def setUp(self):
self.assertDictEqual.__self__.maxDiff = None
# generate molecule
molecule = Structure(coordinates=[[0.0, 1.0, 0.0], [0.0, 0.0, 1.0],
[0.0, 0.0, -1.0]],
symbols=['O', 'H', 'H'],
charge=0,
multiplicity=1)
# optimization
txt_input = create_qchem_input(molecule,
jobtype='opt',
exchange='hf',
basis='sto-3g',
geom_opt_tol_gradient=300,
geom_opt_tol_energy=100,
geom_opt_coords=-1,
geom_opt_tol_displacement=1200)
parsed_data = get_output_from_qchem(txt_input,
processors=4,
parser=basic_optimization,
force_recalculation=recalculate,
store_full_output=True)
self.molecule = parsed_data['optimized_molecule']
def test_eth_00_ras22(self):
rasci = dict(self.rem)
if do_alpha_beta:
rasci.update({'ras_elec_alpha': 1,
'ras_elec_beta': 1})
# create qchem input
txt_input = create_qchem_input(self.molecule, **rasci)
# calculate and parse qchem output
output = get_output_from_qchem(txt_input,
processors=4,
store_full_output=True,
force_recalculation=recalculate)
data = parser_rasci(output)
filename = self.__class__.__name__ + '_ras22.yaml'
# create reference file
if ctrl_print:
with open(filename, 'w') as outfile:
yaml.dump(data, outfile, default_flow_style=False, allow_unicode=True)
with open(filename, 'r') as stream:
data_loaded = yaml.load(stream, Loader=yaml.Loader)
data = standardize_dictionary(data, decimal=2)
#print(data)
print(data_loaded)
data_loaded = standardize_dictionary(data_loaded, decimal=2)
self.assertDictEqual(data, data_loaded)
def test_srdft(self):
# create qchem input
qc_input = create_qchem_input(
self.molecule,
jobtype='sp',
exchange='hf',
correlation='rasci',
basis='6-31G(d,p)',
ras_act=2,
ras_elec=2,
ras_spin_mult=0,
ras_roots=2,
ras_do_hole=True,
ras_sts_tm=True,
# rasci sr-dft
ras_omega=400,
ras_srdft_cor='srpw92',
ras_srdft_exc='srpbe',
ras_natorb=False,
set_iter=30,
ras_srdft_damp=0.5)
#from pyqchem.cache import SqlCache as CacheSystem
#cache = CacheSystem()
#cache.list_database()
#output = cache.retrieve_calculation_data(qc_input, 'fullout')
#print(output)
# calculate and parse qchem output
output = get_output_from_qchem(qc_input,
processors=4,
force_recalculation=recalculate,
store_full_output=True)
print(output)
data = parser_rasci(output)
filename = dir_path + '/' + self.__class__.__name__ + '_srdft.yaml'
if remake_tests:
with open(filename, 'w') as outfile:
yaml.dump(data,
outfile,
default_flow_style=False,
allow_unicode=True)
data = standardize_dictionary(data, decimal=2)
with open(filename, 'r') as stream:
data_loaded = yaml.load(stream, Loader=yaml.Loader)
print(data_loaded)
data_loaded = standardize_dictionary(data_loaded, decimal=2)
self.assertDictEqual(data, data_loaded)
def test_srdft(self):
# create qchem input
txt_input = create_qchem_input(
self.molecule,
jobtype='sp',
exchange='hf',
correlation='rasci',
basis='6-31G(d,p)',
ras_act=4,
ras_elec=4,
ras_spin_mult=0,
ras_roots=6,
ras_do_hole=True,
ras_sts_tm=True,
# rasci sr-dft
ras_omega=300,
ras_srdft_cor='srpbe',
ras_srdft_exc='srlsda',
ras_natorb=False,
set_iter=30,
ras_srdft_damp=0.5)
print(txt_input.get_txt())
# calculate and parse qchem output
output = get_output_from_qchem(txt_input,
processors=4,
force_recalculation=recalculate,
store_full_output=True)
print(output)
data = parser_rasci(output)
print(data)
filename = dir_path + '/' + self.__class__.__name__ + '_srdft.yaml'
if remake_tests:
with open(filename, 'w') as outfile:
yaml.dump(data,
outfile,
default_flow_style=False,
allow_unicode=True)
data = standardize_dictionary(data)
with open(filename, 'r') as stream:
data_loaded = yaml.load(stream, Loader=yaml.Loader)
print(data_loaded)
data_loaded = standardize_dictionary(data_loaded)
self.assertDictEqual(data, data_loaded)
def test_rasci(self):
# create qchem input
txt_input = create_qchem_input(self.molecule,
jobtype='sp',
exchange='hf',
correlation='rasci',
basis='sto-3g',
ras_act=4,
ras_elec=4,
ras_spin_mult=1,
ras_roots=6,
ras_print=5,
ras_do_hole=True,
ras_sts_tm=True)
# calculate and parse qchem output
output = get_output_from_qchem(txt_input,
processors=4,
force_recalculation=recalculate,
store_full_output=True)
print(output)
data = parser_rasci(output)
print(data)
filename = dir_path + '/' + self.__class__.__name__ + '_rasci.yaml'
if remake_tests:
with open(filename, 'w') as outfile:
yaml.dump(data,
outfile,
default_flow_style=False,
allow_unicode=True)
data = standardize_dictionary(data, decimal=2)
with open(filename, 'r') as stream:
data_loaded = yaml.load(stream, Loader=yaml.Loader)
print(data_loaded)
data_loaded = standardize_dictionary(data_loaded, decimal=2)
self.assertDictEqual(data, data_loaded)
def test_eth_00_ras44(self):
rasci = dict(self.rem)
rasci.update({'ras_act': 4,
'ras_elec': 4,
'ras_occ': 6})
if do_alpha_beta:
rasci.update({'ras_elec_alpha': 2,
'ras_elec_beta': 2})
# create qchem input
txt_input = create_qchem_input(self.molecule, **rasci)
# calculate and parse qchem output
output = get_output_from_qchem(txt_input, processors=4)
print(output)
data = basic_rasci(output)
print(data)
filename = self.__class__.__name__ + '_ras44.yaml'
# creat reference file
if ctrl_print:
with open(filename, 'w') as outfile:
yaml.dump(data, outfile, default_flow_style=False, allow_unicode=True)
with open(filename, 'r') as stream:
data_loaded = yaml.safe_load(stream)
data = standardize_dictionary(data)
print(data_loaded)
data_loaded = standardize_dictionary(data_loaded)
self.assertDictEqual(data, data_loaded)
'H', 'H', 'H'
]
molecule = Structure(coordinates=coordinates,
symbols=symbols,
charge=0,
multiplicity=1)
molecule.get_coordinates()
print('optimize molecule')
txt_input = create_qchem_input(molecule,
jobtype='opt',
method='b3lyp',
basis='cc-pVDZ',
geom_opt_tol_gradient=50,
geom_opt_coords=-1,
geom_opt_tol_displacement=800)
parsed_data = get_output_from_qchem(txt_input,
processors=4,
use_mpi=True,
parser=basic_optimization,
force_recalculation=False)
#parsed_data = basic_optimization(data)
opt_molecule = parsed_data['optimized_molecule']
print(opt_molecule)
[0.00000, -2.49029, 0.00000],
[1.21479, -0.70136, 0.00000],
[2.15666, -1.24515, 0.00000],
[1.21479, 0.70136, 0.00000],
[2.15666, 1.24515, 0.00000]]
symbols = ['C', 'H', 'C', 'H', 'C', 'H', 'C', 'H', 'C', 'H', 'C', 'F']
benzene_coordinates = np.array(benzene_coordinates)
molecule = Structure(coordinates=benzene_coordinates,
symbols=symbols,
charge=0)
parameters = {'jobtype': 'sp', 'exchange': 'hf', 'basis': '6-31G'}
qc_input = create_qchem_input(molecule, **parameters)
_, _, fchk_data = get_output_from_qchem(qc_input,
processors=4,
force_recalculation=True,
read_fchk=True)
from pyqchem.file_io import build_fchk
open('test.fchk', 'w').write(build_fchk(fchk_data))
mo_coeff = _set_zero_to_coefficients(fchk_data['basis'],
fchk_data['coefficients'],
range(6, 12))
fchk_data['coefficients'] = mo_coeff
structure = fchk_data['structure']
# define molecule
coordinates = [[0.0, 1.0, 0.0], [0.0, 0.0, 1.0], [0.0, 0.0, -1.0]]
symbols = ['O', 'H', 'H']
molecule = Structure(coordinates=coordinates,
symbols=symbols,
charge=0,
multiplicity=1)
print('Initial structure')
print(molecule)
# calculation
qc_input = create_qchem_input(molecule,
jobtype='freq',
exchange='hf',
basis='sto-3g')
out, electronic_structure = get_output_from_qchem(
qc_input,
processors=4,
read_fchk=True,
force_recalculation=True,
remote=remote_data, # Set remote data
parser=basic_frequencies)
# Show output
print(out)
# Show Electronic structure data
print(electronic_structure)
symbols = ['O', 'H', 'H']
molecule = Structure(coordinates=coordinates,
symbols=symbols,
charge=0,
multiplicity=1)
print('Initial structure')
print(molecule)
# optimization
qc_input = create_qchem_input(molecule,
jobtype='opt',
exchange='hf',
basis='sto-3g',
geom_opt_tol_gradient=300,
geom_opt_tol_energy=100,
geom_opt_coords=-1,
geom_opt_tol_displacement=1200)
parsed_data, electronic_structure = get_output_from_qchem(
qc_input, processors=4, parser=basic_optimization, read_fchk=True)
opt_molecule = parsed_data['optimized_molecule']
print('Optimized structure')
print(opt_molecule)
# frequencies calculation
qc_input = create_qchem_input(opt_molecule,
jobtype='freq',
charge=0,
multiplicity=1)
# print(molecule)
for x in range(len(geom_opt_max_cycles_l)):
# create_qchem_input is the function responsible for creating the input file for the calculation
# This should mostly be left unchanged as the Job object takes care of passing in the correct parameters and if a
# change is required it should be done using the input_variation function in the job class
txt_input = create_qchem_input(
molecule,
jobtype=Test.jobtype,
gui=Test.gui,
basis=Test.basis,
method=Test.method,
max_scf_cycles=Test.max_scf_cycles,
geom_opt_max_cycles=Test.geom_opt_max_cycles,
scf_convergence=Test.scf_convergence)
txt_input_freq = create_qchem_input(
molecule,
jobtype='freq',
gui=Test.gui,
basis=Test.basis,
method=Test.method,
max_scf_cycles=Test.max_scf_cycles,
geom_opt_max_cycles=Test.geom_opt_max_cycles,
scf_convergence=Test.scf_convergence)
[3.7, -0.92281, -1.22792], [3.7, 0.92281, -1.22792]]
symbols = ['C', 'C', 'H', 'H', 'H', 'H', 'C', 'C', 'H', 'H', 'H', 'H']
range_f1 = range(0, 6)
range_f2 = range(6, 12)
# create molecule
molecule = Structure(coordinates=dimer_ethene,
symbols=symbols,
charge=0,
multiplicity=1)
# create Q-Chem input
qc_input = create_qchem_input(molecule,
jobtype='sp',
exchange='hf',
basis='6-31G')
print(qc_input.get_txt())
# get data from Q-Chem calculation
output, electronic_structure = get_output_from_qchem(qc_input,
processors=4,
force_recalculation=False,
read_fchk=True,
fchk_only=True)
# store original fchk info in file
open('test.fchk', 'w').write(build_fchk(electronic_structure))
# get symmetry classification
electronic_structure_f1 = crop_electronic_structure(electronic_structure,
molecule = Structure(coordinates=coordinates,
symbols=symbols,
charge=0,
multiplicity=1)
print('Initial structure')
print(molecule)
# optimization
qc_input = create_qchem_input(molecule,
jobtype='sp',
exchange='hf',
basis='sto-3g',
unrestricted=True,
solvent_method='pcm',
solvent_params={'Dielectric': 8.93}, # Cl2CH2
pcm_params={'Theory': 'CPCM',
'Method': 'SWIG',
'Solver': 'Inversion',
'Radii': 'Bondi'}
)
data, electronic_structure = get_output_from_qchem(qc_input,
force_recalculation=True,
processors=4,
parser=basic_parser_qchem,
read_fchk=True)
print('scf energy', data['scf_energy'], 'H')
