5 15 1 0 vectors hcore enter rungamess t ed2 t ed3 1 edO n nicch2 nicch2_rhf Closed shell SCF Restart Data Contents of file nicch2_swap in restart new title ni cch2 1a1 rhf restart hay s ni bar s nm ecp s mult 1 bypass super force zmat angstrom ni nica 1 0 1 90 0 cacb 3 90 0 1 180 0 1 0 2 90 0 3 0 0 hcb 2 hcc 5 90 0 4 hcb 2 hcc 5 90 0 variables nica 2 0895 cacb 1 3604 hcb 1 1047 hcc 122 646 5b KO K O BB DND 55 24 ECP CASSCF AND DIRECT CI CALCULATIONS ON NICCHp2 end basis sh 0 032828 13 3615 0 231208 2 0133 0 817238 0 4538 sh 1 000000 0 1233 sc 1 000000 0 4962 sc 1 000000 0 1533 pec 0 018534 18 1557 0 115442 3 9864 0 386206 1 1429 0 640089 0 3594 pec 1 000000 0 1146 s ni 0 4372528 0 6778 1889453 0 1116 ni 0000000 0 0387 ni 0000000 0 0840 ni 0000000 0 0240 ni 03604
55. t is followed by a character string specifying the type of calculation for which the restart may be required Valid key strings and their effects are given in Table 1 Clearly the r argument must be given on the start up job as well as the restart job 2 USAGE OF THE RUNGAMESS SCRIPT 7 The r option is equivalent to using a series of t options one for each relevant file as given in Table 1 Files saved in this way thus reside on the directory GAMESS_TMP with names of the form myjob ed11 Since rungamess processes file arguments in the order they are presented any of the file assignments implied by r may be overridden if the appropriate option is placed after r 2 4 Accessing Library Files The library argument short form l can be used to associate a logical file name with the corresponding library file The two LFNs which are accepted are edO for the non local pseu dopotential library file and table for the Table Cl database used by the MRDCI module The directory in which the library files are to be found is obtained from the environment variable GAMESS LIB 2 5 Batch Job Submission Provided the local setup has been performed the rungamess script will submit a job to a batch queuing system if the q option is provided A job file with suffix script is generated and submitted The exact behaviour of the script and any additional arguments that can be presented will depend on the queuing system in use Template
56. te steps performing the symmetry adaptation integral transformation followed by configuration selection construction of the Cl Hamiltonian the diagonalisation and finally the subsequent analysis of the Cl wavefunctions Open shell SCF Job Contents of file nh3_rohf title 23 TABLE CI CALCULATIONS ON THE AMMONIA CATION to run nh3 3 21g scf energy 55 53325817 hartree super off nosym charge 1 mult 2 zmat angstrom n h 1 roh h 1 roh 2 theta h 1 roh 2 theta 3 theta 1 variables roh 1 03 hessian 0 7 theta 104 2 hessian 0 2 end enter rungamess t ed2 t ed3 n nh3 nh3_rohf Table CI Job Contents of file nh3_mrdci in restart title nh3 3 21g mrdci energies ir 55 6393336 2r 55 4116210 bypass scf charge 1 mult 2 zmat angstrom n h 1 roh h 1 roh 2 theta h 1 roh 2 theta 3 theta 1 variables roh 1 03 hessian 0 7 theta 104 2 hessian 0 2 end runtype ci mrdci adapt tran table select symmetry 1 spin 2 cntrl 9 conf 141283 12 13124 12 roots 2 thresh 5 5 ci diag 48 23 TABLE CI CALCULATIONS ON THE AMMONIA CATION 49 extrap 3 dthr 0 0001 0 0001 natorb cive i 2 prop cive i 2 14 123 12 13 124 12 moment 36 1 36 2 1 enter to run rungamess t ed2 t ed3 t table n nh3 nh3_mrdci The orbitals employed in the Cl calculation will be taken from the default section associated with the open shell RHF module section 5 that containing the energy or
57. tem diagnostics will appear at the terminal stderr unless redirected rungamess myjob gt amp myjob err amp To retain the ed2 and ed3 files in the scratch directory rungamess myjob t ed2 t ed3 gt amp myjob err amp 5 Sequence of Calculations on H0O In this example we include a sequence of input files and for performing various calculations based on the H20 example given above To simplify the commands required water is used as the root of the filename of all binary datasets using the n argument 1 The first job as above generates the starting vectors In this and subsequent jobs the mainfile ed2 is saved in case a restart due to lack of time occurs Contents of file water_scf in 5 SEQUENCE OF CALCULATIONS ON H gt O 10 to run title h2o 3 21g scf zmat angstrom o h 1 roh h 1 roh 2 theta variables roh 0 956 hess 0 7 theta 104 5 hess 0 2 end enter rungamess t ed2 t ed3 n water water_scf 2 This run utilises the vectors made above Both bond length and bond angle are to be optimised Contents of file water_opt in to run restart new title water optimisation at scf level 3 21g basis set zmat angstrom o h 1 oh h 1 oh 2 hoh variables oh 0 956 hoh 104 5 end runtype optimise enter rungamess t ed2 t ed3 n water water_opt 3 This example would be used to complete if necessary the run started in 1 Contents of file water_restopt in to run restart optimise title
58. to section 10 of the Dumpfile on convergence the default section used for NO output e Integral evaluation has been bypassed as the initial SCF job specified the necessary integral format for the subsequent SCF In the above we have assumed that the MCSCF calculation completes in the time allocated with the associated direct access files allocated in default scratch status The following rungamess invocation is typical of that required if restarts of the MCSCF step are envisaged rungamess r mcscf n beo beo_mcscf Note that the symmetry adapted list of integrals are sorted at the outset of processing to ED13 and this file should be preserved across restart jobs given that the DONT SORT data line is presented to the restart job Assuming the above job terminated prior to convergence the calculation might be restarted as follows Contents of file beo_mcscf_rest in restart scf super off nosym title beo dzp zmat angstrom be o 1 beo variables beo 1 300 hessian 0 7 end basis dzp scftype mcscf thresh 4 mcscf orbital 3cor1 doci doc3 doc2 uoci uoc2 uoc3 end dont sort enter to run rungamess r mcscf n beo beo_mcscf_rest Now let us consider performing the MCSCF calculation under RUNTYPE CI specification where having performed the 6 electrons in 6 orbital CASSCF we use the natural orbitals in carrying out a second order Cl using the Direct Cl module Specifically we aim to use a reference space in the Cl consisting of
59. water optimisation at scf level 3 21g basis set zmat angstrom o h 1 oh h 1 oh 2 hoh variables oh 0 956 hoh 104 5 end runtype optimise enter rungamess t ed2 t ed3 n water water_restopt 5 SEQUENCE OF CALCULATIONS ON H gt O 11 4 This example performs an open shell RHF calculation at the optimised geometry from 2 note the RESTART usage Contents of file water_orhf in to run restart title h2o doublet bi state ground state geometry charge 1 mult 2 zmat angs o h 1 oh h 1 oh 2 hoh variables oh 0 956 hoh 104 5 end enter rungamess t ed2 t ed3 n water water_orhf 5 The valence shell scf mos are to be localised For the purpose of the example below it is assumed that orbitals 2 and 3 are the bond orbitals The CHARGE and MULT directives are required to override the values set in the preceding job on the doublet cation Contents of file water_loc in to run restart title lmos for h20 ground state geometry charge 0 mult 1 zmat angs o h 1 oh h 1 oh 2 hoh variables oh 0 956 hoh 104 5 end runtype analyse local 2 to 5 end vectors 1 enter 5 rungamess t ed2 t ed3 n water water_loc 6 SCF CALCULATIONS ON C4F4 CeH NO2 AND Cs H NO2 3 CH3 12 6 The localised orbitals are restored from section 5 and the NOGEN facility used to generate the virtual pairs of the two bond orbitals The SWAP directive has been used to move the localised bond orbitals to the top of the
60. xyz myjob ed2 The way in which saved files are reused is dependent on the preference of the user If a job needs to be restarted one option is simply to edit the input file say to add a restart directive and re issue the command given above This is the simplest method but obviously results in the input and output files being overwritten If it is preferred that the restart job has a different name it is necessary to ensure that the old files are correctly associated with the new job name This is the model adopted in this Chapter because of the need to include all the input files with unique names in the examples directory This can simply be achieved by giving the filename as part of the argument to k or t the following command will re use the dumpfile ed3 but not ed2 from the above job rungamess k ed3 myjob ed3 myjob_new If many files are to be carried over between jobs of different names it is simpler to rename them all using the name or n option This sets the first part of the filename for all direct access and Fortran datasets but leaves the names of the names input output punch and NQS job files unchanged The following sequence uses water as the root part of the filename for both jobs rungamess t ed2 t ed3 n water water_scf rungamess t ed2 t ed3 n water water_opt To simplify the file arguments required to allow restarting of a job as a result of time out the r argument has been provided I

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