# This Source Code Form is subject to the terms of the Mozilla Public
# License, v. 2.0. If a copy of the MPL was not distributed with this
# file, You can obtain one at https://mozilla.org/MPL/2.0/.
from __future__ import annotations
"""
Sile object for reading the force constant matrix written by GULP
"""
import numpy as np
from scipy.sparse import lil_matrix
from sisl._internal import set_module
from sisl.messages import deprecation
from ..sile import add_sile, sile_fh_open
from .sile import SileGULP
__all__ = ["fcSileGULP"]
@set_module("sisl.io.gulp")
class fcSileGULP(SileGULP):
"""GULP output file object"""
[docs]
@sile_fh_open()
def read_hessian(self, **kwargs):
"""Returns a sparse matrix in coo format which contains the GULP Hessian (force constant) matrix.
This routine expects the units to be in eV/Ang**2.
Parameters
----------
cutoff : float, optional
absolute values below the cutoff are considered 0. Defaults to 0 eV/Ang**2.
dtype: np.dtype (np.float64)
default data-type of the matrix
Returns
-------
M : Hessian/force constant in `scipy.sparse.coo_matrix` format
"""
# Default cutoff
cutoff = kwargs.get("cutoff", 0.0)
dtype = kwargs.get("dtype", np.float64)
# Read number of atoms in the file...
na = int(self.readline())
no = na * 3
fc = lil_matrix((no, no), dtype=dtype)
tmp = np.empty([3, na, 3], dtype=dtype)
# Reduce overhead...
rl = self.fh.readline
for ia in range(na):
i = ia * 3
for ja in range(na):
# read line that should contain:
# ia ja
lsplit = rl().split()
assert int(lsplit[0]) == ia + 1, "Inconsistent 2ND file data"
assert int(lsplit[1]) == ja + 1, "Inconsistent 2ND file data"
# Read 3x3 data
tmp[0, ja, :] = rl().split()
tmp[1, ja, :] = rl().split()
tmp[2, ja, :] = rl().split()
# much faster assignment
fc[i, :] = tmp[0].ravel()
fc[i + 1, :] = tmp[1].ravel()
fc[i + 2, :] = tmp[2].ravel()
# Convert to COO format
fc = fc.tocoo()
fc.data[np.fabs(fc.data) < cutoff] = 0.0
fc.eliminate_zeros()
return fc
read_force_constant = deprecation(
"read_force_constant is deprecated in favor of read_hessian", "0.15", "0.16"
)(read_hessian)
add_sile("FORCE_CONSTANTS_2ND", fcSileGULP, gzip=True)