from pypospack.task.lammps import LammpsSimulationError
from pypospack.task.task_manager import PypospackTaskManagerError
import scipy.stats
import Ni__eam__morse_exp_universal as Ni_eam
filename_out = 'pypospack.results.out'
#------------------------------------------------------------------------------
# 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')
# <---------------- end make configuration file
filename_in = 'pypospack.config.in'
filename_out = 'pypospack.results.out'
engine = PyposmatMonteCarloSampler(filename_in=filename_in,
filename_out=filename_out)
# <---------------- printout for debugging purposes
print('base_directory:{}'.format(engine.base_directory))
print('input_filename:{}'.format(engine.pyposmat_filename_in))
print('output_filename:{}'.format(engine.pyposmat_filename_out))
# <---------------- the steps of engine.configure() tested individually
from mpi4py import MPI
from pypospack.pyposmat import PyposmatConfigurationFile
from pypospack.pyposmat import PyposmatIterativeSampler
from pypospack.pyposmat import PyposmatDataFile
if __name__ == "__main__":
import Ni__eam__morse_exp_fs as config
#------------------------------------------------------------------------------
# WRITE CONFIGURATION FILE
#------------------------------------------------------------------------------
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='pypospack.config.in')
configuration.read(filename='pypospack.config.in')
import argparse
arg_parser = argparse.ArgumentParser()
arg_parser.add_argument('-i',
'--input',
type=str,
help="input file to be processed")
args = vars(arg_parser.parse_args())
filename = args['input']
structure_db['structure_directory'] = 'structure_db'
structure_db['structures'] = OrderedDict()
structure_db['structures']['MgO_NaCl'] = 'MgO_NaCl_unit.gga.relax.vasp'
structure_db['structures']['MgO_NaCl_fr_a'] = 'MgO_NaCl_333_fr_a.vasp'
structure_db['structures']['MgO_NaCl_fr_c'] = 'MgO_NaCl_333_fr_c.vasp'
structure_db['structures']['MgO_NaCl_sch'] = 'MgO_NaCl_333_sch.vasp'
structure_db['structures']['MgO_NaCl_001s'] = 'MgO_NaCl_001s.vasp'
#------------------------------------------------------------------------------
# WRITE CONFIGURATION FILE
#------------------------------------------------------------------------------
configuration = PyposmatConfigurationFile()
configuration.qois = qoi_db.qois
configuration.potential = potential_formalism
configuration.structures = structure_db
configuration.sampling_type = parameter_sampling
configuration.sampling_distribution = parameter_distribution
configuration.parameter_constraints = parameter_constraints
configuration.qoi_constraints = qoi_constraints
configuration.write(filename='pypospack.config.in')
configuration.read(filename='pypospack.config.in')
# <---------------- end make configuration file
filename_in='pypospack.config.in'
filename_out='pypospack.results.out'
engine = PyposmatMonteCarloSampler(
filename_in=filename_in,
filename_out=filename_out)
# <---------------- printout for debugging purposes
print('base_directory:{}'.format(engine.base_directory))
print('input_filename:{}'.format(engine.pyposmat_filename_in))
Si_sw_structures = OrderedDict()
Si_sw_structures['structure_directory'] = 'test__PyposmatMonteCarloSampler'
Si_sw_structures['structures'] = OrderedDict()
Si_sw_structures['structures']['Si'] = 'Si_dia_unit.vasp'
Si_sw_structures['structures']['Si_vac'] = 'Si_vac_333.vasp'
#------------------------------------------------------------------------------
# WRITE CONFIGURATION FILE
#------------------------------------------------------------------------------
Si_sw_configuration = PyposmatConfigurationFile()
Si_sw_configuration.qois = Si_sw_qoi_db.qois
Si_sw_configuration.potential = Si_sw_potential
Si_sw_configuration.structures = Si_sw_structures
Si_sw_configuration.sampling_type = sampling
Si_sw_configuration.sampling_distribution = Si_sw_param_dist
Si_sw_configuration.write(filename='pypospack.config.in')
Si_sw_configuration.read(filename='pypospack.config.in')
# <---------------- end make configuration file
filename_in='pypospack.config.in'
filename_out='pypospack.results.out'
engine = PyposmatMonteCarloSampler(
filename_in=filename_in,
filename_out=filename_out)
# <---------------- printout for debugging purposes
print('base_directory:{}'.format(engine.base_directory))
print('input_filename:{}'.format(engine.pyposmat_filename_in))
print('output_filename:{}'.format(engine.pyposmat_filename_out))
plt.close('all')
f, ax = plt.subplots()
ax.hist(data, normed=1)
f.savefig(dst_file)
if __name__ == "__main__":
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.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_param_dist
Si_sw_configuration.write(filename='pypospack.config.in')
Si_sw_configuration.read(filename='pypospack.config.in')
pypospack_filename_in = 'pypospack.config.in'
datafile_filename = os.path.join('data', 'pyposmat.kde.2.out')
datafile = PyposmatDataFile(filename=datafile_filename)
datafile.read()
histogram_dir = 'histograms'
if os.path.isdir(histogram_dir):
shutil.rmtree(histogram_dir)
os.mkdir(histogram_dir)