def test_get_excitation_spectrum(self):
nwo = NwOutput(os.path.join(test_dir, "phen_tddft.log"))
spectrum = nwo.get_excitation_spectrum()
self.assertEqual(len(spectrum.x), 2000)
self.assertAlmostEqual(spectrum.x[0], 1.9291)
self.assertAlmostEqual(spectrum.y[0], 0.0)
self.assertAlmostEqual(spectrum.y[1000], 0.0007423569947114812)
def test_parse_tddft(self):
nwo = NwOutput(os.path.join(test_dir, "phen_tddft.log"))
roots = nwo.parse_tddft()
self.assertEqual(roots["singlet"].shape, (20, 2))
self.assertAlmostEqual(roots["singlet"][0, 0], 3.9291)
self.assertAlmostEqual(roots["singlet"][0, 1], 0.0)
self.assertAlmostEqual(roots["singlet"][1, 1], 0.00177)
def test_parse_tddft(self):
nwo = NwOutput(os.path.join(test_dir, "phen_tddft.log"))
roots = nwo.parse_tddft()
self.assertEqual(len(roots["singlet"]), 20)
self.assertAlmostEqual(roots["singlet"][0]["energy"], 3.9291)
self.assertAlmostEqual(roots["singlet"][0]["osc_strength"], 0.0)
self.assertAlmostEqual(roots["singlet"][1]["osc_strength"], 0.00177)
def test_get_excitation_spectrum(self):
nwo = NwOutput(os.path.join(test_dir, "phen_tddft.log"))
spectrum = nwo.get_excitation_spectrum()
self.assertEqual(len(spectrum.x), 2000)
self.assertAlmostEqual(spectrum.x[0], 1.9291)
self.assertAlmostEqual(spectrum.y[0], 0.0)
self.assertAlmostEqual(spectrum.y[1000], 0.0007423569947114812)
def test_parse_tddft(self):
nwo = NwOutput(os.path.join(test_dir, "phen_tddft.log"))
roots = nwo.parse_tddft()
self.assertEqual(len(roots["singlet"]), 20)
self.assertAlmostEqual(roots["singlet"][0]["energy"], 3.9291)
self.assertAlmostEqual(roots["singlet"][0]["osc_strength"], 0.0)
self.assertAlmostEqual(roots["singlet"][1]["osc_strength"], 0.00177)
def check(self):
# Checks output file for errors.
out = NwOutput(self.output_filename)
self.errors = []
self.input_file = out.job_info['input']
if out.data[-1]["has_error"]:
self.errors.extend(out.data[-1]["errors"])
self.errors = list(set(self.errors))
self.ntasks = len(out.data)
return len(self.errors) > 0
def _get_output_nodes(self, output_path, error_path):
"""
Extracts output nodes from the standard output and standard error
files.
"""
from pymatgen.io.nwchem import NwOutput
from aiida.orm.data.structure import StructureData
from aiida.orm.data.array.trajectory import TrajectoryData
ret_dict = []
nwo = NwOutput(output_path)
for out in nwo.data:
molecules = out.pop('molecules', None)
structures = out.pop('structures', None)
if molecules:
structlist = [
StructureData(pymatgen_molecule=m) for m in molecules
]
ret_dict.append(
('trajectory', TrajectoryData(structurelist=structlist)))
if structures:
structlist = [
StructureData(pymatgen_structure=s) for s in structures
]
ret_dict.append(
('trajectory', TrajectoryData(structurelist=structlist)))
ret_dict.append(('output', ParameterData(dict=out)))
# Since ParameterData rewrites it's properties (using _set_attr())
# with keys from the supplied dictionary, ``source`` has to be
# moved to another key. See issue #9 for details:
# (https://bitbucket.org/epfl_theos/aiida_epfl/issues/9)
nwo.job_info['program_source'] = nwo.job_info.pop('source', None)
ret_dict.append(('job_info', ParameterData(dict=nwo.job_info)))
return ret_dict
def test_read(self):
nwo = NwOutput(os.path.join(test_dir, "CH4.nwout"))
nwo_cosmo = NwOutput(os.path.join(test_dir, "N2O4.nwout"))
self.assertEqual(0, nwo[0]["charge"])
self.assertEqual(-1, nwo[-1]["charge"])
self.assertEqual(len(nwo), 5)
self.assertAlmostEqual(-1102.6224491715582, nwo[0]["energies"][-1], 2)
self.assertAlmostEqual(-1102.9986291578023, nwo[2]["energies"][-1], 3)
self.assertAlmostEqual(-11156.354030653656,
nwo_cosmo[5]["energies"][0]["cosmo scf"], 3)
self.assertAlmostEqual(-11153.374133394364,
nwo_cosmo[5]["energies"][0]["gas phase"], 3)
self.assertAlmostEqual(-11156.353632962995,
nwo_cosmo[5]["energies"][0]["sol phase"], 2)
self.assertAlmostEqual(-11168.818934311605,
nwo_cosmo[6]["energies"][0]["cosmo scf"], 2)
self.assertAlmostEqual(-11166.3624424611462,
nwo_cosmo[6]["energies"][0]["gas phase"], 2)
self.assertAlmostEqual(-11168.818934311605,
nwo_cosmo[6]["energies"][0]["sol phase"], 2)
self.assertAlmostEqual(-11165.227959110889,
nwo_cosmo[7]["energies"][0]["cosmo scf"], 2)
self.assertAlmostEqual(-11165.025443612385,
nwo_cosmo[7]["energies"][0]["gas phase"], 2)
self.assertAlmostEqual(-11165.227959110154,
nwo_cosmo[7]["energies"][0]["sol phase"], 2)
self.assertAlmostEqual(nwo[1]["hessian"][0][0], 4.60187e01)
self.assertAlmostEqual(nwo[1]["hessian"][1][2], -1.14030e-08)
self.assertAlmostEqual(nwo[1]["hessian"][2][3], 2.60819e01)
self.assertAlmostEqual(nwo[1]["hessian"][6][6], 1.45055e02)
self.assertAlmostEqual(nwo[1]["hessian"][11][14], 1.35078e01)
# CH4.nwout, line 722
self.assertAlmostEqual(nwo[0]["forces"][0][3], -0.001991)
# N2O4.nwout, line 1071
self.assertAlmostEqual(nwo_cosmo[0]["forces"][0][4], 0.011948)
# There should be four DFT gradients.
self.assertEqual(len(nwo_cosmo[0]["forces"]), 4)
ie = nwo[4]["energies"][-1] - nwo[2]["energies"][-1]
ea = nwo[2]["energies"][-1] - nwo[3]["energies"][-1]
self.assertAlmostEqual(0.7575358648355177, ie)
self.assertAlmostEqual(-14.997877958701338, ea, 3)
self.assertEqual(nwo[4]["basis_set"]["C"]["description"], "6-311++G**")
nwo = NwOutput(os.path.join(test_dir, "H4C3O3_1.nwout"))
self.assertTrue(nwo[-1]["has_error"])
self.assertEqual(nwo[-1]["errors"][0], "Bad convergence")
nwo = NwOutput(os.path.join(test_dir, "CH3CH2O.nwout"))
self.assertTrue(nwo[-1]["has_error"])
self.assertEqual(nwo[-1]["errors"][0], "Bad convergence")
nwo = NwOutput(os.path.join(test_dir, "C1N1Cl1_1.nwout"))
self.assertTrue(nwo[-1]["has_error"])
self.assertEqual(nwo[-1]["errors"][0], "autoz error")
nwo = NwOutput(
os.path.join(test_dir, "anthrachinon_wfs_16_ethyl.nwout"))
self.assertTrue(nwo[-1]["has_error"])
self.assertEqual(nwo[-1]["errors"][0], "Geometry optimization failed")
nwo = NwOutput(
os.path.join(test_dir, "anthrachinon_wfs_15_carboxyl.nwout"))
self.assertEqual(nwo[1]["frequencies"][0][0], -70.47)
self.assertEqual(len(nwo[1]["frequencies"][0][1]), 27)
self.assertEqual(nwo[1]["frequencies"][-1][0], 3696.74)
self.assertEqual(nwo[1]["frequencies"][-1][1][-1],
(0.20498, -0.94542, -0.00073))
self.assertEqual(nwo[1]["normal_frequencies"][1][0], -70.72)
self.assertEqual(nwo[1]["normal_frequencies"][3][0], -61.92)
self.assertEqual(nwo[1]["normal_frequencies"][1][1][-1],
(0.00056, 0.00042, 0.06781))
def test_read(self):
nwo = NwOutput(os.path.join(test_dir, "CH4.nwout"))
nwo_cosmo = NwOutput(os.path.join(test_dir, "N2O4.nwout"))
self.assertEqual(0, nwo.data[0]["charge"])
self.assertEqual(-1, nwo.data[-1]["charge"])
self.assertAlmostEqual(-1102.6224098664698,
nwo.data[0]["energies"][-1])
self.assertAlmostEqual(-1102.9985898393043,
nwo.data[2]["energies"][-1])
self.assertAlmostEqual(-11156.353632964056,
nwo_cosmo.data[5]["energies"][0]["cosmo scf"])
self.assertAlmostEqual(-11153.373735810987,
nwo_cosmo.data[5]["energies"][0]["gas phase"])
self.assertAlmostEqual(-11156.353632962995,
nwo_cosmo.data[5]["energies"][0]["sol phase"])
self.assertAlmostEqual(-11168.818934311605,
nwo_cosmo.data[6]["energies"][0]["cosmo scf"])
self.assertAlmostEqual(-11166.3624424611462,
nwo_cosmo.data[6]["energies"][0]['gas phase'])
self.assertAlmostEqual(-11168.818934311605,
nwo_cosmo.data[6]["energies"][0]['sol phase'])
self.assertAlmostEqual(-11165.227959110889,
nwo_cosmo.data[7]["energies"][0]['cosmo scf'])
self.assertAlmostEqual(-11165.025443612385,
nwo_cosmo.data[7]["energies"][0]['gas phase'])
self.assertAlmostEqual(-11165.227959110154,
nwo_cosmo.data[7]["energies"][0]['sol phase'])
self.assertAlmostEqual(nwo.data[1]["hessian"][0][0], 4.60187e+01)
self.assertAlmostEqual(nwo.data[1]["hessian"][1][2], -1.14030e-08)
self.assertAlmostEqual(nwo.data[1]["hessian"][2][3], 2.60819e+01)
self.assertAlmostEqual(nwo.data[1]["hessian"][6][6], 1.45055e+02)
self.assertAlmostEqual(nwo.data[1]["hessian"][11][14], 1.35078e+01)
# CH4.nwout, line 722
self.assertAlmostEqual(nwo.data[0]["forces"][0][3], -0.001991)
# N2O4.nwout, line 1071
self.assertAlmostEqual(nwo_cosmo.data[0]["forces"][0][4], 0.011948)
# There should be four DFT gradients.
self.assertEqual(len(nwo_cosmo.data[0]["forces"]), 4)
ie = (nwo.data[4]["energies"][-1] - nwo.data[2]["energies"][-1])
ea = (nwo.data[2]["energies"][-1] - nwo.data[3]["energies"][-1])
self.assertAlmostEqual(0.7575358046858582, ie)
self.assertAlmostEqual(-14.997877424073295, ea)
self.assertEqual(nwo.data[4]["basis_set"]["C"]["description"],
"6-311++G**")
nwo = NwOutput(os.path.join(test_dir, "H4C3O3_1.nwout"))
self.assertTrue(nwo.data[-1]["has_error"])
self.assertEqual(nwo.data[-1]["errors"][0], "Bad convergence")
nwo = NwOutput(os.path.join(test_dir, "CH3CH2O.nwout"))
self.assertTrue(nwo.data[-1]["has_error"])
self.assertEqual(nwo.data[-1]["errors"][0], "Bad convergence")
nwo = NwOutput(os.path.join(test_dir, "C1N1Cl1_1.nwout"))
self.assertTrue(nwo.data[-1]["has_error"])
self.assertEqual(nwo.data[-1]["errors"][0], "autoz error")
nwo = NwOutput(
os.path.join(test_dir, "anthrachinon_wfs_16_ethyl.nwout"))
self.assertTrue(nwo.data[-1]["has_error"])
self.assertEqual(nwo.data[-1]["errors"][0],
"Geometry optimization failed")
nwo = NwOutput(
os.path.join(test_dir, "anthrachinon_wfs_15_carboxyl.nwout"))
self.assertEqual(nwo.data[1]['frequencies'][0][0], -70.47)
self.assertEqual(len(nwo.data[1]['frequencies'][0][1]), 27)
self.assertEqual(nwo.data[1]['frequencies'][-1][0], 3696.74)
self.assertEqual(nwo.data[1]['frequencies'][-1][1][-1],
(0.20498, -0.94542, -0.00073))
self.assertEqual(nwo.data[1]["normal_frequencies"][1][0], -70.72)
self.assertEqual(nwo.data[1]["normal_frequencies"][3][0], -61.92)
self.assertEqual(nwo.data[1]["normal_frequencies"][1][1][-1],
(0.00056, 0.00042, 0.06781))
import os
import dlite
from pymatgen.io.nwchem import NwOutput
from pymatgen.io.ase import AseAtomsAdaptor
data = NwOutput('nwchem_result1.nwout')
keys = data.data[0].keys()