def test__send_results_to_the_qoi_manager():
engine = PyposmatEngine(filename_in=config_fn,
filename_out='pyposmat.config.out')
engine.configure()
engine.task_manager.evaluate_tasks(
parameters=parameters, potential=engine.configuration.potential)
engine.qoi_manager.calculate_qois(task_results=engine.task_manager.results)
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__create_base_directories():
engine = PyposmatEngine(filename_in=config_fn,
filename_out='pyposmat.config.out')
engine.create_base_directories()
assert all([os.path.isdir(d) for d in simulation_directories])
cleanup_simulation_directories()
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 __init__(self,
filename_in='pyposmat.config.in',
filename_out='pyposmat.results.out',
o_log=None,
mpi_rank=None,
mpi_size=None,
base_directory=None):
"""Additional attributes are set by the base class :obj:PyposmatEngine
Args:
filename_in (str) - path of the configuration file
filename_out (str) - path of the output file
o_log (PyposmatLogFile) - if type(o_log) is a string, then the string is treated as a path in which to log information to. If type(o_log) is PyposmatLogFile then it is set as an attribute for the refernce.
mpi_rank (int)
mpi_size (int)
base_directory (str,optional): Either the relative or full path which provides a
unique drive addressing space for simultaneously running simulations.
Attributes:
mpi_rank (int) - this is passed in
mpi_size (int) - this is passed in
pyposmat_data_in_filename (str) - the path of the datafile to read in
pyposmat_data_out_filename (str) - the path of the datafile to write simulation results to
"""
assert isinstance(filename_in, str)
assert isinstance(filename_out, str)
assert type(base_directory) in [str, type(None)]
PyposmatEngine.__init__(self,
filename_in=filename_in,
filename_out=filename_out,
base_directory=base_directory,
fullauto=False)
if mpi_rank is None:
self.mpi_rank = 0
else:
self.mpi_rank = mpi_rank
if mpi_size is None:
self.mpi_size = 1
else:
self.mpi_size = mpi_size
assert self.mpi_rank < self.mpi_size
self.mpi_rank = mpi_rank
self.mpi_size = mpi_size
self.pyposmat_data_in_filename = None
self.pyposmat_data_out_filename = filename_out
self.pyposmat_badparameters_filename = 'pyposmat.badparameters.out'
try:
self.configure_logger(o_log)
except TypeError as e:
m = "Unable to to configure obj_log based on attribute log:{}".format(
str(o_log))
raise TypeError(m)
def test__initialize_w_filenames():
engine = PyposmatEngine(filename_in=config_fn,
filename_out='pyposmat.config.out')
engine.configure()
for d in simulation_directories:
assert os.path.isdir(d)
cleanup_simulation_directories()
def __init__(self,
config_fn='pyposmat.config.in',
data_in_fn='pyposmat.results.in',
data_out_fn='pyposmat.results.out',
mpi_rank = None,
mpi_size=None,
o_log = None,
log_to_stdout=True,
base_directory = None,
fullauto=True):
self.DEBUG = False
self.configuration = None
self.datafile_in = None
self.datafile_out = None
self.mpi_rank = None
self.mpi_size = None
self.qoi_mananger = None
self.task_manager = None
PyposmatEngine.__init__(self,
filename_in=config_fn,
filename_out=data_out_fn,
base_directory=base_directory,
fullauto=fullauto)
self.configuration_fn = config_fn
self.datafile_in_fn = data_in_fn
self.datafile_out_fn = data_out_fn
self.pyposmat_badparameters_filename = 'pyposmat.badparameters.out'
self.configuration = None
self.datafile = None
self.subselect_df = None
self.reference_potentials = None
self.qoi_validation_names = None
self.error_validation_names = None
self.normed_error_validation_names = None
self.qoi_validation_target = None
self.obj_log = None
self.log_to_stdout = None
self.initialize_mpi_information(mpi_rank=mpi_rank,
mpi_size=mpi_size)
self.configure_logger(o_log=o_log,
log_to_stdout=log_to_stdout)
if fullauto is True:
self.read_configuration_file(filename=self.configuration_fn)
self.read_datafile_in(filename=data_in_fn)
self.configure_datafile_out(filename=data_out_fn)
def test__evaluate_tasks_through_the_task_mananager():
engine = PyposmatEngine(filename_in=config_fn,
filename_out='pyposmat.config.out')
engine.configure()
assert type(parameters) is OrderedDict
assert type(engine.configuration.potential) is OrderedDict
engine.task_manager.evaluate_tasks(
parameters=parameters, potential=engine.configuration.potential)
assert type(engine.task_manager.results) is OrderedDict
def test__configure_task_manager():
engine = PyposmatEngine(filename_in=config_fn,
filename_out='pyposmat.config.out')
engine.create_base_directories()
engine.read_configuration_file()
engine.configure_qoi_manager()
engine.configure_task_manager()
from pypospack.task import TaskManager
assert type(engine.task_manager) is TaskManager
cleanup_simulation_directories()
def test__evaluate_parameter_set():
engine = PyposmatEngine(filename_in=config_fn,
filename_out='pyposmat.config.out')
engine.configure()
results = engine.evaluate_parameter_set(parameters=parameters)
assert 'parameters' in results
assert 'qois' in results
assert type(results['parameters']) is OrderedDict
assert type(results['qois']) is OrderedDict
assert all([v is not None for k, v in results['parameters'].items()])
assert all([v is not None for k, v in results['qois'].items()])
def configure_qoi_manager(self,qois=None,use_fitting_qois=True,use_testing_qois=False):
if qois is not None:
_qois = copy.deepcopy(qois)
else:
_qois = OrderedDict()
if use_fitting_qois:
for k,v in self.configuration.qois.items():
_qois[k]=v
if use_testing_qois:
for k,v in self.configuration.qois_validation.items():
_qois[k]=v
PyposmatEngine.configure_qoi_manager(self,_qois)
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__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()
from pypospack.pyposmat.engines import PyposmatEngine
from pypospack.pyposmat.data import PyposmatDataFile
from pypospack.pyposmat.data import PyposmatConfigurationFile
# from pypospack.qoi import QoiManager
# from pypospack.task import TaskManager
filename_config = 'pypospack.config.in'
write_configuration_file(
filename=filename_config,
qois=qoi_db.qois,
potential_definition=potential_definition,
structures=structures)
#Ni_configuration = PyposmatConfigurationFile()
#Ni_configuration.qois = Ni_qoi_db.qois
#Ni_configuration.potential = potential_definition
#Ni_configuration.structures = Ni_structures
#Ni_configuration.write(filename='pypospack.config.in')
#Ni_configuration.read(filename='pypospack.config.in')
engine = PyposmatEngine(
filename_in = 'pypospack.config.in',
filename_out = 'pypospack.config.out')
engine.configure()
_parameters = potential_parameters
results = engine.evaluate_parameter_set(parameters=_parameters)
print(results)
('SiSiSi_a', 1.927303534824485),
('SiSiSi_lambda', 12.109230909182934),
('SiSiSi_gamma', 2.242334213331301),
('SiSiSi_costheta0',
-0.3333333333333333),
('SiSiSi_A', 19.19755654803364),
('SiSiSi_B', 0.16452955359488666),
('SiSiSi_p', 4.313046208558489),
('SiSiSi_q', 0.7433313641477534),
('SiSiSi_tol', 0.0)])
def cleanup(testing_set):
import shutil
if os.path.exists(testing_set['base_directory']):
if os.path.isdir(testing_set['base_directory']):
shutil.rmtree(testing_set['base_directory'])
elif os.path.isfile(testing_set['base_directory']):
os.remove(testing_set['base_directory'])
else:
raise ValueError('path:{}'.format(testing_set['base_directory']))
if __name__ == "__main__":
cleanup(testing_set)
o = PyposmatEngine(filename_in=testing_set['config_fn'],
base_directory=testing_set['base_directory'])
o.configure()
o.evaluate_parameter_set(parameters=testing_set['parameters'])
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)
def test__configure():
engine = PyposmatEngine(filename_in=_pyposmat_config_fn,
filename_out='pyposmat.config.out')
engine.configure()
parameters=parameters, potential=engine.configuration.potential)
assert type(engine.task_manager.results) is OrderedDict
def test__send_results_to_the_qoi_manager():
engine = PyposmatEngine(filename_in=config_fn,
filename_out='pyposmat.config.out')
engine.configure()
engine.task_manager.evaluate_tasks(
parameters=parameters, potential=engine.configuration.potential)
engine.qoi_manager.calculate_qois(task_results=engine.task_manager.results)
if __name__ == "__main__":
engine = PyposmatEngine(filename_in=config_fn,
filename_out='pyposmat.config.out')
engine.configure()
results = engine.evaluate_parameter_set(parameters=parameters)
print(results)
if False:
#print_parameters(parameters=parameters)
m = [80 * '=', '{:^80}'.format('Potential Description'), 80 * '=']
m += ['potential_description']
for k, v in engine.configuration.potential.items():
m += ['\t{} = {}'.format(k, v)]
m += ['parameters']
m += ['\t{} = {}'.format(k, v) for k, v in parameters.items()]
m += [80 * '=', '{:80}'.format('Evaluate Parameter Set'), 80 * '=']
engine.task_manager.evaluate_tasks(
parameters=parameters, potential=engine.configuration.potential)
m += ['engine.task_manager.results:']
def test__create_base_directories():
engine = PyposmatEngine(filename_in=_pyposmat_config_fn,
filename_out='pyposmat.config.out')
engine.create_base_directories()
def configure_task_manager(self):
PyposmatEngine.configure_task_manager(self)
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')
Ni_eam_parameters = OrderedDict()
Ni_eam_parameters['p_NiNi_D0'] = 0.001114
Ni_eam_parameters['p_NiNi_a'] = 3.429506
Ni_eam_parameters['p_NiNi_r0'] = 2.6813
Ni_eam_parameters['d_Ni_rho0'] = 10.0
Ni_eam_parameters['d_Ni_beta'] = 5.0
Ni_eam_parameters['d_Ni_r0'] = 2.0
Ni_eam_parameters['e_Ni_F0'] = 4.10341782e-3
Ni_eam_parameters['e_Ni_p'] = 8.96274624
Ni_eam_parameters['e_Ni_q'] = 8.95940869
Ni_eam_parameters['e_Ni_F1'] = -3.09
_structure_directory = 'test_PypospackEngine'
Ni_structures = OrderedDict()
Ni_structures['Ni_fcc_unit'] = os.path.join(
_structure_directory,
'Ni_fcc_unit.gga.relax.vasp')
Ni_pypospack_config = OrderedDict()
Ni_pypospack_config['qoi_info'] = Ni_qoi
Ni_pypospack_config['structures'] = Ni_structures
_pypospack_root_directory = pypospack.utils.get_pypospack_root_directory()
_pyposmat_config_fn = os.path.join(_pypospack_root_directory,'data','MgO_pareto_data','pyposmat.config.in')
engine = PyposmatEngine(
filename_in = _pyposmat_config_fn,
filename_out = 'pypospack.config.out')
engine.configure()
def test__configure():
engine = PyposmatEngine(filename_in=config_fn,
filename_out='pyposmat.config.out')
engine.configure()
cleanup_simulation_directories()
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__evaluate_parameter_set():
engine = PyposmatEngine(filename_in=config_fn,
filename_out='pyposmat.config.out')
engine.configure()
results = engine.evaluate_parameter_set(parameters=parameters)
cleanup_simulation_directories()
def test__init__():
engine = PyposmatEngine(filename_in=config_fn,
filename_out='pyposmat.config.out')
import os
from collections import OrderedDict
import pypospack.utils
from pypospack.pyposmat.engines import PyposmatEngine
from pypospack.pyposmat.data import PyposmatDataFile
_pypospack_root_directory = pypospack.utils.get_pypospack_root_directory()
_pyposmat_config_fn = os.path.join(_pypospack_root_directory, 'data',
'MgO_pareto_data', 'pyposmat.config.in')
engine = PyposmatEngine(filename_in=_pyposmat_config_fn,
filename_out='pyposmat.config.out')
engine.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()
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)
