def test_incorrect_mol_spec(fd_incorrect_zmatrix_var):
''' Tests that incorrect lines in the molecule
specification fail to be read.'''
# checks parse error raised when freezecode set:
freeze_code_line = 'H 1 1.0 2.0 3.0'
symbol, pos = _get_atoms_info(freeze_code_line)
with pytest.raises(ParseError):
_get_cartesian_atom_coords(symbol, pos)
# checks parse error raised when 'alternate' z-matrix
# definition is used
incorrect_zmatrix = 'C4 O1 0.8 C2 121.4 O2 150.0 1'
with pytest.raises(ParseError):
_get_zmatrix_line(incorrect_zmatrix)
incorrect_symbol = 'C1-7 0 1 2 3'
# Checks parse error raised when
# molecule specifications for molecular mechanics
# calculations have been used.
with pytest.raises(ParseError):
_validate_symbol_string(incorrect_symbol)
# Expect warning as constants aren't supported so they're
# set as vars instead:
with pytest.warns(UserWarning):
# Expect error as undefined var appears in matrix:
with pytest.raises(ParseError):
read_gaussian_in(fd_incorrect_zmatrix_var, True)
def test_read_write_gaussian_cartesian_basis_set(fd_cartesian_basis_set,
cartesian_setup):
# Tests reading a Gaussian input file with:
# - Cartesian coordinates for the atom positions.
# - ASE formatted method and basis
# - Masses defined using readiso section
atoms, params = cartesian_setup
atoms.pbc = None
atoms.cell = None
iso_params = {'temperature': '300', 'pressure': '1.0', 'scale': '1.0'}
params.update(iso_params)
params['opt'] = 'tight maxcyc=100'
params['frequency'] = 'anharmonic'
params['basis'] = 'gen'
params['method'] = 'g1'
params['fitting_basis'] = 'tzvpfit'
params['save'] = ''
params['basis_set'] = _basis_set_text
atoms_new = read_gaussian_in(fd_cartesian_basis_set, True)
atoms_new.set_masses(_get_iso_masses(atoms_new))
_check_atom_properties(atoms, atoms_new, params)
# Now we have tested reading the input, we can test writing it
# and reading it back in.
# Expect warning due to g1 being a composite method:
with pytest.warns(UserWarning):
_test_write_gaussian(atoms_new, params)
def test_read_write_gaussian_cartesian(fd_cartesian, cartesian_setup):
'''Tests the read_gaussian_in and write_gaussian_in methods.
For the input text given by each fixture we do the following:
- Check reading in the text generates the Atoms object and Calculator that
we would expect to get.
- Check that writing out the resulting Atoms object and reading it back in
generates the same Atoms object and parameters. '''
# Tests reading a Gaussian input file with:
# - Cartesian coordinates for the atom positions.
# - ASE formatted method and basis
# - PBCs
# - All nuclei properties set
# - Masses defined using nuclei properties
atoms, params = cartesian_setup
params['nmagmlist'] = np.array([None, -8.89, None])
params['zefflist'] = np.array([None, -1, None])
params['znuclist'] = np.array([None, None, 2])
params['qmomlist'] = np.array([None, None, 1])
params['radnuclearlist'] = np.array([None, None, 1])
params['spinlist'] = np.array([None, None, 1])
# Expect warning due to fragments not being supported:
with pytest.warns(UserWarning):
atoms_new = read_gaussian_in(fd_cartesian, True)
atoms_new.set_masses(_get_iso_masses(atoms_new))
_check_atom_properties(atoms, atoms_new, params)
# Now we have tested reading the input, we can test writing it
# and reading it back in.
_test_write_gaussian(atoms_new, params)
def test_read_write_gaussian_zmatrix(fd_zmatrix):
# Tests reading a Gaussian input file with:
# - Z-matrix format for structure definition
# - Variables in the Z-matrix
# - Masses defined using 'ReadIso'
# - Method and basis not formatted by ASE
# - Basis file used instead of standard basis set.
positions = np.array([
[+0.000, +0.000, +0.000],
[+1.310, +0.000, +0.000],
[-0.160, +1.300, +0.000],
[+1.150, +1.300, +0.000],
[-0.394, -0.446, +1.031],
[-0.394, -0.446, -1.031],
[+1.545, +1.746, -1.031],
[+1.545, +1.746, +1.031],
])
masses = [None] * 8
masses[1] = 0.1134289259
atoms = Atoms('BH2BH4', positions=positions, masses=masses)
params = {
'chk': 'example.chk',
'nprocshared': '16',
'output_type': 't',
'b3lyp': None,
'gen': None,
'opt': 'tight, maxcyc=100',
'freq': None,
'integral': 'ultrafine',
'charge': 0,
'mult': 1,
'temperature': '300',
'pressure': '1.0',
'basisfile': '@basis-set-filename.gbs'
}
params['isolist'] = np.array(masses)
# Note that although the freq is set to ReadIso in the input text,
# here we have set it to None. This is because when reading in a file
# this option does not get saved to the calculator, it instead saves
# the temperature, pressure, scale and masses separately.
# Test reading the gaussian input
atoms_new = read_gaussian_in(fd_zmatrix, True)
atoms_new.set_masses(_get_iso_masses(atoms_new))
_check_atom_properties(atoms, atoms_new, params)
# Now we have tested reading the input, we can test writing it
# and reading it back in.
# ASE does not support reading in output files in 'terse' format, so
# it does not support writing input files with this setting. Therefore,
# the output type automatically set to P in the case that T is chosen
params['output_type'] = 'p'
_test_write_gaussian(atoms_new, params)
def _test_write_gaussian(atoms, params_expected, properties=None):
'''Writes atoms to gaussian input file, reads this back in and
checks that the resulting atoms object is equal to atoms and
the calculator has parameters params_expected'''
atoms.calc.label = 'gaussian_input_file'
out_file = atoms.calc.label + '.com'
atoms_expected = atoms.copy()
atoms.calc.write_input(atoms, properties=properties)
with open(out_file) as fd:
atoms_written = read_gaussian_in(fd, True)
if _get_iso_masses(atoms_written):
atoms_written.set_masses(_get_iso_masses(atoms_written))
_check_atom_properties(atoms_expected, atoms_written, params_expected)
def test_read_gaussian_in_command(fd_command_set):
# Expect error if 'command' is set in link0 section as this
# would try to set the command for the calculator:
with pytest.raises(TypeError):
read_gaussian_in(fd_command_set, True)
def test_read_gaussian_in_errors(fd_command_set, unsupported_file):
with pytest.raises(ParseError):
read_gaussian_in(unsupported_file, True)