def __init__(self, potential_definition, structures_definition,
task_configuration, parameters):
self.potential_definition = potential_definition
self.structure_definition = structures_definition
self.task_configuration = task_configuration
self.parameters = parameters
self.lammps_task = LammpsNptSimulation(**task_configuration)
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 LammpsNptSimulation
lammps_task = LammpsNptSimulation(
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_setfl_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 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 LammpsNptSimulation
lammps_task = LammpsNptSimulation(
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']== 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
class LammpsNptSimulationScaffold(object):
""" a development scafford for LammpsNptSimulation
Tasks are usually run within the TaskManager. This scafford provides a standard
interface for running tasks
"""
def __init__(self,
potential_definition,
structures_definition,
task_configuration,
parameters):
self.potential_definition = potential_definition
self.structure_definition = structures_definition
self.task_configuration = task_configuration
self.parameters = parameters
self.lammps_task = LammpsNptSimulation(**task_configuration)
def run(self,task_configuration=None):
if task_configuration is not None:
self.task_configuration = task_configuration
self.on_init(self.task_configuration)
self.on_config(self.task_configuration)
self.on_ready(self.task_configuration)
def on_init(self,task_configuration):
self.task_configuration['potential'] = self.potential_definition
self.task_configuration['parameters'] = self.parameters
self.lammps_task.on_init(task_configuration)
def on_config(self,task_configuration):
self.lammps_task.on_config(task_configuration)
def on_ready(self,task_configuration):
self.lammps_task.on_ready(task_configuration)
time_sleep = 0.1
while (self.lammps_task.process.poll() is None):
time.sleep(time_sleep)
lammps_task = None
for temperature in range(temp_0, temp_f + 1, 100):
configuration['task']['task_name'] = 'MgO_NaCl_unit.npt.T{}'.format(
temperature)
configuration['task']['task_directory'] = 'MgO_NaCl_unit.npt.T{}'.format(
temperature)
configuration['task']['temperature'] = temperature
configuration['task']['task_type'] = 'lmps_npt'
task_name = configuration['task']['task_name']
task_directory = configuration['task']['task_directory']
structure_filename = configuration['structure']['filename']
restart = False
fullauto = False
if os.path.isdir(task_directory):
shutil.rmtree(task_directory)
lammps_task = LammpsNptSimulation(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)
_time_sleep = 0.1
time.sleep(_time_sleep)
print("t={}".format(temperature))
while (lammps_task.process.poll() is None):
time.sleep(_time_sleep)
lammps_task = None
def create_tasks(self):
self.tasks = OrderedDict()
for k, v in self.task_configurations.items():
self.tasks[k] = LammpsNptSimulation(**v)
MgO_LC_configuration['parameters'] = MgO_LC_parameters
MgO_LC_configuration['structure'] = MgO_structure_definition
configuration = MgO_LC_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 LammpsNptSimulation
lammps_task = LammpsNptSimulation(task_name=task_name,
task_directory=task_directory,
structure_filename=structure_filename,
temperature=100,
time_total=10,
time_step=0.001,
supercell=[5, 5, 5],
pressure=0)
lammps_task.on_init(configuration)
lammps_task.on_config(configuration)
lammps_task.on_ready(configuration)
while lammps_task.status is 'RUNNING':
lammps_task.on_running(configuration)
lammps_task.on_post(configuration)
print(lammps_task.results)
def test__get_task_name():
task_name = LammpsNptSimulation.get_task_name(structure='structure',temperature=10)
assert task_name == 'structure.lmps_npt_10'