Hessians for heterogeneous systems #104
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Currently tests an amorphous polyphosphate system
To mimic CutoffNeighbourhood, MolecularNeighbourhood duplicates the angle connectivity and creates a reference lists triplets -> bonds. The latter needs to be done first otherwise issues arise with bond orders which causes wrong angle values.
This avoids running tests twice in pull requests
…ipy into fix/heterogeneous_hessian
…ipy into fix/heterogeneous_hessian
…ipy into fix/heterogeneous_hessian
Doubling angle connectivity before completing the bonds connectivity is necessary in the hessian computation but leads to errors in other computations. A constructor parameter to MolecularNeighbourhood was therefore added to control this behavior.
Now, modulo a sort operation, the triplet reference lists into the pair list should match the behavior of the cutoff-based routines
Hessians are still failing, need to understand how to compute for fixed connectivities
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Small update: with this last commit I think hessians and other second-order quantities for heterogeneous systems should work with a cutoff. I'm still working on making things work with a fixed connectivity (ie molecules) |
Implemented formulas take derivatives with respect to the reference configuration.
Hypothesis: non-linear potentials have poor FD approximations out of the harmonic zone
pastewka
approved these changes
Jul 10, 2023
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Implementation of hessian computation for systems with multiple atom types.
Closes #103