usage: plotAverageIR.py [-h] [-o OUTFILE]
[-t {transmittance,absorbance,vcd,raman}] [-na]
[-p {pseudo-voigt,gaussian,lorentzian,delta}]
[-m VOIGT_MIXING] [-fwhm FWHM] [-s POINT_SPACING]
[-l LINEAR_SCALE] [-q QUADRATIC_SCALE] [-nr]
[-sc CENTERS] [-sw WIDTHS] [-r RANGES] [-fw FIG_WIDTH]
[-fh FIG_HEIGHT] [-csv EXP_DATA [EXP_DATA ...]]
[-w {electronic,zero-point,enthalpy,free,quasi-rrho,quasi-harmonic}]
[-sp SP_FILES [SP_FILES ...]] [-temp TEMPERATURE]
[-w0 W0] [-rx]
files [files ...]
plot a Boltzmann-averaged IR spectrum
positional arguments:
files frequency job output file(s)
optional arguments:
-h, --help show this help message and exit
-o OUTFILE, --output OUTFILE
output destination
if the file extension is .csv, a CSV file will be written
Default: show plot
-t {transmittance,absorbance,vcd,raman}, --plot-type {transmittance,absorbance,vcd,raman}
type of plot
Default: transmittance
-na, --harmonic force to use harmonic frequencies when anharmonic data is in the file
-s POINT_SPACING, --point-spacing POINT_SPACING
spacing between each x value
Default: a non-uniform spacing that is more dense near peaks
-nr, --no-reverse do not reverse x-axis
-fw FIG_WIDTH, --figure-width FIG_WIDTH
width of figure in inches
-fh FIG_HEIGHT, --figure-height FIG_HEIGHT
height of figure in inches
-csv EXP_DATA [EXP_DATA ...], --experimental-csv EXP_DATA [EXP_DATA ...]
CSV file containing observed spectrum data, which will be plotted on top
frequency job files should not come directly after this flag
-rx, --rotate-x-ticks
rotate x-axis tick labels by 45 degrees
peak options:
-p {pseudo-voigt,gaussian,lorentzian,delta}, --peak-type {pseudo-voigt,gaussian,lorentzian,delta}
function for peaks
Default: pseudo-voigt
-m VOIGT_MIXING, --voigt-mixing VOIGT_MIXING
fraction of pseudo-Voigt that is Gaussian
Default: 0.5
-fwhm FWHM, --full-width-half-max FWHM
full width at half max. of peaks
Default: 15 cm^-1
scale frequencies:
-l LINEAR_SCALE, --linear-scale LINEAR_SCALE
subtract linear_scale * frequency from each mode (i.e. this is 1 - λ)
Default: 0 (no scaling)
-q QUADRATIC_SCALE, --quadratic-scale QUADRATIC_SCALE
subtract quadratic_scale * frequency^2 from each mode
Default: 0 (no scaling)
x-centered interruptions:
-sc CENTERS, --section-centers CENTERS
split plot into sections with a section centered on each of the specified values
values should be separated by commas
-sw WIDTHS, --section-widths WIDTHS
width of each section specified by -sc/--section-centers
should be separated by commas, with one for each section
x-range interruptions:
-r RANGES, --ranges RANGES
split plot into sections (e.g. 0-1900,2900-3300)
energy weighting:
-w {electronic,zero-point,enthalpy,free,quasi-rrho,quasi-harmonic}, --weighting-energy {electronic,zero-point,enthalpy,free,quasi-rrho,quasi-harmonic}
type of energy to use for Boltzmann weighting
Default: quasi-rrho
-sp SP_FILES [SP_FILES ...], --single-point-files SP_FILES [SP_FILES ...]
single point energies to use for thermochem
Default: energies from INFILES
-temp TEMPERATURE, --temperature TEMPERATURE
temperature (K) to use for weighting
Default: 298.15
-w0 W0, --frequency-cutoff W0
cutoff frequency for quasi free energy corrections (1/cm)
Default: 100 cm^-1