ePSman ESgamess class notes & demos: molecule and Gamess job handling class
30/03/21
This class handles Gamess jobs (full pipeline) on a local machine only.
Core functionality is provided by the following libraries:
-
Interface with PubChem.
-
Molecule class/handling routines.
Transformations.
Figures (2D natively, uses py3Dmol on the backend for 3D rendering).
-
Setup Gamess input cards.
Run Gamess calculations (local machine only).
This class creates a pipeline with these tools, and implements a few extra helper routines, with the general aim to make this part of the process as painless as possible.
Minimal method for pipeline to ePolyScat jobs:
PubChem download > Fix reference frame (symmetry axis to Z) > Run Gamess > Export/convert.
Imports
[1]:
# Import class
from epsman.elecStructure.gamess import ESgamess
Molecule creation routines
Currently wraps routines from RDkit + PubChemPy for rapid setup from existing sources. Shows 2D structure and coord tabe on execution.
TODO: add support for manual molecule creation. This can be done via a file at the moment, or via RDkit backend (see, for example, the RDkit docs).
[2]:
# Molecule from PubChem
testDL = ESgamess(searchName = 'N2O')
Set name = N2O
Set smiles = None
Set molFile = None
*** File /home/paul/github/epsman/demos/N2O.SDF already exists, pass overwrite=True to overwrite
Set job = None
Set sym = C1
Set atomList = None
RDKit WARNING: [14:38:36] Warning: molecule is tagged as 3D, but all Z coords are zero
RDKit WARNING: [14:38:36] Warning: molecule is tagged as 3D, but all Z coords are zero
O 8.0 1.3063000000 0.0000000000 0.0000000000
N 7.0 -0.1096000000 0.0000000000 0.0000000000
N 7.0 -1.1967000000 0.0000000000 0.0000000000
[3]:
# Molecule from SMILES
testSmiles = ESgamess(smiles = '[N-]=[N+]=O')
Set name = None
Set smiles = [N-]=[N+]=O
Set molFile = None
Set job = None
Set sym = C1
Set atomList = None
N 7.0 1.1203318954 0.1103129733 0.0000000000
N 7.0 -0.0066842804 -0.3821096381 0.0000000000
O 8.0 -1.1136476150 -0.8657704075 0.0000000000
[4]:
# From file, e.g. SDF file downloaded from PubChem above.
# This uses RDkit Chem.MolFromMolFile() on the backend,
# For details of files supported see https://www.rdkit.org/docs/source/rdkit.Chem.rdmolfiles.html
testFile = ESgamess(molFile = 'N2O.SDF')
Set name = None
Set smiles = None
Set molFile = N2O.SDF
Set job = None
Set sym = C1
Set atomList = None
RDKit WARNING: [14:38:36] Warning: molecule is tagged as 3D, but all Z coords are zero
RDKit WARNING: [14:38:36] Warning: molecule is tagged as 3D, but all Z coords are zero
O 8.0 1.3063000000 0.0000000000 0.0000000000
N 7.0 -0.1096000000 0.0000000000 0.0000000000
N 7.0 -1.1967000000 0.0000000000 0.0000000000
Additional info
If Pandas is available, a fancy print is available with printTable().
[5]:
testDL.printTable()
| Ind | Species | Atomic Num. | x | y | z | |
|---|---|---|---|---|---|---|
| 0 | 0 | O | 8 | 1.3063 | 0.0 | 0.0 |
| 1 | 1 | N | 7 | -0.1096 | 0.0 | 0.0 |
| 2 | 2 | N | 7 | -1.1967 | 0.0 | 0.0 |
If py3Dmol is available, interactive 3D plots are available in notebooks with plot3D().
[6]:
testDL.plot3D()
You appear to be running in JupyterLab (or JavaScript failed to load for some other reason). You need to install the 3dmol extension:
jupyter labextension install jupyterlab_3dmol
The molecule is stored as an RDkit object, self.mol, and RDkit methods are also available.
[7]:
type(testDL.mol)
[7]:
rdkit.Chem.rdchem.Mol
[8]:
# Calling the object will render it
testDL.mol
[8]:
[9]:
# RDkit method example
testDL.mol.GetNumAtoms()
[9]:
3
pyGamess wrapper
Setup Gamess job
[10]:
# Init the pyGamess job.
# This minimally needs a gamess_path set, which defaults to '/opt/gamess'
testDL.initGamess() # Using defaults
*** Init pyGamess job.
Default Gamess input card set (use self.params to modify options dictionary, self.setGamess() to test):
$contrl scftyp=rhf runtyp=energy $end
$basis gbasis=sto ngauss=3 $end
$system mwords=30 $end
$DATA
None
C1
O 8.0 1.3063000000 0.0000000000 0.0000000000
N 7.0 -0.1096000000 0.0000000000 0.0000000000
N 7.0 -1.1967000000 0.0000000000 0.0000000000
$END
This creates a pyGamess object, accessible at self.g.
[11]:
print(type(testDL.g))
print(testDL.g.gamess_path)
<class 'epsman.elecStructure.gamess.gamessInput'>
/opt/gamess
All Gamess job parameters are stored in a dictionary, at self.params (also self.g.options), and can be set there directly. See the pyGamess docs for more info.
pyGamess doesn’t support symmetry or job annotation (uses ‘C1’ only), this can be added via a class wrapper here, and can be set via self.setGamess.
Note that is symmetry is set to anything other than ‘C1’, coordinate transforms may be required -see notes below.
[12]:
testDL.params
[12]:
{'contrl': {'scftyp': 'rhf', 'runtyp': 'energy'},
'basis': {'gbasis': 'sto', 'ngauss': '3'},
'statpt': {'opttol': '0.0001', 'nstep': '20'},
'system': {'mwords': '30'},
'cis': {'nstate': '1'},
'extra': {'job': None, 'sym': 'C1', 'atomList': None}}
This adds an extras item to the params dictionary.
[13]:
testDL.params
[13]:
{'contrl': {'scftyp': 'rhf', 'runtyp': 'energy'},
'basis': {'gbasis': 'sto', 'ngauss': '3'},
'statpt': {'opttol': '0.0001', 'nstep': '20'},
'system': {'mwords': '30'},
'cis': {'nstate': '1'},
'extra': {'job': None, 'sym': 'C1', 'atomList': None}}
Where atomList can additionally be set to sub-select on which atoms are listed on the input card for symmetrized jobs (TODO: make this better/automated!).
The current Gamess input card can always be checked via self.printGamessInput()
[14]:
testDL.printGamessInput()
*** Gamess input card:
$contrl scftyp=rhf runtyp=energy $end
$basis gbasis=sto ngauss=3 $end
$system mwords=30 $end
$DATA
None
C1
O 8.0 1.3063000000 0.0000000000 0.0000000000
N 7.0 -0.1096000000 0.0000000000 0.0000000000
N 7.0 -1.1967000000 0.0000000000 0.0000000000
$END
Run Gamess
If a valid gamess_path is set, then this is simple, and the basic results are returned to self.mol.
[15]:
# Run as per input card
testDL.runGamess()
INFO:pygamess.gamess:Executeing py_rungms with command /opt/gamess/ddikick.x /opt/gamess/gamess.00.x watddq -ddi 1 1 jake -scr /tmp/tmpv0_0f1_d > /tmp/tmpv0_0f1_d/watddq.out
*** Energy run completed
E = -181.1830797993
[16]:
# Run optimization, in this case the updated coord table is also shown.
testDL.runGamess(runType = 'optimize')
INFO:pygamess.gamess:Executeing py_rungms with command /opt/gamess/ddikick.x /opt/gamess/gamess.00.x uopeyh -ddi 1 1 jake -scr /tmp/tmpv0_0f1_d > /tmp/tmpv0_0f1_d/uopeyh.out
*** Optimized self.mol
E = -181.1830797993
| Ind | Species | Atomic Num. | x | y | z | |
|---|---|---|---|---|---|---|
| 0 | 0 | O | 8 | 1.3063 | 0.0 | 0.0 |
| 1 | 1 | N | 7 | -0.1096 | 0.0 | 0.0 |
| 2 | 2 | N | 7 | -1.1967 | 0.0 | 0.0 |
However, in the default case the tmp files are not kept. To keep the full Gamess output, supply a filename (full path).
[17]:
# Check for tmp file
print(testDL.g.gamout)
!cat {testDL.g.gamout}
/tmp/tmpv0_0f1_d/uopeyh.out
cat: /tmp/tmpv0_0f1_d/uopeyh.out: No such file or directory
[18]:
# runGamess wrapper will take a path and move the output file.
testDL.runGamess(fileOut = '/tmp/test.out')
INFO:pygamess.gamess:Executeing py_rungms with command /opt/gamess/ddikick.x /opt/gamess/gamess.00.x ytegoc -ddi 1 1 jake -scr /tmp/tmpv0_0f1_d > /tmp/tmpv0_0f1_d/ytegoc.out
*** Energy run completed
E = -181.1830797993
*** Gamess output file moved to /tmp/test.out
[19]:
# In this case the complete output file can also be printed
testDL.printGamess()
Distributed Data Interface kickoff program.
Initiating 1 compute processes on 1 nodes to run the following command:
/opt/gamess/gamess.00.x ytegoc
******************************************************
* GAMESS VERSION = 30 SEP 2018 (R3) *
* FROM IOWA STATE UNIVERSITY *
* M.W.SCHMIDT, K.K.BALDRIDGE, J.A.BOATZ, S.T.ELBERT, *
* M.S.GORDON, J.H.JENSEN, S.KOSEKI, N.MATSUNAGA, *
* K.A.NGUYEN, S.J.SU, T.L.WINDUS, *
* TOGETHER WITH M.DUPUIS, J.A.MONTGOMERY *
* J.COMPUT.CHEM. 14, 1347-1363(1993) *
**************** 64 BIT LINUX VERSION ****************
SINCE 1993, STUDENTS AND POSTDOCS WORKING AT IOWA STATE UNIVERSITY
AND ALSO IN THEIR VARIOUS JOBS AFTER LEAVING ISU HAVE MADE IMPORTANT
CONTRIBUTIONS TO THE CODE:
IVANA ADAMOVIC, CHRISTINE AIKENS, YURI ALEXEEV, POOJA ARORA,
ANDREY ASADCHEV, ROB BELL, PRADIPTA BANDYOPADHYAY, JONATHAN BENTZ,
BRETT BODE, KURT BRORSEN, CALEB CARLIN, GALINA CHABAN, WEI CHEN,
CHEOL HO CHOI, PAUL DAY, ALBERT DEFUSCO, NUWAN DESILVA, TIM DUDLEY,
DMITRI FEDOROV, ALEX FINDLATER, GRAHAM FLETCHER, MARK FREITAG,
KURT GLAESEMANN, ANASTASIA GUNINA,
DAN KEMP, GRANT MERRILL, NORIYUKI MINEZAWA, JONATHAN MULLIN,
TAKESHI NAGATA, SEAN NEDD, HEATHER NETZLOFF, BOSILJKA NJEGIC, RYAN OLSON,
MIKE PAK, BUU PHAM,
SPENCER PRUITT, LUKE ROSKOP, JIM SHOEMAKER, LYUDMILA SLIPCHENKO,
TONY SMITH, SAROM SOK LEANG, JIE SONG, TETSUYA TAKETSUGU, SIMON WEBB,
PENG XU, SOOHAENG YOO, FEDERICO ZAHARIEV
ADDITIONAL CODE HAS BEEN PROVIDED BY COLLABORATORS IN OTHER GROUPS:
IOWA STATE UNIVERSITY:
JOE IVANIC, AARON WEST, LAIMUTIS BYTAUTAS, KLAUS RUEDENBERG
UNIVERSITY OF TOKYO: KIMIHIKO HIRAO, TAKAHITO NAKAJIMA,
TAKAO TSUNEDA, MUNEAKI KAMIYA, SUSUMU YANAGISAWA,
KIYOSHI YAGI, MAHITO CHIBA, SEIKEN TOKURA, NAOAKI KAWAKAMI
UNIVERSITY OF AARHUS: FRANK JENSEN
UNIVERSITY OF IOWA: VISVALDAS KAIRYS, HUI LI
NATIONAL INST. OF STANDARDS AND TECHNOLOGY: WALT STEVENS, DAVID GARMER
UNIVERSITY OF PISA: BENEDETTA MENNUCCI, JACOPO TOMASI
UNIVERSITY OF MEMPHIS: HENRY KURTZ, PRAKASHAN KORAMBATH
UNIVERSITY OF ALBERTA: TOBY ZENG, MARIUSZ KLOBUKOWSKI
UNIVERSITY OF NEW ENGLAND: MARK SPACKMAN
MIE UNIVERSITY: HIROAKI UMEDA
NAT. INST. OF ADVANCED INDUSTRIAL SCIENCE AND TECHNOLOGY: KAZUO KITAURA
MICHIGAN STATE UNIVERSITY:
KAROL KOWALSKI, MARTA WLOCH, JEFFREY GOUR, JESSE LUTZ,
WEI LI, JUN SHEN, J. EMILIANO DEUSTUA, PIOTR PIECUCH
UNIVERSITY OF MINNESOTA:
YINAN SHU
UNIVERSITY OF SILESIA: MONIKA MUSIAL, STANISLAW KUCHARSKI
FACULTES UNIVERSITAIRES NOTRE-DAME DE LA PAIX:
OLIVIER QUINET, BENOIT CHAMPAGNE
UNIVERSITY OF CALIFORNIA - SANTA BARBARA: BERNARD KIRTMAN
INSTITUTE FOR MOLECULAR SCIENCE:
KAZUYA ISHIMURA, MICHIO KATOUDA, AND SHIGERU NAGASE
UNIVERSITY OF NOTRE DAME: ANNA POMOGAEVA, DAN CHIPMAN
KYUSHU UNIVERSITY:
HARUYUKI NAKANO,
FENG LONG GU, JACEK KORCHOWIEC, MARCIN MAKOWSKI, AND YURIKO AOKI,
HIROTOSHI MORI AND EISAKU MIYOSHI
PENNSYLVANIA STATE UNIVERSITY:
TZVETELIN IORDANOV, CHET SWALINA, JONATHAN SKONE,
SHARON HAMMES-SCHIFFER
WASEDA UNIVERSITY:
MASATO KOBAYASHI, TOMOKO AKAMA, TSUGUKI TOUMA,
TAKESHI YOSHIKAWA, YASUHIRO IKABATA, JUNJI SEINO,
YUYA NAKAJIMA, HIROMI NAKAI
NANJING UNIVERSITY: SHUHUA LI
UNIVERSITY OF NEBRASKA:
PEIFENG SU, DEJUN SI, NANDUN THELLAMUREGE, YALI WANG, HUI LI
UNIVERSITY OF ZURICH: ROBERTO PEVERATI, KIM BALDRIDGE
N. COPERNICUS UNIVERSITY AND JACKSON STATE UNIVERSITY:
MARIA BARYSZ
UNIVERSITY OF COPENHAGEN: Jimmy Kromann, CASPER STEINMANN
TOKYO INSTITUTE OF TECHNOLOGY: HIROYA NAKATA
NAGOYA UNIVERSITY: YOSHIO NISHIMOTO, STEPHAN IRLE
MOSCOW STATE UNIVERSITY: VLADIMIR MIRONOV
EXECUTION OF GAMESS BEGUN Tue Mar 30 14:38:42 2021
ECHO OF THE FIRST FEW INPUT CARDS -
INPUT CARD> $contrl scftyp=rhf runtyp=energy $end
INPUT CARD> $basis gbasis=sto ngauss=3 $end
INPUT CARD> $system mwords=30 $end
INPUT CARD> $DATA
INPUT CARD>None
INPUT CARD>C1
INPUT CARD>O 8.0 1.3063000000 0.0000000000 0.0000000000
INPUT CARD>N 7.0 -0.1096000000 0.0000000000 0.0000000000
INPUT CARD>N 7.0 -1.1967000000 0.0000000000 0.0000000000
INPUT CARD> $END
30000000 WORDS OF MEMORY AVAILABLE
BASIS OPTIONS
-------------
GBASIS=STO IGAUSS= 3 POLAR=NONE
NDFUNC= 0 NFFUNC= 0 DIFFSP= F
NPFUNC= 0 DIFFS= F BASNAM=
RUN TITLE
---------
None
THE POINT GROUP OF THE MOLECULE IS C1
THE ORDER OF THE PRINCIPAL AXIS IS 0
ATOM ATOMIC COORDINATES (BOHR)
CHARGE X Y Z
O 8.0 2.4685490578 0.0000000000 0.0000000000
N 7.0 -0.2071139683 0.0000000000 0.0000000000
N 7.0 -2.2614350895 0.0000000000 0.0000000000
INTERNUCLEAR DISTANCES (ANGS.)
------------------------------
1 O 2 N 3 N
1 O 0.0000000 1.4159000 * 2.5030000 *
2 N 1.4159000 * 0.0000000 1.0871000 *
3 N 2.5030000 * 1.0871000 * 0.0000000
* ... LESS THAN 3.000
ATOMIC BASIS SET
----------------
THE CONTRACTED PRIMITIVE FUNCTIONS HAVE BEEN UNNORMALIZED
THE CONTRACTED BASIS FUNCTIONS ARE NOW NORMALIZED TO UNITY
SHELL TYPE PRIMITIVE EXPONENT CONTRACTION COEFFICIENT(S)
O
1 S 1 130.7093214 0.154328967295
1 S 2 23.8088661 0.535328142282
1 S 3 6.4436083 0.444634542185
2 L 4 5.0331513 -0.099967229187 0.155916274999
2 L 5 1.1695961 0.399512826089 0.607683718598
2 L 6 0.3803890 0.700115468880 0.391957393099
N
3 S 7 99.1061690 0.154328967295
3 S 8 18.0523124 0.535328142282
3 S 9 4.8856602 0.444634542185
4 L 10 3.7804559 -0.099967229187 0.155916274999
4 L 11 0.8784966 0.399512826089 0.607683718598
4 L 12 0.2857144 0.700115468880 0.391957393099
N
5 S 13 99.1061690 0.154328967295
5 S 14 18.0523124 0.535328142282
5 S 15 4.8856602 0.444634542185
6 L 16 3.7804559 -0.099967229187 0.155916274999
6 L 17 0.8784966 0.399512826089 0.607683718598
6 L 18 0.2857144 0.700115468880 0.391957393099
TOTAL NUMBER OF BASIS SET SHELLS = 6
NUMBER OF CARTESIAN GAUSSIAN BASIS FUNCTIONS = 15
NUMBER OF ELECTRONS = 22
CHARGE OF MOLECULE = 0
SPIN MULTIPLICITY = 1
NUMBER OF OCCUPIED ORBITALS (ALPHA) = 11
NUMBER OF OCCUPIED ORBITALS (BETA ) = 11
TOTAL NUMBER OF ATOMS = 3
THE NUCLEAR REPULSION ENERGY IS 56.6209169337
THIS MOLECULE IS RECOGNIZED AS BEING LINEAR,
ORBITAL LZ DEGENERACY TOLERANCE ETOLLZ= 1.00E-06
$CONTRL OPTIONS
---------------
SCFTYP=RHF RUNTYP=ENERGY EXETYP=RUN
MPLEVL= 0 CITYP =NONE CCTYP =NONE VBTYP =NONE
DFTTYP=NONE TDDFT =NONE
MULT = 1 ICHARG= 0 NZVAR = 0 COORD =UNIQUE
PP =NONE RELWFN=NONE LOCAL =NONE NUMGRD= F
ISPHER= -1 NOSYM = 0 MAXIT = 30 UNITS =ANGS
PLTORB= F MOLPLT= F AIMPAC= F FRIEND=
NPRINT= 7 IREST = 0 GEOM =INPUT
NORMF = 0 NORMP = 0 ITOL = 20 ICUT = 9
INTTYP=BEST GRDTYP=BEST QMTTOL= 1.0E-06
$SYSTEM OPTIONS
---------------
REPLICATED MEMORY= 30000000 WORDS (ON EVERY NODE).
DISTRIBUTED MEMDDI= 0 MILLION WORDS IN AGGREGATE,
MEMDDI DISTRIBUTED OVER 1 PROCESSORS IS 0 WORDS/PROCESSOR.
TOTAL MEMORY REQUESTED ON EACH PROCESSOR= 30000000 WORDS.
TIMLIM= 525600.00 MINUTES, OR 365.0 DAYS.
PARALL= F BALTYP= DLB KDIAG= 0 COREFL= F
MXSEQ2= 300 MXSEQ3= 150 mem10= 0
----------------
PROPERTIES INPUT
----------------
MOMENTS FIELD POTENTIAL DENSITY
IEMOM = 1 IEFLD = 0 IEPOT = 0 IEDEN = 0
WHERE =COMASS WHERE =NUCLEI WHERE =NUCLEI WHERE =NUCLEI
OUTPUT=BOTH OUTPUT=BOTH OUTPUT=BOTH OUTPUT=BOTH
IEMINT= 0 IEFINT= 0 IEDINT= 0
MORB = 0
EXTRAPOLATION IN EFFECT
SOSCF IN EFFECT
ORBITAL PRINTING OPTION: NPREO= 1 15 2 1
-------------------------------
INTEGRAL TRANSFORMATION OPTIONS
-------------------------------
NWORD = 0
CUTOFF = 1.0E-09 MPTRAN = 0
DIRTRF = F AOINTS =DUP
----------------------
INTEGRAL INPUT OPTIONS
----------------------
NOPK = 1 NORDER= 0 SCHWRZ= F
------------------------------------------
THE POINT GROUP IS C1 , NAXIS= 0, ORDER= 1
------------------------------------------
DIMENSIONS OF THE SYMMETRY SUBSPACES ARE
A = 15
..... DONE SETTING UP THE RUN .....
STEP CPU TIME = 0.00 TOTAL CPU TIME = 0.0 ( 0.0 MIN)
TOTAL WALL CLOCK TIME= 0.0 SECONDS, CPU UTILIZATION IS 0.00%
********************
1 ELECTRON INTEGRALS
********************
...... END OF ONE-ELECTRON INTEGRALS ......
STEP CPU TIME = 0.00 TOTAL CPU TIME = 0.0 ( 0.0 MIN)
TOTAL WALL CLOCK TIME= 0.0 SECONDS, CPU UTILIZATION IS 0.00%
-------------
GUESS OPTIONS
-------------
GUESS =HUCKEL NORB = 0 NORDER= 0
MIX = F PRTMO = F PUNMO = F
TOLZ = 1.0E-08 TOLE = 1.0E-05
SYMDEN= F PURIFY= F
INITIAL GUESS ORBITALS GENERATED BY HUCKEL ROUTINE.
HUCKEL GUESS REQUIRES 4764 WORDS.
SYMMETRIES FOR INITIAL GUESS ORBITALS FOLLOW. BOTH SET(S).
11 ORBITALS ARE OCCUPIED ( 3 CORE ORBITALS).
4=A 5=A 6=A 7=A 8=A 9=A 10=A
11=A 12=A 13=A 14=A 15=A
...... END OF INITIAL ORBITAL SELECTION ......
STEP CPU TIME = 0.00 TOTAL CPU TIME = 0.0 ( 0.0 MIN)
TOTAL WALL CLOCK TIME= 0.0 SECONDS, CPU UTILIZATION IS 0.00%
----------------------
AO INTEGRAL TECHNOLOGY
----------------------
S,P,L SHELL ROTATED AXIS INTEGRALS, REPROGRAMMED BY
KAZUYA ISHIMURA (IMS) AND JOSE SIERRA (SYNSTAR).
S,P,D,L SHELL ROTATED AXIS INTEGRALS PROGRAMMED BY
KAZUYA ISHIMURA (INSTITUTE FOR MOLECULAR SCIENCE).
S,P,D,F,G SHELL TO TOTAL QUARTET ANGULAR MOMENTUM SUM 5,
ERIC PROGRAM BY GRAHAM FLETCHER (ELORET AND NASA ADVANCED
SUPERCOMPUTING DIVISION, AMES RESEARCH CENTER).
S,P,D,F,G,L SHELL GENERAL RYS QUADRATURE PROGRAMMED BY
MICHEL DUPUIS (PACIFIC NORTHWEST NATIONAL LABORATORY).
--------------------
2 ELECTRON INTEGRALS
--------------------
THE -PK- OPTION IS OFF, THE INTEGRALS ARE NOT IN SUPERMATRIX FORM.
STORING 15000 INTEGRALS/RECORD ON DISK, USING 12 BYTES/INTEGRAL.
TWO ELECTRON INTEGRAL EVALUATION REQUIRES 89377 WORDS OF MEMORY.
II,JST,KST,LST = 1 1 1 1 NREC = 1 INTLOC = 1
II,JST,KST,LST = 2 1 1 1 NREC = 1 INTLOC = 2
II,JST,KST,LST = 3 1 1 1 NREC = 1 INTLOC = 34
II,JST,KST,LST = 4 1 1 1 NREC = 1 INTLOC = 72
II,JST,KST,LST = 5 1 1 1 NREC = 1 INTLOC = 486
II,JST,KST,LST = 6 1 1 1 NREC = 1 INTLOC = 709
TOTAL NUMBER OF NONZERO TWO-ELECTRON INTEGRALS = 2276
1 INTEGRAL RECORDS WERE STORED ON DISK FILE 8.
...... END OF TWO-ELECTRON INTEGRALS .....
STEP CPU TIME = 0.01 TOTAL CPU TIME = 0.0 ( 0.0 MIN)
TOTAL WALL CLOCK TIME= 0.0 SECONDS, CPU UTILIZATION IS 50.00%
--------------------------
RHF SCF CALCULATION
--------------------------
NUCLEAR ENERGY = 56.6209169337
MAXIT = 30 NPUNCH= 2
EXTRAP=T DAMP=F SHIFT=F RSTRCT=F DIIS=F DEM=F SOSCF=T
DENSITY MATRIX CONV= 1.00E-05
SOSCF WILL OPTIMIZE 44 ORBITAL ROTATIONS, SOGTOL= 0.250
MEMORY REQUIRED FOR RHF ITERS= 31961 WORDS.
ITER EX DEM TOTAL ENERGY E CHANGE DENSITY CHANGE ORB. GRAD
1 0 0 -180.6349352246 -180.6349352246 0.842406318 0.000000000
---------------START SECOND ORDER SCF---------------
SOSCF IS SCALING ROTATION ANGLE MATRIX, SQCDF= 0.140487
2 1 0 -180.9447400302 -0.3098048056 0.726548798 0.180297490
3 2 0 -180.9415576650 0.0031823652 0.226517379 0.188684179
4 3 0 -181.1219528866 -0.1803952216 0.333983778 0.064196293
5 4 0 -181.1282578097 -0.0063049231 0.193132621 0.112045845
6 5 0 -181.1769569066 -0.0486990969 0.058052121 0.022286065
7 6 0 -181.1820673078 -0.0051104012 0.028852437 0.008697435
8 7 0 -181.1829582015 -0.0008908937 0.008881127 0.005147896
9 8 0 -181.1830710726 -0.0001128711 0.003193726 0.001343628
10 9 0 -181.1830797930 -0.0000087205 0.000062587 0.000024715
11 10 0 -181.1830797989 -0.0000000059 0.000023347 0.000010068
12 11 0 -181.1830797992 -0.0000000003 0.000008502 0.000002253
13 12 0 -181.1830797993 -0.0000000000 0.000000720 0.000000399
-----------------
DENSITY CONVERGED
-----------------
TIME TO FORM FOCK OPERATORS= 0.0 SECONDS ( 0.0 SEC/ITER)
TIME TO SOLVE SCF EQUATIONS= 0.0 SECONDS ( 0.0 SEC/ITER)
FINAL RHF ENERGY IS -181.1830797993 AFTER 13 ITERATIONS
LZ VALUE ANALYSIS FOR THE MOS
----------------------------------------
MO 1 ( 1) HAS LZ(WEIGHT)= 0.00(100.0%)
MO 2 ( 2) HAS LZ(WEIGHT)= 0.00(100.0%)
MO 3 ( 3) HAS LZ(WEIGHT)= 0.00(100.0%)
MO 4 ( 4) HAS LZ(WEIGHT)= 0.00(100.0%)
MO 5 ( 5) HAS LZ(WEIGHT)= 0.00(100.0%)
MO 6 ( 6) HAS LZ(WEIGHT)= 0.00(100.0%)
MO 7 ( 7) HAS LZ(WEIGHT)= 0.00(100.0%)
MO 8 ( 7) HAS LZ(WEIGHT)= 0.00(100.0%)
MO 9 ( 8) HAS LZ(WEIGHT)= 0.00(100.0%)
MO 10 ( 9) HAS LZ(WEIGHT)= 0.00(100.0%)
MO 11 ( 9) HAS LZ(WEIGHT)= 0.00(100.0%)
MO 12 ( 10) HAS LZ(WEIGHT)= 0.00(100.0%)
MO 13 ( 10) HAS LZ(WEIGHT)= 0.00(100.0%)
MO 14 ( 11) HAS LZ(WEIGHT)= 0.00(100.0%)
MO 15 ( 12) HAS LZ(WEIGHT)= 0.00(100.0%)
------------
EIGENVECTORS
------------
1 2 3 4 5
-20.2387 -15.6547 -15.5635 -1.5103 -1.2294
A A A A A
1 O 1 S 0.994683 0.000366 -0.000022 -0.038574 -0.213755
2 O 1 S 0.022355 -0.002639 0.000103 0.137214 0.780989
3 O 1 X -0.002896 0.001914 -0.000091 -0.042332 -0.077744
4 O 1 Y 0.000000 0.000000 0.000000 0.000000 -0.000000
5 O 1 Z 0.000000 0.000000 0.000000 0.000000 -0.000000
6 N 2 S 0.000363 0.993941 -0.010740 -0.185804 -0.044053
7 N 2 S -0.002852 0.028607 -0.010651 0.525909 0.190276
8 N 2 X -0.004465 -0.005726 0.005685 -0.215881 0.316885
9 N 2 Y 0.000000 0.000000 0.000000 0.000000 -0.000000
10 N 2 Z 0.000000 0.000000 0.000000 0.000000 -0.000000
11 N 3 S -0.000001 0.010985 0.994074 -0.165354 0.071341
12 N 3 S -0.001036 -0.008815 0.028461 0.443033 -0.202824
13 N 3 X -0.000716 -0.004730 0.008917 0.227657 -0.066463
14 N 3 Y 0.000000 0.000000 0.000000 0.000000 -0.000000
15 N 3 Z 0.000000 0.000000 0.000000 0.000000 -0.000000
6 7 8 9 10
-0.7303 -0.6659 -0.6659 -0.5921 -0.3473
A A A A A
1 O 1 S -0.120511 -0.000000 -0.000000 -0.091682 0.000000
2 O 1 S 0.542892 -0.000000 -0.000000 0.441886 0.000000
3 O 1 X 0.212182 -0.000000 -0.000000 0.282393 0.000000
4 O 1 Y 0.000000 0.084683 0.198804 0.000000 0.929990
5 O 1 Z 0.000000 0.198804 -0.084683 0.000000 0.000774
6 N 2 S 0.144709 -0.000000 -0.000000 0.033876 0.000000
7 N 2 S -0.627685 -0.000000 -0.000000 -0.218551 0.000000
8 N 2 X -0.188874 -0.000000 -0.000000 -0.530071 0.000000
9 N 2 Y 0.000000 0.261114 0.612998 0.000000 -0.008727
10 N 2 Z 0.000000 0.612998 -0.261114 0.000000 -0.000007
11 N 3 S -0.156055 -0.000000 -0.000000 0.088708 0.000000
12 N 3 S 0.687898 -0.000000 -0.000000 -0.504406 0.000000
13 N 3 X -0.286433 -0.000000 -0.000000 0.533622 0.000000
14 N 3 Y 0.000000 0.205603 0.482678 0.000000 -0.372349
15 N 3 Z 0.000000 0.482678 -0.205603 0.000000 -0.000310
11 12 13 14 15
-0.3473 0.2381 0.2381 0.4481 1.1895
A A A A A
1 O 1 S 0.000000 0.000000 0.000000 0.053475 0.039502
2 O 1 S 0.000000 0.000000 0.000000 -0.293518 -0.255348
3 O 1 X 0.000000 0.000000 0.000000 0.963127 0.371575
4 O 1 Y -0.000774 0.076671 0.310714 -0.000000 0.000000
5 O 1 Z 0.929990 0.310714 -0.076671 -0.000000 0.000000
6 N 2 S 0.000000 0.000000 0.000000 -0.132767 0.088622
7 N 2 S 0.000000 0.000000 0.000000 0.890822 -1.007362
8 N 2 X 0.000000 0.000000 0.000000 0.180786 1.361082
9 N 2 Y 0.000007 -0.194691 -0.789002 -0.000000 0.000000
10 N 2 Z -0.008727 -0.789002 0.194691 -0.000000 0.000000
11 N 3 S 0.000000 0.000000 0.000000 0.050337 -0.117577
12 N 3 S 0.000000 0.000000 0.000000 -0.328764 1.200088
13 N 3 X 0.000000 0.000000 0.000000 -0.448397 1.180663
14 N 3 Y 0.000310 0.197008 0.798393 -0.000000 0.000000
15 N 3 Z -0.372349 0.798393 -0.197008 -0.000000 0.000000
...... END OF RHF CALCULATION ......
STEP CPU TIME = 0.00 TOTAL CPU TIME = 0.0 ( 0.0 MIN)
TOTAL WALL CLOCK TIME= 0.0 SECONDS, CPU UTILIZATION IS 33.33%
----------------------------------------------------------------
PROPERTY VALUES FOR THE RHF SELF-CONSISTENT FIELD WAVEFUNCTION
----------------------------------------------------------------
-----------------
ENERGY COMPONENTS
-----------------
WAVEFUNCTION NORMALIZATION = 1.0000000000
ONE ELECTRON ENERGY = -360.5175959557
TWO ELECTRON ENERGY = 122.7135992227
NUCLEAR REPULSION ENERGY = 56.6209169337
------------------
TOTAL ENERGY = -181.1830797993
ELECTRON-ELECTRON POTENTIAL ENERGY = 122.7135992227
NUCLEUS-ELECTRON POTENTIAL ENERGY = -539.8773304465
NUCLEUS-NUCLEUS POTENTIAL ENERGY = 56.6209169337
------------------
TOTAL POTENTIAL ENERGY = -360.5428142901
TOTAL KINETIC ENERGY = 179.3597344908
VIRIAL RATIO (V/T) = 2.0101658564
...... PI ENERGY ANALYSIS ......
ENERGY ANALYSIS:
FOCK ENERGY= -115.0903974526
BARE H ENERGY= -360.5175959557
ELECTRONIC ENERGY = -237.8039967041
KINETIC ENERGY= 179.3597344908
N-N REPULSION= 56.6209169337
TOTAL ENERGY= -181.1830797704
SIGMA PART(1+2)= -194.3396030190
(K,V1,2)= 163.1039467435 -440.7455451181 83.3019953555
PI PART(1+2)= -43.4643936851
(K,V1,2)= 16.2557877473 -99.1317853284 39.4116038960
SIGMA SKELETON, ERROR= -137.7186860853 -0.0000000000
MIXED PART= 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00
...... END OF PI ENERGY ANALYSIS ......
---------------------------------------
MULLIKEN AND LOWDIN POPULATION ANALYSES
---------------------------------------
ATOMIC MULLIKEN POPULATION IN EACH MOLECULAR ORBITAL
1 2 3 4 5
2.000000 2.000000 2.000000 2.000000 2.000000
1 2.000401 -0.000189 -0.000000 0.063955 1.380972
2 -0.000400 2.001948 -0.002059 1.046279 0.516360
3 -0.000002 -0.001759 2.002059 0.889766 0.102668
6 7 8 9 10
2.000000 2.000000 2.000000 2.000000 2.000000
1 0.528181 0.127387 0.127387 0.466979 1.724303
2 0.554734 1.120819 1.120819 0.535481 0.000163
3 0.917085 0.751794 0.751794 0.997541 0.275535
11
2.000000
1 1.724303
2 0.000163
3 0.275535
----- POPULATIONS IN EACH AO -----
MULLIKEN LOWDIN
1 O 1 S 1.99935 1.99884
2 O 1 S 1.95707 1.93546
3 O 1 X 0.48387 0.55008
4 O 1 Y 1.85169 1.85258
5 O 1 Z 1.85169 1.85258
6 N 2 S 1.99689 1.99415
7 N 2 S 1.48231 1.37619
8 N 2 X 1.17315 1.20694
9 N 2 Y 1.12098 1.11484
10 N 2 Z 1.12098 1.11484
11 N 3 S 1.99777 1.99730
12 N 3 S 1.73783 1.63940
13 N 3 X 1.17175 1.30164
14 N 3 Y 1.02733 1.03258
15 N 3 Z 1.02733 1.03258
----- MULLIKEN ATOMIC OVERLAP POPULATIONS -----
(OFF-DIAGONAL ELEMENTS NEED TO BE MULTIPLIED BY 2)
1 2 3
1 8.0267637
2 0.1237140 6.1424665
3 -0.0067999 0.6281256 6.3406901
TOTAL MULLIKEN AND LOWDIN ATOMIC POPULATIONS
ATOM MULL.POP. CHARGE LOW.POP. CHARGE
1 O 8.143678 -0.143678 8.189541 -0.189541
2 N 6.894306 0.105694 6.806964 0.193036
3 N 6.962016 0.037984 7.003496 -0.003496
-------------------------------
BOND ORDER AND VALENCE ANALYSIS BOND ORDER THRESHOLD=0.050
-------------------------------
BOND BOND BOND
ATOM PAIR DIST ORDER ATOM PAIR DIST ORDER ATOM PAIR DIST ORDER
1 2 1.416 0.936 1 3 2.503 0.314 2 3 1.087 2.687
TOTAL BONDED FREE
ATOM VALENCE VALENCE VALENCE
1 O 1.251 1.251 -0.000
2 N 3.623 3.623 -0.000
3 N 3.001 3.001 0.000
---------------------
ELECTROSTATIC MOMENTS
---------------------
POINT 1 X Y Z (BOHR) CHARGE
0.111746 0.000000 0.000000 0.00 (A.U.)
DX DY DZ /D/ (DEBYE)
-1.016290 0.000000 0.000000 1.016290
...... END OF PROPERTY EVALUATION ......
STEP CPU TIME = 0.00 TOTAL CPU TIME = 0.0 ( 0.0 MIN)
TOTAL WALL CLOCK TIME= 0.0 SECONDS, CPU UTILIZATION IS 33.33%
580000 WORDS OF DYNAMIC MEMORY USED
EXECUTION OF GAMESS TERMINATED NORMALLY Tue Mar 30 14:38:42 2021
DDI: 263640 bytes (0.3 MB / 0 MWords) used by master data server.
----------------------------------------
CPU timing information for all processes
========================================
0: 0.17 + 0.09 = 0.26
----------------------------------------
ddikick.x: exited gracefully.
Symmetry & frame transformations
To use symmetry in the Gamess calculations, the system must be oriented such that the Z-axis is the highest symmetry axis. In tests both PubChem and RDkit seem to use the X-axis as the symmetry axis, so the frame needs to be rotated in general.
From the Gamess manual:
The 'master frame' is just a standard orientation for
the molecule. By default, the 'master frame' assumes that
1. z is the principal rotation axis (if any),
2. x is a perpendicular two-fold axis (if any),
3. xz is the sigma-v plane (if any), and
4. xy is the sigma-h plane (if any).
Use the lowest number rule that applies to your molecule.
Some examples of these rules:
Ammonia (C3v): the unique H lies in the XZ plane (R1,R3).
Ethane (D3d): the unique H lies in the YZ plane (R1,R2).
Methane (Td): the H lies in the XYZ direction (R2). Since
there is more than one 3-fold, R1 does not apply.
HP=O (Cs): the mirror plane is the XY plane (R4).
In general, it is a poor idea to try to reorient the
molecule. Certain sections of the program, such as the
orbital symmetry assignment, do not know how to deal with
cases where the 'master frame' has been changed.
Linear molecules (C4v or D4h) must lie along the z axis,
so do not try to reorient linear molecules.
This is set with self.rotateFrame(), which can set arbitrary rotations, but defaults to X > Z axis transformation. This uses the RDkit canoicalise and transformation functions, with rotation matrices, as per Github user iwatobipen’s example notebook. (Thanks to iwatobipen and the RDkit list.)
[20]:
testDL.rotateFrame()
*** Set frame rotations, new coord table:
| Ind | Species | Atomic Num. | x | y | z | |
|---|---|---|---|---|---|---|
| 0 | 0 | O | 8 | 7.998781e-17 | 0.0 | -1.3063 |
| 1 | 1 | N | 7 | -6.711064e-18 | 0.0 | 0.1096 |
| 2 | 2 | N | 7 | -7.327674e-17 | 0.0 | 1.1967 |
Symmetry groups supported (from the Gamess manual):
GROUP is the Schoenflies symbol of the symmetry group,
you may choose from
C1, Cs, Ci, Cn, S2n, Cnh, Cnv, Dn, Dnh, Dnd,
T, Th, Td, O, Oh.
NAXIS is the order of the highest rotation axis, and
must be given when the name of the group contains an N.
For example, "Cnv 2" is C2v. "S2n 3" means S6. Use of
NAXIS up to 8 is supported in each axial groups.
For linear molecules, choose either Cnv or Dnh, and enter
NAXIS as 4. Enter atoms as Dnh with NAXIS=2. If the
electronic state of either is degenerate, check the note
about the effect of symmetry in the electronic state
in the SCF section of REFS.DOC.
[21]:
# Set Gamess input with symmetry
testDL.setGamess(note='N2O sym testing', sym='CNV 8')
*** Gamess input card:
$contrl scftyp=rhf runtyp=energy $end
$basis gbasis=sto ngauss=3 $end
$system mwords=30 $end
$DATA
N2O sym testing
CNV 8
O 8.0 0.0000000000 0.0000000000 -1.3063000000
N 7.0 -0.0000000000 0.0000000000 0.1096000000
N 7.0 -0.0000000000 0.0000000000 1.1967000000
$END
Finally, it is worth noting that symmetrized jobs require only the unique atoms given on the input card. This is currently accomplished here rather crudely, via a list of atom indices (rows) to the input builder.
For example…
[22]:
testDL.setGamess(note='N2O sym testing', sym='CNV 8', atomList = [0,2])
*** Gamess input card:
$contrl scftyp=rhf runtyp=energy $end
$basis gbasis=sto ngauss=3 $end
$system mwords=30 $end
$DATA
N2O sym testing
CNV 8
O 8.0 0.0000000000 0.0000000000 -1.3063000000
N 7.0 -0.0000000000 0.0000000000 1.1967000000
$END
Additional Gamess parameters
For the full set of Gamess input options (inc. basis sets), see the manual.
As per the above input cards, pyGamess writes only the minimal set of $contrl, $basis and $system inputs, using the supplied parameters dictionary.
TODO: wrap the input writer for arb sections from the params dictionary.
[23]:
# Basis sets can additionally be set using pyGamess
testDL.g.basis_set("6-31G**")
[23]:
{'gbasis': 'N31', 'ngauss': '6', 'ndfunc': '1', 'npfunc': '1'}
[24]:
# This only has limited support...
testDL.g.basis_set("ACCD")
ERROR:pygamess.gamess:basis type not found
[24]:
{'gbasis': 'N31', 'ngauss': '6', 'ndfunc': '1', 'npfunc': '1'}
[25]:
# ... applying settings manually will always work however
testDL.params['basis'] = {'gbasis':'ACCD'}
testDL.params['contrl']['ISPHER']='1' # For ACCD need this too!
testDL.params
[25]:
{'contrl': {'scftyp': 'rhf', 'runtyp': 'energy', 'ISPHER': '1'},
'basis': {'gbasis': 'ACCD'},
'statpt': {'opttol': '0.0001', 'nstep': '20'},
'system': {'mwords': '30'},
'cis': {'nstate': '1'},
'extra': {'job': 'N2O sym testing', 'sym': 'CNV 8', 'atomList': [0, 2]}}
[26]:
testDL.printGamessInput()
*** Gamess input card:
$contrl scftyp=rhf runtyp=energy ISPHER=1 $end
$basis gbasis=ACCD $end
$system mwords=30 $end
$DATA
N2O sym testing
CNV 8
O 8.0 0.0000000000 0.0000000000 -1.3063000000
N 7.0 -0.0000000000 0.0000000000 1.1967000000
$END
Additional transformations
Bond lengths & angles
These can be addressed using the RDkit functionality.
There is also a wrapper for bond lengths at the moment, self.setBondLength, which takes a dictionary of bonds to set, in the format {'Name':{'a1':0,'a2':1,'l':5}} where ‘a1’ and ‘a2’ give the atom indices for atoms defining the bond. This wraps RDkit’s rdkit.Chem.rdMolTransforms.SetBondLength.
TODO: clean up input, wrap angle setting functions(?).
Here’s a basic bond-length example
[27]:
testDL.printTable()
| Ind | Species | Atomic Num. | x | y | z | |
|---|---|---|---|---|---|---|
| 0 | 0 | O | 8 | 7.998781e-17 | 0.0 | -1.3063 |
| 1 | 1 | N | 7 | -6.711064e-18 | 0.0 | 0.1096 |
| 2 | 2 | N | 7 | -7.327674e-17 | 0.0 | 1.1967 |
[28]:
bonds = {'NO':{'a1':0, 'a2':1, 'l':5}, 'NN':{'a1':1, 'a2':2, 'l':5}}
# testDL.setBondLength(bonds = {'NO':{'a0':0, 'a1':1, 'l':5}})
testDL.setBondLength(bonds)
*** Set bonds, new coord table:
| Ind | Species | Atomic Num. | x | y | z | |
|---|---|---|---|---|---|---|
| 0 | 0 | O | 8 | 7.998781e-17 | 0.0 | -1.3063 |
| 1 | 1 | N | 7 | -2.261739e-16 | 0.0 | 3.6937 |
| 2 | 2 | N | 7 | -5.323356e-16 | 0.0 | 8.6937 |
Note that the RDkit routines move all atoms as appropriate for the new settings.
Manual coords
This is currently a little basic, and just wraps RDkit conformer.SetAtomPosition() routine for each atom. Set & select with a dictionary input, using atom indicies as keys.
[34]:
# Set coords for specified atoms
coordsRef = {0:[0,0,0], 1:[0.7,0,1.0]}
testDL.setCoords(coordsRef)
---------------------------------------------------------------------------
AttributeError Traceback (most recent call last)
<ipython-input-34-3b9ccfb1c4af> in <module>
1 # Set coords for specified atoms
2 coordsRef = {0:[0,0,0], 1:[0.7,0,1.0]}
----> 3 testDL.setCoords(coordsRef)
AttributeError: 'ESgamess' object has no attribute 'setCoords'
[ ]:
# Set all atoms on a specified axes with coord
# This can be useful for symmetrized cases, since otherwise atoms may be erroneously duplicated in Gamess run (even for near-zero coords)
mol.setAxis({'x':0.0, 'y':0.0})
Minimal job pipeline to generate electronic structure & input files for ePolyScat
Possibly not advisable, since errors may go unnoticed, but the whole default pipeline can be executed with self.buildES(), which aims to string together the default cases above and produce a Gamess output file that can be used as input for ePolyScat.
This can be run directly at class creation by passing buildES=True. To keep the Gamess output file, pass fileOut.
[30]:
# Set via build=True - to do
testBuild = ESgamess(searchName = 'N2O', fileOut = '/tmp/autobuild.out', buildES = True)
Set name = N2O
Set smiles = None
Set molFile = None
*** File /home/paul/github/epsman/demos/N2O.SDF already exists, pass overwrite=True to overwrite
Set job = None
Set sym = C1
Set atomList = None
RDKit WARNING: [14:39:01] Warning: molecule is tagged as 3D, but all Z coords are zero
RDKit WARNING: [14:39:01] Warning: molecule is tagged as 3D, but all Z coords are zero
O 8.0 1.3063000000 0.0000000000 0.0000000000
N 7.0 -0.1096000000 0.0000000000 0.0000000000
N 7.0 -1.1967000000 0.0000000000 0.0000000000
*** Running default Gamess job.
*** Set frame rotations, new coord table:
| Ind | Species | Atomic Num. | x | y | z | |
|---|---|---|---|---|---|---|
| 0 | 0 | O | 8 | 7.998781e-17 | 0.0 | -1.3063 |
| 1 | 1 | N | 7 | -6.711064e-18 | 0.0 | 0.1096 |
| 2 | 2 | N | 7 | -7.327674e-17 | 0.0 | 1.1967 |
INFO:pygamess.gamess:Executeing py_rungms with command /opt/gamess/ddikick.x /opt/gamess/gamess.00.x jfqorx -ddi 1 1 jake -scr /tmp/tmpq79qm8ni > /tmp/tmpq79qm8ni/jfqorx.out
*** Init pyGamess job.
Default Gamess input card set (use self.params to modify options dictionary, self.setGamess() to test):
$contrl scftyp=rhf runtyp=energy $end
$basis gbasis=sto ngauss=3 $end
$system mwords=30 $end
$DATA
None
C1
O 8.0 0.0000000000 0.0000000000 -1.3063000000
N 7.0 -0.0000000000 0.0000000000 0.1096000000
N 7.0 -0.0000000000 0.0000000000 1.1967000000
$END
*** Energy run completed
E = -181.1830797993
*** Gamess output file moved to /tmp/autobuild.out
| Ind | Species | Atomic Num. | x | y | z | |
|---|---|---|---|---|---|---|
| 0 | 0 | O | 8 | 7.998781e-17 | 0.0 | -1.3063 |
| 1 | 1 | N | 7 | -6.711064e-18 | 0.0 | 0.1096 |
| 2 | 2 | N | 7 | -7.327674e-17 | 0.0 | 1.1967 |
INFO:pygamess.gamess:deleting tempdir /tmp/tmp35n9bn2b
[32]:
# Running the function independently also works
testDL.buildES(fileOut = '/tmp/autobuild.out')
*** Running default Gamess job.
*** Set frame rotations, new coord table:
| Ind | Species | Atomic Num. | x | y | z | |
|---|---|---|---|---|---|---|
| 0 | 0 | O | 8 | -3.061617e-16 | -1.232595e-32 | 5.0 |
| 1 | 1 | N | 7 | 0.000000e+00 | 0.000000e+00 | 0.0 |
| 2 | 2 | N | 7 | 3.061617e-16 | 0.000000e+00 | -5.0 |
INFO:pygamess.gamess:Executeing py_rungms with command /opt/gamess/ddikick.x /opt/gamess/gamess.00.x eqbqbl -ddi 1 1 jake -scr /tmp/tmpz6c50ibb > /tmp/tmpz6c50ibb/eqbqbl.out
*** Init pyGamess job.
Default Gamess input card set (use self.params to modify options dictionary, self.setGamess() to test):
$contrl scftyp=rhf runtyp=energy $end
$basis gbasis=sto ngauss=3 $end
$system mwords=30 $end
$DATA
None
C1
O 8.0 -0.0000000000 -0.0000000000 5.0000000000
N 7.0 0.0000000000 0.0000000000 0.0000000000
N 7.0 0.0000000000 0.0000000000 -5.0000000000
$END
*** Energy run completed
E = -161.7465089353
*** Gamess output file moved to /tmp/autobuild.out
| Ind | Species | Atomic Num. | x | y | z | |
|---|---|---|---|---|---|---|
| 0 | 0 | O | 8 | -3.061617e-16 | -1.232595e-32 | 5.0 |
| 1 | 1 | N | 7 | 0.000000e+00 | 0.000000e+00 | 0.0 |
| 2 | 2 | N | 7 | 3.061617e-16 | 0.000000e+00 | -5.0 |
Generating electronic strucutres for a range of geometries
In this case, run a single-point calculation for each specified geometry (note this is similar, but slightly distinct, from Gamess native bond-length scan, since one wants to generate a single file for each case here, to be used as ePolyScat input).
[ ]:
# Simply loop over a set of specified coords...