def potential(self, potential_filename):
"""
Execute view_potential() or list_potential() in order to see the pre-defined potential files
Args:
potential_filename:
Returns:
"""
if sys.version_info.major == 2:
stringtypes = (str, unicode)
else:
stringtypes = str
if isinstance(potential_filename, stringtypes):
if '.lmp' in potential_filename:
potential_filename = potential_filename.split('.lmp')[0]
potential_db = LammpsPotentialFile()
potential = potential_db.find_by_name(potential_filename)
elif isinstance(potential_filename, pd.DataFrame):
potential = potential_filename
else:
raise TypeError(
'Potentials have to be strings or pandas dataframes.')
self.input.potential.df = potential
for val in ["units", "atom_style", "dimension"]:
v = self.input.potential[val]
if v is not None:
self.input.control[val] = v
self.input.potential.remove_structure_block()
def potential(self, potential_filename):
"""
Execute view_potential() or list_potential() in order to see the pre-defined potential files
Args:
potential_filename:
Returns:
"""
stringtypes = str
if isinstance(potential_filename, stringtypes):
if ".lmp" in potential_filename:
potential_filename = potential_filename.split(".lmp")[0]
potential_db = LammpsPotentialFile()
potential = potential_db.find_by_name(potential_filename)
elif isinstance(potential_filename, pd.DataFrame):
potential = potential_filename
else:
raise TypeError(
"Potentials have to be strings or pandas dataframes.")
self.input.potential.df = potential
for val in ["units", "atom_style", "dimension"]:
v = self.input.potential[val]
if v is not None:
self.input.control[val] = v
if val == "units" and v != "metal":
warnings.warn(
"WARNING: Non-'metal' units are not fully supported. Your calculation should run OK, but "
"results may not be saved in pyiron units.")
self.input.potential.remove_structure_block()
class TestOpenKimPotential(unittest.TestCase):
def setUp(self):
self.kim = LammpsPotentialFile()
self.potential_path = os.path.join(
os.path.dirname(os.path.abspath(__file__)),
'../../static/lammps/potentials')
def test_find(self):
Fe_lst = ['Fe_C_Becquart_eam', 'Fe_C_Hepburn_Ackland_eam']
self.assertEqual(sorted(list(self.kim.find("Fe")['Name'])),
sorted(Fe_lst))
AlMg_lst = ['Al_Mg_Mendelev_eam']
self.assertEqual(sorted(list(self.kim.find({"Al", "Mg"})['Name'])),
AlMg_lst)
def test_pythonic_functions(self):
self.assertEqual(list(self.kim.find("Fe")['Name']),
list(self.kim["Fe"].list()['Name']))
self.assertEqual(list(self.kim.find("Fe")['Name']),
list(self.kim.Fe.list()['Name']))
self.assertEqual(list(self.kim.find({"Al", "Mg"})['Name']),
list(self.kim["Al"]["Mg"].list()['Name']))
self.assertEqual(list(self.kim.find({"Al", "Mg"})['Name']),
list(self.kim.Mg.Al.list()['Name']))
def view_potentials(self):
"""
List all interatomic potentials for the current atomistic sturcture including all potential parameters.
To quickly get only the names of the potentials you can use: self.potentials_list()
Returns:
pandas.Dataframe: Dataframe including all potential parameters.
"""
from pyiron.lammps.potential import LammpsPotentialFile
if not self.structure:
raise ValueError('No structure set.')
list_of_elements = set(self.structure.get_chemical_symbols())
list_of_potentials = LammpsPotentialFile().find(list_of_elements)
if list_of_potentials is not None:
return list_of_potentials
else:
raise TypeError('No potentials found for this kind of structure: ', str(list_of_elements))
def inspect_emperical_potentials():
return LammpsPotentialFile()
def setUpClass(cls):
cls.kim = LammpsPotentialFile()
cls.potential_path = os.path.join(
os.path.dirname(os.path.abspath(__file__)),
'../../static/lammps/potentials')
def setUp(self):
self.kim = LammpsPotentialFile()
self.potential_path = os.path.join(
os.path.dirname(os.path.abspath(__file__)),
'../../static/lammps/potentials')