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)
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)
# make new configuration file from the old configuration file
from pypospack.pyposmat.data import PyposmatConfigurationFile
_o_config = PyposmatConfigurationFile()
_o_config.read(filename=_pyposmat_config_fn)
pn1 = 'p_NiNi_phi0'
pn2 = 'e_Ni_F0'
# change to normal distribution for parameters of interest
for pn in [pn1,pn2]:
_o_config.configuration['sampling_dist'][pn] = ['normal',{'mu':_best_params[pn],'sigma':_std_params[pn]}]
# change the rest of the free parameters to static
for pn in _o_config.free_parameter_names:
if pn != pn1 and pn != pn2:
_o_config.configuration['sampling_dist'][pn] = ['equals',_best_params[pn]]
_pyposmat_config_fn = os.path.join('data','pyposmat.config.in')
# change the first iteration type to parametric
_o_config.configuration['sampling_type'][0]['type'] = 'parametric'
for k,v in _o_config.configuration['sampling_type'].items():
if type(k) is int:
_o_config.configuration['sampling_type'][k]['n_samples'] = _n_samples
print(_o_config.configuration['sampling_type'])
print("new pyposmat configuration file in:{}".format(_pyposmat_config_fn))
_o_config.write(filename=_pyposmat_config_fn)
_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
#--------------------------------------------------------------------------
data_directory = 'data'
pyposmat_data_filename = 'pyposmat.results.9.out'
pyposmat_configuration_filename = 'pyposmat.config.in'
data_analyzer = PyposmatDataAnalyzer()
data_analyzer.read_configuration_file(
filename=pyposmat_configuration_filename)
data_analyzer.read_data_file(
from pypospack.pyposmat.data import PyposmatDataFile
from pypospack.pyposmat.data import PyposmatDataAnalyzer
import pypospack.pareto as pareto
if __name__ == "__main__":
import Ni__eam__morse_exp_fs_0 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
configuration.write(filename='pyposmat.config.in')
data_directory = 'data__morse_exp_fs'
pyposmat_data_filename = 'pyposmat.results.4.out'
pyposmat_configuration_filename = 'pyposmat.config.in'
data_analyzer = PyposmatDataAnalyzer()
data_analyzer.read_configuration_file(
filename=pyposmat_configuration_filename)
data_analyzer.read_data_file(
filename=os.path.join(data_directory, pyposmat_data_filename))
#data_analyzer.filter_performance_requirements()
#data_analyzer.calculate_pareto_set()
data_analyzer.write_kde_file(filename='pyposmat.kde.out')
exit()
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()
import os,shutil,sys
import numpy as np
from mpi4py import MPI
from pypospack.pyposmat.data import PyposmatConfigurationFile
from pypospack.pyposmat.data import PyposmatDataAnalyzer
from pypospack.pyposmat.engines import PyposmatIterativeSampler
if __name__ == "__main__":
import Ni__eam__morse_exp_universal as Ni_eam
_configuration_filename = 'pyposmat.config.in'
#------------------------------------------------------------------------------
# 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=_configuration_filename)
Ni_eam_configuration.read(filename=_configuration_filename)
pyposmat_app = PyposmatIterativeSampler(
configuration_filename = _configuration_filename)
pyposmat_app.read_configuration_file()
pyposmat_app.run_all()