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#! /usr/bin/python
#
# Copyright (C) 2003-2022 ABINIT group
#
# Written by Gabriel Antonius in python (compatible v2.7).
# This is free software, and you are welcome to redistribute it
# under certain conditions (GNU General Public License,
# see ~abinit/COPYING or http://www.gnu.org/copyleft/gpl.txt).
#
# ABINIT is a project of the Universite Catholique de Louvain,
# Corning Inc. and other collaborators, see ~abinit/doc/developers/contributors.txt.
# Please read ~abinit/doc/biblio/generated_files/bib_acknow.html for suggested
# acknowledgments of the ABINIT effort.
#
# For more information, see https://www.abinit.org .
"""
This script can be run interactively,
but it is recommended to import it as a module:
>>> from merge_ddb_nc import merge_ddb_nc
>>> merge_ddb_nc(out_fname, fnames)
"""
from __future__ import print_function
import numpy as np
import netCDF4 as nc
__version__ = '1.0.0'
def merge_ddb_nc(out_fname, fnames):
"""
Merge a list of DDB.nc files containing different elements of the same qpoint.
Arguments
---------
out_fname: Name for the merged file (will overwrite any existing file).
fnames: List of DDB.nc files.
"""
if not fnames:
raise Exception('Empty list of files given for merge')
fname0 = fnames.pop(0)
with nc.Dataset(out_fname, 'w') as dsout:
with nc.Dataset(fname0, 'r') as dsin:
nc_copy(dsin, dsout)
q0 = dsin.variables[u'q_point_reduced_coord'][...]
for fname in fnames:
with nc.Dataset(fname, 'r') as dsin:
# Check that the qpoints are the same
q = dsin.variables[u'q_point_reduced_coord'][...]
if not all(np.isclose(q0, q)):
raise Exception('Cannot merge DDB.nc at different q-points.')
# Merge dynamical matrix
dynmat = dsin.variables[u'second_derivative_of_energy'][...]
dynmat_mask = dsin.variables[u'second_derivative_of_energy_mask'][...]
out_dynmat = dsin.variables[u'second_derivative_of_energy']
out_dynmat_mask = dsin.variables[u'second_derivative_of_energy_mask']
ni,nj,nk,nl = dynmat_mask.shape
for i in range(ni):
for j in range(nj):
for k in range(nk):
for l in range(nl):
if dynmat_mask[i,j,k,l]:
dsout.variables[u'second_derivative_of_energy'][i,j,k,l,:] = (
dynmat[i,j,k,l,:])
dsout.variables[u'second_derivative_of_energy_mask'][i,j,k,l] = (
dynmat_mask[i,j,k,l])
# Born effective charge tensor
BECT = dsin.variables[u'born_effective_charge_tensor'][...]
BECT_mask = dsin.variables[u'born_effective_charge_tensor_mask'][...]
ni,nj,nk = BECT_mask.shape
for i in range(ni):
for j in range(nj):
for k in range(nk):
if BECT_mask[i,j,k]:
dsout.variables[u'born_effective_charge_tensor'][i,j,k] = (
BECT[i,j,k])
dsout.variables[u'born_effective_charge_tensor_mask'][i,j,k] = (
BECT_mask[i,j,k])
def nc_copy(dsin, dsout):
"""
Copy all dimensions and variable of one nc.Dataset instance into another.
"""
#Copy dimensions
for dname, dim in dsin.dimensions.iteritems():
dsout.createDimension(dname, len(dim))
#Copy variables
for vname, varin in dsin.variables.iteritems():
outVar = dsout.createVariable(vname, varin.datatype, varin.dimensions)
outVar[...] = varin[...]
def interactive_merge_ddb_nc():
"""Get inputs from the user and run merge_ddb_nc."""
program_name = 'merge_ddb_nc'
description = """Merge several DDB.nc files, belonging to the same q-point."""
def get_user(s):
return raw_input(s.rstrip() + '\n').split('#')[0]
print(program_name)
print(len(program_name) * '-')
print(description + '\n')
ui = get_user('Enter a name for the output file in which to merge (will overwrite any existing file):')
out_fname = str(ui)
ui = get_user('Enter the number of files to merge:')
nfiles = int(ui)
fnames = list()
for i in range(nfiles):
ui = get_user('Enter the name of file {}:'.format(i+1))
fname = str(ui)
fnames.append(fname)
# Main execution
print('Executing...')
merge_ddb_nc(out_fname, fnames)
print('All done.')
# =========================================================================== #
# Run interactive program
# =========================================================================== #
if __name__ == '__main__':
interactive_merge_ddb_nc()
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