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Internal coordinate interpolation#166

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leeping wants to merge 48 commits intomasterleeping/geomeTRIC:masterfrom interpolateleeping/geomeTRIC:interpolateCopy head branch name to clipboard

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Commits on May 2, 2023

• Updates to internal.py and molecule.py for interpolation

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Commits on May 5, 2023

• Add interpolation code

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Commits on May 10, 2023

• sum -> np.sum

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Commits on May 13, 2023

• temporary commit, commenting needs to be done

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Commits on May 15, 2023

• Implement erisemax; fix some regression tests

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Commits on May 29, 2023

• Merge branch 'master' of github.com:leeping/geomeTRIC into interpolate

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Commits on Jun 7, 2023

• pull from lpw/interpolate and more comments

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Commits on Jul 6, 2023

• Merge branch 'interpolate' of github.com:leeping/geomeTRIC into interpolate

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Commits on Aug 23, 2023

• args can be passed by users for the interpolation method

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• ignoring nframes and prealign when an interpolated trajectory is provided

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Commits on Sep 10, 2023

• Merge pull request #165 from hjnpark/interpolate

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Commits on Sep 21, 2023

• Merge branch 'interpolate' of github.com:leeping/geomeTRIC into interpolate

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• Merge branch 'master' of github.com:leeping/geomeTRIC into interpolate

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• Resolve an inconsistency in how G condition number was being evaluated

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Commits on Sep 22, 2023

• Improve newCartesian() performance

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• Bug fix - check if rigid is in (None, False)

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• Fix a bug in ov(vi, vi)

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• Tweak two tests in test_openmm.py; still need one that breaks the IC

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Commits on Sep 29, 2023

• Change default behavior of EqualSpacing back to the linear interpolator

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• Interpolate parameter bug fixed

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• Merge pull request #169 from hjnpark/interpolate

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Commits on Sep 30, 2023

• Merge branch 'master' into interpolate

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Commits on Oct 3, 2023

• Implement improved dihedral angle syncing

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Commits on Oct 4, 2023

• Enable warning messages for dihedral angle clash

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Commits on Oct 8, 2023

• Default align reac/prod; split large dihedral angle changes

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Commits on Oct 9, 2023

• interpolation parameter bug fixed

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Commits on Oct 12, 2023

• Lower diagnostic thresholds for dihedrals

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• Merge branch 'interpolate_syncdihedrals2' of github.com:leeping/geomeTRIC into interpolate_syncdihedrals2

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Commits on Oct 18, 2023

• Add group_atoms_by_topology() method

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Commits on Oct 19, 2023

• Don't quit when damping hits 0.2; tweak dihedral diagnostic; align_frags, align_system keywords

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Commits on Oct 24, 2023

• Merge pull request #172 from leeping/interpolate_syncdihedrals2

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• Implement extrapolation feature

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Commits on Oct 30, 2023

• Merge branch 'tmin' into interpolate

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Commits on Oct 31, 2023

• mintrust can be lower than convergence_drms ; conmethod 1 bugfix

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Commits on Nov 4, 2023

• Bug fix for extrapolation not activated

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Commits on Nov 6, 2023

• Merge branch 'master' of github.com:leeping/geomeTRIC into interpolate

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• A strange merge conflict in interpolate branch

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• Merge branch 'interpolate' of github.com:leeping/geomeTRIC into interpolate

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Commits on Dec 6, 2023

• Make align_system option more global

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Commits on Jan 11, 2024

• Add atom deletion support to molecule.py, improve handling of CONECT records

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Commits on Mar 8, 2024

• typo

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• Merge pull request #195 from hjnpark/interpolate

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Commits on Mar 13, 2024

• Merge branch 'master' of github.com:leeping/geomeTRIC into molecule_delatom

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• Fix a "zero divide by zero" error

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• Add interpolation "fast mode" and two new initial guess methods

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• Merge branch 'interpolate' of github.com:leeping/geomeTRIC into interpolate

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• Merge branch 'interpolate' of github.com:leeping/geomeTRIC into interpolate

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• Merge branch 'molecule_delatom' into interpolate

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