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Hessians for heterogeneous systems #104

Merged
merged 44 commits into from
Jul 10, 2023
Merged

Hessians for heterogeneous systems #104

merged 44 commits into from
Jul 10, 2023

Commits on Sep 23, 2022

  1. [ENH] doubling heterogeneous cutoffs for hessian

    @prs513rosewood
    prs513rosewood committed Sep 23, 2022
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  2. [MAINT] simplified a bit hessian term 5

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    prs513rosewood committed Sep 23, 2022
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Commits on Dec 6, 2022

  1. MAINT: moved test potentials out of potentials.py

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    prs513rosewood committed Dec 6, 2022
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Commits on Dec 8, 2022

  1. Moved some numerical functions out of the Ewald calculator

    @griessej
    griessej committed Dec 8, 2022
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  2. MAINT: formatting

    @prs513rosewood
    prs513rosewood committed Dec 8, 2022
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  3. FIX: correct atom order in angles

    @prs513rosewood
    prs513rosewood committed Dec 8, 2022
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  4. Fixed problems with tests

    @griessej
    griessej committed Dec 8, 2022
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  5. TST: added test for manybody heterogeneous system 

    Currently tests an amorphous polyphosphate system
    @prs513rosewood
    prs513rosewood committed Dec 8, 2022
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  6. FIX: fixed angles connectivity doubling 

    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.
    @prs513rosewood
    prs513rosewood committed Dec 8, 2022
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  7. TST: run on push only 

    This avoids running tests twice in pull requests
    @prs513rosewood
    prs513rosewood committed Dec 8, 2022
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  8. Merge branch 'fix/heterogeneous_hessian' of github.com:libAtoms/matsc… 

    …ipy into fix/heterogeneous_hessian
    @prs513rosewood
    prs513rosewood committed Dec 8, 2022
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  9. Fixing more tests

    @griessej
    griessej committed Dec 8, 2022
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  10. Merge branch 'fix/heterogeneous_hessian' of github.com:libAtoms/matsc… 

    …ipy into fix/heterogeneous_hessian
    @griessej
    griessej committed Dec 8, 2022
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  11. Fixing even more tests...

    @griessej
    griessej committed Dec 8, 2022
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  12. TST: birch coefficients

    @prs513rosewood
    prs513rosewood committed Dec 8, 2022
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  13. Merge branch 'fix/heterogeneous_hessian' of github.com:libAtoms/matsc… 

    …ipy into fix/heterogeneous_hessian
    @prs513rosewood
    prs513rosewood committed Dec 8, 2022
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Commits on Dec 9, 2022

  1. FIX: molecule io tests

    @prs513rosewood
    prs513rosewood committed Dec 9, 2022
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  2. removed old molecular calculator

    @prs513rosewood
    prs513rosewood committed Dec 9, 2022
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  3. added polyphosphate stress test

    @prs513rosewood
    prs513rosewood committed Dec 9, 2022
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  4. fixed finite diff hessian tests

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    prs513rosewood committed Dec 9, 2022
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Commits on Dec 13, 2022

  1. fixed double cutoff of molecules 

    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.
    @prs513rosewood
    prs513rosewood committed Dec 13, 2022
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Commits on Dec 15, 2022

  1. simplified polyphosphate tests

    @prs513rosewood
    prs513rosewood committed Dec 15, 2022
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Commits on Dec 19, 2022

  1. moved reversed pair indices and double cutoff to neighbourhood

    @prs513rosewood
    prs513rosewood committed Dec 19, 2022
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Commits on Dec 20, 2022

  1. ignoring debug files in tests

    @prs513rosewood
    prs513rosewood committed Dec 20, 2022
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Commits on Feb 3, 2023

  1. dense cast for hessians in polyphosphate test

    @prs513rosewood
    prs513rosewood committed Feb 3, 2023
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Commits on Feb 13, 2023

  1. added stress test in manybody_molecules

    @prs513rosewood
    prs513rosewood committed Feb 13, 2023
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Commits on Jun 14, 2023

  1. Merge branch 'master' into fix/heterogeneous_hessian_merge

    @prs513rosewood
    prs513rosewood committed Jun 14, 2023
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  2. removing molecular_calculator.py from meson.build

    @prs513rosewood
    prs513rosewood committed Jun 14, 2023
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Commits on Jun 16, 2023

  1. fixing triplet reference lists in MolecularNeighbourhood 

    Now, modulo a sort operation, the triplet reference lists into the pair list
should match the behavior of the cutoff-based routines
    @prs513rosewood
    prs513rosewood committed Jun 16, 2023
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Commits on Jun 28, 2023

  1. fix: added relaxation step to molecule tests for nonaffine + hessian 

    Hessians are still failing, need to understand how to compute for fixed connectivities
    @prs513rosewood
    prs513rosewood committed Jun 28, 2023
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  2. fix: added triplet type in hessian T5

    @prs513rosewood
    prs513rosewood committed Jun 28, 2023
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  3. enh: added heterogeneous test for both pair and triplet types

    @prs513rosewood
    prs513rosewood committed Jun 28, 2023
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Commits on Jun 29, 2023

  1. fix: reset fd deformation in nonaffine_forces

    @prs513rosewood
    prs513rosewood committed Jun 29, 2023
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  2. fix: removed minimization from nonaffine forces + hessian tests

    @prs513rosewood
    prs513rosewood committed Jun 29, 2023
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  3. tst: tighter tolerances on birch coefficients

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    prs513rosewood committed Jun 29, 2023
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Commits on Jun 30, 2023

  1. maint: moved pair masking for hessian to neighbourhood

    @prs513rosewood
    prs513rosewood committed Jun 30, 2023
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  2. fix: added 1/2 correction factor to force-like term in na_forces

    @prs513rosewood
    prs513rosewood committed Jun 30, 2023
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  3. tst: added single pair nonaffine forces test

    @prs513rosewood
    prs513rosewood committed Jun 30, 2023
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  4. fix: fixed manybody nonaffine tests 

    Implemented formulas take derivatives with respect to the reference configuration.
    @prs513rosewood
    prs513rosewood committed Jun 30, 2023
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  5. tst: added analytical test of Tersoff

    @prs513rosewood
    prs513rosewood committed Jun 30, 2023
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  6. tst: fixed hessian tests for Tersoff, Kumagai out of equilibrium 

    Hypothesis: non-linear potentials have poor FD approximations out of the
harmonic zone
    @prs513rosewood
    prs513rosewood committed Jun 30, 2023
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  7. tst: using reference version of FD naforces in test molecules

    @prs513rosewood
    prs513rosewood committed Jun 30, 2023
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  8. tst: marked molecule tests as xfail

    @prs513rosewood
    prs513rosewood committed Jun 30, 2023
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Commits on Jul 7, 2023

  1. maint: updated changelog

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    prs513rosewood committed Jul 7, 2023
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