Swart Lab - Theoretical Chemistry : msxc/pesplot.html

$pesplot$

The script for plotting Potential Energy Surfaces

System set up based loosely on GNUplot script for CDF by L. D'Amore and L. Belpassi

Current version: 2026.02 (shared with CC-BY-NC license). See also all python tools

Installation: mkdir $HOME/msxc ; cd $HOME/msxc ; tar xfz $HOME/Download/pesplot2026.tgz ; export MSXC=$HOME/msxc ; export PATH=$PATH:$MSXC/bin

Usage: pesplot [..options..] files Options: -b IB Indicator if the barrier should be computed globally or per PES profile -1 Do not compute 0 Compute per PES profile 1 Compute globally (default) -c Convert units from kcal/mol to a different one, if a different energy unit is chosen with -u option. Normally, the tool assumes that the energy values are already in that unit. This option allows for using kcal/mol based energy files to be plotted in e.g. eV. -e G Label for the energy type (default G for Gibbs free energy). This text is plotted on the Y-axis label. -f FONT Set global font size (default 24) -k KSIZE Set font size for key legend (default 16) -l TEXT Set location of PES legend (default: BLH): -lb TEXT Set location of barrier legend (default: TLH): L Left-aligned C Centered R Right-aligned T At top B At bottom H Horizontally aligned V Vertically stacked -m MARGIN Set margin between plots and bottom/top of the figure (default: 10.0, in %) -o IDOR Choose orientation of the plot: 2 Portrait 1 Landscape (default) -off Set Set offset between plots and labels (default: 3.6, in %) -p IPAL Choose from a number of color palettes to plot the PES lines (default 9). Use one of the 12 predefined palettes or define your own in the file IPAL. (see: https://www.marcelswart.eu/rtfm/color-blind-palettes.html) -r Plot using rounded lines to connect the stationary points. Default is to plot using squared lines. -s SPACER Set relative size of spacer between columns of PES points (default: 0.5) (NB: PES point columns have width 1.0) -ts IDTS Use dotted lines for the transition states: 1 Do use dotted lines for TSs (default) 0 Use solid lines for TSs -u UNIT Plot PESs in unit: KCAL kcal/mol (default) KJ kJ/mol EV eV AU Hartree NB. See also -c option. --help Help function (this message) --version Display version (2026.02) of the pesplot tool

Note:

You will need at least version 6.0 of Gnuplot
At the moment it works on MacOS/Linux, with Windows coming soon
The first line should be used to label the different PES plots.
The PES input data are separated by a # at all input lines.
For each of the points along the reaction pathway energies should be given with respect to the lowest energy of the reactants.
Indicated in the example below are reactants R, reactant complex RC, transition state TS, and intermediate I. These labels can be changed to {A, B, C, D}, or {I, II, III, IV}, or .. whatever you prefer.
The labels as given in the input-file are used as given for GNU-plot.
Note that formatting instructions can be included:
- E.g., S in italics, in GnuPlot terms is: {/:Italic S}.
- A S in bold can be put with {/:Bold S}.
- Greek letters can be put with {/Symbol a} for α {/Symbol b} for β, etc.
On Mac, GNUPlot (and others) can be installed easily with MacPorts

Examples:

Input file (data from DOI 10.1021/jacs.4c10120): # {/:Italic S} = 1 # {/:Italic S} = 2 R # 0.0 # 0.44 RC # -2.98 # -3.25 TS # 23.30 # 12.16 I # 22.40 # 10.70 Call to pesplot: pesplot -p 2 -ts 0 abhishek.txt Note that you have full control on the font sizes, location of legends, etc. With the following call to pesplot you get the following plot. pesplot -p 2 -ts 0 -f 36 -k 24 -l brh -lb tl -off 5 abhishek.txt -f 36 makes the general font 50% bigger -k 24 makes the font size of the labels and legends 50% bigger -l brh places the legend at the bottom right side, horizontally -lb tl places the barriers description at the top left side -off 5 increases the distance between description of barriers

Input file (data from DOI 10.1021/ja0606529): # Cl^- + POCl_2Cl # Cl^- + P(CH_3)_2Cl # OH^- + P(CH_3)_2OH # OH^- + PO(CH_3)_2OH R # 0.0 # 0.0 # 0.0 # 0.0 RC # -17.5 # -13.0 # -28.7 # -34.3 pre-TS # -2.0 # -12.7 # -26.1 # -20.6 TS/TC # -8.4 # -15.6 # -32.7 # -33.9 Call to pesplot: pesplot -r -p 6 -b 0 -e E^e^l^e^c -c -u KJ -l tch bochove-sn2.txt PS. Note that the input data are in kcal·mol$^{-1}$, but the plot is made in kJ·mol$^{-1}$. This is arranged through the "-c -u KJ" options.

\(pesplot\)