def dev__defect_calculation():
print(80*'-')
print('{:^80}'.format('defect_calculation'))
print(80*'-')
simulation_dir = 'rank_test'
testing_set = testing_set_Si_sw.get_testing_set_Si()
configuration = PyposmatConfigurationFile()
configuration.qois = testing_set['qoi_db'].qois
configuration.structures = testing_set['structure_db']
qoi_manager = QoiManager(
qoi_database=configuration.qois,
fullauto=False
)
qoi_manager.configure()
qoi_manager.determine_tasks()
print('qoi_manager.tasks')
print(len('qoi_manager.tasks')*'-')
for k,v in qoi_manager.tasks.items():
print(k,v)
task_manager = TaskManager(base_directory=simulation_dir)
task_manager.configure(
tasks = qoi_manager.tasks,
structures = testing_set['structure_db']
)
task_managger.evaluate_tasks()
qoi_manager.calculate_qois(
task_results=task_manager.results
)
qoi_manager.qois
def write_configuration_file(filename='pyposmat.config'):
configuration = PyposmatConfigurationFile()
configuration.qois = qoi_db.qois
configuration.qoi_constraints = qoi_constraints
configuration.structures = structure_db
configuration.potential = potential_formalism
configuration.sampling_type = sampling
configuration.sampling_distribution = parameter_distribution
configuration.sampling_constraints = parameter_constraints
configuration.write(filename=filename)
def write_configuration_file(
filename,
qois,
potential_definition,
structures):
configuration = PyposmatConfigurationFile()
configuration.qois = qois
configuration.potential = potential_definition
configuration.sampling_distribution = parameter_distribution
configuration.structures = structures
configuration.write(filename=filename)
def write_configuration_file(config_fn):
import Si_sw
#------------------------------------------------------------------------------
# WRITE CONFIGURATION FILE
#------------------------------------------------------------------------------
Si_sw_configuration = PyposmatConfigurationFile()
Si_sw_configuration.qois = Si_sw.Si_sw_qoi_db.qois
Si_sw_configuration.potential = Si_sw.Si_sw_potential
Si_sw_configuration.structures = Si_sw.Si_sw_structures
Si_sw_configuration.sampling_type = Si_sw.Si_sw_sampling
Si_sw_configuration.sampling_distribution = Si_sw.Si_sw_parameter_distribution
Si_sw_configuration.write(filename=config_fn)
Si_sw_configuration.read(filename=config_fn)
def write_configuration_file(config_fn):
"""
Args:
config_fn(str): the name of the configuration file
"""
from pypospack.pyposmat.data import PyposmatDataFile
import Ni__eam__morse_exp_universal as Ni__eam
Ni_eam_configuration = PyposmatConfigurationFile()
Ni_eam_configuration.qois = Ni_eam.Ni_qoi_db.qois
Ni_eam_configuration.potential = Ni_eam.Ni_eam_potential_formalism
Ni_eam_configuration.structures = Ni_eam.Ni_structure_db
Ni_eam_configuration.sampling_type = Ni_eam.Ni_eam_sampling
Ni_eam_configuration.sampling_distribution =Ni_eam.Ni_eam_parameter_distribution
Ni_eam_configuration.write(filename=config_fn)
Ni_eam_configuration.read(filename=config_fn)
def test__calculate_stacking_fault(potential,qoi_db,structure_db):
simulation_directory = 'rank_test'
configuration = PyposmatConfigurationFile()
configuration.qois = qoi_db.qois
configuration.structures = structure_db
qoi_manager = QoiManager(qoi_database=configuration.qois,fullauto=False)
qoi_manager.configure()
qoi_manager.determine_tasks()
task_manager = TaskManager(base_directory='rank_test')
task_manager.configure(tasks=qoi_manager.tasks,structures=structure_db)
task_manager.evaluate_tasks(parameters=potential,potential=potential)
qoi_manager.calculate_qois(
task_results=task_manager.results)
qoi_manager.qois
qoi_db.add_qoi(qoi_name="MgO_NaCl.G",
qoi_type='shear_modulus',
structures=OrderedDict([('ideal', 'MgO_NaCl')]),
target=92.66)
qoi_db.add_qoi(qoi_name="MgO_NaCl.001s",
qoi_type="E_surface",
structures=OrderedDict([
('slab', 'MgO_NaCl_001s'),
('ideal', 'MgO_NaCl'),
], ),
target=0.05595)
qoi_constraints = OrderedDict()
#------------------------------------------------------------------------------
# WRITE CONFIGURATION FILE
# this is currently creating a race condition, where the file is being written
# by multiple ranks to the same location.
#------------------------------------------------------------------------------
if __name__ == '__main__':
from pypospack.pyposmat.data import PyposmatConfigurationFile
pyposmat_filename_in = 'pyposmat.config.in'
configuration = PyposmatConfigurationFile()
configuration.qois = qoi_db.qois
configuration.qoi_constraints = qoi_constraints
configuration.structures = structure_db
configuration.potential = potential_formalism
configuration.sampling_type = sampling
configuration.sampling_distribution = parameter_distribution
configuration.sampling_constraints = parameter_constraints
configuration.write(filename=pyposmat_filename_in)
'structure_directory'] = '../../../structure_db/MgO_structure_db'
MgO_structure_db['structures'] = OrderedDict()
MgO_structure_db['structures']['MgO_NaCl'] = 'MgO_NaCl_unit.gga.relax.vasp'
print(80 * '-')
print('{:^80}'.format('STRUCTURE DATABASE'))
print(80 * '-')
print('Structure directory:{}'.format(MgO_structure_db['structure_directory']))
print(20 * '-' + ' ' + 59 * '-')
print('{:^20} {:^59}'.format('structure_name', 'structure_filename'))
print(20 * '-' + ' ' + 59 * '-')
for k, v in MgO_structure_db['structures'].items():
print('{:<20} {:<59}'.format(k, v))
MgO_configuration = PyposmatConfigurationFile()
MgO_configuration.qois = MgO_qoi_db.qois
MgO_configuration.structures = MgO_structure_db
_qoi_name = 'MgO_NaCl.thermal_expansion'
_structures = OrderedDict([('ideal', 'MgO_NaCl')])
qoi = ThermalExpansion(qoi_name=_qoi_name, structures=_structures)
qoi.determine_tasks()
print(80 * '-')
print('{:^80}'.format('TASKS DATABASE'))
print(80 * '-')
max_len_task_name = 0
max_len_task_type = 0
for k, v in qoi.tasks.items():
max_len_task_name = max(max_len_task_name, len(k))
import os, copy
import numpy as np
from pypospack.pyposmat.data import PyposmatConfigurationFile
from pypospack.pyposmat.data import PyposmatDataFile
from pypospack.pyposmat.data import PyposmatDataAnalyzer
import pypospack.pareto as pareto
if __name__ == "__main__":
_configuration_filename = 'pyposmat.config.in'
#--------------------------------------------------------------------------
# DEFINE CONFIGURATION FILED
#--------------------------------------------------------------------------
import Si_sw as config
configuration = PyposmatConfigurationFile()
configuration.qois = config.qoi_db.qois
configuration.qoi_constraints = config.qoi_constraints
configuration.structures = config.structure_db
configuration.potential = config.potential_formalism
configuration.sampling_type = config.sampling
configuration.sampling_distribution = config.parameter_distribution
configuration.sampling_constraints = config.parameter_constraints
#<------------- write configuration file
configuration.write(filename=_configuration_filename)
#--------------------------------------------------------------------------
# TEST CONFIGURATION FILE
#--------------------------------------------------------------------------
configuration.read(filename=_configuration_filename)
#--------------------------------------------------------------------------
# ANALYZE DATA
s = [80 * '-']
s += ['{:^80}'.format('ERROR_NAMES')]
s += [80 * '-']
s += [p for p in _error_names]
self.log("\n".join(s))
if __name__ == "__main__":
import Ni__eam__morse_exp_universal as Ni_eam
#------------------------------------------------------------------------------
# WRITE CONFIGURATION FILE
#------------------------------------------------------------------------------
Ni_eam_configuration = PyposmatConfigurationFile()
Ni_eam_configuration.qois = Ni_eam.Ni_qoi_db.qois
Ni_eam_configuration.potential = Ni_eam.Ni_eam_potential_formalism
Ni_eam_configuration.structures = Ni_eam.Ni_structure_db
Ni_eam_configuration.sampling_type = Ni_eam.Ni_eam_sampling
Ni_eam_configuration.sampling_distribution = Ni_eam.Ni_eam_parameter_distribution
Ni_eam_configuration.write(filename='pypospack.config.in')
Ni_eam_configuration.read(filename='pypospack.config.in')
pypospack_filename_in = 'pypospack.config.in'
pyposmat_app = PyposmatIterativeSampler(
configuration_filename=pypospack_filename_in)
pyposmat_app.read_configuration_file()
#pyposmat_app.read_configuration_file(filename=pyposmat_configuration_filename)
pyposmat_app.run_all()