This folder is a proving ground for extension of Melody's alchemical ChIMES
models to atomic systems. This is all only implemented for a 2B system to keep
things simple.

R.K. Lindsey (2024)

The basic premise is described in the file Alchemical ChIMES Ideas.pdf

There are a number of codes and scripts in this repository. Note that these are
not good examples of good coding practice - this is some quick and dirty testing
done over a day or two.

test_chemfit.cpp:

    This file reads in a .xyzf file and produces A.txt and b.txt for an atomic
    alchemical fit
    
test_chemfit.py

    This file reads A.txt and b.txt and produces params.txt and force.txt
    
test_chemfit-energy_evaluator.cpp

    This file reads a .xyzf file and a parameter file and generates predicted
    forces. It is used to verify the parmeter file produced by the first two
    codes does indeed give the results predicted in the force.txt produced by
    test_chemfit.py
    
run_singleatomtype_testfits.sh

    This script can be used to rapidly run through a Oe and Or hyperparameter
    sweep and is intended for use with .xyz files that have only a single
    element type, i.e., Oe is 1, which collapses to the normal ChIMES solution
    
run_twoeatomtype_testfits.sh

    The same as the above, but for multi-element type .xyzfs, i.e., Oe can be
    greater than or equal 1. The trajectory file can also contain a mix of
    single and multi-element type frames.
    
test_chemfit-energy_evaluator-justE.cpp
 
    A potential energy surface generator. Reads a paramter file and prints a
    corresponding PES to stdout
    
The test_trajectories folder contains trajectories that were/planned to be 
used for testing. The .xyzf files for Ar and He were created using the LJ 
potential (parameters below); all other .xyzfs were generated via DFT.

    He: epsilon = 0.021660 kcal/mol; sigma = 2.640 Angstroms
    Ar: epsilon = 0.238066 kcal/mol; sigma = 3.405 Angstroms

    LJ potential: 4*epsilon * ( (sigma/rij)^12 - (sigma/rij)^6 )