def test__on_ready():
symbols = configuration['potential']['symbols']
task_name = configuration['task']['task_name']
task_directory = configuration['task']['task_directory']
structure_filename = configuration['structure']['filename']
restart = False
fullauto = False
cleanup(task_directory)
assert not os.path.exists(task_directory)
assert 'potential' in configuration
assert 'parameters' in configuration
#<--- code setup
from pypospack.task.lammps import LammpsSimulation
lammps_task = LammpsSimulation(task_name=task_name,
task_directory=task_directory,
structure_filename=structure_filename)
lammps_task.on_init(configuration)
lammps_task.on_config(configuration)
#<--- test setup
assert os.path.exists(task_directory)
assert lammps_task.status == 'READY'
#<--- code being testing
lammps_task.on_ready(configuration)
#<--- expected behavior
lammps_setfl_filename = '{}.eam.alloy'.format("".join(symbols))
#<--- check to see if the configuration dictionaries were setup correctly
assert type(lammps_task.conditions_INIT) == OrderedDict
assert type(lammps_task.conditions_CONFIG) == OrderedDict
assert type(lammps_task.conditions_READY) == OrderedDict
assert type(lammps_task.conditions_RUNNING) == OrderedDict
assert type(lammps_task.conditions_POST) == OrderedDict
assert type(lammps_task.conditions_FINISHED) == OrderedDict
assert os.path.isfile(os.path.join(task_directory, lammps_setfl_filename))
assert lammps_task.conditions_INIT['task_directory_created']
assert all([v for k, v in lammps_task.conditions_INIT.items()]) == True
assert lammps_task.conditions_CONFIG['potential_initialized'] == True
assert lammps_task.conditions_CONFIG['parameters_processed'] == True
assert all([v for k, v in lammps_task.conditions_CONFIG.items()]) == True
assert all([v for k, v in lammps_task.conditions_READY.items()]) == True
assert lammps_task.conditions_RUNNING['process_initialized'] == True
assert all([v for k, v in lammps_task.conditions_RUNNING.items()]) == True
assert lammps_task.conditions_POST['process_finished'] == False
assert all([v for k, v in lammps_task.conditions_POST.items()]) == False
assert all([v
for k, v in lammps_task.conditions_FINISHED.items()]) == False
def test__on_init():
symbols = configuration['potential']['symbols']
task_name = configuration['task']['task_name']
task_directory = configuration['task']['task_directory']
structure_filename = configuration['structure']['filename']
restart = False
fullauto = False
cleanup(task_directory)
assert not os.path.exists(task_directory)
assert 'potential' in configuration
assert 'parameters' in configuration
#<--- code setup
from pypospack.task.lammps import LammpsSimulation
lammps_task = LammpsSimulation(task_name=task_name,
task_directory=task_directory,
structure_filename=structure_filename)
#<--- test setup
assert os.path.exists(task_directory)
assert lammps_task.status == 'INIT'
assert lammps_task.potential is None
#<--- code being testing
lammps_task.on_init(configuration)
#<--- expected behavior
lammps_setfl_filename = '{}.eam.alloy'.format("".join(symbols))
#<--- check directory structure
assert os.path.isdir(os.path.abspath(lammps_task.task_directory))
#<--- check attributes
assert lammps_task.task_name == task_name
assert os.path.abspath(lammps_task.task_directory)\
== os.path.abspath(task_directory)
assert lammps_task.task_type == 'single_point'
assert lammps_task.lammps_bin == os.environ['LAMMPS_BIN']
assert lammps_task.lammps_input_filename == 'lammps.in'
assert lammps_task.lammps_output_filename == 'lammps.out'
assert lammps_task.lammps_structure_filename == 'lammps.structure'
assert lammps_task.lammps_setfl_filename is None
assert isinstance(lammps_task.potential, potential.Potential)
assert lammps_task.structure_filename == structure_filename
assert isinstance(lammps_task.structure, crystal.SimulationCell)
assert lammps_task.process is None
if len(lammps_task.conditions_READY) == 0:
assert lammps_task.status == 'READY'
else:
assert lammps_task.status == 'CONFIG'
def test__on_ready():
task_name = configuration['task']['task_name']
task_directory = configuration['task']['task_directory']
structure_filename = configuration['structure']['filename']
restart = False
fullauto = False
cleanup(task_directory)
assert not os.path.exists(task_directory)
assert 'potential' in configuration
assert 'parameters' in configuration
#<--- code setup
from pypospack.task.lammps import LammpsSimulation
lammps_task = LammpsSimulation(task_name=task_name,
task_directory=task_directory,
structure_filename=structure_filename)
lammps_task.on_init(configuration)
lammps_task.on_config(configuration)
#<--- test setup
assert os.path.exists(task_directory)
assert lammps_task.status == 'READY'
#<--- code being testing
lammps_task.on_ready(configuration)
assert type(lammps_task.conditions_INIT) == OrderedDict
assert type(lammps_task.conditions_CONFIG) == OrderedDict
assert type(lammps_task.conditions_READY) == OrderedDict
assert type(lammps_task.conditions_RUNNING) == OrderedDict
assert type(lammps_task.conditions_POST) == OrderedDict
assert type(lammps_task.conditions_FINISHED) == OrderedDict
assert lammps_task.conditions_INIT['task_directory_created']
assert all([v for k, v in lammps_task.conditions_INIT.items()]) == True
assert lammps_task.conditions_CONFIG['potential_initialized'] == True
assert lammps_task.conditions_CONFIG['parameters_processed'] == True
assert all([v for k, v in lammps_task.conditions_CONFIG.items()]) == True
assert all([v for k, v in lammps_task.conditions_READY.items()]) == True
#assert lammps_task.conditions_RUNNING['process_initialized']== False
#assert all([v for k,v in lammps_task.conditions_RUNNING.items()]) == False
assert lammps_task.conditions_POST['process_finished'] == False
assert all([v for k, v in lammps_task.conditions_POST.items()]) == False
assert all([v
for k, v in lammps_task.conditions_FINISHED.items()]) == False
def on_init(self, configuration=None, results=None):
LammpsSimulation.on_init(self, configuration=configuration)
if 'bulk_structure' in configuration:
self.bulk_structure_name = configuration['bulk_structure']
self.bulk_structure_filename = configuration[
'bulk_structure_filename']
self.bulk_structure_lattice = OrderedDict()
_lattice_parameter_variables = [
'lmps_min_all.a11', 'lmps_min_all.a12', 'lmps_min_all.a13',
'lmps_min_all.a21', 'lmps_min_all.a22', 'lmps_min_all.a23',
'lmps_min_all.a31', 'lmps_min_all.a32', 'lmps_min_all.a33'
]
self.bulk_lattice_components = OrderedDict()
for k in _lattice_parameter_variables:
_k = '{}.{}'.format(self.bulk_structure_name, k)
self.bulk_lattice_components[_k] = None
def test__on_init():
task_name = configuration['task']['task_name']
task_directory = configuration['task']['task_directory']
structure_filename = configuration['structure']['filename']
restart = False
fullauto = False
cleanup(task_directory)
assert not os.path.exists(task_directory)
assert 'potential' in configuration
assert 'parameters' in configuration
#<--- code setup
from pypospack.task.lammps import LammpsSimulation
lammps_task = LammpsSimulation(task_name=task_name,
task_directory=task_directory,
structure_filename=structure_filename)
#<--- test setup
assert os.path.exists(task_directory)
assert lammps_task.status == 'INIT'
assert lammps_task.potential is None
#<--- code being testing
lammps_task.on_init(configuration)
#<--- check directory structure
assert os.path.isdir(os.path.abspath(lammps_task.task_directory))
#<--- check attributes
assert lammps_task.task_name == task_name
assert os.path.abspath(lammps_task.task_directory)\
== os.path.abspath(task_directory)
assert lammps_task.task_type == 'single_point'
assert lammps_task.lammps_bin == os.environ['LAMMPS_BIN']
assert lammps_task.lammps_input_filename == 'lammps.in'
assert lammps_task.lammps_output_filename == 'lammps.out'
assert lammps_task.lammps_structure_filename == 'lammps.structure'
# assert lammps_task.lammps_eam_filename is None
assert isinstance(lammps_task.potential, potential.Potential)
assert lammps_task.structure_filename == structure_filename
assert isinstance(lammps_task.structure, crystal.SimulationCell)
assert lammps_task.process is None
print('poscar_filename={}'.format(Ni_structure_definition['filename']))
assert os.path.isfile(Ni_structure_definition['filename'])
Ni_task_configuration = OrderedDict()
Ni_task_configuration['task'] = OrderedDict()
Ni_task_configuration['task']['task_name'] = 'Ni_fcc_unit.E_min_all'
Ni_task_configuration['task']['task_directory'] = 'Ni_fcc_.E_min_all'
Ni_task_configuration['task_type'] = 'min_none'
Ni_task_configuration['potential'] = Ni_eam_potential_definition
Ni_task_configuration['parameters'] = Ni_eam_parameters
Ni_task_configuration['structure'] = Ni_structure_definition
configuration = Ni_task_configuration
task_name = configuration['task']['task_name']
task_directory = configuration['task']['task_directory']
structure_filename = configuration['structure']['filename']
restart = False
fullauto = False
from pypospack.task.lammps import LammpsSimulation
lammps_task = LammpsSimulation(task_name=task_name,
task_directory=task_directory,
structure_filename=structure_filename)
lammps_task.on_init(configuration)
lammps_task.on_config(configuration)
lammps_task.on_ready(configuration)
lammps_task.on_running(configuration)
lammps_task.on_post(configuration)
def on_init(self,configuration=None,results=None):
LammpsSimulation.on_init(self,configuration=configuration)
