Source code for quippy.nmwiz

# HQ XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
# HQ X
# HQ X   quippy writer for normal mode (`.nmd`) files
# HQ X   Copyright Max Veit 2018
# HQ X   File format used by ProDy (http://prody.csb.pitt.edu/)
# HQ X   and VMD's NMWiz plugin
# HQ X   (http://www.ks.uiuc.edu/Research/vmd/plugins/nmwiz/)
# HQ X
# HQ X   Part of:
# HQ X   quippy: Python interface to QUIP atomistic simulation library
# HQ X   Copyright James Kermode 2010
# HQ X
# HQ X   These portions of the source code are released under the GNU General
# HQ X   Public License, version 2, http://www.gnu.org/copyleft/gpl.html
# HQ X
# HQ X   If you would like to license the source code under different terms,
# HQ X   please contact James Kermode, james.kermode@gmail.com
# HQ X
# HQ X   When using this software, please cite the following reference:
# HQ X
# HQ X   http://www.jrkermode.co.uk/quippy
# HQ X
# HQ XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
"""nmwiz: Write atoms and normal modes to '.nmd' format.

Contents:
    NMDWriter   Writer for the .nmd format
"""


from __future__ import division, print_function, unicode_literals
from itertools import izip
import sys

from numpy import abs, sqrt
import quippy
from quippy.io import AtomsWriters


[docs]class NMDWriter(object): """Writer for the '.nmd' format The Atoms object must have normal modes -- both eigenvectors and eigenvalues (force constants in the normal-mode basis) of the Hessian matrix -- stored in 'atoms.info["hessian_eigenvalue_X"]' and 'atoms.arrays["hessian_eigenvector_X"]', where 'X' ranges from 1 to the number of stored normal modes. This writer implements the context manager protocol, so you can use it like so: with NMDWriter(filename) as writer: writer.write(atoms) and the associated file will be closed automatically when done. The '.nmd' file format only supports single configurations, so this writer doesn't accept trajectories. """
[docs] def __init__(self, filename): """Open ``filename`` for writing (use ``-`` for stdout)""" if filename == '-': self._file = sys.stdout else: self._file = open(filename, 'w')
def __enter__(self): # The writer interface requires we open the file in __init__(), # so do nothing here. # In particular, don't reopen the file if it's already been closed. return self
[docs] def write(self, atoms, title='quippy atoms'): """Write out the atoms and modes with an optional title""" # Get the modes from the Atoms object try: mode_idx = 1 eigvecs = [] mode_idces = [] while True: mode_string = 'hessian_eigenvector_{:d}'.format(mode_idx) eigvecs.append(atoms.get_array(mode_string)) mode_idces.append(mode_idx) mode_idx += 1 except KeyError as kerr: if not mode_idces: # Oh great, Python 2 doesn't support exception chaining #py2kfacepalm #raise ValueError("Couldn't find any Hessian eigenvectors " # "in Atoms object") from kerr raise ValueError( "Couldn't find any Hessian eigenvectors in Atoms object " "(key '{:s}' missing)".format(mode_string)) try: eigvals = [] for mode_idx in mode_idces: mode_string = 'hessian_eigenvalue_{:d}'.format(mode_idx) eigvals.append(atoms.info[mode_string]) except KeyError as kerr: # This is how easy it would be in Python 3 #raise ValueError("Couldn't find Hessian eigenvalue number " # "{:d}".format(mode_idx)) from kerr raise ValueError("Couldn't find Hessian eigenvalue number " "{:d} (key '{:s}')".format(mode_idx, mode_string)) # Write the actual file self._file.write('title ' + title + '\n') self._file.write('coordinates ') atoms.get_positions().tofile(self._file, ' ', '%.6f') self._file.write('\n') self._file.write('names ') self._file.write(' '.join(atoms.get_chemical_symbols())) self._file.write('\n') for idx, eigval, eigvec in izip(mode_idces, eigvals, eigvecs): self._file.write('mode {:d} {:.6f} '.format(idx, eigval)) eigvec.tofile(self._file, ' ', '%.6f') self._file.write('\n')
def __exit__(self, exc_type, exc_value, traceback): if self._file is not sys.stdout: self._file.close() # Don't suppress any exceptions return False
[docs] def close(self): """Close the file (unnecessary if using the ``with`` statment)""" self.__exit__(None, None, None)
AtomsWriters['nmd'] = NMDWriter