def test_potcar_file_hash_warning(self):
filename = (
self.TEST_FILES_DIR
/ "modified_potcars_header"
/ "POT_GGA_PAW_PBE"
/ "POTCAR.Fe_pv"
)
with pytest.warns(UnknownPotcarWarning, match="following"):
PotcarSingle.from_file(filename)
def test_potcar_hash_warning(self):
filename = (
self.TEST_FILES_DIR
/ "modified_potcars_data"
/ "POT_GGA_PAW_PBE"
/ "POTCAR.Fe_pv"
)
with pytest.warns(UnknownPotcarWarning, match="integrity"):
PotcarSingle.from_file(filename)
def get_Potcar(self):
''' Reads the file titled POTCAR from the present working directory '''
''' Generates and returns pymatgen.io.vasp.inputs.PotcarSingle object from POTCAR '''
potcar = PotcarSingle.from_file(self.path + '/POTCAR')
return potcar
def test_from_functional_and_symbols(self):
test_potcar_dir = os.path.abspath(
os.path.join(os.path.dirname(__file__),
"..", "..", "..", "..", "test_files"))
SETTINGS["VASP_PSP_DIR"] = test_potcar_dir
p = PotcarSingle.from_symbol_and_functional("Li_sv", "PBE")
self.assertEqual(p.enmax, 271.649)
def test_from_functional_and_symbols(self):
test_potcar_dir = os.path.abspath(
os.path.join(os.path.dirname(__file__),
"..", "..", "..", "..", "test_files"))
SETTINGS["PMG_VASP_PSP_DIR"] = test_potcar_dir
p = PotcarSingle.from_symbol_and_functional("Li_sv", "PBE")
self.assertEqual(p.enmax, 271.649)
def test_identify_potcar(self):
filename = PymatgenTest.TEST_FILES_DIR / "POT_GGA_PAW_PBE_54" / "POTCAR.Fe.gz"
with pytest.warns(None):
psingle = PotcarSingle.from_file(filename)
assert "PBE_54" in psingle.identify_potcar()[0]
assert "Fe" in psingle.identify_potcar()[1]
def isotope (self,before="POMASS = 1.000", change="POMASS = 3.000"):
from pymatgen.io.vasp.outputs import Poscar
from pymatgen.io.vasp.inputs import PotcarSingle
from pymatgen.io.vasp.outputs import Potcar
from pymatgen.io.vasp.sets import MPNMRSet
import shutil
import os
os.chdir(self.dire)
print (os.getcwd())
poscar= Poscar.from_file("POSCAR")
# structure = poscar.structure
print (poscar)
potcar= Potcar.from_file("POTCAR")
potc=str(potcar)
cc= potc.replace(before,change)
vv=PotcarSingle(cc,)
vv.write_file("POTCAR_1")
print (vv)
def test_functional_types(self):
self.assertEqual(self.psingle.functional, "PBE")
self.assertEqual(self.psingle.functional_class, "GGA")
self.assertEqual(self.psingle.potential_type, "PAW")
psingle = PotcarSingle.from_file(PymatgenTest.TEST_FILES_DIR / "POT_LDA_PAW" / "POTCAR.Fe.gz")
self.assertEqual(psingle.functional, "Perdew-Zunger81")
self.assertEqual(psingle.functional_class, "LDA")
self.assertEqual(psingle.potential_type, "PAW")
def test_functional_types(self):
self.assertEqual(self.psingle.functional, 'PBE')
self.assertEqual(self.psingle.functional_class, 'GGA')
self.assertEqual(self.psingle.potential_type, 'PAW')
psingle = PotcarSingle.from_file(self.TEST_FILES_DIR/ "POT_LDA_PAW"/ "POTCAR.Fe.gz")
self.assertEqual(psingle.functional, 'Perdew-Zunger81')
self.assertEqual(psingle.functional_class, 'LDA')
self.assertEqual(psingle.potential_type, 'PAW')
def test_functional_types(self):
self.assertEqual(self.psingle.functional, "PBE")
self.assertEqual(self.psingle.functional_class, "GGA")
self.assertEqual(self.psingle.potential_type, "PAW")
psingle = PotcarSingle.from_file(os.path.join(test_dir, "POT_LDA_PAW", "POTCAR.Fe.gz"))
self.assertEqual(psingle.functional, "Perdew-Zunger81")
self.assertEqual(psingle.functional_class, "LDA")
self.assertEqual(psingle.potential_type, "PAW")
def test_functional_types(self):
self.assertEqual(self.psingle.functional, 'PBE')
self.assertEqual(self.psingle.functional_class, 'GGA')
self.assertEqual(self.psingle.potential_type, 'PAW')
psingle = PotcarSingle.from_file(os.path.join(test_dir, "POT_LDA_PAW",
"POTCAR.Fe.gz"))
self.assertEqual(psingle.functional, 'Perdew-Zunger81')
self.assertEqual(psingle.functional_class, 'LDA')
self.assertEqual(psingle.potential_type, 'PAW')
def potcar_from_linklist(cls, poscar_data, linklist):
"""
Assemble pymatgen Potcar object from a list of VaspPotcarData instances
Reads pseudo-potential from the passed list connecting each element
with it's potential and creates the complete Potcar file according
to the element ordering fodun in the passed poscar data object.
:param poscar_data: input structure for VASP calculations
:type poscar: :class:`aiida_cusp.data.inputs.VaspPoscarData`
:param linklist: dictionary mapping element names to VaspPotcarData
instances
:type linklist: `dict`
:returns: pymatgen Potcar data instance with containing the
concatenated pseudo-potential information for all elements defined
in the linklist
:rtype: :class:`~pymatgen.io.vasp.inputs.Potcar`
"""
# initialize empty Potcar object
complete_potcar = Potcar()
# file empty potcar with potential in order of elements found in the
# passed structure data
site_symbols = poscar_data.get_poscar().site_symbols
for site_symbol in site_symbols:
try:
potential_pointer = linklist[site_symbol]
except KeyError:
raise VaspPotcarDataError(
"Found no potential in passed "
"potential-element map for "
"site symbol '{}'".format(site_symbol))
potential_file = potential_pointer.load_potential_file_node()
potential_contents = potential_file.get_content()
potcar_single = PotcarSingle(potential_contents)
complete_potcar.append(potcar_single)
return complete_potcar
def setUp(self):
self.psingle = PotcarSingle.from_file(
os.path.join(test_dir, "POT_GGA_PAW_PBE", "POTCAR.Mn_pv.gz"))
def test_config_pymatgen():
path_mp_config = os.path.join(os.environ["HOME"], ".pmgrc.yaml")
if os.path.exists(path_mp_config):
mp_config = loadfn(path_mp_config)
print("##########Start to test the PMG_MAPI_KEY paramter##########")
help_cmd = "-mapi YOUR_MP_API_KEY"
param = "PMG_MAPI_KEY"
if param in mp_config:
try:
with MPRester(mp_config[param]) as mpr:
mpr.get_structure_by_material_id("mp-66")
Tips().set_properly(MAPI_KEY=mp_config[param])
except Exception as e:
Tips().set_improper(param, help_cmd)
else:
Tips().set_not_exist(param, help_cmd)
print(
"\n##########Start to test the PMG_DEFAULT_FUNCTIONAL paramter##########"
)
help_cmd = "-df DEFAULT_FUNCTIONAL"
param = "PMG_DEFAULT_FUNCTIONAL"
flag_functional = False
FUNCTIONAL_CHOICES = Potcar.FUNCTIONAL_CHOICES
if param in mp_config:
DF = mp_config[param]
if DF in FUNCTIONAL_CHOICES:
Tips().set_properly(PMG_DEFAULT_FUNCTIONAL=DF)
flag_functional = True
else:
Tips().set_improper(param, help_cmd)
else:
Tips().set_not_exist(param, help_cmd)
print(
"\n##########Start to test the PMG_VASP_PSP_DIR paramter##########"
)
help_cmd = "-psp VASP_PSP_DIR"
param = "PMG_VASP_PSP_DIR"
flag_psp = False
FUNCTIONAL_DIR = list(PotcarSingle.functional_dir.values())
functional_name = {
v: k
for k, v in PotcarSingle.functional_dir.items()
}
if param in mp_config:
psp_dir = mp_config[param]
if os.path.isdir(psp_dir):
flag_psp = False
functional_available = []
sub_dirs = os.listdir(psp_dir)
for item in sub_dirs:
if item in FUNCTIONAL_DIR:
functional = functional_name[item]
try:
p = PotcarSingle.from_symbol_and_functional(
"Fe", functional)
functional_available.append(functional)
flag_psp = True
except Exception as e:
print("There are some problems of " + functional +
" in " + os.path.join(psp_dir, item))
if flag_psp:
Tips().functional_info(param)
print("\t The supported functional is/are: " +
", ".join(functional_available))
flag_psp = True
else:
print("There is no available functional in " + psp_dir)
Tips().set_improper(param, help_cmd)
else:
print("The path " + psp_dir + " not exists.")
Tips().set_improper(param, help_cmd)
else:
Tips().set_not_exist(param, help_cmd)
else:
Tips().set_not_exist("~/.pmgrc.yaml", "-mp")
if flag_psp and flag_functional:
if not (mp_config["PMG_DEFAULT_FUNCTIONAL"] in functional_available):
warnings.warn(
"The default functional '{}' is not supported in current available \
functionals: {}.".format(
mp_config["PMG_DEFAULT_FUNCTIONAL"],
"\n" + ", ".join(functional_available)))
def test_default_functional(self):
p = PotcarSingle.from_symbol_and_functional("Fe")
self.assertEqual(p.functional_class, 'GGA')
SETTINGS["PMG_DEFAULT_FUNCTIONAL"] = "LDA"
p = PotcarSingle.from_symbol_and_functional("Fe")
self.assertEqual(p.functional_class, 'LDA')
def test_default_functional(self):
p = PotcarSingle.from_symbol_and_functional("Fe")
self.assertEqual(p.functional_class, 'GGA')
SETTINGS["PMG_DEFAULT_FUNCTIONAL"] = "LDA"
p = PotcarSingle.from_symbol_and_functional("Fe")
self.assertEqual(p.functional_class, 'LDA')
def setUp(self):
#with zopen(os.path.join(test_dir, "POT_GGA_PAW_PBE",
# "POTCAR.Mn_pv.gz"), 'rb') as f:
self.psingle = PotcarSingle.from_file(os.path.join(test_dir, "POT_GGA_PAW_PBE",
"POTCAR.Mn_pv.gz"))
def setUp(self):
self.psingle = PotcarSingle.from_file(
self.TEST_FILES_DIR / "POT_GGA_PAW_PBE" / "POTCAR.Mn_pv.gz")
def setUp(self):
self.psingle = PotcarSingle.from_file(
self.TEST_FILES_DIR / "POT_GGA_PAW_PBE" / "POTCAR.Mn_pv.gz")
