def load_from_outcar(self, path, structure, mode):
"""
This function reads atom positions, unit cell, forces and stress tensor from the VASP
OUTCAR file
path:
structure:
"""
if mode == 'scf':
filename = os.path.join(path, 'OUTCAR')
self.name = filename.split('/')[-2]
elif mode == 'nscf':
filename = os.path.join(path, 'nscf_SOC/OUTCAR')
self.name = filename.split('/')[-3]
else:
raise Exception(
f"Calculation mode {mode} is wrong. Must be scf or nscf")
if os.access(filename, os.R_OK):
outcar = Outcar(filename)
else:
raise Exception("Missing OUTCAR file in {}".format(filename))
print(self.name)
# ATOMIC PROPERTIES
self.num_atoms = int(
structure.composition.num_atoms) # total number of atoms
self.atoms_frac = structure.frac_coords # fraction coordinates
self.atoms_cart = structure.cart_coords # cartesian coordinates
self.num_per_type = [
int(x) for x in structure.composition.get_el_amt_dict().values()
] # number of atoms per type
self.species = [x.symbol for x in structure.species
] # list with atomic symbols for each specie
self.pomass = [
Element(x.symbol).atomic_mass for x in structure.species
] # list with atomic masses for each specie
self.charges = [x['tot'] for x in outcar.charge] # list with charges
# read zval dict and create a mapping
outcar.read_pseudo_zval()
zval_dict = outcar.zval_dict
self.zvals = [zval_dict[x.symbol] for x in structure.species]
# UNIT CELL
self.unit_cell = structure.lattice.matrix # unit cell
self.recip_cell = structure.lattice.inv_matrix # inverse unit cell
self.volume = structure.lattice.volume
# total energy in eV
self.energy = outcar.final_energy
# atomic positions read from Outcar
self.atoms = np.array(
outcar.read_table_pattern(
header_pattern=r"\sPOSITION\s+TOTAL-FORCE \(eV/Angst\)\n\s-+",
row_pattern=
r"\s+([+-]?\d+\.\d+)\s+([+-]?\d+\.\d+)\s+([+-]?\d+\.\d+)\s+[+-]?\d+\.\d+\s+[+-]?\d+\.\d+\s+[+-]?\d+\.\d+",
footer_pattern=r"\s--+",
postprocess=lambda x: float(x),
last_one_only=False)[0])
# forces acting on atoms from Outcar
self.forces = np.array(
outcar.read_table_pattern(
header_pattern=r"\sPOSITION\s+TOTAL-FORCE \(eV/Angst\)\n\s-+",
row_pattern=
r"\s+[+-]?\d+\.\d+\s+[+-]?\d+\.\d+\s+[+-]?\d+\.\d+\s+([+-]?\d+\.\d+)\s+([+-]?\d+\.\d+)\s+([+-]?\d+\.\d+)",
footer_pattern=r"\s--+",
postprocess=lambda x: float(x),
last_one_only=False)[0])
# READ STRESS: (XX, YY, ZZ, XY, YZ, ZX) and convert values to array
outcar.read_pattern(
{
'stress':
r"in kB\s+([\.\-\d]+)\s+([\.\-\d]+)\s+([\.\-\d]+)\s+([\.\-\d]+)\s+([\.\-\d]+)\s+([\.\-\d]+)"
},
terminate_on_match=False,
postprocess=float)
stress = outcar.data.get("stress")[0]
self.stress = np.array([[stress[0], stress[3], stress[5]],
[stress[3], stress[1], stress[4]],
[stress[5], stress[4], stress[2]]])
# Conversion from kbar to ev/A^3.
self.stress *= KBAR_TO_EVA3
# MAGNETIZATION and its PROJECTION ON EVERY ATOM
try:
# non-collinear
outcar.read_pattern(
{
'total_mag':
r"number of electron\s+\S+\s+magnetization\s+([\.\-\d]+)\s+([\.\-\d]+)\s+([\.\-\d]+)\s"
},
terminate_on_match=False,
postprocess=float)
self.__magnetization = outcar.data.get("total_mag")[-1]
self.proj_magn = np.array([
mag['tot'].moment for mag in outcar.magnetization
]) # 2-D array
except:
# collinear
outcar.read_pattern(
{
'total_mag':
r"number of electron\s+\S+\s+magnetization\s+("
r"\S+)"
},
terminate_on_match=False,
postprocess=float)
self.__magnetization = np.zeros(3)
self.__magnetization[2] = outcar.data.get("total_mag")[-1][0]
self.proj_magn = np.zeros((self.num_atoms, 3))
for i in range(self.num_atoms):
self.proj_magn[i,
2] = outcar.magnetization[i]['tot'] # 2-D array
# NOTE: sum of magnetization projected on atoms differs from the total magnetization
self.proj_magn_sum = np.sum(self.proj_magn, axis=0)
self.get__magnetization()
# POLARIZATION
self.load_polarization(path)
self.fileID = filename
