def test__get_required_tasks(qoi):
_qoidb_filename_in = "pypospack.qoi.yaml"
from pypospack.qoi import QoiDatabase
from pypospack.qoi import QoiManager
_qoi_type = qoi
_qoi_structure = 'MgO_NaCl'
_qoi_name = "{}.{}".format(_qoi_structure, _qoi_type)
_qoi_structures = OrderedDict()
_qoi_structures['ideal'] = 'MgO_NaCl'
_qoidb_QoiDatabase = QoiDatabase()
_qoidb_QoiDatabase.add_qoi(qoi_name=_qoi_name,
qoi_type=_qoi_type,
structures=_qoi_structures,
target=4.5)
qoimanager = QoiManager(qoi_database=_qoidb_QoiDatabase, fullauto=False)
qoimanager.configure()
qoimanager.determine_tasks()
_task_type = 'lmps_min_all'
_qoi_task_name = "{}.{}".format(_qoi_structures['ideal'], _task_type)
assert isinstance(qoimanager.tasks, OrderedDict)
assert _qoi_task_name in qoimanager.tasks
assert qoimanager.tasks[_qoi_task_name]['task_type'] == _task_type
assert qoimanager.tasks[_qoi_task_name]['task_structure'] \
== _qoi_structures['ideal']
def test__read():
_yaml_filename_in = 'pypospack.qoi.yaml'
from pypospack.qoi import QoiDatabase
qoidb = QoiDatabase()
qoidb.read(filename=_yaml_filename_in)
assert isinstance(qoidb.qois, dict)
assert isinstance(qoidb.qois, OrderedDict)
def test__write():
_yaml_filename_in = 'pypospack.qoi.yaml'
_yaml_filename_out = 'pypospack.qoi.yaml.out'
from pypospack.qoi import QoiDatabase
qoidb = QoiDatabase()
qoidb.read(filename=_yaml_filename_in)
qoidb.write(filename=_yaml_filename_out)
qoidb.read(filename=_yaml_filename_out)
def test__init__with_QoiDatabase():
_qoidb_filename_in = "pypospack.qoi.yaml"
from pypospack.qoi import QoiDatabase
qoidb = QoiDatabase()
qoidb.read(filename=_qoidb_filename_in)
from pypospack.qoi import QoiManager
qoimanager = QoiManager(qoi_database=qoidb, fullauto=False)
assert isinstance(qoimanager.qoidb, QoiDatabase)
assert isinstance(qoimanager.qoidb.qoi_names, list)
assert isinstance(qoimanager.qoi_names, list)
def get_testing_set_Si():
testing_set = OrderedDict()
# Stillinger and Weber, Phys. Rev. B, v. 31, p. 5262, (1985)
testing_set['parameters'] = OrderedDict([('SiSiSi_epsilon', 2.1686),
('SiSiSi_sigma', 2.0951),
('SiSiSi_a', 1.80),
('SiSiSi_lambda', 21.0),
('SiSiSi_gamma', 1.20),
('SiSiSi_costheta0', -1 / 3),
('SiSiSi_A', 7.049556277),
('SiSiSi_B', 0.6022245584),
('SiSiSi_p', 4.0),
('SiSiSi_q', 0.0),
('SiSiSi_tol', 0.0)])
testing_set['structure_db'] = OrderedDict()
testing_set['structure_db']['structure_directory'] = os.path.join(
pypospack.utils.get_pypospack_root_directory(), 'data',
'Si__structure_db')
testing_set['structure_db']['structures'] = OrderedDict()
testing_set['structure_db']['structures']['Si_dia'] = 'Si_dia_unit.vasp'
testing_set['structure_db']['structures']['Si_vac'] = 'Si_dia_333_vac.vasp'
testing_set['qoi_db'] = QoiDatabase()
testing_set['qoi_db'].add_qoi(qoi_name='Si_dia.vac',
qoi_type='E_formation',
structures=OrderedDict([('defect', 'Si_vac'),
('ideal', 'Si_dia')
]),
target=3.6)
testing_set['tasks'] = OrderedDict()
testing_set['tasks']['Si_dia.lmps_min_all'] = OrderedDict([
('task_type', 'lmps_min_all'), ('task_structure', 'Si_dia')
])
testing_set['tasks']['Si_vac.lmps_min_pos'] = OrderedDict([
('task_type', 'lmps_min_pos'), ('task_structure', 'Si_vac'),
('bulk_structure', 'Si_dia')
])
return testing_set
def write_configuration_file(qoi_name,qoi_type,structures,target):
qoidb = QoiDatabase()
qoidb.add_qoi(
qoi_name=qoi_name,
qoi_type=qoi_type,
structures=structures,
target=target
)
potential = OrderedDict()
potential['potential_type'] = 'buckingham'
potential['symbols'] = ['Mg','O']
potential['cutoff_global'] = 10.0
structures = OrderedDict()
structures['structure_directory'] = 'test_PypospackEngine'
structures['structures'] = OrderedDict()
structures['structures']['MgO_NaCl'] = 'MgO_NaCl_unit.gga.relax.vasp'
configuration = PyposmatConfigurationFile()
configuration.qois = qoidb.qois
configuration.potential = potential
configuration.structures = structures
configuration.write(filename='pyposmat.config.in')
parameter_constraints['OO_C > 0'] = 'OO_C > 0.'
#------------------------------------------------------------------------------
# STRUCTURE DATABASE DEFINITION
#------------------------------------------------------------------------------
structure_db = OrderedDict()
structure_db['structure_directory'] = _pyposmat_structure_directory
structure_db['structures'] = OrderedDict()
structure_db['structures']['MgO_NaCl'] = 'MgO_NaCl_unit.vasp'
structure_db['structures']['MgO_NaCl_001s'] = 'MgO_NaCl_001s.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'
#------------------------------------------------------------------------------
# FITTING DATABASE
#------------------------------------------------------------------------------
qoi_db = QoiDatabase()
qoi_db.add_qoi(qoi_name="MgO_NaCl.a0",
qoi_type="a11_min_all",
structures=OrderedDict([('ideal', 'MgO_NaCl')]),
target=4.246)
qoi_db.add_qoi(qoi_name="MgO_NaCl.c11",
qoi_type="c11",
structures=OrderedDict([('ideal', 'MgO_NaCl')]),
target=277.0)
qoi_db.add_qoi(qoi_name="MgO_NaCl.c12",
qoi_type="c12",
structures=OrderedDict([('ideal', 'MgO_NaCl')]),
target=91.67)
qoi_db.add_qoi(qoi_name="MgO_NaCl.c44",
qoi_type="c44",
structures=OrderedDict([('ideal', 'MgO_NaCl')]),
MgO_LewisCatlow['potential']['potential_type'] = 'buckingham'
MgO_LewisCatlow['potential']['symbols'] = ['Mg', 'O']
MgO_LewisCatlow['parameters'] = OrderedDict()
MgO_LewisCatlow['parameters']['chrg_Mg'] = +2.0
MgO_LewisCatlow['parameters']['chrg_O'] = -2.0
MgO_LewisCatlow['parameters']['MgMg_A'] = 0.0
MgO_LewisCatlow['parameters']['MgMg_rho'] = 0.5
MgO_LewisCatlow['parameters']['MgMg_C'] = 0.0
MgO_LewisCatlow['parameters']['MgO_A'] = 821.6
MgO_LewisCatlow['parameters']['MgO_rho'] = 0.3242
MgO_LewisCatlow['parameters']['MgO_C'] = 0.0
MgO_LewisCatlow['parameters']['OO_A'] = 2274.00
MgO_LewisCatlow['parameters']['OO_rho'] = 0.1490
MgO_LewisCatlow['parameters']['OO_C'] = 27.88
MgO_qoi_db_gga = QoiDatabase()
MgO_qoi_db_gga.add_qoi(qoi_name='MgO_NaCl.a0',
qoi_type='a11_min_all',
structures=OrderedDict([('ideal', 'MgO_NaCl')]),
target=4.246)
MgO_qoi_db_gga.add_qoi(qoi_name='MgO_NaCl.c11',
qoi_type='c11',
structures=OrderedDict([('ideal', 'MgO_NaCl')]),
target=277.00)
MgO_qoi_db_gga.add_qoi(qoi_name='MgO_NaCl.c12',
qoi_type='c12',
structures=OrderedDict([('ideal', 'MgO_NaCl')]),
target=91.67)
MgO_qoi_db_gga.add_qoi(qoi_name='MgO_NaCl.c44',
qoi_type='c44',
structures=OrderedDict([('ideal', 'MgO_NaCl')]),
#------------------------------------------------------------------------------
# STRUCTURE DATABASE DEFINITION
#------------------------------------------------------------------------------
structure_db = OrderedDict()
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_prim'] = 'MgO_NaCl_prim.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'
#------------------------------------------------------------------------------
# FITTING DATABASE
#------------------------------------------------------------------------------
qoi_db = QoiDatabase()
qoi_db.add_qoi(qoi_name='MgO_NaCl.a0',
qoi_type='a11_min_all',
structures=OrderedDict([('ideal', 'MgO_NaCl')]),
target=4.246)
qoi_db.add_qoi(qoi_name='MgO_NaCl.c11',
qoi_type='c11',
structures=OrderedDict([('ideal', 'MgO_NaCl')]),
target=277.00)
qoi_db.add_qoi(qoi_name='MgO_NaCl.c12',
qoi_type='c12',
structures=OrderedDict([('ideal', 'MgO_NaCl')]),
target=91.67)
qoi_db.add_qoi(qoi_name='MgO_NaCl.c44',
qoi_type='c44',
structures=OrderedDict([('ideal', 'MgO_NaCl')]),
#MgO_parameter_constraints['OO_rho_gt_0'] = ['OO_rho > 0']
#MgO_parameter_constraints['OO_C_gt_0'] = ['OO_C > 0']
# <---------------- STRUCTURE DATABASE
Si_sw_structures = OrderedDict()
Si_sw_structures['structure_directory'] = 'test__PyposmatMonteCarloSampler'
Si_sw_structures['structures'] = OrderedDict()
Si_sw_structures['structures']['Si_dia'] = 'Si_dia_unit.vasp'
#<00--------------- QOI DATABASE
#Si reference database
# LDA-DFT reference data, originally from:
# Pizzagalli et al. Phil. Mag A (2008) A 83 1191
# Taken from table
# Pizzagalli et al. J Phys. Condens. Matter (2013) 055801
Si_sw_qoi_db = QoiDatabase()
# <----------------- STRUCTURAL PROPERTIES
Si_sw_qoi_db.add_qoi(qoi_name='Si_dia.Ecoh',
qoi_type='Ecoh_min_all',
structures=OrderedDict([('ideal', 'Si_dia')]),
target=-4.63)
Si_sw_qoi_db.add_qoi(qoi_name='Si_dia.a0',
qoi_type='a11_min_all',
structures=OrderedDict([('ideal', 'Si_dia')]),
target=5.43)
# <----------------- ELASTIC PROPERTIES
Si_sw_qoi_db.add_qoi(qoi_name='Si_dia.c11',
qoi_type='c11',
structures=OrderedDict([('ideal', 'Si_dia')]),
target=166.0)
Si_sw_qoi_db.add_qoi(qoi_name='Si_dia.c12',
def __init_QoiDatabase_from_OrderedDict(self, qoi_database_OrderedDict):
assert isinstance(qoi_database_OrderedDict, OrderedDict)
self.qoidb = QoiDatabase(qoi_database_OrderedDict)
def __init_QoiDatabase_from_file(self, qoi_database_filename):
assert isinstance(qoi_database_filename, str)
self.qoidb = QoiDatabase()
self.qoidb.read(filename=qoi_database_filename)
def __init_QoiDatabase_from_None(self):
self.qoidb = QoiDatabase()
from pypospack.task import TaskManager
from pypospack.qoi import QoiDatabase,QoiManager
from pypospack.qoi import StackingFaultEnergyCalculation
NiAl_eam__Mishin2009 = OrderedDict()
NiAl_eam__Mishin2009['potential_type'] = 'eam'
NiAl_eam__Mishin2009['symbols'] = ['Ni,Al']
NiAl_eam__Mishin2009['setfl_filename'] = os.path.join('potential_db','Mishin-Ni-Al-2009.eam.alloy')
NiAl_eam__Mishin2009['reference'] = 'Purja Pun and Y. Mishin (2009). Phil. Mag., 89(34-36)'
Ni_fcc_isf = OrderedDict()
Ni_fcc_isf['qoi_name'] = 'Ni_fcc.isf'
Ni_fcc_isf['qoi_type'] = 'E_stacking_fault'
Ni_fcc_isf['structures'] = OrderedDict([('defect','Ni_fcc_isf'),('ideal','Ni_fcc_111_unit')])
Ni_fcc_isf['target'] = 100.
Ni_qoi_db = QoiDatabase()
Ni_qoi_db.add_qoi(
qoi_name=Ni_fcc_isf['qoi_name'],
qoi_type=Ni_fcc_isf['qoi_type'],
structures=Ni_fcc_isf['structures'],
target=Ni_fcc_isf['target'])
Ni_structure_db = OrderedDict()
Ni_structure_db['structure_directory'] = 'structure_db'
Ni_structure_db['structures'] = OrderedDict()
Ni_structure_db['structures']['Ni_fcc_111_unit'] = 'Ni_fcc_111_unit.gga.relaxed.vasp'
Ni_structure_db['structures']['Ni_fcc_isf'] = 'Ni_fcc_isf.vasp'
Ni_structure_db['structures']['Ni_fcc_esf'] = 'Ni_fcc_esf.vasp'
Ni_structure_db['structures']['Ni_fcc_usf'] = 'Ni_fcc_usf.vasp'