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 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 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 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 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__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 test__create_base_directories():
engine = PyposmatEngine(filename_in=_pyposmat_config_fn,
filename_out='pyposmat.config.out')
engine.create_base_directories()
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:']
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__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__configure_qoi_manager():
engine = PyposmatEngine(filename_in=_pyposmat_config_fn,
filename_out='pyposmat.config.out')
engine.read_configuration_file()
engine.configure_qoi_manager()
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')
('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'])
def test__configure():
engine = PyposmatEngine(filename_in=_pyposmat_config_fn,
filename_out='pyposmat.config.out')
engine.configure()
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)
def test__init__():
engine = PyposmatEngine(filename_in=config_fn,
filename_out='pyposmat.config.out')
