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f! parser test
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@alongd
alongd committed Sep 11, 2024
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26 changes: 16 additions & 10 deletions arc/parser_test.py
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Original file line number Diff line number Diff line change
Expand Up @@ -722,24 +722,30 @@ def test_parse_conformers(self):
def test_parse_active_space(self):
"""Test parsing active space information"""
path = os.path.join(ARC_PATH, 'arc', 'testing', 'sp', 'mehylamine_CCSD(T).out')
active_space = parser.parse_active_space(sp_path=path,
species=ARCSpecies(label='mehylamine', smiles='CN'))
self.assertEqual(active_space, (14, 7))
active = parser.parse_active_space(sp_path=path,
species=ARCSpecies(label='mehylamine', smiles='CN'))
self.assertEqual(active, {'e_o': (14, 7), 'occ': [7, 2], 'closed': [5, 2]})

path = os.path.join(ARC_PATH, 'arc', 'testing', 'sp', 'ONHO(T)_sp_CCSD(T).out')
active_space = parser.parse_active_space(sp_path=path,
species=ARCSpecies(label='ONHO', smiles='[O]N[O]'))
self.assertEqual(active_space, (18, 10))
active = parser.parse_active_space(sp_path=path,
species=ARCSpecies(label='ONHO', smiles='[O]N[O]'))
self.assertEqual(active, {'e_o': (18, 10), 'occ': [13], 'closed': [8]})

path = os.path.join(ARC_PATH, 'arc', 'testing', 'sp', 'TS_x118_sp_CCSD(T).out')
active_space = parser.parse_active_space(sp_path=path,
species=ARCSpecies(label='x118', is_ts=True,
xyz="""N -0.0 -1.36720300 0.15499300
active = parser.parse_active_space(sp_path=path,
species=ARCSpecies(label='x118', is_ts=True,
xyz="""N -0.0 -1.36720300 0.15499300
O -0.0 -1.10333100 -0.98685800
H -0.0 -0.28110100 0.76732400
O 0.0 0.97476200 0.91364300
O 0.0 1.44007500 -0.27062400"""))
self.assertEqual(active_space, (24, 13))
self.assertEqual(active, {'e_o': (24, 13), 'occ': [14, 3], 'closed': [9, 2]})

path = os.path.join(ARC_PATH, 'arc', 'testing', 'sp', 'N_CCSD.out')
active = parser.parse_active_space(sp_path=path,
species=ARCSpecies(label='N', is_ts=False,
xyz="""N 0.0 0.0 0.0"""))
self.assertEqual(active, {'e_o': (5, 4), 'occ': [3, 1, 1, 0, 1, 0, 0, 0], 'closed': [1, 0, 0, 0, 0, 0, 0, 0]})


if __name__ == '__main__':
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340 changes: 340 additions & 0 deletions arc/testing/sp/N_CCSD.out
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@@ -0,0 +1,340 @@

Working directory : /gtmp/molpro.YUwB5GrZBI/
Global scratch directory : /gtmp/molpro.YUwB5GrZBI/
Wavefunction directory : /home/alon/wfu/
Main file repository : /gtmp/molpro.YUwB5GrZBI/

id : dana

Nodes nprocs
n134 16
GA implementation: MPI file
GA implementation (serial work in mppx): MPI file

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


Variables initialized (1025), CPU time= 0.01 sec
***,N
memory,Total=7813,m;

geometry={angstrom;
N 0.00000000 0.00000000 0.00000000}

gprint,orbitals;

basis=cc-pvdz



int;
{hf;
maxit,999;
wf,spin=3,charge=0;}

uccsd;



Commands initialized (840), CPU time= 0.03 sec, 684 directives.
Default parameters read. Elapsed time= 1.35 sec

Checking input...
Passed
1


*** PROGRAM SYSTEM MOLPRO ***
Copyright, TTI GmbH Stuttgart, 2015
Version 2022.3 linked Wed Nov 30 13:40:34 2022


**********************************************************************************************************************************
LABEL * N
64 bit mpp version DATE: 07-Sep-24 TIME: 22:47:54
**********************************************************************************************************************************

SHA1: e31ec9a5ea85254ab76f59d122cbdd51c71cf98b
**********************************************************************************************************************************

Memory per process: 366 MW
Total memory per node: 7813 MW
Total GA space: 1953 MW

GA preallocation enabled
GA check enabled

Variable memory set to 366.2 MW


Geometry recognized as XYZ


SETTING BASIS = CC-PVDZ


Using spherical harmonics

Library entry N S cc-pVDZ selected for orbital group 1
Library entry N P cc-pVDZ selected for orbital group 1
Library entry N D cc-pVDZ selected for orbital group 1


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

Geometry written to block 1 of record 700

Orientation using atomic masses
Molecule type: Atom
Symmetry elements: X,Y,Z
Rotational constants: 0.0000000 0.0000000 0.0000000 GHz (calculated with average atomic masses)

Point group D2h



ATOMIC COORDINATES

NR ATOM CHARGE X Y Z

1 N 7.00 0.000000000 0.000000000 0.000000000

NUCLEAR CHARGE: 7
NUMBER OF PRIMITIVE AOS: 27
NUMBER OF SYMMETRY AOS: 26
NUMBER OF CONTRACTIONS: 14 ( 5Ag + 2B3u + 2B2u + 1B1g + 2B1u + 1B2g + 1B3g + 0Au )
NUMBER OF INNER CORE ORBITALS: 0 ( 0Ag + 0B3u + 0B2u + 0B1g + 0B1u + 0B2g + 0B3g + 0Au )
NUMBER OF OUTER CORE ORBITALS: 1 ( 1Ag + 0B3u + 0B2u + 0B1g + 0B1u + 0B2g + 0B3g + 0Au )
NUMBER OF VALENCE ORBITALS: 4 ( 1Ag + 1B3u + 1B2u + 0B1g + 1B1u + 0B2g + 0B3g + 0Au )


NUCLEAR REPULSION ENERGY 0.00000000


Allocated 123 MW GA space on the current processor, total: 1954 MW. Time: 0.05 sec

EXTRA SYMMETRY OF AOS IN SYMMETRY 1: 1 1 1 2 3

Eigenvalues of metric

1 0.451E-01 0.100E+01 0.100E+01 0.100E+01 0.195E+01
2 0.184E+00 0.182E+01
3 0.184E+00 0.182E+01
4 0.100E+01
5 0.184E+00 0.182E+01
6 0.100E+01
7 0.100E+01


Contracted 2-electron integrals neglected if value below 1.0D-11
AO integral compression algorithm 1 Integral accuracy 1.0D-11

4.194 MB (compressed) written to integral file (100.0%)

Node minimum: 0.262 MB, node maximum: 0.262 MB


NUMBER OF SORTED TWO-ELECTRON INTEGRALS: 129. BUFFER LENGTH: 32768
NUMBER OF SEGMENTS: 1 SEGMENT LENGTH: 129 RECORD LENGTH: 524288

Memory used in sort: 0.56 MW

SORT1 READ 1852. AND WROTE 126. INTEGRALS IN 1 RECORDS. CPU TIME: 0.01 SEC, REAL TIME: 0.01 SEC
SORT2 READ 968. AND WROTE 1083. INTEGRALS IN 16 RECORDS. CPU TIME: 0.00 SEC, REAL TIME: 0.00 SEC

Node minimum: 4. Node maximum: 490. integrals

OPERATOR DM FOR CENTER 0 COORDINATES: 0.000000 0.000000 0.000000


**********************************************************************************************************************************
DATASETS * FILE NREC LENGTH (MB) RECORD NAMES
1 18 28.55 500 610 700 900 950 970 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 * 0.85 0.39
REAL TIME * 2.76 SEC
DISK USED * 28.80 MB (local), 524.87 MB (total)
GA USED * 0.00 MB (max) 0.00 MB (current)
**********************************************************************************************************************************


Program * Restricted Hartree-Fock

Orbital guess generated from atomic densities. Full valence occupancy: 2 1 1 0 1 0 0 0


Initial alpha occupancy: 2 1 1 0 1 0 0
Initial beta occupancy: 2 0 0 0 0 0 0

NELEC= 7 SYM=8 MS2= 3 THRE=1.0D-08 THRD=3.2D-06 THRG=3.2D-06 HFMA2=F DIIS_START=2 DIIS_MAX=10 DIIS_INCORE=F

Level shifts: 0.00 (CLOSED) 0.00 (OPEN) 0.30 (GAP_MIN)

ITER ETOT DE GRAD DDIFF DIIS NEXP TIME(IT) TIME(TOT) DIAG
1 -54.35871954 -54.35871954 0.00D+00 0.59D+00 0 0 0.00 0.02 start
2 -54.38773225 -0.02901271 0.37D-01 0.11D+00 1 0 0.00 0.02 diag2
3 -54.38832005 -0.00058780 0.84D-02 0.27D-01 2 0 0.00 0.02 diag2
4 -54.38841370 -0.00009365 0.25D-02 0.13D-01 3 0 0.00 0.02 diag2
5 -54.38841424 -0.00000053 0.18D-03 0.99D-03 4 0 0.00 0.02 diag2
6 -54.38841424 -0.00000000 0.42D-06 0.15D-05 5 0 0.01 0.03 diag2
7 -54.38841424 0.00000000 0.29D-08 0.11D-07 0 0 0.00 0.03 diag

Final alpha occupancy: 2 1 1 0 1 0 0
Final beta occupancy: 2 0 0 0 0 0 0

!RHF STATE 1.8 Energy -54.388414236937
RHF One-electron energy -73.949784753221
RHF Two-electron energy 19.561370516285
RHF Kinetic energy 54.388183347818
RHF Nuclear energy 0.000000000000
RHF Virial quotient -1.000004245207

!RHF STATE 1.8 Dipole moment 0.00000000 0.00000000 0.00000000
Dipole moment /Debye 0.00000000 0.00000000 0.00000000

ELECTRON ORBITALS
=================

Orbital Occupation Energy Cen Mu Typ Coefficients
1.1 2.00000 -15.62769 1 1 s 1.00000
2.1 2.00000 -0.94227 1 2 s 1.00000
1.2 1.00000 -0.56237 1 1 px 1.00000
1.3 1.00000 -0.56237 1 1 py 1.00000
1.5 1.00000 -0.56237 1 1 pz 1.00000


HOMO 1.5 -0.562370 = -15.3029eV
LUMO 2.2 0.880431 = 23.9578eV
LUMO-HOMO 1.442802 = 39.2606eV

Orbitals saved in record 2100.2


**********************************************************************************************************************************
DATASETS * FILE NREC LENGTH (MB) RECORD NAMES
1 18 28.55 500 610 700 900 950 970 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 0.35 700 1000 520 2100
GEOM BASIS MCVARS RHF

PROGRAMS * TOTAL HF-SCF INT
CPU TIMES * 1.63 0.74 0.39
REAL TIME * 7.19 SEC
DISK USED * 28.94 MB (local), 527.14 MB (total)
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

Number of core orbitals: 1 ( 1 0 0 0 0 0 0 0 )
Number of closed-shell orbitals: 1 ( 1 0 0 0 0 0 0 0 )
Number of active orbitals: 3 ( 0 1 1 0 1 0 0 0 )
Number of external orbitals: 9 ( 3 1 1 1 1 1 1 0 )

Number of N-1 electron functions: 5
Number of N-2 electron functions: 10
Number of singly external CSFs: 12
Number of doubly external CSFs: 138
Total number of CSFs: 150

Molecular orbitals read from record 2100.2 Type=RHF/CANONICAL

Integral transformation finished. Total CPU: 0.04 sec, npass= 1 Memory used: 0.07 MW

Starting RMP2 calculation, locsing= 0

ITER. SQ.NORM CORR.ENERGY TOTAL ENERGY ENERGY CHANGE DEN1 VAR(S) VAR(P) DIIS TIME
1 1.02039334 -0.07278335 -54.46119759 -0.07278335 -0.00020471 0.38D-05 0.52D-04 1 1 0.10
2 1.02053061 -0.07300412 -54.46141836 -0.00022076 -0.00000014 0.10D-09 0.34D-07 2 2 0.12
3 1.02053183 -0.07300573 -54.46141997 -0.00000161 -0.00000000 0.18D-11 0.95D-11 3 3 0.12
4 1.02053182 -0.07300572 -54.46141996 0.00000001 -0.00000000 0.67D-15 0.25D-14 4 4 0.12

Norm of t1 vector: 0.02959147 S-energy: -0.00172365 T1 diagnostic: 0.00068731
Norm of t2 vector: 0.14020043 P-energy: -0.07128207
Alpha-Beta: -0.04979092
Alpha-Alpha: -0.02149115
Beta-Beta: 0.00000000

Spin contamination <S**2-Sz**2-Sz> 0.00013927
Reference energy -54.388414236937
RHF-RMP2 correlation energy -0.073005721083
!RHF-RMP2 energy -54.461419958020

Starting UCCSD calculation

ITER. SQ.NORM CORR.ENERGY TOTAL ENERGY ENERGY CHANGE DEN1 VAR(S) VAR(P) DIIS TIME
1 1.02800792 -0.08499385 -54.47340809 -0.08499385 -0.00353707 0.44D-04 0.94D-03 1 1 0.16
2 1.03107787 -0.08914846 -54.47756270 -0.00415461 -0.00004118 0.24D-06 0.11D-04 2 2 0.20
3 1.03127367 -0.08932326 -54.47773749 -0.00017479 -0.00000065 0.11D-06 0.14D-06 3 3 0.22
4 1.03128825 -0.08933977 -54.47775400 -0.00001651 -0.00000002 0.91D-09 0.47D-08 4 4 0.24
5 1.03128271 -0.08933243 -54.47774667 0.00000733 -0.00000000 0.67D-10 0.16D-09 5 5 0.26
6 1.03128507 -0.08933541 -54.47774965 -0.00000298 -0.00000000 0.64D-11 0.28D-11 6 6 0.27
7 1.03128438 -0.08933448 -54.47774872 0.00000093 -0.00000000 0.14D-12 0.10D-12 6 1 0.29

Norm of t1 vector: 0.03509621 S-energy: -0.00204908 T1 diagnostic: 0.00030073
D1 diagnostic: 0.00063963
D2 diagnostic: 0.15004576 (internal)
Norm of t2 vector: 0.17335696 P-energy: -0.08728541
Alpha-Beta: -0.06323921
Alpha-Alpha: -0.02404620
Beta-Beta: 0.00000000

Spin contamination <S**2-Sz**2-Sz> 0.00001507


RESULTS
=======

Reference energy -54.388414236937
UCCSD singles energy -0.002049075709
UCCSD pair energy -0.087285409135
UCCSD correlation energy -0.089334484844

!RHF-UCCSD energy -54.477748721781

Program statistics:

Available memory in ccsd: 366234205
Min. memory needed in ccsd: 1745
Max. memory used in ccsd: 1831
Max. memory used in cckext: 34467 ( 7 integral passes)
Max. memory used in cckint: 66459 ( 1 integral passes)



**********************************************************************************************************************************
DATASETS * FILE NREC LENGTH (MB) RECORD NAMES
1 18 28.55 500 610 700 900 950 970 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 0.35 700 1000 520 2100
GEOM BASIS MCVARS RHF

PROGRAMS * TOTAL UCCSD HF-SCF INT
CPU TIMES * 2.15 0.47 0.74 0.39
REAL TIME * 7.88 SEC
DISK USED * 28.95 MB (local), 527.36 MB (total)
SF USED * 0.04 MB
GA USED * 0.00 MB (max) 0.00 MB (current)
**********************************************************************************************************************************

UCCSD/cc-pVDZ energy= -54.477748721781

UCCSD HF-SCF
-54.47774872 -54.38841424
**********************************************************************************************************************************
Molpro calculation terminated

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