From d8833f9166b61fe651960c308d1f55dba4027a85 Mon Sep 17 00:00:00 2001 From: Alon Grinberg Dana Date: Sun, 8 Sep 2024 08:41:32 +0300 Subject: [PATCH] f! parser test --- arc/parser_test.py | 26 +-- arc/testing/sp/N_CCSD.out | 340 ++++++++++++++++++++++++++++++++++++++ 2 files changed, 356 insertions(+), 10 deletions(-) create mode 100644 arc/testing/sp/N_CCSD.out diff --git a/arc/parser_test.py b/arc/parser_test.py index d1d4373f14..9950be9c17 100644 --- a/arc/parser_test.py +++ b/arc/parser_test.py @@ -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__': diff --git a/arc/testing/sp/N_CCSD.out b/arc/testing/sp/N_CCSD.out new file mode 100644 index 0000000000..201df9f26d --- /dev/null +++ b/arc/testing/sp/N_CCSD.out @@ -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 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 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