from __future__ import division, print_function
# Import sile objects
from .sile import SileScaleUp
from ..sile import *
# Import the geometry object
import sisl._array as _a
from sisl import Geometry, Atom, SuperCell
from sisl.unit import unit_convert
import numpy as np
__all__ = ['refSileScaleUp', 'restartSileScaleUp']
Bohr2Ang = unit_convert('Bohr', 'Ang')
Ang2Bohr = unit_convert('Ang', 'Bohr')
[docs]class refSileScaleUp(SileScaleUp):
""" REF file object for ScaleUp """
[docs] @sile_fh_open()
def read_supercell(self):
""" Reads a supercell from the Sile """
# 1st line is number of supercells
nsc = _a.fromiteri(map(int, self.readline().split()[:3]))
self.readline() # natoms, nspecies
self.readline() # species
cell = _a.fromiterd(map(float, self.readline().split()[:9]))
# Typically ScaleUp uses very large unit-cells
# so supercells will typically be restricted to [3, 3, 3]
return SuperCell(cell * Bohr2Ang, nsc=nsc)
[docs] @sile_fh_open()
def read_geometry(self, primary=False, **kwargs):
""" Reads a geometry from the Sile """
# 1st line is number of supercells
nsc = _a.fromiteri(map(int, self.readline().split()[:3]))
na, ns = map(int, self.readline().split()[:2])
# Convert species to atom objects
try:
species = get_sile(self.file.rsplit('REF', 1)[0] + 'orbocc').read_atom()
except:
species = [Atom(s) for s in self.readline().split()[:ns]]
# Total number of super-cells
if primary:
# Only read in the primary unit-cell
ns = 1
else:
ns = np.prod(nsc)
cell = _a.fromiterd(map(float, self.readline().split()))
try:
cell.shape = (3, 3)
if primary:
cell[0, :] /= nsc[0]
cell[1, :] /= nsc[1]
cell[2, :] /= nsc[2]
except:
c = np.empty([3, 3], np.float64)
c[0, 0] = 1. + cell[0]
c[0, 1] = cell[5] / 2.
c[0, 2] = cell[4] / 2.
c[1, 0] = cell[5] / 2.
c[1, 1] = 1. + cell[1]
c[1, 2] = cell[3] / 2.
c[2, 0] = cell[4] / 2.
c[2, 1] = cell[3] / 2.
c[2, 2] = 1. + cell[2]
cell = c * Ang2Bohr
sc = SuperCell(cell * Bohr2Ang, nsc=nsc)
# Create list of coordinates and atoms
xyz = np.empty([na * ns, 3], np.float64)
atoms = [None] * na * ns
# Read the geometry
for ia in range(na * ns):
# Retrieve line
# ix iy iz ia is x y z
line = self.readline().split()
atoms[ia] = species[int(line[4]) - 1]
xyz[ia, :] = _a.fromiterd(map(float, line[5:8]))
return Geometry(xyz * Bohr2Ang, atoms, sc=sc)
[docs] @sile_fh_open()
def write_geometry(self, geom, fmt='18.8e'):
""" Writes the geometry to the contained file """
# Check that we can write to the file
sile_raise_write(self)
# 1st line is number of supercells
self._write('{:5d}{:5d}{:5d}\n'.format(*geom.sc.nsc // 2 + 1))
# natoms, nspecies
self._write('{:5d}{:5d}\n'.format(len(geom), len(geom.atom.atom)))
s = ''
for a in geom.atom.atom:
# Append the species label
s += '{:<10}'.format(a.tag)
self._write(s + '\n')
fmt_str = '{{:{0}}} '.format(fmt) * 9 + '\n'
self._write(fmt_str.format(*(geom.cell*Ang2Bohr).reshape(-1)))
# Create line
# ix iy iz ia is x y z
line = '{:5d}{:5d}{:5d}{:5d}{:5d}' + '{{:{0}}}'.format(fmt) * 3 + '\n'
args = [None] * 8
for _, isc in geom.sc:
if np.any(isc < 0):
continue
# Write the geometry
for ia in geom:
args[0] = isc[0]
args[1] = isc[1]
args[2] = isc[2]
args[3] = ia + 1
args[4] = geom.atom.specie[ia] + 1
args[5] = geom.xyz[ia, 0] * Ang2Bohr
args[6] = geom.xyz[ia, 1] * Ang2Bohr
args[7] = geom.xyz[ia, 2] * Ang2Bohr
self._write(line.format(*args))
def ArgumentParser(self, p=None, *args, **kwargs):
""" Returns the arguments that is available for this Sile """
newkw = Geometry._ArgumentParser_args_single()
newkw.update(kwargs)
return self.read_geometry().ArgumentParser(p, *args, **newkw)
# The restart file is _equivalent_ but with displacements
class restartSileScaleUp(refSileScaleUp):
@sile_fh_open()
def read_geometry(self, *args, **kwargs):
""" Read geometry of the restart file
This will also try and read the corresponding .REF file
such that final coordinates are returned.
Note that a .restart file from ScaleUp only contains the displacements
from a .REF file and thus it is not the *actual* atomic coordinates.
If the .REF file does not exist the returned cell vectors correspond
to the strain tensor (+1 along the diagonal).
"""
try:
ref = get_sile(self.file.rsplit('restart', 1)[0] + 'REF').read_geometry()
except:
ref = None
restart = super(restartSileScaleUp, self).read_geometry()
if not ref is None:
restart.sc = SuperCell(np.dot(ref.sc.cell, restart.sc.cell.T),
nsc=restart.nsc)
restart.xyz += ref.xyz
return restart
add_sile('REF', refSileScaleUp, case=False, gzip=True)
add_sile('restart', restartSileScaleUp, case=False, gzip=True)