Add internal coordinate harmonic model #26
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* see freqs * Add computing Hessians using MBTR forcefield (#8) * Add a ASE calculator for MBTR * Move back to Py3.9 for dscribe I get an error "from collections import Iterable" stemming from the sparse module used by dscribe * Add force computation * Add ability to compute Hessian from MBTR * Remove unused import * Add an example notebook with MBTR * Adjust the scale to be a unit normal Should reduce the likelihood of numerical issues * Update proof-of-concept with more data, better KRR * Allow use of MOPAC in proof of concept (#13) * Separate notebooks for exact answer, steps in fitting (#14) * Add utility for making calculator Avoid copying code between notebooks * Separate exact, sampling and approximation * Accept "None" as an option * Sample as if computing numerical derivatives (#17) * Start notebook for displacing along axes * Add code for combining perturbations into single tasks * Add example of using this new data * Refactor and add linear terms Fixes #2 Fixes #4 * Make the second-order terms 1/2 the first order * Update with the newer model * Update the proof of concept notebooks * see freqs * internal coordinate model * flake8 cleanup * added pytest for internals * more flake8 cleanup * geometric package to convert to internal coordinates --------- Co-authored-by: snelliott <[email protected]> Co-authored-by: Logan Ward <[email protected]> Co-authored-by: Logan Ward <[email protected]>
We can recreate these in the new directory structure if need be
Also remove some temporary files
It fails randomly
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Completing #25 . Fixes #7