mirror of https://github.com/phonopy/phonopy.git
Merge branch 'merge-dftb-interface' into develop
This commit is contained in:
Atsushi Togo
commit
7cc8ca802e
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@ -0,0 +1,51 @@
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.. _dftbp_interface:
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|
||||
DFTB+ & phonopy calculation
|
||||
=========================================
|
||||
|
||||
How to run
|
||||
-----------
|
||||
|
||||
DFTB+ phonon band structures are created as follows:
|
||||
|
||||
1) Create a DFTB+ input file dftb_in.hsd that is set up to perform a
|
||||
single-point energy and force calculation for a structure which is named
|
||||
``geo.gen``. The dftb_in.hsd file should turn on force evaluation by setting
|
||||
``CalculateForces = Yes`` in its analysis block, and write the tagged results
|
||||
by enabling ``WriteResultsTag = Yes`` in its options.
|
||||
|
||||
2) Generate the the required set of structures and the ``disp.yaml`` file by
|
||||
issuing the command ::
|
||||
|
||||
% phonopy -d --dim="4 4 4" --dftb+
|
||||
|
||||
This example builds 2 x 2 x 2 supercell files. The undistorted supercell is
|
||||
stored in ``geo.genS``, while the required displacements are stored in files
|
||||
matching the pattern ``geo.genS-*``. Note that you have to increase the
|
||||
supercell dimension until you reach convergence of the band structure.
|
||||
|
||||
2) For each each ``geo.genS-*`` structure perform a DFTB+ calculations,
|
||||
retaining the resulting ``detailed.out`` file.
|
||||
|
||||
3) Create the ``FORCE_SETS`` file with the command ::
|
||||
|
||||
% phonopy -f disp-*/results.tag --dftb+ ...
|
||||
|
||||
Where the location of all of the ``results.tag`` files is given on the
|
||||
command line. To run this command, the ``disp.yaml`` file has to be located
|
||||
in the current directory, because the atomic displacements are written into
|
||||
the FORCE_SETS file.
|
||||
|
||||
4) Create a ``band.conf`` file to specify the path in the Brillouin zone you are
|
||||
interested in (see the phonopy documentation). Then post-process the phonopy
|
||||
data, either in the settings file (DIM) or by providing the dimensions of the
|
||||
the supercell repeat on the command line ::
|
||||
|
||||
% phonopy -p band.conf --dim="4 4 4" --dftb+
|
||||
|
||||
|
||||
5) Create a band structure in gnuplot format ::
|
||||
|
||||
% phonopy-bandplot --gnuplot band.yaml > band.dat
|
||||
|
||||
All major phonopy options should be available for the DFTB+ interface.
|
||||
|
|
@ -0,0 +1,18 @@
|
|||
This is an example of the use of the DFTB+ interface. An input is
|
||||
given in the dftb_in.hsd file along with the conventional unit cell in
|
||||
geo.gen. This example also requires the pbc-0-3 Slater-Koster
|
||||
parameteters for carbon
|
||||
(https://www.dftb.org/parameters/download/pbc/pbc-0-3-cc/).
|
||||
|
||||
1) Create the (one) displaced supercell structure(s):
|
||||
phonopy -d --dim="4 4 4" --dftb+
|
||||
|
||||
2) Run the supercell input with dftb+. This has been pre-calculated
|
||||
with DFTB+ version 18.2, with the required data stored in the file
|
||||
results.tag.
|
||||
|
||||
3) Collect the forces:
|
||||
phonopy -f results.tag --dftb+ ...
|
||||
|
||||
4) Calculate phonon dispersion data into band.yaml and save band.pdf:
|
||||
phonopy --dftb+ --dim="4 4 4" -p -s band.conf
|
||||
|
|
@ -0,0 +1,3 @@
|
|||
BAND = 0 0 0 1/2 0 1/2 1/2 1/4 3/4 3/8 3/8 3/4 0 0 0 1/2 1/2 1/2 5/8 1/4 5/8 1/2 1/4 3/4 1/2 1/2 1/2 3/8 3/8 3/4, 5/8 1/4 5/8 1/2 0 1/2
|
||||
BAND_LABELS = $\Gamma$ X W K $\Gamma$ L U W L K:U X
|
||||
BAND_POINTS = 101
|
||||
|
|
@ -0,0 +1,48 @@
|
|||
# Input for DFTB+ diamond primitive cell example, see
|
||||
# https://www.dftbplus.org/ for details of code useage
|
||||
|
||||
Geometry = GenFormat {
|
||||
# geometry input file
|
||||
<<< geo.genS-001
|
||||
}
|
||||
|
||||
Hamiltonian = DFTB {
|
||||
|
||||
SCC = No # non-self-consistent, as diamond
|
||||
|
||||
MaxAngularMomentum = {
|
||||
C = "p" # s and p functions, read parameter file for details
|
||||
}
|
||||
|
||||
# local location of Slater-Koster parameter data files.
|
||||
# These are available at https://www.dftb.org/parameters
|
||||
SlaterKosterFiles = Type2FileNames {
|
||||
Separator = "-"
|
||||
Suffix = ".skf"
|
||||
}
|
||||
|
||||
# Example uses a fairly large supercell, so not many k-points are included
|
||||
KPointsAndWeights = SupercellFolding {
|
||||
2 0 0
|
||||
0 2 0
|
||||
0 0 2
|
||||
0.5 0.5 0.5
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
Options = {
|
||||
# Required options for storing data needed by phonopy
|
||||
WriteResultsTag = Yes
|
||||
}
|
||||
|
||||
ParserOptions = {
|
||||
# input parser version for DFTB+ 18.2, but this is backward
|
||||
# compatible
|
||||
ParserVersion = 6
|
||||
}
|
||||
|
||||
Analysis = {
|
||||
# required option for phonopy
|
||||
CalculateForces = Yes
|
||||
}
|
||||
|
|
@ -0,0 +1,14 @@
|
|||
8 F
|
||||
C
|
||||
1 1 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00
|
||||
2 1 0.2500000000E+00 0.2500000000E+00 0.2500000000E+00
|
||||
3 1 0.5000000000E+00 0.5000000000E+00 0.0000000000E+00
|
||||
4 1 0.7500000000E+00 0.7500000000E+00 0.2500000000E+00
|
||||
5 1 0.5000000000E+00 0.0000000000E+00 0.5000000000E+00
|
||||
6 1 0.7500000000E+00 0.2500000000E+00 0.7500000000E+00
|
||||
7 1 0.0000000000E+00 0.5000000000E+00 0.5000000000E+00
|
||||
8 1 0.2500000000E+00 0.7500000000E+00 0.7500000000E+00
|
||||
0.0000000000E+00 0.0000000000E+00 0.0000000000E+00
|
||||
0.3561772125E+01 0.0000000000E+00 0.0000000000E+00
|
||||
0.0000000000E+00 0.3561772125E+01 0.0000000000E+00
|
||||
0.0000000000E+00 0.0000000000E+00 0.3561772125E+01
|
||||
File diff suppressed because it is too large
Load Diff
|
|
@ -83,7 +83,8 @@ def get_parser():
|
|||
elk_mode=False,
|
||||
siesta_mode=False,
|
||||
cp2k_mode=False,
|
||||
fc_symmetry=False,
|
||||
dftbp_mode=False,
|
||||
fc_symmetry=None,
|
||||
fc_format=None,
|
||||
fc_spg_symmetry=False,
|
||||
fits_debye_model=False,
|
||||
|
|
@ -220,6 +221,9 @@ def get_parser():
|
|||
parser.add_argument(
|
||||
"-d", "--displacement", dest="is_displacement", action="store_true",
|
||||
help="Create supercells with displacements")
|
||||
parser.add_argument(
|
||||
"--dftb+", dest="dftbp_mode", action="store_true",
|
||||
help="Invoke dftb+ mode")
|
||||
parser.add_argument(
|
||||
"--dim", nargs='+', dest="supercell_dimension",
|
||||
help="Same behavior as DIM tag")
|
||||
|
|
|
|||
|
|
@ -48,14 +48,13 @@ def get_interface_mode(args):
|
|||
"""
|
||||
|
||||
calculator_list = ['wien2k', 'abinit', 'qe', 'elk', 'siesta', 'cp2k',
|
||||
'crystal', 'vasp']
|
||||
'crystal', 'vasp','dftbp']
|
||||
for calculator in calculator_list:
|
||||
mode = "%s_mode" % calculator
|
||||
if mode in args and args.__dict__[mode]:
|
||||
return calculator
|
||||
return None
|
||||
|
||||
|
||||
def write_supercells_with_displacements(interface_mode,
|
||||
supercell,
|
||||
cells_with_disps,
|
||||
|
|
@ -103,6 +102,9 @@ def write_supercells_with_displacements(interface_mode,
|
|||
optional_structure_info[1],
|
||||
num_unitcells_in_supercell,
|
||||
template_file="TEMPLATE")
|
||||
elif interface_mode == 'dftbp':
|
||||
from phonopy.interface.dftbp import write_supercells_with_displacements
|
||||
write_supercells_with_displacements(supercell, cells_with_disps)
|
||||
|
||||
|
||||
def read_crystal_structure(filename=None,
|
||||
|
|
@ -181,7 +183,10 @@ def read_crystal_structure(filename=None,
|
|||
from phonopy.interface.crystal import read_crystal
|
||||
unitcell, conv_numbers = read_crystal(cell_filename)
|
||||
return unitcell, (cell_filename, conv_numbers)
|
||||
|
||||
elif interface_mode == 'dftbp':
|
||||
from phonopy.interface.dftbp import read_dftbp
|
||||
unitcell = read_dftbp(cell_filename)
|
||||
return unitcell, (cell_filename,)
|
||||
|
||||
def get_default_cell_filename(interface_mode):
|
||||
if interface_mode == 'phonopy_yaml':
|
||||
|
|
@ -200,10 +205,11 @@ def get_default_cell_filename(interface_mode):
|
|||
return "unitcell.inp"
|
||||
elif interface_mode == 'crystal':
|
||||
return "crystal.o"
|
||||
elif interface_mode == 'dftbp':
|
||||
return "geo.gen"
|
||||
else:
|
||||
return None
|
||||
|
||||
|
||||
def get_default_supercell_filename(interface_mode):
|
||||
if interface_mode == 'phonopy_yaml':
|
||||
return "phonopy_disp.yaml"
|
||||
|
|
@ -219,6 +225,8 @@ def get_default_supercell_filename(interface_mode):
|
|||
return "supercell.inp"
|
||||
elif interface_mode == 'crystal':
|
||||
return None # supercell.ext can not be parsed by crystal interface.
|
||||
elif interface_mode == 'dftbp':
|
||||
return "geo.gen"
|
||||
else:
|
||||
return None
|
||||
|
||||
|
|
@ -244,12 +252,13 @@ def get_default_physical_units(interface_mode):
|
|||
qe : Ry, au, AMU, Ry/au
|
||||
siesta : eV, au, AMU, eV/Angstroem
|
||||
CRYSTAL : eV, Angstrom, AMU, eV/Angstroem
|
||||
DFTB+ : hartree, au, AMU hartree/au
|
||||
|
||||
"""
|
||||
|
||||
from phonopy.units import (Wien2kToTHz, AbinitToTHz, PwscfToTHz, ElkToTHz,
|
||||
SiestaToTHz, VaspToTHz, CP2KToTHz, CrystalToTHz,
|
||||
Hartree, Bohr)
|
||||
DftbpToTHz, Hartree, Bohr)
|
||||
|
||||
units = {'factor': None,
|
||||
'nac_factor': None,
|
||||
|
|
@ -305,6 +314,12 @@ def get_default_physical_units(interface_mode):
|
|||
units['distance_to_A'] = 1.0
|
||||
units['force_constants_unit'] = 'eV/Angstrom^2'
|
||||
units['length_unit'] = 'Angstrom'
|
||||
elif interface_mode == 'dftbp':
|
||||
units['factor'] = DftbpToTHz
|
||||
units['nac_factor'] = Hartree * Bohr
|
||||
units['distance_to_A'] = Bohr
|
||||
units['force_constants_unit'] = 'hartree/au^2'
|
||||
units['length_unit'] = 'Angstrom'
|
||||
|
||||
return units
|
||||
|
||||
|
|
@ -334,7 +349,7 @@ def create_FORCE_SETS(interface_mode,
|
|||
"other files." % force_filenames[0])
|
||||
|
||||
if interface_mode in (None, 'vasp', 'abinit', 'elk', 'qe', 'siesta',
|
||||
'cp2k', 'crystal'):
|
||||
'cp2k', 'crystal', 'dftbp'):
|
||||
disp_dataset = parse_disp_yaml(filename=disp_filename)
|
||||
num_atoms = disp_dataset['natom']
|
||||
num_displacements = len(disp_dataset['first_atoms'])
|
||||
|
|
@ -415,6 +430,8 @@ def get_force_sets(interface_mode,
|
|||
from phonopy.interface.cp2k import parse_set_of_forces
|
||||
elif interface_mode == 'crystal':
|
||||
from phonopy.interface.crystal import parse_set_of_forces
|
||||
elif interface_mode == 'dftbp':
|
||||
from phonopy.interface.dftbp import parse_set_of_forces
|
||||
else:
|
||||
return []
|
||||
|
||||
|
|
|
|||
|
|
@ -0,0 +1,219 @@
|
|||
# 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.structure.atoms import Atoms
|
||||
from phonopy.units import dftbpToBohr
|
||||
from phonopy.file_IO import collect_forces
|
||||
from phonopy.interface.vasp import (get_scaled_positions_lines, check_forces,
|
||||
get_drift_forces)
|
||||
|
||||
def parse_set_of_forces(num_atoms, forces_filenames, verbose=True):
|
||||
hook = 'forces :real:2:'
|
||||
is_parsed = True
|
||||
force_sets = []
|
||||
for i, filename in enumerate(forces_filenames):
|
||||
if verbose:
|
||||
sys.stdout.write("%d. " % (i + 1))
|
||||
|
||||
f = open(filename)
|
||||
dftbp_forces = collect_forces(f, num_atoms, hook, [0, 1, 2])
|
||||
if check_forces(dftbp_forces, num_atoms, filename, verbose=verbose):
|
||||
drift_force = get_drift_forces(dftbp_forces,
|
||||
filename=filename,
|
||||
verbose=verbose)
|
||||
force_sets.append(np.array(dftbp_forces) - drift_force)
|
||||
else:
|
||||
is_parsed = False
|
||||
|
||||
if is_parsed:
|
||||
return force_sets
|
||||
else:
|
||||
return []
|
||||
|
||||
|
||||
#
|
||||
# read dftbp-files
|
||||
#
|
||||
|
||||
def read_dftbp(filename):
|
||||
""" Reads DFTB+ structure files in gen format.
|
||||
|
||||
Args:
|
||||
filename: name of the gen-file to be read
|
||||
|
||||
Returns:
|
||||
atoms: an object of the phonopy.Atoms class, representing the structure
|
||||
found in filename
|
||||
"""
|
||||
|
||||
infile = open(filename, 'r')
|
||||
|
||||
lines = infile.readlines()
|
||||
|
||||
# remove any comments
|
||||
for ss in lines:
|
||||
if ss.strip().startswith('#'):
|
||||
lines.remove(ss)
|
||||
|
||||
natoms = int(lines[0].split()[0])
|
||||
symbols = lines[1].split()
|
||||
|
||||
if (lines[0].split()[1].lower() == 'f'):
|
||||
is_scaled = True
|
||||
scale_pos = 1
|
||||
scale_latvecs = dftbpToBohr
|
||||
else:
|
||||
is_scaled = False
|
||||
scale_pos = dftbpToBohr
|
||||
scale_latvecs = dftbpToBohr
|
||||
|
||||
# assign positions and expanded symbols
|
||||
positions = []
|
||||
expaned_symbols = []
|
||||
|
||||
for ii in range(2, natoms+2):
|
||||
lsplit = lines[ii].split()
|
||||
|
||||
expaned_symbols.append(symbols[int(lsplit[1]) - 1])
|
||||
positions.append([float(ss)*scale_pos for ss in lsplit[2:5]])
|
||||
|
||||
# origin is ignored, may be used in future
|
||||
origin = [float(ss) for ss in lines[natoms+2].split()]
|
||||
|
||||
# assign coords of unitcell
|
||||
cell = []
|
||||
|
||||
for ii in range(natoms+3, natoms+6):
|
||||
lsplit = lines[ii].split()
|
||||
|
||||
cell.append([float(ss)*scale_latvecs for ss in lsplit[:3]])
|
||||
cell = np.array(cell)
|
||||
|
||||
if is_scaled:
|
||||
atoms = Atoms(symbols=expaned_symbols,
|
||||
cell=cell,
|
||||
scaled_positions=positions)
|
||||
else:
|
||||
atoms = Atoms(symbols=expaned_symbols,
|
||||
cell=cell,
|
||||
positions=positions)
|
||||
|
||||
return atoms
|
||||
|
||||
#
|
||||
# write dftb+ .gen-file
|
||||
#
|
||||
def get_reduced_symbols(symbols):
|
||||
"""Reduces expanded list of symbols.
|
||||
|
||||
Args:
|
||||
symbols: list containing any chemical symbols as often as
|
||||
the atom appears in the structure
|
||||
|
||||
Returns:
|
||||
reduced_symbols: any symbols appears only once
|
||||
"""
|
||||
|
||||
reduced_symbols = []
|
||||
|
||||
for ss in symbols:
|
||||
if not (ss in reduced_symbols):
|
||||
reduced_symbols.append(ss)
|
||||
|
||||
return reduced_symbols
|
||||
|
||||
def write_dftbp(filename, atoms):
|
||||
"""Writes DFTB+ readable, gen-formatted structure files
|
||||
|
||||
Args:
|
||||
filename: name of the gen-file to be written
|
||||
atoms: object containing information about structure
|
||||
"""
|
||||
scale_pos = dftbpToBohr
|
||||
|
||||
lines = ""
|
||||
|
||||
# 1. line, use absolute positions
|
||||
natoms = atoms.get_number_of_atoms()
|
||||
lines += str(natoms)
|
||||
lines += ' S \n'
|
||||
|
||||
# 2. line
|
||||
expaned_symbols = atoms.get_chemical_symbols()
|
||||
symbols = get_reduced_symbols(expaned_symbols)
|
||||
lines += ' '.join(symbols) + '\n'
|
||||
|
||||
atom_numbers = []
|
||||
for ss in expaned_symbols:
|
||||
atom_numbers.append(symbols.index(ss) + 1)
|
||||
|
||||
positions = atoms.get_positions()/scale_pos
|
||||
|
||||
for ii in range(natoms):
|
||||
pos = positions[ii]
|
||||
pos_str = "{:3d} {:3d} {:20.15f} {:20.15f} {:20.15f}\n".format(
|
||||
ii + 1, atom_numbers[ii], pos[0], pos[1], pos[2])
|
||||
lines += pos_str
|
||||
|
||||
# origin arbitrary
|
||||
lines +='0.0 0.0 0.0\n'
|
||||
|
||||
cell = atoms.get_cell()/scale_pos
|
||||
|
||||
for ii in range(3):
|
||||
cell_str = "{:20.15f} {:20.15f} {:20.15f}\n".format(
|
||||
cell[ii][0], cell[ii][1], cell[ii][2])
|
||||
lines += cell_str
|
||||
|
||||
outfile = open(filename, 'w')
|
||||
outfile.write(lines)
|
||||
|
||||
def write_supercells_with_displacements(supercell, cells_with_disps, filename="geo.gen"):
|
||||
"""Writes perfect supercell and supercells with displacements
|
||||
|
||||
Args:
|
||||
supercell: perfect supercell
|
||||
cells_with_disps: supercells with displaced atoms
|
||||
filename: root-filename
|
||||
"""
|
||||
|
||||
# original cell
|
||||
write_dftbp(filename + "S", supercell)
|
||||
|
||||
# displaced cells
|
||||
for ii in range(len(cells_with_disps)):
|
||||
write_dftbp(filename + "S-{:03d}".format(ii+1), cells_with_disps[ii])
|
||||
|
|
@ -68,4 +68,6 @@ ElkToTHz = sqrt(Hartree*EV/AMU)/(Bohr*1e-10)/(2*pi)/1e12 # [THz] 154.10794
|
|||
SiestaToTHz = sqrt(EV/(AMU*Bohr))/Angstrom/(2*pi)/1e12 # [THz] 21.49068
|
||||
CP2KToTHz = ElkToTHz # CP2K uses a.u. units (Hartree/Bohr)
|
||||
CrystalToTHz = VaspToTHz
|
||||
DftbpToTHz = sqrt(Hartree*EV/AMU)/(Bohr*1e-10)/(2*pi)/1e12 # [THz] 154.10794344
|
||||
dftbpToBohr = 0.188972598857892E+01
|
||||
EVAngstromToGPa = EV * 1e21
|
||||
|
|
|
|||
Loading…
Reference in New Issue