First version of Gaussian parser including geometry

parent 51277673
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,
......
%mem=24000000
#B1B95/6-31G**
atom calc
casno=7429905
method=55
basis=3
0 2
Al
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.
%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
Entering Gaussian System, Link 0=g09
Initial command:
/aplic/Gaussian/g09d01_prebuilt/g09/l1.exe "/work/g4rosendo/Gau-24710.inp" -scrdir="/work/g4rosendo/"
Entering Link 1 = /aplic/Gaussian/g09d01_prebuilt/g09/l1.exe PID= 24711.
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
23-Nov-2015
******************************************
%chk=ZnO10pbe
%mem=1500mb
%nproc=12
Will use up to 12 processors via shared memory.
----------------------------------------
#p pbepbe/6-31G* td(singlets,nstates=10)
----------------------------------------
1/38=1/1;
2/12=2,17=6,18=5,40=1/2;
3/5=1,6=6,7=1,11=9,16=1,25=1,30=1,74=1009/1,2,8,3;
4//1;
5/5=2,38=5/2;
8/6=1,10=2,108=10/1;
9/41=10,42=1,48=1,70=2/14;
6/7=2,8=2,9=2,10=2/1;
99/5=1,9=1/99;
Leave Link 1 at Mon Nov 23 17:00:44 2015, MaxMem= 196608000 cpu: 1.0
(Enter /aplic/Gaussian/g09d01_prebuilt/g09/l101.exe)
------
ZnO 10
------
Symbolic Z-matrix:
Charge = 0 Multiplicity = 1
O 3.25423 1.27931 -2.5453
Zn 2.2486 -0.44791 -2.74547
O 3.22448 -2.01425 -3.19003
Zn 3.40375 -1.80554 -5.2096
O 5.25271 -2.2956 -5.24775
Zn 5.99419 -0.54287 -5.22935
O 6.28848 -0.42881 -3.16158
Zn 5.12325 -1.93266 -3.19034
Zn 4.96041 0.94342 -3.28777
O 5.13698 1.15173 -5.30696
Zn 0.60202 -0.16612 -5.28309
O 2.30612 -0.50268 -6.02914
Zn 3.31139 1.2242 -5.82287
O -0.72661 1.20584 -5.41057
Zn -0.43367 1.32094 -3.34239
O 0.42395 -0.37365 -3.26432
Zn 2.15599 2.58444 -3.36103
O 0.30717 3.07376 -3.32446
Zn 0.43812 2.71027 -5.38147
O 2.33665 2.79214 -5.38101
NAtoms= 20 NQM= 20 NQMF= 0 NMMI= 0 NMMIF= 0
NMic= 0 NMicF= 0.
Isotopes and Nuclear Properties:
(Nuclear quadrupole moments (NQMom) in fm**2, nuclear magnetic moments (NMagM)
in nuclear magnetons)
Atom 1 2 3 4 5 6 7 8 9 10
IAtWgt= 16 64 16 64 16 64 16 64 64 16
AtmWgt= 15.9949146 63.9291454 15.9949146 63.9291454 15.9949146 63.9291454 15.9949146 63.9291454 63.9291454 15.9949146
NucSpn= 0 0 0 0 0 0 0 0 0 0
AtZEff= 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
NQMom= 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
NMagM= 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
AtZNuc= 8.0000000 30.0000000 8.0000000 30.0000000 8.0000000 30.0000000 8.0000000 30.0000000 30.0000000 8.0000000
Atom 11 12 13 14 15 16 17 18 19 20
IAtWgt= 64 16 64 16 64 16 64 16 64 16
AtmWgt= 63.9291454 15.9949146 63.9291454 15.9949146 63.9291454 15.9949146 63.9291454 15.9949146 63.9291454 15.9949146
NucSpn= 0 0 0 0 0 0 0 0 0 0
AtZEff= 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
NQMom= 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
NMagM= 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
AtZNuc= 30.0000000 8.0000000 30.0000000 8.0000000 30.0000000 8.0000000 30.0000000 8.0000000 30.0000000 8.0000000
Leave Link 101 at Mon Nov 23 17:00:44 2015, MaxMem= 196608000 cpu: 1.4
(Enter /aplic/Gaussian/g09d01_prebuilt/g09/l202.exe)
Input orientation:
---------------------------------------------------------------------
Center Atomic Atomic Coordinates (Angstroms)
Number Number Type X Y Z
---------------------------------------------------------------------
1 8 0 3.254226 1.279306 -2.545296
2 30 0 2.248597 -0.447906 -2.745470
3 8 0 3.224484 -2.014252 -3.190027
4 30 0 3.403746 -1.805543 -5.209595
5 8 0 5.252709 -2.295604 -5.247745
6 30 0 5.994191 -0.542868 -5.229353
7 8 0 6.288483 -0.428812 -3.161576
8 30 0 5.123246 -1.932659 -3.190337
9 30 0 4.960409 0.943418 -3.287771
10 8 0 5.136985 1.151726 -5.306959
11 30 0 0.602019 -0.166115 -5.283088
12 8 0 2.306120 -0.502678 -6.029138
13 30 0 3.311391 1.224196 -5.822871
14 8 0 -0.726613 1.205842 -5.410571
15 30 0 -0.433671 1.320945 -3.342386
16 8 0 0.423947 -0.373652 -3.264322
17 30 0 2.155991 2.584440 -3.361029
18 8 0 0.307166 3.073761 -3.324464
19 30 0 0.438122 2.710270 -5.381465
20 8 0 2.336653 2.792143 -5.381008
---------------------------------------------------------------------
Distance matrix (angstroms):
1 2 3 4 5
1 O 0.000000
2 Zn 2.008637 0.000000
3 O 3.356201 1.898269 0.000000
4 Zn 4.078865 3.041292 2.038222 0.000000
5 O 4.906847 4.324356 2.902941 1.913186 0.000000
6 Zn 4.246396 4.495348 3.741002 2.881864 1.903212
7 O 3.536125 4.061303 3.450003 3.796245 2.984936
8 Zn 3.771741 3.265885 1.900515 2.655229 2.093184
9 Zn 1.890806 3.095771 3.430861 3.697756 3.797131
10 O 3.344823 4.178855 4.261746 3.429146 3.449781
11 Zn 4.076635 3.038113 3.830644 3.246969 5.115164
12 O 4.026354 3.284629 3.344967 1.890474 3.536602
13 Zn 3.278536 3.660034 4.174562 3.092565 4.060601
14 O 4.905332 4.323138 5.559765 5.115536 6.931013
15 Zn 3.773284 3.267982 4.952661 5.290290 7.003195
16 O 3.355555 1.898439 3.246551 3.835832 5.562806
17 Zn 1.890745 3.095580 4.724288 4.924028 6.079819
18 O 3.537278 4.062823 5.866574 6.078662 7.549006
19 Zn 4.245228 4.494482 5.906549 5.405279 6.946719
20 O 3.342436 4.177527 5.356312 4.723006 5.865690
6 7 8 9 10
6 Zn 0.000000
7 O 2.091726 0.000000
8 Zn 2.616801 1.902672 0.000000
9 Zn 2.654711 1.913824 2.882331 0.000000
10 O 1.900651 2.902881 3.740817 2.037570 0.000000
11 Zn 5.405585 6.075006 5.285999 4.920155 4.722626
12 O 3.774008 4.907910 4.247334 4.080630 3.357439
13 Zn 3.266833 4.321805 4.492081 3.037240 1.898476
14 O 6.946944 7.545969 7.000035 6.075967 5.864763
15 Zn 6.953549 6.948503 6.441148 5.407551 5.909348
16 O 5.909111 5.865695 4.951706 4.723845 5.358346
17 Zn 5.291736 5.118297 5.407211 3.250090 3.837400
18 O 7.003632 6.933304 6.948155 5.117849 5.563421
19 Zn 6.440182 7.000605 6.950412 5.287381 4.951154
20 O 4.952058 5.560341 5.906598 3.831908 3.246276
11 12 13 14 15
11 Zn 0.000000
12 O 1.890457 0.000000
13 Zn 3.092738 2.008783 0.000000
14 O 1.914101 3.535412 4.059040 0.000000
15 Zn 2.655245 4.248610 4.493067 2.091998 0.000000
16 O 2.037203 3.347153 4.175718 2.902581 1.900858
17 Zn 3.697931 4.083093 3.040704 3.796125 2.881513
18 O 3.797360 4.909378 4.322996 2.984906 1.903030
19 Zn 2.882730 3.772523 3.264801 1.902829 2.616886
20 O 3.430720 3.358102 1.898371 3.449758 3.741002
16 17 18 19 20
16 O 0.000000
17 Zn 3.429233 0.000000
18 O 3.449915 1.912832 0.000000
19 Zn 3.740732 2.655009 2.092972 0.000000
20 O 4.261580 2.038650 2.903016 1.900296 0.000000
Stoichiometry O10Zn10
Framework group C1[X(O10Zn10)]
Deg. of freedom 54
Full point group C1 NOp 1
Largest Abelian subgroup C1 NOp 1
Largest concise Abelian subgroup C1 NOp 1
Standard orientation:
---------------------------------------------------------------------
Center Atomic Atomic Coordinates (Angstroms)
Number Number Type X Y Z
---------------------------------------------------------------------
1 8 0 -0.000734 0.864150 1.816326
2 30 0 -0.000417 -1.111812 1.455499
3 8 0 1.622447 -1.928655 0.905496
4 30 0 1.624848 -1.495870 -1.086247
5 8 0 3.466647 -0.979626 -1.125596
6 30 0 3.221338 0.899462 -0.949335
7 8 0 3.465548 0.979375 1.126548
8 30 0 3.219307 -0.899145 0.951365
9 30 0 1.623676 1.497522 1.084697
10 8 0 1.623969 1.928575 -0.906756
11 30 0 -1.622120 -1.496989 -1.084550
12 8 0 0.000752 -0.864960 -1.819840
13 30 0 0.000438 1.110039 -1.452976
14 8 0 -3.464366 -0.979255 -1.127718
15 30 0 -3.221840 -0.899157 0.948629
16 8 0 -1.624103 -1.928101 0.906515
17 30 0 -1.626413 1.496394 1.086702
18 8 0 -3.467756 0.979712 1.124414
19 30 0 -3.218843 0.899483 -0.952154
20 8 0 -1.622306 1.929055 -0.905504
---------------------------------------------------------------------
Rotational constants (GHZ): 0.2194629 0.0952492 0.0914800
Leave Link 202 at Mon Nov 23 17:00:44 2015, MaxMem= 196608000 cpu: 0.5
(Enter /aplic/Gaussian/g09d01_prebuilt/g09/l301.exe)
Standard basis: 6-31G(d) (6D, 7F)
Ernie: Thresh= 0.10000D-02 Tol= 0.10000D-05 Strict=F.
There are 540 symmetry adapted cartesian basis functions of A symmetry.
There are 510 symmetry adapted basis functions of A symmetry.
510 basis functions, 1320 primitive gaussians, 540 cartesian basis functions
190 alpha electrons 190 beta electrons
nuclear repulsion energy 10193.3392886135 Hartrees.
IExCor= 1009 DFT=T Ex=PBE Corr=PBE ExCW=0 ScaHFX= 0.000000
ScaDFX= 1.000000 1.000000 1.000000 1.000000 ScalE2= 1.000000 1.000000
IRadAn= 0 IRanWt= -1 IRanGd= 0 ICorTp=0 IEmpDi= 4
NAtoms= 20 NActive= 20 NUniq= 20 SFac= 1.00D+00 NAtFMM= 60 NAOKFM=F Big=F
Integral buffers will be 131072 words long.
Regular integral format.
Two-electron integral symmetry is turned on.
Leave Link 301 at Mon Nov 23 17:00:44 2015, MaxMem= 196608000 cpu: 1.2
(Enter /aplic/Gaussian/g09d01_prebuilt/g09/l302.exe)
NPDir=0 NMtPBC= 1 NCelOv= 1 NCel= 1 NClECP= 1 NCelD= 1
NCelK= 1 NCelE2= 1 NClLst= 1 CellRange= 0.0.
One-electron integrals computed using PRISM.
NBasis= 510 RedAO= T EigKep= 1.05D-03 NBF= 510
NBsUse= 510 1.00D-06 EigRej= -1.00D+00 NBFU= 510
Precomputing XC quadrature grid using
IXCGrd= 4 IRadAn= 0 IRanWt= -1 IRanGd= 0 AccXCQ= 0.00D+00.
Generated NRdTot= 0 NPtTot= 0 NUsed= 0 NTot= 32
NSgBfM= 520 520 524 524 524 MxSgAt= 20 MxSgA2= 20.
Leave Link 302 at Mon Nov 23 17:00:45 2015, MaxMem= 196608000 cpu: 10.2
(Enter /aplic/Gaussian/g09d01_prebuilt/g09/l308.exe)
Leave Link 308 at Mon Nov 23 17:00:46 2015, MaxMem= 196608000 cpu: 2.3
(Enter /aplic/Gaussian/g09d01_prebuilt/g09/l303.exe)
DipDrv: MaxL=1.
Leave Link 303 at Mon Nov 23 17:00:46 2015, MaxMem= 196608000 cpu: 1.4
(Enter /aplic/Gaussian/g09d01_prebuilt/g09/l401.exe)
ExpMin= 4.93D-02 ExpMax= 8.24D+04 ExpMxC= 1.24D+04 IAcc=2 IRadAn= 4 AccDes= 0.00D+00
Harris functional with IExCor= 1009 and IRadAn= 4 diagonalized for initial guess.
HarFok: IExCor= 1009 AccDes= 0.00D+00 IRadAn= 4 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.
Harris En= -18539.5549992387
JPrj=0 DoOrth=F DoCkMO=F.
Leave Link 401 at Mon Nov 23 17:00:48 2015, MaxMem= 196608000 cpu: 20.5
(Enter /aplic/Gaussian/g09d01_prebuilt/g09/l502.exe)
Closed shell SCF:
Using DIIS extrapolation, IDIIS= 1040.
Integral symmetry usage will be decided dynamically.
IVT= 903740 IEndB= 903740 NGot= 196608000 MDV= 196013041
LenX= 196013041 LenY= 195720901
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.
Fock matrices will be formed incrementally for 20 cycles.
Cycle 1 Pass 1 IDiag 1:
FoFJK: IHMeth= 1 ICntrl= 500 DoSepK=F KAlg= 0 I1Cent= 0 FoldK=F
IRaf= 740000000 NMat= 1 IRICut= 1 DoRegI=T DoRafI=F ISym2E= 0.
FoFCou: FMM=F IPFlag= 0 FMFlag= 100000 FMFlg1= 0
NFxFlg= 0 DoJE=T BraDBF=F KetDBF=F FulRan=T
wScrn= 0.000000 ICntrl= 500 IOpCl= 0 I1Cent= 0 NGrid= 0
NMat0= 1 NMatS0= 1 NMatT0= 0 NMatD0= 1 NMtDS0= 0 NMtDT0= 0
Symmetry not used in FoFCou.
E= -18538.0224425364
DIIS: error= 5.75D-02 at cycle 1 NSaved= 1.
NSaved= 1 IEnMin= 1 EnMin= -18538.0224425364 IErMin= 1 ErrMin= 5.75D-02
ErrMax= 5.75D-02 0.00D+00 EMaxC= 1.00D-01 BMatC= 3.81D+00 BMatP= 3.81D+00
IDIUse=3 WtCom= 4.25D-01 WtEn= 5.75D-01
Coeff-Com: 0.100D+01
Coeff-En: 0.100D+01
Coeff: 0.100D+01
Gap= 0.280 Goal= None Shift= 0.000
GapD= 0.280 DampG=1.000 DampE=0.250 DampFc=0.2500 IDamp=-1.
Damping current iteration by 2.50D-01
RMSDP=2.71D-02 MaxDP=2.15D+00 OVMax= 7.92D-01
Cycle 2 Pass 1 IDiag 1:
RMSU= 6.77D-03 CP: 1.01D+00
E= -18538.3616365454 Delta-E= -0.339194008964 Rises=F Damp=T
DIIS: error= 4.12D-02 at cycle 2 NSaved= 2.
NSaved= 2 IEnMin= 2 EnMin= -18538.3616365454 IErMin= 2 ErrMin= 4.12D-02
ErrMax= 4.12D-02 0.00D+00 EMaxC= 1.00D-01 BMatC= 3.73D-01 BMatP= 3.81D+00
IDIUse=3 WtCom= 5.88D-01 WtEn= 4.12D-01
Coeff-Com: -0.943D-01 0.109D+01
Coeff-En: 0.404D+00 0.596D+00
Coeff: 0.111D+00 0.889D+00
Gap= -0.018 Goal= None Shift= 0.000
RMSDP=8.14D-03 MaxDP=6.90D-01 DE=-3.39D-01 OVMax= 7.75D-01
Cycle 3 Pass 1 IDiag 1:
RMSU= 4.68D-03 CP: 9.66D-01 3.45D-02
E= -18539.7579340111 Delta-E= -1.396297465722 Rises=F Damp=F