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 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
