def get_madelung_tag_single(rundict, force=False, verbose=0, oxi_int=False):
struct_data = rundict.structure_data
if not force and struct_data[0].properties.get("E_mad", None) is not None:
print("skipping")
return True
poscar, potcar = [p.from_file(rundict.job_folder+f) for (p, f) in
[(Poscar, "/POSCAR"), (Potcar, "/POTCAR")]]
s_dict = {}
if verbose > 0:
print("poscar/potcar parsed")
if oxi_int:
oxi = rundict.structure.copy()
try:
oxi.add_oxidation_state_by_guess()
except ValueError:
print("Forced to set oxidation by hand")
oxi.add_oxidation_state_by_element({"Na": 1,
"Mg": 2,
"Mn": 3.5,
"O": -2,
"Li": 1,
"Ca": 2,
"Fe": 3,
"Zn": 4,
"Co": 2.5,
"Ti": 4,
"S": -2,
'P': 5})
ew_sum_int = EwaldSummation(oxi)
oxi.add_site_property("E_mad_int",
[ew_sum_int.get_site_energy(i)
for i in range(oxi.num_sites)])
s_dict['oxi_int'] = oxi
struct_data.add_site_property("E_mad_int",
[ew_sum_int.get_site_energy(i)
for i in range(oxi.num_sites)])
if verbose > 0:
print("integer oxidation state computed")
if struct_data[0].properties.get("charge", None) is None:
print("No bader charges => no bader madelung")
return False
# Test if bader charges were computed correctly
get_oxidation_state_decorated_structure(struct_data,
potcar, poscar)
if verbose > 0:
print("bader oxidation state computed")
ew_sum = EwaldSummation(rundict.structure_data)
# madelung_array = []
struct_data.add_site_property("E_mad",
[ew_sum.get_site_energy(i)
for i in range(struct_data.num_sites)])
s_dict["oxi_bader"] = struct_data
print(" ".join(s_dict.values()))
return True
def test_site(self):
"""Test that uses an uncharged structure"""
filepath = os.path.join(test_dir, "POSCAR")
p = Poscar.from_file(filepath, check_for_POTCAR=False)
original_s = p.structure
s = original_s.copy()
s.add_oxidation_state_by_element({"Li": 1, "Fe": 3, "P": 5, "O": -2})
# Comparison to LAMMPS result
ham = EwaldSummation(s, compute_forces=True)
self.assertAlmostEquals(-1226.3335, ham.total_energy, 3)
self.assertAlmostEquals(-45.8338, ham.get_site_energy(0), 3)
self.assertAlmostEquals(-27.2978, ham.get_site_energy(8), 3)
def test_site(self):
"""Test that uses an uncharged structure"""
filepath = os.path.join(test_dir, 'POSCAR')
p = Poscar.from_file(filepath, check_for_POTCAR=False)
original_s = p.structure
s = original_s.copy()
s.add_oxidation_state_by_element({"Li": 1, "Fe": 3,
"P": 5, "O": -2})
# Comparison to LAMMPS result
ham = EwaldSummation(s, compute_forces=True)
self.assertAlmostEquals(-1226.3335, ham.total_energy, 3)
self.assertAlmostEquals(-45.8338, ham.get_site_energy(0), 3)
self.assertAlmostEquals(-27.2978, ham.get_site_energy(8), 3)
def calc_elem_max_potential(structure_oxid: mg.Structure,
full_list=False,
check_vesta=False):
"""
Return the maximum Madelung potential for all elements in a structure.
:param structure_oxid: Pymatgen Structure with oxidation states for each site
:param full_list: Boolean, if True, return all the site potentials associated with the element
:param check_vesta: Boolean, if True, convert all site potentials' units from V to e/Angstrom
:return: Dictionary: {Pymatgen Element: maximum Madelung potential for that element}
or {Pymatgen Element: list of all Madelung potentials for that element}
"""
# set the conversion factor if the potential values needs to be compared with the ones from VESTA
# conversion value obtained from page 107 of https://jp-minerals.org/vesta/archives/VESTA_Manual.pdf
if check_vesta:
vesta_conversion = 14.39965
else:
vesta_conversion = 1
# define a dictionary that stores the oxidation states for all the element
elem_charge_lookup = {
specie.element: specie.oxi_state
for specie in structure_oxid.composition.elements
}
# if there is only one element, then ewald summation will not work
if len(elem_charge_lookup) == 1:
return {elem: None for elem in elem_charge_lookup.keys()}
# initialize the Ewald Summation object in order to calculate Ewald site energy
ews = EwaldSummation(structure_oxid)
# obtain the site indices where each element occupies
elem_indices, *_ = get_elem_info(structure_oxid, makesupercell=False)
# get the site potential using indices
# the Ewald site energy is converted to site potential using V=2E/q
# TODO: need to resolve division by zero error message
site_potentials = {
elem: [
2 * ews.get_site_energy(index) /
(elem_charge_lookup[elem] * vesta_conversion) for index in indices
]
for elem, indices in elem_indices.items()
}
if full_list:
return site_potentials
return {
elem: max(potentials)
for elem, potentials in site_potentials.items()
}
def featurize(self, strc, idx):
"""
Args:
struct (Structure): Pymatgen Structure object.
idx (int): index of target site in structure.
Returns:
([float]) - Electrostatic energy of the site
"""
# Check if the new input is the last
# Note: We use 'is' rather than structure comparisons for speed
if strc is self.__last_structure:
ewald = self.__last_ewald
else:
self.__last_structure = strc
ewald = EwaldSummation(strc, acc_factor=self.accuracy)
self.__last_ewald = ewald
return [ewald.get_site_energy(idx)]
def get_I_mads(struc):
# Add oxidation states
try:
struc = bva.get_oxi_state_decorated_structure(struc)
#print (struc)
except:
struc.add_oxidation_state_by_guess()
# Check if a specific species is present
if (Specie('I',-1) in struc.species):
ews = EwaldSummation(struc)
print (ews)
I_indices = [n for n,site in enumerate(struc) if
site.specie.symbol == 'I']
I_mads = np.array([ews.get_site_energy(n) for n in I_indices])
print (I_indices)
print (I_mads)
return I_mads
return ews.total_energy
print (ews.total_energy)
def featurize(self, strc, idx):
"""
Args:
struct (Structure): Pymatgen Structure object.
idx (int): index of target site in structure.
Returns:
([float]) - Electrostatic energy of the site
"""
# Check if the new input is the last
# Note: We use 'is' rather than structure comparisons for speed
#
# TODO: Figure out if this implementation is thread-safe! I was debating adding
# Locks, but think we are OK
if strc is self.__last_structure:
ewald = self.__last_ewald
else:
self.__last_structure = strc
ewald = EwaldSummation(strc, acc_factor=self.accuracy)
self.__last_ewald = ewald
return [ewald.get_site_energy(idx)]
