def one_off(crystal_name):
config = load_config_file(
os.path.join(os.path.dirname(os.path.dirname(non_pseudo.__file__)),
'settings', 'non_pseudo.yaml'))
crystal = Material(crystal_name)
crystal.run_id = 'one_off'
print('SCREENING : {}'.format(crystal_name))
run_all_simulations(config, crystal)
print('...done!\n')
print('Crystal name :\t\t{}'.format(crystal_name))
print('CH4 v/v 35bar :\t\t{}'.format(
crystal.ga1_absolute_volumetric_loading))
print('CH4 v/v 65bar :\t\t{}'.format(
crystal.ga0_absolute_volumetric_loading))
print('He void fraction :\t{}'.format(crystal.vf_helium_void_fraction))
print('Vol. surface area :\t{}\n'.format(
crystal.sa_volumetric_surface_area))
avg_sig, avg_ep = calculate_average_sigma_epsilon(crystal_name)
v, nd = calculate_vol_nden(crystal_name)
print('\nAvg. sigma-value :\t{}'.format(avg_sig))
print('Avg. epsilon-value :\t{}'.format(avg_ep))
print('Unit cell vol. :\t{}'.format(v))
print('Number density :\t{}'.format(nd))
def _init(run_id):
"""Load config for run.
Args:
run_id (str): identification string for run.
Returns:
config (dict): parameters specified in config.
"""
non_pseudo_dir = os.path.dirname(os.path.dirname(non_pseudo.__file__))
run_dir = os.path.join(non_pseudo_dir, run_id)
config_file = os.path.join(run_dir, 'config.yaml')
config.update(load_config_file(config_file))
return config
def start_run(config_path):
config = load_config_file(config_path)
non_pseudo_dir = os.path.dirname(os.path.dirname(non_pseudo.__file__))
run_id = datetime.now().isoformat()
config['run_id'] = run_id
config['raspa2_dir'] = os.path.dirname(RASPA2.__file__)
config['non_pseudo_dir'] = non_pseudo_dir
run_dir = os.path.join(non_pseudo_dir, run_id)
os.makedirs(run_dir, exist_ok=True)
file_name = os.path.join(run_dir, 'config.yaml')
with open(file_name, 'w') as config_file:
yaml.dump(config, config_file, default_flow_style=False)
print('Run created with id: {}'.format(run_id))
return config
def worker_run_loop(run_id):
"""
Args:
run_id (str): identification string for run.
Finds next-to-be-simulated hypothetical or real material and calculates
properties of interest, saving results to database.
"""
config = load_config_file(os.path.join(run_id, 'config.yaml'))
non_pseudo_dir = os.path.dirname(os.path.dirname(non_pseudo.__file__))
materials_dir = config['materials_directory']
mat_dir = os.path.join(non_pseudo_dir, materials_dir)
mat_names = os.listdir(mat_dir)
for cif_name in mat_names:
name = cif_name[:-4]
add_material_to_database(config, name)
def start(config_path):
"""Create new run.
Args:
config_path (str): path to config file (ex: settings/non_pseudo.sample.yaml)
Prints run_id, creates run-directory with config-file.
"""
config = load_config_file(config_path)
non_pseudo_dir = os.path.dirname(os.path.dirname(non_pseudo.__file__))
run_id = datetime.now().isoformat()
config['run_id'] = run_id
config['raspa2_dir'] = os.path.dirname(RASPA2.__file__)
config['non_pseudo_dir'] = non_pseudo_dir
run_dir = os.path.join(non_pseudo_dir, run_id)
os.makedirs(run_dir, exist_ok=True)
file_name = os.path.join(run_dir, 'config.yaml')
with open(file_name, 'w') as config_file:
yaml.dump(config, config_file, default_flow_style=False)
print('Run created with id: {}'.format(run_id))