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Create RestCapableHybridTopologyFactory #848

Merged
merged 106 commits into from
Apr 13, 2022
Merged

Create RestCapableHybridTopologyFactory #848

merged 106 commits into from
Apr 13, 2022

Commits on Aug 20, 2021

  1. add initial version

    @zhang-ivy
    zhang-ivy committed Aug 20, 2021
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Commits on Aug 25, 2021

  1. address dominic's comments and fix rest scale bug

    @zhang-ivy
    zhang-ivy committed Aug 25, 2021
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Commits on Aug 26, 2021

  1. set alpha to 0 for NoCutofF

    @zhang-ivy
    zhang-ivy committed Aug 26, 2021
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Commits on Aug 30, 2021

  1. map CBs

    @zhang-ivy
    zhang-ivy committed Aug 30, 2021
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Commits on Oct 26, 2021

  1. update with scaled water rest changes

    @zhang-ivy
    zhang-ivy committed Oct 26, 2021
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  2. Merge branch 'rest-over-protocol' of ssh://github.com/choderalab/pers… 

    …es into rest-over-protocol
    @zhang-ivy
    zhang-ivy committed Oct 26, 2021
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  3. change continue to pass

    @zhang-ivy
    zhang-ivy committed Oct 26, 2021
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  4. Merge branch 'rest-over-protocol' of ssh://github.com/choderalab/pers… 

    …es into rest-over-protocol

n setup.py in
    @zhang-ivy
    zhang-ivy committed Oct 26, 2021
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  5. fix r_cutoff

    @zhang-ivy
    zhang-ivy committed Oct 26, 2021
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  6. Merge branch 'rest-over-protocol' of ssh://github.com/choderalab/pers

    @zhang-ivy
    zhang-ivy committed Oct 26, 2021
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Commits on Oct 27, 2021

  1. fix bugs

    @zhang-ivy
    zhang-ivy committed Oct 27, 2021
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Commits on Oct 28, 2021

  1. temp changes to allow small molecule pipeline

    @zhang-ivy
    zhang-ivy committed Oct 28, 2021
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  2. Merge branch 'master' into rest-over-protocol

    @zhang-ivy
    zhang-ivy committed Oct 28, 2021
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Commits on Oct 29, 2021

  1. add more comments and fix valence problems

    @zhang-ivy
    zhang-ivy committed Oct 29, 2021
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  2. Merge branch 'rest-over-protocol' of ssh://github.com/choderalab/pers… 

    …es into rest-over-protocol
    @zhang-ivy
    zhang-ivy committed Oct 29, 2021
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Commits on Nov 1, 2021

  1. fix torsions

    @zhang-ivy
    zhang-ivy committed Nov 1, 2021
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  2. Merge branch 'rest-over-protocol' of ssh://github.com/choderalab/pers… 

    …es into rest-over-protocol
    @zhang-ivy
    zhang-ivy committed Nov 1, 2021
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  3. fix K_old/new

    @zhang-ivy
    zhang-ivy committed Nov 1, 2021
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  4. Merge branch 'rest-over-protocol' of ssh://github.com/choderalab/pers… 

    …es into rest-over-protocol

n
    @zhang-ivy
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  5. don't add torsions twice

    @zhang-ivy
    zhang-ivy committed Nov 1, 2021
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  6. Merge branch 'rest-over-protocol' of ssh://github.com/choderalab/pers… 

    …es into rest-over-protocol
    @zhang-ivy
    zhang-ivy committed Nov 1, 2021
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  7. fix keys and add print statements:

    @zhang-ivy
    zhang-ivy committed Nov 1, 2021
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  8. Merge branch 'rest-over-protocol' of ssh://github.com/choderalab/pers… 

    …es into rest-over-protocol
    @zhang-ivy
    zhang-ivy committed Nov 1, 2021
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  9. fix keys again

    @zhang-ivy
    zhang-ivy committed Nov 1, 2021
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  10. Merge branch 'rest-over-protocol' of ssh://github.com/choderalab/pers… 

    …es into rest-over-protocol
    @zhang-ivy
    zhang-ivy committed Nov 1, 2021
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  11. fix torsions

    @zhang-ivy
    zhang-ivy committed Nov 1, 2021
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Commits on Nov 2, 2021

  1. add core/env torsions twice

    @zhang-ivy
    zhang-ivy committed Nov 2, 2021
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  2. fix nonbondeds

    @zhang-ivy
    zhang-ivy committed Nov 2, 2021
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Commits on Nov 3, 2021

  1. speed up nonbondeds

    @zhang-ivy
    zhang-ivy committed Nov 3, 2021
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  2. fixes to enable speed up and simplify some other stuff

    @zhang-ivy
    zhang-ivy committed Nov 3, 2021
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  3. resolve comments from johns first reviewg

    @zhang-ivy
    zhang-ivy committed Nov 3, 2021
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Commits on Nov 4, 2021

  1. remove PME in name of class

    @zhang-ivy
    zhang-ivy committed Nov 4, 2021
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  2. change Rest to REST in class name

    @zhang-ivy
    zhang-ivy committed Nov 4, 2021
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  3. add first attempt at lambda protocol and alchemical state

    @zhang-ivy
    zhang-ivy committed Nov 4, 2021
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  4. allow lambda protocol input

    @zhang-ivy
    zhang-ivy committed Nov 4, 2021
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  5. change no_alchemy to no-alchemy

    @zhang-ivy
    zhang-ivy committed Nov 4, 2021
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Commits on Nov 8, 2021

  1. fix set parameters alch lambdas for rest at endstates

    @zhang-ivy
    zhang-ivy committed Nov 8, 2021
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  2. fix endstate param

    @zhang-ivy
    zhang-ivy committed Nov 8, 2021
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Commits on Nov 9, 2021

  1. add reciprocal space lambda

    @zhang-ivy
    zhang-ivy committed Nov 9, 2021
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  2. forgot to add reciprocal space lambda to state

    @zhang-ivy
    zhang-ivy committed Nov 9, 2021
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  3. allow specificatoin of rest radius

    @zhang-ivy
    zhang-ivy committed Nov 9, 2021
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  4. fix merge conflicts

    @zhang-ivy
    zhang-ivy committed Nov 9, 2021
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  5. remove need to pass residue id through top proposal

    @zhang-ivy
    zhang-ivy committed Nov 9, 2021
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  6. add import

    @zhang-ivy
    zhang-ivy committed Nov 9, 2021
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  7. fix small molecule api bug

    @zhang-ivy
    zhang-ivy committed Nov 9, 2021
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  8. fix another small molecule api bug

    @zhang-ivy
    zhang-ivy committed Nov 9, 2021
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  9. remove small molecule api changes

    @zhang-ivy
    zhang-ivy committed Nov 9, 2021
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Commits on Nov 10, 2021

  1. speed up co copy exceptions and do not set sigma to 0

    @zhang-ivy
    zhang-ivy committed Nov 10, 2021
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  2. fix sterics expression

    @zhang-ivy
    zhang-ivy committed Nov 10, 2021
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  3. Merge branch 'rest-over-protocol' of ssh://github.com/choderalab/pers… 

    …es into rest-over-protocol
    @zhang-ivy
    zhang-ivy committed Nov 10, 2021
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  4. change min to max

    @zhang-ivy
    zhang-ivy committed Nov 10, 2021
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  5. fix custom expression logic for electrostatics and exceptions

    @zhang-ivy
    zhang-ivy committed Nov 10, 2021
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  6. add max() to exceptions sigma expression

    @zhang-ivy
    zhang-ivy committed Nov 10, 2021
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  7. remove remaining sigmas that are zeroed in copy_*

    @zhang-ivy
    zhang-ivy committed Nov 10, 2021
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  8. remove zeros from _copy() functions again

    @zhang-ivy
    zhang-ivy committed Nov 10, 2021
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  9. Merge branch 'rest-over-protocol' of ssh://github.com/choderalab/pers… 

    …es into rest-over-protocol
    @zhang-ivy
    zhang-ivy committed Nov 10, 2021
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Commits on Nov 11, 2021

  1. fix units

    @zhang-ivy
    zhang-ivy committed Nov 11, 2021
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  2. undo typo

    @zhang-ivy
    zhang-ivy committed Nov 11, 2021
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  3. remove checks for nb params old*new != 0

    @zhang-ivy
    zhang-ivy committed Nov 11, 2021
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Commits on Nov 12, 2021

  1. remove lifting from exceptions

    @zhang-ivy
    zhang-ivy committed Nov 12, 2021
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  2. clean up code

    @zhang-ivy
    zhang-ivy committed Nov 12, 2021
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  3. take average mass for mapped atoms

    @zhang-ivy
    zhang-ivy committed Nov 12, 2021
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  4. fix bug 0.5 -> 0.05

    @zhang-ivy
    zhang-ivy committed Nov 12, 2021
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Commits on Nov 15, 2021

  1. remove checks

    @zhang-ivy
    zhang-ivy committed Nov 15, 2021
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  2. Merge branch 'master' into rest-over-protocol

    @zhang-ivy
    zhang-ivy committed Nov 15, 2021
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Commits on Nov 17, 2021

  1. set name of forces with duplicate names

    @zhang-ivy
    zhang-ivy committed Nov 17, 2021
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Commits on Nov 22, 2021

  1. fix flags for test

    @zhang-ivy
    zhang-ivy committed Nov 22, 2021
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Commits on Nov 24, 2021

  1. allow vanilla and rest htf generation at same time

    @zhang-ivy
    zhang-ivy committed Nov 24, 2021
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  2. fix test_rest

    @zhang-ivy
    zhang-ivy committed Nov 24, 2021
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  3. fix test rest pt 2

    @zhang-ivy
    zhang-ivy committed Nov 24, 2021
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  4. add tests

    @zhang-ivy
    zhang-ivy committed Nov 24, 2021
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  5. add minimization to all test cases

    @zhang-ivy
    zhang-ivy committed Nov 24, 2021
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Commits on Nov 25, 2021

  1. remove os.chdir()

    @zhang-ivy
    zhang-ivy committed Nov 25, 2021
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  2. load htf before md test and fix formatting

    @zhang-ivy
    zhang-ivy committed Nov 25, 2021
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Commits on Dec 6, 2021

  1. Merge branch 'master' into rest-over-protocol

    @mikemhenry
    mikemhenry committed Dec 6, 2021
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Commits on Dec 23, 2021

  1. rework tests

    @zhang-ivy
    zhang-ivy committed Dec 23, 2021
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Commits on Jan 3, 2022

  1. first attempt at fixing endstate validation cases

    @zhang-ivy
    zhang-ivy committed Jan 3, 2022
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  2. add endstate validation for each type of htf

    @zhang-ivy
    zhang-ivy committed Jan 3, 2022
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  3. fix variable name in test

    @zhang-ivy
    zhang-ivy committed Jan 3, 2022
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Commits on Jan 11, 2022

  1. add step to set epsilon to 0 if negative

    @zhang-ivy
    zhang-ivy committed Jan 11, 2022
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  2. add step to set epsilon to 0 if negative

    @zhang-ivy
    zhang-ivy committed Jan 11, 2022
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Commits on Jan 19, 2022

  1. finish fixes for endstate validation

    @zhang-ivy
    zhang-ivy committed Jan 19, 2022
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  2. add copy import

    @zhang-ivy
    zhang-ivy committed Jan 19, 2022
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  3. fix bugs in endstate validation code

    @zhang-ivy
    zhang-ivy committed Jan 19, 2022
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Commits on Jan 21, 2022

  1. move nonscale interactions to NonbondedForce and update tests

    @zhang-ivy
    zhang-ivy committed Jan 21, 2022
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  2. use reference platform for generate_dipeptide_top_pos_sys

    @zhang-ivy
    zhang-ivy committed Jan 21, 2022
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Commits on Jan 28, 2022

  1. use compute values feature

    @zhang-ivy
    zhang-ivy committed Jan 28, 2022
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Commits on Mar 6, 2022

  1. select full residues when defining rest region

    @zhang-ivy
    zhang-ivy committed Mar 6, 2022
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Commits on Mar 7, 2022

  1. add class attributes to docstring

    @zhang-ivy
    zhang-ivy committed Mar 7, 2022
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  2. fixed lifting term lambdas

    @zhang-ivy
    zhang-ivy committed Mar 7, 2022
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  3. update lambda protocol docstrings

    @zhang-ivy
    zhang-ivy committed Mar 7, 2022
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  4. update docstrings

    @zhang-ivy
    zhang-ivy committed Mar 7, 2022
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  5. Merge branch 'main' into rest-over-protocol

    @mikemhenry
    mikemhenry committed Mar 7, 2022
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  6. run slower tets only on the GPU

    @mikemhenry
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Commits on Mar 16, 2022

  1. fix bug in test

    @zhang-ivy
    zhang-ivy committed Mar 16, 2022
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Commits on Mar 21, 2022

  1. only use computed values if CustomNonbondedForce hasattr

    @zhang-ivy
    zhang-ivy committed Mar 21, 2022
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Commits on Mar 22, 2022

  1. Merge branch 'main' into rest-over-protocol

    @mikemhenry
    mikemhenry committed Mar 22, 2022
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  2. added import I forgot to add

    @mikemhenry
    mikemhenry committed Mar 22, 2022
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Commits on Mar 29, 2022

  1. turn LRC off for scaled sterics force

    @zhang-ivy
    zhang-ivy committed Mar 29, 2022
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  2. Merge branch 'rest-over-protocol' of ssh://github.com/choderalab/pers… 

    …es into rest-over-protocol
    @zhang-ivy
    zhang-ivy committed Mar 29, 2022
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  3. Merge branch 'main' into rest-over-protocol

    @mikemhenry
    mikemhenry committed Mar 29, 2022
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Commits on Apr 12, 2022

  1. Update perses/tests/test_relative_point_mutation_setup.py 

    Co-authored-by: Iván Pulido <ivanpulido@protonmail.com>
    @zhang-ivy @ijpulidos
    zhang-ivy and ijpulidos committed Apr 12, 2022
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  2. Update perses/tests/test_topology_proposal.py 

    Co-authored-by: Iván Pulido <ivanpulido@protonmail.com>
    @zhang-ivy @ijpulidos
    zhang-ivy and ijpulidos committed Apr 12, 2022
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  3. Update perses/tests/test_topology_proposal.py 

    Co-authored-by: Iván Pulido <ivanpulido@protonmail.com>
    @zhang-ivy @ijpulidos
    zhang-ivy and ijpulidos committed Apr 12, 2022
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  4. turn LRC on for scaled sterics force to make tests pass for now

    @zhang-ivy
    zhang-ivy committed Apr 12, 2022
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  5. Merge branch 'main' into rest-over-protocol

    @ijpulidos
    ijpulidos committed Apr 12, 2022
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