def get_sample(calculation_path):
structure = Structure(file_path=Path.join(calculation_path, 'POSCAR'))
structure.shift_sites_so_first_atom_is_at_origin()
outcar = Outcar(file_path=Path.join(calculation_path, 'OUTCAR'))
lattice_information = structure.get_magnitudes_and_angles()
ideal_perovskite_structure = Perovskite(
supercell_dimensions=[1, 1, 1],
lattice=copy.deepcopy(structure.lattice),
species_list=structure.get_species_list())
displacement_vector = DisplacementVector.get_instance_from_displaced_structure_relative_to_reference_structure(
reference_structure=ideal_perovskite_structure,
displaced_structure=structure,
coordinate_mode='Cartesian')
energy = outcar.energy
forces = outcar.final_forces_list
stresses = outcar.final_stresses_list
volume = structure.lattice.get_volume() #in A^3
for z in range(len(stresses)):
stresses[z] /= volume
row_of_data = lattice_information + displacement_vector.to_list() + [
energy
] + forces + stresses
output_string = ' '.join([str(x) for x in row_of_data])
return row_of_data, output_string
def __init__(self, vasp_calculation_input_dictionary):
vasp_calculation_input_dictionary = copy.deepcopy(
vasp_calculation_input_dictionary)
vasp_calculation_input_dictionary = {
k.lower(): v
for k, v in vasp_calculation_input_dictionary.items()
} #enforce all keys lowercase
path = Path.clean(vasp_calculation_input_dictionary.pop('path'))
information_structure = None #used for number of nodes and potcar
if isinstance(vasp_calculation_input_dictionary['structure'],
Structure):
initial_structure = vasp_calculation_input_dictionary.pop(
'structure')
information_structure = initial_structure
contcar_path = None
else:
initial_structure = None
contcar_path = vasp_calculation_input_dictionary.pop('structure')
information_structure = Structure(contcar_path)
wavecar_path = vasp_calculation_input_dictionary.pop(
'wavecar_path'
) if 'wavecar_path' in vasp_calculation_input_dictionary else None
chargecar_path = vasp_calculation_input_dictionary.pop(
'chargecar_path'
) if 'chargecar_path' in vasp_calculation_input_dictionary else None
incar_template = vasp_calculation_input_dictionary.pop(
'incar_template'
) if 'incar_template' in vasp_calculation_input_dictionary else None
kpoints_scheme = vasp_calculation_input_dictionary.pop(
'kpoints_scheme'
) if 'kpoints_scheme' in vasp_calculation_input_dictionary else None
kpoints_list = [
int(x) for x in vasp_calculation_input_dictionary.pop(
'kpoints_list').split(' ')
] if ('kpoints_list' in vasp_calculation_input_dictionary
and vasp_calculation_input_dictionary['kpoints_list'] != None
) else None
potcar_type = vasp_calculation_input_dictionary.pop(
'potcar_type'
) if 'potcar_type' in vasp_calculation_input_dictionary else 'lda_paw'
vasp_code_type = vasp_calculation_input_dictionary.pop(
'vasp_code_type'
) if 'vasp_code_type' in vasp_calculation_input_dictionary else 'standard'
node_count = vasp_calculation_input_dictionary.pop(
'node_count'
) if 'node_count' in vasp_calculation_input_dictionary else None
use_mp_hubbard_u = vasp_calculation_input_dictionary.pop(
'use_mp_hubbard_u'
) if 'use_mp_hubbard_u' in vasp_calculation_input_dictionary else None
for file_path in [wavecar_path, chargecar_path]:
if file_path != None and not Path.exists(file_path):
print "Warning: Path " + str(
file_path) + " specified does not exist. Not using."
#raise Exception("Path " + str(file_path) + " specified does not exist.")
if kpoints_scheme != None and kpoints_list != None:
kpoints = Kpoints(scheme_string=kpoints_scheme,
subdivisions_list=kpoints_list)
if 'kspacing' in vasp_calculation_input_dictionary:
raise Exception(
"kpoints are being specified by more than one method.")
elif 'kspacing' not in vasp_calculation_input_dictionary:
raise Exception(
"If kpoints aren't explicitly defined through a scheme and a list, the kspacing tag must be present in the incar."
)
else:
kpoints = None
potcar = Potcar(elements_list=information_structure.get_species_list(),
calculation_type=potcar_type)
submission_script_file = QueueAdapter.get_submission_file()
if os.environ['QUEUE_ADAPTER_HOST'] != 'Savio':
if node_count == None:
submission_script_file = QueueAdapter.modify_number_of_cores_from_num_atoms(
submission_script_file, information_structure.site_count)
else:
submission_script_file = QueueAdapter.set_number_of_nodes(
submission_script_file, node_count)
submission_script_file = QueueAdapter.modify_submission_script(
submission_script_file, modification_key=vasp_code_type)
incar_modifiers = vasp_calculation_input_dictionary #whatever is left should only be incar modifiers - we popped all other keys
for key, value in incar_modifiers.items(
): #make sure there are no None values - these should not be put in INCAR
if value in [None, 'None']:
del incar_modifiers[key]
if 'encut' in incar_modifiers and (
0.1 < incar_modifiers['encut']) and (
incar_modifiers['encut'] <
10.0): #Should use this as a multiplier times enmax
enmax = potcar.get_enmax()
incar_modifiers['encut'] = int(incar_modifiers['encut'] * enmax)
if incar_template == 'static':
incar = IncarMaker.get_static_incar(
custom_parameters_dictionary=incar_modifiers)
elif incar_template == 'external_relaxation':
incar = IncarMaker.get_external_relaxation_incar(
custom_parameters_dictionary=incar_modifiers)
elif incar_template != None:
raise Exception("Incar template " + str(incar_template) +
" not valid")
else:
incar = Incar()
incar.modify_from_dictionary(incar_modifiers)
if 'lreal' not in incar:
if information_structure.site_count > 20:
incar['lreal'] = 'Auto'
else:
incar['lreal'] = False
if 'npar' not in incar:
if os.environ['QUEUE_ADAPTER_HOST'] == 'Savio':
incar['npar'] = 4
else:
incar['npar'] = QueueAdapter.get_optimal_npar(
submission_script_file)
elif incar['npar'] in ['Remove', 'remove']:
del incar['npar']
###################TEMPORARILY HARDCODED FOR PEROVSKITES##########################################
if use_mp_hubbard_u:
u_species = initial_structure.get_species_list()[1]
mp_hubbard_u_values = {
'Co': 3.32,
'Cr': 3.7,
'Fe': 5.3,
'Mn': 3.9,
'Mo': 4.38,
'Ni': 6.2,
'V': 3.25,
'W': 6.2
}
if u_species in mp_hubbard_u_values.keys():
u_value = mp_hubbard_u_values[u_species]
incar['LDAU'] = True
incar['LDAUJ'] = '0 0 0'
incar['LDAUL'] = '0 2 0'
incar['LDAUPRINT'] = 1
incar['LDAUTYPE'] = 2
incar['LDAUU'] = '0 ' + str(u_value) + ' 0'
incar['LMAXMIX'] = 4
incar['LORBIT'] = 11
super(VaspCalculationGenerator,
self).__init__(path=path,
initial_structure=initial_structure,
incar=incar,
kpoints=kpoints,
potcar=potcar,
submission_script_file=submission_script_file,
contcar_path=contcar_path,
wavecar_path=wavecar_path,
chargecar_path=chargecar_path)