Source code for inout.vasp
import numpy as np
import os.path
from typing import List
[docs]def read_input_lines(structure_file: str) -> tuple:
"""
Parser function to read VASP input file.
:param structure_file: Path of VASP input file
:type structure_file: str
:return: A standardized set of data that defines a crystal structure such as lattice_matrix and atom_type
:rtype: tuple
"""
try:
with open(structure_file, 'r') as infile:
_lines = infile.readlines()
except IOError:
print("\nFail to open '{0}' file".format(structure_file))
print("Please check the path of VASP input file\n")
raise
# comment = _lines[0]
lattice_ratio = float(_lines[1].split()[0])
lattice_matrix = np.asfarray([line.split()[0:3] for line in _lines[2:5]]) * lattice_ratio
num_atom = [int(num) for num in _lines[6].split()]
num_total = 0
for num in num_atom:
num_total += num
__atom_type = []
for ind_atom, num in enumerate(num_atom):
__atom_type.extend([_lines[5].split()[ind_atom] for _ in range(num)])
coordinate = 'cartesian'
if _lines[7].split()[0][0] in ('S', 's'):
selective = True
pos_atom = _lines[9:9 + num_total]
if _lines[8].split()[0][0] in ('D', 'd'):
coordinate = 'direct'
atom = [pos.split()[0:3] for pos in pos_atom]
atom_direct = np.asfarray(atom)
__atom_cart = np.dot(atom_direct, lattice_matrix)
elif _lines[8].split()[0][0] in ('C', 'c', 'K', 'k'):
atom = [pos.split()[0:3] for pos in pos_atom]
__atom_cart = np.asfarray(atom)
__atom_true = [i for i, v in enumerate(pos_atom) if 'T' in v.split()]
else:
selective = False
pos_atom = _lines[8:8 + num_total]
if _lines[7].split()[0][0] in ('D', 'd'):
coordinate = 'direct'
atom = [pos.split()[0:3] for pos in pos_atom]
atom_direct = np.asfarray(atom)
__atom_cart = np.dot(atom_direct, lattice_matrix)
elif _lines[7].split()[0][0] in ('C', 'c', 'K', 'k'):
atom = [pos.split()[0:3] for pos in pos_atom]
__atom_cart = np.asfarray(atom)
__atom_true = [i for i, _ in enumerate(pos_atom)] # set all the atoms as True if not selective dynamics
# # Rearrangement of the atomic position sequence according to the atomic type
# set_atom_type = []
# for atom in __atom_type:
# if atom not in set_atom_type:
# set_atom_type.append(atom)
#
# tmp_atom = []
# for atom in __atom_type:
# for ind_set_atom, set_atom in enumerate(set_atom_type):
# if atom == set_atom:
# tmp_atom.append(ind_set_atom)
# set_atom_arg = np.argsort(np.array(tmp_atom))
#
# _atom_cart = __atom_cart[set_atom_arg]
# atom_type = []
# _atom_true = []
# for ind_atom_arg, atom_arg in enumerate(set_atom_arg):
# atom_type.append(__atom_type[atom_arg])
# if atom_arg in __atom_true:
# _atom_true.append(ind_atom_arg)
#
# # Rearrangement of the atomic position sequence according to the z-position in ascending order
# num_atom = [atom_type.count(atom) for atom in set_atom_type]
# num1 = 0
# set_atom_arg = np.array([], dtype=int)
# for num in num_atom:
# set_atom_arg = np.concatenate((set_atom_arg, np.argsort(_atom_cart[num1:num1 + num, 2]) + num1), axis=0)
# num1 += num
#
# atom_cart = _atom_cart[set_atom_arg]
# atom_true = []
# for ind_atom_arg, atom_arg in enumerate(set_atom_arg):
# if atom_arg in _atom_true:
# atom_true.append(ind_atom_arg)
# Define the index of xyz selective dynamics True
xyz_true = []
for ind_T in __atom_true:
xyz_true.extend([ind_T for i in range(3)])
return lattice_matrix, __atom_type, num_atom, selective, coordinate, __atom_cart, __atom_true, xyz_true
[docs]def write_input_lines(unit_cell,
comment: str) -> List[str]:
"""
Parser function to write VASP input file.
:param unit_cell: Instance of UnitCell class
:type unit_cell: :class:`core.UnitCell`
:param comment: Comment to display in VASP input file
:type comment: str
:return: List of each line of VASP input file
:rtype: List[str]
"""
lines = ["%s" % comment + '\n', "%s" % '1.00000000000000' + '\n']
for v in unit_cell.lattice_matrix:
_line = " {0:>20.16f} {1:>20.16f} {2:20.16f}".format(v[0], v[1], v[2])
lines.append(_line + '\n')
ind_atom = 0
set_atom_type = [unit_cell.atom_type[ind_atom]]
for num in unit_cell.num_atom[:-1]:
ind_atom += num
set_atom_type.append(unit_cell.atom_type[ind_atom])
lines.append("%s" % " ".join(set_atom_type) + '\n')
num_atom = [str(num) for num in unit_cell.num_atom]
lines.append("%s" % " ".join(num_atom) + '\n')
if unit_cell.selective:
lines.append("Selective dynamics" + '\n')
else:
pass
lines.append("Cartesian" + '\n')
if unit_cell.selective:
for i, v in enumerate(unit_cell.atom_cart):
if i in unit_cell.atom_true:
_line = " {0:>20.16f} {1:>20.16f} {2:20.16f} T T T".format(v[0], v[1], v[2])
lines.append(_line + '\n')
else:
_line = " {0:>20.16f} {1:>20.16f} {2:20.16f} F F F".format(v[0], v[1], v[2])
lines.append(_line + '\n')
else:
for v in unit_cell.atom_cart:
_line = " {0:>20.16f} {1:>20.16f} {2:20.16f}".format(v[0], v[1], v[2])
lines.append(_line + '\n')
return lines
[docs]def read_output_lines(force_file: str,
num_super_atom: int) -> np.ndarray:
"""
Parser function to read VASP output file in which the atomic forces are written.
:param force_file: Path of VASP output file
:type force_file: str
:param num_super_atom: The number of atoms in super cell
:type num_super_atom: int
:return: A standardized atomic forces, _force_matrix
:rtype: np.ndarray[float]
"""
try:
with open(force_file, 'r') as infile:
_lines = infile.readlines()
except IOError:
print("\nFail to open '{0}' file".format(force_file))
print("Please check the path of VASP output file\n")
raise
_, _filename = os.path.split(force_file)
_unit_convert = (1.602 * 10 ** (-19)) / 10 ** (-10) # (eV/Angst) to (J/m)
_force_index = None
if _filename == 'vasprun.xml':
_tag_atomic_force = 'forces'
for _ind_line, _line in enumerate(_lines):
if _tag_atomic_force in _line:
_force_index = _ind_line
break
if _force_index is None:
print("'Forces acting on atoms' is not written in '{0}'".format(force_file))
print("Corresponding DFT calculation may be incompletely stopped")
assert False
_atomic_forces = _lines[_force_index + 1: _force_index + 1 + num_super_atom]
_force_matrix = np.asfarray([atomic_force.split()[1:4] for atomic_force in _atomic_forces]) * _unit_convert
elif _filename == 'OUTCAR':
_tag_atomic_force = 'TOTAL-FORCE'
for _ind_line, _line in enumerate(_lines):
if _tag_atomic_force in _line:
_force_index = _ind_line
break
if _force_index is None:
print("'Forces acting on atoms' is not written in '{0}'".format(force_file))
print("Check: corresponding DFT calculation must have been incompletely stopped")
assert False
_atomic_forces = _lines[_force_index + 2: _force_index + 2 + num_super_atom]
_force_matrix = np.asfarray([atomic_force.split()[3:6] for atomic_force in _atomic_forces]) * _unit_convert
return _force_matrix