Swart Lab - Theoretical Chemistry : msxc/pesplot.html

\(pesplot\)

The script for plotting Potential Energy Surfaces, pesplot, version 2025.03
System set up based on GNUplot script for CDF by L. D'Amore and L. Belpassi
Current version: 2025.03 (shared with CC-BY-NC license). See also all python tools

Usage: pesplot [-b IB] [-c] [-e G] [-h HEADER] [-o IDOR] [-p IDPAL] [-r] [-ts IDTS] [-u UNIT] [..technical-options..] files

Description:
 -b IB       Indicator if the barrier should be computed globally or per PES profile
    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.
 -h HEADER   Possibility to use your own header instead of the default one:
     1       Use $MSXC/pesplot/header1*.gnu (font 18, thickness 3/8)
     2       Use $MSXC/pesplot/header2*.gnu (font 24, thickness 4/11) (default)
     3       Use $MSXC/pesplot/header3*.gnu (font 30, thickness 5/14)
     FILE    Use your own FILE
 -o IDOR     Choose orientation of the plot:
     2       Portrait
     1       Landscape (default)
 -p IPAL     Choose out of a number of color palettes to plot the PES lines (default 10).
             Use one of the 12 predefined palettes or define your own in the file IPAL.
 -r          Plot using rounded lines to connect the stationary points.
             Default is to plot using squared lines.
 -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.

Technical options:
 --help      Help function (this message)
 --version   Display version (2025.02) of the pesplot tool
 -dx DX      Set distance (along X-axis) between stationary points (default 1.0)
 -ddx DDX    Set the width of the stationary points (default 0.5)
 -gap GAP    Set the gap-size between stationary points (default 0.5)
 -dup DUP    Set the size of white space above maximum energy value, per PES profile (default 2.0 [1])
 -ddn DDN    Set the size of white space below minimum energy value, per PES profile (default 2.0 [1])
 -dy DY      Vertical offset between labels

[1]:  These default values (in kcal/mol) are automatically transformed,
      if a different energy unit is chosen with -u option.
      

Note:

The labels as given in the input-file are used as given for GNU-plot.
The first line should be used to label the different PES plots.
The PES plots 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 above are the 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.
Note that formatting instructions can be included, as shown for S in italics, which in GnuPlot terms is: {/:Italic S}. A S in bold can be put with {/:Bold S}.

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
          
        

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 -h 1 -r -p 6 -b 0 -e E^e^l^e^c -c -u KJ 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.
        