Platypus-QM β ( )

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1 Platypus-QM β ( )

3 MPI MPI RHF &Atoms &Basis &Atoms &PointCahrges

4 &Control &QM &Integral &RHF A 25 A.1 HF B 27 C 29 C.1 Platypus-QM

5 bash $HOME/local/platypus-qm/bin Platypus-QM $HOME/work/platypus (1) (Typewriter) ( ) 1: &RHF 1 &RHF 2 &rhf 2: platypus qm energy rhf platypus qm energy rhf (2) (Italic) 1

6 ( ) integer ( ) real number ( ) digit ( : 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 0) string ( ) file name ( ) basis name ( ) symbol ( ) id (, 1 digit ) 1: PRINT = integer 1 PRINT = 1 2 PRINT = 2 2: BasisSet = basis name 1 BasisSet = MINI-4 2 BasisSet = 6-31G (3) [ A ] [ ] 1: [ PRINT = integer ] 1! (PRINT ) 2 PRINT = 1! ( ) (4) { A B C } { } 1 1: PRUNED = { YES NO } 1 PRUNED = YES 2 PRUNED = NO (5) [... ] 1: A [... ] 1 A 2 A A A 2

7 (6) A + B + + 1: symbol + id Mg123 (7) $ 1: $ (8) 1: $ command [ arg [...] ] (9) 1: line1 line2 line3 (10) ( \) 1: $ command arg1 \ arg2 3

9 2. MPI 2 MPI 2.1 Platypus-QM./bahrc export PLATYPUSQMDIR=/usr/local/platypus-qm export PATH="$PLATYPUSQMDIR/bin:$PATH" 2.2 MPI MPI mpiexec/mpirun mpiexec -np 2 $ mpirun -np 2 program Flat MPI (go K.sh) #!/bin/bash -x # #PJM --rsc-list "node=2" #PJM --rsc-list "elapse=00:05:00" #PJM --mpi "rank-map-bynode" #PJM --mpi "use-rankdir" #PJM --stgin "rank=*./platypus_qm %r:./" #PJM --stgin "rank=*./qm.inp %r:./" #PJM --stgin "rank=*./basisfile %r:./" #PJM -s #. /work/system/env_base export OMP_NUM_THREADS=8 LPGPARM="lpgparm -s 32MB -d 32MB -h 32MB -t 32MB -p 32MB" 5

10 2. MPI 2.2 MPI mpiexec ${LPGPARM}./platypus_qm $ pjsub go.sh $ pjstat $ pjstat -v ID (REQID) $ pjdel REQID 6

11 3. 3 qm.inp BASISFILE 3.1 RHF &qm wftype = rhf &end &rhf energyconv = 1.d-7 scfconv = 1.d-04 maxcyc = 20 &end &basis BasisFile = BASISFILE BasisSet = MINI-4 &end &atoms units = au O H H &end 7

13 (1) (2) 1: Print = 1 2: Print = 1 (3) 1: Print = 1 2: Print = 1 (4)!, #, ; 1: Print = 1! 2: Print = 1 # 3: Print = 1 ; (5) 9

14 : PRINT = 1 # 2: Print = 1 # (6) & &END 1: &RHF &END (7) 1: &RHF &END # (8) 2 (i) (ii) ( ) &Atoms &Basis &PointCharges &GaussianCharges (9) = = ( 1 [ 2 [...] ] ) ( ) 1: WeightFactors = 1 10

15 : WeightFactors = ( 1 1 ) (10) 11

16 (1) &Atoms &Basis &PointCharges (2) &Control &QM &Integral &RHF QM/MD RHF, RDFT 12

17 &Atoms 4.3 &Atoms &Atoms [ Units = { ang au } ] atom name1 x1 y1 z1 [ charge1 ] [ basis name1 [ basis library name1 ]] [ atom name2 x2 y2 z2 [ charge2 ] [ basis name2 [ basis library name2 ]]] [... ] &End Units ang au [ : ang ] (Å) (a.u.) atom name symbol id x y z charge symbol [ + id ] (H Ba) ( : H, Mg) &Basis digit [ + digit [... ] ] ( : H1, Mg12) X real number Y real number Z real number ( : a.u.) real number [ : ] 13

18 &Atoms (continued) basis name string [ : &Basis ] basis library name basis name string PLATYPUS QM BASIS DIR [ : &Basis ] units (a.u.) &atoms units = au O H H &end 2. &atoms units = au O MINI-4 H MINI-4 H MINI-4 &end 14

19 &Basis 4.4 &Basis &Atoms [ &Basis [ BasisFile = basis library name ] [ BasisSet = basis name ] [ # basis set definition block def symbol = basis name # shell definition block shell type number of primitives [ scale factor ] # primitive function definition line orbital exponent coefficient [ coefficient ] [... ] [... ] [... ] ] [ # basis set assignment line set { symbol symbol+id } = basis name [ basis library name ] [... ] ] &End ] symbol basis name &Basis [ # basis set definition block def symbol = basis name # shell definition block shell type number of primitives [ scale factor ] # primitive definition line orbital exponent coefficient [ coefficient ] [... ] [... ] [... ] ] 15

20 &Basis PLATYPUS BASISDIR PLATYPUS BASISFILE PLATYPUS BASISSET string [ :./ ] PLATYPUS BASISDIR string [ : BASISFILE ] string [ : STO-3G ] BasisFile BasisSet string string PLATYPUS BASISDIR [ : PLATYPUS BASISFILE ] [ : PLATYPUS BASISSET ] def set atom name symbol symbol+id id basis name basis library name symbol [ + id ] ( : H, Mg) + ( : H1, Mg12) digit [ + digit [... ] ] string basis name PLATYPUS BASISDIR string [ : BasisFile ] 16

21 &Basis (continued) shell type { S P D SP } number of primitives integer scale factor real number [ : 1.0] orbital exponent real number coefficient real number SP coefficient basis library name def basis name def &Atoms 1. &Atoms 2. set symbol+id = basis name [ basis library name ] symbol+id ( symbol+id ) 3. set symbol = basis name [ basis library name ] symbol ( symbol symbol+id ) 4. BasisSet &Basis BasisFile =../BasisLib BasisSet = 6-31G &End 2. 17

22 &Basis &Basis BasisFile =../BasisLib set H = 6-31G set O = 6-31G** &End 3. H H &Basis BasisFile =../BasisLib set H = 6-31G set O = 6-31G** def H = 6-31G S S &End 4. def H = 6-31G S S

23 &PointCahrges 4.5 &PointCahrges [ &PointCharges [ Units = { ang au } ] x1 y1 z1 charge1 [ x2 y2 z2 charge2 ] [... ] &End ] Units ang au [ : ang ] (Å) (a.u.) atom name x y z charge X real number Y real number Z real number ( : a.u.) real number &PointCharges # x y z charge &End 19

24 &Control 4.6 &Control [ &Control [ PRINT = integer ] &End ] PRINT integer [ : 0 ] &Control print = 1 &End 20

25 &QM 4.7 &QM [ &QM [ WFType = { RHF } ] [ Check = { NO Energy } ] &End ] WFTYPE Check RHF NO Energy [ : RHF ] RHF QM [ : NO ] &QM wftype = rhf &End 21

26 &Integral 4.8 &Integral [ &Integral [ ERITHRES = real number ] &End ] ERITHRES ERI real number [ : 1.0E-8 ] &Integral erithres = 1.0d-8 &End 22

27 &RHF 4.9 &RHF [ &RHF [ ION = integer ] [ MAXCYC = integer ] [ SCFCONV = real number ] [ ENERGYCONV = real number ] [ DIISSIZE = integer ] &End ] ION MAXCYC SCFCONV ENERGYCONV DIISSIZE integer [ : 0 ] integer [ : 30 ] RMS real number [ : 1.0E-6 ] real number [ : 1.0E-10 ] DIIS real number [ : 8 ] SCFCONV ENERGYCONV &RHF MAXCYC = 20 SCFCONV = 1.0E-4 ENERGYCONV = 1.0E-8 &END 23

29 A. A ĤΨ = EΨ (A.1) Ĥ Ψ E Platypus-QM A.1 HF HF (Hartree-Fock) Ψ Φ 0 Ψ = Φ 0 (A.2) MO ( ; Molecular Orbital) ϕ i MO N Φ 0 = ϕ 1 (1)ϕ 2 (2)... ϕ N (N) MOϕ i α ϕ i β ϕ i (A.3) Φ RHF 0 = ϕ 1 (1)ϕ 1 (2)... ϕ N/2 (N 1)ϕ N/2 (N) (A.4) MO 2 RHF (Restricted Hartree-Fock) 1 MO N open high spin Φ ROHF 0 = ϕ 1 ϕ 1... ϕ (N Nopen)/2ϕ (N Nopen)/2ϕ (N Nopen)/ ϕ (N Nopen)/2+N open (A.5) ROHF (Restricted Open shell Hartree-Fock) α MO β MO Φ UHF 0 = ϕ 1 (1)ϕ 2 (2)... ϕ Nα (N α )ϕ Nα+1(N α + 1)... ϕ Nα+N β (N α + N β ) (A.6) UHF (Unrestricted Hartree-Fock) HF E MO { C } { ϵ } CI CASSCF HF HF MO ϕ i AO ( ; Atomic Orbital) χ µ AO (basis function) ϕ i = N AO µ C iµ χ µ (A.7) 25

30 A. A.1 HF (Basis set) N AO HF F SC = Cϵ (A.8) F Fock S C MO ϵ (A.8) Fock F MO C MO C init C (A.8) MO C init 26

31 B. B / 200 File Not Found 201 File Open Error 202 File Close Error 203 File Rrewind Error 204 File Read Error 205 File Write Error 300 Group Not Specified 301 Group Begin 302 Group End 303 Group EOF 304 Invalid Group Name 305 Duplicate Group 311 Incorrect Option Syntax 312 Invalid Option Name 313 Duplicate Option 321 Invalid Value 322 Out Of Range 27

32 B. / 323 Inconsistent Value 331 Invalid Format 341 Invalid Name 351 Duplicate 352 No Atoms 355 No Basis Set 999 Internal Error 28

33 C. C Platypus-QM (1) Fortran (2) MPI (3) BLAS, LAPACK (1) C.1 Platypus-QM 1. $ tar xvf platypus-qm-0.63-k.tar.bz2 2. $./runconfigure_k $ make 3. (1) (2) src/platypus qm data/qm.inp data/basisfile data/go K.sh (3) go K.sh (4) $ pjsub go_k.sh (5) data/qm C6H6 H2O PC.out ref 29

main.dvi

main.dvi 1 F77 5 hmogi-2008f@kiban.civil.saitama-u.ac.jp 2013/5/13 1 2 f77... f77.exe f77.exe CDROM (CDROM D D: setupond E E: setupone 5 C:work\T66160\20130422>f77 menseki.f -o menseki f77(.exe) f77 f77(.exe) C:work\T66160\20130422>set