def dev__defect_calculation():
print(80*'-')
print('{:^80}'.format('defect_calculation'))
print(80*'-')
simulation_dir = 'rank_test'
testing_set = testing_set_Si_sw.get_testing_set_Si()
configuration = PyposmatConfigurationFile()
configuration.qois = testing_set['qoi_db'].qois
configuration.structures = testing_set['structure_db']
qoi_manager = QoiManager(
qoi_database=configuration.qois,
fullauto=False
)
qoi_manager.configure()
qoi_manager.determine_tasks()
print('qoi_manager.tasks')
print(len('qoi_manager.tasks')*'-')
for k,v in qoi_manager.tasks.items():
print(k,v)
task_manager = TaskManager(base_directory=simulation_dir)
task_manager.configure(
tasks = qoi_manager.tasks,
structures = testing_set['structure_db']
)
task_managger.evaluate_tasks()
qoi_manager.calculate_qois(
task_results=task_manager.results
)
qoi_manager.qois
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__calculate_stacking_fault(potential,qoi_db,structure_db):
simulation_directory = 'rank_test'
configuration = PyposmatConfigurationFile()
configuration.qois = qoi_db.qois
configuration.structures = structure_db
qoi_manager = QoiManager(qoi_database=configuration.qois,fullauto=False)
qoi_manager.configure()
qoi_manager.determine_tasks()
task_manager = TaskManager(base_directory='rank_test')
task_manager.configure(tasks=qoi_manager.tasks,structures=structure_db)
task_manager.evaluate_tasks(parameters=potential,potential=potential)
qoi_manager.calculate_qois(
task_results=task_manager.results)
qoi_manager.qois
print(80*'-')
print('{:^80}'.format('STRUCTURE DATABASE'))
print(80*'-')
print('Structure directory:{}'.format(structure_db['structure_directory']))
print(20*'-' + ' ' + 59*'-')
print('{:^20} {:^59}'.format('structure_name','structure_filename'))
print(20*'-' + ' ' + 59*'-')
for k,v in structure_db['structures'].items():
print('{:<20} {:<59}'.format(k,v))
qoi_manager = QoiManager(
qoi_database=configuration.qois,
fullauto=False)
qoi_manager.configure()
qoi_manager.determine_tasks()
print(80*'-')
print('{:^80}'.format('TASKS DATABASE'))
print(80*'-')
for k,v in qoi_manager.tasks.items():
tsk_name = k
tsk_type = v['task_type']
tsk_structure = v['task_structure']
print(tsk_name,tsk_type,tsk_structure,tsk_structure)
task_manager = TaskManager(base_directory='rank_test')
task_manager.configure(
tasks=qoi_manager.tasks,
structures=structure_db
)
class TestQoi(object):
def __init__(self,qoi_db,structure_db,potential):
self.configuration = None
self.qoi_manager = None
self.task_directory = 'rank_test'
self.task_manager = None
self.setup_configuration_file(qoi_db=qoi_db,structure_db=structure_db)
self.check_structure_db(structure_db)
self.configure_qoi_manager(qoi_database=self.configuration.qois)
self.check_task_database()
self.configure_task_manager(task_directory=self.task_directory,
tasks=self.qoi_manager.tasks,
structures=self.configuration.structures)
self.evaluate_tasks(parameters=potential,
potential=potential)
self.check_task_results(task_results=self.task_manager.results)
self.calculate_qois()
self.check_qoi_results()
def setup_configuration_file(self,qoi_db,structure_db):
print('setup_configuration_file')
self.configuration = PyposmatConfigurationFile()
self.configuration.qois = qoi_db.qois
self.configuration.structures = structure_db
def check_structure_db(self,structure_db):
print('check_structures')
structure_directory = self.configuration.structures['structure_directory']
assert os.path.isdir(structure_directory)
for structure_name,structure_fn in self.configuration.structures['structures'].items():
print(structure_name,structure_fn)
assert os.path.isfile(os.path.join(structure_directory,structure_fn))
def configure_qoi_manager(self,qoi_database):
self.qoi_manager = QoiManager(qoi_database=qoi_database,fullauto=False)
self.qoi_manager.configure()
self.qoi_manager.determine_tasks()
def check_task_database(self):
print('{} {} {}'.format('task_name','task_type','task_structure'))
for k,v in self.qoi_manager.tasks.items():
task_name = k
task_type = v['task_type']
task_structure = v['task_structure']
print('{} {} {}'.format(task_name,task_type,task_structure))
assert k in task_list
assert task_type == task_list[k]['task_type']
assert task_structure == task_list[k]['task_structure']
assert len(self.qoi_manager.tasks) == len(task_list)
def configure_task_manager(self,task_directory,tasks,structures):
self.task_manager = TaskManager(base_directory=task_directory)
self.task_manager.configure(tasks=tasks,
structures=structures)
def evaluate_tasks(self,parameters,potential):
self.task_manager.evaluate_tasks(parameters=parameters,potential=potential)
def check_task_results(self,task_results):
table_col_names = ['name','value']
table_rows = []
for k,v in task_results.items():
table_rows.append([str(k),str(v)])
print('\n'.join([','.join(v) for v in table_rows]))
def calculate_qois(self):
self.qoi_manager.calculate_qois(task_results=self.task_manager.results)
def check_qoi_results(self):
print(self.qoi_manager.qois)