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Expanded ensemble#421

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ajsilveira wants to merge 179 commits intochoderalab:expanded-ensemblechoderalab/openmmtools:expanded-ensemblefrom ajsilveira:expanded-ensembleajsilveira/openmmtools:expanded-ensembleCopy head branch name to clipboard

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Commits

Commits on Mar 15, 2019

• Properly send CV coordinates to root MPI process

  andrrizzi

  committed
  27517bc

Commits on Mar 19, 2019

• Add test for uniform mixing with MPI

  andrrizzi

  committed
  e6f9cae

Commits on May 9, 2019

• option for performing expanded ensemble simulations

  

  Silveira

  committed
  35a719c

• fix typo

  

  Silveira

  committed
  f2782d2

• fix typo

  

  Silveira

  committed
  6e9689c

• fix typo

  

  Silveira

  committed
  e3253e1

Commits on May 10, 2019

• store weight_update in reporter

  

  Silveira

  committed
  af94050

• print histogram for the expanded ensemble

  

  Silveira

  committed
  4bf9551

• remove sampler options from write online data

  

  Silveira

  committed
  f38263d

• add weight update option in example

  

  Silveira

  committed
  89b338d

Commits on May 14, 2019

• fix bug related to the beta factor variable

  

  Silveira

  committed
  97546ac

Commits on May 23, 2019

• Update everything to match MolSSI cookiecutter

  jchodera

  committed
  fdeb728

• Update changelog

  jchodera

  committed
  973e60a

• Add channels to conda envs

  jchodera

  committed
  d5a27f9

Commits on May 24, 2019

• Add missing dependencies

  jchodera

  committed
  55908fd

• Fix logsumexp import

  jchodera

  committed
  b1b361e

• Update changelog

  jchodera

  committed
  e206d1b

• Merge pull request choderalab#424 from choderalab/cookiecutter

  Show description for 7d83a1a
  jchodera

  authored
  7d83a1a

Commits on May 29, 2019

• Update setup.py to use cookiecutter and versioneer

  andrrizzi

  authored
  8181bb5

• Create _version.py

  andrrizzi

  authored
  54dded2

• Update releasehistory.rst

  andrrizzi

  authored
  a4b62e4

• Let versioneer set the version

  andrrizzi

  authored
  030cc13

• Determine version in __init__ with versioneer

  andrrizzi

  authored
  1e14040

• Use versioneer version when initializing netcdf

  andrrizzi

  authored
  d827d20

• Fix version reference

  andrrizzi

  authored
  727e6a5

Commits on May 30, 2019

• Fix error handling

  andrrizzi

  committed
  53170a1

• Attempt setting env var HDF5_USE_FILE_LOCKING to false when opening netcdf file on failure

  andrrizzi

  committed
  27c43ce

• Merge pull request choderalab#426 from choderalab/release-0.18.2

  Show description for ce39205
  andrrizzi

  authored
  ce39205

• Update releasehistory.rst

  andrrizzi

  authored
  7642908

• Merge pull request choderalab#427 from choderalab/update-releasenotes

  Show description for 6b31737
  andrrizzi

  authored
  6b31737

• add round trips as criteria for changing sams stage

  

  Silveira

  committed
  92e72b7

• sams accepts multiple criteria for switching stages

  

  Silveira

  committed
  c77bbf3

• fix bug

  

  Silveira

  committed
  093a361

• fix error

  

  Silveira

  committed
  4ab5fdd

Commits on May 31, 2019

• first revised version

  

  Ana Silveira

  committed
  c729b73

• fix in error statement

  

  Ana Silveira

  committed
  f8318c1

Commits on Jun 1, 2019

• delete debug statement

  

  Silveira

  committed
  4d2c176

Commits on Jun 3, 2019

• Merge branch 'master' into expanded-ensemble

  

  Silveira

  committed
  cb99ca5

Commits on Jun 6, 2019

• add histogram flatness as default criteria

  Show description for 250da68
  

  Ana Silveira

  committed
  250da68

Commits on Jun 7, 2019

• fix bug in the advance dict

  

  Ana Silveira

  committed
  38f5eab

Commits on Jun 13, 2019

• [WIP] Changes to update multi region from 0.15 to 0.18

  Show description for 6f0717f
  adw62

  authored
  6f0717f

• fix bugs

  adw62

  authored
  cdcd7ba

Commits on Jun 18, 2019

• [WIP] PME not working

  adw62

  authored
  c61bd97

Commits on Jun 24, 2019

• [WIP] PME working

  adw62

  authored
  399e4f4

• change offset behaviour

  adw62

  authored
  e367907

• correct error in exceptions

  adw62

  authored
  a549254

Commits on Jun 26, 2019

• Few simplifications/style changes

  andrrizzi

  committed
  fbaeb11

• Rename AlchemicalRegion.region_name to AlchemicalRegion.name

  andrrizzi

  committed
  d4d496e

• Fix bug where reference force is modified instead of copy

  andrrizzi

  committed
  e6a9a30

• More style fixes

  andrrizzi

  committed
  664f89f

• Fix bug in determining nonbonded lambda variables

  andrrizzi

  committed
  97b8c77

• More PEP8 fixes

  andrrizzi

  committed
  0947a76

• Fix bug where exceptions where added to the reference force instead of its copy.

  andrrizzi

  committed
  f02ed2b

• variables mis named

  adw62

  authored
  675e7af

Commits on Jul 8, 2019

• check for flatness criteria

  

  Ana Silveira

  committed
  b988a8c

Commits on Jul 19, 2019

• FIx module path

  andrrizzi

  authored
  d04d416

• Update releasehistory.rst

  andrrizzi

  authored
  c16fc7d

• Temporarily allow macOS tests to fail

  andrrizzi

  authored
  c641385

• Temporarily allow macOS tests to fail

  andrrizzi

  authored
  1cc66de

• Fix YAML dict -> list

  andrrizzi

  authored
  7712c07

• Fix choderalab#409: rename restart_attempts in docstring

  andrrizzi

  authored
  c01b5b0

• Fix choderalab#418: Fix tutorial comment

  Show description for 0a39769
  andrrizzi

  authored
  0a39769

• Merge pull request choderalab#430 from choderalab/fix-module-path

  Show description for 2ea991c
  andrrizzi

  authored
  2ea991c

Commits on Jul 20, 2019

• Fix choderalab#408: Add util function to API sphinx docs

  andrrizzi

  authored
  c831c14

• Remove duplicate pyyaml requirement

  andrrizzi

  authored
  92fe2f2

• Fix choderalab#400: dummy cache cannot replace ContextCache

  andrrizzi

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  3c30819

• PEP8

  andrrizzi

  authored
  bc83976

Commits on Jul 21, 2019

• Fix choderalab#422: Set chunksize=1 for iteration dimension

  andrrizzi

  authored
  15bfeb1

• Update releasehistory.rst

  andrrizzi

  authored
  7a9dd32

• Merge branch 'master' into fix-docs

  andrrizzi

  authored
  d1434ab

• Update releasehistory.rst

  andrrizzi

  authored
  14adf7b

• Merge pull request choderalab#432 from choderalab/fix-docs

  Show description for 6cf88cc
  andrrizzi

  authored
  6cf88cc

Commits on Jul 25, 2019

• Corrections for current tests

  Show description for a66b013
  adw62

  authored
  a66b013

• Fix TolueneImplicitOBC2

  adw62

  authored
  56d2eba

• remove print

  adw62

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  3e44c94

Commits on Jul 26, 2019

• Compatabilty for MultiReg tests

  adw62

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  11fda47

• MultiReg TIP3P Box test

  adw62

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  cba7cc5

• LennardJonesCluster and LennardJonesFluid

  adw62

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  412e5ed

Commits on Aug 2, 2019

• make tests clearer

  adw62

  authored
  17dd9ba

• make tests clearer

  adw62

  authored
  81755a9

Commits on Aug 9, 2019

• tests working

  adw62

  authored
  aeb45ee

• tests working

  adw62

  authored
  a353409

• remove extra lines

  adw62

  authored
  eb032f1

• remove extra lines

  adw62

  authored
  5ea2b1c

Commits on Aug 10, 2019

• fix single region tests

  adw62

  authored
  d9fd743

• fix single region tests

  adw62

  authored
  192a587

• compare_system_energies working

  adw62

  authored
  ece15ea

Commits on Aug 12, 2019

• all fast test working

  adw62

  authored
  fcaacb9

• all fast tests working

  adw62

  authored
  8c4793b

Commits on Sep 4, 2019

• fix for Long range correction did not converge

  adw62

  authored
  805ba45

• correct typo

  Show description for 938a34b
  adw62

  authored
  938a34b

Commits on Sep 11, 2019

• All test working

  adw62

  authored
  62fa036

• all tests working

  adw62

  authored
  793b6c4

Commits on Sep 24, 2019

• ThermodynamicState support for more barostats

  Show description for b11fc6a
  Olllom

  committed
  b11fc6a

Commits on Sep 25, 2019

• Add files via upload

  adw62

  authored
  548e779

• Add files via upload

  adw62

  authored
  25df3cf

• Correct mistaken push

  adw62

  authored
  f26e55c

• Add files via upload

  adw62

  authored
  25162ae

Commits on Sep 26, 2019

• added ThermodynamicState support for non-zero surface tension

  Olllom

  committed
  37f4cf6

• removed old comment

  Olllom

  committed
  e75f212

Commits on Sep 27, 2019

• enable platform properties in ThermodynamicState.create_context

  Olllom

  committed
  a6f1f38

• enable platform properties in ContextCache

  Olllom

  committed
  b6a60d6

• added platform properties to ContextCache serialization

  Olllom

  committed
  03158ef

Commits on Oct 14, 2019

• Avoid modifying reference nonbonded force and more docs

  andrrizzi

  committed
  b7a9e7e

• Style fixes

  andrrizzi

  committed
  f5a6557

Commits on Oct 15, 2019

• Comments from review choderalab#1

  adw62

  authored
  6d9c6e3

• Delete alchemy.py

  adw62

  authored
  1b88dc9

• Comments from review choderalab#1

  adw62

  authored
  315492a

• Small code simplification

  andrrizzi

  committed
  03034c4

• remove one if in Distribute exceptions contributions in appropriate bond forces

  adw62

  authored
  eb7e305

• stop at_least_one_alchemical being treated multiple times

  adw62

  authored
  02c9746

• rework _find_force_components

  adw62

  authored
  47e027b

Commits on Oct 17, 2019

• _find_force_components reworked

  adw62

  authored
  1212447

Commits on Oct 19, 2019

• Test nightly and conda-forge openmm builds on travis

  jchodera

  committed
  5879558

• Update force-install of openmm

  jchodera

  committed
  3b630f6

• Make sure to use 'latest' openmm for osx

  jchodera

  committed
  6ab23d5

• Fix alchemy test that was previously trying to alchemically modify only part of a TIP4P-Ew molecule

  jchodera

  committed
  e7090e0

• Clean up contexts in test that is segfaulting

  jchodera

  committed
  debcf2b

• Update releasehistory.rst

  andrrizzi

  authored
  28a429d

• Merge branch 'master' into alchemical-regions

  andrrizzi

  authored
  1f38908

• Merge pull request choderalab#438 from choderalab/alchemical-regions

  Show description for 048265d
  andrrizzi

  authored
  048265d

• Fix reduced_potentials_at_states

  andrrizzi

  authored
  b500c6d

• Update releasehistory.rst

  andrrizzi

  authored
  4b8155f

• Force removal of ocl-icd and ocl-icd-system to see if this prevents OpenMM from trying to use OpenCL platform on travis

  

  Chodera

  committed
  0704db1

• Merge remote-tracking branch 'origin/master' into travis-test-conda-forge

  jchodera

  committed
  861dfb6

• Fix bug introduced in last commit

  jchodera

  committed
  1de5a17

Commits on Oct 20, 2019

• Merge pull request choderalab#442 from choderalab/travis-test-conda-forge

  Show description for 8ca9fb0
  jchodera

  authored
  8ca9fb0

Commits on Oct 21, 2019

• Merge branch 'master' into other_barostats

  Show description for 171d5b1
  Olllom

  committed
  171d5b1

• Merge branch 'master' into other_barostats

  Show description for ba91110
  Olllom

  committed
  ba91110

Commits on Oct 22, 2019

• ContextCache refactoring

  Olllom

  committed
  e4b6b06

Commits on Oct 23, 2019

• ThermodynamicState refactoring for surface tension

  Olllom

  committed
  fb94572

• ThermodynamicState._is_barostat_type_consistent

  Olllom

  committed
  101915a

Commits on Oct 26, 2019

• final cleanup of other barostats in ThermodynamicState

  Olllom

  committed
  d1c1812

• Convert API warnings from warnings.warn() to logger.warn()

  jchodera

  committed
  8f61441

• Rework harmonic oscillator free energy tests with/without unsampled states to run on travis

  jchodera

  committed
  f25f6f6

• Minor cleanup of comments

  jchodera

  committed
  6ad1427

• Update changelog

  jchodera

  committed
  1934693

Commits on Oct 28, 2019

• Fix sphinx formatting in changelog

  jchodera

  committed
  f89d318

Commits on Oct 29, 2019

• attempted fix of surface tension test

  Olllom

  committed
  46308b0

• Merge pull request choderalab#446 from choderalab/sams-endpoint-tests

  Show description for 21dee06
  jchodera

  authored
  21dee06

Commits on Oct 30, 2019

• Merge pull request choderalab#437 from Olllom/other_barostats

  Show description for 6e07232
  andrrizzi

  authored
  6e07232

Commits on Nov 5, 2019

• Add test reduced_potential_at_states

  andrrizzi

  committed
  383a22a

Commits on Nov 6, 2019

• Merge pull request choderalab#444 from choderalab/fix-reduced-potentials

  Show description for 110524b
  andrrizzi

  authored
  110524b

Commits on Nov 7, 2019

• Merge branch 'master' into fix-mpi-mixing

  andrrizzi

  authored
  b22711c

Commits on Nov 8, 2019

• Merge pull request choderalab#407 from choderalab/fix-mpi-mixing

  Show description for 2cd8310
  andrrizzi

  authored
  2cd8310

• Fix SEM in test

  andrrizzi

  committed
  e5a8f8f

• Better comment

  andrrizzi

  committed
  7980ea9

• Fix release history

  andrrizzi

  committed
  acdcd8c

• Merge pull request choderalab#450 from choderalab/fix-release-notes

  Show description for 64dd4c7
  andrrizzi

  authored
  64dd4c7

• Fix release notes

  andrrizzi

  committed
  7de78f8

• Merge pull request choderalab#451 from choderalab/fix-release

  Show description for 82f14f0
  andrrizzi

  authored
  82f14f0

Commits on Mar 21, 2020

• Fix restrained atom indices

  andrrizzi

  committed
  9bd05c0

• Fix release history

  andrrizzi

  committed
  9019ae9

Commits on Mar 22, 2020

• Merge pull request choderalab#462 from choderalab/fix-restrained-indices

  Show description for c2b61c4
  jchodera

  authored
  c2b61c4

Commits on Apr 10, 2020

• add a loopy customintegrator

  dominicrufa

  committed
  61f6e00

• help example

  dominicrufa

  committed
  9eed89c

Commits on Apr 13, 2020

• Update openmmtools/integrators.py

  Show description for bc21606
  

  dominicrufa

  and

  maxentile

  authored
  bc21606

• deleting x_annealing as it is a redundant placeholder variable

  dominicrufa

  committed
  8f1a26f

• Merge branch 'loopy_alchemical_customintegrator' of https://github.com/choderalab/openmmtools into loopy_alchemical_customintegrator

  dominicrufa

  committed
  dbc157f

Commits on Apr 14, 2020

• Fix travis since miniconda changed location

  Show description for b3bd3c3
  jchodera

  committed
  b3bd3c3

• Fix the fix

  jchodera

  committed
  a515540

• Merge pull request choderalab#465 from choderalab/fix-travis-2

  Show description for 506c354
  jchodera

  authored
  506c354

• Merge remote-tracking branch 'origin/master' into loopy_alchemical_customintegrator

  jchodera

  committed
  aa14549

Commits on Apr 15, 2020

• Remove accidentally committed C vile

  jchodera

  committed
  115d1fb

• Add PeriodicNonequilibriumIntegrator to docs

  jchodera

  committed
  fa871d1

• Add PeriodicNonequilibriumIntegrator (heavily based on loopy integrators from @domrufa)

  jchodera

  committed
  fe6042f

• Update changelog

  jchodera

  committed
  88baad8

• Add back C file

  jchodera

  committed
  1585fdd

• Remove unused Jupyter

  jchodera

  committed
  442fab2

• Address helpful comments from @dominicrufa

  jchodera

  committed
  9924e5b

Commits on Apr 17, 2020

• fixing string syntax error and make 'cycle' variable consistent

  dominicrufa

  committed
  fa3fd80

Commits on Apr 18, 2020

• Merge pull request choderalab#466 from choderalab/periodic-nonequilibrium-integrator

  Show description for 9fa56df
  jchodera

  authored
  9fa56df

Commits on Apr 21, 2020

• Fix an issue with accidentally resetting PeriodicNonequilibriumIntegrator

  jchodera

  committed
  3cab265

• Ensure alchemical parameters are correctly set at beginning of nonequilibrium periodic integration cycle

  jchodera

  committed
  141ac5f

• Use more robust scheme to initialize PeriodicNonequilibriumIntegrator

  jchodera

  committed
  fb672f3

Commits on Apr 28, 2020

• Merge pull request choderalab#467 from choderalab/fix-periodic-nonequilibrium

  Show description for 2a8537b
  jchodera

  authored
  2a8537b

Commits on May 4, 2020

• Update neq integrator tests to generate trajectory.

  jchodera

  committed
  6f865a2

Commits on May 11, 2020

• Merge pull request choderalab#469 from choderalab/update-neq-test

  Show description for d409771
  jchodera

  authored
  d409771

Commits on Aug 20, 2020

• resolved merge conflict

  

  Ana Silveira

  committed
  be5a0df