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plot_modes.py
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plot_modes.py
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#!/usr/bin/env python
import sys
import numpy as np
import argparse as arg
import matplotlib.pyplot as plt
from matplotlib import ticker, gridspec
from matplotlib import rc
import matplotlib as mpl
rc('font',**{'family':'sans-serif','sans-serif':['Helvetica']})
## for Palatino and other serif fonts use:
#rc('font',**{'family':'serif','serif':['Palatino']})
rc('text', usetex=True)
pgf_with_latex = { # setup matplotlib to use latex for output
"pgf.texsystem": "pdflatex", # change this if using xetex or lautex
"text.usetex": True, # use LaTeX to write all text
"font.family": "serif",
"font.serif": [], # blank entries should cause plots
"font.sans-serif": [], # to inherit fonts from the document
"font.monospace": [],
# "pgf.preamble": [
# r"\usepackage[utf8x]{inputenc}",
# r"\usepackage[T1]{fontenc}",
# r"\usepackage{siunitx}",
# ]
}
mpl.rcParams.update(pgf_with_latex)
def options():
'''Defines the options of the script.'''
parser = arg.ArgumentParser(
formatter_class=arg.ArgumentDefaultsHelpFormatter)
#
# Input Options
#
inp = parser.add_argument_group("Input Data")
inp.add_argument('-f', '--file', type=str, dest='ModesFile',
help='''Normal Modes comparison file.''')
inp.add_argument('-c', '--color', type=str, default="b", dest='Color',
help='''Color of the plot.''')
#
# Output Options
#
out = parser.add_argument_group("Output Options")
out.add_argument('-p', '--pre', default=None, type=str, dest='OutPre',
help='''Output File Prefix.''')
out.add_argument('-o', '--output', default=None, type=str, dest='Out',
help='''Output File Format.''')
args = parser.parse_args()
Opts = vars(args)
return Opts
def plot_modes(modes, color="b"):
fig = plt.figure(figsize=(12, 6))
gs = gridspec.GridSpec(1, 1)
# Plot
ax = plt.subplot(gs[0])
x = np.arange(0, modes.max() + modes.max() / 10)
y = x
ax.plot(x, y, color="k", ls="--")
ax.scatter(np.sort(modes[:,0]), np.sort(modes[:,1]), color=color)
ax.set_xlabel(r"$\nu^{QM}$ / cm$^{-1}$", size=18, labelpad=5)
ax.set_ylabel(r"$\nu^{MM}$ / cm$^{-1}$", size=18, labelpad=5)
xtickmaj = ticker.MultipleLocator(500)
xtickmin = ticker.AutoMinorLocator(5)
ytickmaj = ticker.MultipleLocator(500)
ytickmin = ticker.AutoMinorLocator(5)
ax.xaxis.set_major_locator(xtickmaj)
ax.xaxis.set_minor_locator(xtickmin)
ax.yaxis.set_major_locator(ytickmaj)
ax.yaxis.set_minor_locator(ytickmin)
ax.xaxis.set_ticks_position('both')
ax.yaxis.set_ticks_position('both')
ax.tick_params(axis='both', which='major', direction='in', labelsize=16, pad=10, length=5)
ax.tick_params(axis='both', which='minor', direction='in', labelsize=16, pad=10, length=2)
ax.set_xlim(0, modes.max() + 50)
ax.set_ylim(0, modes.max() + 50)
return
def plot_overlap(overlap, color="b"):
fig = plt.figure(figsize=(12, 6))
gs = gridspec.GridSpec(1, 1)
# Sort
overlap = overlap[overlap[:,0].argsort()]
# Plot
ax = plt.subplot(gs[0])
ax.bar(overlap[:,0], overlap[:,1], color=color, width=1.0)
ax.set_xlabel(r"Normal Mode", size=18, labelpad=5)
# ax.set_ylabel(r"overlap", size=18, labelpad=5)
ax.set_ylabel(r"$\langle Q_i^{MM} \vert Q_i^{QM} \rangle$", size=18, labelpad=5)
ax.xaxis.set_label_position('top')
xtickmaj = ticker.MultipleLocator(20)
xtickmin = ticker.AutoMinorLocator(5)
ytickmaj = ticker.MultipleLocator(0.2)
ytickmin = ticker.AutoMinorLocator(3)
ax.xaxis.set_major_locator(xtickmaj)
ax.xaxis.set_minor_locator(xtickmin)
ax.yaxis.set_major_locator(ytickmaj)
ax.yaxis.set_minor_locator(ytickmin)
ax.xaxis.set_ticks_position('both')
ax.yaxis.set_ticks_position('both')
ax.tick_params(axis='both', which='major', direction='in', labelsize=16, pad=10, length=5, labeltop=True, labelbottom=False)
ax.tick_params(axis='both', which='minor', direction='in', labelsize=16, pad=10, length=2)
ax.set_xlim(0, overlap[:,0].max())
ax.set_ylim(0, 1)
return
if __name__ == '__main__':
Opts = options()
modes_file = np.loadtxt(Opts["ModesFile"])
modes = np.c_ [ modes_file[:,3], modes_file[:,1] ]
ovlp = np.c_ [ modes_file[:,0], modes_file[:,-2] ]
plot_modes(modes, color=Opts["Color"])
if Opts["Out"]:
if Opts["OutPre"]:
name = "%s_modes.%s" % (Opts["OutPre"], Opts["Out"])
else:
name = "modes.%s" % Opts["Out"]
plt.savefig(name, dpi=600)
else:
plt.show()
plot_overlap(ovlp, color=Opts["Color"])
if Opts["Out"]:
if Opts["OutPre"]:
name = "%s_ovlp.%s" % (Opts["OutPre"], Opts["Out"])
else:
name = "ovlp.%s" % Opts["Out"]
plt.savefig(name, dpi=600)
else:
plt.show()