from __future__ import print_function, division
from numbers import Integral
import numpy as np
from .sile import SileVASP
from ..sile import *
from .car import carSileVASP
from sisl import Grid
__all__ = ['locpotSileVASP']
[docs]class locpotSileVASP(carSileVASP):
""" Electrostatic (or total) potential plus geometry
This file-object handles the electrostatic(total) potential from VASP
"""
[docs] @sile_fh_open(True)
def read_grid(self, index=0, dtype=np.float64):
""" Reads the potential (in eV) from the file and returns with a grid (plus geometry)
Parameters
----------
index : int or array_like, optional
the index of the potential to read. For a spin-polarized VASP calculation 0 and 1 are
allowed, UP/DOWN. For non-collinear 0, 1, 2 or 3 is allowed which equals,
TOTAL, x, y, z total potential with the Cartesian directions equal to the potential
for the magnetization directions. For array-like they refer to the fractional
contributions for each corresponding index.
dtype : numpy.dtype, optional
grid stored dtype
Returns
-------
Grid : potential with associated geometry
"""
geom = self.read_geometry()
V = geom.sc.volume
# Now we are past the cell and geometry
# We can now read the size of LOCPOT
self.readline()
nx, ny, nz = list(map(int, self.readline().split()))
n = nx * ny * nz
is_index = True
if isinstance(index, Integral):
max_index = index + 1
else:
is_index = False
max_index = len(index)
rl = self.readline
vals = []
vapp = vals.append
i = 0
while i < n * max_index:
dat = [l for l in rl().split()]
vapp(dat)
i += len(dat)
if i % n == 0 and i < n * max_index:
# Each time a new spin-index is present, we need to read the coordinates
j = 0
while j < geom.na:
j += len(rl().split())
# one line of nx, ny, nz
rl()
# Cut size before proceeding (otherwise it *may* fail)
vals = np.array(vals).astype(dtype).ravel()
if is_index:
val = vals[n * index:n * (index + 1)].reshape(nz, ny, nx)
else:
vals = vals[:n * max_index].reshape(-1, nz, ny, nx)
val = vals[0] * index[0]
for i, scale in enumerate(index[1:]):
val += vals[i + 1] * scale
del vals
# Make it C-ordered with nx, ny, nz
val = np.swapaxes(val, 0, 2) / V
# Create the grid with data
# Since we populate the grid data afterwards there
# is no need to create a bigger grid than necessary.
grid = Grid([1, 1, 1], dtype=dtype, geometry=geom)
grid.grid = val
return grid
add_sile('LOCPOT', locpotSileVASP, gzip=True)