===> Testing for py38-qcengine-0.20.1 ===> py38-qcengine-0.20.1 depends on package: py38-pytest>0 - found ===> py38-qcengine-0.20.1 depends on executable: nwchem - found ===> py38-qcengine-0.20.1 depends on package: rdkit>0 - found ===> py38-qcengine-0.20.1 depends on package: py38-pyberny>0 - found ===> py38-qcengine-0.20.1 depends on package: py38-geometric>0 - found ===> py38-qcengine-0.20.1 depends on file: /usr/local/bin/python3.8 - found ============================= test session starts ============================== platform freebsd13 -- Python 3.8.12, pytest-4.6.11, py-1.9.0, pluggy-0.13.1 rootdir: /disk-samsung/freebsd-ports/science/py-qcengine/work-py38/qcengine-0.20.1, inifile: setup.cfg plugins: forked-1.0.2, hypothesis-6.23.1, xdist-1.32.0, cov-2.9.0, rerunfailures-10.1, timeout-1.4.2, mock-1.10.4 collected 935 items / 3 skipped / 932 selected qcengine/programs/tests/test_adcc.py s [ 0%] qcengine/programs/tests/test_alignment.py ssssssssssssssssssssssss..FF.. 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[100%] =================================== FAILURES =================================== ___________ test_hf_alignment[hf rhf ae: nwchem-dz-grd1-fixed-SRM9] ___________ self = NWChemHarness(name='NWChem', scratch=True, thread_safe=False, thread_parallel=False, node_parallel=True, managed_memory=True, extras=None, version_cache={'/usr/local/bin/nwchem': '7.0.2+11.eol.2499.gbbee7e139269'}) outfiles = {'nwchem.grad': None, 'nwchem.hess': None} input_model = AtomicInput(driver='gradient', model={'method': 'hf', 'basis': 'cc-pvdz'}, molecule_hash='c213da7') def parse_output( self, outfiles: Dict[str, str], input_model: "AtomicInput" ) -> AtomicResult: # lgtm: [py/similar-function] # Get the stdout from the calculation (required) stdout = outfiles.pop("stdout") stderr = outfiles.pop("stderr") method = input_model.model.method.lower() method = method[4:] if method.startswith("nwc-") else method # Read the NWChem stdout file and, if needed, the hess or grad files # July 2021: nwmol & vector returns now atin/outfile orientation depending on fix_com,orientation=T/F. previously always atin orientation try: qcvars, nwhess, nwgrad, nwmol, version, module, errorTMP = harvest( input_model.molecule, method, stdout, **outfiles ) except Exception as e: raise UnknownError(error_stamp(stdout=stdout, stderr=stderr)) try: if nwgrad is not None: qcvars[f"{method.upper()} TOTAL GRADIENT"] = nwgrad qcvars["CURRENT GRADIENT"] = nwgrad if nwhess is not None: qcvars[f"{method.upper()} TOTAL HESSIAN"] = nwhess qcvars["CURRENT HESSIAN"] = nwhess # Normalize the output as a float or list of floats if input_model.driver.upper() == "PROPERTIES": retres = qcvars[f"CURRENT ENERGY"] else: > retres = qcvars[f"CURRENT {input_model.driver.upper()}"] E KeyError: 'CURRENT GRADIENT' qcengine/programs/nwchem/runner.py:275: KeyError During handling of the above exception, another exception occurred: inp = {'call': 'nwchem', 'fcae': 'ae', 'keywords': {'scf__thresh': 1e-06}, 'reference': 'rhf'} scramble = {'do_resort': True, 'do_rotate': True, 'do_shift': True} frame = 'fixed', driver = 'gradient', basis = 'cc-pvdz' subjects = ['hf', 'bh3p', 'bh3p'] clsd_open_pmols = {'bh3p': Molecule(name='bh3p', formula='BH3', hash='f532294'), 'bh3p-fixed': Molecule(name='bh3p', formula='BH3', hash...cule(name='h2o', formula='H2O', hash='4684da5'), 'h2o-fixed': Molecule(name='h2o', formula='H2O', hash='4684da5'), ...} request = > @pytest.mark.parametrize( "scramble", # * this parameter alters the input molecule by Cartesian frame and/or atom ordering to imitate real-world inputs. # * scramble dictionary are arguments to qcdb.Molecule.scramble() or qcel.models.Molecule.scramble() that computes a shifted/rotated/atom-mapped input molecule from `subjects` below and the transformations to be applied to the reference data. # * arguments do_shift=T/F and other boolean values generate random perturbations, so multiple lines or runs makes a fuller test. # * specific shifts etc or problematic runs can be reproduced by specifying arrays like the commented example below. note that b/c do_resort is natom-dependent, may need to exclude subjects while debugging. # * `id`s below are numbered since `pytest -k` doesn't recognize case and so duplicate entries can be added. the 0, 1, 2, 3, 9 progression is handy for debugging since perturbations are added systematically [ # pytest.param({"do_shift": [ 2.660760432055, 1.477336796939, -2.098045335573], "do_rotate": [[ 0.321861140022, 0.445246880671, 0.835560064745], [-0.447874157747, 0.849136107328, -0.279958229125], [-0.834154749052, -0.28411808546 , 0.472718487209]], "do_resort": [2, 0, 1]}, id="mTTT3"), # pytest.param({"do_shift": False, "do_rotate": False, "do_resort": False}, id="srm0"), # pytest.param({"do_shift": True, "do_rotate": False, "do_resort": False}, id="Srm1"), # pytest.param({"do_shift": True, "do_rotate": True, "do_resort": False}, id="SRm2"), # pytest.param({"do_shift": False, "do_rotate": False, "do_resort": True}, id="srM3"), # pytest.param({"do_shift": True, "do_rotate": True, "do_resort": True}, id="SRM8"), pytest.param({"do_shift": True, "do_rotate": True, "do_resort": True}, id="SRM9"), ], ) @pytest.mark.parametrize( "frame", # * this parameter alters the input molecule by fix_com and fix_orientation to imitate user signaling frame matters or not. [ pytest.param("fixed"), # fix_=True (no_com/no_reorient); atres.mol.geom = atin.mol.geom aka scrambled pytest.param("free"), # fix_=False (def) ; atres.mol.geom = dsl internal orientation ], ) @pytest.mark.parametrize( "driver", [ pytest.param("energy", id="ene0"), pytest.param("gradient", id="grd1"), pytest.param("hessian", id="hes2"), ], ) @pytest.mark.parametrize( "basis, subjects", # this parameter, along with rhf/uhf below covers four different molecules, with nat=2-4. [ pytest.param("cc-pvdz", ["hf", "bh3p", "bh3p"], id="dz"), pytest.param("aug-cc-pvdz", ["h2o", "nh2", "nh2"], id="adz", marks=pytest.mark.long), ], ) @pytest.mark.parametrize( "inp", [ # yapf: disable pytest.param({"call": "cfour", "reference": "rhf", "fcae": "ae", "keywords": {"scf_conv": 12}, }, id="hf rhf ae: cfour", marks=using("cfour")), pytest.param({"call": "gamess", "reference": "rhf", "fcae": "ae", "keywords": {}, }, id="hf rhf ae: gamess", marks=using("gamess")), pytest.param({"call": "nwchem", "reference": "rhf", "fcae": "ae", "keywords": {"scf__thresh": 1.e-6}, }, id="hf rhf ae: nwchem", marks=using("nwchem")), pytest.param({"call": "psi4", "reference": "rhf", "fcae": "ae", "keywords": {"scf_type": "pk"}, }, id="hf rhf ae: psi4", marks=using("psi4_derqcsk")), pytest.param({"call": "cfour", "reference": "uhf", "fcae": "ae", "keywords": {"reference": "uhf", "scf_conv": 12}, }, id="hf uhf ae: cfour", marks=using("cfour")), pytest.param({"call": "gamess", "reference": "uhf", "fcae": "ae", "keywords": {"contrl__scftyp": "uhf"}, }, id="hf uhf ae: gamess", marks=using("gamess")), pytest.param({"call": "nwchem", "reference": "uhf", "fcae": "ae", "keywords": {"scf__uhf": True, "scf__thresh": 1.e-6}, }, id="hf uhf ae: nwchem", marks=using("nwchem")), pytest.param({"call": "psi4", "reference": "uhf", "fcae": "ae", "keywords": {"reference": "uhf", "scf_type": "pk"}, }, id="hf uhf ae: psi4", marks=using("psi4_derqcsk")), # yapf: enable ], ) def test_hf_alignment(inp, scramble, frame, driver, basis, subjects, clsd_open_pmols, request): > runner_asserter( *_processor(inp, "", basis, subjects, clsd_open_pmols, request, driver, "hf", scramble=scramble, frame=frame) ) qcengine/programs/tests/test_alignment.py:96: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ qcengine/programs/tests/standard_suite_runner.py:177: in runner_asserter wfn = qcng.compute(atin, qcprog, raise_error=True, local_options=local_options) qcengine/compute.py:91: in compute output_data = executor.compute(input_data, config) qcengine/programs/model.py:116: in compute result = self._compute(local_input_data, config) qcengine/programs/nwchem/runner.py:137: in _compute return self.parse_output(dexe["outfiles"], input_model) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = NWChemHarness(name='NWChem', scratch=True, thread_safe=False, thread_parallel=False, node_parallel=True, managed_memory=True, extras=None, version_cache={'/usr/local/bin/nwchem': '7.0.2+11.eol.2499.gbbee7e139269'}) outfiles = {'nwchem.grad': None, 'nwchem.hess': None} input_model = AtomicInput(driver='gradient', model={'method': 'hf', 'basis': 'cc-pvdz'}, molecule_hash='c213da7') def parse_output( self, outfiles: Dict[str, str], input_model: "AtomicInput" ) -> AtomicResult: # lgtm: [py/similar-function] # Get the stdout from the calculation (required) stdout = outfiles.pop("stdout") stderr = outfiles.pop("stderr") method = input_model.model.method.lower() method = method[4:] if method.startswith("nwc-") else method # Read the NWChem stdout file and, if needed, the hess or grad files # July 2021: nwmol & vector returns now atin/outfile orientation depending on fix_com,orientation=T/F. previously always atin orientation try: qcvars, nwhess, nwgrad, nwmol, version, module, errorTMP = harvest( input_model.molecule, method, stdout, **outfiles ) except Exception as e: raise UnknownError(error_stamp(stdout=stdout, stderr=stderr)) try: if nwgrad is not None: qcvars[f"{method.upper()} TOTAL GRADIENT"] = nwgrad qcvars["CURRENT GRADIENT"] = nwgrad if nwhess is not None: qcvars[f"{method.upper()} TOTAL HESSIAN"] = nwhess qcvars["CURRENT HESSIAN"] = nwhess # Normalize the output as a float or list of floats if input_model.driver.upper() == "PROPERTIES": retres = qcvars[f"CURRENT ENERGY"] else: retres = qcvars[f"CURRENT {input_model.driver.upper()}"] except KeyError as e: > raise UnknownError(error_stamp(stdout=stdout, stderr=stderr)) E qcengine.exceptions.UnknownError: STDOUT: E E E E ============================== echo of input deck ============================== E echo E geometry units bohr E H -1.898036207571 -3.040824317013 -1.409570406918 E F -2.027560649775 -1.342644053478 -1.729377153012 E E end E memory 879931424 double E charge 0 E E basis spherical E H library cc-pvdz E bqH library H cc-pvdz E F library cc-pvdz E bqF library F cc-pvdz E end E E scf E thresh 1e-06 E end E E task scf gradient E E E python E grad = rtdb_get('scf:gradient') E if ga_nodeid() == 0: E import json E with open('nwchem.grad', 'w') as fp: E json.dump(grad, fp) E end E E task python E E ================================================================================ E E E E E E E Northwest Computational Chemistry Package (NWChem) 7.0.2 E -------------------------------------------------------- E E E Environmental Molecular Sciences Laboratory E Pacific Northwest National Laboratory E Richland, WA 99352 E E Copyright (c) 1994-2020 E Pacific Northwest National Laboratory E Battelle Memorial Institute E E NWChem is an open-source computational chemistry package E distributed under the terms of the E Educational Community License (ECL) 2.0 E A copy of the license is included with this distribution E in the LICENSE.TXT file E E ACKNOWLEDGMENT E -------------- E E This software and its documentation were developed at the E EMSL at Pacific Northwest National Laboratory, a multiprogram E national laboratory, operated for the U.S. Department of Energy E by Battelle under Contract Number DE-AC05-76RL01830. Support E for this work was provided by the Department of Energy Office E of Biological and Environmental Research, Office of Basic E Energy Sciences, and the Office of Advanced Scientific Computing. E E E Job information E --------------- E E hostname = yv.noip.me E program = /usr/local/bin/nwchem E date = Thu Oct 21 12:46:58 2021 E E compiled = Thu_Oct_21_12:11:03_2021 E source = /disk-samsung/freebsd-ports/science/nwchem/work/nwchem-7.0.2-release/src/.. E nwchem branch = 7.0.2 E nwchem revision = 11-eol-2499-gbbee7e139269 E ga revision = 5.8.0 E use scalapack = T E input = nwchem.nw E prefix = nwchem. E data base = ./nwchem.db E status = startup E nproc = 1 E time left = -1s E E E E Memory information E ------------------ E E heap = 219982852 doubles = 1678.3 Mbytes E stack = 219982857 doubles = 1678.3 Mbytes E global = 439965712 doubles = 3356.7 Mbytes (distinct from heap & stack) E total = 879931421 doubles = 6713.3 Mbytes E verify = yes E hardfail = no E E E Directory information E --------------------- E E 0 permanent = . E 0 scratch = . E E E E E NWChem Input Module E ------------------- E E E ORDER OF PRIMARY AXIS IS BEING SET TO 4 E C4V symmetry detected E E ------ E auto-z E ------ E no constraints, skipping 0.0000000000000000 E no constraints, skipping 0.0000000000000000 E E E Geometry "geometry" -> "" E ------------------------- E E Output coordinates in a.u. (scale by 1.000000000 to convert to a.u.) E E No. Tag Charge X Y Z E ---- ---------------- ---------- -------------- -------------- -------------- E 1 H 1.0000 0.00000000 0.00000000 -1.55959097 E 2 F 9.0000 0.00000000 0.00000000 0.17328789 E E Atomic Mass E ----------- E E H 1.007825 E F 18.998400 E E E Effective nuclear repulsion energy (a.u.) 5.1936694525 E E Nuclear Dipole moment (a.u.) E ---------------------------- E X Y Z E ---------------- ---------------- ---------------- E 0.0000000000 0.0000000000 0.0000000000 E E Symmetry information E -------------------- E E Group name C4v E Group number 18 E Group order 8 E No. of unique centers 2 E E Symmetry unique atoms E E 1 2 E E E E Z-matrix (autoz) E -------- E E Units are Angstrom for bonds and degrees for angles E E Type Name I J K L M Value E ----------- -------- ----- ----- ----- ----- ----- ---------- E 1 Stretch 1 2 0.91700 E E E XYZ format geometry E ------------------- E 2 E geometry E H 0.00000000 0.00000000 -0.82530006 E F 0.00000000 0.00000000 0.09170001 E E ============================================================================== E internuclear distances E ------------------------------------------------------------------------------ E center one | center two | atomic units | a.u. E ------------------------------------------------------------------------------ E 2 F | 1 H | 1.73288 | 1.73288 E ------------------------------------------------------------------------------ E number of included internuclear distances: 1 E ============================================================================== E E E E library name resolved from: .nwchemrc E library file name is: E E Basis "ao basis" -> "" (spherical) E ----- E H (Hydrogen) E ------------ E Exponent Coefficients E -------------- --------------------------------------------------------- E 1 S 1.30100000E+01 0.019685 E 1 S 1.96200000E+00 0.137977 E 1 S 4.44600000E-01 0.478148 E E 2 S 1.22000000E-01 1.000000 E E 3 P 7.27000000E-01 1.000000 E E bqH E --- E Exponent Coefficients E -------------- --------------------------------------------------------- E 1 S 1.30100000E+01 0.019685 E 1 S 1.96200000E+00 0.137977 E 1 S 4.44600000E-01 0.478148 E E 2 S 1.22000000E-01 1.000000 E E 3 P 7.27000000E-01 1.000000 E E F (Fluorine) E ------------ E Exponent Coefficients E -------------- --------------------------------------------------------- E 1 S 1.47100000E+04 0.000721 E 1 S 2.20700000E+03 0.005553 E 1 S 5.02800000E+02 0.028267 E 1 S 1.42600000E+02 0.106444 E 1 S 4.64700000E+01 0.286814 E 1 S 1.67000000E+01 0.448641 E 1 S 6.35600000E+00 0.264761 E 1 S 1.31600000E+00 0.015333 E E 2 S 1.47100000E+04 -0.000165 E 2 S 2.20700000E+03 -0.001308 E 2 S 5.02800000E+02 -0.006495 E 2 S 1.42600000E+02 -0.026691 E 2 S 4.64700000E+01 -0.073690 E 2 S 1.67000000E+01 -0.170776 E 2 S 6.35600000E+00 -0.112327 E 2 S 1.31600000E+00 0.562814 E E 3 S 3.89700000E-01 1.000000 E E 4 P 2.26700000E+01 0.044878 E 4 P 4.97700000E+00 0.235718 E 4 P 1.34700000E+00 0.508521 E E 5 P 3.47100000E-01 1.000000 E E 6 D 1.64000000E+00 1.000000 E E bqF E --- E Exponent Coefficients E -------------- --------------------------------------------------------- E 1 S 1.47100000E+04 0.000721 E 1 S 2.20700000E+03 0.005553 E 1 S 5.02800000E+02 0.028267 E 1 S 1.42600000E+02 0.106444 E 1 S 4.64700000E+01 0.286814 E 1 S 1.67000000E+01 0.448641 E 1 S 6.35600000E+00 0.264761 E 1 S 1.31600000E+00 0.015333 E E 2 S 1.47100000E+04 -0.000165 E 2 S 2.20700000E+03 -0.001308 E 2 S 5.02800000E+02 -0.006495 E 2 S 1.42600000E+02 -0.026691 E 2 S 4.64700000E+01 -0.073690 E 2 S 1.67000000E+01 -0.170776 E 2 S 6.35600000E+00 -0.112327 E 2 S 1.31600000E+00 0.562814 E E 3 S 3.89700000E-01 1.000000 E E 4 P 2.26700000E+01 0.044878 E 4 P 4.97700000E+00 0.235718 E 4 P 1.34700000E+00 0.508521 E E 5 P 3.47100000E-01 1.000000 E E 6 D 1.64000000E+00 1.000000 E E E E Summary of "ao basis" -> "" (spherical) E ------------------------------------------------------------------------------ E Tag Description Shells Functions and Types E ---------------- ------------------------------ ------ --------------------- E H cc-pvdz 3 5 2s1p E bqH cc-pvdz 3 5 2s1p E F cc-pvdz 6 14 3s2p1d E bqF cc-pvdz 6 14 3s2p1d E E E NWChem SCF Module E ----------------- E E E E ao basis = "ao basis" E functions = 19 E atoms = 2 E closed shells = 5 E open shells = 0 E charge = 0.00 E wavefunction = RHF E input vectors = atomic E output vectors = ./nwchem.movecs E use symmetry = T E symmetry adapt = T E E E Summary of "ao basis" -> "ao basis" (spherical) E ------------------------------------------------------------------------------ E Tag Description Shells Functions and Types E ---------------- ------------------------------ ------ --------------------- E H cc-pvdz 3 5 2s1p E bqH cc-pvdz 3 5 2s1p E F cc-pvdz 6 14 3s2p1d E bqF cc-pvdz 6 14 3s2p1d E E E Symmetry analysis of basis E -------------------------- E E a1 9 E a2 0 E b1 1 E b2 1 E e 8 E E E Forming initial guess at 0.0s E E E Superposition of Atomic Density Guess E ------------------------------------- E E Sum of atomic energies: -99.88314519 E E Non-variational initial energy E ------------------------------ E E Total energy = -99.865715 E 1-e energy = -149.649522 E 2-e energy = 44.590137 E HOMO = -0.637960 E LUMO = 0.109607 E E E Symmetry analysis of molecular orbitals - initial E ------------------------------------------------- E E E !! scf_movecs_sym_adapt: 2 vectors were symmetry contaminated E E Symmetry fudging E E !! scf_movecs_sym_adapt: 2 vectors were symmetry contaminated E E Numbering of irreducible representations: E E 1 a1 2 a2 3 b1 4 b2 5 e E E Orbital symmetries: E E 1 a1 2 a1 3 a1 4 e 5 e E 6 a1 7 a1 8 a1 9 e 10 e E 11 e 12 e 13 a1 14 a1 15 b2 E E E Starting SCF solution at 0.1s E E E E ---------------------------------------------- E Quadratically convergent ROHF E E Convergence threshold : 1.000E-06 E Maximum no. of iterations : 30 E Final Fock-matrix accuracy: 1.000E-08 E ---------------------------------------------- E E E #quartets = 1.035D+03 #integrals = 4.841D+03 #direct = 0.0% #cached =100.0% E E E Integral file = ./nwchem.aoints.0 E Record size in doubles = 65536 No. of integs per rec = 43688 E Max. records in memory = 2 Max. records in file = 124819 E No. of bits per label = 8 No. of bits per value = 64 E E E iter energy gnorm gmax time E ----- ------------------- --------- --------- -------- E 1 -99.9944094325 7.27D-01 3.80D-01 0.1 E 2 -100.0177379586 1.62D-01 6.40D-02 0.2 E 3 -100.0193962961 1.41D-02 6.37D-03 0.2 E 4 -100.0194112693 2.02D-05 8.98D-06 0.2 E 5 -100.0194112693 4.87D-08 2.24D-08 0.3 E E E Final RHF results E ------------------ E E Total SCF energy = -100.019411269305 E One-electron energy = -150.693050028557 E Two-electron energy = 45.479969306790 E Nuclear repulsion energy = 5.193669452462 E E Time for solution = 0.2s E E E E Symmetry analysis of molecular orbitals - final E ----------------------------------------------- E E Numbering of irreducible representations: E E 1 a1 2 a2 3 b1 4 b2 5 e E E Orbital symmetries: E E 1 a1 2 a1 3 a1 4 e 5 e E 6 a1 7 a1 8 e 9 e 10 a1 E 11 e 12 e 13 a1 14 a1 15 b2 E E Final eigenvalues E ----------------- E E 1 E 1 -26.2781 E 2 -1.5835 E 3 -0.7472 E 4 -0.6289 E 5 -0.6289 E 6 0.1838 E 7 0.8100 E 8 1.4119 E 9 1.4119 E 10 1.4156 E 11 1.6041 E 12 1.6041 E 13 2.1341 E 14 2.4989 E 15 4.0044 E E ROHF Final Molecular Orbital Analysis E ------------------------------------- E E Vector 2 Occ=2.000000D+00 E=-1.583452D+00 Symmetry=a1 E MO Center= 2.0D-17, 1.9D-16, -2.4D-02, r^2= 3.7D-01 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 7 0.481194 2 F s 8 0.480605 2 F s E 1 0.174632 1 H s E E Vector 3 Occ=2.000000D+00 E=-7.471972D-01 Symmetry=a1 E MO Center= -1.7D-16, -8.4D-17, -1.4D-02, r^2= 5.6D-01 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 11 0.555850 2 F pz 1 -0.387490 1 H s E 14 0.299645 2 F pz 8 0.289834 2 F s E E Vector 4 Occ=2.000000D+00 E=-6.288892D-01 Symmetry=e E MO Center= 3.3D-17, -3.1D-18, 7.5D-02, r^2= 4.4D-01 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 10 0.573600 2 F py 13 0.410308 2 F py E 9 0.335256 2 F px 12 0.239816 2 F px E E Vector 5 Occ=2.000000D+00 E=-6.288892D-01 Symmetry=e E MO Center= 1.9D-16, -1.8D-16, 7.5D-02, r^2= 4.4D-01 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 9 0.573600 2 F px 12 0.410308 2 F px E 10 -0.335256 2 F py 13 -0.239816 2 F py E E Vector 6 Occ=0.000000D+00 E= 1.838400D-01 Symmetry=a1 E MO Center= -4.5D-16, 5.0D-16, -1.0D+00, r^2= 2.1D+00 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 2 1.265475 1 H s 8 -0.670151 2 F s E 14 0.336135 2 F pz 11 0.217915 2 F pz E E Vector 7 Occ=0.000000D+00 E= 8.100489D-01 Symmetry=a1 E MO Center= -8.6D-16, 9.0D-17, -8.0D-01, r^2= 1.1D+00 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 1 1.275533 1 H s 2 -0.907033 1 H s E 11 0.370721 2 F pz 5 -0.327559 1 H pz E 14 0.194975 2 F pz E E Vector 8 Occ=0.000000D+00 E= 1.411878D+00 Symmetry=e E MO Center= 2.0D-15, -1.7D-15, -2.1D-01, r^2= 8.6D-01 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 9 0.652391 2 F px 12 -0.577659 2 F px E 10 -0.545553 2 F py 13 0.483060 2 F py E 3 -0.334186 1 H px 4 0.279458 1 H py E E Vector 9 Occ=0.000000D+00 E= 1.411878D+00 Symmetry=e E MO Center= -2.2D-15, -2.6D-15, -2.1D-01, r^2= 8.6D-01 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 10 0.652391 2 F py 13 -0.577659 2 F py E 9 0.545553 2 F px 12 -0.483060 2 F px E 4 -0.334186 1 H py 3 -0.279458 1 H px E E Vector 10 Occ=0.000000D+00 E= 1.415619D+00 Symmetry=a1 E MO Center= 1.9D-15, 7.7D-15, 4.9D-01, r^2= 9.0D-01 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 14 1.618091 2 F pz 1 1.084020 1 H s E 11 -0.644892 2 F pz 8 -0.591943 2 F s E 5 0.513224 1 H pz 7 -0.226860 2 F s E E Vector 11 Occ=0.000000D+00 E= 1.604149D+00 Symmetry=e E MO Center= -2.2D-15, -5.1D-16, -4.0D-01, r^2= 1.0D+00 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 3 0.956399 1 H px 12 -0.838793 2 F px E 9 0.380981 2 F px 4 0.217740 1 H py E 13 -0.190966 2 F py E E Vector 12 Occ=0.000000D+00 E= 1.604149D+00 Symmetry=e E MO Center= 1.3D-15, -5.5D-15, -4.0D-01, r^2= 1.0D+00 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 4 0.956399 1 H py 13 -0.838793 2 F py E 10 0.380981 2 F py 3 -0.217740 1 H px E 12 0.190966 2 F px E E Vector 13 Occ=0.000000D+00 E= 2.134096D+00 Symmetry=a1 E MO Center= 6.0D-16, 2.2D-15, -1.1D-01, r^2= 9.6D-01 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 8 2.403587 2 F s 7 -1.664197 2 F s E 6 -0.716261 2 F s 14 -0.714895 2 F pz E 1 -0.707619 1 H s 2 -0.543054 1 H s E 5 -0.349676 1 H pz E E Vector 14 Occ=0.000000D+00 E= 2.498873D+00 Symmetry=a1 E MO Center= -6.7D-17, -3.2D-16, -6.9D-01, r^2= 6.0D-01 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 5 1.405944 1 H pz 8 -0.968301 2 F s E 1 0.776130 1 H s 11 0.759152 2 F pz E 14 0.288474 2 F pz 2 0.275079 1 H s E 7 -0.249146 2 F s E E Vector 15 Occ=0.000000D+00 E= 4.004354D+00 Symmetry=b2 E MO Center= -4.9D-18, 6.7D-17, 9.2D-02, r^2= 3.0D-01 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 15 1.000000 2 F d -2 E E E center of mass E -------------- E x = 0.00000000 y = 0.00000000 z = 0.08599312 E E moments of inertia (a.u.) E ------------------ E 2.873911650430 0.000000000000 0.000000000000 E 0.000000000000 2.873911650430 0.000000000000 E 0.000000000000 0.000000000000 0.000000000000 E E Mulliken analysis of the total density E -------------------------------------- E E Atom Charge Shell Charges E ----------- ------ ------------------------------------------------------- E 1 H 1 0.76 0.63 0.03 0.11 E 2 F 9 9.24 2.00 0.89 0.97 3.32 2.05 0.00 E E Multipole analysis of the density wrt the origin E ------------------------------------------------ E E L x y z total open nuclear E - - - - ----- ---- ------- E 0 0 0 0 -0.000000 0.000000 10.000000 E E 1 1 0 0 -0.000000 0.000000 0.000000 E 1 0 1 0 0.000000 0.000000 0.000000 E 1 0 0 1 -0.767022 0.000000 0.000000 E E 2 2 0 0 -4.007314 0.000000 0.000000 E 2 1 1 0 -0.000000 0.000000 0.000000 E 2 1 0 1 0.000000 0.000000 0.000000 E 2 0 2 0 -4.007314 0.000000 0.000000 E 2 0 1 1 0.000000 0.000000 0.000000 E 2 0 0 2 -2.493425 0.000000 2.702582 E E E Parallel integral file used 1 records with 0 large values E E NWChem Gradients Module E ----------------------- E E E E wavefunction = RHF E E Using symmetry E E STDERR: E E Program received signal SIGSEGV: Segmentation fault - invalid memory reference. E E Backtrace for this error: E #0 0x804a1f6db in ??? E #1 0x804a1e896 in ??? E #2 0x803729f6f in handle_signal E at /disk-samsung/freebsd-src/lib/libthr/thread/thr_sig.c:303 E #3 0x80372953e in thr_sighandler E at /disk-samsung/freebsd-src/lib/libthr/thread/thr_sig.c:246 E #4 0x7ffffffff192 in ??? E #5 0x803dd91b1 in ??? E #6 0x803badeb5 in ??? E #7 0x803298434 in ??? E #8 0x80329901d in ??? E #9 0x802f076a9 in ??? E #10 0x802e70b74 in ??? E #11 0x9f45dc in ??? E #12 0x9e382f in ??? E #13 0x7ebc84 in ??? E #14 0x7e6a23 in ??? E #15 0x7fdbf4 in ??? E #16 0x7ec987 in ??? E #17 0x4219d7 in ??? E #18 0x422db0 in ??? E #19 0x41462d in ??? E #20 0x40e0e1 in ??? E #21 0x40c71c in ??? E #22 0x40c82f in ??? E E TRACEBACK: E Traceback (most recent call last): E File "/disk-samsung/freebsd-ports/science/py-qcengine/work-py38/qcengine-0.20.1/qcengine/programs/nwchem/runner.py", line 275, in parse_output E retres = qcvars[f"CURRENT {input_model.driver.upper()}"] E KeyError: 'CURRENT GRADIENT' qcengine/programs/nwchem/runner.py:277: UnknownError ___________ test_hf_alignment[hf rhf ae: nwchem-dz-grd1-free-SRM9] ____________ self = NWChemHarness(name='NWChem', scratch=True, thread_safe=False, thread_parallel=False, node_parallel=True, managed_memory=True, extras=None, version_cache={'/usr/local/bin/nwchem': '7.0.2+11.eol.2499.gbbee7e139269'}) outfiles = {'nwchem.grad': None, 'nwchem.hess': None} input_model = AtomicInput(driver='gradient', model={'method': 'hf', 'basis': 'cc-pvdz'}, molecule_hash='e737d71') def parse_output( self, outfiles: Dict[str, str], input_model: "AtomicInput" ) -> AtomicResult: # lgtm: [py/similar-function] # Get the stdout from the calculation (required) stdout = outfiles.pop("stdout") stderr = outfiles.pop("stderr") method = input_model.model.method.lower() method = method[4:] if method.startswith("nwc-") else method # Read the NWChem stdout file and, if needed, the hess or grad files # July 2021: nwmol & vector returns now atin/outfile orientation depending on fix_com,orientation=T/F. previously always atin orientation try: qcvars, nwhess, nwgrad, nwmol, version, module, errorTMP = harvest( input_model.molecule, method, stdout, **outfiles ) except Exception as e: raise UnknownError(error_stamp(stdout=stdout, stderr=stderr)) try: if nwgrad is not None: qcvars[f"{method.upper()} TOTAL GRADIENT"] = nwgrad qcvars["CURRENT GRADIENT"] = nwgrad if nwhess is not None: qcvars[f"{method.upper()} TOTAL HESSIAN"] = nwhess qcvars["CURRENT HESSIAN"] = nwhess # Normalize the output as a float or list of floats if input_model.driver.upper() == "PROPERTIES": retres = qcvars[f"CURRENT ENERGY"] else: > retres = qcvars[f"CURRENT {input_model.driver.upper()}"] E KeyError: 'CURRENT GRADIENT' qcengine/programs/nwchem/runner.py:275: KeyError During handling of the above exception, another exception occurred: inp = {'call': 'nwchem', 'fcae': 'ae', 'keywords': {'scf__thresh': 1e-06}, 'reference': 'rhf'} scramble = {'do_resort': True, 'do_rotate': True, 'do_shift': True} frame = 'free', driver = 'gradient', basis = 'cc-pvdz' subjects = ['hf', 'bh3p', 'bh3p'] clsd_open_pmols = {'bh3p': Molecule(name='bh3p', formula='BH3', hash='f532294'), 'bh3p-fixed': Molecule(name='bh3p', formula='BH3', hash...cule(name='h2o', formula='H2O', hash='4684da5'), 'h2o-fixed': Molecule(name='h2o', formula='H2O', hash='4684da5'), ...} request = > @pytest.mark.parametrize( "scramble", # * this parameter alters the input molecule by Cartesian frame and/or atom ordering to imitate real-world inputs. # * scramble dictionary are arguments to qcdb.Molecule.scramble() or qcel.models.Molecule.scramble() that computes a shifted/rotated/atom-mapped input molecule from `subjects` below and the transformations to be applied to the reference data. # * arguments do_shift=T/F and other boolean values generate random perturbations, so multiple lines or runs makes a fuller test. # * specific shifts etc or problematic runs can be reproduced by specifying arrays like the commented example below. note that b/c do_resort is natom-dependent, may need to exclude subjects while debugging. # * `id`s below are numbered since `pytest -k` doesn't recognize case and so duplicate entries can be added. the 0, 1, 2, 3, 9 progression is handy for debugging since perturbations are added systematically [ # pytest.param({"do_shift": [ 2.660760432055, 1.477336796939, -2.098045335573], "do_rotate": [[ 0.321861140022, 0.445246880671, 0.835560064745], [-0.447874157747, 0.849136107328, -0.279958229125], [-0.834154749052, -0.28411808546 , 0.472718487209]], "do_resort": [2, 0, 1]}, id="mTTT3"), # pytest.param({"do_shift": False, "do_rotate": False, "do_resort": False}, id="srm0"), # pytest.param({"do_shift": True, "do_rotate": False, "do_resort": False}, id="Srm1"), # pytest.param({"do_shift": True, "do_rotate": True, "do_resort": False}, id="SRm2"), # pytest.param({"do_shift": False, "do_rotate": False, "do_resort": True}, id="srM3"), # pytest.param({"do_shift": True, "do_rotate": True, "do_resort": True}, id="SRM8"), pytest.param({"do_shift": True, "do_rotate": True, "do_resort": True}, id="SRM9"), ], ) @pytest.mark.parametrize( "frame", # * this parameter alters the input molecule by fix_com and fix_orientation to imitate user signaling frame matters or not. [ pytest.param("fixed"), # fix_=True (no_com/no_reorient); atres.mol.geom = atin.mol.geom aka scrambled pytest.param("free"), # fix_=False (def) ; atres.mol.geom = dsl internal orientation ], ) @pytest.mark.parametrize( "driver", [ pytest.param("energy", id="ene0"), pytest.param("gradient", id="grd1"), pytest.param("hessian", id="hes2"), ], ) @pytest.mark.parametrize( "basis, subjects", # this parameter, along with rhf/uhf below covers four different molecules, with nat=2-4. [ pytest.param("cc-pvdz", ["hf", "bh3p", "bh3p"], id="dz"), pytest.param("aug-cc-pvdz", ["h2o", "nh2", "nh2"], id="adz", marks=pytest.mark.long), ], ) @pytest.mark.parametrize( "inp", [ # yapf: disable pytest.param({"call": "cfour", "reference": "rhf", "fcae": "ae", "keywords": {"scf_conv": 12}, }, id="hf rhf ae: cfour", marks=using("cfour")), pytest.param({"call": "gamess", "reference": "rhf", "fcae": "ae", "keywords": {}, }, id="hf rhf ae: gamess", marks=using("gamess")), pytest.param({"call": "nwchem", "reference": "rhf", "fcae": "ae", "keywords": {"scf__thresh": 1.e-6}, }, id="hf rhf ae: nwchem", marks=using("nwchem")), pytest.param({"call": "psi4", "reference": "rhf", "fcae": "ae", "keywords": {"scf_type": "pk"}, }, id="hf rhf ae: psi4", marks=using("psi4_derqcsk")), pytest.param({"call": "cfour", "reference": "uhf", "fcae": "ae", "keywords": {"reference": "uhf", "scf_conv": 12}, }, id="hf uhf ae: cfour", marks=using("cfour")), pytest.param({"call": "gamess", "reference": "uhf", "fcae": "ae", "keywords": {"contrl__scftyp": "uhf"}, }, id="hf uhf ae: gamess", marks=using("gamess")), pytest.param({"call": "nwchem", "reference": "uhf", "fcae": "ae", "keywords": {"scf__uhf": True, "scf__thresh": 1.e-6}, }, id="hf uhf ae: nwchem", marks=using("nwchem")), pytest.param({"call": "psi4", "reference": "uhf", "fcae": "ae", "keywords": {"reference": "uhf", "scf_type": "pk"}, }, id="hf uhf ae: psi4", marks=using("psi4_derqcsk")), # yapf: enable ], ) def test_hf_alignment(inp, scramble, frame, driver, basis, subjects, clsd_open_pmols, request): > runner_asserter( *_processor(inp, "", basis, subjects, clsd_open_pmols, request, driver, "hf", scramble=scramble, frame=frame) ) qcengine/programs/tests/test_alignment.py:96: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ qcengine/programs/tests/standard_suite_runner.py:177: in runner_asserter wfn = qcng.compute(atin, qcprog, raise_error=True, local_options=local_options) qcengine/compute.py:91: in compute output_data = executor.compute(input_data, config) qcengine/programs/model.py:116: in compute result = self._compute(local_input_data, config) qcengine/programs/nwchem/runner.py:137: in _compute return self.parse_output(dexe["outfiles"], input_model) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = NWChemHarness(name='NWChem', scratch=True, thread_safe=False, thread_parallel=False, node_parallel=True, managed_memory=True, extras=None, version_cache={'/usr/local/bin/nwchem': '7.0.2+11.eol.2499.gbbee7e139269'}) outfiles = {'nwchem.grad': None, 'nwchem.hess': None} input_model = AtomicInput(driver='gradient', model={'method': 'hf', 'basis': 'cc-pvdz'}, molecule_hash='e737d71') def parse_output( self, outfiles: Dict[str, str], input_model: "AtomicInput" ) -> AtomicResult: # lgtm: [py/similar-function] # Get the stdout from the calculation (required) stdout = outfiles.pop("stdout") stderr = outfiles.pop("stderr") method = input_model.model.method.lower() method = method[4:] if method.startswith("nwc-") else method # Read the NWChem stdout file and, if needed, the hess or grad files # July 2021: nwmol & vector returns now atin/outfile orientation depending on fix_com,orientation=T/F. previously always atin orientation try: qcvars, nwhess, nwgrad, nwmol, version, module, errorTMP = harvest( input_model.molecule, method, stdout, **outfiles ) except Exception as e: raise UnknownError(error_stamp(stdout=stdout, stderr=stderr)) try: if nwgrad is not None: qcvars[f"{method.upper()} TOTAL GRADIENT"] = nwgrad qcvars["CURRENT GRADIENT"] = nwgrad if nwhess is not None: qcvars[f"{method.upper()} TOTAL HESSIAN"] = nwhess qcvars["CURRENT HESSIAN"] = nwhess # Normalize the output as a float or list of floats if input_model.driver.upper() == "PROPERTIES": retres = qcvars[f"CURRENT ENERGY"] else: retres = qcvars[f"CURRENT {input_model.driver.upper()}"] except KeyError as e: > raise UnknownError(error_stamp(stdout=stdout, stderr=stderr)) E qcengine.exceptions.UnknownError: STDOUT: E E E E ============================== echo of input deck ============================== E echo E geometry units bohr E H -1.311364448397 0.571853917270 -2.039061637661 E F -1.222314592045 2.286447787232 -2.273810711375 E E end E memory 879931424 double E charge 0 E E basis spherical E H library cc-pvdz E bqH library H cc-pvdz E F library cc-pvdz E bqF library F cc-pvdz E end E E scf E thresh 1e-06 E end E E task scf gradient E E E python E grad = rtdb_get('scf:gradient') E if ga_nodeid() == 0: E import json E with open('nwchem.grad', 'w') as fp: E json.dump(grad, fp) E end E E task python E E ================================================================================ E E E E E E E Northwest Computational Chemistry Package (NWChem) 7.0.2 E -------------------------------------------------------- E E E Environmental Molecular Sciences Laboratory E Pacific Northwest National Laboratory E Richland, WA 99352 E E Copyright (c) 1994-2020 E Pacific Northwest National Laboratory E Battelle Memorial Institute E E NWChem is an open-source computational chemistry package E distributed under the terms of the E Educational Community License (ECL) 2.0 E A copy of the license is included with this distribution E in the LICENSE.TXT file E E ACKNOWLEDGMENT E -------------- E E This software and its documentation were developed at the E EMSL at Pacific Northwest National Laboratory, a multiprogram E national laboratory, operated for the U.S. Department of Energy E by Battelle under Contract Number DE-AC05-76RL01830. Support E for this work was provided by the Department of Energy Office E of Biological and Environmental Research, Office of Basic E Energy Sciences, and the Office of Advanced Scientific Computing. E E E Job information E --------------- E E hostname = yv.noip.me E program = /usr/local/bin/nwchem E date = Thu Oct 21 12:46:59 2021 E E compiled = Thu_Oct_21_12:11:03_2021 E source = /disk-samsung/freebsd-ports/science/nwchem/work/nwchem-7.0.2-release/src/.. E nwchem branch = 7.0.2 E nwchem revision = 11-eol-2499-gbbee7e139269 E ga revision = 5.8.0 E use scalapack = T E input = nwchem.nw E prefix = nwchem. E data base = ./nwchem.db E status = startup E nproc = 1 E time left = -1s E E E E Memory information E ------------------ E E heap = 219982852 doubles = 1678.3 Mbytes E stack = 219982857 doubles = 1678.3 Mbytes E global = 439965712 doubles = 3356.7 Mbytes (distinct from heap & stack) E total = 879931421 doubles = 6713.3 Mbytes E verify = yes E hardfail = no E E E Directory information E --------------------- E E 0 permanent = . E 0 scratch = . E E E E E NWChem Input Module E ------------------- E E E ORDER OF PRIMARY AXIS IS BEING SET TO 4 E C4V symmetry detected E E ------ E auto-z E ------ E no constraints, skipping 0.0000000000000000 E no constraints, skipping 0.0000000000000000 E E E Geometry "geometry" -> "" E ------------------------- E E Output coordinates in a.u. (scale by 1.000000000 to convert to a.u.) E E No. Tag Charge X Y Z E ---- ---------------- ---------- -------------- -------------- -------------- E 1 H 1.0000 0.00000000 0.00000000 -1.55959097 E 2 F 9.0000 0.00000000 0.00000000 0.17328789 E E Atomic Mass E ----------- E E H 1.007825 E F 18.998400 E E E Effective nuclear repulsion energy (a.u.) 5.1936694525 E E Nuclear Dipole moment (a.u.) E ---------------------------- E X Y Z E ---------------- ---------------- ---------------- E 0.0000000000 0.0000000000 0.0000000000 E E Symmetry information E -------------------- E E Group name C4v E Group number 18 E Group order 8 E No. of unique centers 2 E E Symmetry unique atoms E E 1 2 E E E E Z-matrix (autoz) E -------- E E Units are Angstrom for bonds and degrees for angles E E Type Name I J K L M Value E ----------- -------- ----- ----- ----- ----- ----- ---------- E 1 Stretch 1 2 0.91700 E E E XYZ format geometry E ------------------- E 2 E geometry E H 0.00000000 0.00000000 -0.82530006 E F 0.00000000 0.00000000 0.09170001 E E ============================================================================== E internuclear distances E ------------------------------------------------------------------------------ E center one | center two | atomic units | a.u. E ------------------------------------------------------------------------------ E 2 F | 1 H | 1.73288 | 1.73288 E ------------------------------------------------------------------------------ E number of included internuclear distances: 1 E ============================================================================== E E E E library name resolved from: .nwchemrc E library file name is: E E Basis "ao basis" -> "" (spherical) E ----- E H (Hydrogen) E ------------ E Exponent Coefficients E -------------- --------------------------------------------------------- E 1 S 1.30100000E+01 0.019685 E 1 S 1.96200000E+00 0.137977 E 1 S 4.44600000E-01 0.478148 E E 2 S 1.22000000E-01 1.000000 E E 3 P 7.27000000E-01 1.000000 E E bqH E --- E Exponent Coefficients E -------------- --------------------------------------------------------- E 1 S 1.30100000E+01 0.019685 E 1 S 1.96200000E+00 0.137977 E 1 S 4.44600000E-01 0.478148 E E 2 S 1.22000000E-01 1.000000 E E 3 P 7.27000000E-01 1.000000 E E F (Fluorine) E ------------ E Exponent Coefficients E -------------- --------------------------------------------------------- E 1 S 1.47100000E+04 0.000721 E 1 S 2.20700000E+03 0.005553 E 1 S 5.02800000E+02 0.028267 E 1 S 1.42600000E+02 0.106444 E 1 S 4.64700000E+01 0.286814 E 1 S 1.67000000E+01 0.448641 E 1 S 6.35600000E+00 0.264761 E 1 S 1.31600000E+00 0.015333 E E 2 S 1.47100000E+04 -0.000165 E 2 S 2.20700000E+03 -0.001308 E 2 S 5.02800000E+02 -0.006495 E 2 S 1.42600000E+02 -0.026691 E 2 S 4.64700000E+01 -0.073690 E 2 S 1.67000000E+01 -0.170776 E 2 S 6.35600000E+00 -0.112327 E 2 S 1.31600000E+00 0.562814 E E 3 S 3.89700000E-01 1.000000 E E 4 P 2.26700000E+01 0.044878 E 4 P 4.97700000E+00 0.235718 E 4 P 1.34700000E+00 0.508521 E E 5 P 3.47100000E-01 1.000000 E E 6 D 1.64000000E+00 1.000000 E E bqF E --- E Exponent Coefficients E -------------- --------------------------------------------------------- E 1 S 1.47100000E+04 0.000721 E 1 S 2.20700000E+03 0.005553 E 1 S 5.02800000E+02 0.028267 E 1 S 1.42600000E+02 0.106444 E 1 S 4.64700000E+01 0.286814 E 1 S 1.67000000E+01 0.448641 E 1 S 6.35600000E+00 0.264761 E 1 S 1.31600000E+00 0.015333 E E 2 S 1.47100000E+04 -0.000165 E 2 S 2.20700000E+03 -0.001308 E 2 S 5.02800000E+02 -0.006495 E 2 S 1.42600000E+02 -0.026691 E 2 S 4.64700000E+01 -0.073690 E 2 S 1.67000000E+01 -0.170776 E 2 S 6.35600000E+00 -0.112327 E 2 S 1.31600000E+00 0.562814 E E 3 S 3.89700000E-01 1.000000 E E 4 P 2.26700000E+01 0.044878 E 4 P 4.97700000E+00 0.235718 E 4 P 1.34700000E+00 0.508521 E E 5 P 3.47100000E-01 1.000000 E E 6 D 1.64000000E+00 1.000000 E E E E Summary of "ao basis" -> "" (spherical) E ------------------------------------------------------------------------------ E Tag Description Shells Functions and Types E ---------------- ------------------------------ ------ --------------------- E H cc-pvdz 3 5 2s1p E bqH cc-pvdz 3 5 2s1p E F cc-pvdz 6 14 3s2p1d E bqF cc-pvdz 6 14 3s2p1d E E E NWChem SCF Module E ----------------- E E E E ao basis = "ao basis" E functions = 19 E atoms = 2 E closed shells = 5 E open shells = 0 E charge = 0.00 E wavefunction = RHF E input vectors = atomic E output vectors = ./nwchem.movecs E use symmetry = T E symmetry adapt = T E E E Summary of "ao basis" -> "ao basis" (spherical) E ------------------------------------------------------------------------------ E Tag Description Shells Functions and Types E ---------------- ------------------------------ ------ --------------------- E H cc-pvdz 3 5 2s1p E bqH cc-pvdz 3 5 2s1p E F cc-pvdz 6 14 3s2p1d E bqF cc-pvdz 6 14 3s2p1d E E E Symmetry analysis of basis E -------------------------- E E a1 9 E a2 0 E b1 1 E b2 1 E e 8 E E E Forming initial guess at 0.0s E E E Superposition of Atomic Density Guess E ------------------------------------- E E Sum of atomic energies: -99.88314519 E E Non-variational initial energy E ------------------------------ E E Total energy = -99.865715 E 1-e energy = -149.649522 E 2-e energy = 44.590137 E HOMO = -0.637960 E LUMO = 0.109607 E E E Symmetry analysis of molecular orbitals - initial E ------------------------------------------------- E E E !! scf_movecs_sym_adapt: 2 vectors were symmetry contaminated E E Symmetry fudging E E !! scf_movecs_sym_adapt: 2 vectors were symmetry contaminated E E Numbering of irreducible representations: E E 1 a1 2 a2 3 b1 4 b2 5 e E E Orbital symmetries: E E 1 a1 2 a1 3 a1 4 e 5 e E 6 a1 7 a1 8 a1 9 e 10 e E 11 e 12 e 13 a1 14 a1 15 b2 E E E Starting SCF solution at 0.1s E E E E ---------------------------------------------- E Quadratically convergent ROHF E E Convergence threshold : 1.000E-06 E Maximum no. of iterations : 30 E Final Fock-matrix accuracy: 1.000E-08 E ---------------------------------------------- E E E #quartets = 1.035D+03 #integrals = 4.841D+03 #direct = 0.0% #cached =100.0% E E E Integral file = ./nwchem.aoints.0 E Record size in doubles = 65536 No. of integs per rec = 43688 E Max. records in memory = 2 Max. records in file = 124808 E No. of bits per label = 8 No. of bits per value = 64 E E E iter energy gnorm gmax time E ----- ------------------- --------- --------- -------- E 1 -99.9944094325 7.27D-01 3.80D-01 0.1 E 2 -100.0177379586 1.62D-01 6.40D-02 0.2 E 3 -100.0193962961 1.41D-02 6.21D-03 0.2 E 4 -100.0194112693 2.02D-05 8.98D-06 0.2 E 5 -100.0194112693 4.87D-08 2.24D-08 0.2 E E E Final RHF results E ------------------ E E Total SCF energy = -100.019411269300 E One-electron energy = -150.693050028556 E Two-electron energy = 45.479969306796 E Nuclear repulsion energy = 5.193669452461 E E Time for solution = 0.1s E E E E Symmetry analysis of molecular orbitals - final E ----------------------------------------------- E E Numbering of irreducible representations: E E 1 a1 2 a2 3 b1 4 b2 5 e E E Orbital symmetries: E E 1 a1 2 a1 3 a1 4 e 5 e E 6 a1 7 a1 8 e 9 e 10 a1 E 11 e 12 e 13 a1 14 a1 15 b2 E E Final eigenvalues E ----------------- E E 1 E 1 -26.2781 E 2 -1.5835 E 3 -0.7472 E 4 -0.6289 E 5 -0.6289 E 6 0.1838 E 7 0.8100 E 8 1.4119 E 9 1.4119 E 10 1.4156 E 11 1.6041 E 12 1.6041 E 13 2.1341 E 14 2.4989 E 15 4.0044 E E ROHF Final Molecular Orbital Analysis E ------------------------------------- E E Vector 2 Occ=2.000000D+00 E=-1.583452D+00 Symmetry=a1 E MO Center= -8.5D-17, -1.5D-16, -2.4D-02, r^2= 3.7D-01 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 7 0.481194 2 F s 8 0.480605 2 F s E 1 0.174632 1 H s E E Vector 3 Occ=2.000000D+00 E=-7.471972D-01 Symmetry=a1 E MO Center= 5.4D-17, 1.4D-16, -1.4D-02, r^2= 5.6D-01 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 11 0.555850 2 F pz 1 -0.387490 1 H s E 14 0.299645 2 F pz 8 0.289834 2 F s E E Vector 4 Occ=2.000000D+00 E=-6.288892D-01 Symmetry=e E MO Center= -1.5D-17, -9.2D-17, 7.5D-02, r^2= 4.4D-01 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 10 0.532129 2 F py 9 0.397810 2 F px E 13 0.380643 2 F py 12 0.284562 2 F px E E Vector 5 Occ=2.000000D+00 E=-6.288892D-01 Symmetry=e E MO Center= -1.9D-16, -4.5D-17, 7.5D-02, r^2= 4.4D-01 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 9 0.532129 2 F px 10 -0.397810 2 F py E 12 0.380643 2 F px 13 -0.284562 2 F py E E Vector 6 Occ=0.000000D+00 E= 1.838400D-01 Symmetry=a1 E MO Center= -2.5D-16, -4.6D-16, -1.0D+00, r^2= 2.1D+00 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 2 1.265475 1 H s 8 -0.670151 2 F s E 14 0.336135 2 F pz 11 0.217915 2 F pz E E Vector 7 Occ=0.000000D+00 E= 8.100489D-01 Symmetry=a1 E MO Center= 1.0D-16, 9.1D-16, -8.0D-01, r^2= 1.1D+00 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 1 1.275533 1 H s 2 -0.907033 1 H s E 11 0.370721 2 F pz 5 -0.327559 1 H pz E 14 0.194975 2 F pz E E Vector 8 Occ=0.000000D+00 E= 1.411878D+00 Symmetry=e E MO Center= 9.4D-16, 2.5D-15, -2.1D-01, r^2= 8.6D-01 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 10 0.795314 2 F py 13 -0.704211 2 F py E 4 -0.407398 1 H py 9 0.301193 2 F px E 12 -0.266691 2 F px 3 -0.154285 1 H px E E Vector 9 Occ=0.000000D+00 E= 1.411878D+00 Symmetry=e E MO Center= 1.2D-15, -4.5D-16, -2.1D-01, r^2= 8.6D-01 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 9 0.795314 2 F px 12 -0.704211 2 F px E 3 -0.407398 1 H px 10 -0.301193 2 F py E 13 0.266691 2 F py 4 0.154285 1 H py E E Vector 10 Occ=0.000000D+00 E= 1.415619D+00 Symmetry=a1 E MO Center= -6.6D-15, -4.9D-15, 4.9D-01, r^2= 9.0D-01 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 14 1.618091 2 F pz 1 1.084020 1 H s E 11 -0.644892 2 F pz 8 -0.591943 2 F s E 5 0.513224 1 H pz 7 -0.226860 2 F s E E Vector 11 Occ=0.000000D+00 E= 1.604149D+00 Symmetry=e E MO Center= 2.6D-15, -1.3D-15, -4.0D-01, r^2= 1.0D+00 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 3 0.881763 1 H px 12 -0.773335 2 F px E 4 -0.429656 1 H py 13 0.376822 2 F py E 9 0.351250 2 F px 10 -0.171153 2 F py E E Vector 12 Occ=0.000000D+00 E= 1.604149D+00 Symmetry=e E MO Center= 1.9D-15, 3.8D-15, -4.0D-01, r^2= 1.0D+00 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 4 0.881763 1 H py 13 -0.773335 2 F py E 3 0.429656 1 H px 12 -0.376822 2 F px E 10 0.351250 2 F py 9 0.171153 2 F px E E Vector 13 Occ=0.000000D+00 E= 2.134096D+00 Symmetry=a1 E MO Center= 2.4D-16, -8.3D-17, -1.1D-01, r^2= 9.6D-01 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 8 2.403587 2 F s 7 -1.664197 2 F s E 6 -0.716261 2 F s 14 -0.714895 2 F pz E 1 -0.707619 1 H s 2 -0.543054 1 H s E 5 -0.349676 1 H pz E E Vector 14 Occ=0.000000D+00 E= 2.498873D+00 Symmetry=a1 E MO Center= 6.7D-17, 9.3D-17, -6.9D-01, r^2= 6.0D-01 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 5 1.405944 1 H pz 8 -0.968301 2 F s E 1 0.776130 1 H s 11 0.759152 2 F pz E 14 0.288474 2 F pz 2 0.275079 1 H s E 7 -0.249146 2 F s E E Vector 15 Occ=0.000000D+00 E= 4.004354D+00 Symmetry=b2 E MO Center= -1.2D-17, 5.8D-19, 9.2D-02, r^2= 3.0D-01 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 15 1.000000 2 F d -2 E E E center of mass E -------------- E x = 0.00000000 y = 0.00000000 z = 0.08599312 E E moments of inertia (a.u.) E ------------------ E 2.873911650432 0.000000000000 0.000000000000 E 0.000000000000 2.873911650432 0.000000000000 E 0.000000000000 0.000000000000 0.000000000000 E E Mulliken analysis of the total density E -------------------------------------- E E Atom Charge Shell Charges E ----------- ------ ------------------------------------------------------- E 1 H 1 0.76 0.63 0.03 0.11 E 2 F 9 9.24 2.00 0.89 0.97 3.32 2.05 0.00 E E Multipole analysis of the density wrt the origin E ------------------------------------------------ E E L x y z total open nuclear E - - - - ----- ---- ------- E 0 0 0 0 -0.000000 0.000000 10.000000 E E 1 1 0 0 0.000000 0.000000 0.000000 E 1 0 1 0 0.000000 0.000000 0.000000 E 1 0 0 1 -0.767022 0.000000 0.000000 E E 2 2 0 0 -4.007314 0.000000 0.000000 E 2 1 1 0 -0.000000 0.000000 0.000000 E 2 1 0 1 -0.000000 0.000000 0.000000 E 2 0 2 0 -4.007314 0.000000 0.000000 E 2 0 1 1 -0.000000 0.000000 0.000000 E 2 0 0 2 -2.493425 0.000000 2.702582 E E E Parallel integral file used 1 records with 0 large values E E NWChem Gradients Module E ----------------------- E E E E wavefunction = RHF E E Using symmetry E E STDERR: E E Program received signal SIGSEGV: Segmentation fault - invalid memory reference. E E Backtrace for this error: E #0 0x804a1f6db in ??? E #1 0x804a1e896 in ??? E #2 0x803729f6f in handle_signal E at /disk-samsung/freebsd-src/lib/libthr/thread/thr_sig.c:303 E #3 0x80372953e in thr_sighandler E at /disk-samsung/freebsd-src/lib/libthr/thread/thr_sig.c:246 E #4 0x7ffffffff192 in ??? E #5 0x803dd91b1 in ??? E #6 0x803badeb5 in ??? E #7 0x803298434 in ??? E #8 0x80329901d in ??? E #9 0x802f076a9 in ??? E #10 0x802e70b74 in ??? E #11 0x9f45dc in ??? E #12 0x9e382f in ??? E #13 0x7ebc84 in ??? E #14 0x7e6a23 in ??? E #15 0x7fdbf4 in ??? E #16 0x7ec987 in ??? E #17 0x4219d7 in ??? E #18 0x422db0 in ??? E #19 0x41462d in ??? E #20 0x40e0e1 in ??? E #21 0x40c71c in ??? E #22 0x40c82f in ??? E E TRACEBACK: E Traceback (most recent call last): E File "/disk-samsung/freebsd-ports/science/py-qcengine/work-py38/qcengine-0.20.1/qcengine/programs/nwchem/runner.py", line 275, in parse_output E retres = qcvars[f"CURRENT {input_model.driver.upper()}"] E KeyError: 'CURRENT GRADIENT' qcengine/programs/nwchem/runner.py:277: UnknownError ___________ test_hf_alignment[hf uhf ae: nwchem-dz-grd1-free-SRM9] ____________ self = NWChemHarness(name='NWChem', scratch=True, thread_safe=False, thread_parallel=False, node_parallel=True, managed_memory=True, extras=None, version_cache={'/usr/local/bin/nwchem': '7.0.2+11.eol.2499.gbbee7e139269'}) outfiles = {'nwchem.grad': None, 'nwchem.hess': None} input_model = AtomicInput(driver='gradient', model={'method': 'hf', 'basis': 'cc-pvdz'}, molecule_hash='96d24d8') def parse_output( self, outfiles: Dict[str, str], input_model: "AtomicInput" ) -> AtomicResult: # lgtm: [py/similar-function] # Get the stdout from the calculation (required) stdout = outfiles.pop("stdout") stderr = outfiles.pop("stderr") method = input_model.model.method.lower() method = method[4:] if method.startswith("nwc-") else method # Read the NWChem stdout file and, if needed, the hess or grad files # July 2021: nwmol & vector returns now atin/outfile orientation depending on fix_com,orientation=T/F. previously always atin orientation try: qcvars, nwhess, nwgrad, nwmol, version, module, errorTMP = harvest( input_model.molecule, method, stdout, **outfiles ) except Exception as e: raise UnknownError(error_stamp(stdout=stdout, stderr=stderr)) try: if nwgrad is not None: qcvars[f"{method.upper()} TOTAL GRADIENT"] = nwgrad qcvars["CURRENT GRADIENT"] = nwgrad if nwhess is not None: qcvars[f"{method.upper()} TOTAL HESSIAN"] = nwhess qcvars["CURRENT HESSIAN"] = nwhess # Normalize the output as a float or list of floats if input_model.driver.upper() == "PROPERTIES": retres = qcvars[f"CURRENT ENERGY"] else: > retres = qcvars[f"CURRENT {input_model.driver.upper()}"] E KeyError: 'CURRENT GRADIENT' qcengine/programs/nwchem/runner.py:275: KeyError During handling of the above exception, another exception occurred: inp = {'call': 'nwchem', 'fcae': 'ae', 'keywords': {'scf__thresh': 1e-06, 'scf__uhf': True}, 'reference': 'uhf'} scramble = {'do_resort': True, 'do_rotate': True, 'do_shift': True} frame = 'free', driver = 'gradient', basis = 'cc-pvdz' subjects = ['hf', 'bh3p', 'bh3p'] clsd_open_pmols = {'bh3p': Molecule(name='bh3p', formula='BH3', hash='f532294'), 'bh3p-fixed': Molecule(name='bh3p', formula='BH3', hash...cule(name='h2o', formula='H2O', hash='4684da5'), 'h2o-fixed': Molecule(name='h2o', formula='H2O', hash='4684da5'), ...} request = > @pytest.mark.parametrize( "scramble", # * this parameter alters the input molecule by Cartesian frame and/or atom ordering to imitate real-world inputs. # * scramble dictionary are arguments to qcdb.Molecule.scramble() or qcel.models.Molecule.scramble() that computes a shifted/rotated/atom-mapped input molecule from `subjects` below and the transformations to be applied to the reference data. # * arguments do_shift=T/F and other boolean values generate random perturbations, so multiple lines or runs makes a fuller test. # * specific shifts etc or problematic runs can be reproduced by specifying arrays like the commented example below. note that b/c do_resort is natom-dependent, may need to exclude subjects while debugging. # * `id`s below are numbered since `pytest -k` doesn't recognize case and so duplicate entries can be added. the 0, 1, 2, 3, 9 progression is handy for debugging since perturbations are added systematically [ # pytest.param({"do_shift": [ 2.660760432055, 1.477336796939, -2.098045335573], "do_rotate": [[ 0.321861140022, 0.445246880671, 0.835560064745], [-0.447874157747, 0.849136107328, -0.279958229125], [-0.834154749052, -0.28411808546 , 0.472718487209]], "do_resort": [2, 0, 1]}, id="mTTT3"), # pytest.param({"do_shift": False, "do_rotate": False, "do_resort": False}, id="srm0"), # pytest.param({"do_shift": True, "do_rotate": False, "do_resort": False}, id="Srm1"), # pytest.param({"do_shift": True, "do_rotate": True, "do_resort": False}, id="SRm2"), # pytest.param({"do_shift": False, "do_rotate": False, "do_resort": True}, id="srM3"), # pytest.param({"do_shift": True, "do_rotate": True, "do_resort": True}, id="SRM8"), pytest.param({"do_shift": True, "do_rotate": True, "do_resort": True}, id="SRM9"), ], ) @pytest.mark.parametrize( "frame", # * this parameter alters the input molecule by fix_com and fix_orientation to imitate user signaling frame matters or not. [ pytest.param("fixed"), # fix_=True (no_com/no_reorient); atres.mol.geom = atin.mol.geom aka scrambled pytest.param("free"), # fix_=False (def) ; atres.mol.geom = dsl internal orientation ], ) @pytest.mark.parametrize( "driver", [ pytest.param("energy", id="ene0"), pytest.param("gradient", id="grd1"), pytest.param("hessian", id="hes2"), ], ) @pytest.mark.parametrize( "basis, subjects", # this parameter, along with rhf/uhf below covers four different molecules, with nat=2-4. [ pytest.param("cc-pvdz", ["hf", "bh3p", "bh3p"], id="dz"), pytest.param("aug-cc-pvdz", ["h2o", "nh2", "nh2"], id="adz", marks=pytest.mark.long), ], ) @pytest.mark.parametrize( "inp", [ # yapf: disable pytest.param({"call": "cfour", "reference": "rhf", "fcae": "ae", "keywords": {"scf_conv": 12}, }, id="hf rhf ae: cfour", marks=using("cfour")), pytest.param({"call": "gamess", "reference": "rhf", "fcae": "ae", "keywords": {}, }, id="hf rhf ae: gamess", marks=using("gamess")), pytest.param({"call": "nwchem", "reference": "rhf", "fcae": "ae", "keywords": {"scf__thresh": 1.e-6}, }, id="hf rhf ae: nwchem", marks=using("nwchem")), pytest.param({"call": "psi4", "reference": "rhf", "fcae": "ae", "keywords": {"scf_type": "pk"}, }, id="hf rhf ae: psi4", marks=using("psi4_derqcsk")), pytest.param({"call": "cfour", "reference": "uhf", "fcae": "ae", "keywords": {"reference": "uhf", "scf_conv": 12}, }, id="hf uhf ae: cfour", marks=using("cfour")), pytest.param({"call": "gamess", "reference": "uhf", "fcae": "ae", "keywords": {"contrl__scftyp": "uhf"}, }, id="hf uhf ae: gamess", marks=using("gamess")), pytest.param({"call": "nwchem", "reference": "uhf", "fcae": "ae", "keywords": {"scf__uhf": True, "scf__thresh": 1.e-6}, }, id="hf uhf ae: nwchem", marks=using("nwchem")), pytest.param({"call": "psi4", "reference": "uhf", "fcae": "ae", "keywords": {"reference": "uhf", "scf_type": "pk"}, }, id="hf uhf ae: psi4", marks=using("psi4_derqcsk")), # yapf: enable ], ) def test_hf_alignment(inp, scramble, frame, driver, basis, subjects, clsd_open_pmols, request): > runner_asserter( *_processor(inp, "", basis, subjects, clsd_open_pmols, request, driver, "hf", scramble=scramble, frame=frame) ) qcengine/programs/tests/test_alignment.py:96: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ qcengine/programs/tests/standard_suite_runner.py:177: in runner_asserter wfn = qcng.compute(atin, qcprog, raise_error=True, local_options=local_options) qcengine/compute.py:91: in compute output_data = executor.compute(input_data, config) qcengine/programs/model.py:116: in compute result = self._compute(local_input_data, config) qcengine/programs/nwchem/runner.py:137: in _compute return self.parse_output(dexe["outfiles"], input_model) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = NWChemHarness(name='NWChem', scratch=True, thread_safe=False, thread_parallel=False, node_parallel=True, managed_memory=True, extras=None, version_cache={'/usr/local/bin/nwchem': '7.0.2+11.eol.2499.gbbee7e139269'}) outfiles = {'nwchem.grad': None, 'nwchem.hess': None} input_model = AtomicInput(driver='gradient', model={'method': 'hf', 'basis': 'cc-pvdz'}, molecule_hash='96d24d8') def parse_output( self, outfiles: Dict[str, str], input_model: "AtomicInput" ) -> AtomicResult: # lgtm: [py/similar-function] # Get the stdout from the calculation (required) stdout = outfiles.pop("stdout") stderr = outfiles.pop("stderr") method = input_model.model.method.lower() method = method[4:] if method.startswith("nwc-") else method # Read the NWChem stdout file and, if needed, the hess or grad files # July 2021: nwmol & vector returns now atin/outfile orientation depending on fix_com,orientation=T/F. previously always atin orientation try: qcvars, nwhess, nwgrad, nwmol, version, module, errorTMP = harvest( input_model.molecule, method, stdout, **outfiles ) except Exception as e: raise UnknownError(error_stamp(stdout=stdout, stderr=stderr)) try: if nwgrad is not None: qcvars[f"{method.upper()} TOTAL GRADIENT"] = nwgrad qcvars["CURRENT GRADIENT"] = nwgrad if nwhess is not None: qcvars[f"{method.upper()} TOTAL HESSIAN"] = nwhess qcvars["CURRENT HESSIAN"] = nwhess # Normalize the output as a float or list of floats if input_model.driver.upper() == "PROPERTIES": retres = qcvars[f"CURRENT ENERGY"] else: retres = qcvars[f"CURRENT {input_model.driver.upper()}"] except KeyError as e: > raise UnknownError(error_stamp(stdout=stdout, stderr=stderr)) E qcengine.exceptions.UnknownError: STDOUT: E E E E ============================== echo of input deck ============================== E echo E geometry units bohr E B -1.159833210256 -1.751039165054 1.781558984342 E H 0.363850363318 -3.517850652388 1.906899932953 E H -5.167492355814 1.983502578635 1.117523876554 E H -4.290792499041 2.792117474457 1.858358512607 E E end E memory 879931424 double E charge 1 E E basis spherical E H library cc-pvdz E bqH library H cc-pvdz E B library cc-pvdz E bqB library B cc-pvdz E end E E dft E mult 2 E end E E mcscf E multiplicity 2 E end E E scf E uhf E thresh 1e-06 E nopen 1 E end E E task scf gradient E E E python E grad = rtdb_get('scf:gradient') E if ga_nodeid() == 0: E import json E with open('nwchem.grad', 'w') as fp: E json.dump(grad, fp) E end E E task python E E ================================================================================ E E E E E E E Northwest Computational Chemistry Package (NWChem) 7.0.2 E -------------------------------------------------------- E E E Environmental Molecular Sciences Laboratory E Pacific Northwest National Laboratory E Richland, WA 99352 E E Copyright (c) 1994-2020 E Pacific Northwest National Laboratory E Battelle Memorial Institute E E NWChem is an open-source computational chemistry package E distributed under the terms of the E Educational Community License (ECL) 2.0 E A copy of the license is included with this distribution E in the LICENSE.TXT file E E ACKNOWLEDGMENT E -------------- E E This software and its documentation were developed at the E EMSL at Pacific Northwest National Laboratory, a multiprogram E national laboratory, operated for the U.S. Department of Energy E by Battelle under Contract Number DE-AC05-76RL01830. Support E for this work was provided by the Department of Energy Office E of Biological and Environmental Research, Office of Basic E Energy Sciences, and the Office of Advanced Scientific Computing. E E E Job information E --------------- E E hostname = yv.noip.me E program = /usr/local/bin/nwchem E date = Thu Oct 21 12:47:29 2021 E E compiled = Thu_Oct_21_12:11:03_2021 E source = /disk-samsung/freebsd-ports/science/nwchem/work/nwchem-7.0.2-release/src/.. E nwchem branch = 7.0.2 E nwchem revision = 11-eol-2499-gbbee7e139269 E ga revision = 5.8.0 E use scalapack = T E input = nwchem.nw E prefix = nwchem. E data base = ./nwchem.db E status = startup E nproc = 1 E time left = -1s E E E E Memory information E ------------------ E E heap = 219982852 doubles = 1678.3 Mbytes E stack = 219982857 doubles = 1678.3 Mbytes E global = 439965712 doubles = 3356.7 Mbytes (distinct from heap & stack) E total = 879931421 doubles = 6713.3 Mbytes E verify = yes E hardfail = no E E E Directory information E --------------------- E E 0 permanent = . E 0 scratch = . E E E E E NWChem Input Module E ------------------- E E E CS symmetry detected E E ------ E auto-z E ------ E autoz: The atoms group into disjoint clusters E cluster 1: 1 2 E cluster 2: 3 4 E Connecting clusters 1 2 via atoms 1 3 r = 2.92 E autoz: regenerating connections with new bonds E no constraints, skipping 0.0000000000000000 E no constraints, skipping 0.0000000000000000 E E E Geometry "geometry" -> "" E ------------------------- E E Output coordinates in a.u. (scale by 1.000000000 to convert to a.u.) E E No. Tag Charge X Y Z E ---- ---------------- ---------- -------------- -------------- -------------- E 1 B 5.0000 -0.00000000 1.07625282 0.00000000 E 2 H 1.0000 0.00000000 3.41269131 0.00000000 E 3 H 1.0000 0.00000000 -4.39697770 -0.70201436 E 4 H 1.0000 0.00000000 -4.39697770 0.70201436 E E Atomic Mass E ----------- E E B 11.009310 E H 1.007825 E E E Effective nuclear repulsion energy (a.u.) 4.9195381997 E E Nuclear Dipole moment (a.u.) E ---------------------------- E X Y Z E ---------------- ---------------- ---------------- E 0.0000000000 0.0000000000 0.0000000000 E E Symmetry information E -------------------- E E Group name Cs E Group number 2 E Group order 2 E No. of unique centers 3 E E Symmetry unique atoms E E 1 2 3 E E E E Z-matrix (autoz) E -------- E E Units are Angstrom for bonds and degrees for angles E E Type Name I J K L M Value E ----------- -------- ----- ----- ----- ----- ----- ---------- E 1 Stretch 1 3 2.92004 E 2 Stretch 1 2 1.23639 E 3 Stretch 3 4 0.74298 E 4 Bend 1 3 4 82.69096 E 5 Bend 2 1 3 172.69096 E 6 Torsion 2 1 3 4 180.00000 E E E XYZ format geometry E ------------------- E 4 E geometry E B -0.00000000 0.56952851 0.00000000 E H 0.00000000 1.80591860 0.00000000 E H 0.00000000 -2.32678056 -0.37149003 E H 0.00000000 -2.32678056 0.37149003 E E ============================================================================== E internuclear distances E ------------------------------------------------------------------------------ E center one | center two | atomic units | a.u. E ------------------------------------------------------------------------------ E 2 H | 1 B | 2.33644 | 2.33644 E ------------------------------------------------------------------------------ E number of included internuclear distances: 1 E ============================================================================== E E E E library name resolved from: .nwchemrc E library file name is: E E Basis "ao basis" -> "" (spherical) E ----- E H (Hydrogen) E ------------ E Exponent Coefficients E -------------- --------------------------------------------------------- E 1 S 1.30100000E+01 0.019685 E 1 S 1.96200000E+00 0.137977 E 1 S 4.44600000E-01 0.478148 E E 2 S 1.22000000E-01 1.000000 E E 3 P 7.27000000E-01 1.000000 E E bqH E --- E Exponent Coefficients E -------------- --------------------------------------------------------- E 1 S 1.30100000E+01 0.019685 E 1 S 1.96200000E+00 0.137977 E 1 S 4.44600000E-01 0.478148 E E 2 S 1.22000000E-01 1.000000 E E 3 P 7.27000000E-01 1.000000 E E B (Boron) E --------- E Exponent Coefficients E -------------- --------------------------------------------------------- E 1 S 4.57000000E+03 0.000696 E 1 S 6.85900000E+02 0.005353 E 1 S 1.56500000E+02 0.027134 E 1 S 4.44700000E+01 0.101380 E 1 S 1.44800000E+01 0.272055 E 1 S 5.13100000E+00 0.448403 E 1 S 1.89800000E+00 0.290123 E 1 S 3.32900000E-01 0.014322 E E 2 S 4.57000000E+03 -0.000139 E 2 S 6.85900000E+02 -0.001097 E 2 S 1.56500000E+02 -0.005444 E 2 S 4.44700000E+01 -0.021916 E 2 S 1.44800000E+01 -0.059751 E 2 S 5.13100000E+00 -0.138732 E 2 S 1.89800000E+00 -0.131482 E 2 S 3.32900000E-01 0.539526 E E 3 S 1.04300000E-01 1.000000 E E 4 P 6.00100000E+00 0.035481 E 4 P 1.24100000E+00 0.198072 E 4 P 3.36400000E-01 0.505230 E E 5 P 9.53800000E-02 1.000000 E E 6 D 3.43000000E-01 1.000000 E E bqB E --- E Exponent Coefficients E -------------- --------------------------------------------------------- E 1 S 4.57000000E+03 0.000696 E 1 S 6.85900000E+02 0.005353 E 1 S 1.56500000E+02 0.027134 E 1 S 4.44700000E+01 0.101380 E 1 S 1.44800000E+01 0.272055 E 1 S 5.13100000E+00 0.448403 E 1 S 1.89800000E+00 0.290123 E 1 S 3.32900000E-01 0.014322 E E 2 S 4.57000000E+03 -0.000139 E 2 S 6.85900000E+02 -0.001097 E 2 S 1.56500000E+02 -0.005444 E 2 S 4.44700000E+01 -0.021916 E 2 S 1.44800000E+01 -0.059751 E 2 S 5.13100000E+00 -0.138732 E 2 S 1.89800000E+00 -0.131482 E 2 S 3.32900000E-01 0.539526 E E 3 S 1.04300000E-01 1.000000 E E 4 P 6.00100000E+00 0.035481 E 4 P 1.24100000E+00 0.198072 E 4 P 3.36400000E-01 0.505230 E E 5 P 9.53800000E-02 1.000000 E E 6 D 3.43000000E-01 1.000000 E E E E Summary of "ao basis" -> "" (spherical) E ------------------------------------------------------------------------------ E Tag Description Shells Functions and Types E ---------------- ------------------------------ ------ --------------------- E H cc-pvdz 3 5 2s1p E bqH cc-pvdz 3 5 2s1p E B cc-pvdz 6 14 3s2p1d E bqB cc-pvdz 6 14 3s2p1d E E E NWChem SCF Module E ----------------- E E E E ao basis = "ao basis" E functions = 29 E atoms = 4 E alpha electrons = 4 E beta electrons = 3 E charge = 1.00 E wavefunction = UHF E input vectors = atomic E output vectors = ./nwchem.movecs E use symmetry = T E symmetry adapt = T E E E Summary of "ao basis" -> "ao basis" (spherical) E ------------------------------------------------------------------------------ E Tag Description Shells Functions and Types E ---------------- ------------------------------ ------ --------------------- E H cc-pvdz 3 5 2s1p E bqH cc-pvdz 3 5 2s1p E B cc-pvdz 6 14 3s2p1d E bqB cc-pvdz 6 14 3s2p1d E E E Symmetry analysis of basis E -------------------------- E E a' 19 E a" 10 E E E Forming initial guess at 0.0s E E E Superposition of Atomic Density Guess E ------------------------------------- E E Sum of atomic energies: -26.03078371 E E Renormalizing density from 8.00 to 7 E E Non-variational initial energy E ------------------------------ E E Total energy = -23.356783 E 1-e energy = -37.930394 E 2-e energy = 9.654074 E HOMO = -0.541143 E LUMO = -0.369125 E E E Symmetry analysis of molecular orbitals - initial alpha E ------------------------------------------------------- E E Numbering of irreducible representations: E E 1 a' 2 a" E E Orbital symmetries: E E 1 a' 2 a' 3 a' 4 a' 5 a" E 6 a' 7 a" 8 a' 9 a' 10 a' E 11 a" 12 a' 13 a' 14 a' E E E Symmetry analysis of molecular orbitals - initial beta E ------------------------------------------------------ E E Numbering of irreducible representations: E E 1 a' 2 a" E E Orbital symmetries: E E 1 a' 2 a' 3 a' 4 a' 5 a" E 6 a' 7 a" 8 a' 9 a' 10 a' E 11 a" 12 a' 13 a' 14 a' E E E Starting SCF solution at 0.1s E E E E ---------------------------------------------- E Quadratically convergent UHF E E Convergence threshold : 1.000E-06 E Maximum no. of iterations : 30 E Integral*density screening: 1.000E-08 E ---------------------------------------------- E E E #quartets = 4.385D+03 #integrals = 2.659D+04 #direct = 0.0% #cached =100.0% E E E Integral file = ./nwchem.aoints.0 E Record size in doubles = 65536 No. of integs per rec = 43688 E Max. records in memory = 4 Max. records in file = 124666 E No. of bits per label = 8 No. of bits per value = 64 E E E iter energy gnorm gmax time E ----- ------------------- --------- --------- -------- E 1 -25.9180776106 2.39D-01 1.30D-01 0.2 E 2 -25.9425949473 1.02D-01 4.13D-02 0.3 E 3 -25.9450986421 9.04D-03 3.62D-03 0.3 E 4 -25.9451384267 4.23D-05 2.22D-05 0.4 E 5 -25.9451384275 4.21D-08 1.45D-08 0.5 E E E Final UHF results E ------------------ E E Total SCF energy = -25.945138427483 E One electron energy = -41.231566793914 E Two electron energy = 10.366890166699 E Nuclear repulsion energy = 4.919538199732 E E Sz = 0.5000 E Sz(Sz+1) = 0.7500 E S^2 = 0.7561 E E Time for solution = 0.4s E E E E Symmetry analysis of molecular orbitals - alpha E ----------------------------------------------- E E Numbering of irreducible representations: E E 1 a' 2 a" E E Orbital symmetries: E E 1 a' 2 a' 3 a' 4 a' 5 a" E 6 a' 7 a' 8 a" 9 a' 10 a' E 11 a" 12 a' 13 a' 14 a' E E E Symmetry analysis of molecular orbitals - beta E ---------------------------------------------- E E Numbering of irreducible representations: E E 1 a' 2 a" E E Orbital symmetries: E E 1 a' 2 a' 3 a' 4 a' 5 a" E 6 a' 7 a' 8 a" 9 a' 10 a' E 11 a" 12 a' 13 a' 14 a' E E Final alpha eigenvalues E ----------------------- E E 1 E 1 -8.1252 E 2 -1.0028 E 3 -0.8149 E 4 -0.7527 E 5 -0.2658 E 6 -0.2653 E 7 -0.0033 E 8 0.0346 E 9 0.1374 E 10 0.1737 E 11 0.1852 E 12 0.1870 E 13 0.3755 E 14 0.4824 E E Final beta eigenvalues E ---------------------- E E 1 E 1 -8.0993 E 2 -0.9423 E 3 -0.7607 E 4 -0.2719 E 5 -0.2266 E 6 -0.2261 E 7 0.0300 E 8 0.0357 E 9 0.1561 E 10 0.1930 E 11 0.2052 E 12 0.2792 E 13 0.3851 E 14 0.5236 E E UHF Final Alpha Molecular Orbital Analysis E ------------------------------------------ E E Vector 2 Occ=1.000000D+00 E=-1.002800D+00 Symmetry=a' E MO Center= 3.7D-14, 1.1D+00, -6.4D-17, r^2= 1.0D+00 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 2 0.492039 1 B s 15 0.356568 2 H s E 3 0.268302 1 B s E E Vector 3 Occ=1.000000D+00 E=-8.148572D-01 Symmetry=a' E MO Center= -6.4D-14, -1.7D-01, 1.1D-18, r^2= 2.3D+00 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 5 0.524956 1 B py 2 -0.287247 1 B s E 15 0.250333 2 H s 3 -0.229648 1 B s E 20 -0.178467 3 H s 25 -0.178467 4 H s E 8 0.153927 1 B py E E Vector 4 Occ=1.000000D+00 E=-7.526730D-01 Symmetry=a' E MO Center= -2.3D-14, -1.7D+00, 4.0D-17, r^2= 2.1D+00 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 20 0.369617 3 H s 25 0.369617 4 H s E 5 0.299059 1 B py 2 -0.206142 1 B s E 3 -0.177075 1 B s 21 0.153232 3 H s E 26 0.153232 4 H s E E Vector 5 Occ=0.000000D+00 E=-2.658293D-01 Symmetry=a" E MO Center= -3.0D-14, 5.6D-01, -8.1D-17, r^2= 1.9D+00 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 6 0.582936 1 B pz 9 0.546644 1 B pz E E Vector 6 Occ=0.000000D+00 E=-2.653212D-01 Symmetry=a' E MO Center= -2.3D-13, 5.7D-01, -6.7D-16, r^2= 1.9D+00 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 4 0.584131 1 B px 7 0.548015 1 B px E E Vector 7 Occ=0.000000D+00 E=-3.254915D-03 Symmetry=a' E MO Center= 2.4D-13, 1.6D+00, -5.2D-17, r^2= 2.9D+00 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 16 2.513675 2 H s 3 -1.726187 1 B s E 8 -1.359052 1 B py 5 -0.459433 1 B py E 2 -0.197244 1 B s 15 0.163347 2 H s E E Vector 8 Occ=0.000000D+00 E= 3.464398D-02 Symmetry=a" E MO Center= 6.3D-15, -2.2D+00, -2.3D-17, r^2= 3.0D+00 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 21 1.880424 3 H s 26 -1.880424 4 H s E 6 0.218083 1 B pz 20 0.155442 3 H s E 25 -0.155442 4 H s E E Vector 9 Occ=0.000000D+00 E= 1.373915D-01 Symmetry=a' E MO Center= -3.1D-14, 6.8D-01, 2.4D-16, r^2= 4.1D+00 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 8 1.565287 1 B py 3 0.876108 1 B s E 5 -0.611109 1 B py 16 -0.565268 2 H s E 15 -0.381927 2 H s 2 -0.284879 1 B s E E Vector 10 Occ=0.000000D+00 E= 1.736780D-01 Symmetry=a' E MO Center= -2.0D-12, 5.7D-01, 1.5D-16, r^2= 3.2D+00 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 7 -1.057622 1 B px 4 1.031213 1 B px E E Vector 11 Occ=0.000000D+00 E= 1.852048D-01 Symmetry=a" E MO Center= -1.3D-14, 5.1D-01, -2.9D-17, r^2= 3.6D+00 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 9 -1.082206 1 B pz 6 1.012051 1 B pz E 21 -0.546308 3 H s 26 0.546308 4 H s E E Vector 12 Occ=0.000000D+00 E= 1.869628D-01 Symmetry=a' E MO Center= 1.8D-12, 1.1D-01, 5.3D-18, r^2= 3.0D+00 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 3 1.562996 1 B s 2 -1.344584 1 B s E 1 -0.561416 1 B s 5 0.382259 1 B py E 15 -0.262114 2 H s 8 -0.248097 1 B py E E Vector 13 Occ=0.000000D+00 E= 3.755379D-01 Symmetry=a' E MO Center= -5.7D-14, -2.5D+00, 4.8D-16, r^2= 3.1D+00 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 8 1.168231 1 B py 16 -1.154228 2 H s E 21 0.866207 3 H s 26 0.866207 4 H s E 20 -0.686717 3 H s 25 -0.686717 4 H s E 3 0.430641 1 B s 5 -0.192688 1 B py E 2 0.159785 1 B s E E Vector 14 Occ=0.000000D+00 E= 4.823578D-01 Symmetry=a' E MO Center= 3.7D-13, 1.4D+00, -4.4D-16, r^2= 3.2D+00 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 16 3.175248 2 H s 3 -2.835358 1 B s E 8 -1.723478 1 B py 2 0.959608 1 B s E 15 -0.712612 2 H s 14 0.520262 1 B d 2 E 1 0.401160 1 B s 5 0.374529 1 B py E 12 0.299989 1 B d 0 18 -0.172951 2 H py E E Vector 15 Occ=0.000000D+00 E= 5.031629D-01 Symmetry=a' E MO Center= -2.5D-13, 6.6D-01, -1.2D-16, r^2= 1.5D+00 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 10 0.938633 1 B d -2 E E E UHF Final Beta Molecular Orbital Analysis E ----------------------------------------- E E Vector 2 Occ=1.000000D+00 E=-9.422736D-01 Symmetry=a' E MO Center= 1.9D-13, 1.3D+00, -3.0D-17, r^2= 8.3D-01 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 2 0.421960 1 B s 15 0.336134 2 H s E 5 0.284707 1 B py 3 0.271792 1 B s E E Vector 3 Occ=1.000000D+00 E=-7.607244D-01 Symmetry=a' E MO Center= 9.1D-15, -2.3D+00, -8.7D-18, r^2= 7.8D-01 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 20 0.402771 3 H s 25 0.402771 4 H s E 21 0.162503 3 H s 26 0.162503 4 H s E E Vector 4 Occ=0.000000D+00 E=-2.718526D-01 Symmetry=a' E MO Center= -6.0D-13, 2.9D-01, 2.1D-17, r^2= 1.9D+00 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 3 0.705918 1 B s 5 -0.338926 1 B py E 16 -0.308194 2 H s 8 -0.233155 1 B py E 2 0.227759 1 B s 15 -0.223693 2 H s E E Vector 5 Occ=0.000000D+00 E=-2.266266D-01 Symmetry=a" E MO Center= -3.6D-15, 6.1D-01, -1.1D-16, r^2= 2.1D+00 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 9 0.599323 1 B pz 6 0.529471 1 B pz E E Vector 6 Occ=0.000000D+00 E=-2.260711D-01 Symmetry=a' E MO Center= 1.5D-13, 6.2D-01, 5.7D-17, r^2= 2.1D+00 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 7 0.600383 1 B px 4 0.531054 1 B px E E Vector 7 Occ=0.000000D+00 E= 3.001982D-02 Symmetry=a' E MO Center= 7.2D-14, 1.4D+00, -7.3D-18, r^2= 3.6D+00 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 16 2.639808 2 H s 3 -1.531133 1 B s E 8 -1.487851 1 B py 5 -0.429957 1 B py E 2 -0.305419 1 B s E E Vector 8 Occ=0.000000D+00 E= 3.574049D-02 Symmetry=a" E MO Center= 6.7D-15, -2.2D+00, 7.8D-18, r^2= 2.9D+00 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 21 1.891959 3 H s 26 -1.891959 4 H s E 6 0.202702 1 B pz 20 0.154623 3 H s E 25 -0.154623 4 H s E E Vector 9 Occ=0.000000D+00 E= 1.561029D-01 Symmetry=a' E MO Center= 1.0D-13, 9.6D-01, 2.8D-16, r^2= 3.7D+00 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 8 1.605617 1 B py 3 1.529250 1 B s E 16 -0.869834 2 H s 2 -0.663008 1 B s E 5 -0.504745 1 B py 15 -0.431092 2 H s E 1 -0.305631 1 B s E E Vector 10 Occ=0.000000D+00 E= 1.930289D-01 Symmetry=a' E MO Center= -1.9D-13, 5.6D-01, 2.7D-17, r^2= 3.0D+00 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 4 1.057013 1 B px 7 -1.029531 1 B px E E Vector 11 Occ=0.000000D+00 E= 2.052377D-01 Symmetry=a" E MO Center= -1.6D-14, 5.1D-01, -1.1D-15, r^2= 3.4D+00 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 9 -1.057692 1 B pz 6 1.044129 1 B pz E 21 -0.524946 3 H s 26 0.524946 4 H s E E Vector 12 Occ=0.000000D+00 E= 2.791950D-01 Symmetry=a' E MO Center= 1.2D-13, -1.7D-01, 7.0D-16, r^2= 2.9D+00 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 3 1.664699 1 B s 2 -1.301347 1 B s E 16 -0.637546 2 H s 5 0.605256 1 B py E 1 -0.514144 1 B s 20 -0.255596 3 H s E 25 -0.255596 4 H s 21 0.187973 3 H s E 26 0.187973 4 H s E E Vector 13 Occ=0.000000D+00 E= 3.851311D-01 Symmetry=a' E MO Center= -4.7D-14, -2.4D+00, 3.4D-16, r^2= 3.1D+00 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 8 1.023957 1 B py 21 0.842520 3 H s E 26 0.842520 4 H s 16 -0.777885 2 H s E 20 -0.663959 3 H s 25 -0.663959 4 H s E 2 0.463839 1 B s 5 -0.293595 1 B py E 1 0.188724 1 B s E E Vector 14 Occ=0.000000D+00 E= 5.236087D-01 Symmetry=a' E MO Center= 1.4D-13, 1.4D+00, -1.8D-16, r^2= 2.8D+00 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 16 3.042146 2 H s 3 -2.551174 1 B s E 8 -1.667587 1 B py 15 -0.791150 2 H s E 2 0.763908 1 B s 14 0.521066 1 B d 2 E 5 0.462802 1 B py 1 0.324811 1 B s E 12 0.299262 1 B d 0 18 -0.181150 2 H py E E Vector 15 Occ=0.000000D+00 E= 5.576254D-01 Symmetry=a' E MO Center= -1.4D-13, 6.2D-01, -7.3D-16, r^2= 1.5D+00 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 10 0.934530 1 B d -2 E E E center of mass E -------------- E x = -0.00000000 y = 0.45788690 z = 0.00000000 E E moments of inertia (a.u.) E ------------------ E 61.510536153688 -0.000000000000 0.000000000000 E -0.000000000000 0.993361021423 0.000000000000 E 0.000000000000 0.000000000000 60.517175132265 E E Mulliken analysis of the total density E -------------------------------------- E E Atom Charge Shell Charges E ----------- ------ ------------------------------------------------------- E 1 B 5 4.26 2.00 0.87 0.52 0.69 0.16 0.01 E 2 H 1 0.78 0.65 0.10 0.02 E 3 H 1 0.98 0.70 0.27 0.01 E 4 H 1 0.98 0.70 0.27 0.01 E E Mulliken analysis of the alpha density E -------------------------------------- E E Atom Charge Shell Charges E ----------- ------ ------------------------------------------------------- E 1 B 5 2.54 1.00 0.55 0.32 0.55 0.12 0.01 E 2 H 1 0.47 0.39 0.07 0.01 E 3 H 1 0.49 0.35 0.13 0.01 E 4 H 1 0.49 0.35 0.13 0.01 E E Mulliken analysis of the beta density E ------------------------------------- E E Atom Charge Shell Charges E ----------- ------ ------------------------------------------------------- E 1 B 5 1.72 1.00 0.32 0.20 0.14 0.05 0.00 E 2 H 1 0.30 0.26 0.03 0.01 E 3 H 1 0.49 0.35 0.14 0.01 E 4 H 1 0.49 0.35 0.14 0.01 E E Mulliken analysis of the spin density E ------------------------------------- E E Atom Charge Shell Charges E ----------- ------ ------------------------------------------------------- E 1 B 5 0.82 0.00 0.24 0.12 0.40 0.07 0.00 E 2 H 1 0.17 0.13 0.04 0.00 E 3 H 1 0.01 0.01 -0.00 0.00 E 4 H 1 0.01 0.01 -0.00 0.00 E E Multipole analysis of the density wrt the origin E ------------------------------------------------ E E L x y z total alpha beta nuclear E - - - - ----- ----- ---- ------- E 0 0 0 0 1.000000 -4.000000 -3.000000 8.000000 E E 1 1 0 0 -0.000000 0.000000 -0.000000 0.000000 E 1 0 1 0 1.267538 0.421377 0.846161 0.000000 E 1 0 0 1 -0.000000 -0.000000 -0.000000 0.000000 E E 2 2 0 0 -4.410694 -2.645046 -1.765648 0.000000 E 2 1 1 0 -0.000000 -0.000000 -0.000000 0.000000 E 2 1 0 1 0.000000 0.000000 0.000000 0.000000 E 2 0 2 0 -1.707399 -30.308540 -27.503748 56.104888 E 2 0 1 1 0.000000 0.000000 0.000000 0.000000 E 2 0 0 2 -3.959912 -2.912730 -2.032830 0.985648 E E E Parallel integral file used 1 records with 0 large values E E NWChem Gradients Module E ----------------------- E E E E wavefunction = UHF E E Using symmetry E E STDERR: E E Program received signal SIGSEGV: Segmentation fault - invalid memory reference. E E Backtrace for this error: E #0 0x804a1f6db in ??? E #1 0x804a1e896 in ??? E #2 0x803729f6f in handle_signal E at /disk-samsung/freebsd-src/lib/libthr/thread/thr_sig.c:303 E #3 0x80372953e in thr_sighandler E at /disk-samsung/freebsd-src/lib/libthr/thread/thr_sig.c:246 E #4 0x7ffffffff192 in ??? E #5 0x803dd91b1 in ??? E #6 0x803badeb5 in ??? E #7 0x803298434 in ??? E #8 0x80329901d in ??? E #9 0x802f076a9 in ??? E #10 0x802e70b74 in ??? E #11 0x9f45dc in ??? E #12 0x9e382f in ??? E #13 0x7f38de in ??? E #14 0x7e7ba4 in ??? E #15 0x7fdbf4 in ??? E #16 0x7ec987 in ??? E #17 0x4219d7 in ??? E #18 0x422db0 in ??? E #19 0x41462d in ??? E #20 0x40e0e1 in ??? E #21 0x40c71c in ??? E #22 0x40c82f in ??? E E TRACEBACK: E Traceback (most recent call last): E File "/disk-samsung/freebsd-ports/science/py-qcengine/work-py38/qcengine-0.20.1/qcengine/programs/nwchem/runner.py", line 275, in parse_output E retres = qcvars[f"CURRENT {input_model.driver.upper()}"] E KeyError: 'CURRENT GRADIENT' qcengine/programs/nwchem/runner.py:277: UnknownError ___________________________ test_atom_labels[nwchem] ___________________________ qcprog = 'nwchem', basis = 'aug-cc-pvdz' keywords = {'scf__nr': 1.0, 'scf__thresh': 1e-08} @pytest.mark.parametrize( "qcprog, basis, keywords", [ pytest.param("cfour", "aug-pvdz", {"scf_conv": 12}, id="cfour", marks=using("cfour")), pytest.param( "gamess", "accd", {"mp2__nacore": 0, "contrl__ispher": 1}, id="gamess", marks=using("gamess"), ), pytest.param( "nwchem", "aug-cc-pvdz", {"scf__nr": 1.0, "scf__thresh": 1.0e-8}, id="nwchem", marks=using("nwchem") ), pytest.param( "psi4", "aug-cc-pvdz", { "scf_type": "pk", "mp2_type": "conv", }, id="psi4", marks=using("psi4"), ), ], ) def test_atom_labels(qcprog, basis, keywords): kmol = qcel.models.Molecule.from_data( """ H 0 0 0 H5 5 0 0 H_other 0 5 0 H_4sq 5 5 0 units au """ ) assert compare(["H", "H", "H", "H"], kmol.symbols, "elem") assert compare(["", "5", "_other", "_4sq"], kmol.atom_labels, "elbl") atin = qcel.models.AtomicInput( **{"molecule": kmol, "model": {"method": "mp2", "basis": basis}, "driver": "energy", "keywords": keywords} ) atres = qcng.compute(atin, qcprog) pprint.pprint(atres.dict(), width=200) nre = 1.0828427 assert compare_values( nre, atres.properties.nuclear_repulsion_energy, atol=1.0e-4, label="nre" ), f"nre: {atres.properties.nuclear_repulsion_energy} != {nre}" nmo = 36 assert compare(nmo, atres.properties.calcinfo_nmo, label="nmo"), f"nmo: {atres.properties.calcinfo_nmo} != {nmo}" scf = -1.656138508 > assert compare_values( scf, atres.properties.scf_total_energy, atol=3.0e-6, label="scf ene" ), f"scf ene: {atres.properties.scf_total_energy} != {scf}" E AssertionError: scf ene: -1.705577612556 != -1.656138508 E assert False E + where False = compare_values(-1.656138508, -1.705577612556, atol=3e-06, label='scf ene') E + where -1.705577612556 = AtomicResultProperties(calcinfo_nbasis=36, calcinfo_nmo=36, calcinfo_nalpha=2, calcinfo_nbeta=2, calcinfo_natom=4, nuc...ergy=0.0, mp2_doubles_energy=-0.164673847343, mp2_correlation_energy=-0.164673847343, mp2_total_energy=-1.870251459898).scf_total_energy E + where AtomicResultProperties(calcinfo_nbasis=36, calcinfo_nmo=36, calcinfo_nalpha=2, calcinfo_nbeta=2, calcinfo_natom=4, nuc...ergy=0.0, mp2_doubles_energy=-0.164673847343, mp2_correlation_energy=-0.164673847343, mp2_total_energy=-1.870251459898) = AtomicResult(driver='energy', model={'method': 'mp2', 'basis': 'aug-cc-pvdz'}, molecule_hash='3f6b259').properties qcengine/programs/tests/test_ghost.py:205: AssertionError ----------------------------- Captured stdout call ----------------------------- {'driver': , 'error': None, 'extras': {'outfiles': {'nwchem.grad': None, 'nwchem.hess': None}, 'qcvars': {'CURRENT CORRELATION ENERGY': '-0.164673847343', 'CURRENT ENERGY': '-1.870251459899', 'CURRENT REFERENCE ENERGY': '-1.705577612556', 'HF TOTAL ENERGY': '-1.705577612556', 'MP2 CORRELATION ENERGY': '-0.164673847343', 'MP2 DOUBLES ENERGY': '-0.164673847343', 'MP2 OPPOSITE-SPIN CORRELATION ENERGY': '-0.160769906581', 'MP2 SAME-SPIN CORRELATION ENERGY': '-0.003903940762', 'MP2 SINGLES ENERGY': '0', 'MP2 TOTAL ENERGY': '-1.870251459898', 'N ALPHA ELECTRONS': '2', 'N ATOMS': '4', 'N BASIS FUNCTIONS': '36', 'N BETA ELECTRONS': '2', 'N MOLECULAR ORBITALS': '36', 'NUCLEAR REPULSION ENERGY': '1.0828427125', 'SCF TOTAL ENERGY': '-1.705577612556', 'SCS(N)-MP2 CORRELATION ENERGY': '-0.006870935741120000034673959366', 'SCS(N)-MP2 TOTAL ENERGY': '-1.712448548297120000034673959', 'SCS-MP2 CORRELATION ENERGY': '-0.1942252014845333333333333333', 'SCS-MP2 TOTAL ENERGY': '-1.899802814040533333333333333', 'SCS-MP2-VDW CORRELATION ENERGY': '-0.2077374508046800042837708469', 'SCS-MP2-VDW TOTAL ENERGY': '-1.913315063360680004283770847'}}, 'id': None, 'keywords': {'scf__nr': 1.0, 'scf__thresh': 1e-08}, 'model': {'basis': 'aug-cc-pvdz', 'method': 'mp2'}, 'molecule': {'atom_labels': array(['', '5', '_other', '_4sq'], dtype=' ""\n' ' -------------------------\n' '\n' ' Output coordinates in a.u. (scale by 1.000000000 to convert to a.u.)\n' '\n' ' No. Tag Charge X Y Z\n' ' ---- ---------------- ---------- -------------- -------------- --------------\n' ' 1 H 1.0000 3.53553391 0.00000000 0.00000000\n' ' 2 H5 1.0000 0.00000000 3.53553391 0.00000000\n' ' 3 H_other 1.0000 0.00000000 -3.53553391 0.00000000\n' ' 4 H_4sq 1.0000 -3.53553391 0.00000000 0.00000000\n' '\n' ' Atomic Mass \n' ' ----------- \n' '\n' ' H 1.007825\n' ' H5 1.007825\n' ' H_other 1.007825\n' ' H_4sq 1.007825\n' '\n' '\n' ' Effective nuclear repulsion energy (a.u.) 1.0828427125\n' '\n' ' Nuclear Dipole moment (a.u.) \n' ' ----------------------------\n' ' X Y Z\n' ' ---------------- ---------------- ----------------\n' ' 0.0000000000 0.0000000000 0.0000000000\n' '\n' ' Symmetry information\n' ' --------------------\n' '\n' ' Group name Cs \n' ' Group number 2\n' ' Group order 2\n' ' No. of unique centers 4\n' '\n' ' Symmetry unique atoms\n' '\n' ' 1 2 3 4\n' '\n' '\n' ' XYZ format geometry\n' ' -------------------\n' ' 4\n' ' geometry\n' ' H 1.87092411 0.00000000 0.00000000\n' ' H5 0.00000000 1.87092411 0.00000000\n' ' H_other 0.00000000 -1.87092411 0.00000000\n' ' H_4sq -1.87092411 0.00000000 0.00000000\n' '\n' ' library name resolved from: .nwchemrc\n' ' library file name is: \n' ' \n' ' Basis "ao basis" -> "" (cartesian)\n' ' -----\n' ' H (Hydrogen)\n' ' ------------\n' ' Exponent Coefficients \n' ' -------------- ---------------------------------------------------------\n' ' 1 S 1.30100000E+01 0.019685\n' ' 1 S 1.96200000E+00 0.137977\n' ' 1 S 4.44600000E-01 0.478148\n' '\n' ' 2 S 1.22000000E-01 1.000000\n' '\n' ' 3 S 2.97400000E-02 1.000000\n' '\n' ' 4 P 7.27000000E-01 1.000000\n' '\n' ' 5 P 1.41000000E-01 1.000000\n' '\n' ' bqH\n' ' ---\n' ' Exponent Coefficients \n' ' -------------- ---------------------------------------------------------\n' ' 1 S 1.30100000E+01 0.019685\n' ' 1 S 1.96200000E+00 0.137977\n' ' 1 S 4.44600000E-01 0.478148\n' '\n' ' 2 S 1.22000000E-01 1.000000\n' '\n' ' 3 S 2.97400000E-02 1.000000\n' '\n' ' 4 P 7.27000000E-01 1.000000\n' '\n' ' 5 P 1.41000000E-01 1.000000\n' '\n' '\n' '\n' ' Summary of "ao basis" -> "" (cartesian)\n' ' ------------------------------------------------------------------------------\n' ' Tag Description Shells Functions and Types\n' ' ---------------- ------------------------------ ------ ---------------------\n' ' H aug-cc-pvdz 5 9 3s2p\n' ' bqH aug-cc-pvdz 5 9 3s2p\n' '\n' '\n' ' NWChem SCF Module\n' ' -----------------\n' '\n' '\n' '\n' ' ao basis = "ao basis"\n' ' functions = 36\n' ' atoms = 4\n' ' closed shells = 2\n' ' open shells = 0\n' ' charge = 0.00\n' ' wavefunction = RHF \n' ' input vectors = atomic\n' ' output vectors = ./nwchem.movecs\n' ' use symmetry = T\n' ' symmetry adapt = T\n' '\n' '\n' ' Summary of "ao basis" -> "ao basis" (cartesian)\n' ' ------------------------------------------------------------------------------\n' ' Tag Description Shells Functions and Types\n' ' ---------------- ------------------------------ ------ ---------------------\n' ' H aug-cc-pvdz 5 9 3s2p\n' ' bqH aug-cc-pvdz 5 9 3s2p\n' '\n' '\n' ' Symmetry analysis of basis\n' ' --------------------------\n' '\n' " a' 28\n" ' a" 8\n' '\n' '\n' ' Forming initial guess at 0.0s\n' '\n' '\n' ' Superposition of Atomic Density Guess\n' ' -------------------------------------\n' '\n' ' Sum of atomic energies: -1.99733851\n' '\n' ' Non-variational initial energy\n' ' ------------------------------\n' '\n' ' Total energy = -1.383269\n' ' 1-e energy = -4.162689\n' ' 2-e energy = 1.696577\n' ' HOMO = -0.194035\n' ' LUMO = -0.194035\n' '\n' '\n' ' !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n' ' Warning - the HOMO and LUMO are degenerate and you are using symmetry.\n' ' This can lead to non-variational energies and poor convergence.\n' ' Modify the initial guess, or use an open-shell wavefunction, or turn\n' ' off symmetry.\n' ' !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n' '\n' '\n' ' Symmetry analysis of molecular orbitals - initial\n' ' -------------------------------------------------\n' '\n' ' Numbering of irreducible representations: \n' '\n' ' 1 a\' 2 a" \n' '\n' ' Orbital symmetries:\n' '\n' " 1 a' 2 a' 3 a' 4 a' 5 a' \n" ' 6 a\' 7 a\' 8 a\' 9 a" 10 a\' \n' ' 11 a\' 12 a" \n' '\n' '\n' ' Starting SCF solution at 0.1s\n' '\n' '\n' '\n' ' ----------------------------------------------\n' ' Quadratically convergent ROHF\n' '\n' ' Convergence threshold : 1.000E-08\n' ' Maximum no. of iterations : 30\n' ' Final Fock-matrix accuracy: 1.000E-10\n' '\n' ' PCG initial level shift : 5.000\n' ' PCG change shift at maxg : 0.500\n' ' PCG final level shift : 0.000\n' ' NR initial level shift : 0.000\n' ' NR change shift at maxg : 0.000\n' ' NR final level shift : 0.000\n' ' NR enabled at maxg : 1.000\n' ' ----------------------------------------------\n' '\n' '\n' ' Integral file = ./nwchem.aoints.0\n' ' Record size in doubles = 65536 No. of integs per rec = 43688\n' ' Max. records in memory = 6 Max. records in file = 124964\n' ' No. of bits per label = 8 No. of bits per value = 64\n' '\n' '\n' ' #quartets = 2.212D+04 #integrals = 1.177D+05 #direct = 0.0% #cached =100.0%\n' '\n' '\n' ' iter energy gnorm gmax time\n' ' ----- ------------------- --------- --------- --------\n' ' 1 -1.6404986441 3.05D-01 1.68D-01 0.1\n' ' 2 -1.6562970051 2.98D-02 1.55D-02 0.2\n' ' 3 -1.6606305329 2.42D-01 1.28D-01 0.3\n' ' ga_iter_lsolve: convergence stagnant ... aborting solve\n' '\n' ' Disabled NR: increased maxiter to 40\n' '\n' ' 4 -1.6898295392 1.56D-01 1.04D-01 0.3\n' ' 5 -1.7027985834 1.18D-01 6.59D-02 0.4\n' ' 6 -1.7055194814 1.36D-02 7.03D-03 0.4\n' ' 7 -1.7055669904 4.33D-03 2.97D-03 0.4\n' ' 8 -1.7055763134 2.64D-03 1.33D-03 0.4\n' ' 9 -1.7055775578 5.15D-04 2.58D-04 0.5\n' ' 10 -1.7055776052 1.06D-04 6.86D-05 0.5\n' ' 11 -1.7055776110 6.54D-05 4.01D-05 0.5\n' ' 12 -1.7055776124 2.31D-05 9.90D-06 0.5\n' ' 13 -1.7055776126 3.30D-06 2.20D-06 0.5\n' ' 14 -1.7055776126 3.07D-07 1.29D-07 0.6\n' ' 15 -1.7055776126 3.55D-08 1.89D-08 0.6\n' ' 16 -1.7055776126 4.12D-09 2.29D-09 0.6\n' '\n' '\n' ' Final RHF results \n' ' ------------------ \n' '\n' ' Total SCF energy = -1.705577612556\n' ' One-electron energy = -4.201323937448\n' ' Two-electron energy = 1.412903612418\n' ' Nuclear repulsion energy = 1.082842712475\n' '\n' ' Time for solution = 0.5s\n' '\n' '\n' '\n' ' Symmetry analysis of molecular orbitals - final\n' ' -----------------------------------------------\n' '\n' ' Numbering of irreducible representations: \n' '\n' ' 1 a\' 2 a" \n' '\n' ' Orbital symmetries:\n' '\n' " 1 a' 2 a' 3 a' 4 a' 5 a' \n" ' 6 a\' 7 a\' 8 a\' 9 a" 10 a\' \n' ' 11 a\' 12 a" \n' '\n' ' Final eigenvalues\n' ' -----------------\n' '\n' ' 1 \n' ' 1 -0.3728\n' ' 2 -0.3149\n' ' 3 -0.1250\n' ' 4 -0.0759\n' ' 5 0.0909\n' ' 6 0.0918\n' ' 7 0.0939\n' ' 8 0.1068\n' ' 9 0.2191\n' ' 10 0.2442\n' ' 11 0.2581\n' ' 12 0.3044\n' '\n' ' ROHF Final Molecular Orbital Analysis\n' ' -------------------------------------\n' '\n' " Vector 1 Occ=2.000000D+00 E=-3.728485D-01 Symmetry=a'\n" ' MO Center= 2.2D-14, -2.3D-14, 1.7D-16, r^2= 4.2D+00\n' ' Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function \n' ' ----- ------------ --------------- ----- ------------ ---------------\n' ' 2 0.232172 1 H s 11 0.232172 2 H s \n' ' 20 0.232172 3 H s 29 0.232172 4 H s \n' ' 1 0.207614 1 H s 10 0.207614 2 H s \n' ' 19 0.207614 3 H s 28 0.207614 4 H s \n' '\n' " Vector 2 Occ=2.000000D+00 E=-3.149099D-01 Symmetry=a'\n" ' MO Center= 1.2D-14, -1.1D-14, -5.8D-16, r^2= 4.8D+00\n' ' Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function \n' ' ----- ------------ --------------- ----- ------------ ---------------\n' ' 2 0.277062 1 H s 11 0.277062 2 H s \n' ' 20 -0.277062 3 H s 29 -0.277062 4 H s \n' ' 1 0.229099 1 H s 10 0.229099 2 H s \n' ' 19 -0.229099 3 H s 28 -0.229099 4 H s \n' '\n' " Vector 3 Occ=0.000000D+00 E=-1.250010D-01 Symmetry=a'\n" ' MO Center= -2.2D-14, 3.5D-14, 5.2D-16, r^2= 5.3D+00\n' ' Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function \n' ' ----- ------------ --------------- ----- ------------ ---------------\n' ' 2 0.252551 1 H s 11 -0.252551 2 H s \n' ' 20 0.252551 3 H s 29 -0.252551 4 H s \n' ' 1 0.221043 1 H s 10 -0.221043 2 H s \n' ' 19 0.221043 3 H s 28 -0.221043 4 H s \n' '\n' " Vector 4 Occ=0.000000D+00 E=-7.585474D-02 Symmetry=a'\n" ' MO Center= -2.0D-14, 1.1D-14, 6.0D-17, r^2= 5.8D+00\n' ' Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function \n' ' ----- ------------ --------------- ----- ------------ ---------------\n' ' 2 0.298787 1 H s 11 -0.298787 2 H s \n' ' 20 -0.298787 3 H s 29 0.298787 4 H s \n' ' 3 0.272602 1 H s 12 -0.272602 2 H s \n' ' 21 -0.272602 3 H s 30 0.272602 4 H s \n' ' 1 0.245185 1 H s 10 -0.245185 2 H s \n' '\n' " Vector 5 Occ=0.000000D+00 E= 9.094428D-02 Symmetry=a'\n" ' MO Center= -4.3D-12, 6.4D-12, -4.0D-16, r^2= 1.8D+01\n' ' Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function \n' ' ----- ------------ --------------- ----- ------------ ---------------\n' ' 3 0.947333 1 H s 12 -0.947333 2 H s \n' ' 21 0.947333 3 H s 30 -0.947333 4 H s \n' ' 2 -0.414802 1 H s 11 0.414802 2 H s \n' ' 20 -0.414802 3 H s 29 0.414802 4 H s \n' '\n' " Vector 6 Occ=0.000000D+00 E= 9.183389D-02 Symmetry=a'\n" ' MO Center= 4.7D-12, -6.0D-12, 2.6D-16, r^2= 1.5D+01\n' ' Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function \n' ' ----- ------------ --------------- ----- ------------ ---------------\n' ' 3 -0.486114 1 H s 12 -0.486114 2 H s \n' ' 21 -0.486114 3 H s 30 -0.486114 4 H s \n' ' 2 0.470368 1 H s 11 0.470368 2 H s \n' ' 20 0.470368 3 H s 29 0.470368 4 H s \n' '\n' " Vector 7 Occ=0.000000D+00 E= 9.391311D-02 Symmetry=a'\n" ' MO Center= 4.5D-13, 8.4D-13, 6.1D-16, r^2= 1.8D+01\n' ' Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function \n' ' ----- ------------ --------------- ----- ------------ ---------------\n' ' 3 0.950700 1 H s 12 0.950700 2 H s \n' ' 21 -0.950700 3 H s 30 -0.950700 4 H s \n' ' 2 -0.390633 1 H s 11 -0.390633 2 H s \n' ' 20 0.390633 3 H s 29 0.390633 4 H s \n' '\n' " Vector 8 Occ=0.000000D+00 E= 1.068491D-01 Symmetry=a'\n" ' MO Center= -8.4D-13, -1.2D-12, 3.4D-18, r^2= 2.2D+01\n' ' Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function \n' ' ----- ------------ --------------- ----- ------------ ---------------\n' ' 3 1.985671 1 H s 12 -1.985671 2 H s \n' ' 21 -1.985671 3 H s 30 1.985671 4 H s \n' ' 2 -0.350640 1 H s 11 0.350640 2 H s \n' ' 20 0.350640 3 H s 29 -0.350640 4 H s \n' '\n' ' Vector 9 Occ=0.000000D+00 E= 2.190739D-01 Symmetry=a"\n' ' MO Center= -7.0D-14, 9.4D-14, -6.8D-16, r^2= 5.5D+00\n' ' Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function \n' ' ----- ------------ --------------- ----- ------------ ---------------\n' ' 9 0.431003 1 H pz 18 0.431003 2 H pz \n' ' 27 0.431003 3 H pz 36 0.431003 4 H pz \n' '\n' " Vector 10 Occ=0.000000D+00 E= 2.442052D-01 Symmetry=a'\n" ' MO Center= -8.8D-14, 8.9D-14, 2.2D-16, r^2= 5.7D+00\n' ' Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function \n' ' ----- ------------ --------------- ----- ------------ ---------------\n' ' 8 0.386737 1 H py 16 0.386737 2 H px \n' ' 25 -0.386737 3 H px 35 -0.386737 4 H py \n' '\n' " Vector 11 Occ=0.000000D+00 E= 2.581071D-01 Symmetry=a'\n" ' MO Center= -4.8D-14, 4.9D-14, -2.8D-16, r^2= 5.5D+00\n' ' Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function \n' ' ----- ------------ --------------- ----- ------------ ---------------\n' ' 7 0.377112 1 H px 17 0.377112 2 H py \n' ' 26 -0.377112 3 H py 34 -0.377112 4 H px \n' ' 2 0.259475 1 H s 11 0.259475 2 H s \n' ' 20 0.259475 3 H s 29 0.259475 4 H s \n' '\n' ' Vector 12 Occ=0.000000D+00 E= 3.044166D-01 Symmetry=a"\n' ' MO Center= -1.0D-13, 8.0D-14, 4.0D-18, r^2= 6.1D+00\n' ' Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function \n' ' ----- ------------ --------------- ----- ------------ ---------------\n' ' 9 0.512506 1 H pz 18 0.512506 2 H pz \n' ' 27 -0.512506 3 H pz 36 -0.512506 4 H pz \n' '\n' ' Vector 13 Occ=0.000000D+00 E= 3.068497D-01 Symmetry=a"\n' ' MO Center= 8.2D-14, -8.2D-14, -6.6D-16, r^2= 6.1D+00\n' ' Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function \n' ' ----- ------------ --------------- ----- ------------ ---------------\n' ' 9 0.513256 1 H pz 18 -0.513256 2 H pz \n' ' 27 0.513256 3 H pz 36 -0.513256 4 H pz \n' '\n' " Vector 14 Occ=0.000000D+00 E= 3.295674D-01 Symmetry=a'\n" ' MO Center= 1.1D-13, -9.9D-14, 3.2D-16, r^2= 6.2D+00\n' ' Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function \n' ' ----- ------------ --------------- ----- ------------ ---------------\n' ' 8 0.418305 1 H py 16 -0.418305 2 H px \n' ' 25 -0.418305 3 H px 35 0.418305 4 H py \n' ' 7 0.234806 1 H px 17 -0.234806 2 H py \n' ' 26 -0.234806 3 H py 34 0.234806 4 H px \n' '\n' " Vector 15 Occ=0.000000D+00 E= 3.297333D-01 Symmetry=a'\n" ' MO Center= -5.0D-14, 3.8D-14, -4.0D-16, r^2= 6.3D+00\n' ' Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function \n' ' ----- ------------ --------------- ----- ------------ ---------------\n' ' 8 0.410208 1 H py 16 0.410208 2 H px \n' ' 25 0.410208 3 H px 35 0.410208 4 H py \n' ' 7 -0.246652 1 H px 17 -0.246652 2 H py \n' ' 26 -0.246652 3 H py 34 -0.246652 4 H px \n' ' 2 -0.168401 1 H s 11 -0.168401 2 H s \n' '\n' ' Vector 16 Occ=0.000000D+00 E= 3.905678D-01 Symmetry=a"\n' ' MO Center= 9.2D-14, -9.2D-14, -5.8D-27, r^2= 6.8D+00\n' ' Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function \n' ' ----- ------------ --------------- ----- ------------ ---------------\n' ' 9 0.610176 1 H pz 18 -0.610176 2 H pz \n' ' 27 -0.610176 3 H pz 36 0.610176 4 H pz \n' '\n' " Vector 17 Occ=0.000000D+00 E= 4.418726D-01 Symmetry=a'\n" ' MO Center= 9.3D-14, 3.1D-14, -4.5D-17, r^2= 8.4D+00\n' ' Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function \n' ' ----- ------------ --------------- ----- ------------ ---------------\n' ' 7 0.598503 1 H px 17 -0.598503 2 H py \n' ' 26 -0.598503 3 H py 34 0.598503 4 H px \n' ' 3 -0.477114 1 H s 12 0.477114 2 H s \n' ' 21 -0.477114 3 H s 30 0.477114 4 H s \n' ' 8 -0.456037 1 H py 16 0.456037 2 H px \n' '\n' " Vector 18 Occ=0.000000D+00 E= 4.447587D-01 Symmetry=a'\n" ' MO Center= -1.4D-13, 1.5D-13, 2.2D-16, r^2= 8.5D+00\n' ' Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function \n' ' ----- ------------ --------------- ----- ------------ ---------------\n' ' 7 0.591768 1 H px 17 0.591768 2 H py \n' ' 26 0.591768 3 H py 34 0.591768 4 H px \n' ' 3 -0.477540 1 H s 12 -0.477540 2 H s \n' ' 21 0.477540 3 H s 30 0.477540 4 H s \n' ' 8 0.468619 1 H py 16 0.468619 2 H px \n' '\n' " Vector 19 Occ=0.000000D+00 E= 4.875859D-01 Symmetry=a'\n" ' MO Center= 2.1D-14, -1.5D-13, 6.5D-17, r^2= 9.6D+00\n' ' Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function \n' ' ----- ------------ --------------- ----- ------------ ---------------\n' ' 3 0.948483 1 H s 12 -0.948483 2 H s \n' ' 21 -0.948483 3 H s 30 0.948483 4 H s \n' ' 7 -0.807595 1 H px 17 0.807595 2 H py \n' ' 26 -0.807595 3 H py 34 0.807595 4 H px \n' ' 8 0.247492 1 H py 16 -0.247492 2 H px \n' '\n' " Vector 20 Occ=0.000000D+00 E= 4.974799D-01 Symmetry=a'\n" ' MO Center= 9.6D-14, -1.0D-13, -7.2D-17, r^2= 7.8D+00\n' ' Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function \n' ' ----- ------------ --------------- ----- ------------ ---------------\n' ' 8 0.806352 1 H py 16 -0.806352 2 H px \n' ' 25 0.806352 3 H px 35 -0.806352 4 H py \n' ' 3 -0.282694 1 H s 12 0.282694 2 H s \n' ' 21 0.282694 3 H s 30 -0.282694 4 H s \n' ' 7 0.253577 1 H px 17 -0.253577 2 H py \n' '\n' " Vector 21 Occ=0.000000D+00 E= 7.263901D-01 Symmetry=a'\n" ' MO Center= -1.2D-13, 6.7D-14, -1.9D-17, r^2= 6.6D+00\n' ' Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function \n' ' ----- ------------ --------------- ----- ------------ ---------------\n' ' 2 0.823082 1 H s 11 0.823082 2 H s \n' ' 20 0.823082 3 H s 29 0.823082 4 H s \n' ' 1 -0.685535 1 H s 10 -0.685535 2 H s \n' ' 19 -0.685535 3 H s 28 -0.685535 4 H s \n' ' 3 -0.257861 1 H s 12 -0.257861 2 H s \n' '\n' '\n' ' center of mass\n' ' --------------\n' ' x = 0.00000000 y = 0.00000000 z = 0.00000000\n' '\n' ' moments of inertia (a.u.)\n' ' ------------------\n' ' 25.195625000000 0.000000000000 0.000000000000\n' ' 0.000000000000 25.195625000000 0.000000000000\n' ' 0.000000000000 0.000000000000 50.391250000000\n' '\n' ' Mulliken analysis of the total density\n' ' --------------------------------------\n' '\n' ' Atom Charge Shell Charges\n' ' ----------- ------ -------------------------------------------------------\n' ' 1 H 1 1.00 0.38 0.53 0.08 0.00 0.02\n' ' 2 H 1 1.00 0.38 0.53 0.08 0.00 0.02\n' ' 3 H 1 1.00 0.38 0.53 0.08 0.00 0.02\n' ' 4 H 1 1.00 0.38 0.53 0.08 0.00 0.02\n' '\n' ' Multipole analysis of the density wrt the origin\n' ' ------------------------------------------------\n' '\n' ' L x y z total open nuclear\n' ' - - - - ----- ---- -------\n' ' 0 0 0 0 -0.000000 0.000000 4.000000\n' '\n' ' 1 1 0 0 -0.000000 0.000000 0.000000\n' ' 1 0 1 0 0.000000 0.000000 0.000000\n' ' 1 0 0 1 0.000000 0.000000 0.000000\n' '\n' ' 2 2 0 0 -4.159376 0.000000 25.000000\n' ' 2 1 1 0 -2.949281 0.000000 0.000000\n' ' 2 1 0 1 -0.000000 0.000000 0.000000\n' ' 2 0 2 0 -4.159376 0.000000 25.000000\n' ' 2 0 1 1 -0.000000 0.000000 0.000000\n' ' 2 0 0 2 -5.949450 0.000000 0.000000\n' '\n' '\n' ' Parallel integral file used 3 records with 0 large values\n' '\n' ' NWChem MP2 Semi-direct Energy/Gradient Module\n' ' ---------------------------------------------\n' '\n' '\n' ' Basis functions = 36\n' ' Molecular orbitals = 36\n' ' Frozen core = 0\n' ' Frozen virtuals = 0\n' ' Active alpha occupied = 2\n' ' Active beta occupied = 2\n' ' Active alpha virtual = 34\n' ' Active beta virtual = 34\n' ' Use MO symmetry = T\n' ' Use skeleton AO sym = T\n' '\n' ' AO/Fock/Back tols = 1.0D-09 1.0D-09 1.0D-09\n' '\n' ' GA uses MA = F GA memory limited = T\n' '\n' ' Available: \n' ' local mem= 4.40D+08\n' ' global mem= 4.40D+08\n' ' local disk= 8.62D+09\n' ' mp2_memr nvloc 34\n' ' nvloc new 34\n' ' 1 passes of 2: 256876 3268 156250.\n' '\n' ' Semi-direct pass number 1 of 1 for RHF alpha+beta at 0.8s\n' ' vrange nnbf 666\n' 'Node 0 wrote 0.4 Mb in 0.0 s Agg I/O rate: 976.6 Mb/s\n' ' Done moints_semi at 0.9s\n' ' Done maket at 0.9s\n' ' Done multipass loop at 0.9s\n' '\n' '\n' ' -------------------------------------------\n' ' SCF energy -1.705577612556\n' ' Correlation energy -0.164673847343\n' ' Singlet pairs -0.158817936199\n' ' Triplet pairs -0.005855911143\n' ' Total MP2 energy -1.870251459898\n' ' -------------------------------------------\n' '\n' '\n' '\n' ' ---------------------------------------------------\n' ' Spin Component Scaled (SCS) MP2\n' ' Same spin pairs -0.003903940762\n' ' Same spin scaling factor 0.333333333333\n' ' Opposite spin pairs -0.160769906581\n' ' Opposite spin scaling fact. 1.200000000000\n' ' SCS-MP2 correlation energy -0.194225201484\n' ' Total SCS-MP2 energy -1.899802814040\n' ' ---------------------------------------------------\n' '\n' ' -----------------------\n' ' Performance information\n' ' -----------------------\n' '\n' ' Timer overhead = 9.21D-07 seconds/call\n' '\n' ' Nr. of calls CPU time (s) Wall time (s) GFlops\n' ' --------------- ------------------- ------------------------------ -------------------\n' 'Name Min Avg Max Min Avg Max Min Avg Max Mx/calls Min Max Sum\n' 'mp2: moin 1 1 1 9.30E-2 9.30E-2 9.30E-2 9.26E-2 9.26E-2 9.26E-2 9.26E-2 0.0 0.0 0.0 \n' 'mp2: make 1 1 1 1.67E-2 1.67E-2 1.67E-2 3.27E-2 3.27E-2 3.27E-2 3.27E-2 0.0 0.0 0.0 \n' 'mp2: tota 1 1 1 0.14 0.14 0.14 0.18 0.18 0.18 0.18 0.0 0.0 0.0 \n' '\n' ' The average no. of pstat calls per process was 3.00D+00\n' ' with a timing overhead of 2.76D-06s\n' '\n' '\n' ' Task times cpu: 0.8s wall: 0.9s\n' '\n' '\n' ' NWChem Input Module\n' ' -------------------\n' '\n' '\n' ' Summary of allocated global arrays\n' '-----------------------------------\n' ' No active global arrays\n' '\n' '\n' '\n' ' GA Statistics for process 0\n' ' ------------------------------\n' '\n' ' create destroy get put acc scatter gather read&inc\n' 'calls: 892 892 1.30e+04 3729 1.10e+04 0 0 1580 \n' 'number of processes/call 0.00e+00 0.00e+00 0.00e+00 0.00e+00 0.00e+00\n' 'bytes total: 1.21e+07 8.82e+06 3.12e+06 0.00e+00 0.00e+00 1.26e+04\n' 'bytes remote: 0.00e+00 0.00e+00 0.00e+00 0.00e+00 0.00e+00 0.00e+00\n' 'Max memory consumed for GA by this process: 1430792 bytes\n' '\n' 'MA_summarize_allocated_blocks: starting scan ...\n' 'MA_summarize_allocated_blocks: scan completed: 0 heap blocks, 0 stack blocks\n' 'MA usage statistics:\n' '\n' '\tallocation statistics:\n' '\t\t\t\t\t heap\t stack\n' '\t\t\t\t\t ----\t -----\n' '\tcurrent number of blocks\t 0\t 0\n' '\tmaximum number of blocks\t 18\t 22\n' '\tcurrent total bytes\t\t 0\t 0\n' '\tmaximum total bytes\t\t 3157312\t 22509864\n' '\tmaximum total K-bytes\t\t 3158\t 22510\n' '\tmaximum total M-bytes\t\t 4\t 23\n' '\n' '\n' ' CITATION\n' ' --------\n' ' Please cite the following reference when publishing\n' ' results obtained with NWChem:\n' '\n' ' E. Aprà, E. J. Bylaska, W. A. de Jong, N. Govind, K. Kowalski,\n' ' T. P. Straatsma, M. Valiev, H. J. J. van Dam, Y. Alexeev, J. Anchell,\n' ' V. Anisimov, F. W. Aquino, R. Atta-Fynn, J. Autschbach, N. P. Bauman,\n' ' J. C. Becca, D. E. Bernholdt, K. Bhaskaran-Nair, S. Bogatko, P. Borowski,\n' ' J. Boschen, J. Brabec, A. Bruner, E. Cauët, Y. Chen, G. N. Chuev,\n' ' C. J. Cramer, J. Daily, M. J. O. Deegan, T. H. Dunning Jr., M. Dupuis,\n' ' K. G. Dyall, G. I. Fann, S. A. Fischer, A. Fonari, H. Früchtl, L. Gagliardi,\n' ' J. Garza, N. Gawande, S. Ghosh, K. Glaesemann, A. W. Götz, J. Hammond,\n' ' V. Helms, E. D. Hermes, K. Hirao, S. Hirata, M. Jacquelin, L. Jensen,\n' ' B. G. Johnson, H. Jónsson, R. A. Kendall, M. Klemm, R. Kobayashi, V. Konkov,\n' ' S. Krishnamoorthy, M. Krishnan, Z. Lin, R. D. Lins, R. J. Littlefield,\n' ' A. J. Logsdail, K. Lopata, W. Ma, A. V. Marenich, J. Martin del Campo,\n' ' D. Mejia-Rodriguez, J. E. Moore, J. M. Mullin, T. Nakajima, D. R. Nascimento,\n' ' J. A. Nichols, P. J. Nichols, J. Nieplocha, A. Otero-de-la-Roza, B. Palmer,\n' ' A. Panyala, T. Pirojsirikul, B. Peng, R. Peverati, J. Pittner, L. Pollack,\n' ' R. M. Richard, P. Sadayappan, G. C. Schatz, W. A. Shelton, D. W. Silverstein,\n' ' D. M. A. Smith, T. A. Soares, D. Song, M. Swart, H. L. Taylor, G. S. Thomas,\n' ' V. Tipparaju, D. G. Truhlar, K. Tsemekhman, T. Van Voorhis,\n' ' Á. Vázquez-Mayagoitia, P. Verma, O. Villa, A. Vishnu, K. D. Vogiatzis,\n' ' D. Wang, J. H. Weare, M. J. Williamson, T. L. Windus, K. Woliński,\n' ' A. T. Wong, Q. Wu, C. Yang, Q. Yu, M. Zacharias, Z. Zhang, Y. Zhao,\n' ' and R. J. Harrison\n' ' "NWChem: Past, present, and future\n' ' J. Chem. Phys. 152, 184102 (2020)\n' ' doi:10.1063/5.0004997\n' '\n' ' AUTHORS\n' ' -------\n' ' E. Apra, E. J. Bylaska, N. Govind, K. Kowalski, M. Valiev, W. A. de Jong,\n' ' T. P. Straatsma, H. J. J. van Dam, D. Wang, T. L. Windus, N. P. Bauman,\n' ' A. Panyala, J. Hammond, J. Autschbach, K. Bhaskaran-Nair, J. Brabec,\n' ' K. Lopata, S. A. Fischer, S. Krishnamoorthy, M. Jacquelin, W. Ma, M. Klemm,\n' ' O. Villa, Y. Chen, V. Anisimov, F. Aquino, S. Hirata, M. T. Hackler,\n' ' Eric Hermes, L. Jensen, J. E. Moore, J. C. Becca, V. Konjkov,\n' ' D. Mejia-Rodriguez, T. Risthaus, M. Malagoli, A. Marenich,\n' ' A. Otero-de-la-Roza, J. Mullin, P. Nichols, R. Peverati, J. Pittner, Y. Zhao,\n' ' P.-D. Fan, A. Fonari, M. J. Williamson, R. J. Harrison, J. R. Rehr,\n' ' M. Dupuis, D. Silverstein, D. M. A. Smith, J. Nieplocha, V. Tipparaju,\n' ' M. Krishnan, B. E. Van Kuiken, A. Vazquez-Mayagoitia, M. Swart, Q. Wu,\n' ' T. Van Voorhis, A. A. Auer, M. Nooijen, L. D. Crosby, E. Brown, G. Cisneros,\n' ' G. I. Fann, H. Fruchtl, J. Garza, K. Hirao, R. A. Kendall, J. A. Nichols,\n' ' K. Tsemekhman, K. Wolinski, J. Anchell, D. E. Bernholdt, P. Borowski,\n' ' T. Clark, D. Clerc, H. Dachsel, M. J. O. Deegan, K. Dyall, D. Elwood,\n' ' E. Glendening, M. Gutowski, A. C. Hess, J. Jaffe, B. G. Johnson, J. Ju,\n' ' R. Kobayashi, R. Kutteh, Z. Lin, R. Littlefield, X. Long, B. Meng,\n' ' T. Nakajima, S. Niu, L. Pollack, M. Rosing, K. Glaesemann, G. Sandrone,\n' ' M. Stave, H. Taylor, G. Thomas, J. H. van Lenthe, A. T. Wong, Z. Zhang.\n' '\n' ' Total times cpu: 0.8s wall: 1.0s\n', 'success': True, 'wavefunction': None} ------------------------------ Captured log call ------------------------------- ERROR root:testing.py:20 scf ene..............................................FAILED ERROR root:testing.py:21 scf ene: computed value (-1.7055776) does not match (-1.6561385) to atol=3e-06 by difference (-0.0494391). ________________________________ test_gradient _________________________________ self = NWChemHarness(name='NWChem', scratch=True, thread_safe=False, thread_parallel=False, node_parallel=True, managed_memory=True, extras=None, version_cache={'/usr/local/bin/nwchem': '7.0.2+11.eol.2499.gbbee7e139269'}) outfiles = {'nwchem.grad': None, 'nwchem.hess': None} input_model = AtomicInput(driver='gradient', model={'method': 'b3lyp', 'basis': '3-21g'}, molecule_hash='4002acf') def parse_output( self, outfiles: Dict[str, str], input_model: "AtomicInput" ) -> AtomicResult: # lgtm: [py/similar-function] # Get the stdout from the calculation (required) stdout = outfiles.pop("stdout") stderr = outfiles.pop("stderr") method = input_model.model.method.lower() method = method[4:] if method.startswith("nwc-") else method # Read the NWChem stdout file and, if needed, the hess or grad files # July 2021: nwmol & vector returns now atin/outfile orientation depending on fix_com,orientation=T/F. previously always atin orientation try: qcvars, nwhess, nwgrad, nwmol, version, module, errorTMP = harvest( input_model.molecule, method, stdout, **outfiles ) except Exception as e: raise UnknownError(error_stamp(stdout=stdout, stderr=stderr)) try: if nwgrad is not None: qcvars[f"{method.upper()} TOTAL GRADIENT"] = nwgrad qcvars["CURRENT GRADIENT"] = nwgrad if nwhess is not None: qcvars[f"{method.upper()} TOTAL HESSIAN"] = nwhess qcvars["CURRENT HESSIAN"] = nwhess # Normalize the output as a float or list of floats if input_model.driver.upper() == "PROPERTIES": retres = qcvars[f"CURRENT ENERGY"] else: > retres = qcvars[f"CURRENT {input_model.driver.upper()}"] E KeyError: 'CURRENT GRADIENT' qcengine/programs/nwchem/runner.py:275: KeyError During handling of the above exception, another exception occurred: nh2 = Molecule(name='H2N', formula='H2N', hash='4002acf') @using("nwchem") def test_gradient(nh2): resi = { "molecule": nh2, "driver": "gradient", "model": {"method": "b3lyp", "basis": "3-21g"}, "keywords": {"dft__convergence__gradient": "1e-6"}, } > res = qcng.compute(resi, "nwchem", raise_error=True, return_dict=True) qcengine/programs/tests/test_nwchem.py:114: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ qcengine/compute.py:91: in compute output_data = executor.compute(input_data, config) qcengine/programs/model.py:116: in compute result = self._compute(local_input_data, config) qcengine/programs/nwchem/runner.py:137: in _compute return self.parse_output(dexe["outfiles"], input_model) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = NWChemHarness(name='NWChem', scratch=True, thread_safe=False, thread_parallel=False, node_parallel=True, managed_memory=True, extras=None, version_cache={'/usr/local/bin/nwchem': '7.0.2+11.eol.2499.gbbee7e139269'}) outfiles = {'nwchem.grad': None, 'nwchem.hess': None} input_model = AtomicInput(driver='gradient', model={'method': 'b3lyp', 'basis': '3-21g'}, molecule_hash='4002acf') def parse_output( self, outfiles: Dict[str, str], input_model: "AtomicInput" ) -> AtomicResult: # lgtm: [py/similar-function] # Get the stdout from the calculation (required) stdout = outfiles.pop("stdout") stderr = outfiles.pop("stderr") method = input_model.model.method.lower() method = method[4:] if method.startswith("nwc-") else method # Read the NWChem stdout file and, if needed, the hess or grad files # July 2021: nwmol & vector returns now atin/outfile orientation depending on fix_com,orientation=T/F. previously always atin orientation try: qcvars, nwhess, nwgrad, nwmol, version, module, errorTMP = harvest( input_model.molecule, method, stdout, **outfiles ) except Exception as e: raise UnknownError(error_stamp(stdout=stdout, stderr=stderr)) try: if nwgrad is not None: qcvars[f"{method.upper()} TOTAL GRADIENT"] = nwgrad qcvars["CURRENT GRADIENT"] = nwgrad if nwhess is not None: qcvars[f"{method.upper()} TOTAL HESSIAN"] = nwhess qcvars["CURRENT HESSIAN"] = nwhess # Normalize the output as a float or list of floats if input_model.driver.upper() == "PROPERTIES": retres = qcvars[f"CURRENT ENERGY"] else: retres = qcvars[f"CURRENT {input_model.driver.upper()}"] except KeyError as e: > raise UnknownError(error_stamp(stdout=stdout, stderr=stderr)) E qcengine.exceptions.UnknownError: STDOUT: E E E E ============================== echo of input deck ============================== E echo E geometry units bohr E N 0.000000000000 0.000000000000 -0.145912920000 E H 0.000000000000 -1.511214300000 1.013682600000 E H 0.000000000000 1.511214300000 1.013682600000 E symmetry c1 E end E memory 879931424 double E charge 0 E E basis E H library 3-21g E bqH library H 3-21g E N library 3-21g E bqN library N 3-21g E end E E dft E convergence gradient 1e-6 E mult 2 E xc b3lyp E end E E mcscf E multiplicity 2 E end E E scf E nopen 1 E end E E task dft gradient E E E python E grad = rtdb_get('dft:gradient') E if ga_nodeid() == 0: E import json E with open('nwchem.grad', 'w') as fp: E json.dump(grad, fp) E end E E task python E E ================================================================================ E E E E E E E Northwest Computational Chemistry Package (NWChem) 7.0.2 E -------------------------------------------------------- E E E Environmental Molecular Sciences Laboratory E Pacific Northwest National Laboratory E Richland, WA 99352 E E Copyright (c) 1994-2020 E Pacific Northwest National Laboratory E Battelle Memorial Institute E E NWChem is an open-source computational chemistry package E distributed under the terms of the E Educational Community License (ECL) 2.0 E A copy of the license is included with this distribution E in the LICENSE.TXT file E E ACKNOWLEDGMENT E -------------- E E This software and its documentation were developed at the E EMSL at Pacific Northwest National Laboratory, a multiprogram E national laboratory, operated for the U.S. Department of Energy E by Battelle under Contract Number DE-AC05-76RL01830. Support E for this work was provided by the Department of Energy Office E of Biological and Environmental Research, Office of Basic E Energy Sciences, and the Office of Advanced Scientific Computing. E E E Job information E --------------- E E hostname = yv.noip.me E program = /usr/local/bin/nwchem E date = Thu Oct 21 12:49:03 2021 E E compiled = Thu_Oct_21_12:11:03_2021 E source = /disk-samsung/freebsd-ports/science/nwchem/work/nwchem-7.0.2-release/src/.. E nwchem branch = 7.0.2 E nwchem revision = 11-eol-2499-gbbee7e139269 E ga revision = 5.8.0 E use scalapack = T E input = nwchem.nw E prefix = nwchem. E data base = ./nwchem.db E status = startup E nproc = 1 E time left = -1s E E E E Memory information E ------------------ E E heap = 219982852 doubles = 1678.3 Mbytes E stack = 219982857 doubles = 1678.3 Mbytes E global = 439965712 doubles = 3356.7 Mbytes (distinct from heap & stack) E total = 879931421 doubles = 6713.3 Mbytes E verify = yes E hardfail = no E E E Directory information E --------------------- E E 0 permanent = . E 0 scratch = . E E E E E NWChem Input Module E ------------------- E E E Turning off AUTOSYM since E SYMMETRY directive was detected! E E E ------ E auto-z E ------ E no constraints, skipping 0.0000000000000000 E no constraints, skipping 0.0000000000000000 E E E Geometry "geometry" -> "" E ------------------------- E E Output coordinates in a.u. (scale by 1.000000000 to convert to a.u.) E E No. Tag Charge X Y Z E ---- ---------------- ---------- -------------- -------------- -------------- E 1 N 7.0000 0.00000000 0.00000000 -0.25768789 E 2 H 1.0000 0.00000000 -1.51121430 0.90190763 E 3 H 1.0000 0.00000000 1.51121430 0.90190763 E E Atomic Mass E ----------- E E N 14.003070 E H 1.007825 E E E Effective nuclear repulsion energy (a.u.) 7.6805432250 E E Nuclear Dipole moment (a.u.) E ---------------------------- E X Y Z E ---------------- ---------------- ---------------- E 0.0000000000 0.0000000000 0.0000000000 E E E E Z-matrix (autoz) E -------- E E Units are Angstrom for bonds and degrees for angles E E Type Name I J K L M Value E ----------- -------- ----- ----- ----- ----- ----- ---------- E 1 Stretch 1 2 1.00800 E 2 Stretch 1 3 1.00800 E 3 Bend 2 1 3 105.00000 E E E XYZ format geometry E ------------------- E 3 E geometry E N 0.00000000 0.00000000 -0.13636257 E H 0.00000000 -0.79970023 0.47726900 E H 0.00000000 0.79970023 0.47726900 E E ============================================================================== E internuclear distances E ------------------------------------------------------------------------------ E center one | center two | atomic units | a.u. E ------------------------------------------------------------------------------ E 2 H | 1 N | 1.90484 | 1.90484 E 3 H | 1 N | 1.90484 | 1.90484 E ------------------------------------------------------------------------------ E number of included internuclear distances: 2 E ============================================================================== E E E E ============================================================================== E internuclear angles E ------------------------------------------------------------------------------ E center 1 | center 2 | center 3 | degrees E ------------------------------------------------------------------------------ E 2 H | 1 N | 3 H | 105.00 E ------------------------------------------------------------------------------ E number of included internuclear angles: 1 E ============================================================================== E E E E library name resolved from: .nwchemrc E library file name is: E E Basis "ao basis" -> "" (cartesian) E ----- E H (Hydrogen) E ------------ E Exponent Coefficients E -------------- --------------------------------------------------------- E 1 S 5.44717800E+00 0.156285 E 1 S 8.24547000E-01 0.904691 E E 2 S 1.83192000E-01 1.000000 E E bqH E --- E Exponent Coefficients E -------------- --------------------------------------------------------- E 1 S 5.44717800E+00 0.156285 E 1 S 8.24547000E-01 0.904691 E E 2 S 1.83192000E-01 1.000000 E E N (Nitrogen) E ------------ E Exponent Coefficients E -------------- --------------------------------------------------------- E 1 S 2.42766000E+02 0.059866 E 1 S 3.64851000E+01 0.352955 E 1 S 7.81449000E+00 0.706513 E E 2 S 5.42522000E+00 -0.413301 E 2 S 1.14915000E+00 1.224420 E E 3 P 5.42522000E+00 0.237972 E 3 P 1.14915000E+00 0.858953 E E 4 S 2.83205000E-01 1.000000 E E 5 P 2.83205000E-01 1.000000 E E bqN E --- E Exponent Coefficients E -------------- --------------------------------------------------------- E 1 S 2.42766000E+02 0.059866 E 1 S 3.64851000E+01 0.352955 E 1 S 7.81449000E+00 0.706513 E E 2 S 5.42522000E+00 -0.413301 E 2 S 1.14915000E+00 1.224420 E E 3 P 5.42522000E+00 0.237972 E 3 P 1.14915000E+00 0.858953 E E 4 S 2.83205000E-01 1.000000 E E 5 P 2.83205000E-01 1.000000 E E E E Summary of "ao basis" -> "" (cartesian) E ------------------------------------------------------------------------------ E Tag Description Shells Functions and Types E ---------------- ------------------------------ ------ --------------------- E H 3-21g 2 2 2s E bqH 3-21g 2 2 2s E N 3-21g 5 9 3s2p E bqN 3-21g 5 9 3s2p E E E E NWChem DFT Module E ----------------- E E E E E Summary of "ao basis" -> "ao basis" (cartesian) E ------------------------------------------------------------------------------ E Tag Description Shells Functions and Types E ---------------- ------------------------------ ------ --------------------- E H 3-21g 2 2 2s E bqH 3-21g 2 2 2s E N 3-21g 5 9 3s2p E bqN 3-21g 5 9 3s2p E E E Caching 1-el integrals E E General Information E ------------------- E SCF calculation type: DFT E Wavefunction type: spin polarized. E No. of atoms : 3 E No. of electrons : 9 E Alpha electrons : 5 E Beta electrons : 4 E Charge : 0 E Spin multiplicity: 2 E Use of symmetry is: off; symmetry adaption is: off E Maximum number of iterations: 30 E AO basis - number of functions: 13 E number of shells: 9 E Convergence on energy requested: 1.00D-06 E Convergence on density requested: 1.00D-05 E Convergence on gradient requested: 1.00D-06 E E XC Information E -------------- E B3LYP Method XC Potential E Hartree-Fock (Exact) Exchange 0.200 E Slater Exchange Functional 0.800 local E Becke 1988 Exchange Functional 0.720 non-local E Lee-Yang-Parr Correlation Functional 0.810 E VWN I RPA Correlation Functional 0.190 local E E Grid Information E ---------------- E Grid used for XC integration: medium E Radial quadrature: Mura-Knowles E Angular quadrature: Lebedev. E Tag B.-S. Rad. Rad. Pts. Rad. Cut. Ang. Pts. E --- ---------- --------- --------- --------- E N 0.65 49 5.0 434 E H 0.35 45 6.0 434 E Grid pruning is: on E Number of quadrature shells: 139 E Spatial weights used: Erf1 E E Convergence Information E ----------------------- E Convergence aids based upon iterative change in E total energy or number of iterations. E Levelshifting, if invoked, occurs when the E HOMO/LUMO gap drops below (HL_TOL): 1.00D-02 E DIIS, if invoked, will attempt to extrapolate E using up to (NFOCK): 10 stored Fock matrices. E E Damping( 0%) Levelshifting(0.5) DIIS E --------------- ------------------- --------------- E dE on: start ASAP start E dE off: 2 iters 30 iters 30 iters E E E Screening Tolerance Information E ------------------------------- E Density screening/tol_rho: 1.00D-10 E AO Gaussian exp screening on grid/accAOfunc: 14 E CD Gaussian exp screening on grid/accCDfunc: 20 E XC Gaussian exp screening on grid/accXCfunc: 20 E Schwarz screening/accCoul: 1.00D-08 E E E Superposition of Atomic Density Guess E ------------------------------------- E E Sum of atomic energies: -55.00575769 E E Non-variational initial energy E ------------------------------ E E Total energy = -55.098827 E 1-e energy = -89.297923 E 2-e energy = 26.518553 E HOMO = -0.254418 E LUMO = 0.208647 E E Time after variat. SCF: 0.1 E Time prior to 1st pass: 0.1 E E #quartets = 1.035D+03 #integrals = 2.423D+03 #direct = 0.0% #cached =100.0% E E E Integral file = ./nwchem.aoints.0 E Record size in doubles = 65536 No. of integs per rec = 43688 E Max. records in memory = 2 Max. records in file = 126087 E No. of bits per label = 8 No. of bits per value = 64 E E E Grid_pts file = ./nwchem.gridpts.0 E Record size in doubles = 12289 No. of grid_pts per rec = 3070 E Max. records in memory = 23 Max. recs in file = 672262 E E E Memory utilization after 1st SCF pass: E Heap Space remaining (MW): 219.57 219567932 E Stack Space remaining (MW): 219.98 219982596 E E convergence iter energy DeltaE RMS-Dens Diis-err time E ---------------- ----- ----------------- --------- --------- --------- ------ E d= 0,ls=0.0,diis 1 -55.5381145899 -6.32D+01 1.43D-02 3.69D-02 0.3 E 1.27D-02 3.50D-02 E d= 0,ls=0.0,diis 2 -55.5536750786 -1.56D-02 2.33D-03 8.16D-04 0.5 E 1.69D-03 2.41D-04 E d= 0,ls=0.0,diis 3 -55.5539245810 -2.50D-04 6.55D-04 1.79D-04 0.6 E 8.87D-04 3.12D-04 E d= 0,ls=0.0,diis 4 -55.5540280623 -1.03D-04 2.88D-04 2.44D-05 0.8 E 8.94D-05 2.51D-06 E d= 0,ls=0.0,diis 5 -55.5540368117 -8.75D-06 9.91D-05 4.44D-07 1.0 E 8.89D-05 3.55D-07 E d= 0,ls=0.0,diis 6 -55.5540374684 -6.57D-07 1.33D-05 3.92D-09 1.1 E 1.78D-05 4.50D-09 E d= 0,ls=0.0,diis 7 -55.5540374771 -8.76D-09 1.49D-06 3.75D-11 1.3 E 1.61D-06 2.75D-11 E E E Total DFT energy = -55.554037477144 E One electron energy = -90.135977635636 E Coulomb energy = 34.520280766762 E Exchange-Corr. energy = -7.618883833320 E Nuclear repulsion energy = 7.680543225050 E E Numeric. integr. density = 9.000001805107 E E Total iterative time = 1.2s E E E E DFT Final Alpha Molecular Orbital Analysis E ------------------------------------------ E E Vector 1 Occ=1.000000D+00 E=-1.425003D+01 E MO Center= -4.3D-14, 2.8D-13, -1.4D-01, r^2= 2.0D-02 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 1 0.984055 1 N s 2 0.104479 1 N s E 6 -0.049248 1 N s E E Vector 2 Occ=1.000000D+00 E=-8.570840D-01 E MO Center= -1.4D-11, -4.4D-10, 1.5D-01, r^2= 6.3D-01 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 6 0.654549 1 N s 1 -0.218593 1 N s E 2 0.213070 1 N s 10 0.141610 2 H s E 12 0.141610 3 H s 5 0.134652 1 N pz E 9 0.124342 1 N pz E E Vector 3 Occ=1.000000D+00 E=-4.725099D-01 E MO Center= 2.5D-23, 4.1D-10, 1.3D-01, r^2= 9.5D-01 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 4 0.409573 1 N py 8 0.297229 1 N py E 10 -0.242571 2 H s 12 0.242571 3 H s E 11 -0.212552 2 H s 13 0.212552 3 H s E E Vector 4 Occ=1.000000D+00 E=-2.902855D-01 E MO Center= -7.1D-10, 1.8D-21, -1.4D-01, r^2= 6.9D-01 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 7 0.610168 1 N px 3 0.537692 1 N px E E Vector 5 Occ=1.000000D+00 E=-2.846159D-01 E MO Center= 7.2D-10, -8.9D-11, -3.1D-01, r^2= 7.7D-01 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 6 0.528699 1 N s 9 -0.458426 1 N pz E 5 -0.434272 1 N pz 11 -0.135656 2 H s E 13 -0.135656 3 H s 10 -0.122879 2 H s E 12 -0.122879 3 H s 1 -0.111887 1 N s E 2 0.092321 1 N s E E Vector 6 Occ=0.000000D+00 E= 1.122910D-01 E MO Center= -7.3D-13, -2.0D-09, 5.7D-01, r^2= 2.3D+00 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 6 1.258816 1 N s 11 -0.998718 2 H s E 13 -0.998718 3 H s 9 0.581699 1 N pz E 5 0.258262 1 N pz 1 -0.120746 1 N s E 10 -0.072567 2 H s 12 -0.072567 3 H s E 2 0.060997 1 N s E E Vector 7 Occ=0.000000D+00 E= 1.911021D-01 E MO Center= 4.6D-22, 2.1D-09, 4.8D-01, r^2= 2.3D+00 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 11 1.204566 2 H s 13 -1.204566 3 H s E 8 0.906360 1 N py 4 0.380319 1 N py E 10 0.080687 2 H s 12 -0.080687 3 H s E E Vector 8 Occ=0.000000D+00 E= 8.935097D-01 E MO Center= -1.9D-21, -2.4D-09, 2.0D-01, r^2= 1.7D+00 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 10 0.932129 2 H s 12 -0.932129 3 H s E 11 -0.636865 2 H s 13 0.636865 3 H s E 8 0.559954 1 N py E E Vector 9 Occ=0.000000D+00 E= 9.779868D-01 E MO Center= -1.8D-11, 2.3D-09, 4.9D-01, r^2= 1.2D+00 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 10 0.946465 2 H s 12 0.946465 3 H s E 11 -0.536368 2 H s 13 -0.536368 3 H s E 5 -0.341848 1 N pz 9 -0.151839 1 N pz E 2 -0.065630 1 N s 1 0.061945 1 N s E 6 -0.026069 1 N s E E Vector 10 Occ=0.000000D+00 E= 1.019549D+00 E MO Center= -3.6D-13, 5.6D-23, -1.4D-01, r^2= 1.0D+00 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 3 1.036225 1 N px 7 -0.995274 1 N px E E Vector 11 Occ=0.000000D+00 E= 1.119679D+00 E MO Center= 8.6D-12, -4.5D-11, -3.4D-01, r^2= 1.0D+00 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 9 1.238697 1 N pz 5 -0.998126 1 N pz E 6 0.338629 1 N s 10 -0.260494 2 H s E 12 -0.260494 3 H s 11 -0.193704 2 H s E 13 -0.193704 3 H s 2 0.111902 1 N s E 1 -0.055193 1 N s E E Vector 12 Occ=0.000000D+00 E= 1.236048D+00 E MO Center= -3.2D-22, 6.7D-11, -9.5D-02, r^2= 1.3D+00 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 8 1.506342 1 N py 4 -1.078878 1 N py E 11 0.833877 2 H s 13 -0.833877 3 H s E 10 -0.100253 2 H s 12 0.100253 3 H s E E Vector 13 Occ=0.000000D+00 E= 2.081951D+00 E MO Center= 1.0D-11, 5.6D-11, 8.1D-02, r^2= 1.0D+00 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 6 2.323423 1 N s 2 -1.714033 1 N s E 9 0.605423 1 N pz 11 -0.580577 2 H s E 13 -0.580577 3 H s 10 -0.211280 2 H s E 12 -0.211280 3 H s 5 -0.152103 1 N pz E 1 0.049169 1 N s E E E DFT Final Beta Molecular Orbital Analysis E ----------------------------------------- E E Vector 1 Occ=1.000000D+00 E=-1.423161D+01 E MO Center= -3.1D-14, 2.6D-13, -1.4D-01, r^2= 2.0D-02 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 1 0.984377 1 N s 2 0.103209 1 N s E 6 -0.049164 1 N s E E Vector 2 Occ=1.000000D+00 E=-8.041484D-01 E MO Center= -6.5D-12, -5.1D-10, 1.8D-01, r^2= 6.5D-01 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 6 0.606042 1 N s 1 -0.208882 1 N s E 2 0.200945 1 N s 10 0.163440 2 H s E 12 0.163440 3 H s 5 0.140990 1 N pz E 9 0.118873 1 N pz 11 0.045253 2 H s E 13 0.045253 3 H s E E Vector 3 Occ=1.000000D+00 E=-4.587022D-01 E MO Center= 1.7D-22, 4.9D-10, 1.5D-01, r^2= 9.8D-01 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 4 0.393684 1 N py 8 0.278272 1 N py E 10 -0.253005 2 H s 12 0.253005 3 H s E 11 -0.232472 2 H s 13 0.232472 3 H s E E Vector 4 Occ=1.000000D+00 E=-2.555375D-01 E MO Center= 2.6D-11, -9.5D-11, -3.4D-01, r^2= 7.6D-01 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 6 0.554623 1 N s 9 -0.462659 1 N pz E 5 -0.421251 1 N pz 11 -0.134532 2 H s E 13 -0.134532 3 H s 1 -0.118556 1 N s E 10 -0.116052 2 H s 12 -0.116052 3 H s E 2 0.094394 1 N s E E Vector 5 Occ=0.000000D+00 E=-7.405122D-02 E MO Center= -2.0D-11, 2.0D-22, -1.4D-01, r^2= 7.6D-01 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 7 0.668341 1 N px 3 0.475045 1 N px E E Vector 6 Occ=0.000000D+00 E= 1.244482D-01 E MO Center= -3.5D-12, -2.1D-09, 5.7D-01, r^2= 2.3D+00 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 6 1.289451 1 N s 11 -1.007196 2 H s E 13 -1.007196 3 H s 9 0.587551 1 N pz E 5 0.257024 1 N pz 1 -0.125194 1 N s E 10 -0.059181 2 H s 12 -0.059181 3 H s E 2 0.055688 1 N s E E Vector 7 Occ=0.000000D+00 E= 1.997159D-01 E MO Center= 3.2D-22, 2.2D-09, 4.7D-01, r^2= 2.3D+00 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 11 1.208746 2 H s 13 -1.208746 3 H s E 8 0.922549 1 N py 4 0.381818 1 N py E 10 0.068992 2 H s 12 -0.068992 3 H s E E Vector 8 Occ=0.000000D+00 E= 8.939907D-01 E MO Center= -7.3D-22, -2.2D-09, 2.0D-01, r^2= 1.7D+00 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 10 0.931268 2 H s 12 -0.931268 3 H s E 11 -0.640322 2 H s 13 0.640322 3 H s E 8 0.553095 1 N py E E Vector 9 Occ=0.000000D+00 E= 9.861348D-01 E MO Center= 3.2D-12, 2.1D-09, 4.9D-01, r^2= 1.2D+00 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 10 0.945595 2 H s 12 0.945595 3 H s E 11 -0.525267 2 H s 13 -0.525267 3 H s E 5 -0.343290 1 N pz 9 -0.164895 1 N pz E 2 -0.070811 1 N s 1 0.066739 1 N s E 6 -0.050728 1 N s E E Vector 10 Occ=0.000000D+00 E= 1.121024D+00 E MO Center= 2.0D-11, -5.1D-22, -1.4D-01, r^2= 9.2D-01 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 3 1.066399 1 N px 7 -0.957181 1 N px E E Vector 11 Occ=0.000000D+00 E= 1.138230D+00 E MO Center= -2.6D-11, -4.2D-11, -3.3D-01, r^2= 1.0D+00 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 9 1.235869 1 N pz 5 -1.002873 1 N pz E 6 0.350363 1 N s 10 -0.257675 2 H s E 12 -0.257675 3 H s 11 -0.197586 2 H s E 13 -0.197586 3 H s 2 0.109427 1 N s E 1 -0.056481 1 N s E E Vector 12 Occ=0.000000D+00 E= 1.253439D+00 E MO Center= -4.2D-22, 5.8D-11, -1.0D-01, r^2= 1.3D+00 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 8 1.502665 1 N py 4 -1.084099 1 N py E 11 0.819747 2 H s 13 -0.819747 3 H s E 10 -0.090743 2 H s 12 0.090743 3 H s E E Vector 13 Occ=0.000000D+00 E= 2.130353D+00 E MO Center= 7.1D-12, 5.5D-11, 7.7D-02, r^2= 1.0D+00 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 6 2.311562 1 N s 2 -1.715595 1 N s E 9 0.599990 1 N pz 11 -0.573675 2 H s E 13 -0.573675 3 H s 10 -0.210906 2 H s E 12 -0.210906 3 H s 5 -0.150599 1 N pz E 1 0.050437 1 N s E E E alpha - beta orbital overlaps E ----------------------------- E E E alpha 1 2 3 4 5 6 7 8 9 10 E beta 1 2 3 5 4 6 7 8 9 10 E overlap 1.000 0.999 1.000 0.998 0.999 1.000 1.000 1.000 1.000 0.998 E E E alpha 11 12 13 E beta 11 12 13 E overlap 1.000 1.000 1.000 E E -------------------------- E Expectation value of S2: E -------------------------- E = 0.7519 (Exact = 0.7500) E E E center of mass E -------------- E x = 0.00000000 y = 0.00000000 z = -0.11177494 E E moments of inertia (a.u.) E ------------------ E 6.972597808146 0.000000000000 0.000000000000 E 0.000000000000 2.369319507560 0.000000000000 E 0.000000000000 0.000000000000 4.603278300586 E E Multipole analysis of the density E --------------------------------- E E L x y z total alpha beta nuclear E - - - - ----- ----- ---- ------- E 0 0 0 0 -0.000000 -5.000000 -4.000000 9.000000 E E 1 1 0 0 -0.000000 0.000000 -0.000000 0.000000 E 1 0 1 0 0.000000 0.000000 0.000000 0.000000 E 1 0 0 1 0.839909 0.570768 0.269141 0.000000 E E 2 2 0 0 -4.918206 -3.189775 -1.728432 0.000000 E 2 1 1 0 -0.000000 -0.000000 -0.000000 0.000000 E 2 1 0 1 0.000000 0.000000 0.000000 0.000000 E 2 0 2 0 -3.994399 -4.446461 -4.115476 4.567537 E 2 0 1 1 0.000000 0.000000 0.000000 0.000000 E 2 0 0 2 -5.331260 -3.946066 -3.476890 2.091696 E E E Parallel integral file used 1 records with 0 large values E E E General Information E ------------------- E SCF calculation type: DFT E Wavefunction type: spin polarized. E No. of atoms : 3 E No. of electrons : 9 E Alpha electrons : 5 E Beta electrons : 4 E Charge : 0 E Spin multiplicity: 2 E Use of symmetry is: off; symmetry adaption is: off E Maximum number of iterations: 30 E AO basis - number of functions: 13 E number of shells: 9 E Convergence on energy requested: 1.00D-06 E Convergence on density requested: 1.00D-05 E Convergence on gradient requested: 1.00D-06 E E XC Information E -------------- E B3LYP Method XC Potential E Hartree-Fock (Exact) Exchange 0.200 E Slater Exchange Functional 0.800 local E Becke 1988 Exchange Functional 0.720 non-local E Lee-Yang-Parr Correlation Functional 0.810 E VWN I RPA Correlation Functional 0.190 local E E Grid Information E ---------------- E Grid used for XC integration: medium E Radial quadrature: Mura-Knowles E Angular quadrature: Lebedev. E Tag B.-S. Rad. Rad. Pts. Rad. Cut. Ang. Pts. E --- ---------- --------- --------- --------- E N 0.65 49 5.0 434 E H 0.35 45 6.0 434 E Grid pruning is: on E Number of quadrature shells: 139 E Spatial weights used: Erf1 E E Convergence Information E ----------------------- E Convergence aids based upon iterative change in E total energy or number of iterations. E Levelshifting, if invoked, occurs when the E HOMO/LUMO gap drops below (HL_TOL): 1.00D-02 E DIIS, if invoked, will attempt to extrapolate E using up to (NFOCK): 10 stored Fock matrices. E E Damping( 0%) Levelshifting(0.5) DIIS E --------------- ------------------- --------------- E dE on: start ASAP start E dE off: 2 iters 30 iters 30 iters E E E Screening Tolerance Information E ------------------------------- E Density screening/tol_rho: 1.00D-10 E AO Gaussian exp screening on grid/accAOfunc: 14 E CD Gaussian exp screening on grid/accCDfunc: 20 E XC Gaussian exp screening on grid/accXCfunc: 20 E Schwarz screening/accCoul: 1.00D-08 E E E E NWChem DFT Gradient Module E -------------------------- E E E E charge = 0.00 E wavefunction = open shell E E E STDERR: E E Program received signal SIGSEGV: Segmentation fault - invalid memory reference. E E Backtrace for this error: E #0 0x804a1f6db in ??? E #1 0x804a1e896 in ??? E #2 0x803729f6f in handle_signal E at /disk-samsung/freebsd-src/lib/libthr/thread/thr_sig.c:303 E #3 0x80372953e in thr_sighandler E at /disk-samsung/freebsd-src/lib/libthr/thread/thr_sig.c:246 E #4 0x7ffffffff192 in ??? E #5 0x803dd91b1 in ??? E #6 0x803badeb5 in ??? E #7 0x803298434 in ??? E #8 0x80329901d in ??? E #9 0x802f076a9 in ??? E #10 0x802e70b74 in ??? E #11 0x9f45dc in ??? E #12 0x9e382f in ??? E #13 0x7f38de in ??? E #14 0x7e7ba4 in ??? E #15 0x582d21 in ??? E #16 0x583157 in ??? E #17 0x421a14 in ??? E #18 0x422db0 in ??? E #19 0x41462d in ??? E #20 0x40e0e1 in ??? E #21 0x40c71c in ??? E #22 0x40c82f in ??? E E TRACEBACK: E Traceback (most recent call last): E File "/disk-samsung/freebsd-ports/science/py-qcengine/work-py38/qcengine-0.20.1/qcengine/programs/nwchem/runner.py", line 275, in parse_output E retres = qcvars[f"CURRENT {input_model.driver.upper()}"] E KeyError: 'CURRENT GRADIENT' qcengine/programs/nwchem/runner.py:277: UnknownError ______________________________ test_geometry_bug _______________________________ self = NWChemHarness(name='NWChem', scratch=True, thread_safe=False, thread_parallel=False, node_parallel=True, managed_memory=True, extras=None, version_cache={'/usr/local/bin/nwchem': '7.0.2+11.eol.2499.gbbee7e139269'}) outfiles = {'nwchem.grad': None, 'nwchem.hess': None} input_model = AtomicInput(driver='gradient', model={'method': 'b3lyp', 'basis': '6-31g'}, molecule_hash='02bbc5a') def parse_output( self, outfiles: Dict[str, str], input_model: "AtomicInput" ) -> AtomicResult: # lgtm: [py/similar-function] # Get the stdout from the calculation (required) stdout = outfiles.pop("stdout") stderr = outfiles.pop("stderr") method = input_model.model.method.lower() method = method[4:] if method.startswith("nwc-") else method # Read the NWChem stdout file and, if needed, the hess or grad files # July 2021: nwmol & vector returns now atin/outfile orientation depending on fix_com,orientation=T/F. previously always atin orientation try: qcvars, nwhess, nwgrad, nwmol, version, module, errorTMP = harvest( input_model.molecule, method, stdout, **outfiles ) except Exception as e: raise UnknownError(error_stamp(stdout=stdout, stderr=stderr)) try: if nwgrad is not None: qcvars[f"{method.upper()} TOTAL GRADIENT"] = nwgrad qcvars["CURRENT GRADIENT"] = nwgrad if nwhess is not None: qcvars[f"{method.upper()} TOTAL HESSIAN"] = nwhess qcvars["CURRENT HESSIAN"] = nwhess # Normalize the output as a float or list of floats if input_model.driver.upper() == "PROPERTIES": retres = qcvars[f"CURRENT ENERGY"] else: > retres = qcvars[f"CURRENT {input_model.driver.upper()}"] E KeyError: 'CURRENT GRADIENT' qcengine/programs/nwchem/runner.py:275: KeyError During handling of the above exception, another exception occurred: @using("nwchem") def test_geometry_bug(): """Make sure that the harvester does not crash if NWChem's autosym moves atoms too far""" # Example molecule that has an RMSD of 2e-4 after NWChem symmetrizes the coordinates xyz = """6 Properties=species:S:1:pos:R:3 unique_id=2da214efcf4e4c277fabc5b2b6ca6f32 pbc="F F F" C -0.00828817 1.39046978 -0.00560069 O -0.00797038 -0.02504537 0.02030606 H 1.00658338 1.81556366 0.00348335 H -0.54657475 1.79916975 -0.87390126 H -0.52288871 1.72555240 0.89907326 H 0.44142019 -0.33354425 -0.77152059""" mol = qcel.models.Molecule.from_data(xyz) > qcng.compute( {"molecule": mol, "model": {"method": "b3lyp", "basis": "6-31g"}, "driver": "gradient"}, "nwchem", raise_error=True, ) qcengine/programs/tests/test_nwchem.py:242: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ qcengine/compute.py:91: in compute output_data = executor.compute(input_data, config) qcengine/programs/model.py:116: in compute result = self._compute(local_input_data, config) qcengine/programs/nwchem/runner.py:137: in _compute return self.parse_output(dexe["outfiles"], input_model) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = NWChemHarness(name='NWChem', scratch=True, thread_safe=False, thread_parallel=False, node_parallel=True, managed_memory=True, extras=None, version_cache={'/usr/local/bin/nwchem': '7.0.2+11.eol.2499.gbbee7e139269'}) outfiles = {'nwchem.grad': None, 'nwchem.hess': None} input_model = AtomicInput(driver='gradient', model={'method': 'b3lyp', 'basis': '6-31g'}, molecule_hash='02bbc5a') def parse_output( self, outfiles: Dict[str, str], input_model: "AtomicInput" ) -> AtomicResult: # lgtm: [py/similar-function] # Get the stdout from the calculation (required) stdout = outfiles.pop("stdout") stderr = outfiles.pop("stderr") method = input_model.model.method.lower() method = method[4:] if method.startswith("nwc-") else method # Read the NWChem stdout file and, if needed, the hess or grad files # July 2021: nwmol & vector returns now atin/outfile orientation depending on fix_com,orientation=T/F. previously always atin orientation try: qcvars, nwhess, nwgrad, nwmol, version, module, errorTMP = harvest( input_model.molecule, method, stdout, **outfiles ) except Exception as e: raise UnknownError(error_stamp(stdout=stdout, stderr=stderr)) try: if nwgrad is not None: qcvars[f"{method.upper()} TOTAL GRADIENT"] = nwgrad qcvars["CURRENT GRADIENT"] = nwgrad if nwhess is not None: qcvars[f"{method.upper()} TOTAL HESSIAN"] = nwhess qcvars["CURRENT HESSIAN"] = nwhess # Normalize the output as a float or list of floats if input_model.driver.upper() == "PROPERTIES": retres = qcvars[f"CURRENT ENERGY"] else: retres = qcvars[f"CURRENT {input_model.driver.upper()}"] except KeyError as e: > raise UnknownError(error_stamp(stdout=stdout, stderr=stderr)) E qcengine.exceptions.UnknownError: STDOUT: E E E E ============================== echo of input deck ============================== E echo E geometry units bohr E C -0.015662370000 2.627607070000 -0.010583770000 E O -0.015061840000 -0.047328890000 0.038372890000 E H 1.902166910000 3.430918080000 0.006582580000 E H -1.032876580000 3.399938080000 -1.651434040000 E H -0.988116460000 3.260821450000 1.699002230000 E H 0.834163270000 -0.630307280000 -1.457962620000 E E end E memory 879931424 double E charge 0 E E basis E H library 6-31g E bqH library H 6-31g E O library 6-31g E bqO library O 6-31g E C library 6-31g E bqC library C 6-31g E end E E dft E xc b3lyp E end E E task dft gradient E E E python E grad = rtdb_get('dft:gradient') E if ga_nodeid() == 0: E import json E with open('nwchem.grad', 'w') as fp: E json.dump(grad, fp) E end E E task python E E ================================================================================ E E E E E E E Northwest Computational Chemistry Package (NWChem) 7.0.2 E -------------------------------------------------------- E E E Environmental Molecular Sciences Laboratory E Pacific Northwest National Laboratory E Richland, WA 99352 E E Copyright (c) 1994-2020 E Pacific Northwest National Laboratory E Battelle Memorial Institute E E NWChem is an open-source computational chemistry package E distributed under the terms of the E Educational Community License (ECL) 2.0 E A copy of the license is included with this distribution E in the LICENSE.TXT file E E ACKNOWLEDGMENT E -------------- E E This software and its documentation were developed at the E EMSL at Pacific Northwest National Laboratory, a multiprogram E national laboratory, operated for the U.S. Department of Energy E by Battelle under Contract Number DE-AC05-76RL01830. Support E for this work was provided by the Department of Energy Office E of Biological and Environmental Research, Office of Basic E Energy Sciences, and the Office of Advanced Scientific Computing. E E E Job information E --------------- E E hostname = yv.noip.me E program = /usr/local/bin/nwchem E date = Thu Oct 21 12:49:07 2021 E E compiled = Thu_Oct_21_12:11:03_2021 E source = /disk-samsung/freebsd-ports/science/nwchem/work/nwchem-7.0.2-release/src/.. E nwchem branch = 7.0.2 E nwchem revision = 11-eol-2499-gbbee7e139269 E ga revision = 5.8.0 E use scalapack = T E input = nwchem.nw E prefix = nwchem. E data base = ./nwchem.db E status = startup E nproc = 1 E time left = -1s E E E E Memory information E ------------------ E E heap = 219982852 doubles = 1678.3 Mbytes E stack = 219982857 doubles = 1678.3 Mbytes E global = 439965712 doubles = 3356.7 Mbytes (distinct from heap & stack) E total = 879931421 doubles = 6713.3 Mbytes E verify = yes E hardfail = no E E E Directory information E --------------------- E E 0 permanent = . E 0 scratch = . E E E E E NWChem Input Module E ------------------- E E E CS symmetry detected E E ------ E auto-z E ------ E no constraints, skipping 0.0000000000000000 E no constraints, skipping 0.0000000000000000 E E E Geometry "geometry" -> "" E ------------------------- E E Output coordinates in a.u. (scale by 1.000000000 to convert to a.u.) E E No. Tag Charge X Y Z E ---- ---------------- ---------- -------------- -------------- -------------- E 1 C 6.0000 -0.02036890 1.24889593 0.00000000 E 2 O 8.0000 -0.16536789 -1.42255589 0.00000000 E 3 H 1.0000 0.93753153 2.00052872 1.68555959 E 4 H 1.0000 0.93753153 2.00052872 -1.68555959 E 5 H 1.0000 -1.96141013 1.95717945 0.00000000 E 6 H 1.0000 1.53150359 -2.07116535 0.00000000 E E Atomic Mass E ----------- E E C 12.000000 E O 15.994910 E H 1.007825 E E E Effective nuclear repulsion energy (a.u.) 40.3062465888 E E Nuclear Dipole moment (a.u.) E ---------------------------- E X Y Z E ---------------- ---------------- ---------------- E 0.0000000000 0.0000000000 0.0000000000 E E Symmetry information E -------------------- E E Group name Cs E Group number 2 E Group order 2 E No. of unique centers 5 E E Symmetry unique atoms E E 1 2 3 5 6 E E E E Z-matrix (autoz) E -------- E E Units are Angstrom for bonds and degrees for angles E E Type Name I J K L M Value E ----------- -------- ----- ----- ----- ----- ----- ---------- E 1 Stretch 1 2 1.41575 E 2 Stretch 1 3 1.10034 E 3 Stretch 1 4 1.10034 E 4 Stretch 1 5 1.09340 E 5 Stretch 2 6 0.96131 E 6 Bend 1 2 6 107.81197 E 7 Bend 2 1 3 112.70047 E 8 Bend 2 1 4 112.70047 E 9 Bend 2 1 5 106.94016 E 10 Bend 3 1 4 108.31392 E 11 Bend 3 1 5 107.99017 E 12 Bend 4 1 5 107.99017 E 13 Torsion 3 1 2 6 -61.48499 E 14 Torsion 4 1 2 6 61.48499 E 15 Torsion 5 1 2 6 180.00000 E E E XYZ format geometry E ------------------- E 6 E geometry E C -0.01077876 0.66088731 0.00000000 E O -0.08750893 -0.75278421 0.00000000 E H 0.49612035 1.05863429 0.89195979 E H 0.49612035 1.05863429 -0.89195979 E H -1.03793362 1.03569484 0.00000000 E H 0.81043685 -1.09601358 0.00000000 E E ============================================================================== E internuclear distances E ------------------------------------------------------------------------------ E center one | center two | atomic units | a.u. E ------------------------------------------------------------------------------ E 2 O | 1 C | 2.67538 | 2.67538 E 3 H | 1 C | 2.07934 | 2.07934 E 4 H | 1 C | 2.07934 | 2.07934 E 5 H | 1 C | 2.06623 | 2.06623 E 6 H | 2 O | 1.81661 | 1.81661 E ------------------------------------------------------------------------------ E number of included internuclear distances: 5 E ============================================================================== E E E E ============================================================================== E internuclear angles E ------------------------------------------------------------------------------ E center 1 | center 2 | center 3 | degrees E ------------------------------------------------------------------------------ E 2 O | 1 C | 3 H | 112.70 E 2 O | 1 C | 4 H | 112.70 E 2 O | 1 C | 5 H | 106.94 E 3 H | 1 C | 4 H | 108.31 E 3 H | 1 C | 5 H | 107.99 E 4 H | 1 C | 5 H | 107.99 E 1 C | 2 O | 6 H | 107.81 E ------------------------------------------------------------------------------ E number of included internuclear angles: 7 E ============================================================================== E E E E library name resolved from: .nwchemrc E library file name is: E E Basis "ao basis" -> "" (cartesian) E ----- E H (Hydrogen) E ------------ E Exponent Coefficients E -------------- --------------------------------------------------------- E 1 S 1.87311370E+01 0.033495 E 1 S 2.82539370E+00 0.234727 E 1 S 6.40121700E-01 0.813757 E E 2 S 1.61277800E-01 1.000000 E E bqH E --- E Exponent Coefficients E -------------- --------------------------------------------------------- E 1 S 1.87311370E+01 0.033495 E 1 S 2.82539370E+00 0.234727 E 1 S 6.40121700E-01 0.813757 E E 2 S 1.61277800E-01 1.000000 E E O (Oxygen) E ---------- E Exponent Coefficients E -------------- --------------------------------------------------------- E 1 S 5.48467170E+03 0.001831 E 1 S 8.25234950E+02 0.013950 E 1 S 1.88046960E+02 0.068445 E 1 S 5.29645000E+01 0.232714 E 1 S 1.68975700E+01 0.470193 E 1 S 5.79963530E+00 0.358521 E E 2 S 1.55396160E+01 -0.110778 E 2 S 3.59993360E+00 -0.148026 E 2 S 1.01376180E+00 1.130767 E E 3 P 1.55396160E+01 0.070874 E 3 P 3.59993360E+00 0.339753 E 3 P 1.01376180E+00 0.727159 E E 4 S 2.70005800E-01 1.000000 E E 5 P 2.70005800E-01 1.000000 E E bqO E --- E Exponent Coefficients E -------------- --------------------------------------------------------- E 1 S 5.48467170E+03 0.001831 E 1 S 8.25234950E+02 0.013950 E 1 S 1.88046960E+02 0.068445 E 1 S 5.29645000E+01 0.232714 E 1 S 1.68975700E+01 0.470193 E 1 S 5.79963530E+00 0.358521 E E 2 S 1.55396160E+01 -0.110778 E 2 S 3.59993360E+00 -0.148026 E 2 S 1.01376180E+00 1.130767 E E 3 P 1.55396160E+01 0.070874 E 3 P 3.59993360E+00 0.339753 E 3 P 1.01376180E+00 0.727159 E E 4 S 2.70005800E-01 1.000000 E E 5 P 2.70005800E-01 1.000000 E E C (Carbon) E ---------- E Exponent Coefficients E -------------- --------------------------------------------------------- E 1 S 3.04752490E+03 0.001835 E 1 S 4.57369510E+02 0.014037 E 1 S 1.03948690E+02 0.068843 E 1 S 2.92101550E+01 0.232184 E 1 S 9.28666300E+00 0.467941 E 1 S 3.16392700E+00 0.362312 E E 2 S 7.86827240E+00 -0.119332 E 2 S 1.88128850E+00 -0.160854 E 2 S 5.44249300E-01 1.143456 E E 3 P 7.86827240E+00 0.068999 E 3 P 1.88128850E+00 0.316424 E 3 P 5.44249300E-01 0.744308 E E 4 S 1.68714400E-01 1.000000 E E 5 P 1.68714400E-01 1.000000 E E bqC E --- E Exponent Coefficients E -------------- --------------------------------------------------------- E 1 S 3.04752490E+03 0.001835 E 1 S 4.57369510E+02 0.014037 E 1 S 1.03948690E+02 0.068843 E 1 S 2.92101550E+01 0.232184 E 1 S 9.28666300E+00 0.467941 E 1 S 3.16392700E+00 0.362312 E E 2 S 7.86827240E+00 -0.119332 E 2 S 1.88128850E+00 -0.160854 E 2 S 5.44249300E-01 1.143456 E E 3 P 7.86827240E+00 0.068999 E 3 P 1.88128850E+00 0.316424 E 3 P 5.44249300E-01 0.744308 E E 4 S 1.68714400E-01 1.000000 E E 5 P 1.68714400E-01 1.000000 E E E E Summary of "ao basis" -> "" (cartesian) E ------------------------------------------------------------------------------ E Tag Description Shells Functions and Types E ---------------- ------------------------------ ------ --------------------- E H 6-31g 2 2 2s E bqH 6-31g 2 2 2s E O 6-31g 5 9 3s2p E bqO 6-31g 5 9 3s2p E C 6-31g 5 9 3s2p E bqC 6-31g 5 9 3s2p E E E E NWChem DFT Module E ----------------- E E E E E Summary of "ao basis" -> "ao basis" (cartesian) E ------------------------------------------------------------------------------ E Tag Description Shells Functions and Types E ---------------- ------------------------------ ------ --------------------- E H 6-31g 2 2 2s E bqH 6-31g 2 2 2s E O 6-31g 5 9 3s2p E bqO 6-31g 5 9 3s2p E C 6-31g 5 9 3s2p E bqC 6-31g 5 9 3s2p E E E Symmetry analysis of basis E -------------------------- E E a' 20 E a" 6 E E Caching 1-el integrals E E General Information E ------------------- E SCF calculation type: DFT E Wavefunction type: closed shell. E No. of atoms : 6 E No. of electrons : 18 E Alpha electrons : 9 E Beta electrons : 9 E Charge : 0 E Spin multiplicity: 1 E Use of symmetry is: on ; symmetry adaption is: on E Maximum number of iterations: 30 E AO basis - number of functions: 26 E number of shells: 18 E Convergence on energy requested: 1.00D-06 E Convergence on density requested: 1.00D-05 E Convergence on gradient requested: 5.00D-04 E E XC Information E -------------- E B3LYP Method XC Potential E Hartree-Fock (Exact) Exchange 0.200 E Slater Exchange Functional 0.800 local E Becke 1988 Exchange Functional 0.720 non-local E Lee-Yang-Parr Correlation Functional 0.810 E VWN I RPA Correlation Functional 0.190 local E E Grid Information E ---------------- E Grid used for XC integration: medium E Radial quadrature: Mura-Knowles E Angular quadrature: Lebedev. E Tag B.-S. Rad. Rad. Pts. Rad. Cut. Ang. Pts. E --- ---------- --------- --------- --------- E C 0.70 49 7.0 434 E O 0.60 49 7.0 434 E H 0.35 45 8.0 434 E Grid pruning is: on E Number of quadrature shells: 233 E Spatial weights used: Erf1 E E Convergence Information E ----------------------- E Convergence aids based upon iterative change in E total energy or number of iterations. E Levelshifting, if invoked, occurs when the E HOMO/LUMO gap drops below (HL_TOL): 1.00D-02 E DIIS, if invoked, will attempt to extrapolate E using up to (NFOCK): 10 stored Fock matrices. E E Damping( 0%) Levelshifting(0.5) DIIS E --------------- ------------------- --------------- E dE on: start ASAP start E dE off: 2 iters 30 iters 30 iters E E E Screening Tolerance Information E ------------------------------- E Density screening/tol_rho: 1.00D-10 E AO Gaussian exp screening on grid/accAOfunc: 14 E CD Gaussian exp screening on grid/accCDfunc: 20 E XC Gaussian exp screening on grid/accXCfunc: 20 E Schwarz screening/accCoul: 1.00D-08 E E E Superposition of Atomic Density Guess E ------------------------------------- E E Sum of atomic energies: -114.40753654 E E Non-variational initial energy E ------------------------------ E E Total energy = -115.281416 E 1-e energy = -234.910594 E 2-e energy = 79.322931 E HOMO = -0.363031 E LUMO = 0.127665 E E E Symmetry analysis of molecular orbitals - initial E ------------------------------------------------- E E Numbering of irreducible representations: E E 1 a' 2 a" E E Orbital symmetries: E E 1 a' 2 a' 3 a' 4 a' 5 a' E 6 a" 7 a' 8 a' 9 a" 10 a' E 11 a' 12 a' 13 a" 14 a' 15 a' E 16 a" 17 a' 18 a' 19 a" E E Time after variat. SCF: 0.2 E Time prior to 1st pass: 0.2 E E #quartets = 1.045D+04 #integrals = 3.565D+04 #direct = 0.0% #cached =100.0% E E E Integral file = ./nwchem.aoints.0 E Record size in doubles = 65536 No. of integs per rec = 43688 E Max. records in memory = 3 Max. records in file = 126083 E No. of bits per label = 8 No. of bits per value = 64 E E E Grid_pts file = ./nwchem.gridpts.0 E Record size in doubles = 12289 No. of grid_pts per rec = 3070 E Max. records in memory = 38 Max. recs in file = 672251 E E E Memory utilization after 1st SCF pass: E Heap Space remaining (MW): 219.32 219317340 E Stack Space remaining (MW): 219.98 219982540 E E convergence iter energy DeltaE RMS-Dens Diis-err time E ---------------- ----- ----------------- --------- --------- --------- ------ E d= 0,ls=0.0,diis 1 -115.6346747298 -1.56D+02 3.26D-02 3.57D-01 0.6 E d= 0,ls=0.0,diis 2 -115.6312557818 3.42D-03 1.68D-02 4.75D-01 0.8 E d= 0,ls=0.0,diis 3 -115.6766948011 -4.54D-02 2.57D-03 1.68D-02 1.0 E d= 0,ls=0.0,diis 4 -115.6781351426 -1.44D-03 6.58D-04 5.56D-04 1.2 E d= 0,ls=0.0,diis 5 -115.6782044116 -6.93D-05 1.62D-04 3.10D-05 1.4 E Resetting Diis E d= 0,ls=0.0,diis 6 -115.6782083625 -3.95D-06 1.40D-05 8.15D-08 1.7 E d= 0,ls=0.0,diis 7 -115.6782083782 -1.56D-08 2.22D-06 9.27D-10 1.9 E E E Total DFT energy = -115.678208378154 E One electron energy = -236.880028840293 E Coulomb energy = 96.419913913445 E Exchange-Corr. energy = -15.524340040065 E Nuclear repulsion energy = 40.306246588759 E E Numeric. integr. density = 17.999998635402 E E Total iterative time = 1.7s E E E E Occupations of the irreducible representations E ---------------------------------------------- E E irrep alpha beta E -------- -------- -------- E a' 7.0 7.0 E a" 2.0 2.0 E E E DFT Final Molecular Orbital Analysis E ------------------------------------ E E Vector 1 Occ=2.000000D+00 E=-1.913620D+01 Symmetry=a' E MO Center= -8.7D-02, -7.5D-01, 8.8D-20, r^2= 1.5D-02 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 10 0.995089 2 O s 11 0.028888 2 O s E E Vector 2 Occ=2.000000D+00 E=-1.022263D+01 Symmetry=a' E MO Center= -1.1D-02, 6.6D-01, 6.8D-19, r^2= 2.8D-02 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 1 0.995204 1 C s 2 0.035621 1 C s E 6 -0.026476 1 C s E E Vector 3 Occ=2.000000D+00 E=-1.027665D+00 Symmetry=a' E MO Center= 9.2D-02, -5.6D-01, 5.4D-16, r^2= 5.9D-01 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 15 0.452877 2 O s 11 0.443256 2 O s E 10 -0.202544 2 O s 2 0.146708 1 C s E 25 0.141968 6 H s 12 0.117114 2 O px E 4 -0.105693 1 C py 13 0.076009 2 O py E 1 -0.075273 1 C s 16 0.052752 2 O px E E Vector 4 Occ=2.000000D+00 E=-6.872622D-01 Symmetry=a' E MO Center= 1.3D-02, 4.6D-01, -7.3D-16, r^2= 1.5D+00 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 2 0.363613 1 C s 6 0.349332 1 C s E 1 -0.180316 1 C s 13 0.178720 2 O py E 15 -0.176439 2 O s 23 0.140276 5 H s E 25 -0.137204 6 H s 11 -0.133612 2 O s E 19 0.131546 3 H s 21 0.131546 4 H s E E Vector 5 Occ=2.000000D+00 E=-5.080327D-01 Symmetry=a' E MO Center= 1.4D-01, -6.8D-02, -1.0D-15, r^2= 1.5D+00 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 12 0.313764 2 O px 13 -0.283857 2 O py E 4 0.262454 1 C py 25 0.221244 6 H s E 3 0.203440 1 C px 16 0.152788 2 O px E 15 -0.149951 2 O s 17 -0.131864 2 O py E 26 0.127965 6 H s 19 0.123739 3 H s E E Vector 6 Occ=2.000000D+00 E=-4.412865D-01 Symmetry=a" E MO Center= 1.5D-01, 5.5D-01, -9.4D-16, r^2= 1.4D+00 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 5 0.429643 1 C pz 14 0.249017 2 O pz E 19 0.207183 3 H s 21 -0.207183 4 H s E 9 0.187205 1 C pz 20 0.161421 3 H s E 22 -0.161421 4 H s 18 0.153610 2 O pz E E Vector 7 Occ=2.000000D+00 E=-4.233119D-01 Symmetry=a' E MO Center= -3.1D-01, 3.2D-01, 1.7D-15, r^2= 1.5D+00 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 3 0.348088 1 C px 13 0.319548 2 O py E 23 -0.251821 5 H s 4 -0.247468 1 C py E 7 0.190417 1 C px 17 0.191017 2 O py E 24 -0.173280 5 H s 8 -0.092410 1 C py E 15 -0.091639 2 O s 12 0.089719 2 O px E E Vector 8 Occ=2.000000D+00 E=-3.221820D-01 Symmetry=a' E MO Center= -1.8D-01, -3.2D-01, -1.5D-15, r^2= 1.6D+00 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 12 0.421363 2 O px 15 -0.291219 2 O s E 16 0.286101 2 O px 3 -0.240199 1 C px E 13 0.236246 2 O py 17 0.185471 2 O py E 24 0.183031 5 H s 23 0.168834 5 H s E 11 -0.159077 2 O s 25 0.156755 6 H s E E Vector 9 Occ=2.000000D+00 E=-2.642870D-01 Symmetry=a" E MO Center= 7.5D-03, -4.0D-01, 8.2D-16, r^2= 1.3D+00 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 14 0.600673 2 O pz 18 0.467521 2 O pz E 20 -0.200263 3 H s 22 0.200263 4 H s E 5 -0.174915 1 C pz 19 -0.153626 3 H s E 21 0.153626 4 H s E E Vector 10 Occ=0.000000D+00 E= 7.072652D-02 Symmetry=a' E MO Center= 7.5D-01, -6.2D-01, -4.8D-16, r^2= 2.7D+00 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 26 1.194269 6 H s 15 -0.998498 2 O s E 6 -0.622542 1 C s 8 -0.563608 1 C py E 20 0.449977 3 H s 22 0.449977 4 H s E 16 -0.437560 2 O px 24 0.305574 5 H s E 12 -0.263483 2 O px 4 -0.209459 1 C py E E Vector 11 Occ=0.000000D+00 E= 1.266880D-01 Symmetry=a' E MO Center= 1.5D-01, 9.3D-01, 1.5D-14, r^2= 3.7D+00 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 6 2.368491 1 C s 20 -1.123310 3 H s E 22 -1.123310 4 H s 24 -0.975082 5 H s E 15 -0.603716 2 O s 26 0.463642 6 H s E 17 -0.224772 2 O py 2 0.207209 1 C s E 16 -0.196583 2 O px 8 0.170942 1 C py E E Vector 12 Occ=0.000000D+00 E= 1.618830D-01 Symmetry=a' E MO Center= -5.5D-01, 9.1D-01, -4.2D-15, r^2= 2.8D+00 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 24 1.805731 5 H s 7 1.244406 1 C px E 20 -0.671034 3 H s 22 -0.671034 4 H s E 8 -0.452945 1 C py 3 0.411069 1 C px E 26 -0.326138 6 H s 17 -0.255552 2 O py E 13 -0.148312 2 O py 23 0.124969 5 H s E E Vector 13 Occ=0.000000D+00 E= 1.701269D-01 Symmetry=a" E MO Center= 4.8D-01, 1.0D+00, -9.3D-15, r^2= 2.8D+00 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 20 1.523080 3 H s 22 -1.523080 4 H s E 9 -1.314347 1 C pz 5 -0.466533 1 C pz E 18 0.238612 2 O pz 14 0.107190 2 O pz E 19 0.075734 3 H s 21 -0.075734 4 H s E E Vector 14 Occ=0.000000D+00 E= 2.037186D-01 Symmetry=a' E MO Center= 7.3D-02, 2.1D-01, 2.0D-16, r^2= 2.7D+00 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 8 1.300298 1 C py 26 0.904002 6 H s E 17 0.840447 2 O py 6 -0.705625 1 C s E 15 0.609183 2 O s 7 0.550276 1 C px E 24 0.505078 5 H s 20 -0.452133 3 H s E 22 -0.452133 4 H s 13 0.380179 2 O py E E Vector 15 Occ=0.000000D+00 E= 5.480992D-01 Symmetry=a' E MO Center= -7.2D-02, 6.6D-01, 1.5D-16, r^2= 1.7D+00 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 8 1.450283 1 C py 4 -1.020760 1 C py E 15 0.673455 2 O s 2 0.362356 1 C s E 13 -0.298127 2 O py 6 -0.274302 1 C s E 26 0.243307 6 H s 7 0.231627 1 C px E 11 -0.152605 2 O s 19 -0.148047 3 H s E E Vector 16 Occ=0.000000D+00 E= 5.749326D-01 Symmetry=a' E MO Center= 3.2D-01, 5.6D-01, -7.2D-15, r^2= 2.1D+00 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 7 1.852235 1 C px 3 -0.805275 1 C px E 24 0.596279 5 H s 23 0.463213 5 H s E 8 -0.259002 1 C py 20 -0.245484 3 H s E 22 -0.245484 4 H s 26 -0.212882 6 H s E 19 -0.200570 3 H s 21 -0.200570 4 H s E E Vector 17 Occ=0.000000D+00 E= 5.855805D-01 Symmetry=a" E MO Center= -2.8D-01, 5.4D-01, 6.8D-15, r^2= 2.1D+00 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 9 1.859626 1 C pz 5 -0.781720 1 C pz E 20 -0.522206 3 H s 22 0.522206 4 H s E 19 -0.390463 3 H s 21 0.390463 4 H s E 14 -0.242642 2 O pz 18 -0.162469 2 O pz E E Vector 18 Occ=0.000000D+00 E= 8.343174D-01 Symmetry=a' E MO Center= 3.5D-01, -4.4D-01, 1.9D-15, r^2= 2.6D+00 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 25 1.056346 6 H s 24 0.933523 5 H s E 7 0.823953 1 C px 26 -0.740466 6 H s E 20 -0.493337 3 H s 22 -0.493337 4 H s E 3 -0.451071 1 C px 19 0.396730 3 H s E 21 0.396730 4 H s 12 -0.382921 2 O px E E Vector 19 Occ=0.000000D+00 E= 8.811457D-01 Symmetry=a" E MO Center= 3.8D-01, 7.5D-01, -2.0D-14, r^2= 2.3D+00 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 20 -1.389251 3 H s 22 1.389251 4 H s E 9 1.341949 1 C pz 5 -0.789226 1 C pz E 19 0.728630 3 H s 21 -0.728630 4 H s E 18 -0.557318 2 O pz 14 0.407754 2 O pz E E Vector 20 Occ=0.000000D+00 E= 8.974384D-01 Symmetry=a' E MO Center= -2.8D-01, 1.1D-01, 7.4D-15, r^2= 2.7D+00 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 24 1.113525 5 H s 7 0.962590 1 C px E 20 -0.750413 3 H s 22 -0.750413 4 H s E 23 -0.741495 5 H s 16 -0.654570 2 O px E 12 0.619296 2 O px 3 -0.596934 1 C px E 6 0.526002 1 C s 26 0.429435 6 H s E E Vector 21 Occ=0.000000D+00 E= 9.018199D-01 Symmetry=a' E MO Center= -1.4D-01, 8.3D-01, 7.0D-15, r^2= 2.1D+00 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 6 1.152929 1 C s 23 0.769473 5 H s E 24 -0.771931 5 H s 19 0.647199 3 H s E 21 0.647199 4 H s 20 -0.593542 3 H s E 22 -0.593542 4 H s 2 -0.577558 1 C s E 17 -0.432448 2 O py 4 -0.428907 1 C py E E Vector 22 Occ=0.000000D+00 E= 1.004436D+00 Symmetry=a" E MO Center= -3.8D-02, -4.2D-01, -7.7D-18, r^2= 2.1D+00 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 18 1.150101 2 O pz 14 -0.843157 2 O pz E 19 0.481757 3 H s 21 -0.481757 4 H s E 9 -0.461824 1 C pz 20 -0.264513 3 H s E 22 0.264513 4 H s 5 -0.175838 1 C pz E E Vector 23 Occ=0.000000D+00 E= 1.035223D+00 Symmetry=a' E MO Center= -7.5D-02, 1.4D-01, 3.9D-16, r^2= 3.0D+00 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 6 3.848708 1 C s 2 -1.587155 1 C s E 24 -1.082996 5 H s 20 -0.676461 3 H s E 22 -0.676461 4 H s 26 -0.654004 6 H s E 11 -0.579837 2 O s 25 0.544559 6 H s E 17 -0.499558 2 O py 16 -0.464245 2 O px E E Vector 24 Occ=0.000000D+00 E= 1.063191D+00 Symmetry=a' E MO Center= 4.5D-02, -2.8D-01, 3.5D-15, r^2= 2.6D+00 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 6 2.617375 1 C s 2 -1.459195 1 C s E 17 0.807211 2 O py 20 -0.788875 3 H s E 22 -0.788875 4 H s 24 -0.681646 5 H s E 13 -0.655474 2 O py 26 0.580044 6 H s E 15 -0.510151 2 O s 8 0.493226 1 C py E E Vector 25 Occ=0.000000D+00 E= 1.167354D+00 Symmetry=a' E MO Center= -8.8D-02, -5.9D-01, 1.4D-17, r^2= 2.0D+00 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 6 1.755594 1 C s 16 1.474015 2 O px E 17 -1.183723 2 O py 26 -0.872579 6 H s E 12 -0.650831 2 O px 23 -0.540714 5 H s E 25 -0.526281 6 H s 2 -0.507121 1 C s E 13 0.444977 2 O py 8 -0.357744 1 C py E E Vector 26 Occ=0.000000D+00 E= 1.727181D+00 Symmetry=a' E MO Center= 3.6D-02, -2.5D-01, -3.7D-17, r^2= 1.6D+00 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 15 -3.419092 2 O s 6 3.172175 1 C s E 11 1.705797 2 O s 17 -1.353946 2 O py E 8 -0.792587 1 C py 2 -0.505420 1 C s E 25 0.492822 6 H s 16 -0.431328 2 O px E 24 -0.372262 5 H s 4 -0.348346 1 C py E E E center of mass E -------------- E x = -0.04474480 y = -0.12019575 z = 0.00000000 E E moments of inertia (a.u.) E ------------------ E 72.599920360901 -0.000000356572 0.000000000000 E -0.000000356572 14.117727032640 0.000000000000 E 0.000000000000 0.000000000000 75.264276065896 E E Multipole analysis of the density E --------------------------------- E E L x y z total alpha beta nuclear E - - - - ----- ----- ---- ------- E 0 0 0 0 -0.000000 -9.000000 -9.000000 18.000000 E E 1 1 0 0 0.684410 0.342205 0.342205 0.000000 E 1 0 1 0 0.416192 0.208096 0.208096 0.000000 E 1 0 0 1 -0.000000 -0.000000 -0.000000 0.000000 E E 2 2 0 0 -8.877758 -8.524792 -8.524792 8.171825 E 2 1 1 0 -1.826678 -0.148148 -0.148148 -1.530382 E 2 1 0 1 0.000000 0.000000 0.000000 0.000000 E 2 0 2 0 -9.672325 -25.672300 -25.672300 41.672276 E 2 0 1 1 0.000000 0.000000 0.000000 0.000000 E 2 0 0 2 -10.142365 -7.912293 -7.912293 5.682222 E E E Parallel integral file used 1 records with 0 large values E E E General Information E ------------------- E SCF calculation type: DFT E Wavefunction type: closed shell. E No. of atoms : 6 E No. of electrons : 18 E Alpha electrons : 9 E Beta electrons : 9 E Charge : 0 E Spin multiplicity: 1 E Use of symmetry is: on ; symmetry adaption is: on E Maximum number of iterations: 30 E AO basis - number of functions: 26 E number of shells: 18 E Convergence on energy requested: 1.00D-06 E Convergence on density requested: 1.00D-05 E Convergence on gradient requested: 5.00D-04 E E XC Information E -------------- E B3LYP Method XC Potential E Hartree-Fock (Exact) Exchange 0.200 E Slater Exchange Functional 0.800 local E Becke 1988 Exchange Functional 0.720 non-local E Lee-Yang-Parr Correlation Functional 0.810 E VWN I RPA Correlation Functional 0.190 local E E Grid Information E ---------------- E Grid used for XC integration: medium E Radial quadrature: Mura-Knowles E Angular quadrature: Lebedev. E Tag B.-S. Rad. Rad. Pts. Rad. Cut. Ang. Pts. E --- ---------- --------- --------- --------- E C 0.70 49 7.0 434 E O 0.60 49 7.0 434 E H 0.35 45 8.0 434 E Grid pruning is: on E Number of quadrature shells: 233 E Spatial weights used: Erf1 E E Convergence Information E ----------------------- E Convergence aids based upon iterative change in E total energy or number of iterations. E Levelshifting, if invoked, occurs when the E HOMO/LUMO gap drops below (HL_TOL): 1.00D-02 E DIIS, if invoked, will attempt to extrapolate E using up to (NFOCK): 10 stored Fock matrices. E E Damping( 0%) Levelshifting(0.5) DIIS E --------------- ------------------- --------------- E dE on: start ASAP start E dE off: 2 iters 30 iters 30 iters E E E Screening Tolerance Information E ------------------------------- E Density screening/tol_rho: 1.00D-10 E AO Gaussian exp screening on grid/accAOfunc: 14 E CD Gaussian exp screening on grid/accCDfunc: 20 E XC Gaussian exp screening on grid/accXCfunc: 20 E Schwarz screening/accCoul: 1.00D-08 E E E E NWChem DFT Gradient Module E -------------------------- E E E E charge = 0.00 E wavefunction = closed shell E E Using symmetry E E STDERR: E E Program received signal SIGSEGV: Segmentation fault - invalid memory reference. E E Backtrace for this error: E #0 0x804a1f6db in ??? E #1 0x804a1e896 in ??? E #2 0x803729f6f in handle_signal E at /disk-samsung/freebsd-src/lib/libthr/thread/thr_sig.c:303 E #3 0x80372953e in thr_sighandler E at /disk-samsung/freebsd-src/lib/libthr/thread/thr_sig.c:246 E #4 0x7ffffffff192 in ??? E #5 0x803dd91b1 in ??? E #6 0x803badeb5 in ??? E #7 0x803298434 in ??? E #8 0x80329901d in ??? E #9 0x802f076a9 in ??? E #10 0x802e70b74 in ??? E #11 0x9f45dc in ??? E #12 0x9e382f in ??? E #13 0x7f38de in ??? E #14 0x7e7ba4 in ??? E #15 0x582d21 in ??? E #16 0x583157 in ??? E #17 0x421a14 in ??? E #18 0x422db0 in ??? E #19 0x41462d in ??? E #20 0x40e0e1 in ??? E #21 0x40c71c in ??? E #22 0x40c82f in ??? E E TRACEBACK: E Traceback (most recent call last): E File "/disk-samsung/freebsd-ports/science/py-qcengine/work-py38/qcengine-0.20.1/qcengine/programs/nwchem/runner.py", line 275, in parse_output E retres = qcvars[f"CURRENT {input_model.driver.upper()}"] E KeyError: 'CURRENT GRADIENT' qcengine/programs/nwchem/runner.py:277: UnknownError ______________ test_hf_energy_module[hf rohf ae: nwchem-adz-ene0] ______________ self = NWChemHarness(name='NWChem', scratch=True, thread_safe=False, thread_parallel=False, node_parallel=True, managed_memory=True, extras=None, version_cache={'/usr/local/bin/nwchem': '7.0.2+11.eol.2499.gbbee7e139269'}) outfiles = {'nwchem.grad': None, 'nwchem.hess': None} input_model = AtomicInput(driver='energy', model={'method': 'hf', 'basis': 'aug-cc-pvdz'}, molecule_hash='4002acf') def parse_output( self, outfiles: Dict[str, str], input_model: "AtomicInput" ) -> AtomicResult: # lgtm: [py/similar-function] # Get the stdout from the calculation (required) stdout = outfiles.pop("stdout") stderr = outfiles.pop("stderr") method = input_model.model.method.lower() method = method[4:] if method.startswith("nwc-") else method # Read the NWChem stdout file and, if needed, the hess or grad files # July 2021: nwmol & vector returns now atin/outfile orientation depending on fix_com,orientation=T/F. previously always atin orientation try: qcvars, nwhess, nwgrad, nwmol, version, module, errorTMP = harvest( input_model.molecule, method, stdout, **outfiles ) except Exception as e: raise UnknownError(error_stamp(stdout=stdout, stderr=stderr)) try: if nwgrad is not None: qcvars[f"{method.upper()} TOTAL GRADIENT"] = nwgrad qcvars["CURRENT GRADIENT"] = nwgrad if nwhess is not None: qcvars[f"{method.upper()} TOTAL HESSIAN"] = nwhess qcvars["CURRENT HESSIAN"] = nwhess # Normalize the output as a float or list of floats if input_model.driver.upper() == "PROPERTIES": retres = qcvars[f"CURRENT ENERGY"] else: > retres = qcvars[f"CURRENT {input_model.driver.upper()}"] E KeyError: 'CURRENT ENERGY' qcengine/programs/nwchem/runner.py:275: KeyError During handling of the above exception, another exception occurred: inp = {'call': 'nwchem', 'fcae': 'ae', 'keywords': {'scf__rohf': True}, 'reference': 'rohf'} dertype = 0, basis = 'aug-cc-pvdz', subjects = ['h2o', 'nh2', 'nh2'] clsd_open_pmols = {'bh3p': Molecule(name='bh3p', formula='BH3', hash='f532294'), 'h2o': Molecule(name='h2o', formula='H2O', hash='4684da5'), 'hf': Molecule(name='hf', formula='FH', hash='25205df'), 'nh2': Molecule(name='nh2', formula='H2N', hash='4002acf')} request = > @pytest.mark.parametrize( "dertype", [ pytest.param(0, id="ene0"), ], ) @pytest.mark.parametrize( "basis, subjects", [ pytest.param("cc-pvdz", ["hf", "bh3p", "bh3p"], id="dz"), pytest.param("aug-cc-pvdz", ["h2o", "nh2", "nh2"], id="adz", marks=pytest.mark.long), pytest.param("cfour-qz2p", ["h2o", "nh2", "nh2"], id="qz2p", marks=pytest.mark.long), ], ) @pytest.mark.parametrize( "inp", [ # yapf: disable ######## Are all possible ways of computing working? pytest.param({"call": "cfour", "reference": "rhf", "fcae": "ae", "keywords": {"scf_conv": 12}, }, id="hf rhf ae: cfour", marks=using("cfour")), pytest.param({"call": "gamess", "reference": "rhf", "fcae": "ae", "keywords": {}, }, id="hf rhf ae: gamess", marks=using("gamess")), pytest.param({"call": "nwchem", "reference": "rhf", "fcae": "ae", "keywords": {}, }, id="hf rhf ae: nwchem", marks=using("nwchem")), pytest.param({"call": "psi4", "reference": "rhf", "fcae": "ae", "keywords": {"scf_type": "pk"}, }, id="hf rhf ae: psi4", marks=using("psi4_mp2qcsk")), pytest.param({"call": "cfour", "reference": "uhf", "fcae": "ae", "keywords": {"reference": "uhf", "scf_conv": 12}, }, id="hf uhf ae: cfour", marks=using("cfour")), pytest.param({"call": "gamess", "reference": "uhf", "fcae": "ae", "keywords": {"contrl__scftyp": "uhf"}, }, id="hf uhf ae: gamess", marks=using("gamess")), pytest.param({"call": "nwchem", "reference": "uhf", "fcae": "ae", "keywords": {"scf__uhf": True}, }, id="hf uhf ae: nwchem", marks=using("nwchem")), pytest.param({"call": "psi4", "reference": "uhf", "fcae": "ae", "keywords": {"reference": "uhf", "scf_type": "pk"}, }, id="hf uhf ae: psi4", marks=using("psi4_mp2qcsk")), pytest.param({"call": "cfour", "reference": "rohf", "fcae": "ae", "keywords": {"reference": "rohf", "scf_conv": 12}, }, id="hf rohf ae: cfour", marks=using("cfour")), pytest.param({"call": "gamess", "reference": "rohf", "fcae": "ae", "keywords": {"contrl__scftyp": "rohf"}, }, id="hf rohf ae: gamess", marks=using("gamess")), pytest.param({"call": "nwchem", "reference": "rohf", "fcae": "ae", "keywords": {"scf__rohf": True}, }, id="hf rohf ae: nwchem", marks=using("nwchem")), pytest.param({"call": "psi4", "reference": "rohf", "fcae": "ae", "keywords": {"reference": "rohf", "scf_type": "pk"}, }, id="hf rohf ae: psi4", marks=using("psi4_mp2qcsk")), # yapf: enable ], ) def test_hf_energy_module(inp, dertype, basis, subjects, clsd_open_pmols, request): > runner_asserter(*_processor(inp, dertype, basis, subjects, clsd_open_pmols, request, "energy", "hf")) qcengine/programs/tests/test_standard_suite.py:162: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ qcengine/programs/tests/standard_suite_runner.py:177: in runner_asserter wfn = qcng.compute(atin, qcprog, raise_error=True, local_options=local_options) qcengine/compute.py:91: in compute output_data = executor.compute(input_data, config) qcengine/programs/model.py:116: in compute result = self._compute(local_input_data, config) qcengine/programs/nwchem/runner.py:137: in _compute return self.parse_output(dexe["outfiles"], input_model) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = NWChemHarness(name='NWChem', scratch=True, thread_safe=False, thread_parallel=False, node_parallel=True, managed_memory=True, extras=None, version_cache={'/usr/local/bin/nwchem': '7.0.2+11.eol.2499.gbbee7e139269'}) outfiles = {'nwchem.grad': None, 'nwchem.hess': None} input_model = AtomicInput(driver='energy', model={'method': 'hf', 'basis': 'aug-cc-pvdz'}, molecule_hash='4002acf') def parse_output( self, outfiles: Dict[str, str], input_model: "AtomicInput" ) -> AtomicResult: # lgtm: [py/similar-function] # Get the stdout from the calculation (required) stdout = outfiles.pop("stdout") stderr = outfiles.pop("stderr") method = input_model.model.method.lower() method = method[4:] if method.startswith("nwc-") else method # Read the NWChem stdout file and, if needed, the hess or grad files # July 2021: nwmol & vector returns now atin/outfile orientation depending on fix_com,orientation=T/F. previously always atin orientation try: qcvars, nwhess, nwgrad, nwmol, version, module, errorTMP = harvest( input_model.molecule, method, stdout, **outfiles ) except Exception as e: raise UnknownError(error_stamp(stdout=stdout, stderr=stderr)) try: if nwgrad is not None: qcvars[f"{method.upper()} TOTAL GRADIENT"] = nwgrad qcvars["CURRENT GRADIENT"] = nwgrad if nwhess is not None: qcvars[f"{method.upper()} TOTAL HESSIAN"] = nwhess qcvars["CURRENT HESSIAN"] = nwhess # Normalize the output as a float or list of floats if input_model.driver.upper() == "PROPERTIES": retres = qcvars[f"CURRENT ENERGY"] else: retres = qcvars[f"CURRENT {input_model.driver.upper()}"] except KeyError as e: > raise UnknownError(error_stamp(stdout=stdout, stderr=stderr)) E qcengine.exceptions.UnknownError: STDOUT: E E E E ============================== echo of input deck ============================== E echo E geometry units bohr E N 0.000000000000 0.000000000000 -0.145912920000 E H 0.000000000000 -1.511214300000 1.013682600000 E H 0.000000000000 1.511214300000 1.013682600000 E E end E memory 879931424 double E charge 0 E E basis spherical E H library aug-cc-pvdz E bqH library H aug-cc-pvdz E N library aug-cc-pvdz E bqN library N aug-cc-pvdz E end E E dft E mult 2 E end E E mcscf E multiplicity 2 E end E E scf E rohf E nopen 1 E end E E task scf energy E E ================================================================================ E E E E E E E Northwest Computational Chemistry Package (NWChem) 7.0.2 E -------------------------------------------------------- E E E Environmental Molecular Sciences Laboratory E Pacific Northwest National Laboratory E Richland, WA 99352 E E Copyright (c) 1994-2020 E Pacific Northwest National Laboratory E Battelle Memorial Institute E E NWChem is an open-source computational chemistry package E distributed under the terms of the E Educational Community License (ECL) 2.0 E A copy of the license is included with this distribution E in the LICENSE.TXT file E E ACKNOWLEDGMENT E -------------- E E This software and its documentation were developed at the E EMSL at Pacific Northwest National Laboratory, a multiprogram E national laboratory, operated for the U.S. Department of Energy E by Battelle under Contract Number DE-AC05-76RL01830. Support E for this work was provided by the Department of Energy Office E of Biological and Environmental Research, Office of Basic E Energy Sciences, and the Office of Advanced Scientific Computing. E E E Job information E --------------- E E hostname = yv.noip.me E program = /usr/local/bin/nwchem E date = Thu Oct 21 12:50:05 2021 E E compiled = Thu_Oct_21_12:11:03_2021 E source = /disk-samsung/freebsd-ports/science/nwchem/work/nwchem-7.0.2-release/src/.. E nwchem branch = 7.0.2 E nwchem revision = 11-eol-2499-gbbee7e139269 E ga revision = 5.8.0 E use scalapack = T E input = nwchem.nw E prefix = nwchem. E data base = ./nwchem.db E status = startup E nproc = 1 E time left = -1s E E E E Memory information E ------------------ E E heap = 219982852 doubles = 1678.3 Mbytes E stack = 219982857 doubles = 1678.3 Mbytes E global = 439965712 doubles = 3356.7 Mbytes (distinct from heap & stack) E total = 879931421 doubles = 6713.3 Mbytes E verify = yes E hardfail = no E E E Directory information E --------------------- E E 0 permanent = . E 0 scratch = . E E E E E NWChem Input Module E ------------------- E E E C2V symmetry detected E E ------ E auto-z E ------ E no constraints, skipping 0.0000000000000000 E no constraints, skipping 0.0000000000000000 E E E Geometry "geometry" -> "" E ------------------------- E E Output coordinates in a.u. (scale by 1.000000000 to convert to a.u.) E E No. Tag Charge X Y Z E ---- ---------------- ---------- -------------- -------------- -------------- E 1 N 7.0000 0.00000000 0.00000000 -0.25768789 E 2 H 1.0000 1.51121430 0.00000000 0.90190763 E 3 H 1.0000 -1.51121430 0.00000000 0.90190763 E E Atomic Mass E ----------- E E N 14.003070 E H 1.007825 E E E Effective nuclear repulsion energy (a.u.) 7.6805432250 E E Nuclear Dipole moment (a.u.) E ---------------------------- E X Y Z E ---------------- ---------------- ---------------- E 0.0000000000 0.0000000000 0.0000000000 E E Symmetry information E -------------------- E E Group name C2v E Group number 16 E Group order 4 E No. of unique centers 2 E E Symmetry unique atoms E E 1 2 E E E E Z-matrix (autoz) E -------- E E Units are Angstrom for bonds and degrees for angles E E Type Name I J K L M Value E ----------- -------- ----- ----- ----- ----- ----- ---------- E 1 Stretch 1 2 1.00800 E 2 Stretch 1 3 1.00800 E 3 Bend 2 1 3 105.00000 E E E XYZ format geometry E ------------------- E 3 E geometry E N 0.00000000 0.00000000 -0.13636257 E H 0.79970023 0.00000000 0.47726900 E H -0.79970023 0.00000000 0.47726900 E E ============================================================================== E internuclear distances E ------------------------------------------------------------------------------ E center one | center two | atomic units | a.u. E ------------------------------------------------------------------------------ E 2 H | 1 N | 1.90484 | 1.90484 E 3 H | 1 N | 1.90484 | 1.90484 E ------------------------------------------------------------------------------ E number of included internuclear distances: 2 E ============================================================================== E E E E ============================================================================== E internuclear angles E ------------------------------------------------------------------------------ E center 1 | center 2 | center 3 | degrees E ------------------------------------------------------------------------------ E 2 H | 1 N | 3 H | 105.00 E ------------------------------------------------------------------------------ E number of included internuclear angles: 1 E ============================================================================== E E E E library name resolved from: .nwchemrc E library file name is: E E Basis "ao basis" -> "" (spherical) E ----- E H (Hydrogen) E ------------ E Exponent Coefficients E -------------- --------------------------------------------------------- E 1 S 1.30100000E+01 0.019685 E 1 S 1.96200000E+00 0.137977 E 1 S 4.44600000E-01 0.478148 E E 2 S 1.22000000E-01 1.000000 E E 3 S 2.97400000E-02 1.000000 E E 4 P 7.27000000E-01 1.000000 E E 5 P 1.41000000E-01 1.000000 E E bqH E --- E Exponent Coefficients E -------------- --------------------------------------------------------- E 1 S 1.30100000E+01 0.019685 E 1 S 1.96200000E+00 0.137977 E 1 S 4.44600000E-01 0.478148 E E 2 S 1.22000000E-01 1.000000 E E 3 S 2.97400000E-02 1.000000 E E 4 P 7.27000000E-01 1.000000 E E 5 P 1.41000000E-01 1.000000 E E N (Nitrogen) E ------------ E Exponent Coefficients E -------------- --------------------------------------------------------- E 1 S 9.04600000E+03 0.000700 E 1 S 1.35700000E+03 0.005389 E 1 S 3.09300000E+02 0.027406 E 1 S 8.77300000E+01 0.103207 E 1 S 2.85600000E+01 0.278723 E 1 S 1.02100000E+01 0.448540 E 1 S 3.83800000E+00 0.278238 E 1 S 7.46600000E-01 0.015440 E E 2 S 9.04600000E+03 -0.000153 E 2 S 1.35700000E+03 -0.001208 E 2 S 3.09300000E+02 -0.005992 E 2 S 8.77300000E+01 -0.024544 E 2 S 2.85600000E+01 -0.067459 E 2 S 1.02100000E+01 -0.158078 E 2 S 3.83800000E+00 -0.121831 E 2 S 7.46600000E-01 0.549003 E E 3 S 2.24800000E-01 1.000000 E E 4 S 6.12400000E-02 1.000000 E E 5 P 1.35500000E+01 0.039919 E 5 P 2.91700000E+00 0.217169 E 5 P 7.97300000E-01 0.510319 E E 6 P 2.18500000E-01 1.000000 E E 7 P 5.61100000E-02 1.000000 E E 8 D 8.17000000E-01 1.000000 E E 9 D 2.30000000E-01 1.000000 E E bqN E --- E Exponent Coefficients E -------------- --------------------------------------------------------- E 1 S 9.04600000E+03 0.000700 E 1 S 1.35700000E+03 0.005389 E 1 S 3.09300000E+02 0.027406 E 1 S 8.77300000E+01 0.103207 E 1 S 2.85600000E+01 0.278723 E 1 S 1.02100000E+01 0.448540 E 1 S 3.83800000E+00 0.278238 E 1 S 7.46600000E-01 0.015440 E E 2 S 9.04600000E+03 -0.000153 E 2 S 1.35700000E+03 -0.001208 E 2 S 3.09300000E+02 -0.005992 E 2 S 8.77300000E+01 -0.024544 E 2 S 2.85600000E+01 -0.067459 E 2 S 1.02100000E+01 -0.158078 E 2 S 3.83800000E+00 -0.121831 E 2 S 7.46600000E-01 0.549003 E E 3 S 2.24800000E-01 1.000000 E E 4 S 6.12400000E-02 1.000000 E E 5 P 1.35500000E+01 0.039919 E 5 P 2.91700000E+00 0.217169 E 5 P 7.97300000E-01 0.510319 E E 6 P 2.18500000E-01 1.000000 E E 7 P 5.61100000E-02 1.000000 E E 8 D 8.17000000E-01 1.000000 E E 9 D 2.30000000E-01 1.000000 E E E E Summary of "ao basis" -> "" (spherical) E ------------------------------------------------------------------------------ E Tag Description Shells Functions and Types E ---------------- ------------------------------ ------ --------------------- E H aug-cc-pvdz 5 9 3s2p E bqH aug-cc-pvdz 5 9 3s2p E N aug-cc-pvdz 9 23 4s3p2d E bqN aug-cc-pvdz 9 23 4s3p2d E E E NWChem SCF Module E ----------------- E E E E ao basis = "ao basis" E functions = 41 E atoms = 3 E closed shells = 4 E open shells = 1 E charge = 0.00 E wavefunction = ROHF E input vectors = atomic E output vectors = ./nwchem.movecs E use symmetry = T E symmetry adapt = T E E E Summary of "ao basis" -> "ao basis" (spherical) E ------------------------------------------------------------------------------ E Tag Description Shells Functions and Types E ---------------- ------------------------------ ------ --------------------- E H aug-cc-pvdz 5 9 3s2p E bqH aug-cc-pvdz 5 9 3s2p E N aug-cc-pvdz 9 23 4s3p2d E bqN aug-cc-pvdz 9 23 4s3p2d E E E Symmetry analysis of basis E -------------------------- E E a1 18 E a2 4 E b1 12 E b2 7 E E E Forming initial guess at 0.0s E E E Superposition of Atomic Density Guess E ------------------------------------- E E Sum of atomic energies: -55.30138077 E E Non-variational initial energy E ------------------------------ E E Total energy = -55.390877 E 1-e energy = -89.431618 E 2-e energy = 26.360198 E HOMO = -0.293603 E LUMO = 0.025716 E E E Symmetry analysis of molecular orbitals - initial E ------------------------------------------------- E E Numbering of irreducible representations: E E 1 a1 2 a2 3 b1 4 b2 E E Orbital symmetries: E E 1 a1 2 a1 3 b1 4 a1 5 b2 E 6 a1 7 b1 8 a1 9 b2 10 a1 E 11 b1 12 b1 13 a1 14 a1 15 a2 E E E Starting SCF solution at 0.1s E E E E ---------------------------------------------- E Quadratically convergent ROHF E E Convergence threshold : 1.000E-04 E Maximum no. of iterations : 30 E Final Fock-matrix accuracy: 1.000E-07 E ---------------------------------------------- E E E Integral file = ./nwchem.aoints.0 E Record size in doubles = 65536 No. of integs per rec = 43688 E Max. records in memory = 5 Max. records in file = 125783 E No. of bits per label = 8 No. of bits per value = 64 E E E #quartets = 1.144D+04 #integrals = 1.161D+05 #direct = 0.0% #cached =100.0% E E E iter energy gnorm gmax time E ----- ------------------- --------- --------- -------- E 1 -55.5584036896 3.87D-01 1.66D-01 0.2 E 2 -55.5698996105 7.16D-02 2.45D-02 0.3 E 3 -55.5707238110 1.81D-03 7.98D-04 0.4 E E STDERR: E E Program received signal SIGSEGV: Segmentation fault - invalid memory reference. E E Backtrace for this error: E #0 0x804a1f6db in ??? E #1 0x804a1e896 in ??? E #2 0x803729f6f in handle_signal E at /disk-samsung/freebsd-src/lib/libthr/thread/thr_sig.c:303 E #3 0x80372953e in thr_sighandler E at /disk-samsung/freebsd-src/lib/libthr/thread/thr_sig.c:246 E #4 0x7ffffffff192 in ??? E #5 0x803dd91b1 in ??? E #6 0x803badeb5 in ??? E #7 0x803298434 in ??? E #8 0x80329901d in ??? E #9 0x802f076a9 in ??? E #10 0x802e70b74 in ??? E #11 0x9f45dc in ??? E #12 0x9e382f in ??? E #13 0x97509a in ??? E #14 0x84896a in ??? E #15 0x83f524 in ??? E #16 0x9dff9d in ??? E #17 0x841794 in ??? E #18 0x83e215 in ??? E #19 0x83d230 in ??? E #20 0x826574 in ??? E #21 0x420197 in ??? E #22 0x4213f1 in ??? E #23 0x414589 in ??? E #24 0x40e0e1 in ??? E #25 0x40c71c in ??? E #26 0x40c82f in ??? E E TRACEBACK: E Traceback (most recent call last): E File "/disk-samsung/freebsd-ports/science/py-qcengine/work-py38/qcengine-0.20.1/qcengine/programs/nwchem/runner.py", line 275, in parse_output E retres = qcvars[f"CURRENT {input_model.driver.upper()}"] E KeyError: 'CURRENT ENERGY' qcengine/programs/nwchem/runner.py:277: UnknownError _____________ test_hf_gradient_module[hf rhf ae: nwchem-dz-grd1] ______________ self = NWChemHarness(name='NWChem', scratch=True, thread_safe=False, thread_parallel=False, node_parallel=True, managed_memory=True, extras=None, version_cache={'/usr/local/bin/nwchem': '7.0.2+11.eol.2499.gbbee7e139269'}) outfiles = {'nwchem.grad': None, 'nwchem.hess': None} input_model = AtomicInput(driver='gradient', model={'method': 'hf', 'basis': 'cc-pvdz'}, molecule_hash='25205df') def parse_output( self, outfiles: Dict[str, str], input_model: "AtomicInput" ) -> AtomicResult: # lgtm: [py/similar-function] # Get the stdout from the calculation (required) stdout = outfiles.pop("stdout") stderr = outfiles.pop("stderr") method = input_model.model.method.lower() method = method[4:] if method.startswith("nwc-") else method # Read the NWChem stdout file and, if needed, the hess or grad files # July 2021: nwmol & vector returns now atin/outfile orientation depending on fix_com,orientation=T/F. previously always atin orientation try: qcvars, nwhess, nwgrad, nwmol, version, module, errorTMP = harvest( input_model.molecule, method, stdout, **outfiles ) except Exception as e: raise UnknownError(error_stamp(stdout=stdout, stderr=stderr)) try: if nwgrad is not None: qcvars[f"{method.upper()} TOTAL GRADIENT"] = nwgrad qcvars["CURRENT GRADIENT"] = nwgrad if nwhess is not None: qcvars[f"{method.upper()} TOTAL HESSIAN"] = nwhess qcvars["CURRENT HESSIAN"] = nwhess # Normalize the output as a float or list of floats if input_model.driver.upper() == "PROPERTIES": retres = qcvars[f"CURRENT ENERGY"] else: > retres = qcvars[f"CURRENT {input_model.driver.upper()}"] E KeyError: 'CURRENT GRADIENT' qcengine/programs/nwchem/runner.py:275: KeyError During handling of the above exception, another exception occurred: inp = {'call': 'nwchem', 'fcae': 'ae', 'keywords': {'scf__thresh': 1e-06}, 'reference': 'rhf'} dertype = 1, basis = 'cc-pvdz', subjects = ['hf', 'bh3p', 'bh3p'] clsd_open_pmols = {'bh3p': Molecule(name='bh3p', formula='BH3', hash='f532294'), 'h2o': Molecule(name='h2o', formula='H2O', hash='4684da5'), 'hf': Molecule(name='hf', formula='FH', hash='25205df'), 'nh2': Molecule(name='nh2', formula='H2N', hash='4002acf')} request = > @pytest.mark.parametrize( "dertype", [ pytest.param(1, id="grd1"), # pytest.param(0, id="grd0", marks=pytest.mark.long), ], ) @pytest.mark.parametrize( "basis, subjects", [ pytest.param("cc-pvdz", ["hf", "bh3p", "bh3p"], id="dz"), pytest.param("aug-cc-pvdz", ["h2o", "nh2", "nh2"], id="adz", marks=pytest.mark.long), pytest.param("cfour-qz2p", ["h2o", "nh2", "nh2"], id="qz2p", marks=pytest.mark.long), ], ) @pytest.mark.parametrize( "inp", [ # yapf: disable ######## Are all possible ways of computing working? pytest.param({"call": "cfour", "reference": "rhf", "fcae": "ae", "keywords": {"scf_conv": 12}, }, id="hf rhf ae: cfour", marks=using("cfour")), pytest.param({"call": "gamess", "reference": "rhf", "fcae": "ae", "keywords": {}, }, id="hf rhf ae: gamess", marks=using("gamess")), pytest.param({"call": "nwchem", "reference": "rhf", "fcae": "ae", "keywords": {"scf__thresh": 1.e-6}, }, id="hf rhf ae: nwchem", marks=using("nwchem")), pytest.param({"call": "psi4", "reference": "rhf", "fcae": "ae", "keywords": {"scf_type": "pk"}, }, id="hf rhf ae: psi4", marks=using("psi4_derqcsk")), pytest.param({"call": "cfour", "reference": "uhf", "fcae": "ae", "keywords": {"reference": "uhf", "scf_conv": 12}, }, id="hf uhf ae: cfour", marks=using("cfour")), pytest.param({"call": "gamess", "reference": "uhf", "fcae": "ae", "keywords": {"contrl__scftyp": "uhf"}, }, id="hf uhf ae: gamess", marks=using("gamess")), pytest.param({"call": "nwchem", "reference": "uhf", "fcae": "ae", "keywords": {"scf__uhf": True, "scf__thresh": 1.e-6}, }, id="hf uhf ae: nwchem", marks=using("nwchem")), pytest.param({"call": "psi4", "reference": "uhf", "fcae": "ae", "keywords": {"reference": "uhf", "scf_type": "pk"}, }, id="hf uhf ae: psi4", marks=using("psi4_derqcsk")), pytest.param({"call": "cfour", "reference": "rohf", "fcae": "ae", "keywords": {"reference": "rohf", "scf_conv": 12}, }, id="hf rohf ae: cfour", marks=using("cfour")), pytest.param({"call": "gamess", "reference": "rohf", "fcae": "ae", "keywords": {"contrl__scftyp": "rohf"}, }, id="hf rohf ae: gamess", marks=using("gamess")), pytest.param({"call": "nwchem", "reference": "rohf", "fcae": "ae", "keywords": {"scf__rohf": True, "scf__thresh": 1.e-6}, }, id="hf rohf ae: nwchem", marks=using("nwchem")), pytest.param({"call": "psi4", "reference": "rohf", "fcae": "ae", "keywords": {"reference": "rohf", "scf_type": "pk"}, }, id="hf rohf ae: psi4", marks=using("psi4_derqcsk")), # yapf: enable ], ) def test_hf_gradient_module(inp, dertype, basis, subjects, clsd_open_pmols, request): > runner_asserter(*_processor(inp, dertype, basis, subjects, clsd_open_pmols, request, "gradient", "hf")) qcengine/programs/tests/test_standard_suite.py:214: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ qcengine/programs/tests/standard_suite_runner.py:177: in runner_asserter wfn = qcng.compute(atin, qcprog, raise_error=True, local_options=local_options) qcengine/compute.py:91: in compute output_data = executor.compute(input_data, config) qcengine/programs/model.py:116: in compute result = self._compute(local_input_data, config) qcengine/programs/nwchem/runner.py:137: in _compute return self.parse_output(dexe["outfiles"], input_model) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = NWChemHarness(name='NWChem', scratch=True, thread_safe=False, thread_parallel=False, node_parallel=True, managed_memory=True, extras=None, version_cache={'/usr/local/bin/nwchem': '7.0.2+11.eol.2499.gbbee7e139269'}) outfiles = {'nwchem.grad': None, 'nwchem.hess': None} input_model = AtomicInput(driver='gradient', model={'method': 'hf', 'basis': 'cc-pvdz'}, molecule_hash='25205df') def parse_output( self, outfiles: Dict[str, str], input_model: "AtomicInput" ) -> AtomicResult: # lgtm: [py/similar-function] # Get the stdout from the calculation (required) stdout = outfiles.pop("stdout") stderr = outfiles.pop("stderr") method = input_model.model.method.lower() method = method[4:] if method.startswith("nwc-") else method # Read the NWChem stdout file and, if needed, the hess or grad files # July 2021: nwmol & vector returns now atin/outfile orientation depending on fix_com,orientation=T/F. previously always atin orientation try: qcvars, nwhess, nwgrad, nwmol, version, module, errorTMP = harvest( input_model.molecule, method, stdout, **outfiles ) except Exception as e: raise UnknownError(error_stamp(stdout=stdout, stderr=stderr)) try: if nwgrad is not None: qcvars[f"{method.upper()} TOTAL GRADIENT"] = nwgrad qcvars["CURRENT GRADIENT"] = nwgrad if nwhess is not None: qcvars[f"{method.upper()} TOTAL HESSIAN"] = nwhess qcvars["CURRENT HESSIAN"] = nwhess # Normalize the output as a float or list of floats if input_model.driver.upper() == "PROPERTIES": retres = qcvars[f"CURRENT ENERGY"] else: retres = qcvars[f"CURRENT {input_model.driver.upper()}"] except KeyError as e: > raise UnknownError(error_stamp(stdout=stdout, stderr=stderr)) E qcengine.exceptions.UnknownError: STDOUT: E E E E ============================== echo of input deck ============================== E echo E geometry units bohr E H 0.000000000000 0.000000000000 -1.645584110000 E F 0.000000000000 0.000000000000 0.087294750000 E E end E memory 879931424 double E charge 0 E E basis spherical E H library cc-pvdz E bqH library H cc-pvdz E F library cc-pvdz E bqF library F cc-pvdz E end E E scf E thresh 1e-06 E end E E task scf gradient E E E python E grad = rtdb_get('scf:gradient') E if ga_nodeid() == 0: E import json E with open('nwchem.grad', 'w') as fp: E json.dump(grad, fp) E end E E task python E E ================================================================================ E E E E E E E Northwest Computational Chemistry Package (NWChem) 7.0.2 E -------------------------------------------------------- E E E Environmental Molecular Sciences Laboratory E Pacific Northwest National Laboratory E Richland, WA 99352 E E Copyright (c) 1994-2020 E Pacific Northwest National Laboratory E Battelle Memorial Institute E E NWChem is an open-source computational chemistry package E distributed under the terms of the E Educational Community License (ECL) 2.0 E A copy of the license is included with this distribution E in the LICENSE.TXT file E E ACKNOWLEDGMENT E -------------- E E This software and its documentation were developed at the E EMSL at Pacific Northwest National Laboratory, a multiprogram E national laboratory, operated for the U.S. Department of Energy E by Battelle under Contract Number DE-AC05-76RL01830. Support E for this work was provided by the Department of Energy Office E of Biological and Environmental Research, Office of Basic E Energy Sciences, and the Office of Advanced Scientific Computing. E E E Job information E --------------- E E hostname = yv.noip.me E program = /usr/local/bin/nwchem E date = Thu Oct 21 12:50:06 2021 E E compiled = Thu_Oct_21_12:11:03_2021 E source = /disk-samsung/freebsd-ports/science/nwchem/work/nwchem-7.0.2-release/src/.. E nwchem branch = 7.0.2 E nwchem revision = 11-eol-2499-gbbee7e139269 E ga revision = 5.8.0 E use scalapack = T E input = nwchem.nw E prefix = nwchem. E data base = ./nwchem.db E status = startup E nproc = 1 E time left = -1s E E E E Memory information E ------------------ E E heap = 219982852 doubles = 1678.3 Mbytes E stack = 219982857 doubles = 1678.3 Mbytes E global = 439965712 doubles = 3356.7 Mbytes (distinct from heap & stack) E total = 879931421 doubles = 6713.3 Mbytes E verify = yes E hardfail = no E E E Directory information E --------------------- E E 0 permanent = . E 0 scratch = . E E E E E NWChem Input Module E ------------------- E E E ORDER OF PRIMARY AXIS IS BEING SET TO 4 E C4V symmetry detected E E ------ E auto-z E ------ E no constraints, skipping 0.0000000000000000 E no constraints, skipping 0.0000000000000000 E E E Geometry "geometry" -> "" E ------------------------- E E Output coordinates in a.u. (scale by 1.000000000 to convert to a.u.) E E No. Tag Charge X Y Z E ---- ---------------- ---------- -------------- -------------- -------------- E 1 H 1.0000 0.00000000 0.00000000 -1.55959097 E 2 F 9.0000 0.00000000 0.00000000 0.17328789 E E Atomic Mass E ----------- E E H 1.007825 E F 18.998400 E E E Effective nuclear repulsion energy (a.u.) 5.1936694525 E E Nuclear Dipole moment (a.u.) E ---------------------------- E X Y Z E ---------------- ---------------- ---------------- E 0.0000000000 0.0000000000 0.0000000000 E E Symmetry information E -------------------- E E Group name C4v E Group number 18 E Group order 8 E No. of unique centers 2 E E Symmetry unique atoms E E 1 2 E E E E Z-matrix (autoz) E -------- E E Units are Angstrom for bonds and degrees for angles E E Type Name I J K L M Value E ----------- -------- ----- ----- ----- ----- ----- ---------- E 1 Stretch 1 2 0.91700 E E E XYZ format geometry E ------------------- E 2 E geometry E H 0.00000000 0.00000000 -0.82530006 E F 0.00000000 0.00000000 0.09170001 E E ============================================================================== E internuclear distances E ------------------------------------------------------------------------------ E center one | center two | atomic units | a.u. E ------------------------------------------------------------------------------ E 2 F | 1 H | 1.73288 | 1.73288 E ------------------------------------------------------------------------------ E number of included internuclear distances: 1 E ============================================================================== E E E E library name resolved from: .nwchemrc E library file name is: E E Basis "ao basis" -> "" (spherical) E ----- E H (Hydrogen) E ------------ E Exponent Coefficients E -------------- --------------------------------------------------------- E 1 S 1.30100000E+01 0.019685 E 1 S 1.96200000E+00 0.137977 E 1 S 4.44600000E-01 0.478148 E E 2 S 1.22000000E-01 1.000000 E E 3 P 7.27000000E-01 1.000000 E E bqH E --- E Exponent Coefficients E -------------- --------------------------------------------------------- E 1 S 1.30100000E+01 0.019685 E 1 S 1.96200000E+00 0.137977 E 1 S 4.44600000E-01 0.478148 E E 2 S 1.22000000E-01 1.000000 E E 3 P 7.27000000E-01 1.000000 E E F (Fluorine) E ------------ E Exponent Coefficients E -------------- --------------------------------------------------------- E 1 S 1.47100000E+04 0.000721 E 1 S 2.20700000E+03 0.005553 E 1 S 5.02800000E+02 0.028267 E 1 S 1.42600000E+02 0.106444 E 1 S 4.64700000E+01 0.286814 E 1 S 1.67000000E+01 0.448641 E 1 S 6.35600000E+00 0.264761 E 1 S 1.31600000E+00 0.015333 E E 2 S 1.47100000E+04 -0.000165 E 2 S 2.20700000E+03 -0.001308 E 2 S 5.02800000E+02 -0.006495 E 2 S 1.42600000E+02 -0.026691 E 2 S 4.64700000E+01 -0.073690 E 2 S 1.67000000E+01 -0.170776 E 2 S 6.35600000E+00 -0.112327 E 2 S 1.31600000E+00 0.562814 E E 3 S 3.89700000E-01 1.000000 E E 4 P 2.26700000E+01 0.044878 E 4 P 4.97700000E+00 0.235718 E 4 P 1.34700000E+00 0.508521 E E 5 P 3.47100000E-01 1.000000 E E 6 D 1.64000000E+00 1.000000 E E bqF E --- E Exponent Coefficients E -------------- --------------------------------------------------------- E 1 S 1.47100000E+04 0.000721 E 1 S 2.20700000E+03 0.005553 E 1 S 5.02800000E+02 0.028267 E 1 S 1.42600000E+02 0.106444 E 1 S 4.64700000E+01 0.286814 E 1 S 1.67000000E+01 0.448641 E 1 S 6.35600000E+00 0.264761 E 1 S 1.31600000E+00 0.015333 E E 2 S 1.47100000E+04 -0.000165 E 2 S 2.20700000E+03 -0.001308 E 2 S 5.02800000E+02 -0.006495 E 2 S 1.42600000E+02 -0.026691 E 2 S 4.64700000E+01 -0.073690 E 2 S 1.67000000E+01 -0.170776 E 2 S 6.35600000E+00 -0.112327 E 2 S 1.31600000E+00 0.562814 E E 3 S 3.89700000E-01 1.000000 E E 4 P 2.26700000E+01 0.044878 E 4 P 4.97700000E+00 0.235718 E 4 P 1.34700000E+00 0.508521 E E 5 P 3.47100000E-01 1.000000 E E 6 D 1.64000000E+00 1.000000 E E E E Summary of "ao basis" -> "" (spherical) E ------------------------------------------------------------------------------ E Tag Description Shells Functions and Types E ---------------- ------------------------------ ------ --------------------- E H cc-pvdz 3 5 2s1p E bqH cc-pvdz 3 5 2s1p E F cc-pvdz 6 14 3s2p1d E bqF cc-pvdz 6 14 3s2p1d E E E NWChem SCF Module E ----------------- E E E E ao basis = "ao basis" E functions = 19 E atoms = 2 E closed shells = 5 E open shells = 0 E charge = 0.00 E wavefunction = RHF E input vectors = atomic E output vectors = ./nwchem.movecs E use symmetry = T E symmetry adapt = T E E E Summary of "ao basis" -> "ao basis" (spherical) E ------------------------------------------------------------------------------ E Tag Description Shells Functions and Types E ---------------- ------------------------------ ------ --------------------- E H cc-pvdz 3 5 2s1p E bqH cc-pvdz 3 5 2s1p E F cc-pvdz 6 14 3s2p1d E bqF cc-pvdz 6 14 3s2p1d E E E Symmetry analysis of basis E -------------------------- E E a1 9 E a2 0 E b1 1 E b2 1 E e 8 E E E Forming initial guess at 0.0s E E E Superposition of Atomic Density Guess E ------------------------------------- E E Sum of atomic energies: -99.88314519 E E Non-variational initial energy E ------------------------------ E E Total energy = -99.865715 E 1-e energy = -149.649522 E 2-e energy = 44.590137 E HOMO = -0.637960 E LUMO = 0.109607 E E E Symmetry analysis of molecular orbitals - initial E ------------------------------------------------- E E Numbering of irreducible representations: E E 1 a1 2 a2 3 b1 4 b2 5 e E E Orbital symmetries: E E 1 a1 2 a1 3 a1 4 e 5 e E 6 a1 7 a1 8 a1 9 e 10 e E 11 e 12 e 13 a1 14 a1 15 b2 E E E Starting SCF solution at 0.1s E E E E ---------------------------------------------- E Quadratically convergent ROHF E E Convergence threshold : 1.000E-06 E Maximum no. of iterations : 30 E Final Fock-matrix accuracy: 1.000E-08 E ---------------------------------------------- E E E #quartets = 1.035D+03 #integrals = 4.841D+03 #direct = 0.0% #cached =100.0% E E E Integral file = ./nwchem.aoints.0 E Record size in doubles = 65536 No. of integs per rec = 43688 E Max. records in memory = 2 Max. records in file = 125785 E No. of bits per label = 8 No. of bits per value = 64 E E E iter energy gnorm gmax time E ----- ------------------- --------- --------- -------- E 1 -99.9944094325 7.27D-01 3.80D-01 0.2 E 2 -100.0177379586 1.62D-01 6.40D-02 0.2 E 3 -100.0193962961 1.41D-02 6.34D-03 0.2 E 4 -100.0194112693 2.02D-05 8.98D-06 0.2 E 5 -100.0194112693 4.87D-08 2.24D-08 0.3 E E E Final RHF results E ------------------ E E Total SCF energy = -100.019411269308 E One-electron energy = -150.693050028575 E Two-electron energy = 45.479969306805 E Nuclear repulsion energy = 5.193669452462 E E Time for solution = 0.2s E E E E Symmetry analysis of molecular orbitals - final E ----------------------------------------------- E E Numbering of irreducible representations: E E 1 a1 2 a2 3 b1 4 b2 5 e E E Orbital symmetries: E E 1 a1 2 a1 3 a1 4 e 5 e E 6 a1 7 a1 8 e 9 e 10 a1 E 11 e 12 e 13 a1 14 a1 15 b2 E E Final eigenvalues E ----------------- E E 1 E 1 -26.2781 E 2 -1.5835 E 3 -0.7472 E 4 -0.6289 E 5 -0.6289 E 6 0.1838 E 7 0.8100 E 8 1.4119 E 9 1.4119 E 10 1.4156 E 11 1.6041 E 12 1.6041 E 13 2.1341 E 14 2.4989 E 15 4.0044 E E ROHF Final Molecular Orbital Analysis E ------------------------------------- E E Vector 2 Occ=2.000000D+00 E=-1.583452D+00 Symmetry=a1 E MO Center= 1.3D-16, -3.0D-16, -2.4D-02, r^2= 3.7D-01 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 7 0.481194 2 F s 8 0.480605 2 F s E 1 0.174632 1 H s E E Vector 3 Occ=2.000000D+00 E=-7.471972D-01 Symmetry=a1 E MO Center= 2.9D-16, -4.9D-16, -1.4D-02, r^2= 5.6D-01 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 11 0.555850 2 F pz 1 -0.387490 1 H s E 14 0.299645 2 F pz 8 0.289834 2 F s E E Vector 4 Occ=2.000000D+00 E=-6.288892D-01 Symmetry=e E MO Center= 1.0D-16, 1.6D-16, 7.5D-02, r^2= 4.4D-01 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 10 0.663525 2 F py 13 0.474633 2 F py E E Vector 5 Occ=2.000000D+00 E=-6.288892D-01 Symmetry=e E MO Center= -1.6D-16, -3.2D-17, 7.5D-02, r^2= 4.4D-01 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 9 0.663525 2 F px 12 0.474633 2 F px E E Vector 6 Occ=0.000000D+00 E= 1.838400D-01 Symmetry=a1 E MO Center= 2.0D-16, -7.6D-16, -1.0D+00, r^2= 2.1D+00 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 2 1.265475 1 H s 8 -0.670151 2 F s E 14 0.336135 2 F pz 11 0.217915 2 F pz E E Vector 7 Occ=0.000000D+00 E= 8.100489D-01 Symmetry=a1 E MO Center= -1.0D-15, 2.4D-15, -8.0D-01, r^2= 1.1D+00 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 1 1.275533 1 H s 2 -0.907033 1 H s E 11 0.370721 2 F pz 5 -0.327559 1 H pz E 14 0.194975 2 F pz E E Vector 8 Occ=0.000000D+00 E= 1.411878D+00 Symmetry=e E MO Center= -9.9D-16, -1.5D-16, -2.1D-01, r^2= 8.6D-01 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 9 0.841284 2 F px 12 -0.744914 2 F px E 3 -0.430946 1 H px E E Vector 9 Occ=0.000000D+00 E= 1.411878D+00 Symmetry=e E MO Center= -1.1D-15, 7.5D-15, -2.1D-01, r^2= 8.6D-01 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 10 0.841284 2 F py 13 -0.744914 2 F py E 4 -0.430946 1 H py E E Vector 10 Occ=0.000000D+00 E= 1.415619D+00 Symmetry=a1 E MO Center= 4.0D-15, -1.7D-14, 4.9D-01, r^2= 9.0D-01 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 14 1.618091 2 F pz 1 1.084020 1 H s E 11 -0.644892 2 F pz 8 -0.591943 2 F s E 5 0.513224 1 H pz 7 -0.226860 2 F s E E Vector 11 Occ=0.000000D+00 E= 1.604149D+00 Symmetry=e E MO Center= -8.3D-16, -1.4D-16, -4.0D-01, r^2= 1.0D+00 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 3 0.970170 1 H px 12 -0.850871 2 F px E 9 0.386467 2 F px E E Vector 12 Occ=0.000000D+00 E= 1.604149D+00 Symmetry=e E MO Center= -1.5D-15, 1.1D-14, -4.0D-01, r^2= 1.0D+00 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 4 0.970170 1 H py 13 -0.850871 2 F py E 10 0.386467 2 F py E E Vector 13 Occ=0.000000D+00 E= 2.134096D+00 Symmetry=a1 E MO Center= 1.0D-15, -2.4D-15, -1.1D-01, r^2= 9.6D-01 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 8 2.403587 2 F s 7 -1.664197 2 F s E 6 -0.716261 2 F s 14 -0.714895 2 F pz E 1 -0.707619 1 H s 2 -0.543054 1 H s E 5 -0.349676 1 H pz E E Vector 14 Occ=0.000000D+00 E= 2.498873D+00 Symmetry=a1 E MO Center= -2.0D-16, 5.2D-16, -6.9D-01, r^2= 6.0D-01 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 5 1.405944 1 H pz 8 -0.968301 2 F s E 1 0.776130 1 H s 11 0.759152 2 F pz E 14 0.288474 2 F pz 2 0.275079 1 H s E 7 -0.249146 2 F s E E Vector 15 Occ=0.000000D+00 E= 4.004354D+00 Symmetry=b2 E MO Center= -6.5D-17, 1.8D-17, 9.2D-02, r^2= 3.0D-01 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 15 1.000000 2 F d -2 E E E center of mass E -------------- E x = 0.00000000 y = 0.00000000 z = 0.08599312 E E moments of inertia (a.u.) E ------------------ E 2.873911650429 0.000000000000 0.000000000000 E 0.000000000000 2.873911650429 0.000000000000 E 0.000000000000 0.000000000000 0.000000000000 E E Mulliken analysis of the total density E -------------------------------------- E E Atom Charge Shell Charges E ----------- ------ ------------------------------------------------------- E 1 H 1 0.76 0.63 0.03 0.11 E 2 F 9 9.24 2.00 0.89 0.97 3.32 2.05 0.00 E E Multipole analysis of the density wrt the origin E ------------------------------------------------ E E L x y z total open nuclear E - - - - ----- ---- ------- E 0 0 0 0 -0.000000 0.000000 10.000000 E E 1 1 0 0 -0.000000 0.000000 0.000000 E 1 0 1 0 0.000000 0.000000 0.000000 E 1 0 0 1 -0.767022 0.000000 0.000000 E E 2 2 0 0 -4.007314 0.000000 0.000000 E 2 1 1 0 -0.000000 0.000000 0.000000 E 2 1 0 1 0.000000 0.000000 0.000000 E 2 0 2 0 -4.007314 0.000000 0.000000 E 2 0 1 1 -0.000000 0.000000 0.000000 E 2 0 0 2 -2.493425 0.000000 2.702582 E E E Parallel integral file used 1 records with 0 large values E E NWChem Gradients Module E ----------------------- E E E E wavefunction = RHF E E Using symmetry E E STDERR: E E Program received signal SIGSEGV: Segmentation fault - invalid memory reference. E E Backtrace for this error: E #0 0x804a1f6db in ??? E #1 0x804a1e896 in ??? E #2 0x803729f6f in handle_signal E at /disk-samsung/freebsd-src/lib/libthr/thread/thr_sig.c:303 E #3 0x80372953e in thr_sighandler E at /disk-samsung/freebsd-src/lib/libthr/thread/thr_sig.c:246 E #4 0x7ffffffff192 in ??? E #5 0x803dd91b1 in ??? E #6 0x803badeb5 in ??? E #7 0x803298434 in ??? E #8 0x80329901d in ??? E #9 0x802f076a9 in ??? E #10 0x802e70b74 in ??? E #11 0x9f45dc in ??? E #12 0x9e382f in ??? E #13 0x7ebc84 in ??? E #14 0x7e6a23 in ??? E #15 0x7fdbf4 in ??? E #16 0x7ec987 in ??? E #17 0x4219d7 in ??? E #18 0x422db0 in ??? E #19 0x41462d in ??? E #20 0x40e0e1 in ??? E #21 0x40c71c in ??? E #22 0x40c82f in ??? E E TRACEBACK: E Traceback (most recent call last): E File "/disk-samsung/freebsd-ports/science/py-qcengine/work-py38/qcengine-0.20.1/qcengine/programs/nwchem/runner.py", line 275, in parse_output E retres = qcvars[f"CURRENT {input_model.driver.upper()}"] E KeyError: 'CURRENT GRADIENT' qcengine/programs/nwchem/runner.py:277: UnknownError _____________ test_hf_gradient_module[hf uhf ae: nwchem-dz-grd1] ______________ self = NWChemHarness(name='NWChem', scratch=True, thread_safe=False, thread_parallel=False, node_parallel=True, managed_memory=True, extras=None, version_cache={'/usr/local/bin/nwchem': '7.0.2+11.eol.2499.gbbee7e139269'}) outfiles = {'nwchem.grad': None, 'nwchem.hess': None} input_model = AtomicInput(driver='gradient', model={'method': 'hf', 'basis': 'cc-pvdz'}, molecule_hash='f532294') def parse_output( self, outfiles: Dict[str, str], input_model: "AtomicInput" ) -> AtomicResult: # lgtm: [py/similar-function] # Get the stdout from the calculation (required) stdout = outfiles.pop("stdout") stderr = outfiles.pop("stderr") method = input_model.model.method.lower() method = method[4:] if method.startswith("nwc-") else method # Read the NWChem stdout file and, if needed, the hess or grad files # July 2021: nwmol & vector returns now atin/outfile orientation depending on fix_com,orientation=T/F. previously always atin orientation try: qcvars, nwhess, nwgrad, nwmol, version, module, errorTMP = harvest( input_model.molecule, method, stdout, **outfiles ) except Exception as e: raise UnknownError(error_stamp(stdout=stdout, stderr=stderr)) try: if nwgrad is not None: qcvars[f"{method.upper()} TOTAL GRADIENT"] = nwgrad qcvars["CURRENT GRADIENT"] = nwgrad if nwhess is not None: qcvars[f"{method.upper()} TOTAL HESSIAN"] = nwhess qcvars["CURRENT HESSIAN"] = nwhess # Normalize the output as a float or list of floats if input_model.driver.upper() == "PROPERTIES": retres = qcvars[f"CURRENT ENERGY"] else: > retres = qcvars[f"CURRENT {input_model.driver.upper()}"] E KeyError: 'CURRENT GRADIENT' qcengine/programs/nwchem/runner.py:275: KeyError During handling of the above exception, another exception occurred: inp = {'call': 'nwchem', 'fcae': 'ae', 'keywords': {'scf__thresh': 1e-06, 'scf__uhf': True}, 'reference': 'uhf'} dertype = 1, basis = 'cc-pvdz', subjects = ['hf', 'bh3p', 'bh3p'] clsd_open_pmols = {'bh3p': Molecule(name='bh3p', formula='BH3', hash='f532294'), 'h2o': Molecule(name='h2o', formula='H2O', hash='4684da5'), 'hf': Molecule(name='hf', formula='FH', hash='25205df'), 'nh2': Molecule(name='nh2', formula='H2N', hash='4002acf')} request = > @pytest.mark.parametrize( "dertype", [ pytest.param(1, id="grd1"), # pytest.param(0, id="grd0", marks=pytest.mark.long), ], ) @pytest.mark.parametrize( "basis, subjects", [ pytest.param("cc-pvdz", ["hf", "bh3p", "bh3p"], id="dz"), pytest.param("aug-cc-pvdz", ["h2o", "nh2", "nh2"], id="adz", marks=pytest.mark.long), pytest.param("cfour-qz2p", ["h2o", "nh2", "nh2"], id="qz2p", marks=pytest.mark.long), ], ) @pytest.mark.parametrize( "inp", [ # yapf: disable ######## Are all possible ways of computing working? pytest.param({"call": "cfour", "reference": "rhf", "fcae": "ae", "keywords": {"scf_conv": 12}, }, id="hf rhf ae: cfour", marks=using("cfour")), pytest.param({"call": "gamess", "reference": "rhf", "fcae": "ae", "keywords": {}, }, id="hf rhf ae: gamess", marks=using("gamess")), pytest.param({"call": "nwchem", "reference": "rhf", "fcae": "ae", "keywords": {"scf__thresh": 1.e-6}, }, id="hf rhf ae: nwchem", marks=using("nwchem")), pytest.param({"call": "psi4", "reference": "rhf", "fcae": "ae", "keywords": {"scf_type": "pk"}, }, id="hf rhf ae: psi4", marks=using("psi4_derqcsk")), pytest.param({"call": "cfour", "reference": "uhf", "fcae": "ae", "keywords": {"reference": "uhf", "scf_conv": 12}, }, id="hf uhf ae: cfour", marks=using("cfour")), pytest.param({"call": "gamess", "reference": "uhf", "fcae": "ae", "keywords": {"contrl__scftyp": "uhf"}, }, id="hf uhf ae: gamess", marks=using("gamess")), pytest.param({"call": "nwchem", "reference": "uhf", "fcae": "ae", "keywords": {"scf__uhf": True, "scf__thresh": 1.e-6}, }, id="hf uhf ae: nwchem", marks=using("nwchem")), pytest.param({"call": "psi4", "reference": "uhf", "fcae": "ae", "keywords": {"reference": "uhf", "scf_type": "pk"}, }, id="hf uhf ae: psi4", marks=using("psi4_derqcsk")), pytest.param({"call": "cfour", "reference": "rohf", "fcae": "ae", "keywords": {"reference": "rohf", "scf_conv": 12}, }, id="hf rohf ae: cfour", marks=using("cfour")), pytest.param({"call": "gamess", "reference": "rohf", "fcae": "ae", "keywords": {"contrl__scftyp": "rohf"}, }, id="hf rohf ae: gamess", marks=using("gamess")), pytest.param({"call": "nwchem", "reference": "rohf", "fcae": "ae", "keywords": {"scf__rohf": True, "scf__thresh": 1.e-6}, }, id="hf rohf ae: nwchem", marks=using("nwchem")), pytest.param({"call": "psi4", "reference": "rohf", "fcae": "ae", "keywords": {"reference": "rohf", "scf_type": "pk"}, }, id="hf rohf ae: psi4", marks=using("psi4_derqcsk")), # yapf: enable ], ) def test_hf_gradient_module(inp, dertype, basis, subjects, clsd_open_pmols, request): > runner_asserter(*_processor(inp, dertype, basis, subjects, clsd_open_pmols, request, "gradient", "hf")) qcengine/programs/tests/test_standard_suite.py:214: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ qcengine/programs/tests/standard_suite_runner.py:177: in runner_asserter wfn = qcng.compute(atin, qcprog, raise_error=True, local_options=local_options) qcengine/compute.py:91: in compute output_data = executor.compute(input_data, config) qcengine/programs/model.py:116: in compute result = self._compute(local_input_data, config) qcengine/programs/nwchem/runner.py:137: in _compute return self.parse_output(dexe["outfiles"], input_model) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = NWChemHarness(name='NWChem', scratch=True, thread_safe=False, thread_parallel=False, node_parallel=True, managed_memory=True, extras=None, version_cache={'/usr/local/bin/nwchem': '7.0.2+11.eol.2499.gbbee7e139269'}) outfiles = {'nwchem.grad': None, 'nwchem.hess': None} input_model = AtomicInput(driver='gradient', model={'method': 'hf', 'basis': 'cc-pvdz'}, molecule_hash='f532294') def parse_output( self, outfiles: Dict[str, str], input_model: "AtomicInput" ) -> AtomicResult: # lgtm: [py/similar-function] # Get the stdout from the calculation (required) stdout = outfiles.pop("stdout") stderr = outfiles.pop("stderr") method = input_model.model.method.lower() method = method[4:] if method.startswith("nwc-") else method # Read the NWChem stdout file and, if needed, the hess or grad files # July 2021: nwmol & vector returns now atin/outfile orientation depending on fix_com,orientation=T/F. previously always atin orientation try: qcvars, nwhess, nwgrad, nwmol, version, module, errorTMP = harvest( input_model.molecule, method, stdout, **outfiles ) except Exception as e: raise UnknownError(error_stamp(stdout=stdout, stderr=stderr)) try: if nwgrad is not None: qcvars[f"{method.upper()} TOTAL GRADIENT"] = nwgrad qcvars["CURRENT GRADIENT"] = nwgrad if nwhess is not None: qcvars[f"{method.upper()} TOTAL HESSIAN"] = nwhess qcvars["CURRENT HESSIAN"] = nwhess # Normalize the output as a float or list of floats if input_model.driver.upper() == "PROPERTIES": retres = qcvars[f"CURRENT ENERGY"] else: retres = qcvars[f"CURRENT {input_model.driver.upper()}"] except KeyError as e: > raise UnknownError(error_stamp(stdout=stdout, stderr=stderr)) E qcengine.exceptions.UnknownError: STDOUT: E E E E ============================== echo of input deck ============================== E echo E geometry units bohr E B 0.000000000000 0.000000000000 0.195947860000 E H 0.000000000000 0.000000000000 -2.140490630000 E H 0.000000000000 -0.702014360000 5.669178380000 E H 0.000000000000 0.702014360000 5.669178380000 E E end E memory 879931424 double E charge 1 E E basis spherical E H library cc-pvdz E bqH library H cc-pvdz E B library cc-pvdz E bqB library B cc-pvdz E end E E dft E mult 2 E end E E mcscf E multiplicity 2 E end E E scf E uhf E thresh 1e-06 E nopen 1 E end E E task scf gradient E E E python E grad = rtdb_get('scf:gradient') E if ga_nodeid() == 0: E import json E with open('nwchem.grad', 'w') as fp: E json.dump(grad, fp) E end E E task python E E ================================================================================ E E E E E E E Northwest Computational Chemistry Package (NWChem) 7.0.2 E -------------------------------------------------------- E E E Environmental Molecular Sciences Laboratory E Pacific Northwest National Laboratory E Richland, WA 99352 E E Copyright (c) 1994-2020 E Pacific Northwest National Laboratory E Battelle Memorial Institute E E NWChem is an open-source computational chemistry package E distributed under the terms of the E Educational Community License (ECL) 2.0 E A copy of the license is included with this distribution E in the LICENSE.TXT file E E ACKNOWLEDGMENT E -------------- E E This software and its documentation were developed at the E EMSL at Pacific Northwest National Laboratory, a multiprogram E national laboratory, operated for the U.S. Department of Energy E by Battelle under Contract Number DE-AC05-76RL01830. Support E for this work was provided by the Department of Energy Office E of Biological and Environmental Research, Office of Basic E Energy Sciences, and the Office of Advanced Scientific Computing. E E E Job information E --------------- E E hostname = yv.noip.me E program = /usr/local/bin/nwchem E date = Thu Oct 21 12:50:08 2021 E E compiled = Thu_Oct_21_12:11:03_2021 E source = /disk-samsung/freebsd-ports/science/nwchem/work/nwchem-7.0.2-release/src/.. E nwchem branch = 7.0.2 E nwchem revision = 11-eol-2499-gbbee7e139269 E ga revision = 5.8.0 E use scalapack = T E input = nwchem.nw E prefix = nwchem. E data base = ./nwchem.db E status = startup E nproc = 1 E time left = -1s E E E E Memory information E ------------------ E E heap = 219982852 doubles = 1678.3 Mbytes E stack = 219982857 doubles = 1678.3 Mbytes E global = 439965712 doubles = 3356.7 Mbytes (distinct from heap & stack) E total = 879931421 doubles = 6713.3 Mbytes E verify = yes E hardfail = no E E E Directory information E --------------------- E E 0 permanent = . E 0 scratch = . E E E E E NWChem Input Module E ------------------- E E E CS symmetry detected E E ------ E auto-z E ------ E autoz: The atoms group into disjoint clusters E cluster 1: 1 2 E cluster 2: 3 4 E Connecting clusters 1 2 via atoms 1 3 r = 2.92 E autoz: regenerating connections with new bonds E no constraints, skipping 0.0000000000000000 E no constraints, skipping 0.0000000000000000 E E E Geometry "geometry" -> "" E ------------------------- E E Output coordinates in a.u. (scale by 1.000000000 to convert to a.u.) E E No. Tag Charge X Y Z E ---- ---------------- ---------- -------------- -------------- -------------- E 1 B 5.0000 0.00000000 -1.07625282 0.00000000 E 2 H 1.0000 0.00000000 -3.41269131 0.00000000 E 3 H 1.0000 0.00000000 4.39697770 -0.70201436 E 4 H 1.0000 0.00000000 4.39697770 0.70201436 E E Atomic Mass E ----------- E E B 11.009310 E H 1.007825 E E E Effective nuclear repulsion energy (a.u.) 4.9195381997 E E Nuclear Dipole moment (a.u.) E ---------------------------- E X Y Z E ---------------- ---------------- ---------------- E 0.0000000000 0.0000000000 0.0000000000 E E Symmetry information E -------------------- E E Group name Cs E Group number 2 E Group order 2 E No. of unique centers 3 E E Symmetry unique atoms E E 1 2 3 E E E E Z-matrix (autoz) E -------- E E Units are Angstrom for bonds and degrees for angles E E Type Name I J K L M Value E ----------- -------- ----- ----- ----- ----- ----- ---------- E 1 Stretch 1 3 2.92004 E 2 Stretch 1 2 1.23639 E 3 Stretch 3 4 0.74298 E 4 Bend 1 3 4 82.69096 E 5 Bend 2 1 3 172.69096 E 6 Torsion 2 1 3 4 180.00000 E E E XYZ format geometry E ------------------- E 4 E geometry E B 0.00000000 -0.56952851 0.00000000 E H 0.00000000 -1.80591860 0.00000000 E H 0.00000000 2.32678056 -0.37149003 E H 0.00000000 2.32678056 0.37149003 E E ============================================================================== E internuclear distances E ------------------------------------------------------------------------------ E center one | center two | atomic units | a.u. E ------------------------------------------------------------------------------ E 2 H | 1 B | 2.33644 | 2.33644 E ------------------------------------------------------------------------------ E number of included internuclear distances: 1 E ============================================================================== E E E E library name resolved from: .nwchemrc E library file name is: E E Basis "ao basis" -> "" (spherical) E ----- E H (Hydrogen) E ------------ E Exponent Coefficients E -------------- --------------------------------------------------------- E 1 S 1.30100000E+01 0.019685 E 1 S 1.96200000E+00 0.137977 E 1 S 4.44600000E-01 0.478148 E E 2 S 1.22000000E-01 1.000000 E E 3 P 7.27000000E-01 1.000000 E E bqH E --- E Exponent Coefficients E -------------- --------------------------------------------------------- E 1 S 1.30100000E+01 0.019685 E 1 S 1.96200000E+00 0.137977 E 1 S 4.44600000E-01 0.478148 E E 2 S 1.22000000E-01 1.000000 E E 3 P 7.27000000E-01 1.000000 E E B (Boron) E --------- E Exponent Coefficients E -------------- --------------------------------------------------------- E 1 S 4.57000000E+03 0.000696 E 1 S 6.85900000E+02 0.005353 E 1 S 1.56500000E+02 0.027134 E 1 S 4.44700000E+01 0.101380 E 1 S 1.44800000E+01 0.272055 E 1 S 5.13100000E+00 0.448403 E 1 S 1.89800000E+00 0.290123 E 1 S 3.32900000E-01 0.014322 E E 2 S 4.57000000E+03 -0.000139 E 2 S 6.85900000E+02 -0.001097 E 2 S 1.56500000E+02 -0.005444 E 2 S 4.44700000E+01 -0.021916 E 2 S 1.44800000E+01 -0.059751 E 2 S 5.13100000E+00 -0.138732 E 2 S 1.89800000E+00 -0.131482 E 2 S 3.32900000E-01 0.539526 E E 3 S 1.04300000E-01 1.000000 E E 4 P 6.00100000E+00 0.035481 E 4 P 1.24100000E+00 0.198072 E 4 P 3.36400000E-01 0.505230 E E 5 P 9.53800000E-02 1.000000 E E 6 D 3.43000000E-01 1.000000 E E bqB E --- E Exponent Coefficients E -------------- --------------------------------------------------------- E 1 S 4.57000000E+03 0.000696 E 1 S 6.85900000E+02 0.005353 E 1 S 1.56500000E+02 0.027134 E 1 S 4.44700000E+01 0.101380 E 1 S 1.44800000E+01 0.272055 E 1 S 5.13100000E+00 0.448403 E 1 S 1.89800000E+00 0.290123 E 1 S 3.32900000E-01 0.014322 E E 2 S 4.57000000E+03 -0.000139 E 2 S 6.85900000E+02 -0.001097 E 2 S 1.56500000E+02 -0.005444 E 2 S 4.44700000E+01 -0.021916 E 2 S 1.44800000E+01 -0.059751 E 2 S 5.13100000E+00 -0.138732 E 2 S 1.89800000E+00 -0.131482 E 2 S 3.32900000E-01 0.539526 E E 3 S 1.04300000E-01 1.000000 E E 4 P 6.00100000E+00 0.035481 E 4 P 1.24100000E+00 0.198072 E 4 P 3.36400000E-01 0.505230 E E 5 P 9.53800000E-02 1.000000 E E 6 D 3.43000000E-01 1.000000 E E E E Summary of "ao basis" -> "" (spherical) E ------------------------------------------------------------------------------ E Tag Description Shells Functions and Types E ---------------- ------------------------------ ------ --------------------- E H cc-pvdz 3 5 2s1p E bqH cc-pvdz 3 5 2s1p E B cc-pvdz 6 14 3s2p1d E bqB cc-pvdz 6 14 3s2p1d E E E NWChem SCF Module E ----------------- E E E E ao basis = "ao basis" E functions = 29 E atoms = 4 E alpha electrons = 4 E beta electrons = 3 E charge = 1.00 E wavefunction = UHF E input vectors = atomic E output vectors = ./nwchem.movecs E use symmetry = T E symmetry adapt = T E E E Summary of "ao basis" -> "ao basis" (spherical) E ------------------------------------------------------------------------------ E Tag Description Shells Functions and Types E ---------------- ------------------------------ ------ --------------------- E H cc-pvdz 3 5 2s1p E bqH cc-pvdz 3 5 2s1p E B cc-pvdz 6 14 3s2p1d E bqB cc-pvdz 6 14 3s2p1d E E E Symmetry analysis of basis E -------------------------- E E a' 19 E a" 10 E E E Forming initial guess at 0.0s E E E Superposition of Atomic Density Guess E ------------------------------------- E E Sum of atomic energies: -26.03078371 E E Renormalizing density from 8.00 to 7 E E Non-variational initial energy E ------------------------------ E E Total energy = -23.356783 E 1-e energy = -37.930394 E 2-e energy = 9.654074 E HOMO = -0.541143 E LUMO = -0.369125 E E E Symmetry analysis of molecular orbitals - initial alpha E ------------------------------------------------------- E E Numbering of irreducible representations: E E 1 a' 2 a" E E Orbital symmetries: E E 1 a' 2 a' 3 a' 4 a' 5 a" E 6 a' 7 a" 8 a' 9 a' 10 a' E 11 a" 12 a' 13 a' 14 a' E E E Symmetry analysis of molecular orbitals - initial beta E ------------------------------------------------------ E E Numbering of irreducible representations: E E 1 a' 2 a" E E Orbital symmetries: E E 1 a' 2 a' 3 a' 4 a' 5 a" E 6 a' 7 a" 8 a' 9 a' 10 a' E 11 a" 12 a' 13 a' 14 a' E E E Starting SCF solution at 0.1s E E E E ---------------------------------------------- E Quadratically convergent UHF E E Convergence threshold : 1.000E-06 E Maximum no. of iterations : 30 E Integral*density screening: 1.000E-08 E ---------------------------------------------- E E E #quartets = 4.385D+03 #integrals = 2.659D+04 #direct = 0.0% #cached =100.0% E E E Integral file = ./nwchem.aoints.0 E Record size in doubles = 65536 No. of integs per rec = 43688 E Max. records in memory = 4 Max. records in file = 125783 E No. of bits per label = 8 No. of bits per value = 64 E E E iter energy gnorm gmax time E ----- ------------------- --------- --------- -------- E 1 -25.9180776106 2.39D-01 1.30D-01 0.2 E 2 -25.9425949473 1.02D-01 4.13D-02 0.3 E 3 -25.9450986421 9.04D-03 3.62D-03 0.3 E 4 -25.9451384267 4.23D-05 2.22D-05 0.4 E 5 -25.9451384275 4.21D-08 1.45D-08 0.5 E E E Final UHF results E ------------------ E E Total SCF energy = -25.945138427485 E One electron energy = -41.231566793925 E Two electron energy = 10.366890166706 E Nuclear repulsion energy = 4.919538199733 E E Sz = 0.5000 E Sz(Sz+1) = 0.7500 E S^2 = 0.7561 E E Time for solution = 0.4s E E E E Symmetry analysis of molecular orbitals - alpha E ----------------------------------------------- E E Numbering of irreducible representations: E E 1 a' 2 a" E E Orbital symmetries: E E 1 a' 2 a' 3 a' 4 a' 5 a" E 6 a' 7 a' 8 a" 9 a' 10 a' E 11 a" 12 a' 13 a' 14 a' E E E Symmetry analysis of molecular orbitals - beta E ---------------------------------------------- E E Numbering of irreducible representations: E E 1 a' 2 a" E E Orbital symmetries: E E 1 a' 2 a' 3 a' 4 a' 5 a" E 6 a' 7 a' 8 a" 9 a' 10 a' E 11 a" 12 a' 13 a' 14 a' E E Final alpha eigenvalues E ----------------------- E E 1 E 1 -8.1252 E 2 -1.0028 E 3 -0.8149 E 4 -0.7527 E 5 -0.2658 E 6 -0.2653 E 7 -0.0033 E 8 0.0346 E 9 0.1374 E 10 0.1737 E 11 0.1852 E 12 0.1870 E 13 0.3755 E 14 0.4824 E E Final beta eigenvalues E ---------------------- E E 1 E 1 -8.0993 E 2 -0.9423 E 3 -0.7607 E 4 -0.2719 E 5 -0.2266 E 6 -0.2261 E 7 0.0300 E 8 0.0357 E 9 0.1561 E 10 0.1930 E 11 0.2052 E 12 0.2792 E 13 0.3851 E 14 0.5236 E E UHF Final Alpha Molecular Orbital Analysis E ------------------------------------------ E E Vector 2 Occ=1.000000D+00 E=-1.002800D+00 Symmetry=a' E MO Center= 1.0D-16, -1.1D+00, 7.5D-17, r^2= 1.0D+00 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 2 0.492039 1 B s 15 0.356568 2 H s E 3 0.268302 1 B s E E Vector 3 Occ=1.000000D+00 E=-8.148572D-01 Symmetry=a' E MO Center= -1.3D-17, 1.7D-01, 1.3D-16, r^2= 2.3D+00 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 5 0.524956 1 B py 2 0.287247 1 B s E 15 -0.250333 2 H s 3 0.229648 1 B s E 20 0.178467 3 H s 25 0.178467 4 H s E 8 0.153927 1 B py E E Vector 4 Occ=1.000000D+00 E=-7.526730D-01 Symmetry=a' E MO Center= -3.1D-17, 1.7D+00, -7.8D-17, r^2= 2.1D+00 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 20 0.369617 3 H s 25 0.369617 4 H s E 5 -0.299059 1 B py 2 -0.206142 1 B s E 3 -0.177075 1 B s 21 0.153232 3 H s E 26 0.153232 4 H s E E Vector 5 Occ=0.000000D+00 E=-2.658293D-01 Symmetry=a" E MO Center= -4.9D-18, -5.6D-01, -5.0D-17, r^2= 1.9D+00 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 6 0.582936 1 B pz 9 0.546644 1 B pz E E Vector 6 Occ=0.000000D+00 E=-2.653212D-01 Symmetry=a' E MO Center= -1.2D-16, -5.7D-01, 3.1D-16, r^2= 1.9D+00 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 4 0.584131 1 B px 7 0.548015 1 B px E E Vector 7 Occ=0.000000D+00 E=-3.254915D-03 Symmetry=a' E MO Center= 3.9D-17, -1.6D+00, 3.5D-18, r^2= 2.9D+00 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 16 2.513675 2 H s 3 -1.726187 1 B s E 8 1.359052 1 B py 5 0.459433 1 B py E 2 -0.197244 1 B s 15 0.163347 2 H s E E Vector 8 Occ=0.000000D+00 E= 3.464398D-02 Symmetry=a" E MO Center= 9.8D-18, 2.2D+00, 2.3D-17, r^2= 3.0D+00 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 21 1.880424 3 H s 26 -1.880424 4 H s E 6 0.218083 1 B pz 20 0.155442 3 H s E 25 -0.155442 4 H s E E Vector 9 Occ=0.000000D+00 E= 1.373915D-01 Symmetry=a' E MO Center= 2.8D-16, -6.8D-01, -6.6D-15, r^2= 4.1D+00 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 8 1.565287 1 B py 3 -0.876108 1 B s E 5 -0.611109 1 B py 16 0.565268 2 H s E 15 0.381927 2 H s 2 0.284879 1 B s E E Vector 10 Occ=0.000000D+00 E= 1.736780D-01 Symmetry=a' E MO Center= -1.9D-15, -5.7D-01, -1.7D-17, r^2= 3.2D+00 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 7 -1.057622 1 B px 4 1.031213 1 B px E E Vector 11 Occ=0.000000D+00 E= 1.852048D-01 Symmetry=a" E MO Center= -3.8D-17, -5.1D-01, 7.4D-15, r^2= 3.6D+00 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 9 -1.082206 1 B pz 6 1.012051 1 B pz E 21 -0.546308 3 H s 26 0.546308 4 H s E E Vector 12 Occ=0.000000D+00 E= 1.869628D-01 Symmetry=a' E MO Center= 1.7D-15, -1.1D-01, -5.1D-16, r^2= 3.0D+00 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 3 1.562996 1 B s 2 -1.344584 1 B s E 1 -0.561416 1 B s 5 -0.382259 1 B py E 15 -0.262114 2 H s 8 0.248097 1 B py E E Vector 13 Occ=0.000000D+00 E= 3.755379D-01 Symmetry=a' E MO Center= -1.0D-19, 2.5D+00, 5.7D-16, r^2= 3.1D+00 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 8 1.168231 1 B py 16 1.154228 2 H s E 21 -0.866207 3 H s 26 -0.866207 4 H s E 20 0.686717 3 H s 25 0.686717 4 H s E 3 -0.430641 1 B s 5 -0.192688 1 B py E 2 -0.159785 1 B s E E Vector 14 Occ=0.000000D+00 E= 4.823578D-01 Symmetry=a' E MO Center= -1.3D-17, -1.4D+00, -8.1D-16, r^2= 3.2D+00 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 16 3.175248 2 H s 3 -2.835358 1 B s E 8 1.723478 1 B py 2 0.959608 1 B s E 15 -0.712612 2 H s 14 0.520262 1 B d 2 E 1 0.401160 1 B s 5 -0.374529 1 B py E 12 0.299989 1 B d 0 18 0.172951 2 H py E E Vector 15 Occ=0.000000D+00 E= 5.031629D-01 Symmetry=a' E MO Center= -4.0D-18, -6.6D-01, -9.1D-18, r^2= 1.5D+00 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 10 0.938633 1 B d -2 E E E UHF Final Beta Molecular Orbital Analysis E ----------------------------------------- E E Vector 2 Occ=1.000000D+00 E=-9.422736D-01 Symmetry=a' E MO Center= 8.9D-18, -1.3D+00, 8.6D-17, r^2= 8.3D-01 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 2 0.421960 1 B s 15 0.336134 2 H s E 5 -0.284707 1 B py 3 0.271792 1 B s E E Vector 3 Occ=1.000000D+00 E=-7.607244D-01 Symmetry=a' E MO Center= -2.6D-17, 2.3D+00, -4.3D-18, r^2= 7.8D-01 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 20 0.402771 3 H s 25 0.402771 4 H s E 21 0.162503 3 H s 26 0.162503 4 H s E E Vector 4 Occ=0.000000D+00 E=-2.718526D-01 Symmetry=a' E MO Center= 1.5D-17, -2.9D-01, 3.4D-19, r^2= 1.9D+00 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 3 0.705918 1 B s 5 0.338926 1 B py E 16 -0.308194 2 H s 8 0.233155 1 B py E 2 0.227759 1 B s 15 -0.223693 2 H s E E Vector 5 Occ=0.000000D+00 E=-2.266266D-01 Symmetry=a" E MO Center= -1.0D-17, -6.1D-01, -8.3D-17, r^2= 2.1D+00 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 9 0.599323 1 B pz 6 0.529471 1 B pz E E Vector 6 Occ=0.000000D+00 E=-2.260711D-01 Symmetry=a' E MO Center= -1.8D-16, -6.2D-01, 3.2D-16, r^2= 2.1D+00 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 7 0.600383 1 B px 4 0.531054 1 B px E E Vector 7 Occ=0.000000D+00 E= 3.001982D-02 Symmetry=a' E MO Center= 5.1D-17, -1.4D+00, 1.9D-18, r^2= 3.6D+00 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 16 2.639808 2 H s 3 -1.531133 1 B s E 8 1.487851 1 B py 5 0.429957 1 B py E 2 -0.305419 1 B s E E Vector 8 Occ=0.000000D+00 E= 3.574049D-02 Symmetry=a" E MO Center= 3.6D-17, 2.2D+00, 3.3D-16, r^2= 2.9D+00 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 21 1.891959 3 H s 26 -1.891959 4 H s E 6 0.202702 1 B pz 20 0.154623 3 H s E 25 -0.154623 4 H s E E Vector 9 Occ=0.000000D+00 E= 1.561029D-01 Symmetry=a' E MO Center= 8.4D-16, -9.6D-01, -1.0D-14, r^2= 3.7D+00 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 8 -1.605617 1 B py 3 1.529250 1 B s E 16 -0.869834 2 H s 2 -0.663008 1 B s E 5 0.504745 1 B py 15 -0.431092 2 H s E 1 -0.305631 1 B s E E Vector 10 Occ=0.000000D+00 E= 1.930289D-01 Symmetry=a' E MO Center= -1.8D-15, -5.6D-01, -2.4D-17, r^2= 3.0D+00 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 4 1.057013 1 B px 7 -1.029531 1 B px E E Vector 11 Occ=0.000000D+00 E= 2.052377D-01 Symmetry=a" E MO Center= 1.4D-17, -5.1D-01, 1.1D-14, r^2= 3.4D+00 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 9 -1.057692 1 B pz 6 1.044129 1 B pz E 21 -0.524946 3 H s 26 0.524946 4 H s E E Vector 12 Occ=0.000000D+00 E= 2.791950D-01 Symmetry=a' E MO Center= 7.9D-16, 1.7D-01, -3.8D-16, r^2= 2.9D+00 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 3 1.664699 1 B s 2 -1.301347 1 B s E 16 -0.637546 2 H s 5 -0.605256 1 B py E 1 -0.514144 1 B s 20 -0.255596 3 H s E 25 -0.255596 4 H s 21 0.187973 3 H s E 26 0.187973 4 H s E E Vector 13 Occ=0.000000D+00 E= 3.851311D-01 Symmetry=a' E MO Center= 8.4D-17, 2.4D+00, 5.7D-16, r^2= 3.1D+00 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 8 1.023957 1 B py 21 -0.842520 3 H s E 26 -0.842520 4 H s 16 0.777885 2 H s E 20 0.663959 3 H s 25 0.663959 4 H s E 2 -0.463839 1 B s 5 -0.293595 1 B py E 1 -0.188724 1 B s E E Vector 14 Occ=0.000000D+00 E= 5.236087D-01 Symmetry=a' E MO Center= 4.7D-17, -1.4D+00, 2.9D-17, r^2= 2.8D+00 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 16 3.042146 2 H s 3 -2.551174 1 B s E 8 1.667587 1 B py 15 -0.791150 2 H s E 2 0.763908 1 B s 14 0.521066 1 B d 2 E 5 -0.462802 1 B py 1 0.324811 1 B s E 12 0.299262 1 B d 0 18 0.181150 2 H py E E Vector 15 Occ=0.000000D+00 E= 5.576254D-01 Symmetry=a' E MO Center= 3.0D-16, -6.2D-01, -1.6D-17, r^2= 1.5D+00 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 10 0.934530 1 B d -2 E E E center of mass E -------------- E x = 0.00000000 y = -0.45788690 z = 0.00000000 E E moments of inertia (a.u.) E ------------------ E 61.510536153691 0.000000000000 0.000000000000 E 0.000000000000 0.993361021422 0.000000000000 E 0.000000000000 0.000000000000 60.517175132268 E E Mulliken analysis of the total density E -------------------------------------- E E Atom Charge Shell Charges E ----------- ------ ------------------------------------------------------- E 1 B 5 4.26 2.00 0.87 0.52 0.69 0.16 0.01 E 2 H 1 0.78 0.65 0.10 0.02 E 3 H 1 0.98 0.70 0.27 0.01 E 4 H 1 0.98 0.70 0.27 0.01 E E Mulliken analysis of the alpha density E -------------------------------------- E E Atom Charge Shell Charges E ----------- ------ ------------------------------------------------------- E 1 B 5 2.54 1.00 0.55 0.32 0.55 0.12 0.01 E 2 H 1 0.47 0.39 0.07 0.01 E 3 H 1 0.49 0.35 0.13 0.01 E 4 H 1 0.49 0.35 0.13 0.01 E E Mulliken analysis of the beta density E ------------------------------------- E E Atom Charge Shell Charges E ----------- ------ ------------------------------------------------------- E 1 B 5 1.72 1.00 0.32 0.20 0.14 0.05 0.00 E 2 H 1 0.30 0.26 0.03 0.01 E 3 H 1 0.49 0.35 0.14 0.01 E 4 H 1 0.49 0.35 0.14 0.01 E E Mulliken analysis of the spin density E ------------------------------------- E E Atom Charge Shell Charges E ----------- ------ ------------------------------------------------------- E 1 B 5 0.82 0.00 0.24 0.12 0.40 0.07 0.00 E 2 H 1 0.17 0.13 0.04 0.00 E 3 H 1 0.01 0.01 -0.00 0.00 E 4 H 1 0.01 0.01 -0.00 0.00 E E Multipole analysis of the density wrt the origin E ------------------------------------------------ E E L x y z total alpha beta nuclear E - - - - ----- ----- ---- ------- E 0 0 0 0 1.000000 -4.000000 -3.000000 8.000000 E E 1 1 0 0 0.000000 -0.000000 0.000000 0.000000 E 1 0 1 0 -1.267538 -0.421377 -0.846161 0.000000 E 1 0 0 1 -0.000000 -0.000000 -0.000000 0.000000 E E 2 2 0 0 -4.410694 -2.645046 -1.765648 0.000000 E 2 1 1 0 0.000000 0.000000 0.000000 0.000000 E 2 1 0 1 -0.000000 -0.000000 -0.000000 0.000000 E 2 0 2 0 -1.707399 -30.308540 -27.503748 56.104888 E 2 0 1 1 0.000000 -0.000000 0.000000 0.000000 E 2 0 0 2 -3.959912 -2.912730 -2.032830 0.985648 E E E Parallel integral file used 1 records with 0 large values E E NWChem Gradients Module E ----------------------- E E E E wavefunction = UHF E E Using symmetry E E STDERR: E E Program received signal SIGSEGV: Segmentation fault - invalid memory reference. E E Backtrace for this error: E #0 0x804a1f6db in ??? E #1 0x804a1e896 in ??? E #2 0x803729f6f in handle_signal E at /disk-samsung/freebsd-src/lib/libthr/thread/thr_sig.c:303 E #3 0x80372953e in thr_sighandler E at /disk-samsung/freebsd-src/lib/libthr/thread/thr_sig.c:246 E #4 0x7ffffffff192 in ??? E #5 0x803dd91b1 in ??? E #6 0x803badeb5 in ??? E #7 0x803298434 in ??? E #8 0x80329901d in ??? E #9 0x802f076a9 in ??? E #10 0x802e70b74 in ??? E #11 0x9f45dc in ??? E #12 0x9e382f in ??? E #13 0x7f38de in ??? E #14 0x7e7ba4 in ??? E #15 0x7fdbf4 in ??? E #16 0x7ec987 in ??? E #17 0x4219d7 in ??? E #18 0x422db0 in ??? E #19 0x41462d in ??? E #20 0x40e0e1 in ??? E #21 0x40c71c in ??? E #22 0x40c82f in ??? E E TRACEBACK: E Traceback (most recent call last): E File "/disk-samsung/freebsd-ports/science/py-qcengine/work-py38/qcengine-0.20.1/qcengine/programs/nwchem/runner.py", line 275, in parse_output E retres = qcvars[f"CURRENT {input_model.driver.upper()}"] E KeyError: 'CURRENT GRADIENT' qcengine/programs/nwchem/runner.py:277: UnknownError _____________ test_hf_gradient_module[hf rohf ae: nwchem-dz-grd1] ______________ self = NWChemHarness(name='NWChem', scratch=True, thread_safe=False, thread_parallel=False, node_parallel=True, managed_memory=True, extras=None, version_cache={'/usr/local/bin/nwchem': '7.0.2+11.eol.2499.gbbee7e139269'}) outfiles = {'nwchem.grad': None, 'nwchem.hess': None} input_model = AtomicInput(driver='gradient', model={'method': 'hf', 'basis': 'cc-pvdz'}, molecule_hash='f532294') def parse_output( self, outfiles: Dict[str, str], input_model: "AtomicInput" ) -> AtomicResult: # lgtm: [py/similar-function] # Get the stdout from the calculation (required) stdout = outfiles.pop("stdout") stderr = outfiles.pop("stderr") method = input_model.model.method.lower() method = method[4:] if method.startswith("nwc-") else method # Read the NWChem stdout file and, if needed, the hess or grad files # July 2021: nwmol & vector returns now atin/outfile orientation depending on fix_com,orientation=T/F. previously always atin orientation try: qcvars, nwhess, nwgrad, nwmol, version, module, errorTMP = harvest( input_model.molecule, method, stdout, **outfiles ) except Exception as e: raise UnknownError(error_stamp(stdout=stdout, stderr=stderr)) try: if nwgrad is not None: qcvars[f"{method.upper()} TOTAL GRADIENT"] = nwgrad qcvars["CURRENT GRADIENT"] = nwgrad if nwhess is not None: qcvars[f"{method.upper()} TOTAL HESSIAN"] = nwhess qcvars["CURRENT HESSIAN"] = nwhess # Normalize the output as a float or list of floats if input_model.driver.upper() == "PROPERTIES": retres = qcvars[f"CURRENT ENERGY"] else: > retres = qcvars[f"CURRENT {input_model.driver.upper()}"] E KeyError: 'CURRENT GRADIENT' qcengine/programs/nwchem/runner.py:275: KeyError During handling of the above exception, another exception occurred: inp = {'call': 'nwchem', 'fcae': 'ae', 'keywords': {'scf__rohf': True, 'scf__thresh': 1e-06}, 'reference': 'rohf'} dertype = 1, basis = 'cc-pvdz', subjects = ['hf', 'bh3p', 'bh3p'] clsd_open_pmols = {'bh3p': Molecule(name='bh3p', formula='BH3', hash='f532294'), 'h2o': Molecule(name='h2o', formula='H2O', hash='4684da5'), 'hf': Molecule(name='hf', formula='FH', hash='25205df'), 'nh2': Molecule(name='nh2', formula='H2N', hash='4002acf')} request = > @pytest.mark.parametrize( "dertype", [ pytest.param(1, id="grd1"), # pytest.param(0, id="grd0", marks=pytest.mark.long), ], ) @pytest.mark.parametrize( "basis, subjects", [ pytest.param("cc-pvdz", ["hf", "bh3p", "bh3p"], id="dz"), pytest.param("aug-cc-pvdz", ["h2o", "nh2", "nh2"], id="adz", marks=pytest.mark.long), pytest.param("cfour-qz2p", ["h2o", "nh2", "nh2"], id="qz2p", marks=pytest.mark.long), ], ) @pytest.mark.parametrize( "inp", [ # yapf: disable ######## Are all possible ways of computing working? pytest.param({"call": "cfour", "reference": "rhf", "fcae": "ae", "keywords": {"scf_conv": 12}, }, id="hf rhf ae: cfour", marks=using("cfour")), pytest.param({"call": "gamess", "reference": "rhf", "fcae": "ae", "keywords": {}, }, id="hf rhf ae: gamess", marks=using("gamess")), pytest.param({"call": "nwchem", "reference": "rhf", "fcae": "ae", "keywords": {"scf__thresh": 1.e-6}, }, id="hf rhf ae: nwchem", marks=using("nwchem")), pytest.param({"call": "psi4", "reference": "rhf", "fcae": "ae", "keywords": {"scf_type": "pk"}, }, id="hf rhf ae: psi4", marks=using("psi4_derqcsk")), pytest.param({"call": "cfour", "reference": "uhf", "fcae": "ae", "keywords": {"reference": "uhf", "scf_conv": 12}, }, id="hf uhf ae: cfour", marks=using("cfour")), pytest.param({"call": "gamess", "reference": "uhf", "fcae": "ae", "keywords": {"contrl__scftyp": "uhf"}, }, id="hf uhf ae: gamess", marks=using("gamess")), pytest.param({"call": "nwchem", "reference": "uhf", "fcae": "ae", "keywords": {"scf__uhf": True, "scf__thresh": 1.e-6}, }, id="hf uhf ae: nwchem", marks=using("nwchem")), pytest.param({"call": "psi4", "reference": "uhf", "fcae": "ae", "keywords": {"reference": "uhf", "scf_type": "pk"}, }, id="hf uhf ae: psi4", marks=using("psi4_derqcsk")), pytest.param({"call": "cfour", "reference": "rohf", "fcae": "ae", "keywords": {"reference": "rohf", "scf_conv": 12}, }, id="hf rohf ae: cfour", marks=using("cfour")), pytest.param({"call": "gamess", "reference": "rohf", "fcae": "ae", "keywords": {"contrl__scftyp": "rohf"}, }, id="hf rohf ae: gamess", marks=using("gamess")), pytest.param({"call": "nwchem", "reference": "rohf", "fcae": "ae", "keywords": {"scf__rohf": True, "scf__thresh": 1.e-6}, }, id="hf rohf ae: nwchem", marks=using("nwchem")), pytest.param({"call": "psi4", "reference": "rohf", "fcae": "ae", "keywords": {"reference": "rohf", "scf_type": "pk"}, }, id="hf rohf ae: psi4", marks=using("psi4_derqcsk")), # yapf: enable ], ) def test_hf_gradient_module(inp, dertype, basis, subjects, clsd_open_pmols, request): > runner_asserter(*_processor(inp, dertype, basis, subjects, clsd_open_pmols, request, "gradient", "hf")) qcengine/programs/tests/test_standard_suite.py:214: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ qcengine/programs/tests/standard_suite_runner.py:177: in runner_asserter wfn = qcng.compute(atin, qcprog, raise_error=True, local_options=local_options) qcengine/compute.py:91: in compute output_data = executor.compute(input_data, config) qcengine/programs/model.py:116: in compute result = self._compute(local_input_data, config) qcengine/programs/nwchem/runner.py:137: in _compute return self.parse_output(dexe["outfiles"], input_model) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = NWChemHarness(name='NWChem', scratch=True, thread_safe=False, thread_parallel=False, node_parallel=True, managed_memory=True, extras=None, version_cache={'/usr/local/bin/nwchem': '7.0.2+11.eol.2499.gbbee7e139269'}) outfiles = {'nwchem.grad': None, 'nwchem.hess': None} input_model = AtomicInput(driver='gradient', model={'method': 'hf', 'basis': 'cc-pvdz'}, molecule_hash='f532294') def parse_output( self, outfiles: Dict[str, str], input_model: "AtomicInput" ) -> AtomicResult: # lgtm: [py/similar-function] # Get the stdout from the calculation (required) stdout = outfiles.pop("stdout") stderr = outfiles.pop("stderr") method = input_model.model.method.lower() method = method[4:] if method.startswith("nwc-") else method # Read the NWChem stdout file and, if needed, the hess or grad files # July 2021: nwmol & vector returns now atin/outfile orientation depending on fix_com,orientation=T/F. previously always atin orientation try: qcvars, nwhess, nwgrad, nwmol, version, module, errorTMP = harvest( input_model.molecule, method, stdout, **outfiles ) except Exception as e: raise UnknownError(error_stamp(stdout=stdout, stderr=stderr)) try: if nwgrad is not None: qcvars[f"{method.upper()} TOTAL GRADIENT"] = nwgrad qcvars["CURRENT GRADIENT"] = nwgrad if nwhess is not None: qcvars[f"{method.upper()} TOTAL HESSIAN"] = nwhess qcvars["CURRENT HESSIAN"] = nwhess # Normalize the output as a float or list of floats if input_model.driver.upper() == "PROPERTIES": retres = qcvars[f"CURRENT ENERGY"] else: retres = qcvars[f"CURRENT {input_model.driver.upper()}"] except KeyError as e: > raise UnknownError(error_stamp(stdout=stdout, stderr=stderr)) E qcengine.exceptions.UnknownError: STDOUT: E E E E ============================== echo of input deck ============================== E echo E geometry units bohr E B 0.000000000000 0.000000000000 0.195947860000 E H 0.000000000000 0.000000000000 -2.140490630000 E H 0.000000000000 -0.702014360000 5.669178380000 E H 0.000000000000 0.702014360000 5.669178380000 E E end E memory 879931424 double E charge 1 E E basis spherical E H library cc-pvdz E bqH library H cc-pvdz E B library cc-pvdz E bqB library B cc-pvdz E end E E dft E mult 2 E end E E mcscf E multiplicity 2 E end E E scf E rohf E thresh 1e-06 E nopen 1 E end E E task scf gradient E E E python E grad = rtdb_get('scf:gradient') E if ga_nodeid() == 0: E import json E with open('nwchem.grad', 'w') as fp: E json.dump(grad, fp) E end E E task python E E ================================================================================ E E E E E E E Northwest Computational Chemistry Package (NWChem) 7.0.2 E -------------------------------------------------------- E E E Environmental Molecular Sciences Laboratory E Pacific Northwest National Laboratory E Richland, WA 99352 E E Copyright (c) 1994-2020 E Pacific Northwest National Laboratory E Battelle Memorial Institute E E NWChem is an open-source computational chemistry package E distributed under the terms of the E Educational Community License (ECL) 2.0 E A copy of the license is included with this distribution E in the LICENSE.TXT file E E ACKNOWLEDGMENT E -------------- E E This software and its documentation were developed at the E EMSL at Pacific Northwest National Laboratory, a multiprogram E national laboratory, operated for the U.S. Department of Energy E by Battelle under Contract Number DE-AC05-76RL01830. Support E for this work was provided by the Department of Energy Office E of Biological and Environmental Research, Office of Basic E Energy Sciences, and the Office of Advanced Scientific Computing. E E E Job information E --------------- E E hostname = yv.noip.me E program = /usr/local/bin/nwchem E date = Thu Oct 21 12:50:11 2021 E E compiled = Thu_Oct_21_12:11:03_2021 E source = /disk-samsung/freebsd-ports/science/nwchem/work/nwchem-7.0.2-release/src/.. E nwchem branch = 7.0.2 E nwchem revision = 11-eol-2499-gbbee7e139269 E ga revision = 5.8.0 E use scalapack = T E input = nwchem.nw E prefix = nwchem. E data base = ./nwchem.db E status = startup E nproc = 1 E time left = -1s E E E E Memory information E ------------------ E E heap = 219982852 doubles = 1678.3 Mbytes E stack = 219982857 doubles = 1678.3 Mbytes E global = 439965712 doubles = 3356.7 Mbytes (distinct from heap & stack) E total = 879931421 doubles = 6713.3 Mbytes E verify = yes E hardfail = no E E E Directory information E --------------------- E E 0 permanent = . E 0 scratch = . E E E E E NWChem Input Module E ------------------- E E E CS symmetry detected E E ------ E auto-z E ------ E autoz: The atoms group into disjoint clusters E cluster 1: 1 2 E cluster 2: 3 4 E Connecting clusters 1 2 via atoms 1 3 r = 2.92 E autoz: regenerating connections with new bonds E no constraints, skipping 0.0000000000000000 E no constraints, skipping 0.0000000000000000 E E E Geometry "geometry" -> "" E ------------------------- E E Output coordinates in a.u. (scale by 1.000000000 to convert to a.u.) E E No. Tag Charge X Y Z E ---- ---------------- ---------- -------------- -------------- -------------- E 1 B 5.0000 0.00000000 -1.07625282 0.00000000 E 2 H 1.0000 0.00000000 -3.41269131 0.00000000 E 3 H 1.0000 0.00000000 4.39697770 -0.70201436 E 4 H 1.0000 0.00000000 4.39697770 0.70201436 E E Atomic Mass E ----------- E E B 11.009310 E H 1.007825 E E E Effective nuclear repulsion energy (a.u.) 4.9195381997 E E Nuclear Dipole moment (a.u.) E ---------------------------- E X Y Z E ---------------- ---------------- ---------------- E 0.0000000000 0.0000000000 0.0000000000 E E Symmetry information E -------------------- E E Group name Cs E Group number 2 E Group order 2 E No. of unique centers 3 E E Symmetry unique atoms E E 1 2 3 E E E E Z-matrix (autoz) E -------- E E Units are Angstrom for bonds and degrees for angles E E Type Name I J K L M Value E ----------- -------- ----- ----- ----- ----- ----- ---------- E 1 Stretch 1 3 2.92004 E 2 Stretch 1 2 1.23639 E 3 Stretch 3 4 0.74298 E 4 Bend 1 3 4 82.69096 E 5 Bend 2 1 3 172.69096 E 6 Torsion 2 1 3 4 180.00000 E E E XYZ format geometry E ------------------- E 4 E geometry E B 0.00000000 -0.56952851 0.00000000 E H 0.00000000 -1.80591860 0.00000000 E H 0.00000000 2.32678056 -0.37149003 E H 0.00000000 2.32678056 0.37149003 E E ============================================================================== E internuclear distances E ------------------------------------------------------------------------------ E center one | center two | atomic units | a.u. E ------------------------------------------------------------------------------ E 2 H | 1 B | 2.33644 | 2.33644 E ------------------------------------------------------------------------------ E number of included internuclear distances: 1 E ============================================================================== E E E E library name resolved from: .nwchemrc E library file name is: E E Basis "ao basis" -> "" (spherical) E ----- E H (Hydrogen) E ------------ E Exponent Coefficients E -------------- --------------------------------------------------------- E 1 S 1.30100000E+01 0.019685 E 1 S 1.96200000E+00 0.137977 E 1 S 4.44600000E-01 0.478148 E E 2 S 1.22000000E-01 1.000000 E E 3 P 7.27000000E-01 1.000000 E E bqH E --- E Exponent Coefficients E -------------- --------------------------------------------------------- E 1 S 1.30100000E+01 0.019685 E 1 S 1.96200000E+00 0.137977 E 1 S 4.44600000E-01 0.478148 E E 2 S 1.22000000E-01 1.000000 E E 3 P 7.27000000E-01 1.000000 E E B (Boron) E --------- E Exponent Coefficients E -------------- --------------------------------------------------------- E 1 S 4.57000000E+03 0.000696 E 1 S 6.85900000E+02 0.005353 E 1 S 1.56500000E+02 0.027134 E 1 S 4.44700000E+01 0.101380 E 1 S 1.44800000E+01 0.272055 E 1 S 5.13100000E+00 0.448403 E 1 S 1.89800000E+00 0.290123 E 1 S 3.32900000E-01 0.014322 E E 2 S 4.57000000E+03 -0.000139 E 2 S 6.85900000E+02 -0.001097 E 2 S 1.56500000E+02 -0.005444 E 2 S 4.44700000E+01 -0.021916 E 2 S 1.44800000E+01 -0.059751 E 2 S 5.13100000E+00 -0.138732 E 2 S 1.89800000E+00 -0.131482 E 2 S 3.32900000E-01 0.539526 E E 3 S 1.04300000E-01 1.000000 E E 4 P 6.00100000E+00 0.035481 E 4 P 1.24100000E+00 0.198072 E 4 P 3.36400000E-01 0.505230 E E 5 P 9.53800000E-02 1.000000 E E 6 D 3.43000000E-01 1.000000 E E bqB E --- E Exponent Coefficients E -------------- --------------------------------------------------------- E 1 S 4.57000000E+03 0.000696 E 1 S 6.85900000E+02 0.005353 E 1 S 1.56500000E+02 0.027134 E 1 S 4.44700000E+01 0.101380 E 1 S 1.44800000E+01 0.272055 E 1 S 5.13100000E+00 0.448403 E 1 S 1.89800000E+00 0.290123 E 1 S 3.32900000E-01 0.014322 E E 2 S 4.57000000E+03 -0.000139 E 2 S 6.85900000E+02 -0.001097 E 2 S 1.56500000E+02 -0.005444 E 2 S 4.44700000E+01 -0.021916 E 2 S 1.44800000E+01 -0.059751 E 2 S 5.13100000E+00 -0.138732 E 2 S 1.89800000E+00 -0.131482 E 2 S 3.32900000E-01 0.539526 E E 3 S 1.04300000E-01 1.000000 E E 4 P 6.00100000E+00 0.035481 E 4 P 1.24100000E+00 0.198072 E 4 P 3.36400000E-01 0.505230 E E 5 P 9.53800000E-02 1.000000 E E 6 D 3.43000000E-01 1.000000 E E E E Summary of "ao basis" -> "" (spherical) E ------------------------------------------------------------------------------ E Tag Description Shells Functions and Types E ---------------- ------------------------------ ------ --------------------- E H cc-pvdz 3 5 2s1p E bqH cc-pvdz 3 5 2s1p E B cc-pvdz 6 14 3s2p1d E bqB cc-pvdz 6 14 3s2p1d E E E NWChem SCF Module E ----------------- E E E E ao basis = "ao basis" E functions = 29 E atoms = 4 E closed shells = 3 E open shells = 1 E charge = 1.00 E wavefunction = ROHF E input vectors = atomic E output vectors = ./nwchem.movecs E use symmetry = T E symmetry adapt = T E E E Summary of "ao basis" -> "ao basis" (spherical) E ------------------------------------------------------------------------------ E Tag Description Shells Functions and Types E ---------------- ------------------------------ ------ --------------------- E H cc-pvdz 3 5 2s1p E bqH cc-pvdz 3 5 2s1p E B cc-pvdz 6 14 3s2p1d E bqB cc-pvdz 6 14 3s2p1d E E E Symmetry analysis of basis E -------------------------- E E a' 19 E a" 10 E E E Forming initial guess at 0.0s E E E Superposition of Atomic Density Guess E ------------------------------------- E E Sum of atomic energies: -26.03078371 E E Renormalizing density from 8.00 to 7 E E Non-variational initial energy E ------------------------------ E E Total energy = -23.356783 E 1-e energy = -37.930394 E 2-e energy = 9.654074 E HOMO = -0.541143 E LUMO = -0.369125 E E E Symmetry analysis of molecular orbitals - initial E ------------------------------------------------- E E Numbering of irreducible representations: E E 1 a' 2 a" E E Orbital symmetries: E E 1 a' 2 a' 3 a' 4 a' 5 a" E 6 a' 7 a" 8 a' 9 a' 10 a' E 11 a" 12 a' 13 a' 14 a' E E E Starting SCF solution at 0.1s E E E E ---------------------------------------------- E Quadratically convergent ROHF E E Convergence threshold : 1.000E-06 E Maximum no. of iterations : 30 E Final Fock-matrix accuracy: 1.000E-08 E ---------------------------------------------- E E E #quartets = 4.401D+03 #integrals = 2.699D+04 #direct = 0.0% #cached =100.0% E E E Integral file = ./nwchem.aoints.0 E Record size in doubles = 65536 No. of integs per rec = 43688 E Max. records in memory = 4 Max. records in file = 125777 E No. of bits per label = 8 No. of bits per value = 64 E E E iter energy gnorm gmax time E ----- ------------------- --------- --------- -------- E 1 -25.9180776105 2.35D-01 1.30D-01 0.2 E 2 -25.9397896780 1.79D-01 8.18D-02 0.2 E 3 -25.9435939778 8.82D-03 3.79D-03 0.3 E 4 -25.9436143154 7.37D-05 4.38D-05 0.4 E 5 -25.9436143167 8.47D-08 5.90D-08 0.4 E E E Final ROHF results E ------------------ E E Total SCF energy = -25.943614316734 E One-electron energy = -41.234112642237 E Two-electron energy = 10.370960125770 E Nuclear repulsion energy = 4.919538199733 E E Time for solution = 0.3s E E E E Symmetry analysis of molecular orbitals - final E ----------------------------------------------- E E Numbering of irreducible representations: E E 1 a' 2 a" E E Orbital symmetries: E E 1 a' 2 a' 3 a' 4 a' 5 a" E 6 a' 7 a' 8 a" 9 a' 10 a' E 11 a" 12 a' 13 a' 14 a' E E Final eigenvalues E ----------------- E E 1 E 1 -8.1120 E 2 -0.9661 E 3 -0.7661 E 4 -0.5185 E 5 -0.2450 E 6 -0.2444 E 7 0.0118 E 8 0.0352 E 9 0.1473 E 10 0.1835 E 11 0.1953 E 12 0.2179 E 13 0.3787 E 14 0.5013 E E ROHF Final Molecular Orbital Analysis E ------------------------------------- E E Vector 2 Occ=2.000000D+00 E=-9.660846D-01 Symmetry=a' E MO Center= 7.8D-17, -1.3D+00, 9.0D-17, r^2= 8.1D-01 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 2 0.410308 1 B s 15 0.373215 2 H s E 5 -0.267159 1 B py 3 0.233597 1 B s E E Vector 3 Occ=2.000000D+00 E=-7.661266D-01 Symmetry=a' E MO Center= -1.9D-17, 2.3D+00, 1.1D-16, r^2= 7.7D-01 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 20 0.404977 3 H s 25 0.404977 4 H s E 21 0.161577 3 H s 26 0.161577 4 H s E E Vector 4 Occ=1.000000D+00 E=-5.185390D-01 Symmetry=a' E MO Center= -1.9D-17, -1.6D-01, -2.1D-17, r^2= 1.1D+00 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 5 0.573859 1 B py 2 0.445346 1 B s E 3 0.331254 1 B s 15 -0.185478 2 H s E E Vector 5 Occ=0.000000D+00 E=-2.449572D-01 Symmetry=a" E MO Center= -3.7D-18, -5.8D-01, 8.6D-16, r^2= 2.0D+00 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 9 0.574269 1 B pz 6 0.555745 1 B pz E E Vector 6 Occ=0.000000D+00 E=-2.444242D-01 Symmetry=a' E MO Center= -1.1D-16, -5.9D-01, 3.2D-16, r^2= 2.0D+00 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 7 0.575505 1 B px 4 0.557142 1 B px E E Vector 7 Occ=0.000000D+00 E= 1.176677D-02 Symmetry=a' E MO Center= -3.2D-17, -1.6D+00, 3.1D-17, r^2= 3.0D+00 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 16 2.593266 2 H s 3 -1.695546 1 B s E 8 1.390763 1 B py 5 0.430647 1 B py E 2 -0.246575 1 B s E E Vector 8 Occ=0.000000D+00 E= 3.518159D-02 Symmetry=a" E MO Center= 6.5D-18, 2.2D+00, 1.5D-16, r^2= 2.9D+00 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 21 1.886688 3 H s 26 -1.886688 4 H s E 6 0.210300 1 B pz 20 0.154971 3 H s E 25 -0.154971 4 H s E E Vector 9 Occ=0.000000D+00 E= 1.473221D-01 Symmetry=a' E MO Center= -5.8D-16, -8.4D-01, -1.1D-15, r^2= 3.9D+00 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 8 1.594147 1 B py 3 -1.209527 1 B s E 16 0.708668 2 H s 5 -0.548273 1 B py E 2 0.495446 1 B s 15 0.409117 2 H s E 1 0.229671 1 B s E E Vector 10 Occ=0.000000D+00 E= 1.834688D-01 Symmetry=a' E MO Center= 1.2D-15, -5.6D-01, -2.1D-17, r^2= 3.1D+00 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 4 1.046004 1 B px 7 -1.043453 1 B px E E Vector 11 Occ=0.000000D+00 E= 1.953350D-01 Symmetry=a" E MO Center= 3.7D-17, -5.1D-01, -1.1D-16, r^2= 3.5D+00 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 9 -1.070035 1 B pz 6 1.030182 1 B pz E 21 -0.534965 3 H s 26 0.534965 4 H s E E Vector 12 Occ=0.000000D+00 E= 2.179420D-01 Symmetry=a' E MO Center= -7.1D-16, 8.9D-02, -7.6D-18, r^2= 2.9D+00 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 3 1.606918 1 B s 2 -1.307238 1 B s E 1 -0.544688 1 B s 5 -0.460210 1 B py E 8 0.300715 1 B py 16 -0.193751 2 H s E 15 -0.191106 2 H s 20 -0.178430 3 H s E 25 -0.178430 4 H s E E Vector 13 Occ=0.000000D+00 E= 3.786984D-01 Symmetry=a' E MO Center= -5.0D-19, 2.5D+00, 7.7D-16, r^2= 3.0D+00 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 8 1.113320 1 B py 16 1.026767 2 H s E 21 -0.863700 3 H s 26 -0.863700 4 H s E 20 0.684480 3 H s 25 0.684480 4 H s E 3 -0.264928 1 B s 2 -0.239565 1 B s E 5 -0.202555 1 B py E E Vector 14 Occ=0.000000D+00 E= 5.013068D-01 Symmetry=a' E MO Center= -5.0D-18, -1.4D+00, -4.6D-17, r^2= 3.0D+00 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 16 3.122566 2 H s 3 -2.721614 1 B s E 8 1.694920 1 B py 2 0.899151 1 B s E 15 -0.753606 2 H s 14 0.523535 1 B d 2 E 5 -0.388772 1 B py 1 0.374829 1 B s E 12 0.301461 1 B d 0 18 0.176239 2 H py E E E center of mass E -------------- E x = 0.00000000 y = -0.45788690 z = 0.00000000 E E moments of inertia (a.u.) E ------------------ E 61.510536153691 0.000000000000 0.000000000000 E 0.000000000000 0.993361021422 0.000000000000 E 0.000000000000 0.000000000000 60.517175132268 E E Mulliken analysis of the total density E -------------------------------------- E E Atom Charge Shell Charges E ----------- ------ ------------------------------------------------------- E 1 B 5 4.26 2.00 0.85 0.51 0.71 0.17 0.01 E 2 H 1 0.78 0.65 0.11 0.02 E 3 H 1 0.98 0.70 0.27 0.01 E 4 H 1 0.98 0.70 0.27 0.01 E E Mulliken analysis of the open-shell density E ------------------------------------------- E E Atom Charge Shell Charges E ----------- ------ ------------------------------------------------------- E 1 B 5 0.94 0.00 0.25 0.17 0.44 0.08 -0.00 E 2 H 1 0.06 0.05 0.00 0.00 E 3 H 1 0.00 0.00 -0.00 0.00 E 4 H 1 0.00 0.00 -0.00 0.00 E E Multipole analysis of the density wrt the origin E ------------------------------------------------ E E L x y z total open nuclear E - - - - ----- ---- ------- E 0 0 0 0 1.000000 -1.000000 8.000000 E E 1 1 0 0 -0.000000 0.000000 0.000000 E 1 0 1 0 -1.259798 0.294814 0.000000 E 1 0 0 1 -0.000000 0.000000 0.000000 E E 2 2 0 0 -4.396207 -0.978057 0.000000 E 2 1 1 0 0.000000 0.000000 0.000000 E 2 1 0 1 -0.000000 -0.000000 0.000000 E 2 0 2 0 -1.774839 -1.989875 56.104888 E 2 0 1 1 -0.000000 0.000000 0.000000 E 2 0 0 2 -3.945662 -0.979636 0.985648 E E E Parallel integral file used 1 records with 0 large values E E NWChem Gradients Module E ----------------------- E E E E wavefunction = ROHF E E Using symmetry E E STDERR: E E Program received signal SIGSEGV: Segmentation fault - invalid memory reference. E E Backtrace for this error: E #0 0x804a1f6db in ??? E #1 0x804a1e896 in ??? E #2 0x803729f6f in handle_signal E at /disk-samsung/freebsd-src/lib/libthr/thread/thr_sig.c:303 E #3 0x80372953e in thr_sighandler E at /disk-samsung/freebsd-src/lib/libthr/thread/thr_sig.c:246 E #4 0x7ffffffff192 in ??? E #5 0x803dd91b1 in ??? E #6 0x803badeb5 in ??? E #7 0x803298434 in ??? E #8 0x80329901d in ??? E #9 0x802f076a9 in ??? E #10 0x802e70b74 in ??? E #11 0x9f45dc in ??? E #12 0x9e382f in ??? E #13 0x7f38de in ??? E #14 0x7e7ba4 in ??? E #15 0x7fdbf4 in ??? E #16 0x7ec987 in ??? E #17 0x4219d7 in ??? E #18 0x422db0 in ??? E #19 0x41462d in ??? E #20 0x40e0e1 in ??? E #21 0x40c71c in ??? E #22 0x40c82f in ??? E E TRACEBACK: E Traceback (most recent call last): E File "/disk-samsung/freebsd-ports/science/py-qcengine/work-py38/qcengine-0.20.1/qcengine/programs/nwchem/runner.py", line 275, in parse_output E retres = qcvars[f"CURRENT {input_model.driver.upper()}"] E KeyError: 'CURRENT GRADIENT' qcengine/programs/nwchem/runner.py:277: UnknownError ______________ test_hf_hessian_module[hf rohf ae: nwchem-dz-hes2] ______________ self = NWChemHarness(name='NWChem', scratch=True, thread_safe=False, thread_parallel=False, node_parallel=True, managed_memory=True, extras=None, version_cache={'/usr/local/bin/nwchem': '7.0.2+11.eol.2499.gbbee7e139269'}) outfiles = {'nwchem.grad': None, 'nwchem.hess': None} input_model = AtomicInput(driver='hessian', model={'method': 'hf', 'basis': 'cc-pvdz'}, molecule_hash='f532294') def parse_output( self, outfiles: Dict[str, str], input_model: "AtomicInput" ) -> AtomicResult: # lgtm: [py/similar-function] # Get the stdout from the calculation (required) stdout = outfiles.pop("stdout") stderr = outfiles.pop("stderr") method = input_model.model.method.lower() method = method[4:] if method.startswith("nwc-") else method # Read the NWChem stdout file and, if needed, the hess or grad files # July 2021: nwmol & vector returns now atin/outfile orientation depending on fix_com,orientation=T/F. previously always atin orientation try: qcvars, nwhess, nwgrad, nwmol, version, module, errorTMP = harvest( input_model.molecule, method, stdout, **outfiles ) except Exception as e: raise UnknownError(error_stamp(stdout=stdout, stderr=stderr)) try: if nwgrad is not None: qcvars[f"{method.upper()} TOTAL GRADIENT"] = nwgrad qcvars["CURRENT GRADIENT"] = nwgrad if nwhess is not None: qcvars[f"{method.upper()} TOTAL HESSIAN"] = nwhess qcvars["CURRENT HESSIAN"] = nwhess # Normalize the output as a float or list of floats if input_model.driver.upper() == "PROPERTIES": retres = qcvars[f"CURRENT ENERGY"] else: > retres = qcvars[f"CURRENT {input_model.driver.upper()}"] E KeyError: 'CURRENT HESSIAN' qcengine/programs/nwchem/runner.py:275: KeyError During handling of the above exception, another exception occurred: inp = {'call': 'nwchem', 'fcae': 'ae', 'keywords': {'scf__rohf': True, 'scf__thresh': 1e-07}, 'reference': 'rohf'} dertype = 2, basis = 'cc-pvdz', subjects = ['hf', 'bh3p', 'bh3p'] clsd_open_pmols = {'bh3p': Molecule(name='bh3p', formula='BH3', hash='f532294'), 'h2o': Molecule(name='h2o', formula='H2O', hash='4684da5'), 'hf': Molecule(name='hf', formula='FH', hash='25205df'), 'nh2': Molecule(name='nh2', formula='H2N', hash='4002acf')} request = > @pytest.mark.parametrize( "dertype", [ pytest.param(2, id="hes2"), # pytest.param(1, id="hes1", marks=pytest.mark.long), # pytest.param(0, id="hes0", marks=pytest.mark.long), ], ) @pytest.mark.parametrize( "basis, subjects", [ pytest.param("cc-pvdz", ["hf", "bh3p", "bh3p"], id="dz"), pytest.param("aug-cc-pvdz", ["h2o", "nh2", "nh2"], id="adz", marks=pytest.mark.long), pytest.param("cfour-qz2p", ["h2o", "nh2", "nh2"], id="qz2p", marks=pytest.mark.long), ], ) @pytest.mark.parametrize( "inp", [ # yapf: disable pytest.param({"call": "cfour", "reference": "rhf", "fcae": "ae", "keywords": {"scf_conv": 12}, }, id="hf rhf ae: cfour", marks=using("cfour")), pytest.param({"call": "gamess", "reference": "rhf", "fcae": "ae", "keywords": {}, }, id="hf rhf ae: gamess", marks=using("gamess")), pytest.param({"call": "nwchem", "reference": "rhf", "fcae": "ae", "keywords": {}, }, id="hf rhf ae: nwchem", marks=using("nwchem")), pytest.param({"call": "psi4", "reference": "rhf", "fcae": "ae", "keywords": {"scf_type": "pk"}, }, id="hf rhf ae: psi4", marks=using("psi4_derqcsk")), pytest.param({"call": "cfour", "reference": "uhf", "fcae": "ae", "keywords": {"reference": "uhf", "scf_conv": 12}, }, id="hf uhf ae: cfour", marks=using("cfour")), pytest.param({"call": "gamess", "reference": "uhf", "fcae": "ae", "keywords": {"contrl__scftyp": "uhf"}, }, id="hf uhf ae: gamess", marks=using("gamess")), pytest.param({"call": "nwchem", "reference": "uhf", "fcae": "ae", "keywords": {"scf__uhf": True}, }, id="hf uhf ae: nwchem", marks=using("nwchem")), pytest.param({"call": "psi4", "reference": "uhf", "fcae": "ae", "keywords": {"reference": "uhf", "scf_type": "pk"}, }, id="hf uhf ae: psi4", marks=using("psi4_derqcsk")), pytest.param({"call": "cfour", "reference": "rohf", "fcae": "ae", "keywords": {"reference": "rohf", "scf_conv": 12}, }, id="hf rohf ae: cfour", marks=using("cfour")), pytest.param({"call": "gamess", "reference": "rohf", "fcae": "ae", "keywords": {"contrl__scftyp": "rohf", "scf__dirscf": True}, }, id="hf rohf ae: gamess", marks=using("gamess")), pytest.param({"call": "nwchem", "reference": "rohf", "fcae": "ae", "keywords": {"scf__rohf": True, "scf__thresh": 1.e-7}, }, id="hf rohf ae: nwchem", marks=using("nwchem")), pytest.param({"call": "psi4", "reference": "rohf", "fcae": "ae", "keywords": {"reference": "rohf", "scf_type": "pk"}, "error": {2: _q6 }}, id="hf rohf ae: psi4", marks=using("psi4_mp2qcsk")), # yapf: enable ], ) def test_hf_hessian_module(inp, dertype, basis, subjects, clsd_open_pmols, request): > runner_asserter(*_processor(inp, dertype, basis, subjects, clsd_open_pmols, request, "hessian", "hf")) qcengine/programs/tests/test_standard_suite.py:265: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ qcengine/programs/tests/standard_suite_runner.py:177: in runner_asserter wfn = qcng.compute(atin, qcprog, raise_error=True, local_options=local_options) qcengine/compute.py:91: in compute output_data = executor.compute(input_data, config) qcengine/programs/model.py:116: in compute result = self._compute(local_input_data, config) qcengine/programs/nwchem/runner.py:137: in _compute return self.parse_output(dexe["outfiles"], input_model) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = NWChemHarness(name='NWChem', scratch=True, thread_safe=False, thread_parallel=False, node_parallel=True, managed_memory=True, extras=None, version_cache={'/usr/local/bin/nwchem': '7.0.2+11.eol.2499.gbbee7e139269'}) outfiles = {'nwchem.grad': None, 'nwchem.hess': None} input_model = AtomicInput(driver='hessian', model={'method': 'hf', 'basis': 'cc-pvdz'}, molecule_hash='f532294') def parse_output( self, outfiles: Dict[str, str], input_model: "AtomicInput" ) -> AtomicResult: # lgtm: [py/similar-function] # Get the stdout from the calculation (required) stdout = outfiles.pop("stdout") stderr = outfiles.pop("stderr") method = input_model.model.method.lower() method = method[4:] if method.startswith("nwc-") else method # Read the NWChem stdout file and, if needed, the hess or grad files # July 2021: nwmol & vector returns now atin/outfile orientation depending on fix_com,orientation=T/F. previously always atin orientation try: qcvars, nwhess, nwgrad, nwmol, version, module, errorTMP = harvest( input_model.molecule, method, stdout, **outfiles ) except Exception as e: raise UnknownError(error_stamp(stdout=stdout, stderr=stderr)) try: if nwgrad is not None: qcvars[f"{method.upper()} TOTAL GRADIENT"] = nwgrad qcvars["CURRENT GRADIENT"] = nwgrad if nwhess is not None: qcvars[f"{method.upper()} TOTAL HESSIAN"] = nwhess qcvars["CURRENT HESSIAN"] = nwhess # Normalize the output as a float or list of floats if input_model.driver.upper() == "PROPERTIES": retres = qcvars[f"CURRENT ENERGY"] else: retres = qcvars[f"CURRENT {input_model.driver.upper()}"] except KeyError as e: > raise UnknownError(error_stamp(stdout=stdout, stderr=stderr)) E qcengine.exceptions.UnknownError: STDOUT: E E E E ============================== echo of input deck ============================== E echo E geometry units bohr E B 0.000000000000 0.000000000000 0.195947860000 E H 0.000000000000 0.000000000000 -2.140490630000 E H 0.000000000000 -0.702014360000 5.669178380000 E H 0.000000000000 0.702014360000 5.669178380000 E E end E memory 879931424 double E charge 1 E E basis spherical E H library cc-pvdz E bqH library H cc-pvdz E B library cc-pvdz E bqB library B cc-pvdz E end E E dft E mult 2 E end E E mcscf E multiplicity 2 E end E E scf E rohf E thresh 1e-07 E nopen 1 E end E E task scf hessian E E ================================================================================ E E E E E E E Northwest Computational Chemistry Package (NWChem) 7.0.2 E -------------------------------------------------------- E E E Environmental Molecular Sciences Laboratory E Pacific Northwest National Laboratory E Richland, WA 99352 E E Copyright (c) 1994-2020 E Pacific Northwest National Laboratory E Battelle Memorial Institute E E NWChem is an open-source computational chemistry package E distributed under the terms of the E Educational Community License (ECL) 2.0 E A copy of the license is included with this distribution E in the LICENSE.TXT file E E ACKNOWLEDGMENT E -------------- E E This software and its documentation were developed at the E EMSL at Pacific Northwest National Laboratory, a multiprogram E national laboratory, operated for the U.S. Department of Energy E by Battelle under Contract Number DE-AC05-76RL01830. Support E for this work was provided by the Department of Energy Office E of Biological and Environmental Research, Office of Basic E Energy Sciences, and the Office of Advanced Scientific Computing. E E E Job information E --------------- E E hostname = yv.noip.me E program = /usr/local/bin/nwchem E date = Thu Oct 21 12:50:43 2021 E E compiled = Thu_Oct_21_12:11:03_2021 E source = /disk-samsung/freebsd-ports/science/nwchem/work/nwchem-7.0.2-release/src/.. E nwchem branch = 7.0.2 E nwchem revision = 11-eol-2499-gbbee7e139269 E ga revision = 5.8.0 E use scalapack = T E input = nwchem.nw E prefix = nwchem. E data base = ./nwchem.db E status = startup E nproc = 1 E time left = -1s E E E E Memory information E ------------------ E E heap = 219982852 doubles = 1678.3 Mbytes E stack = 219982857 doubles = 1678.3 Mbytes E global = 439965712 doubles = 3356.7 Mbytes (distinct from heap & stack) E total = 879931421 doubles = 6713.3 Mbytes E verify = yes E hardfail = no E E E Directory information E --------------------- E E 0 permanent = . E 0 scratch = . E E E E E NWChem Input Module E ------------------- E E E CS symmetry detected E E ------ E auto-z E ------ E autoz: The atoms group into disjoint clusters E cluster 1: 1 2 E cluster 2: 3 4 E Connecting clusters 1 2 via atoms 1 3 r = 2.92 E autoz: regenerating connections with new bonds E no constraints, skipping 0.0000000000000000 E no constraints, skipping 0.0000000000000000 E E E Geometry "geometry" -> "" E ------------------------- E E Output coordinates in a.u. (scale by 1.000000000 to convert to a.u.) E E No. Tag Charge X Y Z E ---- ---------------- ---------- -------------- -------------- -------------- E 1 B 5.0000 0.00000000 -1.07625282 0.00000000 E 2 H 1.0000 0.00000000 -3.41269131 0.00000000 E 3 H 1.0000 0.00000000 4.39697770 -0.70201436 E 4 H 1.0000 0.00000000 4.39697770 0.70201436 E E Atomic Mass E ----------- E E B 11.009310 E H 1.007825 E E E Effective nuclear repulsion energy (a.u.) 4.9195381997 E E Nuclear Dipole moment (a.u.) E ---------------------------- E X Y Z E ---------------- ---------------- ---------------- E 0.0000000000 0.0000000000 0.0000000000 E E Symmetry information E -------------------- E E Group name Cs E Group number 2 E Group order 2 E No. of unique centers 3 E E Symmetry unique atoms E E 1 2 3 E E E E Z-matrix (autoz) E -------- E E Units are Angstrom for bonds and degrees for angles E E Type Name I J K L M Value E ----------- -------- ----- ----- ----- ----- ----- ---------- E 1 Stretch 1 3 2.92004 E 2 Stretch 1 2 1.23639 E 3 Stretch 3 4 0.74298 E 4 Bend 1 3 4 82.69096 E 5 Bend 2 1 3 172.69096 E 6 Torsion 2 1 3 4 180.00000 E E E XYZ format geometry E ------------------- E 4 E geometry E B 0.00000000 -0.56952851 0.00000000 E H 0.00000000 -1.80591860 0.00000000 E H 0.00000000 2.32678056 -0.37149003 E H 0.00000000 2.32678056 0.37149003 E E ============================================================================== E internuclear distances E ------------------------------------------------------------------------------ E center one | center two | atomic units | a.u. E ------------------------------------------------------------------------------ E 2 H | 1 B | 2.33644 | 2.33644 E ------------------------------------------------------------------------------ E number of included internuclear distances: 1 E ============================================================================== E E E E library name resolved from: .nwchemrc E library file name is: E E Basis "ao basis" -> "" (spherical) E ----- E H (Hydrogen) E ------------ E Exponent Coefficients E -------------- --------------------------------------------------------- E 1 S 1.30100000E+01 0.019685 E 1 S 1.96200000E+00 0.137977 E 1 S 4.44600000E-01 0.478148 E E 2 S 1.22000000E-01 1.000000 E E 3 P 7.27000000E-01 1.000000 E E bqH E --- E Exponent Coefficients E -------------- --------------------------------------------------------- E 1 S 1.30100000E+01 0.019685 E 1 S 1.96200000E+00 0.137977 E 1 S 4.44600000E-01 0.478148 E E 2 S 1.22000000E-01 1.000000 E E 3 P 7.27000000E-01 1.000000 E E B (Boron) E --------- E Exponent Coefficients E -------------- --------------------------------------------------------- E 1 S 4.57000000E+03 0.000696 E 1 S 6.85900000E+02 0.005353 E 1 S 1.56500000E+02 0.027134 E 1 S 4.44700000E+01 0.101380 E 1 S 1.44800000E+01 0.272055 E 1 S 5.13100000E+00 0.448403 E 1 S 1.89800000E+00 0.290123 E 1 S 3.32900000E-01 0.014322 E E 2 S 4.57000000E+03 -0.000139 E 2 S 6.85900000E+02 -0.001097 E 2 S 1.56500000E+02 -0.005444 E 2 S 4.44700000E+01 -0.021916 E 2 S 1.44800000E+01 -0.059751 E 2 S 5.13100000E+00 -0.138732 E 2 S 1.89800000E+00 -0.131482 E 2 S 3.32900000E-01 0.539526 E E 3 S 1.04300000E-01 1.000000 E E 4 P 6.00100000E+00 0.035481 E 4 P 1.24100000E+00 0.198072 E 4 P 3.36400000E-01 0.505230 E E 5 P 9.53800000E-02 1.000000 E E 6 D 3.43000000E-01 1.000000 E E bqB E --- E Exponent Coefficients E -------------- --------------------------------------------------------- E 1 S 4.57000000E+03 0.000696 E 1 S 6.85900000E+02 0.005353 E 1 S 1.56500000E+02 0.027134 E 1 S 4.44700000E+01 0.101380 E 1 S 1.44800000E+01 0.272055 E 1 S 5.13100000E+00 0.448403 E 1 S 1.89800000E+00 0.290123 E 1 S 3.32900000E-01 0.014322 E E 2 S 4.57000000E+03 -0.000139 E 2 S 6.85900000E+02 -0.001097 E 2 S 1.56500000E+02 -0.005444 E 2 S 4.44700000E+01 -0.021916 E 2 S 1.44800000E+01 -0.059751 E 2 S 5.13100000E+00 -0.138732 E 2 S 1.89800000E+00 -0.131482 E 2 S 3.32900000E-01 0.539526 E E 3 S 1.04300000E-01 1.000000 E E 4 P 6.00100000E+00 0.035481 E 4 P 1.24100000E+00 0.198072 E 4 P 3.36400000E-01 0.505230 E E 5 P 9.53800000E-02 1.000000 E E 6 D 3.43000000E-01 1.000000 E E E E Summary of "ao basis" -> "" (spherical) E ------------------------------------------------------------------------------ E Tag Description Shells Functions and Types E ---------------- ------------------------------ ------ --------------------- E H cc-pvdz 3 5 2s1p E bqH cc-pvdz 3 5 2s1p E B cc-pvdz 6 14 3s2p1d E bqB cc-pvdz 6 14 3s2p1d E E E ROHF detected E E E NWChem Finite-difference Hessian E -------------------------------- E E E NWChem SCF Module E ----------------- E E E E ao basis = "ao basis" E functions = 29 E atoms = 4 E closed shells = 3 E open shells = 1 E charge = 1.00 E wavefunction = ROHF E input vectors = atomic E output vectors = ./nwchem.movecs E use symmetry = T E symmetry adapt = T E E E Summary of "ao basis" -> "ao basis" (spherical) E ------------------------------------------------------------------------------ E Tag Description Shells Functions and Types E ---------------- ------------------------------ ------ --------------------- E H cc-pvdz 3 5 2s1p E bqH cc-pvdz 3 5 2s1p E B cc-pvdz 6 14 3s2p1d E bqB cc-pvdz 6 14 3s2p1d E E E Symmetry analysis of basis E -------------------------- E E a' 19 E a" 10 E E E Forming initial guess at 0.1s E E E Superposition of Atomic Density Guess E ------------------------------------- E E Sum of atomic energies: -26.03078371 E E Renormalizing density from 8.00 to 7 E E Non-variational initial energy E ------------------------------ E E Total energy = -23.356783 E 1-e energy = -37.930394 E 2-e energy = 9.654074 E HOMO = -0.541143 E LUMO = -0.369125 E E E Symmetry analysis of molecular orbitals - initial E ------------------------------------------------- E E Numbering of irreducible representations: E E 1 a' 2 a" E E Orbital symmetries: E E 1 a' 2 a' 3 a' 4 a' 5 a" E 6 a' 7 a" 8 a' 9 a' 10 a' E 11 a" 12 a' 13 a' 14 a' E E E Starting SCF solution at 0.1s E E E E ---------------------------------------------- E Quadratically convergent ROHF E E Convergence threshold : 1.000E-07 E Maximum no. of iterations : 30 E Final Fock-matrix accuracy: 1.000E-09 E ---------------------------------------------- E E E #quartets = 4.486D+03 #integrals = 2.773D+04 #direct = 0.0% #cached =100.0% E E E Integral file = ./nwchem.aoints.0 E Record size in doubles = 65536 No. of integs per rec = 43688 E Max. records in memory = 4 Max. records in file = 125771 E No. of bits per label = 8 No. of bits per value = 64 E E E iter energy gnorm gmax time E ----- ------------------- --------- --------- -------- E 1 -25.9180776109 2.35D-01 1.30D-01 0.2 E 2 -25.9397896785 1.79D-01 8.18D-02 0.2 E 3 -25.9435939783 8.82D-03 3.79D-03 0.3 E 4 -25.9436143159 7.37D-05 4.38D-05 0.4 E 5 -25.9436143172 4.81D-09 1.98D-09 0.5 E E E Final ROHF results E ------------------ E E Total SCF energy = -25.943614317234 E One-electron energy = -41.234112639159 E Two-electron energy = 10.370960122193 E Nuclear repulsion energy = 4.919538199733 E E Time for solution = 0.3s E E E E Symmetry analysis of molecular orbitals - final E ----------------------------------------------- E E Numbering of irreducible representations: E E 1 a' 2 a" E E Orbital symmetries: E E 1 a' 2 a' 3 a' 4 a' 5 a" E 6 a' 7 a' 8 a" 9 a' 10 a' E 11 a" 12 a' 13 a' 14 a' E E Final eigenvalues E ----------------- E E 1 E 1 -8.1120 E 2 -0.9661 E 3 -0.7661 E 4 -0.5185 E 5 -0.2450 E 6 -0.2444 E 7 0.0118 E 8 0.0352 E 9 0.1473 E 10 0.1835 E 11 0.1953 E 12 0.2179 E 13 0.3787 E 14 0.5013 E E ROHF Final Molecular Orbital Analysis E ------------------------------------- E E Vector 2 Occ=2.000000D+00 E=-9.660846D-01 Symmetry=a' E MO Center= 7.8D-17, -1.3D+00, 1.4D-16, r^2= 8.1D-01 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 2 0.410308 1 B s 15 0.373215 2 H s E 5 -0.267159 1 B py 3 0.233597 1 B s E E Vector 3 Occ=2.000000D+00 E=-7.661266D-01 Symmetry=a' E MO Center= -2.0D-17, 2.3D+00, 1.5D-16, r^2= 7.7D-01 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 20 0.404977 3 H s 25 0.404977 4 H s E 21 0.161577 3 H s 26 0.161577 4 H s E E Vector 4 Occ=1.000000D+00 E=-5.185390D-01 Symmetry=a' E MO Center= -5.4D-17, -1.6D-01, 2.9D-17, r^2= 1.1D+00 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 5 0.573859 1 B py 2 0.445346 1 B s E 3 0.331254 1 B s 15 -0.185478 2 H s E E Vector 5 Occ=0.000000D+00 E=-2.449572D-01 Symmetry=a" E MO Center= -5.2D-18, -5.8D-01, -1.1D-16, r^2= 2.0D+00 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 9 0.574269 1 B pz 6 0.555745 1 B pz E E Vector 6 Occ=0.000000D+00 E=-2.444242D-01 Symmetry=a' E MO Center= -1.2D-16, -5.9D-01, 3.2D-16, r^2= 2.0D+00 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 7 0.575505 1 B px 4 0.557142 1 B px E E Vector 7 Occ=0.000000D+00 E= 1.176677D-02 Symmetry=a' E MO Center= 1.2D-17, -1.6D+00, 3.8D-19, r^2= 3.0D+00 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 16 2.593266 2 H s 3 -1.695546 1 B s E 8 1.390763 1 B py 5 0.430647 1 B py E 2 -0.246575 1 B s E E Vector 8 Occ=0.000000D+00 E= 3.518159D-02 Symmetry=a" E MO Center= -1.5D-17, 2.2D+00, 1.2D-16, r^2= 2.9D+00 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 21 1.886688 3 H s 26 -1.886688 4 H s E 6 0.210300 1 B pz 20 0.154971 3 H s E 25 -0.154971 4 H s E E Vector 9 Occ=0.000000D+00 E= 1.473221D-01 Symmetry=a' E MO Center= -8.2D-16, -8.4D-01, -2.1D-17, r^2= 3.9D+00 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 8 1.594147 1 B py 3 -1.209527 1 B s E 16 0.708668 2 H s 5 -0.548273 1 B py E 2 0.495446 1 B s 15 0.409117 2 H s E 1 0.229671 1 B s E E Vector 10 Occ=0.000000D+00 E= 1.834688D-01 Symmetry=a' E MO Center= 9.3D-16, -5.6D-01, -2.1D-17, r^2= 3.1D+00 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 4 1.046004 1 B px 7 -1.043453 1 B px E E Vector 11 Occ=0.000000D+00 E= 1.953350D-01 Symmetry=a" E MO Center= -4.1D-17, -5.1D-01, -3.7D-17, r^2= 3.5D+00 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 9 -1.070035 1 B pz 6 1.030182 1 B pz E 21 -0.534965 3 H s 26 0.534965 4 H s E E Vector 12 Occ=0.000000D+00 E= 2.179420D-01 Symmetry=a' E MO Center= -1.3D-16, 8.9D-02, -4.0D-16, r^2= 2.9D+00 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 3 1.606918 1 B s 2 -1.307238 1 B s E 1 -0.544688 1 B s 5 -0.460210 1 B py E 8 0.300715 1 B py 16 -0.193751 2 H s E 15 -0.191106 2 H s 20 -0.178430 3 H s E 25 -0.178430 4 H s E E Vector 13 Occ=0.000000D+00 E= 3.786984D-01 Symmetry=a' E MO Center= 1.3D-18, 2.5D+00, -4.2D-16, r^2= 3.0D+00 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 8 1.113320 1 B py 16 1.026767 2 H s E 21 -0.863700 3 H s 26 -0.863700 4 H s E 20 0.684480 3 H s 25 0.684480 4 H s E 3 -0.264928 1 B s 2 -0.239565 1 B s E 5 -0.202555 1 B py E E Vector 14 Occ=0.000000D+00 E= 5.013068D-01 Symmetry=a' E MO Center= -9.6D-18, -1.4D+00, -2.2D-17, r^2= 3.0D+00 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 16 3.122566 2 H s 3 -2.721614 1 B s E 8 1.694920 1 B py 2 0.899151 1 B s E 15 -0.753606 2 H s 14 0.523535 1 B d 2 E 5 -0.388772 1 B py 1 0.374829 1 B s E 12 0.301461 1 B d 0 18 0.176239 2 H py E E E center of mass E -------------- E x = 0.00000000 y = -0.45788690 z = 0.00000000 E E moments of inertia (a.u.) E ------------------ E 61.510536153691 0.000000000000 0.000000000000 E 0.000000000000 0.993361021422 0.000000000000 E 0.000000000000 0.000000000000 60.517175132268 E E Mulliken analysis of the total density E -------------------------------------- E E Atom Charge Shell Charges E ----------- ------ ------------------------------------------------------- E 1 B 5 4.26 2.00 0.85 0.51 0.71 0.17 0.01 E 2 H 1 0.78 0.65 0.11 0.02 E 3 H 1 0.98 0.70 0.27 0.01 E 4 H 1 0.98 0.70 0.27 0.01 E E Mulliken analysis of the open-shell density E ------------------------------------------- E E Atom Charge Shell Charges E ----------- ------ ------------------------------------------------------- E 1 B 5 0.94 0.00 0.25 0.17 0.44 0.08 -0.00 E 2 H 1 0.06 0.05 0.00 0.00 E 3 H 1 0.00 0.00 -0.00 0.00 E 4 H 1 0.00 0.00 -0.00 0.00 E E Multipole analysis of the density wrt the origin E ------------------------------------------------ E E L x y z total open nuclear E - - - - ----- ---- ------- E 0 0 0 0 1.000000 -1.000000 8.000000 E E 1 1 0 0 -0.000000 0.000000 0.000000 E 1 0 1 0 -1.259798 0.294814 0.000000 E 1 0 0 1 -0.000000 -0.000000 0.000000 E E 2 2 0 0 -4.396207 -0.978057 0.000000 E 2 1 1 0 0.000000 -0.000000 0.000000 E 2 1 0 1 -0.000000 0.000000 0.000000 E 2 0 2 0 -1.774839 -1.989876 56.104888 E 2 0 1 1 -0.000000 -0.000000 0.000000 E 2 0 0 2 -3.945662 -0.979636 0.985648 E E E Parallel integral file used 1 records with 0 large values E E E Saving state for scf with suffix hess E ./nwchem.movecs E E E initial hessian E E zero matrix E E E atom: 1 xyz: 1(+) wall time: 0.6 date: Thu Oct 21 12:50:44 2021 E E NWChem SCF Module E ----------------- E E E E ao basis = "ao basis" E functions = 29 E atoms = 4 E closed shells = 3 E open shells = 1 E charge = 1.00 E wavefunction = ROHF E input vectors = ./nwchem.movecs E output vectors = ./nwchem.movecs E use symmetry = F E symmetry adapt = F E E E Forming initial guess at 0.6s E E E Starting SCF solution at 0.6s E E E E Final ROHF results E ------------------ E E Total SCF energy = -25.943614313943 E One-electron energy = -41.234112254690 E Two-electron energy = 10.370959966783 E Nuclear repulsion energy = 4.919537973965 E E Time for solution = 0.1s E E E NWChem Gradients Module E ----------------------- E E E STDERR: E E Program received signal SIGSEGV: Segmentation fault - invalid memory reference. E E Backtrace for this error: E #0 0x804a1f6db in ??? E #1 0x804a1e896 in ??? E #2 0x803729f6f in handle_signal E at /disk-samsung/freebsd-src/lib/libthr/thread/thr_sig.c:303 E #3 0x80372953e in thr_sighandler E at /disk-samsung/freebsd-src/lib/libthr/thread/thr_sig.c:246 E #4 0x7ffffffff192 in ??? E #5 0x803dd91b1 in ??? E #6 0x803badeb5 in ??? E #7 0x803298434 in ??? E #8 0x80329901d in ??? E #9 0x802f076a9 in ??? E #10 0x802e70b74 in ??? E #11 0x9f45dc in ??? E #12 0x9e382f in ??? E #13 0x7f38de in ??? E #14 0x7e7ba4 in ??? E #15 0x7fdbf4 in ??? E #16 0x7ec987 in ??? E #17 0x4219d7 in ??? E #18 0x422db0 in ??? E #19 0x4eb880 in ??? E #20 0x424a09 in ??? E #21 0x424f8c in ??? E #22 0x41477b in ??? E #23 0x40e0e1 in ??? E #24 0x40c71c in ??? E #25 0x40c82f in ??? E E TRACEBACK: E Traceback (most recent call last): E File "/disk-samsung/freebsd-ports/science/py-qcengine/work-py38/qcengine-0.20.1/qcengine/programs/nwchem/runner.py", line 275, in parse_output E retres = qcvars[f"CURRENT {input_model.driver.upper()}"] E KeyError: 'CURRENT HESSIAN' qcengine/programs/nwchem/runner.py:277: UnknownError ________________ test_compute_gradient[nwchem-model5-keywords5] ________________ self = NWChemHarness(name='NWChem', scratch=True, thread_safe=False, thread_parallel=False, node_parallel=True, managed_memory=True, extras=None, version_cache={'/usr/local/bin/nwchem': '7.0.2+11.eol.2499.gbbee7e139269'}) outfiles = {'nwchem.grad': None, 'nwchem.hess': None} input_model = AtomicInput(driver='gradient', model={'method': 'hf', 'basis': '6-31G'}, molecule_hash='55104bb') def parse_output( self, outfiles: Dict[str, str], input_model: "AtomicInput" ) -> AtomicResult: # lgtm: [py/similar-function] # Get the stdout from the calculation (required) stdout = outfiles.pop("stdout") stderr = outfiles.pop("stderr") method = input_model.model.method.lower() method = method[4:] if method.startswith("nwc-") else method # Read the NWChem stdout file and, if needed, the hess or grad files # July 2021: nwmol & vector returns now atin/outfile orientation depending on fix_com,orientation=T/F. previously always atin orientation try: qcvars, nwhess, nwgrad, nwmol, version, module, errorTMP = harvest( input_model.molecule, method, stdout, **outfiles ) except Exception as e: raise UnknownError(error_stamp(stdout=stdout, stderr=stderr)) try: if nwgrad is not None: qcvars[f"{method.upper()} TOTAL GRADIENT"] = nwgrad qcvars["CURRENT GRADIENT"] = nwgrad if nwhess is not None: qcvars[f"{method.upper()} TOTAL HESSIAN"] = nwhess qcvars["CURRENT HESSIAN"] = nwhess # Normalize the output as a float or list of floats if input_model.driver.upper() == "PROPERTIES": retres = qcvars[f"CURRENT ENERGY"] else: > retres = qcvars[f"CURRENT {input_model.driver.upper()}"] E KeyError: 'CURRENT GRADIENT' qcengine/programs/nwchem/runner.py:275: KeyError During handling of the above exception, another exception occurred: program = 'nwchem', model = {'basis': '6-31G', 'method': 'hf'}, keywords = {} @pytest.mark.parametrize("program, model, keywords", _canonical_methods) def test_compute_gradient(program, model, keywords): if not has_program(program): pytest.skip("Program '{}' not found.".format(program)) molecule = _get_molecule(program) inp = AtomicInput( molecule=molecule, driver="gradient", model=model, extras={"mytag": "something"}, keywords=keywords ) if program in ["adcc", "mrchem"]: with pytest.raises(qcng.exceptions.InputError) as e: qcng.compute(inp, program, raise_error=True) assert "Driver gradient not implemented" in str(e.value) else: > ret = qcng.compute(inp, program, raise_error=True) qcengine/tests/test_harness_canonical.py:90: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ qcengine/compute.py:91: in compute output_data = executor.compute(input_data, config) qcengine/programs/model.py:116: in compute result = self._compute(local_input_data, config) qcengine/programs/nwchem/runner.py:137: in _compute return self.parse_output(dexe["outfiles"], input_model) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = NWChemHarness(name='NWChem', scratch=True, thread_safe=False, thread_parallel=False, node_parallel=True, managed_memory=True, extras=None, version_cache={'/usr/local/bin/nwchem': '7.0.2+11.eol.2499.gbbee7e139269'}) outfiles = {'nwchem.grad': None, 'nwchem.hess': None} input_model = AtomicInput(driver='gradient', model={'method': 'hf', 'basis': '6-31G'}, molecule_hash='55104bb') def parse_output( self, outfiles: Dict[str, str], input_model: "AtomicInput" ) -> AtomicResult: # lgtm: [py/similar-function] # Get the stdout from the calculation (required) stdout = outfiles.pop("stdout") stderr = outfiles.pop("stderr") method = input_model.model.method.lower() method = method[4:] if method.startswith("nwc-") else method # Read the NWChem stdout file and, if needed, the hess or grad files # July 2021: nwmol & vector returns now atin/outfile orientation depending on fix_com,orientation=T/F. previously always atin orientation try: qcvars, nwhess, nwgrad, nwmol, version, module, errorTMP = harvest( input_model.molecule, method, stdout, **outfiles ) except Exception as e: raise UnknownError(error_stamp(stdout=stdout, stderr=stderr)) try: if nwgrad is not None: qcvars[f"{method.upper()} TOTAL GRADIENT"] = nwgrad qcvars["CURRENT GRADIENT"] = nwgrad if nwhess is not None: qcvars[f"{method.upper()} TOTAL HESSIAN"] = nwhess qcvars["CURRENT HESSIAN"] = nwhess # Normalize the output as a float or list of floats if input_model.driver.upper() == "PROPERTIES": retres = qcvars[f"CURRENT ENERGY"] else: retres = qcvars[f"CURRENT {input_model.driver.upper()}"] except KeyError as e: > raise UnknownError(error_stamp(stdout=stdout, stderr=stderr)) E qcengine.exceptions.UnknownError: STDOUT: E E E E ============================== echo of input deck ============================== E echo E geometry units bohr E H 0.000000000000 0.000000000000 -0.650000000000 E H 0.000000000000 0.000000000000 0.650000000000 E E end E memory 879931424 double E charge 0 E E basis E H library 6-31G E bqH library H 6-31G E end E E task scf gradient E E E python E grad = rtdb_get('scf:gradient') E if ga_nodeid() == 0: E import json E with open('nwchem.grad', 'w') as fp: E json.dump(grad, fp) E end E E task python E E ================================================================================ E E E E E E E Northwest Computational Chemistry Package (NWChem) 7.0.2 E -------------------------------------------------------- E E E Environmental Molecular Sciences Laboratory E Pacific Northwest National Laboratory E Richland, WA 99352 E E Copyright (c) 1994-2020 E Pacific Northwest National Laboratory E Battelle Memorial Institute E E NWChem is an open-source computational chemistry package E distributed under the terms of the E Educational Community License (ECL) 2.0 E A copy of the license is included with this distribution E in the LICENSE.TXT file E E ACKNOWLEDGMENT E -------------- E E This software and its documentation were developed at the E EMSL at Pacific Northwest National Laboratory, a multiprogram E national laboratory, operated for the U.S. Department of Energy E by Battelle under Contract Number DE-AC05-76RL01830. Support E for this work was provided by the Department of Energy Office E of Biological and Environmental Research, Office of Basic E Energy Sciences, and the Office of Advanced Scientific Computing. E E E Job information E --------------- E E hostname = yv.noip.me E program = /usr/local/bin/nwchem E date = Thu Oct 21 12:54:37 2021 E E compiled = Thu_Oct_21_12:11:03_2021 E source = /disk-samsung/freebsd-ports/science/nwchem/work/nwchem-7.0.2-release/src/.. E nwchem branch = 7.0.2 E nwchem revision = 11-eol-2499-gbbee7e139269 E ga revision = 5.8.0 E use scalapack = T E input = nwchem.nw E prefix = nwchem. E data base = ./nwchem.db E status = startup E nproc = 1 E time left = -1s E E E E Memory information E ------------------ E E heap = 219982852 doubles = 1678.3 Mbytes E stack = 219982857 doubles = 1678.3 Mbytes E global = 439965712 doubles = 3356.7 Mbytes (distinct from heap & stack) E total = 879931421 doubles = 6713.3 Mbytes E verify = yes E hardfail = no E E E Directory information E --------------------- E E 0 permanent = . E 0 scratch = . E E E E E NWChem Input Module E ------------------- E E E ORDER OF PRIMARY AXIS IS BEING SET TO 4 E D4H symmetry detected E E ------ E auto-z E ------ E no constraints, skipping 0.0000000000000000 E no constraints, skipping 0.0000000000000000 E E E Geometry "geometry" -> "" E ------------------------- E E Output coordinates in a.u. (scale by 1.000000000 to convert to a.u.) E E No. Tag Charge X Y Z E ---- ---------------- ---------- -------------- -------------- -------------- E 1 H 1.0000 0.00000000 0.00000000 -0.65000000 E 2 H 1.0000 0.00000000 0.00000000 0.65000000 E E Atomic Mass E ----------- E E H 1.007825 E E E Effective nuclear repulsion energy (a.u.) 0.7692307692 E E Nuclear Dipole moment (a.u.) E ---------------------------- E X Y Z E ---------------- ---------------- ---------------- E 0.0000000000 0.0000000000 0.0000000000 E E Symmetry information E -------------------- E E Group name D4h E Group number 28 E Group order 16 E No. of unique centers 1 E E Symmetry unique atoms E E 1 E E E E Z-matrix (autoz) E -------- E E Units are Angstrom for bonds and degrees for angles E E Type Name I J K L M Value E ----------- -------- ----- ----- ----- ----- ----- ---------- E 1 Stretch 1 2 0.68793 E E E XYZ format geometry E ------------------- E 2 E geometry E H 0.00000000 0.00000000 -0.34396521 E H 0.00000000 0.00000000 0.34396521 E E library name resolved from: .nwchemrc E library file name is: E E Basis "ao basis" -> "" (cartesian) E ----- E H (Hydrogen) E ------------ E Exponent Coefficients E -------------- --------------------------------------------------------- E 1 S 1.87311370E+01 0.033495 E 1 S 2.82539370E+00 0.234727 E 1 S 6.40121700E-01 0.813757 E E 2 S 1.61277800E-01 1.000000 E E bqH E --- E Exponent Coefficients E -------------- --------------------------------------------------------- E 1 S 1.87311370E+01 0.033495 E 1 S 2.82539370E+00 0.234727 E 1 S 6.40121700E-01 0.813757 E E 2 S 1.61277800E-01 1.000000 E E E E Summary of "ao basis" -> "" (cartesian) E ------------------------------------------------------------------------------ E Tag Description Shells Functions and Types E ---------------- ------------------------------ ------ --------------------- E H 6-31G 2 2 2s E bqH 6-31G 2 2 2s E E E NWChem SCF Module E ----------------- E E E E ao basis = "ao basis" E functions = 4 E atoms = 2 E closed shells = 1 E open shells = 0 E charge = 0.00 E wavefunction = RHF E input vectors = atomic E output vectors = ./nwchem.movecs E use symmetry = T E symmetry adapt = T E E E Summary of "ao basis" -> "ao basis" (cartesian) E ------------------------------------------------------------------------------ E Tag Description Shells Functions and Types E ---------------- ------------------------------ ------ --------------------- E H 6-31G 2 2 2s E bqH 6-31G 2 2 2s E E E Symmetry analysis of basis E -------------------------- E E a1g 2 E a1u 0 E a2g 0 E a2u 2 E b1g 0 E b1u 0 E b2g 0 E b2u 0 E eg 0 E eu 0 E E E Forming initial guess at 0.0s E E E Superposition of Atomic Density Guess E ------------------------------------- E E Sum of atomic energies: -0.99646508 E E Non-variational initial energy E ------------------------------ E E Total energy = -0.847860 E 1-e energy = -2.274832 E 2-e energy = 0.657742 E HOMO = -0.608459 E LUMO = 0.189820 E E E Symmetry analysis of molecular orbitals - initial E ------------------------------------------------- E E Numbering of irreducible representations: E E 1 a1g 2 a1u 3 a2g 4 a2u 5 b1g E 6 b1u 7 b2g 8 b2u 9 eg 10 eu E E Orbital symmetries: E E 1 a1g 2 a2u 3 a1g 4 a2u E E E Starting SCF solution at 0.1s E E E E ---------------------------------------------- E Quadratically convergent ROHF E E Convergence threshold : 1.000E-04 E Maximum no. of iterations : 30 E Final Fock-matrix accuracy: 1.000E-07 E ---------------------------------------------- E E E #quartets = 3.700D+01 #integrals = 3.700D+01 #direct = 0.0% #cached =100.0% E E E Integral file = ./nwchem.aoints.0 E Record size in doubles = 65536 No. of integs per rec = 43688 E Max. records in memory = 2 Max. records in file = 125207 E No. of bits per label = 8 No. of bits per value = 64 E E E iter energy gnorm gmax time E ----- ------------------- --------- --------- -------- E 1 -1.1241391460 1.09D-01 1.09D-01 0.1 E 2 -1.1253758406 1.59D-02 1.59D-02 0.1 E 3 -1.1254028862 7.27D-06 7.27D-06 0.1 E E E Final RHF results E ------------------ E E Total SCF energy = -1.125402886195 E One-electron energy = -2.564990972618 E Two-electron energy = 0.670357317192 E Nuclear repulsion energy = 0.769230769231 E E Time for solution = 0.0s E E E E Symmetry analysis of molecular orbitals - final E ----------------------------------------------- E E Numbering of irreducible representations: E E 1 a1g 2 a1u 3 a2g 4 a2u 5 b1g E 6 b1u 7 b2g 8 b2u 9 eg 10 eu E E Orbital symmetries: E E 1 a1g 2 a2u 3 a1g 4 a2u E E Final eigenvalues E ----------------- E E 1 E 1 -0.6121 E 2 0.2522 E 3 0.7501 E 4 1.4785 E E ROHF Final Molecular Orbital Analysis E ------------------------------------- E E Vector 1 Occ=2.000000D+00 E=-6.121382D-01 Symmetry=a1g E MO Center= 0.0D+00, 0.0D+00, 1.4D-17, r^2= 6.9D-01 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 1 0.335462 1 H s 3 0.335462 2 H s E 2 0.258579 1 H s 4 0.258579 2 H s E E Vector 2 Occ=0.000000D+00 E= 2.522278D-01 Symmetry=a2u E MO Center= 0.0D+00, 0.0D+00, 0.0D+00, r^2= 2.1D+00 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 2 1.856396 1 H s 4 -1.856396 2 H s E E Vector 3 Occ=0.000000D+00 E= 7.500515D-01 Symmetry=a1g E MO Center= 0.0D+00, 0.0D+00, -3.3D-16, r^2= 1.6D+00 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 1 0.742884 1 H s 3 0.742884 2 H s E 2 -0.682936 1 H s 4 -0.682936 2 H s E E Vector 4 Occ=0.000000D+00 E= 1.478469D+00 Symmetry=a2u E MO Center= 0.0D+00, 0.0D+00, 3.2D-16, r^2= 9.7D-01 E Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function E ----- ------------ --------------- ----- ------------ --------------- E 2 1.393604 1 H s 4 -1.393604 2 H s E 1 -1.169856 1 H s 3 1.169856 2 H s E E E center of mass E -------------- E x = 0.00000000 y = 0.00000000 z = 0.00000000 E E moments of inertia (a.u.) E ------------------ E 0.851612125000 0.000000000000 0.000000000000 E 0.000000000000 0.851612125000 0.000000000000 E 0.000000000000 0.000000000000 0.000000000000 E E Mulliken analysis of the total density E -------------------------------------- E E Atom Charge Shell Charges E ----------- ------ ------------------------------------------------------- E 1 H 1 1.00 0.54 0.46 E 2 H 1 1.00 0.54 0.46 E E Multipole analysis of the density wrt the origin E ------------------------------------------------ E E L x y z total open nuclear E - - - - ----- ---- ------- E 0 0 0 0 -0.000000 0.000000 2.000000 E E 1 1 0 0 0.000000 0.000000 0.000000 E 1 0 1 0 0.000000 0.000000 0.000000 E 1 0 0 1 -0.000000 0.000000 0.000000 E E 2 2 0 0 -1.458458 0.000000 0.000000 E 2 1 1 0 0.000000 0.000000 0.000000 E 2 1 0 1 0.000000 0.000000 0.000000 E 2 0 2 0 -1.458458 0.000000 0.000000 E 2 0 1 1 0.000000 0.000000 0.000000 E 2 0 0 2 -1.181145 0.000000 0.845000 E E E Parallel integral file used 1 records with 0 large values E E NWChem Gradients Module E ----------------------- E E E E wavefunction = RHF E E Using symmetry E E STDERR: E E Program received signal SIGSEGV: Segmentation fault - invalid memory reference. E E Backtrace for this error: E #0 0x804a1f6db in ??? E #1 0x804a1e896 in ??? E #2 0x803729f6f in handle_signal E at /disk-samsung/freebsd-src/lib/libthr/thread/thr_sig.c:303 E #3 0x80372953e in thr_sighandler E at /disk-samsung/freebsd-src/lib/libthr/thread/thr_sig.c:246 E #4 0x7ffffffff192 in ??? E #5 0x803dd91b1 in ??? E #6 0x803badeb5 in ??? E #7 0x803298434 in ??? E #8 0x80329901d in ??? E #9 0x802f076a9 in ??? E #10 0x802e70b74 in ??? E #11 0x9f45dc in ??? E #12 0x9e382f in ??? E #13 0x7ebc84 in ??? E #14 0x7e6a23 in ??? E #15 0x7fdbf4 in ??? E #16 0x7ec987 in ??? E #17 0x4219d7 in ??? E #18 0x422db0 in ??? E #19 0x41462d in ??? E #20 0x40e0e1 in ??? E #21 0x40c71c in ??? E #22 0x40c82f in ??? E E TRACEBACK: E Traceback (most recent call last): E File "/disk-samsung/freebsd-ports/science/py-qcengine/work-py38/qcengine-0.20.1/qcengine/programs/nwchem/runner.py", line 275, in parse_output E retres = qcvars[f"CURRENT {input_model.driver.upper()}"] E KeyError: 'CURRENT GRADIENT' qcengine/programs/nwchem/runner.py:277: UnknownError ____________________________ test_geometric_stdout _____________________________ input_data = OptimizationInput(model={'method': 'UFF', 'basis': ''}, molecule_hash='d91fd62') @using("rdkit") @using("geometric") def test_geometric_stdout(input_data): input_data["initial_molecule"] = qcng.get_molecule("water") input_data["input_specification"]["model"] = {"method": "UFF", "basis": ""} input_data["keywords"]["program"] = "rdkit" input_data = OptimizationInput(**input_data) > ret = qcng.compute_procedure(input_data, "geometric", raise_error=True) qcengine/tests/test_procedures.py:83: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ qcengine/compute.py:147: in compute_procedure output_data = executor.compute(input_data, config) qcengine/procedures/geometric.py:57: in compute output_data = geometric.run_json.geometric_run_json(input_data) /usr/local/lib/python3.8/site-packages/geometric/run_json.py:159: in geometric_run_json logging.config.fileConfig(logIni,disable_existing_loggers=False) /usr/local/lib/python3.8/logging/config.py:71: in fileConfig formatters = _create_formatters(cp) /usr/local/lib/python3.8/logging/config.py:104: in _create_formatters flist = cp["formatters"]["keys"] _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = , key = 'formatters' def __getitem__(self, key): if key != self.default_section and not self.has_section(key): > raise KeyError(key) E KeyError: 'formatters' /usr/local/lib/python3.8/configparser.py:960: KeyError _________________________ test_optimization_protocols __________________________ input_data = OptimizationInput(model={'method': 'UFF', 'basis': None}, molecule_hash='d91fd62') @using("rdkit") @using("geometric") def test_optimization_protocols(input_data): input_data["initial_molecule"] = qcng.get_molecule("water") input_data["input_specification"]["model"] = {"method": "UFF"} input_data["keywords"]["program"] = "rdkit" input_data["protocols"] = {"trajectory": "initial_and_final"} input_data = OptimizationInput(**input_data) > ret = qcng.compute_procedure(input_data, "geometric", raise_error=True) qcengine/tests/test_procedures.py:129: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ qcengine/compute.py:147: in compute_procedure output_data = executor.compute(input_data, config) qcengine/procedures/geometric.py:57: in compute output_data = geometric.run_json.geometric_run_json(input_data) /usr/local/lib/python3.8/site-packages/geometric/run_json.py:159: in geometric_run_json logging.config.fileConfig(logIni,disable_existing_loggers=False) /usr/local/lib/python3.8/logging/config.py:71: in fileConfig formatters = _create_formatters(cp) /usr/local/lib/python3.8/logging/config.py:104: in _create_formatters flist = cp["formatters"]["keys"] _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = , key = 'formatters' def __getitem__(self, key): if key != self.default_section and not self.has_section(key): > raise KeyError(key) E KeyError: 'formatters' /usr/local/lib/python3.8/configparser.py:960: KeyError ____________________________ test_geometric_retries ____________________________ failure_engine = FailEngine(name='testing_random_name', scratch=False, thread_safe=True, thread_parallel=False, node_parallel=False, ma...', 'pass', 'pass', 'pass', 'pass', 'pass', 'pass', 'pass', 'pass'], ncalls=0, start_distance=5, equilibrium_distance=4) input_data = OptimizationInput(model={'method': 'something', 'basis': None}, molecule_hash='9ef09f1') @using("geometric") @using("rdkit") def test_geometric_retries(failure_engine, input_data): failure_engine.iter_modes = ["random_error", "pass", "random_error", "random_error", "pass"] # Iter 1 # Iter 2 failure_engine.iter_modes.extend(["pass"] * 20) input_data["initial_molecule"] = { "symbols": ["He", "He"], "geometry": [0, 0, 0, 0, 0, failure_engine.start_distance], } input_data["input_specification"]["model"] = {"method": "something"} input_data["keywords"]["program"] = failure_engine.name input_data = OptimizationInput(**input_data) > ret = qcng.compute_procedure(input_data, "geometric", local_options={"ncores": 13}, raise_error=True) qcengine/tests/test_procedures.py:153: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ qcengine/compute.py:147: in compute_procedure output_data = executor.compute(input_data, config) qcengine/procedures/geometric.py:57: in compute output_data = geometric.run_json.geometric_run_json(input_data) /usr/local/lib/python3.8/site-packages/geometric/run_json.py:159: in geometric_run_json logging.config.fileConfig(logIni,disable_existing_loggers=False) /usr/local/lib/python3.8/logging/config.py:71: in fileConfig formatters = _create_formatters(cp) /usr/local/lib/python3.8/logging/config.py:104: in _create_formatters flist = cp["formatters"]["keys"] _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = , key = 'formatters' def __getitem__(self, key): if key != self.default_section and not self.has_section(key): > raise KeyError(key) E KeyError: 'formatters' /usr/local/lib/python3.8/configparser.py:960: KeyError _________________ test_geometric_generic[rdkit-model0-bench0] __________________ input_data = {'initial_molecule': Molecule(name='H2O', formula='H2O', hash='d91fd62'), 'input_specification': {'driver': 'gradient'...'}}, 'keywords': {}, 'model': {'method': 'UFF'}}, 'keywords': {'coordsys': 'tric', 'maxiter': 100, 'program': 'rdkit'}} program = 'rdkit', model = {'method': 'UFF'} bench = [1.87130923886072, 2.959448636243545, 104.5099642579023] @using("geometric") @pytest.mark.parametrize( "program, model, bench", [ pytest.param( "rdkit", {"method": "UFF"}, [1.87130923886072, 2.959448636243545, 104.5099642579023], marks=using("rdkit") ), pytest.param( "rdkit", {"method": "mmff94"}, [1.8310842343589573, 2.884612338953529, 103.93822919865106], marks=using("rdkit"), ), pytest.param( "rdkit", {"method": "MMFF94s"}, [1.8310842343589573, 2.884612338953529, 103.93822919865106], marks=using("rdkit"), ), pytest.param( "torchani", {"method": "ANI1x"}, [1.82581873750194, 2.866376526793269, 103.4332610730292], marks=using("torchani"), ), pytest.param( "mopac", {"method": "PM6"}, [1.7927843431811934, 2.893333237502448, 107.60441967992045], marks=using("mopac"), ), pytest.param( "openmm", {"method": "openff-1.0.0", "basis": "smirnoff"}, [1.8344994291796748, 3.010099477501204, 110.25177977849998], marks=using("openmm"), ), pytest.param( "openmm", {"method": "openff_unconstrained-1.0.0", "basis": "smirnoff"}, [1.8344994291195869, 3.0100994772976124, 110.25259556886984], marks=using("openmm"), ), pytest.param( "openmm", {"method": "smirnoff99Frosst-1.1.0", "basis": "smirnoff"}, [1.814137087600702, 3.025566213038376, 112.9999999990053], marks=using("openmm"), ), pytest.param( "qcore", {"method": "GFN1"}, [1.8104763949897031, 2.9132449420655213, 107.13403040879244], marks=using("qcore"), ), ], ) def test_geometric_generic(input_data, program, model, bench): input_data["initial_molecule"] = qcng.get_molecule("water") input_data["input_specification"]["model"] = model input_data["keywords"]["program"] = program input_data["input_specification"]["extras"] = {"_secret_tags": {"mysecret_tag": "data1"}} > ret = qcng.compute_procedure(input_data, "geometric", raise_error=True) qcengine/tests/test_procedures.py:233: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ qcengine/compute.py:147: in compute_procedure output_data = executor.compute(input_data, config) qcengine/procedures/geometric.py:57: in compute output_data = geometric.run_json.geometric_run_json(input_data) /usr/local/lib/python3.8/site-packages/geometric/run_json.py:159: in geometric_run_json logging.config.fileConfig(logIni,disable_existing_loggers=False) /usr/local/lib/python3.8/logging/config.py:71: in fileConfig formatters = _create_formatters(cp) /usr/local/lib/python3.8/logging/config.py:104: in _create_formatters flist = cp["formatters"]["keys"] _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = , key = 'formatters' def __getitem__(self, key): if key != self.default_section and not self.has_section(key): > raise KeyError(key) E KeyError: 'formatters' /usr/local/lib/python3.8/configparser.py:960: KeyError _________________ test_geometric_generic[rdkit-model1-bench1] __________________ input_data = {'initial_molecule': Molecule(name='H2O', formula='H2O', hash='d91fd62'), 'input_specification': {'driver': 'gradient'..., 'keywords': {}, 'model': {'method': 'mmff94'}}, 'keywords': {'coordsys': 'tric', 'maxiter': 100, 'program': 'rdkit'}} program = 'rdkit', model = {'method': 'mmff94'} bench = [1.8310842343589573, 2.884612338953529, 103.93822919865106] @using("geometric") @pytest.mark.parametrize( "program, model, bench", [ pytest.param( "rdkit", {"method": "UFF"}, [1.87130923886072, 2.959448636243545, 104.5099642579023], marks=using("rdkit") ), pytest.param( "rdkit", {"method": "mmff94"}, [1.8310842343589573, 2.884612338953529, 103.93822919865106], marks=using("rdkit"), ), pytest.param( "rdkit", {"method": "MMFF94s"}, [1.8310842343589573, 2.884612338953529, 103.93822919865106], marks=using("rdkit"), ), pytest.param( "torchani", {"method": "ANI1x"}, [1.82581873750194, 2.866376526793269, 103.4332610730292], marks=using("torchani"), ), pytest.param( "mopac", {"method": "PM6"}, [1.7927843431811934, 2.893333237502448, 107.60441967992045], marks=using("mopac"), ), pytest.param( "openmm", {"method": "openff-1.0.0", "basis": "smirnoff"}, [1.8344994291796748, 3.010099477501204, 110.25177977849998], marks=using("openmm"), ), pytest.param( "openmm", {"method": "openff_unconstrained-1.0.0", "basis": "smirnoff"}, [1.8344994291195869, 3.0100994772976124, 110.25259556886984], marks=using("openmm"), ), pytest.param( "openmm", {"method": "smirnoff99Frosst-1.1.0", "basis": "smirnoff"}, [1.814137087600702, 3.025566213038376, 112.9999999990053], marks=using("openmm"), ), pytest.param( "qcore", {"method": "GFN1"}, [1.8104763949897031, 2.9132449420655213, 107.13403040879244], marks=using("qcore"), ), ], ) def test_geometric_generic(input_data, program, model, bench): input_data["initial_molecule"] = qcng.get_molecule("water") input_data["input_specification"]["model"] = model input_data["keywords"]["program"] = program input_data["input_specification"]["extras"] = {"_secret_tags": {"mysecret_tag": "data1"}} > ret = qcng.compute_procedure(input_data, "geometric", raise_error=True) qcengine/tests/test_procedures.py:233: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ qcengine/compute.py:147: in compute_procedure output_data = executor.compute(input_data, config) qcengine/procedures/geometric.py:57: in compute output_data = geometric.run_json.geometric_run_json(input_data) /usr/local/lib/python3.8/site-packages/geometric/run_json.py:159: in geometric_run_json logging.config.fileConfig(logIni,disable_existing_loggers=False) /usr/local/lib/python3.8/logging/config.py:71: in fileConfig formatters = _create_formatters(cp) /usr/local/lib/python3.8/logging/config.py:104: in _create_formatters flist = cp["formatters"]["keys"] _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = , key = 'formatters' def __getitem__(self, key): if key != self.default_section and not self.has_section(key): > raise KeyError(key) E KeyError: 'formatters' /usr/local/lib/python3.8/configparser.py:960: KeyError _________________ test_geometric_generic[rdkit-model2-bench2] __________________ input_data = {'initial_molecule': Molecule(name='H2O', formula='H2O', hash='d91fd62'), 'input_specification': {'driver': 'gradient'... 'keywords': {}, 'model': {'method': 'MMFF94s'}}, 'keywords': {'coordsys': 'tric', 'maxiter': 100, 'program': 'rdkit'}} program = 'rdkit', model = {'method': 'MMFF94s'} bench = [1.8310842343589573, 2.884612338953529, 103.93822919865106] @using("geometric") @pytest.mark.parametrize( "program, model, bench", [ pytest.param( "rdkit", {"method": "UFF"}, [1.87130923886072, 2.959448636243545, 104.5099642579023], marks=using("rdkit") ), pytest.param( "rdkit", {"method": "mmff94"}, [1.8310842343589573, 2.884612338953529, 103.93822919865106], marks=using("rdkit"), ), pytest.param( "rdkit", {"method": "MMFF94s"}, [1.8310842343589573, 2.884612338953529, 103.93822919865106], marks=using("rdkit"), ), pytest.param( "torchani", {"method": "ANI1x"}, [1.82581873750194, 2.866376526793269, 103.4332610730292], marks=using("torchani"), ), pytest.param( "mopac", {"method": "PM6"}, [1.7927843431811934, 2.893333237502448, 107.60441967992045], marks=using("mopac"), ), pytest.param( "openmm", {"method": "openff-1.0.0", "basis": "smirnoff"}, [1.8344994291796748, 3.010099477501204, 110.25177977849998], marks=using("openmm"), ), pytest.param( "openmm", {"method": "openff_unconstrained-1.0.0", "basis": "smirnoff"}, [1.8344994291195869, 3.0100994772976124, 110.25259556886984], marks=using("openmm"), ), pytest.param( "openmm", {"method": "smirnoff99Frosst-1.1.0", "basis": "smirnoff"}, [1.814137087600702, 3.025566213038376, 112.9999999990053], marks=using("openmm"), ), pytest.param( "qcore", {"method": "GFN1"}, [1.8104763949897031, 2.9132449420655213, 107.13403040879244], marks=using("qcore"), ), ], ) def test_geometric_generic(input_data, program, model, bench): input_data["initial_molecule"] = qcng.get_molecule("water") input_data["input_specification"]["model"] = model input_data["keywords"]["program"] = program input_data["input_specification"]["extras"] = {"_secret_tags": {"mysecret_tag": "data1"}} > ret = qcng.compute_procedure(input_data, "geometric", raise_error=True) qcengine/tests/test_procedures.py:233: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ qcengine/compute.py:147: in compute_procedure output_data = executor.compute(input_data, config) qcengine/procedures/geometric.py:57: in compute output_data = geometric.run_json.geometric_run_json(input_data) /usr/local/lib/python3.8/site-packages/geometric/run_json.py:159: in geometric_run_json logging.config.fileConfig(logIni,disable_existing_loggers=False) /usr/local/lib/python3.8/logging/config.py:71: in fileConfig formatters = _create_formatters(cp) /usr/local/lib/python3.8/logging/config.py:104: in _create_formatters flist = cp["formatters"]["keys"] _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = , key = 'formatters' def __getitem__(self, key): if key != self.default_section and not self.has_section(key): > raise KeyError(key) E KeyError: 'formatters' /usr/local/lib/python3.8/configparser.py:960: KeyError _____________________________ test_nwchem_relax[0] _____________________________ linopt = 0 @using("nwchem") @pytest.mark.parametrize("linopt", [0, 1]) def test_nwchem_relax(linopt): # Make the input file input_data = { "input_specification": { "model": {"method": "HF", "basis": "sto-3g"}, "keywords": {"set__driver:linopt": linopt}, }, "initial_molecule": qcng.get_molecule("hydrogen"), } input_data = OptimizationInput(**input_data) # Run the relaxation > ret = qcng.compute_procedure(input_data, "nwchemdriver", raise_error=True) qcengine/tests/test_procedures.py:262: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ qcengine/compute.py:147: in compute_procedure output_data = executor.compute(input_data, config) qcengine/procedures/nwchem_opt/__init__.py:74: in compute return self.parse_output(dexe["outfiles"], input_data) qcengine/procedures/nwchem_opt/__init__.py:85: in parse_output atomic_results = harvest_as_atomic_result(input_model, stdout) qcengine/procedures/nwchem_opt/harvester.py:97: in harvest_as_atomic_result results.append(AtomicResult(**output_data)) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E pydantic.error_wrappers.ValidationError: 1 validation error for AtomicResult E return_result E none is not an allowed value (type=type_error.none.not_allowed) pydantic/main.py:406: ValidationError _____________________________ test_nwchem_relax[1] _____________________________ linopt = 1 @using("nwchem") @pytest.mark.parametrize("linopt", [0, 1]) def test_nwchem_relax(linopt): # Make the input file input_data = { "input_specification": { "model": {"method": "HF", "basis": "sto-3g"}, "keywords": {"set__driver:linopt": linopt}, }, "initial_molecule": qcng.get_molecule("hydrogen"), } input_data = OptimizationInput(**input_data) # Run the relaxation > ret = qcng.compute_procedure(input_data, "nwchemdriver", raise_error=True) qcengine/tests/test_procedures.py:262: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ qcengine/compute.py:147: in compute_procedure output_data = executor.compute(input_data, config) qcengine/procedures/nwchem_opt/__init__.py:74: in compute return self.parse_output(dexe["outfiles"], input_data) qcengine/procedures/nwchem_opt/__init__.py:85: in parse_output atomic_results = harvest_as_atomic_result(input_model, stdout) qcengine/procedures/nwchem_opt/harvester.py:97: in harvest_as_atomic_result results.append(AtomicResult(**output_data)) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E pydantic.error_wrappers.ValidationError: 1 validation error for AtomicResult E return_result E none is not an allowed value (type=type_error.none.not_allowed) pydantic/main.py:406: ValidationError __________________________ test_torsiondrive_generic ___________________________ @using("rdkit") @using("torsiondrive") def test_torsiondrive_generic(): input_data = TorsionDriveInput( keywords=TDKeywords(dihedrals=[(2, 0, 1, 5)], grid_spacing=[180]), input_specification=QCInputSpecification(driver=DriverEnum.gradient, model=Model(method="UFF", basis=None)), initial_molecule=qcng.get_molecule("ethane"), optimization_spec=OptimizationSpecification( procedure="geomeTRIC", keywords={ "coordsys": "dlc", "maxiter": 300, "program": "rdkit", }, ), ) > ret = qcng.compute_procedure(input_data, "torsiondrive", raise_error=True) qcengine/tests/test_procedures.py:286: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ qcengine/compute.py:149: in compute_procedure return handle_output_metadata(output_data, metadata, raise_error=raise_error, return_dict=return_dict) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ output_data = TorsionDriveResult(schema_name='qcschema_torsion_drive_output', schema_version=1, keywords=TDKeywords(dihedrals=[(2, 0.../local/lib/python3.8/configparser.py", line 960, in __getitem__\n raise KeyError(key)\nKeyError: \'formatters\'\n')) metadata = {'retries': 0, 'stderr': None, 'stdout': None, 'success': True, ...} raise_error = True, return_dict = False def handle_output_metadata( output_data: Union[Dict[str, Any], "BaseModel"], metadata: Dict[str, Any], raise_error: bool = False, return_dict: bool = True, ) -> Union[Dict[str, Any], "BaseModel"]: """ Fuses general metadata and output together. Returns ------- result : dict or pydantic.models.AtomicResult Output type depends on return_dict or a dict if an error was generated in model construction """ if isinstance(output_data, dict): output_fusion = output_data # Error handling else: output_fusion = output_data.dict() # Do not override if computer generates output_fusion["stdout"] = output_fusion.get("stdout", None) or metadata["stdout"] output_fusion["stderr"] = output_fusion.get("stderr", None) or metadata["stderr"] if metadata["success"] is not True: output_fusion["success"] = False output_fusion["error"] = {"error_type": metadata["error_type"], "error_message": metadata["error_message"]} # Raise an error if one exists and a user requested a raise if raise_error and (output_fusion["success"] is not True): msg = "stdout:\n{}".format(output_fusion["stdout"]) msg += "\nstderr:\n{}".format(output_fusion["stderr"]) LOGGER.info(msg) > raise ValueError(output_fusion["error"]["error_message"]) E ValueError: TorsionDrive error at 180: E QCEngine Execution Error: E Traceback (most recent call last): E File "/disk-samsung/freebsd-ports/science/py-qcengine/work-py38/qcengine-0.20.1/qcengine/util.py", line 114, in compute_wrapper E yield metadata E File "/disk-samsung/freebsd-ports/science/py-qcengine/work-py38/qcengine-0.20.1/qcengine/compute.py", line 147, in compute_procedure E output_data = executor.compute(input_data, config) E File "/disk-samsung/freebsd-ports/science/py-qcengine/work-py38/qcengine-0.20.1/qcengine/procedures/geometric.py", line 57, in compute E output_data = geometric.run_json.geometric_run_json(input_data) E File "/usr/local/lib/python3.8/site-packages/geometric/run_json.py", line 159, in geometric_run_json E logging.config.fileConfig(logIni,disable_existing_loggers=False) E File "/usr/local/lib/python3.8/logging/config.py", line 71, in fileConfig E formatters = _create_formatters(cp) E File "/usr/local/lib/python3.8/logging/config.py", line 104, in _create_formatters E flist = cp["formatters"]["keys"] E File "/usr/local/lib/python3.8/configparser.py", line 960, in __getitem__ E raise KeyError(key) E KeyError: 'formatters' qcengine/util.py:177: ValueError =========================== short test summary info ============================ SKIPPED [3] /disk-samsung/freebsd-ports/science/py-qcengine/work-py38/qcengine-0.20.1/qcengine/testing.py:48: Could not find QCEngineRecords in PYTHONPATH SKIPPED [1] qcengine/programs/tests/test_adcc.py:22: Not detecting module adcc. Install package if necessary to enable tests. SKIPPED [24] qcengine/programs/tests/test_alignment.py:38: Not detecting module cfour. Install package if necessary to enable tests. SKIPPED [24] qcengine/programs/tests/test_alignment.py:38: Not detecting module gamess. Install package if necessary to enable tests. SKIPPED [24] qcengine/programs/tests/test_alignment.py:38: Not detecting module psi4_derqcsk. Install package if necessary to enable tests. SKIPPED [4] qcengine/programs/tests/test_dftd3_mp2d.py:15: Not detecting module dftd3. Install package if necessary to enable tests. SKIPPED [1] qcengine/programs/tests/test_dftd3_mp2d.py:32: Not detecting module dftd3. Install package if necessary to enable tests. SKIPPED [1] qcengine/programs/tests/test_dftd3_mp2d.py:1515: Not detecting module dftd3. Install package if necessary to enable tests. SKIPPED [16] qcengine/programs/tests/test_dftd3_mp2d.py:1534: Not detecting module dftd3. Install package if necessary to enable tests. SKIPPED [1] qcengine/programs/tests/test_dftd3_mp2d.py:1579: Not detecting module qcdb. Install package if necessary to enable tests. SKIPPED [18] qcengine/programs/tests/test_dftd3_mp2d.py:1613: Not detecting module mp2d. Install package if necessary to enable tests. SKIPPED [33] qcengine/programs/tests/test_dftd3_mp2d.py:1677: Not detecting module dftd3. Install package if necessary to enable tests. SKIPPED [30] qcengine/programs/tests/test_dftd3_mp2d.py:1677: Not detecting module dftd4. Install package if necessary to enable tests. SKIPPED [6] qcengine/programs/tests/test_dftd3_mp2d.py:1761: Not detecting module dftd3. Install package if necessary to enable tests. SKIPPED [6] qcengine/programs/tests/test_dftd3_mp2d.py:1761: Not detecting module dftd4. Install package if necessary to enable tests. SKIPPED [18] qcengine/programs/tests/test_dftd3_mp2d.py:1808: Not detecting module dftd3_321. Install package if necessary to enable tests. SKIPPED [3] qcengine/programs/tests/test_dftd3_mp2d.py:1869: Not detecting module dftd3. Install package if necessary to enable tests. SKIPPED [3] qcengine/programs/tests/test_dftd3_mp2d.py:1869: Not detecting module dftd4. Install package if necessary to enable tests. SKIPPED [24] qcengine/programs/tests/test_dftd3_mp2d.py:1919: Not detecting module psi4. Install package if necessary to enable tests. SKIPPED [6] qcengine/programs/tests/test_dftd3_mp2d.py:1919: Not detecting module gcp. Install package if necessary to enable tests. SKIPPED [6] qcengine/programs/tests/test_dftd3_mp2d.py:1919: Not detecting module mctc-gcp. Install package if necessary to enable tests. SKIPPED [1] qcengine/programs/tests/test_dftd4.py:16: Not detecting module dftd4. Install package if necessary to enable tests. SKIPPED [1] qcengine/programs/tests/test_dftd4.py:36: Not detecting module dftd4. Install package if necessary to enable tests. SKIPPED [1] qcengine/programs/tests/test_dftd4.py:81: Not detecting module dftd4. Install package if necessary to enable tests. SKIPPED [1] qcengine/programs/tests/test_dftd4.py:121: Not detecting module dftd4. Install package if necessary to enable tests. SKIPPED [1] qcengine/programs/tests/test_dftd4.py:141: Not detecting module dftd4. Install package if necessary to enable tests. SKIPPED [1] qcengine/programs/tests/test_ghost.py:22: Not detecting module cfour. Install package if necessary to enable tests. SKIPPED [1] qcengine/programs/tests/test_ghost.py:22: Not detecting module gamess. Install package if necessary to enable tests. SKIPPED [1] qcengine/programs/tests/test_ghost.py:22: Not detecting module psi4. Install package if necessary to enable tests. SKIPPED [5] qcengine/programs/tests/test_ghost.py:70: Not detecting module cfour. Install package if necessary to enable tests. SKIPPED [5] qcengine/programs/tests/test_ghost.py:70: Not detecting module gamess. Install package if necessary to enable tests. SKIPPED [5] qcengine/programs/tests/test_ghost.py:70: Not detecting module psi4. Install package if necessary to enable tests. SKIPPED [1] qcengine/programs/tests/test_ghost.py:149: Not detecting module cfour. Install package if necessary to enable tests. SKIPPED [1] qcengine/programs/tests/test_ghost.py:149: Not detecting module gamess. Install package if necessary to enable tests. SKIPPED [1] qcengine/programs/tests/test_ghost.py:149: Not detecting module psi4. Install package if necessary to enable tests. SKIPPED [2] /disk-samsung/freebsd-ports/science/py-qcengine/work-py38/qcengine-0.20.1/qcengine/programs/tests/test_harness_canonical.py:84: Program 'cfour' not found. SKIPPED [2] /disk-samsung/freebsd-ports/science/py-qcengine/work-py38/qcengine-0.20.1/qcengine/programs/tests/test_harness_canonical.py:84: Program 'dftd3' not found. SKIPPED [2] /disk-samsung/freebsd-ports/science/py-qcengine/work-py38/qcengine-0.20.1/qcengine/programs/tests/test_harness_canonical.py:84: Program 'gamess' not found. SKIPPED [2] /disk-samsung/freebsd-ports/science/py-qcengine/work-py38/qcengine-0.20.1/qcengine/programs/tests/test_harness_canonical.py:84: Program 'gcp' not found. SKIPPED [2] /disk-samsung/freebsd-ports/science/py-qcengine/work-py38/qcengine-0.20.1/qcengine/programs/tests/test_harness_canonical.py:84: Program 'mctc-gcp' not found. SKIPPED [2] /disk-samsung/freebsd-ports/science/py-qcengine/work-py38/qcengine-0.20.1/qcengine/programs/tests/test_harness_canonical.py:84: Program 'mp2d' not found. SKIPPED [2] /disk-samsung/freebsd-ports/science/py-qcengine/work-py38/qcengine-0.20.1/qcengine/programs/tests/test_harness_canonical.py:84: Program 'psi4' not found. SKIPPED [1] /disk-samsung/freebsd-ports/science/py-qcengine/work-py38/qcengine-0.20.1/qcengine/programs/tests/test_harness_canonical.py:150: Program 'cfour' not found. SKIPPED [1] /disk-samsung/freebsd-ports/science/py-qcengine/work-py38/qcengine-0.20.1/qcengine/programs/tests/test_harness_canonical.py:150: Program 'dftd3' not found. SKIPPED [1] /disk-samsung/freebsd-ports/science/py-qcengine/work-py38/qcengine-0.20.1/qcengine/programs/tests/test_harness_canonical.py:150: Program 'gamess' not found. SKIPPED [1] /disk-samsung/freebsd-ports/science/py-qcengine/work-py38/qcengine-0.20.1/qcengine/programs/tests/test_harness_canonical.py:150: Program 'gcp' not found. SKIPPED [1] /disk-samsung/freebsd-ports/science/py-qcengine/work-py38/qcengine-0.20.1/qcengine/programs/tests/test_harness_canonical.py:150: Program 'mctc-gcp' not found. SKIPPED [1] /disk-samsung/freebsd-ports/science/py-qcengine/work-py38/qcengine-0.20.1/qcengine/programs/tests/test_harness_canonical.py:150: Program 'mp2d' not found. SKIPPED [1] /disk-samsung/freebsd-ports/science/py-qcengine/work-py38/qcengine-0.20.1/qcengine/programs/tests/test_harness_canonical.py:150: Program 'psi4' not found. SKIPPED [2] /disk-samsung/freebsd-ports/science/py-qcengine/work-py38/qcengine-0.20.1/qcengine/programs/tests/test_harness_canonical.py:229: Program 'cfour' not found. SKIPPED [2] /disk-samsung/freebsd-ports/science/py-qcengine/work-py38/qcengine-0.20.1/qcengine/programs/tests/test_harness_canonical.py:229: Program 'dftd3' not found. SKIPPED [2] /disk-samsung/freebsd-ports/science/py-qcengine/work-py38/qcengine-0.20.1/qcengine/programs/tests/test_harness_canonical.py:229: Program 'gamess' not found. SKIPPED [2] /disk-samsung/freebsd-ports/science/py-qcengine/work-py38/qcengine-0.20.1/qcengine/programs/tests/test_harness_canonical.py:229: Program 'gcp' not found. SKIPPED [2] /disk-samsung/freebsd-ports/science/py-qcengine/work-py38/qcengine-0.20.1/qcengine/programs/tests/test_harness_canonical.py:229: Program 'mctc-gcp' not found. SKIPPED [2] /disk-samsung/freebsd-ports/science/py-qcengine/work-py38/qcengine-0.20.1/qcengine/programs/tests/test_harness_canonical.py:229: Program 'mp2d' not found. SKIPPED [2] /disk-samsung/freebsd-ports/science/py-qcengine/work-py38/qcengine-0.20.1/qcengine/programs/tests/test_harness_canonical.py:229: Program 'psi4' not found. SKIPPED [1] qcengine/programs/tests/test_mrchem.py:20: Not detecting module mrchem. Install package if necessary to enable tests. SKIPPED [1] qcengine/programs/tests/test_mrchem.py:54: Not detecting module mrchem. Install package if necessary to enable tests. SKIPPED [1] qcengine/programs/tests/test_programs.py:25: Not detecting module psi4. Install package if necessary to enable tests. SKIPPED [1] qcengine/programs/tests/test_programs.py:46: Not detecting module gcp. Install package if necessary to enable tests. SKIPPED [1] qcengine/programs/tests/test_programs.py:62: Not detecting module psi4_runqcsk. Install package if necessary to enable tests. SKIPPED [1] qcengine/programs/tests/test_programs.py:79: Not detecting module psi4_runqcsk. Install package if necessary to enable tests. SKIPPED [1] qcengine/programs/tests/test_programs.py:94: Not detecting module psi4. Install package if necessary to enable tests. SKIPPED [1] qcengine/programs/tests/test_programs.py:115: Not detecting module psi4. Install package if necessary to enable tests. SKIPPED [1] qcengine/programs/tests/test_programs.py:166: Not detecting module torchani. Install package if necessary to enable tests. SKIPPED [1] qcengine/programs/tests/test_programs.py:181: Not detecting module mopac. Install package if necessary to enable tests. SKIPPED [1] qcengine/programs/tests/test_programs.py:244: Not detecting module openmm. Install package if necessary to enable tests. SKIPPED [1] qcengine/programs/tests/test_programs.py:269: Not detecting module openmm. Install package if necessary to enable tests. SKIPPED [1] qcengine/programs/tests/test_programs.py:299: Not detecting module openmm. Install package if necessary to enable tests. SKIPPED [1] qcengine/programs/tests/test_programs.py:319: Not detecting module openmm. Install package if necessary to enable tests. SKIPPED [6] qcengine/programs/tests/test_programs.py:348: Not detecting module openmm. Install package if necessary to enable tests. SKIPPED [3] qcengine/programs/tests/test_qcore.py:10: Not detecting module qcore. Install package if necessary to enable tests. SKIPPED [1] qcengine/programs/tests/test_qcore.py:35: Not detecting module qcore. Install package if necessary to enable tests. SKIPPED [9] qcengine/programs/tests/test_standard_suite.py:125: Not detecting module cfour. Install package if necessary to enable tests. SKIPPED [9] qcengine/programs/tests/test_standard_suite.py:125: Not detecting module gamess. Install package if necessary to enable tests. SKIPPED [35] /disk-samsung/freebsd-ports/science/py-qcengine/work-py38/qcengine-0.20.1/qcengine/programs/tests/standard_suite_runner.py:62: basis cfour-qz2p not available in nwchem library SKIPPED [9] qcengine/programs/tests/test_standard_suite.py:125: Not detecting module psi4_mp2qcsk. Install package if necessary to enable tests. SKIPPED [9] qcengine/programs/tests/test_standard_suite.py:175: Not detecting module cfour. Install package if necessary to enable tests. SKIPPED [9] qcengine/programs/tests/test_standard_suite.py:175: Not detecting module gamess. Install package if necessary to enable tests. SKIPPED [9] qcengine/programs/tests/test_standard_suite.py:175: Not detecting module psi4_derqcsk. Install package if necessary to enable tests. SKIPPED [9] qcengine/programs/tests/test_standard_suite.py:227: Not detecting module cfour. Install package if necessary to enable tests. SKIPPED [9] qcengine/programs/tests/test_standard_suite.py:227: Not detecting module gamess. Install package if necessary to enable tests. SKIPPED [6] qcengine/programs/tests/test_standard_suite.py:227: Not detecting module psi4_derqcsk. Install package if necessary to enable tests. SKIPPED [3] qcengine/programs/tests/test_standard_suite.py:227: Not detecting module psi4_mp2qcsk. Install package if necessary to enable tests. SKIPPED [18] qcengine/programs/tests/test_standard_suite.py:278: Not detecting module cfour. Install package if necessary to enable tests. SKIPPED [18] qcengine/programs/tests/test_standard_suite.py:278: Not detecting module gamess. Install package if necessary to enable tests. SKIPPED [18] qcengine/programs/tests/test_standard_suite.py:278: Not detecting module psi4_mp2qcsk. Install package if necessary to enable tests. SKIPPED [6] qcengine/programs/tests/test_standard_suite.py:278: Not detecting module qchem. Install package if necessary to enable tests. SKIPPED [42] qcengine/programs/tests/test_standard_suite.py:355: Not detecting module cfour. Install package if necessary to enable tests. SKIPPED [18] qcengine/programs/tests/test_standard_suite.py:355: Not detecting module gamess. Install package if necessary to enable tests. SKIPPED [18] qcengine/programs/tests/test_standard_suite.py:355: Not detecting module psi4_mp2qcsk. Install package if necessary to enable tests. SKIPPED [2] qcengine/programs/tests/test_standard_suite_ccsd(t).py:34: Not detecting module cfour. Install package if necessary to enable tests. SKIPPED [1] qcengine/programs/tests/test_standard_suite_ccsd(t).py:34: Not detecting module psi4. Install package if necessary to enable tests. SKIPPED [1] qcengine/programs/tests/test_standard_suite_ccsd(t).py:34: Not detecting module gamess. Install package if necessary to enable tests. SKIPPED [1] qcengine/programs/tests/test_standard_suite_ccsd(t).py:65: Not detecting module gamess. Install package if necessary to enable tests. SKIPPED [2] qcengine/programs/tests/test_standard_suite_ccsd(t).py:93: Not detecting module cfour. Install package if necessary to enable tests. SKIPPED [1] qcengine/programs/tests/test_standard_suite_ccsd(t).py:93: Not detecting module psi4. Install package if necessary to enable tests. SKIPPED [2] qcengine/programs/tests/test_standard_suite_hf.py:35: Not detecting module cfour. Install package if necessary to enable tests. SKIPPED [1] qcengine/programs/tests/test_standard_suite_hf.py:35: Not detecting module qcore. Install package if necessary to enable tests. SKIPPED [1] qcengine/programs/tests/test_standard_suite_hf.py:35: Not detecting module gamess. Install package if necessary to enable tests. SKIPPED [1] qcengine/programs/tests/test_standard_suite_hf.py:35: Not detecting module molpro. Install package if necessary to enable tests. SKIPPED [1] qcengine/programs/tests/test_standard_suite_hf.py:35: Not detecting module psi4. Install package if necessary to enable tests. SKIPPED [1] qcengine/programs/tests/test_standard_suite_hf.py:35: Not detecting module qchem. Install package if necessary to enable tests. SKIPPED [1] qcengine/programs/tests/test_standard_suite_hf.py:35: Not detecting module turbomole. Install package if necessary to enable tests. SKIPPED [1] qcengine/programs/tests/test_standard_suite_hf.py:35: Not detecting module terachem_pbs. Install package if necessary to enable tests. SKIPPED [2] qcengine/programs/tests/test_standard_suite_hf.py:76: Not detecting module cfour. Install package if necessary to enable tests. SKIPPED [1] qcengine/programs/tests/test_standard_suite_hf.py:76: Not detecting module qcore. Install package if necessary to enable tests. SKIPPED [1] qcengine/programs/tests/test_standard_suite_hf.py:76: Not detecting module gamess. Install package if necessary to enable tests. SKIPPED [1] qcengine/programs/tests/test_standard_suite_hf.py:76: Not detecting module molpro. Install package if necessary to enable tests. SKIPPED [1] qcengine/programs/tests/test_standard_suite_hf.py:76: Not detecting module psi4. Install package if necessary to enable tests. SKIPPED [1] qcengine/programs/tests/test_standard_suite_hf.py:76: Not detecting module qchem. Install package if necessary to enable tests. SKIPPED [1] qcengine/programs/tests/test_standard_suite_hf.py:76: Not detecting module turbomole. Install package if necessary to enable tests. SKIPPED [2] qcengine/programs/tests/test_standard_suite_hf.py:122: Not detecting module cfour. Install package if necessary to enable tests. SKIPPED [1] qcengine/programs/tests/test_standard_suite_hf.py:122: Not detecting module gamess. Install package if necessary to enable tests. SKIPPED [1] qcengine/programs/tests/test_standard_suite_hf.py:122: Not detecting module molpro. Install package if necessary to enable tests. SKIPPED [1] qcengine/programs/tests/test_standard_suite_hf.py:122: Not detecting module psi4. Install package if necessary to enable tests. SKIPPED [1] qcengine/programs/tests/test_standard_suite_hf.py:122: Not detecting module qchem. Install package if necessary to enable tests. SKIPPED [4] qcengine/programs/tests/test_turbomole.py:38: Not detecting module turbomole. Install package if necessary to enable tests. SKIPPED [4] qcengine/programs/tests/test_turbomole.py:58: Not detecting module turbomole. Install package if necessary to enable tests. SKIPPED [1] qcengine/programs/tests/test_turbomole.py:86: Not detecting module turbomole. Install package if necessary to enable tests. SKIPPED [3] qcengine/programs/tests/test_turbomole.py:116: Not detecting module turbomole. Install package if necessary to enable tests. SKIPPED [1] qcengine/programs/tests/test_turbomole.py:146: Not detecting module turbomole. Install package if necessary to enable tests. SKIPPED [1] qcengine/programs/tests/test_xtb.py:17: Not detecting module xtb. Install package if necessary to enable tests. SKIPPED [1] qcengine/programs/tests/test_xtb.py:55: Not detecting module xtb. Install package if necessary to enable tests. SKIPPED [1] qcengine/programs/tests/test_xtb.py:97: Not detecting module xtb. Install package if necessary to enable tests. SKIPPED [1] qcengine/programs/tests/test_xtb.py:138: Not detecting module xtb. Install package if necessary to enable tests. SKIPPED [1] qcengine/programs/tests/test_xtb.py:181: Not detecting module xtb. Install package if necessary to enable tests. SKIPPED [1] qcengine/programs/tests/test_xtb.py:201: Not detecting module xtb. Install package if necessary to enable tests. SKIPPED [1] qcengine/programs/tests/test_xtb.py:239: Not detecting module xtb. Install package if necessary to enable tests. SKIPPED [1] qcengine/programs/tests/test_xtb.py:281: Not detecting module xtb. Install package if necessary to enable tests. SKIPPED [1] qcengine/programs/tests/test_xtb.py:322: Not detecting module xtb. Install package if necessary to enable tests. SKIPPED [1] qcengine/programs/tests/test_xtb.py:365: Not detecting module xtb. Install package if necessary to enable tests. SKIPPED [1] qcengine/programs/tests/test_xtb.py:385: Not detecting module xtb. Install package if necessary to enable tests. SKIPPED [1] qcengine/programs/tests/test_xtb.py:401: Not detecting module xtb. Install package if necessary to enable tests. SKIPPED [1] qcengine/programs/tests/test_xtb.py:419: Not detecting module xtb. Install package if necessary to enable tests. SKIPPED [1] qcengine/tests/test_cli.py:59: Not detecting module psi4. Install package if necessary to enable tests. SKIPPED [1] qcengine/tests/test_cli.py:81: Not detecting module psi4. Install package if necessary to enable tests. SKIPPED [1] /disk-samsung/freebsd-ports/science/py-qcengine/work-py38/qcengine-0.20.1/qcengine/tests/test_harness_canonical.py:64: Program 'dftd3' not found. SKIPPED [1] /disk-samsung/freebsd-ports/science/py-qcengine/work-py38/qcengine-0.20.1/qcengine/tests/test_harness_canonical.py:64: Program 'qcore' not found. SKIPPED [1] /disk-samsung/freebsd-ports/science/py-qcengine/work-py38/qcengine-0.20.1/qcengine/tests/test_harness_canonical.py:64: Program 'molpro' not found. SKIPPED [1] /disk-samsung/freebsd-ports/science/py-qcengine/work-py38/qcengine-0.20.1/qcengine/tests/test_harness_canonical.py:64: Program 'mopac' not found. SKIPPED [1] /disk-samsung/freebsd-ports/science/py-qcengine/work-py38/qcengine-0.20.1/qcengine/tests/test_harness_canonical.py:64: Program 'mp2d' not found. SKIPPED [1] /disk-samsung/freebsd-ports/science/py-qcengine/work-py38/qcengine-0.20.1/qcengine/tests/test_harness_canonical.py:64: Program 'openmm' not found. SKIPPED [1] /disk-samsung/freebsd-ports/science/py-qcengine/work-py38/qcengine-0.20.1/qcengine/tests/test_harness_canonical.py:64: Program 'psi4' not found. SKIPPED [1] /disk-samsung/freebsd-ports/science/py-qcengine/work-py38/qcengine-0.20.1/qcengine/tests/test_harness_canonical.py:64: Program 'qchem' not found. SKIPPED [1] /disk-samsung/freebsd-ports/science/py-qcengine/work-py38/qcengine-0.20.1/qcengine/tests/test_harness_canonical.py:64: Program 'terachem_pbs' not found. SKIPPED [1] /disk-samsung/freebsd-ports/science/py-qcengine/work-py38/qcengine-0.20.1/qcengine/tests/test_harness_canonical.py:64: Program 'torchani' not found. SKIPPED [1] /disk-samsung/freebsd-ports/science/py-qcengine/work-py38/qcengine-0.20.1/qcengine/tests/test_harness_canonical.py:64: Program 'turbomole' not found. SKIPPED [1] /disk-samsung/freebsd-ports/science/py-qcengine/work-py38/qcengine-0.20.1/qcengine/tests/test_harness_canonical.py:64: Program 'xtb' not found. SKIPPED [1] /disk-samsung/freebsd-ports/science/py-qcengine/work-py38/qcengine-0.20.1/qcengine/tests/test_harness_canonical.py:64: Program 'adcc' not found. SKIPPED [1] /disk-samsung/freebsd-ports/science/py-qcengine/work-py38/qcengine-0.20.1/qcengine/tests/test_harness_canonical.py:64: Program 'gcp' not found. SKIPPED [1] /disk-samsung/freebsd-ports/science/py-qcengine/work-py38/qcengine-0.20.1/qcengine/tests/test_harness_canonical.py:64: Program 'mrchem' not found. SKIPPED [1] /disk-samsung/freebsd-ports/science/py-qcengine/work-py38/qcengine-0.20.1/qcengine/tests/test_harness_canonical.py:64: Program 'cfour' not found. SKIPPED [1] /disk-samsung/freebsd-ports/science/py-qcengine/work-py38/qcengine-0.20.1/qcengine/tests/test_harness_canonical.py:64: Program 'gamess' not found. SKIPPED [1] /disk-samsung/freebsd-ports/science/py-qcengine/work-py38/qcengine-0.20.1/qcengine/tests/test_harness_canonical.py:64: Program 'mctc-gcp' not found. SKIPPED [1] /disk-samsung/freebsd-ports/science/py-qcengine/work-py38/qcengine-0.20.1/qcengine/tests/test_harness_canonical.py:77: Program 'dftd3' not found. SKIPPED [1] /disk-samsung/freebsd-ports/science/py-qcengine/work-py38/qcengine-0.20.1/qcengine/tests/test_harness_canonical.py:77: Program 'qcore' not found. SKIPPED [1] /disk-samsung/freebsd-ports/science/py-qcengine/work-py38/qcengine-0.20.1/qcengine/tests/test_harness_canonical.py:77: Program 'molpro' not found. SKIPPED [1] /disk-samsung/freebsd-ports/science/py-qcengine/work-py38/qcengine-0.20.1/qcengine/tests/test_harness_canonical.py:77: Program 'mopac' not found. SKIPPED [1] /disk-samsung/freebsd-ports/science/py-qcengine/work-py38/qcengine-0.20.1/qcengine/tests/test_harness_canonical.py:77: Program 'mp2d' not found. SKIPPED [1] /disk-samsung/freebsd-ports/science/py-qcengine/work-py38/qcengine-0.20.1/qcengine/tests/test_harness_canonical.py:77: Program 'openmm' not found. SKIPPED [1] /disk-samsung/freebsd-ports/science/py-qcengine/work-py38/qcengine-0.20.1/qcengine/tests/test_harness_canonical.py:77: Program 'psi4' not found. SKIPPED [1] /disk-samsung/freebsd-ports/science/py-qcengine/work-py38/qcengine-0.20.1/qcengine/tests/test_harness_canonical.py:77: Program 'qchem' not found. SKIPPED [1] /disk-samsung/freebsd-ports/science/py-qcengine/work-py38/qcengine-0.20.1/qcengine/tests/test_harness_canonical.py:77: Program 'terachem_pbs' not found. SKIPPED [1] /disk-samsung/freebsd-ports/science/py-qcengine/work-py38/qcengine-0.20.1/qcengine/tests/test_harness_canonical.py:77: Program 'torchani' not found. SKIPPED [1] /disk-samsung/freebsd-ports/science/py-qcengine/work-py38/qcengine-0.20.1/qcengine/tests/test_harness_canonical.py:77: Program 'turbomole' not found. SKIPPED [1] /disk-samsung/freebsd-ports/science/py-qcengine/work-py38/qcengine-0.20.1/qcengine/tests/test_harness_canonical.py:77: Program 'xtb' not found. SKIPPED [1] /disk-samsung/freebsd-ports/science/py-qcengine/work-py38/qcengine-0.20.1/qcengine/tests/test_harness_canonical.py:77: Program 'adcc' not found. SKIPPED [1] /disk-samsung/freebsd-ports/science/py-qcengine/work-py38/qcengine-0.20.1/qcengine/tests/test_harness_canonical.py:77: Program 'gcp' not found. SKIPPED [1] /disk-samsung/freebsd-ports/science/py-qcengine/work-py38/qcengine-0.20.1/qcengine/tests/test_harness_canonical.py:77: Program 'mrchem' not found. SKIPPED [1] /disk-samsung/freebsd-ports/science/py-qcengine/work-py38/qcengine-0.20.1/qcengine/tests/test_harness_canonical.py:77: Program 'cfour' not found. SKIPPED [1] /disk-samsung/freebsd-ports/science/py-qcengine/work-py38/qcengine-0.20.1/qcengine/tests/test_harness_canonical.py:77: Program 'gamess' not found. SKIPPED [1] /disk-samsung/freebsd-ports/science/py-qcengine/work-py38/qcengine-0.20.1/qcengine/tests/test_harness_canonical.py:77: Program 'mctc-gcp' not found. SKIPPED [1] /disk-samsung/freebsd-ports/science/py-qcengine/work-py38/qcengine-0.20.1/qcengine/tests/test_harness_canonical.py:103: Program 'adcc' not found. SKIPPED [1] /disk-samsung/freebsd-ports/science/py-qcengine/work-py38/qcengine-0.20.1/qcengine/tests/test_harness_canonical.py:103: Program 'cfour' not found. SKIPPED [1] /disk-samsung/freebsd-ports/science/py-qcengine/work-py38/qcengine-0.20.1/qcengine/tests/test_harness_canonical.py:103: Program 'gamess' not found. SKIPPED [1] /disk-samsung/freebsd-ports/science/py-qcengine/work-py38/qcengine-0.20.1/qcengine/tests/test_harness_canonical.py:103: Program 'molpro' not found. SKIPPED [1] /disk-samsung/freebsd-ports/science/py-qcengine/work-py38/qcengine-0.20.1/qcengine/tests/test_harness_canonical.py:103: Program 'openmm' not found. SKIPPED [1] qcengine/tests/test_harness_canonical.py:99: Not detecting module psi4_mp2qcsk. Install package if necessary to enable tests. SKIPPED [1] /disk-samsung/freebsd-ports/science/py-qcengine/work-py38/qcengine-0.20.1/qcengine/tests/test_harness_canonical.py:103: Program 'qchem' not found. SKIPPED [1] /disk-samsung/freebsd-ports/science/py-qcengine/work-py38/qcengine-0.20.1/qcengine/tests/test_harness_canonical.py:103: Program 'qcore' not found. SKIPPED [1] /disk-samsung/freebsd-ports/science/py-qcengine/work-py38/qcengine-0.20.1/qcengine/tests/test_harness_canonical.py:103: Program 'turbomole' not found. SKIPPED [1] /disk-samsung/freebsd-ports/science/py-qcengine/work-py38/qcengine-0.20.1/qcengine/tests/test_harness_canonical.py:144: Program 'cfour' not found. SKIPPED [2] /disk-samsung/freebsd-ports/science/py-qcengine/work-py38/qcengine-0.20.1/qcengine/tests/test_harness_canonical.py:144: Program 'dftd3' not found. SKIPPED [1] /disk-samsung/freebsd-ports/science/py-qcengine/work-py38/qcengine-0.20.1/qcengine/tests/test_harness_canonical.py:144: Program 'qcore' not found. SKIPPED [1] /disk-samsung/freebsd-ports/science/py-qcengine/work-py38/qcengine-0.20.1/qcengine/tests/test_harness_canonical.py:144: Program 'gamess' not found. SKIPPED [1] /disk-samsung/freebsd-ports/science/py-qcengine/work-py38/qcengine-0.20.1/qcengine/tests/test_harness_canonical.py:144: Program 'mopac' not found. SKIPPED [1] /disk-samsung/freebsd-ports/science/py-qcengine/work-py38/qcengine-0.20.1/qcengine/tests/test_harness_canonical.py:144: Program 'mp2d' not found. SKIPPED [1] /disk-samsung/freebsd-ports/science/py-qcengine/work-py38/qcengine-0.20.1/qcengine/tests/test_harness_canonical.py:144: Program 'openmm' not found. SKIPPED [1] /disk-samsung/freebsd-ports/science/py-qcengine/work-py38/qcengine-0.20.1/qcengine/tests/test_harness_canonical.py:144: Program 'psi4' not found. SKIPPED [1] /disk-samsung/freebsd-ports/science/py-qcengine/work-py38/qcengine-0.20.1/qcengine/tests/test_harness_canonical.py:144: Program 'qchem' not found. SKIPPED [1] /disk-samsung/freebsd-ports/science/py-qcengine/work-py38/qcengine-0.20.1/qcengine/tests/test_harness_canonical.py:144: Program 'terachem_pbs' not found. SKIPPED [1] /disk-samsung/freebsd-ports/science/py-qcengine/work-py38/qcengine-0.20.1/qcengine/tests/test_harness_canonical.py:144: Program 'torchani' not found. SKIPPED [1] /disk-samsung/freebsd-ports/science/py-qcengine/work-py38/qcengine-0.20.1/qcengine/tests/test_harness_canonical.py:144: Program 'turbomole' not found. SKIPPED [1] /disk-samsung/freebsd-ports/science/py-qcengine/work-py38/qcengine-0.20.1/qcengine/tests/test_harness_canonical.py:144: Program 'adcc' not found. SKIPPED [1] /disk-samsung/freebsd-ports/science/py-qcengine/work-py38/qcengine-0.20.1/qcengine/tests/test_harness_canonical.py:144: Program 'gcp' not found. SKIPPED [1] /disk-samsung/freebsd-ports/science/py-qcengine/work-py38/qcengine-0.20.1/qcengine/tests/test_harness_canonical.py:144: Program 'mrchem' not found. SKIPPED [1] /disk-samsung/freebsd-ports/science/py-qcengine/work-py38/qcengine-0.20.1/qcengine/tests/test_harness_canonical.py:144: Program 'mctc-gcp' not found. SKIPPED [1] qcengine/tests/test_mdi.py:12: Not detecting module mdi. Install package if necessary to enable tests. SKIPPED [3] qcengine/tests/test_procedures.py:23: Not detecting module psi4. Install package if necessary to enable tests. SKIPPED [1] qcengine/tests/test_procedures.py:54: Not detecting module psi4. Install package if necessary to enable tests. SKIPPED [1] qcengine/tests/test_procedures.py:88: Not detecting module psi4. Install package if necessary to enable tests. SKIPPED [1] qcengine/tests/test_procedures.py:169: Not detecting module torchani. Install package if necessary to enable tests. SKIPPED [1] qcengine/tests/test_procedures.py:169: Not detecting module mopac. Install package if necessary to enable tests. SKIPPED [3] qcengine/tests/test_procedures.py:169: Not detecting module openmm. Install package if necessary to enable tests. SKIPPED [1] qcengine/tests/test_procedures.py:169: Not detecting module qcore. Install package if necessary to enable tests. SKIPPED [1] qcengine/tests/test_program_utils.py:17: Not detecting module psi4. Install package if necessary to enable tests. SKIPPED [1] qcengine/tests/test_program_utils.py:17: Not detecting module torchani. Install package if necessary to enable tests. ======= 21 failed, 187 passed, 726 skipped, 4 xfailed in 469.76 seconds ======== *** Error code 1 Stop. make: stopped in /disk-samsung/freebsd-ports/science/py-qcengine