PESViewer

Visualize a potential energy surface

Developer: Ruben Van de Vijver, Laboratory for Chemical Technology, Ghent University

The PESViewer is a code to depict and analyze a potential energy surface characterized by wells, bimolecular products, transition states and barrierless reactions. Their energy is needed to plot the potential energy surface. Written values of the energies and 2D plots (structural formulas) of the wells and products can be added to the figure

To run this code, you need python version 2.7, matplotlib, numpy and optionally OpenBabel or RDKit to create 2D plots

INSTALL

Clone the project onto your machine and go to the PESViewer directory. Type:

python setup.py build
python setup.py install 

INPUT

A text file containing the stationary points, energies, names identifiers and options, see the input.txt as example.

For wells, write each well on a separate line as follows (smiles are optional to depict the molecule, if no xyz's are available):

name energy smiles

For bimolecular products (again smiles are optional):

name energy smiles

For reactions (colors are optional, and if available the line of the reaction will be given that color):

name energy reactant product color

For bimolecular products (again colors are optional)

name reactant product color

The plotting options (to be written in the input file) are:

Optionally a folder xyz/ containing the xyz coordinates of the stationary points ($name.xyz) (for bimolecular products, use several xyz coordinates files ($name$index.xyz) )

RUN

With the input file input.inp, type:

pesviewer input.inp

OUTPUT

The output is a modifiable matplotlib figure.

2 modifications are possible

• modifing the x-position of a stationary point by a 'drag and drop' of the energy value
• modifing the position of 2D structure images by a 'drag and drop' of the image