PYREX Motivation

The following quote summarizes my general approach to science:

Both the man of science and the man of art live always at the edge of mystery, surrounded by it; both always, as to the measure of their creation, have had to do with the harmonization of what is new with what is familiar, with the balance between novelty and synthesis, with the struggle to make partial order in total chaos.

—J. Robert Oppenheimer

If you’re interested in using/developing PYREX, you may be familiar with Robert Oppenheimer and his story. He was a father of quantum mechanics and one of the architects of the atomic bomb that devastated Hiroshima, Japan in World War II, he was a man who had to struggle with the weight of his science in a way most of us never will. This message from him details the similarity between science and art, how the idea of both fields is to create order from chaos, to create harmony from disarray, explaining the unexplainable. Living at “the edge of mystery” is something scientists and artists share, a common driver for our work. The motivation behind my development of PYREX is driven by this sentiment, the theoretical study of chemical reactions using quantum chemistry methods is truly an art form. The careful computational artist must use every reaction trajectory as a fine brush stroke to paint a broader picture of how reactions happen. The process of studying small, elementary reaction steps are the chords that lay the foundation for a beautiful symphony. My goal is for PYREX to be a tool to help build the beautiful chemical art you have in mind. In my search of the chemical literature I stumbled across quite a few interesting tools in development that didn’t have a central implementation. One code base that could serve as a hub for multiple methods that can be useful in the explanation of chemical reactions, a tool to help conduct the chemical symphony. It is my hope that you find PYREX a useful utility in your research and even make a contribution to the code base. This documentation will serve to get you started and make you aware of what the code is capable of, if you have any questions about the code feel free to contact me and/or my research group.

–Wallace D. Derricotte

Capabilities

pyREX implements a series of reaction energy methods based on the total reaction energy, conceptual DFT propert ies, derivative properties along the reaction coordinate, and energy decomposition techniques. The following methods are currently available in pyREX:

  1. Intrinsic Reaction Coordinate (IRC) following code
  2. Activation Strain Model (ASM) Decomposition of reaction energy
  3. Reaction Force
  4. Conceptual DFT Properties (chemical potential, chemical hardness, etc.)
  5. Reaction Electronic Flux
  6. Atomic Decomposition of Reaction Force
  7. Reaction Fragility Spectrum
  8. Symmetry-Adapted Perturbation Theory Decomposition of the Reaction Force