def test__read_configuration_file():
engine = PyposmatEngine(filename_in=_pyposmat_config_fn,
filename_out='pyposmat.config.out')
engine.read_configuration_file()
assert isinstance(engine.configuration, PyposmatConfigurationFile)
assert engine.configuration.qois is not None
def read_configuration_file(self, filename=None):
PyposmatEngine.read_configuration_file(self, filename=filename)
# self.structure_directory = self.configuration.structures['structure_directory']
self.n_iterations = self.configuration.sampling_type['n_iterations']
self.parameter_names = [
p for p in self.configuration.sampling_distribution
]
self.qoi_names = [k for k in self.configuration.qois]
self.error_names = ['{}.err'.format(k) for k in self.qoi_names]
self.parameter_distribution_definition =\
self.configuration.sampling_distribution
try:
self.free_parameter_names = [
k for k, v in self.parameter_distribution_definition.items()
if v[0] != 'equals'
]
except KeyError as e:
print(self.parameter_distribution_definition.items())
raise
if self.configuration.sampling_constraints is not None:
self.parameter_constraints = copy.deepcopy(
self.configuration.sampling_constraints)
else:
self.parameter_constraints = OrderedDict()
self.constrained_parameter_names = []
for p in self.parameter_names:
if p not in self.free_parameter_names:
self.constrained_parameter_names.append(p)
def test__configure():
# this test are the submethods in the configure() method
engine = PyposmatEngine(filename_in=_pyposmat_config_fn,
filename_out='pyposmat.config.out')
engine.create_base_directories()
engine.read_configuration_file()
engine.configure_qoi_manager()
engine.configure_task_manager()
def test__read_configuration_file():
engine = PyposmatEngine(filename_in=config_fn,
filename_out='pyposmat.config.out')
engine.create_base_directories()
engine.read_configuration_file()
from pypospack.pyposmat.data import PyposmatConfigurationFile
assert type(engine.configuration) is PyposmatConfigurationFile
cleanup_simulation_directories()
def test__configure_qoi_manager():
engine = PyposmatEngine(filename_in=config_fn,
filename_out='pyposmat.config.out')
engine.create_base_directories()
engine.read_configuration_file()
engine.configure_qoi_manager()
from pypospack.qoi import QoiManager
assert type(engine.qoi_manager) is QoiManager
cleanup_simulation_directories()
def read_configuration_file(self,filename=None):
PyposmatEngine.read_configuration_file(self,filename=filename)
# does this have to be removed?
# self.structure_directory = self.configuration.structures['structure_directory']
if self.DEBUG:
if os.path.isdir(self.structure_directory):
msg = "[OK] structure_directory:".format(self.structure_directory)
self.__log(msg)
else:
msg = "[FAIL] structure_directory:".format(self.structure_directory)
raise PyposmatEngineError(msg)
# set name arrays for validation qois
self.qoi_validation_names = self.configuration.qoi_validation_names
self.error_validation_names = self.configuration.error_validation_names
self.normed_error_validation_names = self.configuration.normed_error_validation_names
# set dictionaries for qoi targets
self.qoi_validation_targets = self.configuration.qoi_validation_targets
# set dictionary for reference potentials
self.reference_potentials = self.configuration.reference_potentials
def test__configure_qoi_manager():
engine = PyposmatEngine(filename_in=_pyposmat_config_fn,
filename_out='pyposmat.config.out')
engine.read_configuration_file()
engine.configure_qoi_manager()
def test__configure():
# this test are the submethods in the configure() method
engine = PyposmatEngine(filename_in=_pyposmat_config_fn,
filename_out='pyposmat.config.out')
engine.create_base_directories()
engine.read_configuration_file()
engine.configure_qoi_manager()
engine.configure_task_manager()
if __name__ == "__main__":
engine = PyposmatEngine(filename_in=_pyposmat_config_fn,
filename_out='pyposmat.config.out')
engine.read_configuration_file()
#print(engine.configuration)
#print(engine.configuration.read(filename=_pyposmat_config_fn))
print(engine.configuration.configuration)
if False:
print("structure_directory:{}".format(engine.structure_directory))
print("structures")
for k, v in engine.structures['structures'].items():
print(k, v)
from pypospack.potentials.MgO import MgO_LewisCatlow
_parameters = MgO_LewisCatlow['parameters']
_results = engine.evaluate_parameter_set(parameters=_parameters)
print(80 * '-')
from pypospack.exceptions import LammpsSimulationError
filename_in = "pypospack.config.in"
filename_out = "pypospack.results.out"
a0 = 3.52
r0 = 1 / (2**0.5) * a0
parameters = OrderedDict()
parameters['p_NiNi_phi0'] = 1.0
parameters['p_NiNi_gamma'] = 2.0
parameters['p_NiNi_r0'] = r0
parameters['d_Ni_rho0'] = 1.0
parameters['d_Ni_beta'] = 4.0
parameters['d_Ni_r0'] = r0
parameters['e_Ni_latticetype'] = 'fcc'
parameters['e_Ni_ecoh'] = -4.45
parameters['e_Ni_B'] = 188.
parameters['e_Ni_a0'] = a0
if __name__ == "__main__":
engine = PyposmatEngine(filename_in=filename_in, filename_out=filename_out)
engine.read_configuration_file(
filename=os.path.join('data', 'pyposmat.config.in'))
engine.configure_qoi_manager()
engine.configure_task_manager()
try:
engine.evaluate_parameter_set(parameters=parameters)
except LammpsSimulationError as e:
print('lammps_simulation_error')
