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Component selection in Raman and spectrum saving added #1

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48 changes: 36 additions & 12 deletions plot_RamanIR.py
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
#! /usr/bin/env python
from chemPackage import collect, dressedT
from numpy import linspace
from numpy import linspace, savetxt, array
from chemPackage.constants import PI
import argparse
import matplotlib.pyplot as plt
Expand All @@ -19,7 +19,7 @@ def main():
"molecule Raman scattering or DIM/QM SERS.")

parser.add_argument("--dressed", "-d", nargs=2, metavar=("dim.out", "freq.out"),
type=str, help="Plot the raman spectrum using dressed tensors formulism. "
type=str, help="Plot the raman spectrum using dressed tensors formalism. "
"Requires the output from a DIM calculation for the field, and the output "
"of a frequency calculation. ", dest="dressed", default=None)

Expand All @@ -37,6 +37,9 @@ def main():

parser.add_argument("--fwhm", metavar="20", default=20, type=float,
help="Full width at half max for the peaks in the spectrum")

parser.add_argument("--component", "-c", metavar="xx", default="all", type=str,
help="Supply the component of the tensor's derivative to calculate Raman intensity")

parser.add_argument("--scalefactor", metavar="30", default=30,
type=float, help="This is a scale factor for the y axis.")
Expand All @@ -52,11 +55,12 @@ def main():
parser.add_argument("--figname", default=None, type=str, metavar="fig.png",
help="Supply a name for the figure if it is to be saved")

parser.add_argument("--specname", default=None, type=str, metavar="spectrum.txt",
help="Supply a name for the spectrum file if it is to be saved in xy format")

parser.add_argument("--no-sticks", default=True, action='store_false',dest='lsticks',
help="If included sticks will not be plotted")



args = parser.parse_args()

# sanity check: did they choose raman or dressed tensors. If not, give up on them
Expand Down Expand Up @@ -92,7 +96,7 @@ def main():

# plot that spectrum
dressedTensors(dimout, freqout, args.translation, args.fwhm, args.scalefactor,
args.xaxis, args.yaxis,args.lsticks, args.figname)
args.xaxis, args.yaxis,args.lsticks, args.figname, args.specname)



Expand All @@ -104,7 +108,8 @@ def main():
exit("Please use the --help option for more information")

# plot the spectrum
plotRaman(freqout, args.fwhm, args.scalefactor, args.xaxis, args.yaxis, args.lsticks, args.figname)
plotRaman(freqout, args.fwhm, args.scalefactor, args.xaxis, args.yaxis, args.component,
args.lsticks, args.figname, args.specname)

# The second real condition: Raman by numerical differentiation.
elif args.IR != None and args.dressed == None:
Expand All @@ -114,7 +119,7 @@ def main():
exit("Please use the --help option for more information")

# plot the spectrum
plotIR(freqout, args.fwhm, args.xaxis, args.yaxis, args.lsticks, args.figname)
plotIR(freqout, args.fwhm, args.xaxis, args.yaxis, args.lsticks, args.figname, args.specname)

else:
exit("This shouldn't even be possible, I guess I'm not as intellegent as I thought I was."
Expand All @@ -124,7 +129,7 @@ def main():



def dressedTensors(dimout, freqout, tr, fwhm, scaleexp, xaxis, yaxis, lsticks, figname):
def dressedTensors(dimout, freqout, tr, fwhm, scaleexp, xaxis, yaxis, lsticks, figname, specname):
"""
This function plots the Raman spectrum of a system using the Dressed Tensors
formulism.
Expand All @@ -143,6 +148,9 @@ def dressedTensors(dimout, freqout, tr, fwhm, scaleexp, xaxis, yaxis, lsticks, f
the form of a list. ie. [lower, upper]
figname ==> If it isn't None then this function will save the figure to
filename supplied.
specname ==> If it isn't None then this function will save the spectrum in the
xy format to the filename supplied.

"""

# collect the dipole-dipole polarizabilities derivatives and
Expand Down Expand Up @@ -181,15 +189,18 @@ def dressedTensors(dimout, freqout, tr, fwhm, scaleexp, xaxis, yaxis, lsticks, f
# check if ranges for the specturm were given. If given apply them
sub.set_xlim(xaxis[0], xaxis[1])
if yaxis != None:
sub.set_ylim(yaxix[0], yaxis[1])
sub.set_ylim(yaxis[0], yaxis[1])


if figname != None:
plt.savefig(figname, dpi=300)
else:
plt.show()

if specname != None:
savetxt(specname, array([domain, y2*scale]).T, fmt=['%.2f', '%4.8g'])

def plotRaman(freqout, fwhm, scaleexp, xaxis, yaxis, lsticks, figname):
def plotRaman(freqout, fwhm, scaleexp, xaxis, yaxis, component, lsticks, figname, specname):
"""
This function plots the Raman spectrum of a system using numerical
differentiation around the normal modes.
Expand All @@ -202,16 +213,20 @@ def plotRaman(freqout, fwhm, scaleexp, xaxis, yaxis, lsticks, figname):
the form of a list. ie. [lower, upper]
yaxis ==> gives the lower and upper bounds for the y-axis. It is supplied in
the form of a list. ie. [lower, upper]
component ==> gives the component of the polarizability tensor for which the
Raman spectrum is to be calculated
figname ==> If it isn't None then this function will save the figure to
filename supplied.
specname ==> If it isn't None then this function will save the spectrum in the
xy format to the filename supplied.
"""
# good news, because the chem package is so great this works for both
# the Raman of the free molecule and SERS calculated with DIM/QM

# collect the dipole-dipole polarizabilities derivatives
freqout.collect_raman_derivatives()
# calculate the raman cross section for the system.
raman_intensity = freqout.cross_section()
raman_intensity = freqout.cross_section(component=component)

scale = 10**scaleexp

Expand Down Expand Up @@ -241,8 +256,11 @@ def plotRaman(freqout, fwhm, scaleexp, xaxis, yaxis, lsticks, figname):
plt.savefig(figname, dpi=300)
else:
plt.show()

if specname != None:
savetxt(specname, array([domain, y2*scale]).T, fmt=['%.2f', '%4.8g'])

def plotIR(freqout, fwhm, xaxis, yaxis, lsticks, figname):
def plotIR(freqout, fwhm, xaxis, yaxis, lsticks, figname, specname):
"""
This function plots the Raman spectrum of a system using numerical
differentiation around the normal modes.
Expand All @@ -253,6 +271,8 @@ def plotIR(freqout, fwhm, xaxis, yaxis, lsticks, figname):
the form of a list. ie. [lower, upper]
figname ==> If it isn't None then this function will save the figure to
filename supplied.
specname ==> If it isn't None then this function will save the spectrum in the
xy format to the filename supplied.
"""

fig = plt.figure()
Expand All @@ -278,6 +298,9 @@ def plotIR(freqout, fwhm, xaxis, yaxis, lsticks, figname):
else:
plt.show()

if specname != None:
savetxt(specname, array([domain, y]).T, fmt=['%.2f', '%4.8g'])


def lorentzian(x, peak=0, height=1.0, fwhm=None, hwhm=None):
'''Calculates a three-parameter lorentzian for a given domain.'''
Expand Down Expand Up @@ -312,6 +335,7 @@ def sum_lorentzian(x, peak=None, height=None, fwhm=None, hwhm=None):
try:
main()
except KeyboardInterrupt:
import sys
sys.exit(1)