Commit 88c0a800 authored by Rosendo Valero Montero's avatar Rosendo Valero Montero
Browse files

g09 tests

parent bfe3311f
......@@ -5,7 +5,7 @@ from nomadcore.caching_backend import CachingLevel
import os, sys, json, logging
import numpy as np
# description of the input
# description of the output
mainFileDescription = SM(
name = 'root',
weak = True,
......@@ -40,13 +40,21 @@ mainFileDescription = SM(
),
SM(name = 'charge_multiplicity',
sections = ['section_system_description','gaussian_section_labels'],
startReStr = r"\s*Symbolic Z-matrix:",
startReStr = r"\s*Charge =",
subFlags = SM.SubFlags.Sequenced,
forwardMatch = True,
subMatchers = [
SM(r"\s*Charge =\s*(?P<total_charge>[-+0-9]+) Multiplicity =\s*(?P<target_multiplicity>[0-9]+)"),
SM(r"\s*(?P<gaussian_atom_label>\D{1,2}?(?=\s*[0-9,-]))",repeats = True),
SM(r"\s*(?P<gaussian_atom_label>\w{1,2}(?=\s))",repeats = True),
SM(r"\s*Variables:|\s*NAtoms=|\s*Z-MATRIX"),
SM(r"\s*"),
SM(r"\sModel"),
SM(r"\sShort"),
SM(r"\s*Atom"),
SM(r"\s*\d\d?\d?\s{7,8}?[A-Za-z-]", repeats = True),
SM(r"\s*Generated"),
SM(r"\sNo Z-Matrix found in file|\sZ-Matrix found in file"),
SM(r"\sRedundant internal coordinates found in file"),
SM(r"\s*(?P<gaussian_atom_label>([A-Za-z][A-Za-z]|[A-WYZa-wyz]|\d\d?\d?))[^A-Za-z]", repeats=True),
SM(r"\sRecover connectivity data from disk."),
SM(r"\s*Variables:|\s*------|\s*\r?\n")
]
),
SM(name = 'geometry',
......
# SP, RHF/STO-3G punch=archive trakio scf=conventional
Gaussian Test Job 00
Water with archiving
0 1
O
H 1 0.96
H 1 0.96 2 109.471221
Entering Gaussian System, Link 0=g09
Initial command:
/mf/frisch/g09/l1.exe "/altuv/s0/scratch/Gau-11282.inp" -scrdir="/altuv/s0/scratch/"
Default CPUs for threads: 0
Entering Link 1 = /mf/frisch/g09/l1.exe PID= 11307.
Copyright (c) 1988,1990,1992,1993,1995,1998,2003,2009,2013,
Gaussian, Inc. All Rights Reserved.
This is part of the Gaussian(R) 09 program. It is based on
the Gaussian(R) 03 system (copyright 2003, Gaussian, Inc.),
the Gaussian(R) 98 system (copyright 1998, Gaussian, Inc.),
the Gaussian(R) 94 system (copyright 1995, Gaussian, Inc.),
the Gaussian 92(TM) system (copyright 1992, Gaussian, Inc.),
the Gaussian 90(TM) system (copyright 1990, Gaussian, Inc.),
the Gaussian 88(TM) system (copyright 1988, Gaussian, Inc.),
the Gaussian 86(TM) system (copyright 1986, Carnegie Mellon
University), and the Gaussian 82(TM) system (copyright 1983,
Carnegie Mellon University). Gaussian is a federally registered
trademark of Gaussian, Inc.
This software contains proprietary and confidential information,
including trade secrets, belonging to Gaussian, Inc.
This software is provided under written license and may be
used, copied, transmitted, or stored only in accord with that
written license.
The following legend is applicable only to US Government
contracts under FAR:
RESTRICTED RIGHTS LEGEND
Use, reproduction and disclosure by the US Government is
subject to restrictions as set forth in subparagraphs (a)
and (c) of the Commercial Computer Software - Restricted
Rights clause in FAR 52.227-19.
Gaussian, Inc.
340 Quinnipiac St., Bldg. 40, Wallingford CT 06492
---------------------------------------------------------------
Warning -- This program may not be used in any manner that
competes with the business of Gaussian, Inc. or will provide
assistance to any competitor of Gaussian, Inc. The licensee
of this program is prohibited from giving any competitor of
Gaussian, Inc. access to this program. By using this program,
the user acknowledges that Gaussian, Inc. is engaged in the
business of creating and licensing software in the field of
computational chemistry and represents and warrants to the
licensee that it is not a competitor of Gaussian, Inc. and that
it will not use this program in any manner prohibited above.
---------------------------------------------------------------
Cite this work as:
Gaussian 09, Revision D.01,
M. J. Frisch, G. W. Trucks, H. B. Schlegel, G. E. Scuseria,
M. A. Robb, J. R. Cheeseman, G. Scalmani, V. Barone, B. Mennucci,
G. A. Petersson, H. Nakatsuji, M. Caricato, X. Li, H. P. Hratchian,
A. F. Izmaylov, J. Bloino, G. Zheng, J. L. Sonnenberg, M. Hada,
M. Ehara, K. Toyota, R. Fukuda, J. Hasegawa, M. Ishida, T. Nakajima,
Y. Honda, O. Kitao, H. Nakai, T. Vreven, J. A. Montgomery, Jr.,
J. E. Peralta, F. Ogliaro, M. Bearpark, J. J. Heyd, E. Brothers,
K. N. Kudin, V. N. Staroverov, T. Keith, R. Kobayashi, J. Normand,
K. Raghavachari, A. Rendell, J. C. Burant, S. S. Iyengar, J. Tomasi,
M. Cossi, N. Rega, J. M. Millam, M. Klene, J. E. Knox, J. B. Cross,
V. Bakken, C. Adamo, J. Jaramillo, R. Gomperts, R. E. Stratmann,
O. Yazyev, A. J. Austin, R. Cammi, C. Pomelli, J. W. Ochterski,
R. L. Martin, K. Morokuma, V. G. Zakrzewski, G. A. Voth,
P. Salvador, J. J. Dannenberg, S. Dapprich, A. D. Daniels,
O. Farkas, J. B. Foresman, J. V. Ortiz, J. Cioslowski,
and D. J. Fox, Gaussian, Inc., Wallingford CT, 2013.
******************************************
Gaussian 09: ES64L-G09RevD.01 24-Apr-2013
24-Apr-2013
******************************************
SetSPE: set environment variable "MP_BIND" = "yes"
SetSPE: set environment variable "MP_BLIST" = "0"
------------------------------------------------------
# SP, RHF/STO-3G punch=archive trakio scf=conventional
------------------------------------------------------
1/38=1/1;
2/12=2,17=6,18=5,40=1/2;
3/6=3,11=1,16=1,25=20,28=1,30=1,116=1/1,2,3,20;
4//1;
5/5=1/2;
6/7=2,8=2,9=2,10=2,28=1/1;
99/5=1,9=1,10=8/99;
-----------------------------------------
Gaussian Test Job 00 Water with archiving
-----------------------------------------
Symbolic Z-matrix:
Charge = 0 Multiplicity = 1
O
H 1 0.96
H 1 0.96 2 109.47122
1 tetrahedral angles replaced.
1 tetrahedral angles replaced.
Input orientation:
---------------------------------------------------------------------
Center Atomic Atomic Coordinates (Angstroms)
Number Number Type X Y Z
---------------------------------------------------------------------
1 8 0 0.000000 0.000000 0.000000
2 1 0 0.000000 0.000000 0.960000
3 1 0 0.905097 0.000000 -0.320000
---------------------------------------------------------------------
Distance matrix (angstroms):
1 2 3
1 O 0.000000
2 H 0.960000 0.000000
3 H 0.960000 1.567673 0.000000
Stoichiometry H2O
Framework group C2V[C2(O),SGV(H2)]
Deg. of freedom 2
Full point group C2V NOp 4
Largest Abelian subgroup C2V NOp 4
Largest concise Abelian subgroup C2 NOp 2
Standard orientation:
---------------------------------------------------------------------
Center Atomic Atomic Coordinates (Angstroms)
Number Number Type X Y Z
---------------------------------------------------------------------
1 8 0 0.000000 0.000000 0.110851
2 1 0 0.000000 0.783837 -0.443405
3 1 0 0.000000 -0.783837 -0.443405
---------------------------------------------------------------------
Rotational constants (GHZ): 919.0227225 408.0852053 282.5991530
Standard basis: STO-3G (5D, 7F)
There are 4 symmetry adapted cartesian basis functions of A1 symmetry.
There are 0 symmetry adapted cartesian basis functions of A2 symmetry.
There are 1 symmetry adapted cartesian basis functions of B1 symmetry.
There are 2 symmetry adapted cartesian basis functions of B2 symmetry.
There are 4 symmetry adapted basis functions of A1 symmetry.
There are 0 symmetry adapted basis functions of A2 symmetry.
There are 1 symmetry adapted basis functions of B1 symmetry.
There are 2 symmetry adapted basis functions of B2 symmetry.
7 basis functions, 21 primitive gaussians, 7 cartesian basis functions
5 alpha electrons 5 beta electrons
nuclear repulsion energy 9.1571759100 Hartrees.
NAtoms= 3 NActive= 3 NUniq= 2 SFac= 2.25D+00 NAtFMM= 60 NAOKFM=F Big=F
Integral buffers will be 131072 words long.
Raffenetti 1 integral format.
Two-electron integral symmetry is turned on.
One-electron integrals computed using PRISM.
NBasis= 7 RedAO= T EigKep= 4.82D-01 NBF= 4 0 1 2
NBsUse= 7 1.00D-06 EigRej= -1.00D+00 NBFU= 4 0 1 2
Enter DskPsm, NBasis= 7 NBas6D= 7 NShell= 4 IDoSP=3.
Generating unsorted Raff 1 combos
Use symmetry via Dacre-Elder procedure.
NGot= 33292271 Memory for integrals= 33289052 for sort= 0.
Out2e will use a cutoff of 1.00D-10
141 integrals produced for a total of 141.
ExpMin= 1.69D-01 ExpMax= 1.31D+02 ExpMxC= 1.31D+02 IAcc=1 IRadAn= 1 AccDes= 0.00D+00
Harris functional with IExCor= 205 and IRadAn= 1 diagonalized for initial guess.
HarFok: IExCor= 205 AccDes= 0.00D+00 IRadAn= 1 IDoV= 1 UseB2=F ITyADJ=14
ICtDFT= 3500011 ScaDFX= 1.000000 1.000000 1.000000 1.000000
FoFCou: FMM=F IPFlag= 0 FMFlag= 100000 FMFlg1= 0
NFxFlg= 0 DoJE=T BraDBF=F KetDBF=T FulRan=T
wScrn= 0.000000 ICntrl= 500 IOpCl= 0 I1Cent= 200000004 NGrid= 0
NMat0= 1 NMatS0= 1 NMatT0= 0 NMatD0= 1 NMtDS0= 0 NMtDT0= 0
Petite list used in FoFCou.
Initial guess orbital symmetries:
Occupied (A1) (A1) (B2) (A1) (B1)
Virtual (A1) (B2)
The electronic state of the initial guess is 1-A1.
Two-electron integrals will be kept in memory, NGetB= 151273.
Requested convergence on RMS density matrix=1.00D-08 within 128 cycles.
Requested convergence on MAX density matrix=1.00D-06.
Requested convergence on energy=1.00D-06.
No special actions if energy rises.
SCF Done: E(RHF) = -74.9607232756 A.U. after 7 cycles
NFock= 7 Conv=0.25D-09 -V/T= 2.0051
**********************************************************************
Population analysis using the SCF density.
**********************************************************************
Orbital symmetries:
Occupied (A1) (A1) (B2) (A1) (B1)
Virtual (A1) (B2)
The electronic state is 1-A1.
Alpha occ. eigenvalues -- -20.23454 -1.26079 -0.62393 -0.44051 -0.38697
Alpha virt. eigenvalues -- 0.59296 0.75410
Condensed to atoms (all electrons):
1 2 3
1 O 7.839228 0.266628 0.266628
2 H 0.266628 0.591638 -0.044508
3 H 0.266628 -0.044508 0.591638
Mulliken charges:
1
1 O -0.372485
2 H 0.186243
3 H 0.186243
Sum of Mulliken charges = 0.00000
Mulliken charges with hydrogens summed into heavy atoms:
1
1 O 0.000000
Electronic spatial extent (au): <R**2>= 17.8525
Charge= 0.0000 electrons
Dipole moment (field-independent basis, Debye):
X= 0.0000 Y= 0.0000 Z= -1.6890 Tot= 1.6890
Quadrupole moment (field-independent basis, Debye-Ang):
XX= -6.0921 YY= -4.1965 ZZ= -5.4605
XY= 0.0000 XZ= 0.0000 YZ= 0.0000
Traceless Quadrupole moment (field-independent basis, Debye-Ang):
XX= -0.8424 YY= 1.0532 ZZ= -0.2108
XY= 0.0000 XZ= 0.0000 YZ= 0.0000
Octapole moment (field-independent basis, Debye-Ang**2):
XXX= 0.0000 YYY= 0.0000 ZZZ= -0.1756 XYY= 0.0000
XXY= 0.0000 XXZ= -0.0059 XZZ= 0.0000 YZZ= 0.0000
YYZ= -0.5889 XYZ= 0.0000
Hexadecapole moment (field-independent basis, Debye-Ang**3):
XXXX= -3.2294 YYYY= -6.5599 ZZZZ= -4.7128 XXXY= 0.0000
XXXZ= 0.0000 YYYX= 0.0000 YYYZ= 0.0000 ZZZX= 0.0000
ZZZY= 0.0000 XXYY= -1.8138 XXZZ= -1.3522 YYZZ= -1.7002
XXYZ= 0.0000 YYXZ= 0.0000 ZZXY= 0.0000
N-N= 9.157175909978D+00 E-N=-1.969263790991D+02 KE= 7.458406050829D+01
Symmetry A1 KE= 6.662722514868D+01
Symmetry A2 KE= 0.000000000000D+00
Symmetry B1 KE= 5.057462452019D+00
Symmetry B2 KE= 2.899372907588D+00
1\1\GINC-ALTUV\SP\RHF\STO-3G\H2O1\FRISCH\24-Apr-2013\0\\# SP, RHF/STO-
3G punch=archive trakio scf=conventional\\Gaussian Test Job 00 Water w
ith archiving\\0,1\O\H,1,0.96\H,1,0.96,2,109.47122063\\Version=ES64L-G
09RevD.01\State=1-A1\HF=-74.9607233\RMSD=2.458e-10\Dipole=0.5425712,0.
,0.3836558\Quadrupole=0.1565292,-0.6262971,0.4697679,0.,-0.4429865,0.\
PG=C02V [C2(O1),SGV(H2)]\\@
The archive entry for this job was punched.
ASKING DUMB QUESTIONS IS EASIER THAN CORECTING DUMB MISTAKES.
Job cpu time: 0 days 0 hours 0 minutes 1.1 seconds.
File lengths (MBytes): RWF= 5 Int= 1 D2E= 0 Chk= 1 Scr= 1
Normal termination of Gaussian 09 at Wed Apr 24 18:58:31 2013.
#P TEST STO-3G COMPLEX pop=full scf=tight
Gaussian Test Job 01
SINGLET DELTA STO-3G//STO-3G DIOXYGEN
0 1
O
O 1 R
R 1.220
This diff is collapsed.
#p rohf/4-31g pop=(reg,npa) test force scf=conventional
Gaussian Test Job 002 (Part 1):
METHYL RADICAL,C3V,2-A-1,UHF/4-31G STRUCTURE using L502
0,2
C
X,1,1.
H,1,R,2,A
H,1,R,2,A,3,120.,0
H,1,R,2,A,3,-120.,0
R=1.07046
A=90.08384
--Link1--
#p rohf/4-31g test force
Gaussian Test Job 002 (Part 2):
METHYL RADICAL,C3V,2-A-1,UHF/4-31G STRUCTURE using L502
in-core
0,2
C
X,1,1.
H,1,R,2,A
H,1,R,2,A,3,120.,0
H,1,R,2,A,3,-120.,0
R=1.07046
A=90.08384
--Link1--
#p rohf/4-31g test force scf=noincore
Gaussian Test Job 002 (Part 3):
METHYL RADICAL,C3V,2-A-1,UHF/4-31G STRUCTURE using L502
direct
0,2
C
X,1,1.
H,1,R,2,A
H,1,R,2,A,3,120.,0
H,1,R,2,A,3,-120.,0
R=1.07046
A=90.08384
--Link1--
#p rohf/4-31g test force scf=noincore raff
Gaussian Test Job 002 (Part 4):
METHYL RADICAL,C3V,2-A-1,UHF/4-31G STRUCTURE using L502
direct, raff
0,2
C
X,1,1.
H,1,R,2,A
H,1,R,2,A,3,120.,0
H,1,R,2,A,3,-120.,0
R=1.07046
A=90.08384
--Link1--
#p rohf/4-31g test force scf=noincore noraff
Gaussian Test Job 002 (Part 5):
METHYL RADICAL,C3V,2-A-1,UHF/4-31G STRUCTURE using L502
direct, reg ints
0,2
C
X,1,1.
H,1,R,2,A
H,1,R,2,A,3,120.,0
H,1,R,2,A,3,-120.,0
R=1.07046
A=90.08384
--Link1--
#p rohf/4-31g test force scf=noincore iop(5/29=3)
Gaussian Test Job 002 (Part 6):
METHYL RADICAL,C3V,2-A-1,UHF/4-31G STRUCTURE using L502
direct, mixed ints
0,2
C
X,1,1.
H,1,R,2,A
H,1,R,2,A,3,120.,0
H,1,R,2,A,3,-120.,0
R=1.07046
A=90.08384
--Link1--
#p gvb(0)/4-31g pop=(reg,npa) test force scf=conventional
Gaussian Test Job 002 (Part 7)
METHYL RADICAL,C3V,2-A-1,UHF/4-31G STRUCTURE using L506
conventional SCF
0,2
C
X,1,1.
H,1,R,2,A
H,1,R,2,A,3,120.,0
H,1,R,2,A,3,-120.,0
R=1.07046
A=90.08384
--Link1--
#p gvb(0)/4-31g test force
Gaussian Test Job 002 (Part 8)
METHYL RADICAL,C3V,2-A-1,UHF/4-31G STRUCTURE using L506
in-core
0,2
C
X,1,1.
H,1,R,2,A
H,1,R,2,A,3,120.,0
H,1,R,2,A,3,-120.,0
R=1.07046
A=90.08384
--Link1--
#p gvb(0)/4-31g test force scf=noincore noraff
Gaussian Test Job 002 (Part 9)
METHYL RADICAL,C3V,2-A-1,UHF/4-31G STRUCTURE, using L506
direct, regular ints
0,2
C
X,1,1.
H,1,R,2,A
H,1,R,2,A,3,120.,0
H,1,R,2,A,3,-120.,0
R=1.07046
A=90.08384
--Link1--
#p gvb(0)/4-31g test force scf=noincore raff
Gaussian Test Job 002 (Part 10)
METHYL RADICAL,C3V,2-A-1,UHF/4-31G STRUCTURE, using L506
direct, raff ints
0,2
C
X,1,1.
H,1,R,2,A
H,1,R,2,A,3,120.,0
H,1,R,2,A,3,-120.,0
R=1.07046
A=90.08384
--Link1--
#p gvb(0)/4-31g test force scf=noincore iop(5/29=3)
Gaussian Test Job 002 (Part 10)
METHYL RADICAL,C3V,2-A-1,UHF/4-31G STRUCTURE, using L506
direct, mixed ints
0,2
C
X,1,1.
H,1,R,2,A
H,1,R,2,A,3,120.,0
H,1,R,2,A,3,-120.,0
R=1.07046
A=90.08384
This diff is collapsed.
#P TEST 3-21G SCFDM
Gaussian Test Job 03
STEEPEST DESCENT SCF 3-21G//3-21G ETHYLENE
0,1
C
C,1,CC
H,1,CH,2,HCC
H,1,CH,2,HCC,3,180.,0
H,2,CH,1,HCC,3,180.,0
H,2,CH,1,HCC,4,180.,0
CC=1.31477
CH=1.07363
HCC=121.8867
This diff is collapsed.
#P TEST UHF/6-31G* scf=conventional
Gaussian Test Job 04
6-31G*//6-31G* ETHYL RADICAL
0,2
C
C,1,RCC
H,1,R1,2,A1
X,1,1.,2,X1,3,180.,0
H,1,R2,4,A2,2,90.,0
H,1,R2,4,A2,2,-90.,0
H,2,R3,1,A3,3,0.,0
H,2,R4,1,A4,3,180.,0
RCC=1.4985
R1=1.08422
R2=1.0886
R3=1.07398
R4=1.07507
A1=111.48882
X1=127.99832
A2=53.40128
A3=121.54216
A4=120.49668
This diff is collapsed.
#P TEST 6-311G** scf=conventional
Gaussian Test Job 05
6-311G**//6-31G* ACETYLENE
0,1
C
C,1,AA
X,1,1.,2,90.
H,1,AH,3,90.,2,180.,0
X,2,1.,1,90.,3,0.,0
H,2,AH,5,90.,1,180.,0
AA=1.18548
AH=1.05698
This diff is collapsed.
#p rhf/gen 6d iop(5/8=2) test pop=reg scfdm
Gaussian Test Job 06
GENERAL BASIS: 6-31G* READ IN, LINK 503 REGULAR SCF, RAF 2-INT
0 1
O
H 1 0.96
H 1 0.96 2 109.471221
O 0
S 6 1.00
5484.67166 0.00183107443
825.234946 0.0139501722
188.046958 0.0684450781
52.9645 0.232714336
16.8975704 0.4701928980
5.79963534 0.358520853
SP 3 0.99
15.8551334 -0.110777549 0.0708742682
3.67302682 -0.148026262 0.339752839
1.03434522 1.13076701 0.727158577
SP 1 0.98
0.281138924 1.0 1.0
D 1 1.
0.8 1.0
****
H 0
S 3 1.20
13.007734 0.03349460434
1.96207942 0.2347269535
0.444528953 0.813757326
S 1 1.15
0.121949156 1.0
****
This diff is collapsed.
#P NONSTD OLDCONSTANTS
1//1;
2//2;
3/5=1,6=6,7=1,11=0,25=14/1,2,3,11,14;
4//1;
5/6=7/2;
6//1;
Gaussian Test Job 07
WATER 6-31G* STANDARD MODEL.
0 1
O
H 1 0.96
H 1 0.96 2 109.471221
This diff is collapsed.
#P rhf/6-31g* use=l310 test scf=conventional
Gaussian Test Job 08
TEST LINK 310 (GENL2E); WATER 6-31G*, STANDARD MODEL
0 1