mirror of https://github.com/phonopy/phonopy.git
196 lines
6.7 KiB
Python
Executable File
196 lines
6.7 KiB
Python
Executable File
#!/usr/bin/env python
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# Copyright (C) 2011 Atsushi Togo
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# All rights reserved.
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#
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# This file is part of phonopy.
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#
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# Redistribution and use in source and binary forms, with or without
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# modification, are permitted provided that the following conditions
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# are met:
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#
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# * Redistributions of source code must retain the above copyright
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# notice, this list of conditions and the following disclaimer.
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#
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# * Redistributions in binary form must reproduce the above copyright
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# notice, this list of conditions and the following disclaimer in
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# the documentation and/or other materials provided with the
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# distribution.
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#
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# * Neither the name of the phonopy project nor the names of its
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# contributors may be used to endorse or promote products derived
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# from this software without specific prior written permission.
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#
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# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
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# "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
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# LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS
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# FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE
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# COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT,
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# INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
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# BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
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# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
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# CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
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# LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN
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# ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
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# POSSIBILITY OF SUCH DAMAGE.
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# Thermal displacement plot (tdplot)
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#
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# Usage:
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# tdplot -i "1 2, 4 5" -o "td.pdf"
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#
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# The axis resolved thermal displacements are averaged by root mean
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# square with the successive indices separated by ",". In this
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# example, values at a temperature with the indices 1 and 2, 3 and 4
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# are averaged by root mean square respectively as follwos:
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# sqrt( ( x_1 ** 2 + x_2 ** 2 + x_3 ** 2 + x_4 ** 2 ) / 4 ),
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# and then they are ploted as a function of temperature.
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#
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# The definition is that indices correspond to those as follows:
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# 1 2 3 : X Y Z of the 1st atom,
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# 4 5 6 : X Y Z of the 2nd atom,
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# ...
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import sys
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import numpy as np
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import matplotlib.pyplot as plt
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try:
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import yaml
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except ImportError:
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print("You need to install python-yaml.")
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sys.exit(1)
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try:
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from yaml import CLoader as Loader
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from yaml import CDumper as Dumper
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except ImportError:
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from yaml import Loader, Dumper
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# Parse options
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from optparse import OptionParser
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parser = OptionParser()
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parser.set_defaults(output_filename=None,
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factor=1.0,
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td_indices=None,
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show_legend=False,
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is_distance=False,
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is_gnuplot=False,
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ymax=None,
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ymin=None,
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tmax=None,
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tmin=None)
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parser.add_option("-i", "--indices", dest="td_indices",
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action="store", type="string",
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help="Indices like 1 2, 3 4 5 6...")
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parser.add_option("--factor", dest="factor", type="float",
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help="Conversion factor of energy unit to internal electronic energy")
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parser.add_option("--ymax", dest="ymax", type="float",
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help="Maximum value of y axis")
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parser.add_option("--ymin", dest="ymin", type="float",
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help="Minimum value of y axis")
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parser.add_option("--tmax", dest="tmax", type="float",
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help="Maximum value of temperature")
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parser.add_option("--tmin", dest="tmin", type="float",
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help="Minimum value of temperature")
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parser.add_option("-o", "--output", dest="output_filename",
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action="store", type="string",
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help="Output filename")
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parser.add_option("-l", "--legend", dest="show_legend",
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action="store_true",
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help="Show legend")
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parser.add_option("--distance", dest="is_distance",
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action="store_true",
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help="Plot thermal distance")
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(options, args) = parser.parse_args()
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if not options.is_distance:
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if len(args) == 0:
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filename = 'thermal_displacements.yaml'
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else:
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filename = args[0]
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yamldata = yaml.load(open(filename).read(), Loader=Loader)
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td = yamldata['thermal_displacements']
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temperatures = [v['temperature'] for v in td]
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displacements = [v['displacements'] for v in td]
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displacements = np.array(displacements).reshape(len(temperatures), -1)
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else:
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if len(args) == 0:
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filename = 'thermal_distances.yaml'
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else:
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filename = args[0]
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yamldata = yaml.load(open(filename).read(), Loader=Loader)
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td = yamldata['thermal_distances']
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temperatures = [v['temperature'] for v in td]
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distances = [v['distance'] for v in td]
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for t, dists in zip(temperatures, distances):
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print(("%14.7f" * (len(dists) + 1)) % ((t,) + tuple(dists)))
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print('')
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print('')
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print('')
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sys.exit(0)
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# Set temperature range
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tmin_index = 0
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tmax_index = len(temperatures)
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if options.tmin is not None:
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for i, t in enumerate(temperatures):
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if t > options.tmin - (temperatures[1] - temperatures[0]) * 0.1:
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tmin_index = i
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break
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if options.tmax is not None:
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for i, t in enumerate(temperatures):
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if t > options.tmax + (temperatures[1] - temperatures[0]) * 0.1:
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tmax_index = i
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break
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# Extract indices
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set_of_indices = []
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if options.td_indices is None:
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set_of_indices.append(range(1, displacements.shape[1] + 1))
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else:
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for v in options.td_indices.split(','):
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set_of_indices.append([int(x) for x in v.split()])
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# Plot
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fig, ax = plt.subplots()
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ax.xaxis.set_ticks_position('both')
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ax.yaxis.set_ticks_position('both')
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ax.xaxis.set_tick_params(which='both', direction='in')
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ax.yaxis.set_tick_params(which='both', direction='in')
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plots = []
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for indices in set_of_indices:
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d = np.zeros(len(temperatures), dtype='double')
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for i in indices:
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d += displacements[:, i-1]
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plots.append(plt.plot(temperatures[tmin_index:tmax_index],
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d[tmin_index:tmax_index] / len(indices)))
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ax.set_xlim((0, temperatures[tmax_index - 1]))
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# Set y range
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if (options.ymin is not None) and (options.ymax is not None):
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plt.ylim(options.ymin, options.ymax)
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elif (options.ymin is None) and (options.ymax is not None):
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plt.ylim(ymax=options.ymax)
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elif (options.ymin is not None) and (options.ymax is None):
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plt.ylim(ymin=options.ymin)
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if options.show_legend:
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plt.legend(plots, set_of_indices, loc='upper left')
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# Set output device and show
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if options.output_filename is not None:
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plt.rcParams['pdf.fonttype'] = 42
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plt.rcParams['font.family'] = 'serif'
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plt.savefig(options.output_filename)
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else:
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plt.show()
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