Source code for sisl.io.siesta.fc

# 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/.
import numpy as np

from sisl._internal import set_module
from sisl.messages import warn
from sisl.unit.siesta import unit_convert

from ..sile import add_sile, sile_fh_open
from .sile import SileSiesta

__all__ = ["fcSileSiesta"]


@set_module("sisl.io.siesta")
class fcSileSiesta(SileSiesta):
    """Force constant file"""

[docs] @sile_fh_open() def read_force(self, displacement=None, na=None): """Reads all displacement forces by multiplying with the displacement value Since the force constant file does not contain the non-displaced configuration this will only return forces on the displaced configurations minus the forces from the non-displaced configuration. This may be used in conjunction with phonopy by noticing that Siesta FC-runs does the displacements in reverse order (-x/+x vs. +x/-x). In this case one should reorder the elements like this: >>> fc = np.roll(fc, 1, axis=2) Parameters ---------- displacement : float, optional the used displacement in the calculation, since Siesta 4.1-b4 this value is written in the FC file and hence not required. If prior Siesta versions are used and this is not supplied the 0.04 Bohr displacement will be assumed. na : int, optional number of atoms in geometry (for returning correct number of atoms), since Siesta 4.1-b4 this value is written in the FC file and hence not required. If prior Siesta versions are used then the file is expected to only contain 1-atom displacement. Returns ------- numpy.ndarray : (displaced atoms, d[xyz], [-+], total atoms, xyz) force constant matrix times the displacement, see `read_force_constant` for details regarding data layout. """ if displacement is None: line = self.readline().split() self.fh.seek(0) try: displacement = float(line[-1]) except Exception: warn( f"{self.__class__.__name__}.read_force assumes displacement=0.04 Bohr!" ) displacement = 0.04 * unit_convert("Bohr", "Ang") # Since the displacements changes sign (starting with a negative sign) # we can convert using this scheme displacement = np.repeat(displacement, 6).ravel() displacement[1::2] *= -1 return self.read_force_constant(na) * displacement.reshape(1, 3, 2, 1, 1)
[docs] @sile_fh_open() def read_force_constant(self, na=None): """Reads the force-constant stored in the FC file Parameters ---------- na : int, optional number of atoms in the unit-cell, if not specified it will guess on only one atom displacement. Returns ------- numpy.ndarray : (displacement, d[xyz], [-+], atoms, xyz) force constant matrix containing all forces. The 2nd dimension contains contains the directions, 3rd dimension contains -/+ displacements. """ # Force constants matrix line = self.readline().split() if na is None: try: na = int(line[-2]) except Exception: na = None fc = list() while True: line = self.readline() if line == "": # empty line or nothing break fc.append(list(map(float, line.split()))) # Units are already eV / Ang ** 2 fc = np.array(fc) # Slice to correct size if na is None: na = fc.size // 6 // 3 # Correct shape of matrix fc.shape = (-1, 3, 2, na, 3) return fc
add_sile("FC", fcSileSiesta, gzip=True) add_sile("FCC", fcSileSiesta, gzip=True)