usage: plotAverageNMR.py [-h] [-o OUTFILE] [-pf PULSE_FREQUENCY] [-e ELEMENT] [-c COUPLE_WITH] [-j COUPLING_THRESHOLD]
[-p {pseudo-voigt,gaussian,lorentzian,delta}] [-m VOIGT_MIXING] [-fwhm FWHM]
[-s POINT_SPACING] [-ss SCALAR_SCALE] [-l LINEAR_SCALE] [-nr] [-sc CENTERS] [-sw WIDTHS]
[-r RANGES] [-fw FIG_WIDTH] [-fh FIG_HEIGHT] [-csv EXP_DATA [EXP_DATA ...]] [-rx]
[-w {electronic,zero-point,enthalpy,free,quasi-rrho,quasi-harmonic}]
[-freq FREQ_FILES [FREQ_FILES ...]] [-sp SP_FILES [SP_FILES ...]] [-temp TEMPERATURE]
[-w0 W0]
files [files ...]
plot NMR spectrum
positional arguments:
files NMR job output file(s)
options:
-h, --help show this help message and exit
-o OUTFILE, --output OUTFILE
output destination
Default: show plot
-pf PULSE_FREQUENCY, --pulse-frequency PULSE_FREQUENCY
pulse frequency
Default: 60 MHz
-e ELEMENT, --element ELEMENT
plot shifts for specified element
Default: H
-c COUPLE_WITH, --couple-with COUPLE_WITH
split only with the specified elements
Default: some common odd isotopes
-j COUPLING_THRESHOLD, --coupling-threshold COUPLING_THRESHOLD
coupling threshold when applying splits
Default: 0 Hz
-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: lorentzian
-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: 2.5 Hz
scale shifts:
-ss SCALAR_SCALE, --scalar-shift SCALAR_SCALE
shift centers
Default: 0 (no shift)
-l LINEAR_SCALE, --linear-scale LINEAR_SCALE
multiply the center of each shift by linear_scale
Default: -1 (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 -c/--centers
should be separated by commas, with one for each section
x-range interruptions:
-r RANGES, --ranges RANGES
split plot into sections (e.g. 0-4,7-10)
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
-freq FREQ_FILES [FREQ_FILES ...], --frequency-files FREQ_FILES [FREQ_FILES ...]
frequency jobs to use for thermochem
-sp SP_FILES [SP_FILES ...], --single-point-files SP_FILES [SP_FILES ...]
single point energies to use for thermochem
Default: TD-DFT energies from INFILES
-temp TEMPERATURE, --temperature TEMPERATURE
temperature (K) to use for weighting
Default: 298.15
-w0 W0, --frequency-cutoff W0
frequency parameter for quasi free energy corrections (1/cm)
Default: 100 cm^-1