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Start to implement ELK interface

This commit is contained in:
Atsushi Togo 2015-03-29 12:27:06 +09:00
parent 122c419cc0
commit 15d0c5a754
2 changed files with 203 additions and 17 deletions
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186
phonopy/interface/elk.py Normal file
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@ -0,0 +1,186 @@
# Copyright (C) 2015 Atsushi Togo
# All rights reserved.
#
# This file is part of phonopy.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions
# are met:
#
# * Redistributions of source code must retain the above copyright
# notice, this list of conditions and the following disclaimer.
#
# * Redistributions in binary form must reproduce the above copyright
# notice, this list of conditions and the following disclaimer in
# the documentation and/or other materials provided with the
# distribution.
#
# * Neither the name of the phonopy project nor the names of its
# contributors may be used to endorse or promote products derived
# from this software without specific prior written permission.
#
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
# "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
# LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS
# FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE
# COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT,
# INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
# BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
# CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
# LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN
# ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
# POSSIBILITY OF SUCH DAMAGE.
import sys
import numpy as np
from phonopy.file_IO import collect_forces, get_drift_forces
from phonopy.interface.vasp import get_scaled_positions_lines, sort_positions_by_symbols
from phonopy.units import Bohr
from phonopy.structure.atoms import Atoms, symbol_map
def parse_set_of_forces(displacements,
forces_filenames,
num_atom):
return True
def read_elk(filename):
elk_in = ElkIn(open(filename).readlines())
tags = elk_in.get_variables()
avec = [tags['scale'][i] * np.array(tags['avec'][i]) for i in range(3)]
symbols = [x.split('.')[0] for x in tags['atoms']['spfnames']]
numbers = []
for s in symbols:
if s in symbols:
numbers.append(symbol_map[s])
else:
numbers.append(0)
for i, n in enumerate(numbers):
if n == 0:
for j in range(1, 119):
if not (j in numbers):
numbers[i] = j
break
pos_all = []
num_all = []
for num, pos in zip(numbers, tags['atoms']['positions']):
pos_all += pos
num_all += [num] * len(pos)
return Atoms(numbers=num_all,
cell=avec,
scaled_positions=pos_all)
def write_elk(filename, cell):
f = open(filename, 'w')
f.write(get_elk_structure(cell))
def write_supercells_with_displacements(supercell,
cells_with_displacements):
write_elk("supercell.in", supercell)
for i, cell in enumerate(cells_with_displacements):
write_elk("supercell-%03d.in" % (i + 1), cell)
def get_elk_structure(cell):
lattice = cell.get_cell()
(num_atoms,
symbols,
scaled_positions,
sort_list) = sort_positions_by_symbols(cell.get_chemical_symbols(),
cell.get_scaled_positions())
lines = ""
lines += "avec\n"
lines += ((" %21.16f" * 3 + "\n") * 3) % tuple(lattice.ravel())
lines += "atoms\n"
n_pos = 0
lines += " %d\n" % len(num_atoms)
for i, (n, s) in enumerate(zip(num_atoms, symbols)):
lines += " \'%s.in\'\n" % s
lines += " %d\n" % n
lines += get_scaled_positions_lines(scaled_positions[n_pos:(n_pos + n)])
if i < len(num_atoms) - 1:
lines += "\n"
n_pos += n
return lines
class ElkIn:
def __init__(self, lines):
self._set_methods = {'atoms': self._set_atoms,
'avec': self._set_avec,
'scale': self._set_scale,
'scale1': self._set_scale1,
'scale2': self._set_scale2,
'scale3': self._set_scale3}
self._tags = {'atoms': None,
'avec': None,
'scale': [1.0, 1.0, 1.0]}
self._lines = iter(lines)
self._collect()
def get_variables(self):
return self._tags
def _collect(self):
elements = {}
while True:
try:
line_str = self._lines.next().strip()
except StopIteration:
break
if len(line_str) == 0:
continue
if line_str[0] == '!':
continue
elems = line_str.split()
if elems[0] in self._set_methods:
self._set_methods[elems[0]]()
def _set_atoms(self):
nspecies = int(self._lines.next().split()[0])
spfnames = []
positions = []
for i in range(nspecies):
spfnames.append(self._lines.next().split()[0].strip('\''))
natoms = int(self._lines.next().split()[0])
pos_sp = []
for j in range(natoms):
pos_sp.append(
[float(x) for x in self._lines.next().split()[:3]])
positions.append(pos_sp)
self._tags['atoms'] = {'spfnames': spfnames,
'positions': positions}
def _set_avec(self):
avec = []
for i in range(3):
avec.append([float(x) for x in self._lines.next().split()[:3]])
self._tags['avec'] = avec
def _set_scale(self):
scale = float(self._lines.next().split()[0])
for i in range(3):
self._tags['scale'][i] = scale
def _set_scale1(self):
self._tags['scale'][0] = float(self._lines.next().split()[0])
def _set_scale2(self):
self._tags['scale'][1] = float(self._lines.next().split()[0])
def _set_scale3(self):
self._tags['scale'][2] = float(self._lines.next().split()[0])
if __name__ == '__main__':
import sys
from phonopy.structure.symmetry import Symmetry
cell = read_elk(sys.argv[1])
symmetry = Symmetry(cell)
print "#", symmetry.get_international_table()
print get_elk_structure(cell)

34
phonopy/interface/vasp.py
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@ -239,8 +239,8 @@ def _write_magnetic_moments(cell):
(num_atoms,
symbols,
scaled_positions,
sort_list) = _sort_positions_by_symbols(cell.get_chemical_symbols(),
cell.get_scaled_positions())
sort_list) = sort_positions_by_symbols(cell.get_chemical_symbols(),
cell.get_scaled_positions())
w.write(" MAGMOM = ")
for i in sort_list:
w.write("%f " % magmoms[i])
@ -260,12 +260,25 @@ def get_scaled_positions_lines(scaled_positions):
return lines
def sort_positions_by_symbols(symbols, positions):
reduced_symbols = _get_reduced_symbols(symbols)
sorted_positions = []
sort_list = []
num_atoms = np.zeros(len(reduced_symbols), dtype=int)
for i, rs in enumerate(reduced_symbols):
for j, (s, p) in enumerate(zip(symbols, positions)):
if rs == s:
sorted_positions.append(p)
sort_list.append(j)
num_atoms[i] += 1
return num_atoms, reduced_symbols, np.array(sorted_positions), sort_list
def _get_vasp_structure(atoms, direct=True):
(num_atoms,
symbols,
scaled_positions,
sort_list) = _sort_positions_by_symbols(atoms.get_chemical_symbols(),
atoms.get_scaled_positions())
sort_list) = sort_positions_by_symbols(atoms.get_chemical_symbols(),
atoms.get_scaled_positions())
lines = ""
for s in symbols:
lines += "%s " % s
@ -287,19 +300,6 @@ def _get_reduced_symbols(symbols):
reduced_symbols.append(s)
return reduced_symbols
def _sort_positions_by_symbols(symbols, positions):
reduced_symbols = _get_reduced_symbols(symbols)
sorted_positions = []
sort_list = []
num_atoms = np.zeros(len(reduced_symbols), dtype=int)
for i, rs in enumerate(reduced_symbols):
for j, (s, p) in enumerate(zip(symbols, positions)):
if rs == s:
sorted_positions.append(p)
sort_list.append(j)
num_atoms[i] += 1
return num_atoms, reduced_symbols, np.array(sorted_positions), sort_list
#
# Non-analytical term
#