#* **************************************************************************
#*
#* CDTK, Chemical Dynamics Toolkit
#* A modular system for chemical dynamics applications and more
#*
#* Copyright (C) 2011, 2012, 2013, 2014, 2015, 2016
#* Oriol Vendrell, DESY, <oriol.vendrell@desy.de>
#*
#* Copyright (C) 2017, 2018, 2019
#* Ralph Welsch, DESY, <ralph.welsch@desy.de>
#*
#* Copyright (C) 2020, 2021, 2022, 2023
#* Ludger Inhester, DESY, ludger.inhester@cfel.de
#*
#* This file is part of CDTK.
#*
#* CDTK is free software: you can redistribute it and/or modify
#* it under the terms of the GNU General Public License as published by
#* the Free Software Foundation, either version 3 of the License, or
#* (at your option) any later version.
#*
#* This program is distributed in the hope that it will be useful,
#* but WITHOUT ANY WARRANTY; without even the implied warranty of
#* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
#* GNU General Public License for more details.
#*
#* You should have received a copy of the GNU General Public License
#* along with this program. If not, see <http://www.gnu.org/licenses/>.
#*
#* **************************************************************************
import os
import os.path
import sys
from optparse import OptionParser
import numpy as np
import matplotlib.pylab as plt
from mpl_toolkits.mplot3d import Axes3D
import CDTK.Tools.Utils as uti
import CDTK.Tools.Mathematics as mat
[docs]
def start():
"""
Wrapper for starting the program. Needed for good unit test coding.
"""
fig = plt.figure()
#ax = Axes3D(fig)
# --------------------------------------------------------------------------
# Parse command line options
# --------------------------------------------------------------------------
parser=OptionParser()
parser.add_option('-n','--name',
dest='name',
type='str',
default=None,
help='Name of file to be found in trj directories')
parser.add_option('-a','--xmin',
dest='xmin',
type='float',
default=0.0,
help='lower limit, x axis')
parser.add_option('-x','--xmax',
dest='xmax',
type='float',
default=10.0,
help='upper limit, x axis')
parser.add_option('-b','--ymin',
dest='ymin',
type='float',
default=0.0,
help='lower limit, y axis')
parser.add_option('-y','--ymax',
dest='ymax',
type='float',
default=10.0,
help='upper limit, y axis')
parser.add_option('-l','--xlabel',
dest='xlabel',
type='str',
default=None,
help='text label for x axis')
parser.add_option('-L','--ylabel',
dest='ylabel',
type='str',
default=None,
help='text label for y axis')
parser.add_option('-u','--xfactor',
dest='xfactor',
type='float',
default=1.0,
help='scaling factor for x axis')
parser.add_option('-v','--yfactor',
dest='yfactor',
type='float',
default=1.0,
help='scaling factor for y axis')
parser.add_option('-w','--fwhm',
dest='fwhm',
type='float',
default=1.0,
help='full with at half maximum for Gaussian smoothing')
parser.add_option('-z','--xsteps',
dest='xsteps',
type='int',
default=500,
help='number of time steps being processed')
parser.add_option('-Z','--ysteps',
dest='ysteps',
type='int',
default=40,
help='number of discrete steps in the y axis')
parser.add_option('-N','--ncountour',
dest='ncontour',
type='int',
default=40,
help='number of contours')
opts, args = parser.parse_args(sys.argv[1:])
if not sys.argv[1:]: # called without any option
parser.print_help()
sys.exit(0)
# --------------------------------------------------------------------------
# Obtain list of trj directories
# --------------------------------------------------------------------------
dirs = uti.getDirectoryList()
# --------------------------------------------------------------------------
# Loop over directories and plot data file
# --------------------------------------------------------------------------
xf = opts.xfactor
yf = opts.yfactor
yy = np.linspace(opts.ymin,opts.ymax,opts.ysteps)*yf
ZZ = np.zeros((opts.xsteps,opts.ysteps),float)
count = np.zeros(opts.xsteps,int)
for d in dirs:
try:
xy = np.loadtxt(d+'/'+opts.name,unpack=True)
dx = xy[0][1] - xy[0][0]
x0 = xy[0][0]
for i,y in enumerate(xy[1]):
gg = mat.GaussianFunction(yy,fwhm=opts.fwhm,xbar=y)
ZZ[i] = ZZ[i] + gg
count[i] += 1
except:
pass
for i,c in enumerate(count):
if c != 0: ZZ[i] = ZZ[i]/float(count[i])
x1 = (opts.xsteps-1)*dx
xx = np.linspace(x0,x1,opts.xsteps)
YY,XX = np.meshgrid(yy,xx)
plt.contour(XX/xf,
YY/yf,
ZZ,
opts.ncontour,
cmap='Spectral_r')
#ax.plot_surface(XX, YY, ZZ/count, rstride=1, cstride=1, cmap='Spectral_r')
if opts.xmin: plt.xlim(xmin=opts.xmin)
if opts.xmax: plt.xlim(xmax=opts.xmax)
if opts.ymin: plt.ylim(ymin=opts.ymin)
if opts.ymax: plt.ylim(ymax=opts.ymax)
if opts.xlabel: plt.xlabel(opts.xlabel)
if opts.ylabel: plt.ylabel(opts.ylabel)
plt.show()
if __name__ == "__main__":
start()