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Commit 827f7b22 authored by Rosendo Valero Montero's avatar Rosendo Valero Montero
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First version of Gaussian parser including geometry

parent 51277673
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parser/parser-gaussian/parser_gaussian.py
View file @ 827f7b22
import setup_paths
from nomadcore.simple_parser import mainFunction, SimpleMatcher as SM
from nomadcore.local_meta_info import loadJsonFile, InfoKindEl
import os, sys, json
from nomadcore.caching_backend import CachingLevel
import os, sys, json, logging
import numpy as np
# description of the input
mainFileDescription = SM(
......@@ -10,14 +12,40 @@ mainFileDescription = SM(
startReStr = "",
subMatchers = [
SM(name = 'newRun',
startReStr = r"\s*# SampleParser #\s*",
startReStr = r"\s*Entering Link 1 ",
repeats = True,
required = True,
forwardMatch = True,
sections = ['section_run'],
sections = ['section_run','section_method'],
subMatchers = [
SM(name = 'header',
startReStr = r"\s*# SampleParser #\s*")
startReStr = r"\s*Entering Link 1 ",
subMatchers = [
SM(r"\s*Cite this work as:"),
SM(r"\s*Gaussian [0-9]+, Revision [A-Za-z0-9.]*,"),
SM(r"\s\*\*\*\*\*\*\*\*\*\*\*\**"),
SM(r"\s*(?P<program_name>Gaussian)\s*(?P<program_version>[0-9]*:\s.*)")
]
),
SM(name = 'globalparams',
startReStr = r"\s*%\w*=",
subFlags = SM.SubFlags.Unordered,
forwardMatch = True,
subMatchers = [
SM(r"\s*%[Cc]hk=(?P<gaussian_chk_file>[A-Za-z0-9.]*)"),
SM(r"\s*%[Mm]em=(?P<gaussian_memory>[A-Za-z0-9.]*)"),
SM(r"\s*%[Nn][Pp]roc=(?P<gaussian_number_of_processors>[A-Za-z0-9.]*)"),
]
),
SM(name = 'geometry_charge_multiplicity',
sections = ['section_system_description','gaussian_section_geometry'],
startReStr = r"\s*Symbolic Z-matrix:",
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>\w+)\s+(?P<gaussian_atom_x_coord__angstrom>[-+0-9EeDd.]+)\s+(?P<gaussian_atom_y_coord__angstrom>[-+0-9EeDd.]+)\s+(?P<gaussian_atom_z_coord__angstrom>[-+0-9EeDd.]+)",
repeats = True)
]),
SM(r"\s*NAtoms=")
])
])
......@@ -33,23 +61,36 @@ parserInfo = {
class GaussianParserContext(object):
"""main place to keep the parser status, open ancillary files,..."""
def __init__(self):
self.scfIterNr = 0
pass
# just examples, you probably want to remove the following two triggers
def startedParsing(self, path, parser):
self.parser = parser
def onClose_section_single_configuration_calculation(self, backend, gIndex, section):
"""trigger called when section_single_configuration_calculation is closed"""
#backend.addValue("", self.scfIterNr)
logging.getLogger("nomadcore.parsing").info("closing section_single_configuration_calculation gIndex %d %s", gIndex, section.simpleValues)
self.scfIterNr = 0
def onClose_section_scf_iteration(self, backend, gIndex, section):
"""trigger called when section_scf_iteration is closed"""
logging.getLogger("nomadcore.parsing").info("closing section_scf_iteration bla gIndex %d %s", gIndex, section.simpleValues)
self.scfIterNr += 1
def onClose_gaussian_section_geometry(self, backend, gIndex, section):
xCoord = section["gaussian_atom_x_coord"]
yCoord = section["gaussian_atom_y_coord"]
zCoord = section["gaussian_atom_z_coord"]
labels = section["gaussian_atom_label"]
logging.error("x:%s",xCoord)
logging.error("y:%s",yCoord)
logging.error("z:%s",zCoord)
logging.error("labels:%s",labels)
atom_positions = np.zeros((len(xCoord),3), dtype=float)
for i in range(len(xCoord)):
atom_positions[i,0] = xCoord[i]
atom_positions[i,1] = yCoord[i]
atom_positions[i,2] = zCoord[i]
backend.addArrayValues("atom_position", atom_positions)
backend.addValue("atom_label", labels)
# which values to cache or forward (mapping meta name -> CachingLevel)
cachingLevelForMetaName = {}
cachingLevelForMetaName = {
"gaussian_atom_x_coord": CachingLevel.Cache,
"gaussian_atom_y_coord": CachingLevel.Cache,
"gaussian_atom_z_coord": CachingLevel.Cache,
"gaussian_atom_label": CachingLevel.Cache,
"gaussian_section_geometry": CachingLevel.Ignore,
}
if __name__ == "__main__":
mainFunction(mainFileDescription, metaInfoEnv, parserInfo,
......
test/examples/Al.inp 0 → 100644
View file @ 827f7b22
%mem=24000000
#B1B95/6-31G**
atom calc
casno=7429905
method=55
basis=3
0 2
Al
test/examples/Al.out 0 → 100644
View file @ 827f7b22
Entering Gaussian System, Link 0=g09
Initial command:
/usr/local/gaussian/g09.b01.em64t.linda/g09/l1.exe /tmp/rdj3/g09-29284/Gau-18735.inp -scrdir=/tmp/rdj3/g09-29284/
Entering Link 1 = /usr/local/gaussian/g09.b01.em64t.linda/g09/l1.exe PID= 18736.
Copyright (c) 1988,1990,1992,1993,1995,1998,2003,2009,2010,
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 B.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, 2010.
******************************************
Gaussian 09: EM64L-G09RevB.01 12-Aug-2010
9-Mar-2012
******************************************
%NProc=8
Will use up to 8 processors via shared memory.
%mem=424000000
---------------------------------------------------------
#B3LYP/aug-cc-pVTZ scf=verytight integral(grid=ultrafine)
---------------------------------------------------------
1/38=1/1;
2/12=2,17=6,18=5,40=1/2;
3/5=16,6=1,7=10,11=2,16=1,25=1,30=1,74=-5,75=-5/1,2,3;
4//1;
5/5=2,17=3,38=5/2;
6/7=2,8=2,9=2,10=2,28=1/1;
99/5=1,9=1/99;
----------------------------------------------------------------------
al- Aluminum atom anion casno=7429905 state=1 config=1 method=2 basis=
20
----------------------------------------------------------------------
Symbolic Z-matrix:
Charge = -1 Multiplicity = 1
AL 0. 0. 0.
Input orientation:
---------------------------------------------------------------------
Center Atomic Atomic Coordinates (Angstroms)
Number Number Type X Y Z
---------------------------------------------------------------------
1 13 0 0.000000 0.000000 0.000000
---------------------------------------------------------------------
Stoichiometry Al(1-)
Framework group OH[O(Al)]
Deg. of freedom 0
Full point group OH NOp 48
Largest Abelian subgroup D2H NOp 8
Largest concise Abelian subgroup C1 NOp 1
Standard orientation:
---------------------------------------------------------------------
Center Atomic Atomic Coordinates (Angstroms)
Number Number Type X Y Z
---------------------------------------------------------------------
1 13 0 0.000000 0.000000 0.000000
---------------------------------------------------------------------
Standard basis: Aug-CC-pVTZ (5D, 7F)
There are 12 symmetry adapted basis functions of AG symmetry.
There are 3 symmetry adapted basis functions of B1G symmetry.
There are 3 symmetry adapted basis functions of B2G symmetry.
There are 3 symmetry adapted basis functions of B3G symmetry.
There are 2 symmetry adapted basis functions of AU symmetry.
There are 9 symmetry adapted basis functions of B1U symmetry.
There are 9 symmetry adapted basis functions of B2U symmetry.
There are 9 symmetry adapted basis functions of B3U symmetry.
Integral buffers will be 131072 words long.
Raffenetti 2 integral format.
Two-electron integral symmetry is turned on.
50 basis functions, 115 primitive gaussians, 59 cartesian basis functions
7 alpha electrons 7 beta electrons
nuclear repulsion energy 0.0000000000 Hartrees.
NAtoms= 1 NActive= 1 NUniq= 1 SFac= 1.00D+00 NAtFMM= 50 NAOKFM=F Big=F
One-electron integrals computed using PRISM.
NBasis= 50 RedAO= T NBF= 12 3 3 3 2 9 9 9
NBsUse= 50 1.00D-06 NBFU= 12 3 3 3 2 9 9 9
Harris functional with IExCor= 402 diagonalized for initial guess.
ExpMin= 1.46D-02 ExpMax= 2.06D+05 ExpMxC= 1.99D+03 IAcc=3 IRadAn= 5 AccDes= 0.00D+00
HarFok: IExCor= 402 AccDes= 0.00D+00 IRadAn= 5 IDoV= 1
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
Omega= 0.000000 0.000000 1.000000 0.000000 0.000000 ICntrl= 500 IOpCl= 0
NMat0= 1 NMatS0= 1 NMatT0= 0 NMatD0= 1 NMtDS0= 0 NMtDT0= 0
I1Cent= 4 NGrid= 0.
Petite list used in FoFCou.
Initial guess orbital symmetries:
Occupied (A1G) (A1G) (T1U) (T1U) (T1U) (A1G) (T1U)
Virtual (T1U) (T1U) (A1G) (T1U) (T1U) (T1U) (T2G) (T2G)
(T2G) (EG) (EG) (T2G) (T2G) (T2G) (EG) (EG) (T1U)
(T1U) (T1U) (A1G) (T2U) (T2U) (T2U) (A2U) (T1U)
(T1U) (T1U) (T2G) (T2G) (T2G) (EG) (EG) (T2U)
(T2U) (T2U) (A2U) (T1U) (T1U) (T1U) (A1G) (T1U)
(T1U) (T1U)
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.
Keep R1 ints in memory in canonical form, NReq=3559651.
Density matrix breaks symmetry, PCut= 1.00D-04
Density has only Abelian symmetry.
Density matrix breaks symmetry, PCut= 1.00D-04
Density has only Abelian symmetry.
Density matrix breaks symmetry, PCut= 1.00D-04
Density has only Abelian symmetry.
Density matrix breaks symmetry, PCut= 1.00D-04
Density has only Abelian symmetry.
Density matrix breaks symmetry, PCut= 1.00D-04
Density has only Abelian symmetry.
Density matrix breaks symmetry, PCut= 1.00D-04
Density has only Abelian symmetry.
Density matrix breaks symmetry, PCut= 1.00D-04
Density has only Abelian symmetry.
Density matrix breaks symmetry, PCut= 1.00D-04
Density has only Abelian symmetry.
Density matrix breaks symmetry, PCut= 1.00D-04
Density has only Abelian symmetry.
Density matrix breaks symmetry, PCut= 1.00D-04
Density has only Abelian symmetry.
SCF Done: E(RB3LYP) = -242.389700912 A.U. after 9 cycles
Convg = 0.7910D-09 -V/T = 2.0034
**********************************************************************
Population analysis using the SCF density.
**********************************************************************
Orbital symmetries:
Occupied (A1G) (A1G) (T1U) (T1U) (T1U) (?A) (?B)
Virtual (?B) (?B) (?A) (?B) (?B) (?B) (?C) (?C) (?C) (?A)
(?A) (?C) (?A) (?C) (?C) (?A) (?B) (?B) (?B) (?A)
(?B) (A2U) (?B) (?B) (?B) (?B) (?B) (T2G) (?A)
(T2G) (T2G) (?A) (?B) (?B) (?B) (A2U) (?B) (?B)
(?B) (A1G) (T1U) (T1U) (T1U)
Unable to determine electronic state: an orbital has unidentified symmetry.
Alpha occ. eigenvalues -- -55.90858 -3.98439 -2.53890 -2.53890 -2.53183
Alpha occ. eigenvalues -- -0.14707 0.04154
Alpha virt. eigenvalues -- 0.06873 0.06873 0.11144 0.11276 0.11649
Alpha virt. eigenvalues -- 0.11649 0.16553 0.16553 0.17309 0.17313
Alpha virt. eigenvalues -- 0.17442 0.36907 0.36908 0.37273 0.37273
Alpha virt. eigenvalues -- 0.37387 0.37412 0.37412 0.37996 0.38088
Alpha virt. eigenvalues -- 0.39755 0.39755 0.39994 0.39994 0.40534
Alpha virt. eigenvalues -- 0.40534 0.40628 0.91783 0.91783 0.92696
Alpha virt. eigenvalues -- 0.92696 0.93384 1.04866 1.04866 1.05411
Alpha virt. eigenvalues -- 1.05411 1.06226 1.06226 1.06431 1.75528
Alpha virt. eigenvalues -- 2.11663 2.11663 2.13025
Condensed to atoms (all electrons):
1
1 Al 14.000000
Mulliken atomic charges:
1
1 Al -1.000000
Sum of Mulliken atomic charges = -1.00000
Mulliken charges with hydrogens summed into heavy atoms:
1
1 Al -1.000000
Sum of Mulliken charges with hydrogens summed into heavy atoms = -1.00000
Electronic spatial extent (au): <R**2>= 89.8727
Charge= -1.0000 electrons
Dipole moment (field-independent basis, Debye):
X= 0.0000 Y= 0.0000 Z= 0.0000 Tot= 0.0000
Quadrupole moment (field-independent basis, Debye-Ang):
XX= -28.0764 YY= -28.0764 ZZ= -64.7292
XY= 0.0000 XZ= 0.0000 YZ= 0.0000
Traceless Quadrupole moment (field-independent basis, Debye-Ang):
XX= 12.2176 YY= 12.2176 ZZ= -24.4352
XY= 0.0000 XZ= 0.0000 YZ= 0.0000
Octapole moment (field-independent basis, Debye-Ang**2):
XXX= 0.0000 YYY= 0.0000 ZZZ= 0.0000 XYY= 0.0000
XXY= 0.0000 XXZ= 0.0000 XZZ= 0.0000 YZZ= 0.0000
YYZ= 0.0000 XYZ= 0.0000
Hexadecapole moment (field-independent basis, Debye-Ang**3):
XXXX= -210.4685 YYYY= -210.4685 ZZZZ= -964.4363 XXXY= 0.0000
XXXZ= 0.0000 YYYX= 0.0000 YYYZ= 0.0000 ZZZX= 0.0000
ZZZY= 0.0000 XXYY= -70.1562 XXZZ= -196.7924 YYZZ= -196.7924
XXYZ= 0.0000 YYXZ= 0.0000 ZZXY= 0.0000
N-N= 0.000000000000D+00 E-N=-5.803947170106D+02 KE= 2.415679408169D+02
Symmetry AG KE= 1.819256577668D+02
Symmetry B1G KE= 0.000000000000D+00
Symmetry B2G KE= 0.000000000000D+00
Symmetry B3G KE= 0.000000000000D+00
Symmetry AU KE= 0.000000000000D+00
Symmetry B1U KE= 2.039512239737D+01
Symmetry B2U KE= 1.962358032638D+01
Symmetry B3U KE= 1.962358032638D+01
1\1\GINC-N233\SP\RB3LYP\Aug-CC-pVTZ\Al1(1-)\RDJ3\09-Mar-2012\0\\#B3LYP
/aug-cc-pVTZ scf=verytight integral(grid=ultrafine)\\al- Aluminum atom
anion casno=7429905 state=1 config=1 method=2 basis=20\\-1,1\Al,0,0.,
0.,0.\\Version=EM64L-G09RevB.01\HF=-242.3897009\RMSD=7.910e-10\Dipole=
0.,0.,0.\Quadrupole=-18.1669729,9.0834864,9.0834864,0.,0.,0.\PG=OH [O(
Al1)]\\@
LAWS OF PROGRAMMING DEFINITION: A WORKING PROGRAM
IS ONE THAT HAS
ONLY UNOBSERVED
BUGS.
Job cpu time: 0 days 0 hours 0 minutes 18.6 seconds.
File lengths (MBytes): RWF= 5 Int= 0 D2E= 0 Chk= 1 Scr= 1
Normal termination of Gaussian 09 at Fri Mar 9 14:47:52 2012.
test/examples/ZnO10pbe.dat 0 → 100644
View file @ 827f7b22
%chk=ZnO10pbe
%mem=1500mb
%nproc=12
#p pbepbe/6-31G* td(singlets,nstates=10)
ZnO 10
0 1
O 3.25422625 1.27930585 -2.54529614
Zn 2.24859735 -0.44790645 -2.74547013
O 3.22448354 -2.01425234 -3.19002709
Zn 3.40374636 -1.80554341 -5.20959503
O 5.25270943 -2.29560427 -5.24774549
Zn 5.99419054 -0.54286846 -5.22935256
O 6.28848283 -0.42881245 -3.16157625
Zn 5.12324614 -1.93265943 -3.19033674
Zn 4.96040891 0.94341796 -3.28777063
O 5.13698492 1.15172617 -5.30695890
Zn 0.60201850 -0.16611529 -5.28308763
O 2.30611968 -0.50267796 -6.02913818
Zn 3.31139087 1.22419605 -5.82287052
O -0.72661336 1.20584185 -5.41057105
Zn -0.43367086 1.32094499 -3.34238586
O 0.42394706 -0.37365245 -3.26432151
Zn 2.15599088 2.58444037 -3.36102890
O 0.30716576 3.07376050 -3.32446397
Zn 0.43812201 2.71026983 -5.38146546
O 2.33665319 2.79214294 -5.38100795
test/examples/ZnO10pbe.out 0 → 100644
View file @ 827f7b22
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