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 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')
import pytest
from collections import OrderedDict
from pypospack.pyposmat import PyposmatConfigurationFile
from pypospack.qoi import QoiDatabase
import MgO
MgO_qoi_db = QoiDatabase()
MgO_qoi_db.add_qoi(qoi_name='MgO_NaCl.fr_a',
qoi_type='point_defect',
structures=OrderedDict([('defect', 'MgO_NaCl_fr_a'),
('ideal', 'MgO_NaCl')]),
target=10.978)
print(80 * '-')
print('{:^80}'.format('QUANTITIES OF INTEREST'))
print(80 * '-')
print(MgO_qoi_db.qois)
MgO_structure_db = OrderedDict()
MgO_structure_db['structure_directory'] = 'test__DefectFormationEnergy'
MgO_structure_db['structures'] = OrderedDict()
MgO_structure_db['structures']['MgO_NaCl'] = 'MgO_NaCl_unit.gga.relax.vasp'
MgO_structure_db['structures']['MgO_NaCl_fr_a'] = 'MgO_NaCl_fr_a.vasp'
print(80 * '-')
print('{:^80}'.format('STRUCTURE DATABASE'))
print(80 * '-')
print('Structure directory:{}'.format(MgO_structure_db['structure_directory']))
print(20 * '-' + ' ' + 59 * '-')
print('{:^20} {:^59}'.format('structure_name', 'structure_filename'))
#------------------------------------------------------------------------------
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')]),
target=144.01)
qoi_db.add_qoi(qoi_name='MgO_NaCl.B',
qoi_type='bulk_modulus',
structure_db['structures'][
'Al_fcc_111_unit'] = 'Al_fcc_111_unit.gga.relaxed.vasp'
structure_db['structures']['Al_fcc_100_s'] = 'Al_fcc_100_surf.vasp'
structure_db['structures']['Al_fcc_110_s'] = 'Al_fcc_110_surf.vasp'
structure_db['structures']['Al_fcc_111_s'] = 'Al_fcc_111_surf.vasp'
structure_db['structures']['Al_fcc_isf'] = 'Al_fcc_isf.vasp'
structure_db['structures']['Al_fcc_esf'] = 'Al_fcc_esf.vasp'
structure_db['structures']['Al_fcc_vac'] = 'Al_fcc_sc_333_vac.vasp'
structure_db['structures']['Al_fcc_o_int'] = 'Al_fcc_sc_333_o_int.vasp'
structure_db['structures']['Al_fcc_i_int'] = 'Al_fcc_sc_333_t_int.vasp'
#------------------------------------------------------------------------------
# FITTING DATABASE
#------------------------------------------------------------------------------
qoi_db = QoiDatabase()
qoi_db.add_qoi(qoi_name='Al_fcc.E_coh',
qoi_type='Ecoh_min_all',
structures=OrderedDict([('ideal', 'Al_fcc')]),
target=-3.36)
qoi_db.add_qoi(qoi_name='Al_fcc.a0',
qoi_type='a11_min_all',
structures=OrderedDict([('ideal', 'Al_fcc')]),
target=4.05)
qoi_db.add_qoi(qoi_name='Al_fcc.c11',
qoi_type='c11',
structures=OrderedDict([('ideal', 'Al_fcc')]),
target=114.)
qoi_db.add_qoi(qoi_name='Al_fcc.c12',
qoi_type='c12',
structures=OrderedDict([('ideal', 'Al_fcc')]),
target=62.)
qoi_db.add_qoi(qoi_name='Al_fcc.c44',
qoi_type='c44',
'Ni_fcc_111_unit'] = 'Ni_fcc_111_unit.gga.relaxed.vasp'
structure_db['structures']['Ni_fcc_100_s'] = 'Ni_fcc_100_surf.vasp'
structure_db['structures']['Ni_fcc_110_s'] = 'Ni_fcc_110_surf.vasp'
structure_db['structures']['Ni_fcc_111_s'] = 'Ni_fcc_111_surf.vasp'
structure_db['structures']['Ni_fcc_isf'] = 'Ni_fcc_isf.vasp'
structure_db['structures']['Ni_fcc_esf'] = 'Ni_fcc_esf.vasp'
structure_db['structures']['Ni_fcc_vac'] = 'Ni_fcc_sc_333_vac.vasp'
structure_db['structures']['Ni_fcc_o_int'] = 'Ni_fcc_sc_333_o_int.vasp'
structure_db['structures']['Ni_fcc_i_int'] = 'Ni_fcc_sc_333_t_int.vasp'
#------------------------------------------------------------------------------
# FITTING DATABASE
#------------------------------------------------------------------------------
qoi_db = QoiDatabase()
qoi_db.add_qoi(
qoi_name='Ni_fcc.E_coh',
qoi_type='Ecoh_min_all',
structures=OrderedDict([('ideal', 'Ni_fcc')]),
target=-4.45 # eV/atom
)
qoi_db.add_qoi(
qoi_name='Ni_fcc.a0',
qoi_type='a11_min_all',
structures=OrderedDict([('ideal', 'Ni_fcc')]),
target=3.52 # Angs
)
qoi_db.add_qoi(
qoi_name='Ni_fcc.c11',
qoi_type='c11',
structures=OrderedDict([('ideal', 'Ni_fcc')]),
target=261. #GPa
)
qoi_db.add_qoi(
Ni_structure_db['structures']['Ni_fcc_110'] = 'Ni_fcc_110.vasp'
Ni_structure_db['structures']['Ni_bcc'] = 'Ni_bcc.vasp'
Ni_structure_db['structures']['Ni_hcp'] = 'Ni_hcp.vasp'
Ni_structure_db['structures']['Ni_sc'] = 'Ni_sc.vasp'
Ni_structure_db['structures']['Ni_fcc_100_s'] = 'Ni_fcc_100_s.vasp'
Ni_structure_db['structures']['Ni_fcc_110_s'] = 'Ni_fcc_110_s.vasp'
Ni_structure_db['structures']['Ni_fcc_111_s'] = 'Ni_fcc_111_s.vasp'
Ni_structure_db['structures']['Ni_fcc_usf'] = 'Ni_fcc_usf.vasp'
Ni_structure_db['structures']['Ni_fcc_ssf'] = 'Ni_fcc_ssf.vasp'
#------------------------------------------------------------------------------
# FITTING DATABASE
#------------------------------------------------------------------------------
Ni_qoi_db = QoiDatabase()
Ni_qoi_db.add_qoi(qoi_name='Ni_fcc.E_coh',
qoi_type='Ecoh_min_all',
structures=OrderedDict([('ideal', 'Ni_fcc')]),
target=-5.7771)
Ni_qoi_db.add_qoi(qoi_name='Ni_fcc.a0',
qoi_type='a11_min_all',
structures=OrderedDict([('ideal', 'Ni_fcc')]),
target=3.508)
Ni_qoi_db.add_qoi(qoi_name='Ni_fcc.c11',
qoi_type='c11',
structures=OrderedDict([('ideal', 'Ni_fcc')]),
target=276.)
Ni_qoi_db.add_qoi(qoi_name='Ni_fcc.c12',
qoi_type='c12',
structures=OrderedDict([('ideal', 'Ni_fcc')]),
target=159.)
Ni_qoi_db.add_qoi(qoi_name='Ni_fcc.c44',
qoi_type='c44',
structure_db['structures'][
'Ni_fcc_111_unit'] = 'Ni_fcc_111_unit.gga.relaxed.vasp'
structure_db['structures']['Ni_fcc_100_s'] = 'Ni_fcc_100_surf.vasp'
structure_db['structures']['Ni_fcc_110_s'] = 'Ni_fcc_110_surf.vasp'
structure_db['structures']['Ni_fcc_111_s'] = 'Ni_fcc_111_surf.vasp'
structure_db['structures']['Ni_fcc_isf'] = 'Ni_fcc_isf.vasp'
structure_db['structures']['Ni_fcc_esf'] = 'Ni_fcc_esf.vasp'
structure_db['structures']['Ni_fcc_vac'] = 'Ni_fcc_sc_333_vac.vasp'
structure_db['structures']['Ni_fcc_o_int'] = 'Ni_fcc_sc_333_o_int.vasp'
structure_db['structures']['Ni_fcc_i_int'] = 'Ni_fcc_sc_333_t_int.vasp'
#------------------------------------------------------------------------------
# FITTING DATABASE
#------------------------------------------------------------------------------
qoi_db = QoiDatabase()
qoi_db.add_qoi(qoi_name='Ni_fcc.E_coh',
qoi_type='Ecoh_min_all',
structures=OrderedDict([('ideal', 'Ni_fcc')]),
target=-4.45)
qoi_db.add_qoi(qoi_name='Ni_fcc.a0',
qoi_type='a11_min_all',
structures=OrderedDict([('ideal', 'Ni_fcc')]),
target=3.52)
qoi_db.add_qoi(qoi_name='Ni_fcc.c11',
qoi_type='c11',
structures=OrderedDict([('ideal', 'Ni_fcc')]),
target=261.)
qoi_db.add_qoi(qoi_name='Ni_fcc.c12',
qoi_type='c12',
structures=OrderedDict([('ideal', 'Ni_fcc')]),
target=151.)
qoi_db.add_qoi(qoi_name='Ni_fcc.c44',
qoi_type='c44',
# refers to the structure file which is contained in
# Si_structures/Si_dia_unit.vasp
#-----------------------------------------------------------------------------
# DEFINE POTENTIAL FORMALISM
#-----------------------------------------------------------------------------
potential_formalism = OrderedDict()
potential_formalism['potential_type'] = 'stillingerweber'
potential_formalism['symbols'] = ['Si']
#potential_formalism['cutoff_global'] = 10.0
#-----------------------------------------------------------------------------
# QOI DEFINITIONS
#-----------------------------------------------------------------------------
qoi_db = QoiDatabase()
qoi_db.add_qoi(qoi_name='Si_dia.a0',
qoi_type='a11_min_all',
structures=OrderedDict([('ideal', 'Si_dia')]),
target=5.431)
qoi_db.add_qoi(qoi_name='Si_dia.c12',
qoi_type='c12',
structures=OrderedDict([('ideal', 'Si_dia')]),
target=75.00)
qoi_db.add_qoi(qoi_name='Si_dia.c44',
qoi_type='c44',
structures=OrderedDict([('ideal', 'Si_dia')]),
target=56.00)
qoi_db.add_qoi(qoi_name='Si_dia.B',
qoi_type='bulk_modulus',
structures=OrderedDict([('ideal', 'Si_dia')]),
target=100.00)
#<----------------- qoi performance constraints
qoi_constraints = OrderedDict()
structure_db['structures'][
'Al_fcc_111_unit'] = 'Al_fcc_111_unit.gga.relaxed.vasp'
structure_db['structures']['Al_fcc_100_s'] = 'Al_fcc_100_surf.vasp'
structure_db['structures']['Al_fcc_110_s'] = 'Al_fcc_110_surf.vasp'
structure_db['structures']['Al_fcc_111_s'] = 'Al_fcc_111_surf.vasp'
structure_db['structures']['Al_fcc_isf'] = 'Al_fcc_isf.vasp'
structure_db['structures']['Al_fcc_esf'] = 'Al_fcc_esf.vasp'
structure_db['structures']['Al_fcc_vac'] = 'Al_fcc_sc_333_vac.vasp'
structure_db['structures']['Al_fcc_o_int'] = 'Al_fcc_sc_333_o_int.vasp'
structure_db['structures']['Al_fcc_i_int'] = 'Al_fcc_sc_333_t_int.vasp'
#------------------------------------------------------------------------------
# FITTING DATABASE
#------------------------------------------------------------------------------
qoi_db = QoiDatabase()
qoi_db.add_qoi(qoi_name='Al_fcc.E_coh',
qoi_type='Ecoh_min_all',
structures=OrderedDict([('ideal', 'Al_fcc')]),
target=-3.36)
qoi_db.add_qoi(qoi_name='Al_fcc.a0',
qoi_type='a11_min_all',
structures=OrderedDict([('ideal', 'Al_fcc')]),
target=4.05)
#qoi_db.add_qoi(
# qoi_name='Al_fcc.c11',
# qoi_type='c11',
# structures=OrderedDict([('ideal','Al_fcc')]),
# target=114.)
#qoi_db.add_qoi(
# qoi_name='Al_fcc.c12',
# qoi_type='c12',
# structures=OrderedDict([('ideal','Al_fcc')]),
# target=62.)
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'
test_data = [
(NiAl_eam__Mishin2009,Ni_qoi_db,Ni_structure_db)
]
structure_db['structures']['Si_dia'] = 'Si_dia_unit.vasp'
structure_db['structures']['Si_vac'] = 'Si_dia_333_vac.vasp'
# in this case 'Si_dia' is the short name which the rest of the file
# refers to the structure file which is contained in
# Si_structures/Si_dia_unit.vasp
#-----------------------------------------------------------------------------
# QOI DEFINITIONS
#-----------------------------------------------------------------------------
# L. Pizzagalli et al, J. J. Phys.: Condens. Matter 25 (2013) 055801
# doi:10.1088/0953-8984/25/5/055801
# reference values from Table 2 and Table 3
qoi_db = QoiDatabase()
qoi_db.add_qoi(
qoi_name='Si_dia.E_coh',
qoi_type='Ecoh_min_all',
structures=OrderedDict([('ideal','Si_dia')]),
target=-4.63)
qoi_db.add_qoi(
qoi_name='Si_dia.a0',
qoi_type='a11_min_all',
structures=OrderedDict([('ideal','Si_dia')]),
target=5.43)
qoi_db.add_qoi(
qoi_name="Si_dia.c11",
qoi_type='c11',
structures=OrderedDict([('ideal','Si_dia')]),
target=166.)
qoi_db.add_qoi(
qoi_name='Si_dia.c12',
qoi_type='c12',
# 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_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.p11',
qoi_type='p_11_min_none',
structures=OrderedDict([('ideal', 'MgO_NaCl')]),
target=4.246)
#------------------------------------------------------------------------------
# QOI CONSTRAINTS
# QOI constraints are performed in the order they are iterated through in
# in the dictionary.
#
# If you want to implement new constraints, they should be implemented in
# pypospack.pyposmat.data.DataAnalyzer
# filter_by_qoi_err:
# key - the qoi_name as in the qoi_db
# value - the maximum allowable absolute error
# filter_by_pareto:
# filters out dominated points if set to True
#------------------------------------------------------------------------------
qoi_constraints = OrderedDict()
# 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_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='a1_min_all',
structures=OrderedDict([('ideal', 'MgO_NaCl')]),
target=4.246)
#------------------------------------------------------------------------------
# QOI CONSTRAINTS
# QOI constraints are performed in the order they are iterated through in
# in the dictionary.
#
# If you want to implement new constraints, they should be implemented in
# pypospack.pyposmat.data.DataAnalyzer
# filter_by_qoi_err:
# key - the qoi_name as in the qoi_db
# value - the maximum allowable absolute error
# filter_by_pareto:
# filters out dominated points if set to True
#------------------------------------------------------------------------------
qoi_constraints = OrderedDict()
from pypospack.qoi import QoiDatabase
from pypospack.qoi import QoiManager
from pypospack.qoi import PhaseOrderCalculation
potential= OrderedDict()
potential['potential_type'] = 'eam'
potential['symbols'] = ['Ni']
potential['setfl_filename'] = os.path.join(
pypospack.utils.get_pypospack_root_directory(),
'data/potentials/Ni__eam/Mishin-Ni-Al-2009.eam.alloy'
)
qoi_db = QoiDatabase()
qoi_db.add_qoi(
qoi_name='E_Ni_fcc_hcp',
qoi_type='phase_order',
structures=OrderedDict([('low','Ni_fcc'),('high','Ni_hcp')]),
target=0.24
)
structure_db = OrderedDict()
structure_db['structure_directory'] = os.path.join(
pypospack.utils.get_pypospack_root_directory(),
'data/Ni_structure_db')
structure_db['structures'] = OrderedDict()
structure_db['structures']['Ni_fcc'] = 'Ni_fcc_100_unit.gga.relaxed.vasp'
structure_db['structures']['Ni_hcp'] = 'Ni_hcp_ortho.vasp'
task_list = OrderedDict()
task_list['Ni_fcc.lmps_min_all'] = OrderedDict([
('task_type','lmps_min_all'),('task_structure','Ni_fcc')])
task_list['Ni_hcp.lmps_min_all'] = OrderedDict([
import pytest
from collections import OrderedDict
from pypospack.pyposmat.data import PyposmatConfigurationFile
from pypospack.qoi import QoiDatabase
from pypospack.qoi import ThermalExpansion
MgO_qoi_db = QoiDatabase()
MgO_qoi_db.add_qoi(qoi_name='MgO_NaCl.th_exp',
qoi_type='thermal_expansion_coefficient',
structures=OrderedDict([('ideal', 'MgO_NaCl')]),
target=0.,
qoi_options={
'temperature_min': 0,
'temperature_max': 1000,
'temperature_step': 100
})
print(MgO_qoi_db.to_string())
MgO_structure_db = OrderedDict()
MgO_structure_db[
'structure_directory'] = '../../../structure_db/MgO_structure_db'
MgO_structure_db['structures'] = OrderedDict()
MgO_structure_db['structures']['MgO_NaCl'] = 'MgO_NaCl_unit.gga.relax.vasp'
print(80 * '-')
print('{:^80}'.format('STRUCTURE DATABASE'))
print(80 * '-')
print('Structure directory:{}'.format(MgO_structure_db['structure_directory']))
print(20 * '-' + ' ' + 59 * '-')
print('{:^20} {:^59}'.format('structure_name', 'structure_filename'))
print(20 * '-' + ' ' + 59 * '-')
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')]),
target=144.01)
MgO_qoi_db_gga.add_qoi(qoi_name='MgO_NaCl.B',
qoi_type='bulk_modulus',
# <---------------- 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',
qoi_type='c12',
structures=OrderedDict([('ideal', 'Si_dia')]),
target=64.0)
Si_sw_qoi_db.add_qoi(qoi_name='Si_dia.c44',
from pypospack.pyposmat import PyposmatDataFile
from pypospack.pyposmat import PyposmatEngine
from pypospack.pyposmat import PyposmatConfigurationFile
#from pypospack.pyposmat import QoiDatabase
from pypospack.qoi import QoiDatabase
from pypospack.io.filesystem import OrderedDictYAMLLoader
import MgO
calc_elastic_properties = False
calc_point_defects = True
# <---------------- making a configuration file
MgO_qoi_db = QoiDatabase()
MgO_qoi_db.add_qoi(
qoi_name='MgO_NaCl.a0',
qoi_type='a11_min_all',
structures=OrderedDict([('ideal','MgO_NaCl')]),
target=4.246)
# <----------------- ELASTIC PROPERTIES
if calc_elastic_properties:
MgO_qoi_db.add_qoi(
qoi_name='MgO_NaCl.c11',
qoi_type='c11',
structures=OrderedDict([('ideal','MgO_NaCl')]),
target=277.00)
MgO_qoi_db.add_qoi(
qoi_name='MgO_NaCl.c12',
qoi_type='c12',
structures=OrderedDict([('ideal','MgO_NaCl')]),
target=91.67)
structure_db['structures'][
'Ni_fcc_111_unit'] = 'Ni_fcc_111_unit.gga.relaxed.vasp'
structure_db['structures']['Ni_fcc_100_s'] = 'Ni_fcc_100_surf.vasp'
structure_db['structures']['Ni_fcc_110_s'] = 'Ni_fcc_110_surf.vasp'
structure_db['structures']['Ni_fcc_111_s'] = 'Ni_fcc_111_surf.vasp'
structure_db['structures']['Ni_fcc_isf'] = 'Ni_fcc_isf.vasp'
structure_db['structures']['Ni_fcc_esf'] = 'Ni_fcc_esf.vasp'
structure_db['structures']['Ni_fcc_vac'] = 'Ni_fcc_sc_333_vac.vasp'
structure_db['structures']['Ni_fcc_o_int'] = 'Ni_fcc_sc_333_o_int.vasp'
structure_db['structures']['Ni_fcc_i_int'] = 'Ni_fcc_sc_333_t_int.vasp'
#------------------------------------------------------------------------------
# FITTING DATABASE
#------------------------------------------------------------------------------
qoi_db = QoiDatabase()
qoi_db.add_qoi(qoi_name='Ni_fcc.E_coh',
qoi_type='Ecoh_min_all',
structures=OrderedDict([('ideal', 'Ni_fcc')]),
target=-5.7771)
qoi_db.add_qoi(qoi_name='Ni_fcc.a0',
qoi_type='a11_min_all',
structures=OrderedDict([('ideal', 'Ni_fcc')]),
target=3.508)
qoi_db.add_qoi(qoi_name='Ni_fcc.c11',
qoi_type='c11',
structures=OrderedDict([('ideal', 'Ni_fcc')]),
target=276.)
qoi_db.add_qoi(qoi_name='Ni_fcc.c12',
qoi_type='c12',
structures=OrderedDict([('ideal', 'Ni_fcc')]),
target=159.)
qoi_db.add_qoi(qoi_name='Ni_fcc.c44',
qoi_type='c44',
import MgO
calc_elastic_properties = False
calc_point_defects = True
# <---------------- making a configuration file
MgO_qoi_db = QoiDatabase()
#MgO_qoi_db.add_qoi(
# qoi_name='MgO_NaCl.a0',
# qoi_type='a11_min_all',
# structures=OrderedDict([('ideal','MgO_NaCl')]),
# target=4.246)
# <----------------- ELASTIC PROPERTIES
if calc_elastic_properties:
MgO_qoi_db.add_qoi(qoi_name='MgO_NaCl.c11',
qoi_type='c11',
structures=OrderedDict([('ideal', 'MgO_NaCl')]),
target=277.00)
MgO_qoi_db.add_qoi(qoi_name='MgO_NaCl.c12',
qoi_type='c12',
structures=OrderedDict([('ideal', 'MgO_NaCl')]),
target=91.67)
MgO_qoi_db.add_qoi(qoi_name='MgO_NaCl.c44',
qoi_type='c44',
structures=OrderedDict([('ideal', 'MgO_NaCl')]),
target=144.01)
MgO_qoi_db.add_qoi(qoi_name='MgO_NaCl.B',
qoi_type='bulk_modulus',
structures=OrderedDict([('ideal', 'MgO_NaCl')]),
target=153.45)
MgO_qoi_db.add_qoi(qoi_name='MgO_NaCl.G',
qoi_type='shear_modulus',
potential_definition['potential_type'] = 'eam'
potential_definition['symbols'] = ['Ni']
potential_definition['setfl_filename'] = os.path.join(
'potential_db',
'Mishin-Ni-Al-2009.eam.alloy'
)
#potential_definition['setfl_filename'] = os.path.join(
# 'potential_db',
# 'Ni99.eam.alloy'
# )
qoi_db = QoiDatabase()
qoi_db.add_qoi(
qoi_name='Ni_fcc.esf',
qoi_type='E_stacking_fault',
structures=OrderedDict([
('defect','Ni_fcc_esf'),
('ideal','Ni_fcc_111_unit')]),
target=7.80e-3)
qoi_db.add_qoi(
qoi_name='Ni_fcc.isf',
qoi_type='E_stacking_fault',
structures=OrderedDict([
('defect','Ni_fcc_isf'),
('ideal','Ni_fcc_111_unit')]),
target=1.45e-02)
qoi_db.add_qoi(
qoi_name='Ni_fcc.usf',
qoi_type='E_stacking_fault',
structures=OrderedDict([
('defect','Ni_fcc_usf'),
structure_db['structures'] = OrderedDict()
structure_db['structures']['Si_dia'] = 'Si_dia_unit.vasp'
structure_db['structures']['Si_vac'] = 'Si_dia_333_vac.vasp'
# in this case 'Si_dia' is the short name which the rest of the file
# refers to the structure file which is contained in
# Si_structures/Si_dia_unit.vasp
#-----------------------------------------------------------------------------
# QOI DEFINITIONS
#-----------------------------------------------------------------------------
# L. Pizzagalli et al, J. J. Phys.: Condens. Matter 25 (2013) 055801
# doi:10.1088/0953-8984/25/5/055801
# reference values from Table 2 and Table 3
qoi_db = QoiDatabase()
qoi_db.add_qoi(qoi_name='Si_dia.a0',
qoi_type='a11_min_all',
structures=OrderedDict([('ideal', 'Si_dia')]),
target=5.43)
qoi_db.add_qoi(qoi_name="Si_dia.c11",
qoi_type='c11',
structures=OrderedDict([('ideal', 'Si_dia')]),
target=166.)
qoi_db.add_qoi(qoi_name='Si_dia.c12',
qoi_type='c12',
structures=OrderedDict([('ideal', 'Si_dia')]),
target=64.00)
qoi_db.add_qoi(qoi_name='Si_dia.c44',
qoi_type='c44',
structures=OrderedDict([('ideal', 'Si_dia')]),
target=80.00)
qoi_db.add_qoi(qoi_name='Si_dia.B',
qoi_type='bulk_modulus',
structure_db['structures'][
'Ni_fcc_111_unit'] = 'Ni_fcc_111_unit.gga.relaxed.vasp'
structure_db['structures']['Ni_fcc_100_s'] = 'Ni_fcc_100_surf.vasp'
structure_db['structures']['Ni_fcc_110_s'] = 'Ni_fcc_110_surf.vasp'
structure_db['structures']['Ni_fcc_111_s'] = 'Ni_fcc_111_surf.vasp'
structure_db['structures']['Ni_fcc_isf'] = 'Ni_fcc_isf.vasp'
structure_db['structures']['Ni_fcc_esf'] = 'Ni_fcc_esf.vasp'
structure_db['structures']['Ni_fcc_vac'] = 'Ni_fcc_sc_333_vac.vasp'
structure_db['structures']['Ni_fcc_o_int'] = 'Ni_fcc_sc_333_o_int.vasp'
structure_db['structures']['Ni_fcc_i_int'] = 'Ni_fcc_sc_333_t_int.vasp'
#------------------------------------------------------------------------------
# FITTING DATABASE
#------------------------------------------------------------------------------
qoi_db = QoiDatabase()
qoi_db.add_qoi(qoi_name='Ni_fcc.E_coh',
qoi_type='Ecoh_min_all',
structures=OrderedDict([('ideal', 'Ni_fcc')]),
target=-4.45)
qoi_db.add_qoi(qoi_name='Ni_fcc.a0',
qoi_type='a11_min_all',
structures=OrderedDict([('ideal', 'Ni_fcc')]),
target=3.52)
#qoi_db.add_qoi(
# qoi_name='Ni_fcc.c11',
# qoi_type='c11',
# structures=OrderedDict([('ideal','Ni_fcc')]),
# target=261.)
#qoi_db.add_qoi(
# qoi_name='Ni_fcc.c12',
# qoi_type='c12',
# structures=OrderedDict([('ideal','Ni_fcc')]),
# target=151.)
# 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')]),
target=144.01)
qoi_db.add_qoi(qoi_name="MgO_NaCl.fr_a",
qoi_type="E_formation",
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)
if __name__ == '__main__':
qoi_db = QoiDatabase()
qoi_db.add_qoi(\
name = 'MgO_NaCl.a0',
qoi_type = 'a0_min_all',
structures = ['MgO_NaCl'],
target = 4.246)
qoi_db.add_qoi(\
name = 'MgO_NaCl.c11',
qoi_type = 'c11',
structures = ['MgO_NaCl'],
target = 277.00)
qoi_db.add_qoi(\
name = 'MgO_NaCl.c12',
qoi_type = 'c12',
structures = ['MgO_NaCl'],
target = 91.67)
qoi_db.add_qoi(\
name = 'MgO_NaCl.c44',
qoi_type = 'c44',
