Code

Much of my research involves writing mathematics-based scientific code (mostly in C++, C, Fortran, Python, and most recently C#). Here’s links to code that I’ve developed and/or contributed to, and which I’ve found to be generally useful to people besides myself:

1) MESMER is a cross platform (Windows, LINUX, OSX), open-source, object oriented C++ code which I have been heavily involved in developing. It is capable of formulating and solving the weak collision kinetic master equation in molecular systems of arbitrary complexity. It’s got all kinds of bells and whistles, and I recently tweaked it to include non-adiabatic RRKM spin-hopping. It is available for free download at SourceForge.

2) CHARMM is a widely used suite of molecular simulation programs to which I have contributed. Most recently, I have implemented the AXD and BXD algorithms in the development version of  CHARMM, as well as methods for adding generic n-state reactive hamiltonians derived from molecular mechanics.

3) fOOm-d (framework for Object Oriented molecular dynamics) is a molecular dynamics framework with an emphasis on methods that require coupling of separate trajectories – e.g., EVB methods and a range of classical-trajectory guided quantum dynamics methods. This project is currently hosted on SourceForge.

4) Here’s a generic and useful Python script for projecting Cartesian velocities & momenta into the molecular normal mode frame… for input, it requires two files: (1) a time series of velocities and coordinates, and (2) a Hessian for the stationary point of interest.

5) Non-adiabatic transition state theory (TST) code for locating a minimum-energy crossing point (MECP) between non-adiabatic surfaces (developed by J.N. Harvey),

6) Code for performing vibrational frequency analysis at an MECP, required for calculating non-adiabatic rate coefficients (developed by D.R. Glowacki)

2 Responses to Code

  1. Richard Best says:

    Daivd, this is amazing stuff. Great job to all of the contributors. This technology has many great capabilities. Fascinating!

    If someone were interested in creating their own scripts and exhibiting it what would the requirements be, in regards to properly crediting the software developers?

    • Hi Richard, thanks for the comment. how did you hear about our stuff? As far as exhibiting DS, the code is all a big jumble and pretty difficult to run unless you’re a developer – although we’re working to stabilize it and make it far more user friendly. At this stage, we are interested in pursuing possible collaborative exhibition opportunities. so if you are really interested, send me an email or something. dave

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