def convert_single_structure(cell_file, param_file, directory="."):
atoms = io.read(cell_file)
io.write(os.path.join(directory, "geo_end.gen"), atoms)
with open(param_file, 'r') as stream:
castep_params = yaml.load(stream)
dftb_params = param_schema.validate({})
# get castep parameters
for castep_name, dftb_name in CASTEP_to_DFTB_map.items():
if castep_name in castep_params:
dftb_params[dftb_name] = castep_params[castep_name]
# get k-points from cell file
k_points = map(int, atoms.calc.cell.kpoints_mp_grid.value.split())
dargs = DFTBArgs(dftb_params['dftb_set'])
custom_species = atoms.get_array('castep_custom_species')
muon_index = np.where(custom_species == dftb_params['mu_symbol'])[0][0]
# Add muon mass
args = dargs.args
args['Driver_'] = 'ConjugateGradient'
args['Driver_Masses_'] = ''
args['Driver_Masses_Mass_'] = ''
args['Driver_Masses_Mass_Atoms'] = '{}'.format(muon_index)
args['Driver_Masses_Mass_MassPerAtom [amu]'] = '0.1138'
args['Driver_MaxSteps'] = dftb_params['geom_steps']
args['Driver_MaxForceComponent [eV/AA]'] = dftb_params['geom_force_tol']
calc = Dftb(atoms=atoms, kpts=k_points, run_manyDftb_steps=True, **args)
calc.write_dftb_in(os.path.join(directory, "dftb_in.hsd"))
def write_dftb_in(self, filename):
if self.read_chg and os.path.exists('charges.bin'):
read_charges = 'Yes'
else:
read_charges = 'No'
self.parameters['Hamiltonian_ReadInitialCharges'] = read_charges
Dftb.write_dftb_in(self, filename)
