Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Internal coordinate interpolation #166

Open
wants to merge 48 commits into
base: master
Choose a base branch
from
Open

Internal coordinate interpolation #166

wants to merge 48 commits into from

Commits on May 2, 2023

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

    @leeping
    leeping committed May 2, 2023
    Configuration menu
    Copy the full SHA
    ee743f5 View commit details
    Browse the repository at this point in the history

Commits on May 5, 2023

  1. Add interpolation code

    @leeping
    leeping committed May 5, 2023
    Configuration menu
    Copy the full SHA
    b27b022 View commit details
    Browse the repository at this point in the history

Commits on May 10, 2023

  1. sum -> np.sum

    @hjnpark
    hjnpark committed May 10, 2023
    Configuration menu
    Copy the full SHA
    f289ea0 View commit details
    Browse the repository at this point in the history

Commits on May 13, 2023

  1. temporary commit, commenting needs to be done

    @hjnpark
    hjnpark committed May 13, 2023
    Configuration menu
    Copy the full SHA
    968aa3b View commit details
    Browse the repository at this point in the history

Commits on May 15, 2023

  1. Implement erisemax; fix some regression tests

    @leeping
    leeping committed May 15, 2023
    Configuration menu
    Copy the full SHA
    82d2536 View commit details
    Browse the repository at this point in the history

Commits on May 29, 2023

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

    Conflicts:
	tools/plot-performance.py
    @leeping
    leeping committed May 29, 2023
    Configuration menu
    Copy the full SHA
    30c5b38 View commit details
    Browse the repository at this point in the history

Commits on Jun 7, 2023

  1. pull from lpw/interpolate and more comments

    @hjnpark
    hjnpark committed Jun 7, 2023
    Configuration menu
    Copy the full SHA
    372bbcd View commit details
    Browse the repository at this point in the history

Commits on Jul 6, 2023

  1. Merge branch 'interpolate' of github.com:leeping/geomeTRIC into inter… 

    …polate
    @leeping
    leeping committed Jul 6, 2023
    Configuration menu
    Copy the full SHA
    0e01123 View commit details
    Browse the repository at this point in the history

Commits on Aug 23, 2023

  1. args can be passed by users for the interpolation method

    @hjnpark
    hjnpark committed Aug 23, 2023
    Configuration menu
    Copy the full SHA
    3585112 View commit details
    Browse the repository at this point in the history

  2. ignoring nframes and prealign when an interpolated trajectory is prov… 

    …ided
    @hjnpark
    hjnpark committed Aug 23, 2023
    Configuration menu
    Copy the full SHA
    4de83d5 View commit details
    Browse the repository at this point in the history

Commits on Sep 10, 2023

  1. Merge pull request #165 from hjnpark/interpolate 

    Interpolate
    @leeping
    leeping authored Sep 10, 2023
    Configuration menu
    Copy the full SHA
    55c0cc6 View commit details
    Browse the repository at this point in the history

Commits on Sep 21, 2023

  1. Merge branch 'interpolate' of github.com:leeping/geomeTRIC into inter… 

    …polate
    @leeping
    leeping committed Sep 21, 2023
    Configuration menu
    Copy the full SHA
    fe335db View commit details
    Browse the repository at this point in the history

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

    @leeping
    leeping committed Sep 21, 2023
    Configuration menu
    Copy the full SHA
    626a5c4 View commit details
    Browse the repository at this point in the history

  3. Resolve an inconsistency in how G condition number was being evaluated

    @leeping
    leeping committed Sep 21, 2023
    Configuration menu
    Copy the full SHA
    9987360 View commit details
    Browse the repository at this point in the history

Commits on Sep 22, 2023

  1. Improve newCartesian() performance

    @leeping
    leeping committed Sep 22, 2023
    Configuration menu
    Copy the full SHA
    225f85d View commit details
    Browse the repository at this point in the history

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

    @leeping
    leeping committed Sep 22, 2023
    Configuration menu
    Copy the full SHA
    72bc66c View commit details
    Browse the repository at this point in the history

  3. Fix a bug in ov(vi, vi)

    @leeping
    leeping committed Sep 22, 2023
    Configuration menu
    Copy the full SHA
    5a68400 View commit details
    Browse the repository at this point in the history

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

    @leeping
    leeping committed Sep 22, 2023
    Configuration menu
    Copy the full SHA
    83f32ed View commit details
    Browse the repository at this point in the history

Commits on Sep 29, 2023

  1. Change default behavior of EqualSpacing back to the linear interpolator

    @leeping
    leeping committed Sep 29, 2023
    Configuration menu
    Copy the full SHA
    cf35814 View commit details
    Browse the repository at this point in the history

  2. Interpolate parameter bug fixed

    @hjnpark
    hjnpark committed Sep 29, 2023
    Configuration menu
    Copy the full SHA
    952a6be View commit details
    Browse the repository at this point in the history

  3. Merge pull request #169 from hjnpark/interpolate 

    Interpolate parameter bug fixed
    @leeping
    leeping authored Sep 29, 2023
    Configuration menu
    Copy the full SHA
    025f49b View commit details
    Browse the repository at this point in the history

Commits on Sep 30, 2023

  1. Merge branch 'master' into interpolate

    @leeping
    leeping committed Sep 30, 2023
    Configuration menu
    Copy the full SHA
    65f2cef View commit details
    Browse the repository at this point in the history

Commits on Oct 3, 2023

  1. Implement improved dihedral angle syncing

    @leeping
    leeping committed Oct 3, 2023
    Configuration menu
    Copy the full SHA
    cfba8c5 View commit details
    Browse the repository at this point in the history

Commits on Oct 4, 2023

  1. Enable warning messages for dihedral angle clash

    @leeping
    leeping committed Oct 4, 2023
    Configuration menu
    Copy the full SHA
    09d48a9 View commit details
    Browse the repository at this point in the history

Commits on Oct 8, 2023

  1. Default align reac/prod; split large dihedral angle changes

    @leeping
    leeping committed Oct 8, 2023
    Configuration menu
    Copy the full SHA
    0a7326d View commit details
    Browse the repository at this point in the history

Commits on Oct 9, 2023

  1. interpolation parameter bug fixed

    @hjnpark
    hjnpark committed Oct 9, 2023
    Configuration menu
    Copy the full SHA
    3bbf667 View commit details
    Browse the repository at this point in the history

Commits on Oct 12, 2023

  1. Lower diagnostic thresholds for dihedrals

    @leeping
    leeping committed Oct 12, 2023
    Configuration menu
    Copy the full SHA
    1d037ee View commit details
    Browse the repository at this point in the history

  2. Merge branch 'interpolate_syncdihedrals2' of github.com:leeping/geome… 

    …TRIC into interpolate_syncdihedrals2
    @leeping
    leeping committed Oct 12, 2023
    Configuration menu
    Copy the full SHA
    04d0231 View commit details
    Browse the repository at this point in the history

Commits on Oct 18, 2023

  1. Add group_atoms_by_topology() method

    @leeping
    leeping committed Oct 18, 2023
    Configuration menu
    Copy the full SHA
    b9e0a0a View commit details
    Browse the repository at this point in the history

Commits on Oct 19, 2023

  1. Don't quit when damping hits 0.2; tweak dihedral diagnostic; align_fr… 

    …ags, align_system keywords
    @leeping
    leeping committed Oct 19, 2023
    Configuration menu
    Copy the full SHA
    e2da27f View commit details
    Browse the repository at this point in the history

Commits on Oct 24, 2023

  1. Merge pull request #172 from leeping/interpolate_syncdihedrals2 

    Interpolate syncdihedrals2
    @leeping
    leeping authored Oct 24, 2023
    Configuration menu
    Copy the full SHA
    60bb0c3 View commit details
    Browse the repository at this point in the history

  2. Implement extrapolation feature

    @leeping
    leeping committed Oct 24, 2023
    Configuration menu
    Copy the full SHA
    0e0f81c View commit details
    Browse the repository at this point in the history

Commits on Oct 30, 2023

  1. Merge branch 'tmin' into interpolate

    @leeping
    leeping committed Oct 30, 2023
    Configuration menu
    Copy the full SHA
    11419ac View commit details
    Browse the repository at this point in the history

Commits on Oct 31, 2023

  1. mintrust can be lower than convergence_drms ; conmethod 1 bugfix

    @leeping
    leeping committed Oct 31, 2023
    Configuration menu
    Copy the full SHA
    ef8c5cd View commit details
    Browse the repository at this point in the history

Commits on Nov 4, 2023

  1. Bug fix for extrapolation not activated

    @leeping
    leeping committed Nov 4, 2023
    Configuration menu
    Copy the full SHA
    862d22b View commit details
    Browse the repository at this point in the history

Commits on Nov 6, 2023

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

    @leeping
    leeping committed Nov 6, 2023
    Configuration menu
    Copy the full SHA
    aa14539 View commit details
    Browse the repository at this point in the history

  2. A strange merge conflict in interpolate branch

    @leeping
    leeping committed Nov 6, 2023
    Configuration menu
    Copy the full SHA
    f0a1e37 View commit details
    Browse the repository at this point in the history

  3. Merge branch 'interpolate' of github.com:leeping/geomeTRIC into inter… 

    …polate

Conflicts:
	geometric/xml_helper.py
    @leeping
    leeping committed Nov 6, 2023
    Configuration menu
    Copy the full SHA
    00ce6af View commit details
    Browse the repository at this point in the history

Commits on Dec 6, 2023

  1. Make align_system option more global

    @leeping
    leeping committed Dec 6, 2023
    Configuration menu
    Copy the full SHA
    fd41651 View commit details
    Browse the repository at this point in the history

Commits on Jan 11, 2024

  1. Add atom deletion support to molecule.py, improve handling of CONECT … 

    …records
    @leeping
    leeping committed Jan 11, 2024
    Configuration menu
    Copy the full SHA
    d5a6170 View commit details
    Browse the repository at this point in the history

Commits on Mar 8, 2024

  1. typo

    @hjnpark
    hjnpark committed Mar 8, 2024
    Configuration menu
    Copy the full SHA
    d8e897e View commit details
    Browse the repository at this point in the history

  2. Merge pull request #195 from hjnpark/interpolate 

    Typo fixed
    @hjnpark
    hjnpark authored Mar 8, 2024
    Configuration menu
    Copy the full SHA
    363de19 View commit details
    Browse the repository at this point in the history

Commits on Mar 13, 2024

  1. Merge branch 'master' of github.com:leeping/geomeTRIC into molecule_d… 

    …elatom
    @leeping
    leeping committed Mar 13, 2024
    Configuration menu
    Copy the full SHA
    b0b5631 View commit details
    Browse the repository at this point in the history

  2. Fix a "zero divide by zero" error

    @leeping
    leeping committed Mar 13, 2024
    Configuration menu
    Copy the full SHA
    086ff87 View commit details
    Browse the repository at this point in the history

  3. Add interpolation "fast mode" and two new initial guess methods

    @leeping
    leeping committed Mar 13, 2024
    Configuration menu
    Copy the full SHA
    90b0bff View commit details
    Browse the repository at this point in the history

  4. Merge branch 'interpolate' of github.com:leeping/geomeTRIC into inter… 

    …polate
    @leeping
    leeping committed Mar 13, 2024
    Configuration menu
    Copy the full SHA
    0196551 View commit details
    Browse the repository at this point in the history

  5. Merge branch 'interpolate' of github.com:leeping/geomeTRIC into inter… 

    …polate
    @leeping
    leeping committed Mar 13, 2024
    Configuration menu
    Copy the full SHA
    8d01391 View commit details
    Browse the repository at this point in the history

  6. Merge branch 'molecule_delatom' into interpolate

    @leeping
    leeping committed Mar 13, 2024
    Configuration menu
    Copy the full SHA
    99dcc3c View commit details
    Browse the repository at this point in the history