Add computing Hessians using MBTR forcefield #8
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I get an error "from collections import Iterable" stemming from the sparse module used by dscribe
Should reduce the likelihood of numerical issues
snelliott
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Nov 17, 2023
* 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
WardLT
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Dec 4, 2023
* 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]>
WardLT
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Dec 4, 2023
* 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 * use internal coordinates in linear model (linear_internals.py) (#25) * 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]> * Remove only notebook directory We can recreate these in the new directory structure if need be * Move the exact answer to be the first dir Also remove some temporary files * Skip accuracy test for Harmonic on cartesian * Make the test even more lenient It fails randomly * Remove deprecated file --------- Co-authored-by: Sarah Elliott <[email protected]> Co-authored-by: snelliott <[email protected]>
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A first stab at training an interatomic potential and using that to compute Hessians.