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Merge pull request #1592 from ReactionMechanismGenerator/no_f12
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Parse CCSD(T) energies (no F12) in Molpro
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Colin Grambow authored May 6, 2019
2 parents 8c2f86a + 20ff313 commit fe57caa
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380 changes: 380 additions & 0 deletions arkane/data/TS_CCSD(T)_no_F12_sp_molpro.out
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Primary working directories : /scratch/alongd/a12145-4440
Secondary working directories : /scratch/alongd/a12145-4440
Wavefunction directory : /home/alongd/wfu/
Main file repository : /scratch/alongd/a12145-4440/

SHA1 : 5e3d8ac6839c721e2824de82269b4736200146bd
NAME : 2015.1.37
ARCHNAME : linux/x86_64
FC : /opt/intel/composer_xe_2015.1.133/bin/intel64/ifort
BLASLIB : -Wl,-_start-group /opt/intel/mkl/lib/intel64/libmkl_intel_ilp64.a /opt/intel/mkl/lib/intel64/libmkl_intel_thread.a /opt/intel/mkl/lib/intel64/libmkl_core.a -Wl,-_end-group
id : phalgunlolur

Nodes nprocs
node02 8

Using customized tuning parameters: mindgm=1; mindgv=20; mindgc=4; mindgr=1; noblas=0; minvec=7
default implementation of scratch files=sf

***,name
memory,1500.0,m;
geometry={angstrom;
O -0.08386036 0.74450390 0.00000000
C -0.03491862 -0.49441450 0.00000000
H -0.12535571 -1.06178181 0.93898289
H -0.12535571 -1.06178181 -0.93898289
H 1.55887339 -0.90581579 0.00000000
}

basis=aug-cc-pvqz

int;

{hf;
maxit,1000;
wf,spin=1,charge=0;}

uccsd(t);



Variables initialized (889), CPU time= 0.01 sec
Commands initialized (702), CPU time= 0.02 sec, 572 directives.
Default parameters read. Elapsed time= 0.15 sec

Checking input...
Passed
1


*** PROGRAM SYSTEM MOLPRO ***
Copyright, TTI GmbH Stuttgart, 2015
Version 2015.1 linked Aug 10 2018 15:00:15


**********************************************************************************************************************************
LABEL * name
64 bit mpp version DATE: 02-May-19 TIME: 06:30:24
**********************************************************************************************************************************

SHA1: 5e3d8ac6839c721e2824de82269b4736200146bd
**********************************************************************************************************************************

Geometry recognized as XYZ


Variable memory set to 1500000000 words, buffer space 230000 words

SETTING BASIS = AUG-CC-PVQZ


Using spherical harmonics

Library entry O S aug-cc-pVQZ selected for orbital group 1
Library entry O P aug-cc-pVQZ selected for orbital group 1
Library entry O D aug-cc-pVQZ selected for orbital group 1
Library entry O F aug-cc-pVQZ selected for orbital group 1
Library entry O G aug-cc-pVQZ selected for orbital group 1
Library entry C S aug-cc-pVQZ selected for orbital group 2
Library entry C P aug-cc-pVQZ selected for orbital group 2
Library entry C D aug-cc-pVQZ selected for orbital group 2
Library entry C F aug-cc-pVQZ selected for orbital group 2
Library entry C G aug-cc-pVQZ selected for orbital group 2
Library entry H S aug-cc-pVQZ selected for orbital group 3
Library entry H P aug-cc-pVQZ selected for orbital group 3
Library entry H D aug-cc-pVQZ selected for orbital group 3
Library entry H F aug-cc-pVQZ selected for orbital group 3


PROGRAM * SEWARD (Integral evaluation for generally contracted gaussian basis sets) Author: Roland Lindh, 1990

Geometry written to block 1 of record 700


Point group Cs



ATOMIC COORDINATES

NR ATOM CHARGE X Y Z

1 O 8.00 -0.158473113 1.406908470 0.000000000
2 C 6.00 -0.065986628 -0.934307997 0.000000000
3 H 1.00 -0.236887960 -2.006476825 1.774420498
4 H 1.00 -0.236887960 -2.006476825 -1.774420498
5 H 1.00 2.945843770 -1.711743762 0.000000000

Bond lengths in Bohr (Angstrom)

1-2 2.343042529 2-3 2.080221470 2-4 2.080221470
( 1.239884711) ( 1.100805796) ( 1.100805796)

Bond angles

1-2-3 120.78155471 1-2-4 120.78155471 3-2-4 117.07807333

NUCLEAR CHARGE: 17
NUMBER OF PRIMITIVE AOS: 407
NUMBER OF SYMMETRY AOS: 330
NUMBER OF CONTRACTIONS: 298 ( 176A' + 122A" )
NUMBER OF CORE ORBITALS: 2 ( 2A' + 0A" )
NUMBER OF VALENCE ORBITALS: 11 ( 8A' + 3A" )


NUCLEAR REPULSION ENERGY 34.98879244

Eigenvalues of metric

1 0.186E-04 0.816E-04 0.110E-03 0.199E-03 0.222E-03 0.358E-03 0.458E-03 0.513E-03
2 0.208E-04 0.832E-04 0.315E-03 0.857E-03 0.917E-03 0.102E-02 0.104E-02 0.139E-02


Contracted 2-electron integrals neglected if value below 1.0D-12
AO integral compression algorithm 1 Integral accuracy 1.0D-12

2750.677 MB (compressed) written to integral file ( 56.9%)

Node minimum: 205.521 MB, node maximum: 478.675 MB


NUMBER OF SORTED TWO-ELECTRON INTEGRALS: 62470784. BUFFER LENGTH: 32768
NUMBER OF SEGMENTS: 4 SEGMENT LENGTH: 15997304 RECORD LENGTH: 524288

Memory used in sort: 16.55 MW

SORT1 READ 604167037. AND WROTE 61315405. INTEGRALS IN 177 RECORDS. CPU TIME: 18.71 SEC, REAL TIME: 19.95 SEC
SORT2 READ 490771955. AND WROTE 500065116. INTEGRALS IN 13792 RECORDS. CPU TIME: 2.64 SEC, REAL TIME: 22.68 SEC

Node minimum: 62470784. Node maximum: 62522131. integrals

OPERATOR DM FOR CENTER 0 COORDINATES: 0.000000 0.000000 0.000000


**********************************************************************************************************************************
DATASETS * FILE NREC LENGTH (MB) RECORD NAMES
1 18 21.68 500 610 700 900 950 970 1000 129 960 1100
VAR BASINP GEOM SYMINP ZMAT AOBASIS BASIS P2S ABASIS S
1400 1410 1200 1210 1080 1600 1650 1700
T V H0 H01 AOSYM SMH MOLCAS OPER

PROGRAMS * TOTAL INT
CPU TIMES * 35.89 35.62
REAL TIME * 65.33 SEC
DISK USED * 8.78 GB
GA USED * 0.00 MB (max) 0.00 MB (current)
**********************************************************************************************************************************


PROGRAM * RHF-SCF (OPEN SHELL) Authors: W. Meyer, H.-J. Werner


NUMBER OF ELECTRONS: 9+ 8-
CONVERGENCE THRESHOLDS: 1.00E-05 (Density) 1.00E-07 (Energy)
MAX. NUMBER OF ITERATIONS: 1000
INTERPOLATION TYPE: DIIS
INTERPOLATION STEPS: 2 (START) 1 (STEP)
LEVEL SHIFTS: -0.60 (CLOSED) -0.30 (OPEN)



Orbital guess generated from atomic densities. Full valence occupancy: 10 3

Molecular orbital dump at record 2100.2

Initial alpha occupancy: 7 2
Initial beta occupancy: 6 2
Wave function symmetry: 1

ITERATION DDIFF GRAD ENERGY 2-EL.EN. DIPOLE MOMENTS DIIS ORB.
1 0.000D+00 0.000D+00 -114.29410445 154.393260 0.96126 -2.11509 0.00000 0 start
2 0.000D+00 0.667D-02 -114.36878038 151.214137 0.41323 -1.19029 0.00000 1 diag,B
3 0.426D-02 0.314D-02 -114.38016278 151.901534 0.34843 -1.23527 0.00000 2 diag,B
4 0.133D-02 0.971D-03 -114.38616372 151.854012 0.21621 -1.15487 0.00000 3 diag,B
5 0.869D-03 0.483D-03 -114.38903362 151.846216 0.14831 -1.14193 0.00000 4 diag,B
6 0.623D-03 0.285D-03 -114.39058898 151.835579 0.12487 -1.15662 0.00000 5 diag,B
7 0.370D-03 0.224D-03 -114.39213816 151.829909 0.10864 -1.17658 0.00000 6 fixocc
8 0.424D-03 0.152D-03 -114.39278138 151.825158 0.10548 -1.19421 0.00000 7 diag,B
9 0.347D-03 0.750D-04 -114.39286032 151.835256 0.10778 -1.20276 0.00000 8 diag,B
10 0.130D-03 0.356D-04 -114.39287360 151.831657 0.10852 -1.20836 0.00000 9 orth
11 0.756D-04 0.127D-04 -114.39287408 151.836494 0.10984 -1.21076 0.00000 9 diag,B
12 0.305D-04 0.799D-05 -114.39287473 151.834574 0.10930 -1.21139 0.00000 9 diag,B
13 0.167D-04 0.218D-05 -114.39287476 151.834943 0.10926 -1.21164 0.00000 9 diag,B
14 0.785D-05 0.781D-06 -114.39287476 151.834910 0.10923 -1.21164 0.00000 0 orth

Final alpha occupancy: 7 2
Final beta occupancy: 6 2

!RHF STATE 1.1 Energy -114.392874762461
Nuclear energy 34.98879244
One-electron energy -225.29912213
Two-electron energy 75.91745493
Virial quotient -1.00158195
!RHF STATE 1.1 Dipole moment 0.10922640 -1.21164314 0.00000000
Dipole moment /Debye 0.27760764 -3.07948798 0.00000000

Orbital energies:

1.1 2.1 3.1 4.1 5.1 6.1 7.1 8.1 9.1
-20.567075 -11.346626 -1.380616 -0.885492 -0.637961 -0.544400 -0.476396 0.022079 0.046074

1.2 2.2 3.2 4.2
-0.688857 -0.442872 0.036979 0.111829

HOMO 2.2 -0.442872 = -12.0512eV
LUMO 8.1 0.022079 = 0.6008eV
LUMO-HOMO 0.464951 = 12.6520eV


**********************************************************************************************************************************
DATASETS * FILE NREC LENGTH (MB) RECORD NAMES
1 18 21.70 500 610 700 900 950 970 1000 129 960 1100
VAR BASINP GEOM SYMINP ZMAT AOBASIS BASIS P2S ABASIS S
1400 1410 1200 1210 1080 1600 1650 1700
T V H0 H01 AOSYM SMH MOLCAS OPER

2 4 4.16 700 1000 520 2100
GEOM BASIS MCVARS RHF

PROGRAMS * TOTAL HF INT
CPU TIMES * 53.54 17.64 35.62
REAL TIME * 86.15 SEC
DISK USED * 9.04 GB
SF USED * 0.18 MB
GA USED * 0.00 MB (max) 0.00 MB (current)
**********************************************************************************************************************************


PROGRAM * CCSD (Unrestricted open-shell coupled cluster) Authors: C. Hampel, H.-J. Werner, 1991, M. Deegan, P.J. Knowles, 1992


Convergence thresholds: THRVAR = 1.00D-08 THRDEN = 1.00D-06

CCSD(T) terms to be evaluated (factor= 1.000)


Number of core orbitals: 2 ( 2 0 )
Number of closed-shell orbitals: 6 ( 4 2 )
Number of active orbitals: 1 ( 1 0 )
Number of external orbitals: 289 ( 169 120 )

Memory could be reduced to 170.09 Mwords without degradation in triples

Number of N-1 electron functions: 13
Number of N-2 electron functions: 78
Number of singly external CSFs: 2010
Number of doubly external CSFs: 2527890
Total number of CSFs: 2529900

Molecular orbitals read from record 2100.2 Type=RHF/CANONICAL (state 1.1)

Integral transformation finished. Total CPU: 23.75 sec, npass= 1 Memory used: 36.77 MW

Starting RMP2 calculation

ITER. SQ.NORM CORR.ENERGY TOTAL ENERGY ENERGY CHANGE DEN1 VAR(S) VAR(P) DIIS TIME
1 1.12362295 -0.44379311 -114.83666788 -0.44379311 -0.00188391 0.75D-04 0.78D-03 1 1 25.99
2 1.12578788 -0.44585827 -114.83873303 -0.00206516 -0.00001423 0.31D-05 0.67D-05 2 2 27.06
3 1.12597093 -0.44594857 -114.83882333 -0.00009030 -0.00000016 0.97D-07 0.49D-07 3 3 28.17
4 1.12598091 -0.44595111 -114.83882588 -0.00000254 -0.00000000 0.21D-08 0.38D-09 4 4 29.12
5 1.12598141 -0.44595118 -114.83882594 -0.00000006 -0.00000000 0.81D-10 0.69D-11 5 5 30.36

Norm of t1 vector: 0.05587229 S-energy: -0.00282109 T1 diagnostic: 0.00179166
Norm of t2 vector: 0.35051348 P-energy: -0.44313009
Alpha-Beta: -0.33883995
Alpha-Alpha: -0.05345496
Beta-Beta: -0.05083518

Spin contamination <S**2-Sz**2-Sz> 0.00524230
Reference energy -114.392874762462
RHF-RMP2 correlation energy -0.445951177778
!RHF-RMP2 energy -114.838825940239

Starting UCCSD calculation

ITER. SQ.NORM CORR.ENERGY TOTAL ENERGY ENERGY CHANGE DEN1 VAR(S) VAR(P) DIIS TIME
1 1.12232761 -0.43486335 -114.82773811 -0.43486335 -0.01361201 0.33D-02 0.25D-02 1 1 43.74
2 1.13748545 -0.44730954 -114.84018431 -0.01244619 -0.00187345 0.55D-03 0.57D-03 2 2 54.91
3 1.14846397 -0.45073841 -114.84361317 -0.00342886 -0.00049169 0.36D-03 0.98D-04 3 3 66.60
4 1.15888126 -0.45276564 -114.84564040 -0.00202723 -0.00019166 0.14D-03 0.40D-04 4 4 78.58
5 1.16799108 -0.45368087 -114.84655563 -0.00091523 -0.00006884 0.51D-04 0.15D-04 5 5 91.74
6 1.17696373 -0.45443548 -114.84731024 -0.00075461 -0.00001408 0.77D-05 0.39D-05 6 6 105.52
7 1.17977392 -0.45458668 -114.84746144 -0.00015120 -0.00000267 0.13D-05 0.76D-06 6 2 119.13
8 1.18053338 -0.45464365 -114.84751842 -0.00005698 -0.00000058 0.27D-06 0.16D-06 6 1 132.57
9 1.18074199 -0.45466121 -114.84753597 -0.00001755 -0.00000014 0.86D-07 0.32D-07 6 4 145.98
10 1.18082230 -0.45466702 -114.84754178 -0.00000581 -0.00000003 0.14D-07 0.74D-08 6 3 159.87
11 1.18083416 -0.45466597 -114.84754073 0.00000105 -0.00000001 0.31D-08 0.19D-08 6 5 174.79
12 1.18083209 -0.45466384 -114.84753860 0.00000213 -0.00000000 0.46D-09 0.58D-09 6 6 188.17
13 1.18082439 -0.45466279 -114.84753755 0.00000105 -0.00000000 0.25D-09 0.19D-09 6 2 200.11
14 1.18081540 -0.45466186 -114.84753662 0.00000093 -0.00000000 0.12D-09 0.62D-10 6 1 213.54

Norm of t1 vector: 0.19518623 S-energy: -0.00524076 T1 diagnostic: 0.03153285
D1 diagnostic: 0.08851186
Norm of t2 vector: 0.37778001 P-energy: -0.44942109
Alpha-Beta: -0.35827401
Alpha-Alpha: -0.04688823
Beta-Beta: -0.04425885

Singles amplitudes (print threshold = 0.500E-01):

I SYM. A A T(IA) [Beta-Beta]

4 1 1 0.12263663
4 1 6 -0.05094434

Spin contamination <S**2-Sz**2-Sz> 0.01513789

Memory could be reduced to 174.40 Mwords without degradation in triples


RESULTS
=======

Reference energy -114.392874762462
UCCSD singles energy -0.005240764964
UCCSD pair energy -0.449421092051
UCCSD correlation energy -0.454661857016
Triples (T) contribution -0.020482748843
Total correlation energy -0.475144605858

RHF-UCCSD energy -114.847536619477
RHF-UCCSD[T] energy -114.869233678808
RHF-UCCSD-T energy -114.867965340657
!RHF-UCCSD(T) energy -114.868019368320

Program statistics:

Available memory in ccsd: 1499999438
Min. memory needed in ccsd: 8049813
Max. memory used in ccsd: 11022119
Max. memory used in cckext: 11623870 (14 integral passes)
Max. memory used in cckint: 36766836 ( 1 integral passes)



**********************************************************************************************************************************
DATASETS * FILE NREC LENGTH (MB) RECORD NAMES
1 18 21.70 500 610 700 900 950 970 1000 129 960 1100
VAR BASINP GEOM SYMINP ZMAT AOBASIS BASIS P2S ABASIS S
1400 1410 1200 1210 1080 1600 1650 1700
T V H0 H01 AOSYM SMH MOLCAS OPER

2 4 4.16 700 1000 520 2100
GEOM BASIS MCVARS RHF

PROGRAMS * TOTAL UCCSD(T) HF INT
CPU TIMES * 442.63 389.08 17.64 35.62
REAL TIME * 499.81 SEC
DISK USED * 11.52 GB
SF USED * 2.34 GB
GA USED * 0.00 MB (max) 0.00 MB (current)
**********************************************************************************************************************************

UCCSD(T)/aug-cc-pVQZ energy= -114.868019368320

UCCSD(T) HF-SCF
-114.86801937 -114.39287476
**********************************************************************************************************************************
Molpro calculation terminated
Variable memory released
2 changes: 1 addition & 1 deletion arkane/gaussian.py
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Original file line number Diff line number Diff line change
Expand Up @@ -52,7 +52,7 @@ class GaussianLog(Log):
"""

def __init__(self, path):
self.path = path
super(GaussianLog, self).__init__(path)

def getNumberOfAtoms(self):
"""
Expand Down
2 changes: 1 addition & 1 deletion arkane/log.py
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Original file line number Diff line number Diff line change
Expand Up @@ -88,7 +88,7 @@ def loadEnergy(self, frequencyScaleFactor=1.):
"""
raise NotImplementedError("loadGeometry is not implemented for the Log class")

def loadZeroPointEnergy(self,frequencyScaleFactor=1.):
def loadZeroPointEnergy(self):
"""
Load the unscaled zero-point energy in J/mol from a QChem output file.
"""
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