def dftb_read_input(folder):
"""Read a DFTB+ output non-destructively.
Args:
directory (str): path to a directory to load DFTB+ results
Returns:
atoms (ase.Atoms): an atomic structure with the results attached in a
SinglePointCalculator
"""
atoms = io.read(os.path.join(folder, 'geo_end.gen'))
atoms.info['name'] = os.path.split(folder)[-1]
results_file = os.path.join(folder, "results.tag")
if os.path.isfile(results_file):
# DFTB+ was used to perform the optimisation
temp_file = os.path.join(folder, "results.tag.bak")
# We need to backup the results file here because
# .read_results() will remove the results file
with BackupFile(results_file, temp_file):
calc = Dftb(atoms=atoms)
calc.atoms_input = atoms
calc.directory = folder
calc.do_forces = True
try:
calc.read_results()
except:
# Failed for ANY reason
atoms.set_calculator(None)
return atoms
energy = calc.get_potential_energy()
forces = calc.get_forces()
charges = calc.get_charges(atoms)
calc = SinglePointCalculator(atoms,
energy=energy,
forces=forces,
charges=charges)
atoms.set_calculator(calc)
return atoms
def create_spinpol_dftbp_calculator(calc=None, param_set='3ob-3-1', kpts=None):
"""Create a calculator containing all necessary parameters for a DFTB+
SCC spin polarised calculation"""
from pymuonsuite.data.dftb_pars import DFTBArgs
if not isinstance(calc, Dftb):
calc = Dftb()
else:
calc = deepcopy(calc)
# A bit of a hack for the k-points
if kpts is not None:
kc = Dftb(kpts=kpts)
kargs = {k: v for k, v in kc.parameters.items() if 'KPoints' in k}
calc.parameters.update(kargs)
# Create the arguments
dargs = DFTBArgs(param_set)
# Make it spin polarised
try:
dargs.set_optional('spinpol.json', True)
except KeyError:
raise ValueError('DFTB+ parameter set does not allow spin polarised'
' calculations')
# Fix a few things, and add a spin on the muon
args = dargs.args
del (args['Hamiltonian_SpinPolarisation'])
args['Hamiltonian_SpinPolarisation_'] = 'Colinear'
args['Hamiltonian_SpinPolarisation_UnpairedElectrons'] = 1
args['Hamiltonian_SpinPolarisation_InitialSpins_'] = ''
args['Hamiltonian_SpinPolarisation_InitialSpins_Atoms'] = '-1'
args['Hamiltonian_SpinPolarisation_InitialSpins_SpinPerAtom'] = 1
calc.parameters.update(args)
calc.do_forces = True
return calc
def read(self, folder, sname=None, read_spinpol=False, read_phonons=False,
**kwargs):
''' Read a DFTB+ output non-destructively.
|
| Args:
| folder (str) : path to a directory to load DFTB+ results
| sname (str): name to label the atoms with and/or of the
| .phonons.pkl file to be read
| Returns:
| atoms (ase.Atoms): an atomic structure with the results
| attached in a SinglePointCalculator
'''
try:
with silence_stdio():
atoms = io.read(os.path.join(folder, 'geo_end.gen'))
except IOError:
raise IOError("ERROR: No geo_end.gen file found in {}."
.format(os.path.abspath(folder)))
except Exception as e:
raise IOError("ERROR: Could not read {file}, due to error: {error}"
.format(file='geo_end.gen', error=e))
if sname is None:
atoms.info['name'] = os.path.split(folder)[-1]
else:
atoms.info['name'] = sname
results_file = os.path.join(folder, "results.tag")
if os.path.isfile(results_file):
# DFTB+ was used to perform the optimisation
temp_file = os.path.join(folder, "results.tag.bak")
# We need to backup the results file here because
# .read_results() will remove the results file
with BackupFile(results_file, temp_file):
calc = Dftb(atoms=atoms)
calc.atoms_input = atoms
calc.directory = folder
calc.do_forces = True
calc.read_results()
energy = calc.get_potential_energy()
forces = calc.get_forces()
charges = calc.get_charges(atoms)
calc = SinglePointCalculator(atoms, energy=energy,
forces=forces, charges=charges)
atoms.calc = calc
if read_spinpol:
try:
pops = parse_spinpol_dftb(folder)
hfine = []
for i in range(len(atoms)):
hf = compute_hfine_mullpop(atoms, pops, self_i=i,
fermi=True, fermi_neigh=True)
hfine.append(hf)
atoms.set_array('hyperfine', np.array(hfine))
except (IndexError, IOError) as e:
raise IOError('Could not read hyperfine details due to error: '
'{0}'.format(e))
if read_phonons:
try:
if sname is not None:
phonon_source_file = os.path.join(folder, sname +
'.phonons.pkl')
else:
print("Phonons filename was not given, searching for any"
" .phonons.pkl file.")
phonon_source_file = glob.glob(
os.path.join(folder, '*.phonons.pkl'))[0]
self._read_dftb_phonons(atoms, phonon_source_file)
except IndexError:
raise IOError("No .phonons.pkl files found in {}."
.format(os.path.abspath(folder)))
except IOError:
raise IOError("{} could not be found."
.format(phonon_source_file))
except Exception as e:
raise IOError('Could not read {file} due to error: {error}'
.format(file=phonon_source_file, error=e))
return atoms
