def __init__(self,
task_name,
task_directory,
structure_filename,
restart=False,
fullauto=False,
temperature=None,
pressure=0,
time_total=None,
time_step=None,
supercell=[10, 10, 10]):
assert temperature is not None
assert time_total is not None
assert time_step is not None
LammpsSimulation.__init__(self,
task_name=task_name,
task_directory=task_directory,
structure_filename=structure_filename)
self.temperature = temperature
self.pressure = pressure
self.time_total = time_total
self.time_step = time_step
self.supercell = supercell
self.lammps_out_fn = 'lammps.out'
self.lattice_fn = 'lattice.out'
def get_conditions_ready(self):
LammpsSimulation.get_conditions_ready(self)
if self.bulk_structure_name is not None:
_is_components_exist = []
for k, v in self.bulk_lattice_components.items():
_is_components_exist.append(v is not None)
_all_components_exist = all(_is_components_exist)
self.conditions_READY['bulk_lattice_components'] =\
_all_components_exist
def __init__(self,
task_name,
task_directory,
structure_filename,
restart=False,
fullauto=False):
_task_type = 'lmps_min_pos'
LammpsSimulation.__init__(self,
task_name=task_name,
task_directory=task_directory,
task_type=_task_type,
structure_filename=structure_filename,
restart=restart,
fullauto=fullauto)
def test____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)
#<--- code being tested
from pypospack.task.lammps import LammpsSimulation
lammps_task = LammpsSimulation(task_name=task_name,
task_directory=task_directory,
structure_filename=structure_filename)
#<--- check directory structure
assert os.path.isdir(os.path.abspath(lammps_task.task_directory))
assert os.listdir(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 lammps_task.potential is None
assert lammps_task.structure_filename == structure_filename
assert isinstance(lammps_task.structure, crystal.SimulationCell)
assert lammps_task.status == 'INIT'
def _lammps_input_create_atoms(self):
str_out = LammpsSimulation._lammps_input_create_atoms(self)
str_out += "replicate {} {} {}\n".format(self.supercell[0],
self.supercell[1],
self.supercell[2])
str_out += "change_box all x scale 1 y scale 1 z scale 1 remap\n"
return str_out
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__configure_potential():
#<--- expected behavior
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.configuration = configuration
#<--- test setup
assert os.path.exists(task_directory)
assert lammps_task.status == 'INIT'
assert lammps_task.potential is None
assert lammps_task.configuration['potential']['potential_type'] \
== configuration['potential']['potential_type']
#<--- code being testing
lammps_task.configure_potential()
#<--- testing to see if the potential is setup correctly
assert isinstance(lammps_task.potential, potential.Potential)
if type(lammps_task.potential) == potential.EamPotential:
assert isinstance(lammps_task.potential.obj_pair,
potential.PairPotential)
assert isinstance(lammps_task.potential.obj_density,
potential.EamDensityFunction)
assert isinstance(lammps_task.potential.obj_embedding,
potential.EamEmbeddingFunction)
if type(lammps_task.potential) == potential.EamPotential \
and 'setfl_filename' in configuration['potential']:
if configuration['potential']['setfl_filename'] is not None:
lammps_setfl_filename = '{}.eam.alloy'.format("".join(symbols))
assert os.path.isfile(
os.path.join(task_directory, lammps_setfl_filename))
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 __init__(self,
task_name,
task_directory,
structure_filename,
restart=False,
fullauto=False):
_task_type = 'lmps_min_sf'
self.bulk_structure_name = None
self.bulk_structure_filename = None
self.bulk_structure_lattice = None
LammpsSimulation.__init__(self,
task_name=task_name,
task_directory=task_directory,
task_type=_task_type,
structure_filename=structure_filename,
restart=restart,
fullauto=fullauto)
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_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 test____init___():
symbols = configuration['potential']['symbols']
task_name = configuration['task']['task_name']
task_directory = configuration['task']['task_directory']
structure_filename = configuration['structure']['filename']
eam_setfl_filename = configuration['potential']['setfl_filename']
restart = False
fullauto = False
cleanup(task_directory)
assert not os.path.exists(task_directory)
assert type(eam_setfl_filename) is str
assert type(structure_filename) is str
poscar = vasp.Poscar()
poscar.read(structure_filename)
assert os.path.isfile(eam_setfl_filename)
assert os.path.isfile(structure_filename)
#<--- code being tested
from pypospack.task.lammps import LammpsSimulation
lammps_task = LammpsSimulation(task_name=task_name,
task_directory=task_directory,
structure_filename=structure_filename)
#<--- expected behavior
lammps_setfl_filename = '{}.eam.alloy'.format("".join(symbols))
#<--- check directory structure
assert os.path.isdir(os.path.abspath(lammps_task.task_directory))
assert os.listdir(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 == None
assert lammps_task.potential is None
assert lammps_task.structure_filename == structure_filename
assert isinstance(lammps_task.structure, crystal.SimulationCell)
assert lammps_task.status == 'INIT'
def on_ready(self,configuration=None,results=None):
LammpsSimulation.on_ready(
self,
configuration=configuration,
results=results)
def on_post(self, configuration=None):
self._get_lattice_parameter_from_lattice_out_file(
filename=os.path.join(self.task_directory, self.lattice_fn),
supercell=self.supercell)
LammpsSimulation.on_post(self, configuration=configuration)
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_ready(self, configuration=None, results=None):
if self.bulk_structure_name is not None:
self.__modify_structure(results=results)
LammpsSimulation.on_ready(self, configuration=configuration)
def on_config(self, configuration, results=None):
if self.bulk_structure_name is not None:
for k, v in results.items():
if k in self.bulk_lattice_components:
self.bulk_lattice_components[k] = v
LammpsSimulation.on_config(self, configuration=None, results=None)
def postprocess(self):
LammpsSimulation.postprocess(self)
def on_post(self, configuration=None):
self.__get_results_from_lammps_outputfile()
LammpsSimulation.on_post(self, configuration=configuration)
def on_config(self,configuration,results=None):
LammpsSimulation.on_config(self,configuration=None,results=None)
def on_init(self,configuration=None,results=None):
LammpsSimulation.on_init(self,configuration=configuration)
