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Expanded ensemble #421

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27517bc
Properly send CV coordinates to root MPI process
andrrizzi Mar 15, 2019
e6f9cae
Add test for uniform mixing with MPI
andrrizzi Mar 19, 2019
35a719c
option for performing expanded ensemble simulations
May 9, 2019
f2782d2
fix typo
May 9, 2019
6e9689c
fix typo
May 9, 2019
e3253e1
fix typo
May 9, 2019
af94050
store weight_update in reporter
May 10, 2019
4bf9551
print histogram for the expanded ensemble
May 10, 2019
f38263d
remove sampler options from write online data
May 10, 2019
89b338d
add weight update option in example
May 10, 2019
97546ac
fix bug related to the beta factor variable
May 14, 2019
fdeb728
Update everything to match MolSSI cookiecutter
jchodera May 23, 2019
973e60a
Update changelog
jchodera May 23, 2019
d5a27f9
Add channels to conda envs
jchodera May 23, 2019
55908fd
Add missing dependencies
jchodera May 24, 2019
b1b361e
Fix logsumexp import
jchodera May 24, 2019
e206d1b
Update changelog
jchodera May 24, 2019
7d83a1a
Merge pull request #424 from choderalab/cookiecutter
jchodera May 24, 2019
8181bb5
Update setup.py to use cookiecutter and versioneer
andrrizzi May 29, 2019
54dded2
Create _version.py
andrrizzi May 29, 2019
a4b62e4
Update releasehistory.rst
andrrizzi May 29, 2019
030cc13
Let versioneer set the version
andrrizzi May 29, 2019
1e14040
Determine version in __init__ with versioneer
andrrizzi May 29, 2019
d827d20
Use versioneer version when initializing netcdf
andrrizzi May 29, 2019
727e6a5
Fix version reference
andrrizzi May 29, 2019
53170a1
Fix error handling
andrrizzi May 30, 2019
27c43ce
Attempt setting env var HDF5_USE_FILE_LOCKING to false when opening n…
andrrizzi May 30, 2019
ce39205
Merge pull request #426 from choderalab/release-0.18.2
andrrizzi May 30, 2019
7642908
Update releasehistory.rst
andrrizzi May 30, 2019
6b31737
Merge pull request #427 from choderalab/update-releasenotes
andrrizzi May 30, 2019
92e72b7
add round trips as criteria for changing sams stage
May 30, 2019
c77bbf3
sams accepts multiple criteria for switching stages
May 30, 2019
093a361
fix bug
May 30, 2019
4ab5fdd
fix error
May 30, 2019
c729b73
first revised version
May 31, 2019
f8318c1
fix in error statement
May 31, 2019
4d2c176
delete debug statement
Jun 1, 2019
cb99ca5
Merge branch 'master' into expanded-ensemble
Jun 3, 2019
250da68
add histogram flatness as default criteria
Jun 6, 2019
38f5eab
fix bug in the advance dict
Jun 7, 2019
6f0717f
[WIP] Changes to update multi region from 0.15 to 0.18
adw62 Jun 13, 2019
cdcd7ba
fix bugs
adw62 Jun 13, 2019
c61bd97
[WIP] PME not working
adw62 Jun 18, 2019
399e4f4
[WIP] PME working
adw62 Jun 24, 2019
e367907
change offset behaviour
adw62 Jun 24, 2019
a549254
correct error in exceptions
adw62 Jun 24, 2019
fbaeb11
Few simplifications/style changes
andrrizzi Jun 26, 2019
d4d496e
Rename AlchemicalRegion.region_name to AlchemicalRegion.name
andrrizzi Jun 26, 2019
e6a9a30
Fix bug where reference force is modified instead of copy
andrrizzi Jun 26, 2019
664f89f
More style fixes
andrrizzi Jun 26, 2019
97b8c77
Fix bug in determining nonbonded lambda variables
andrrizzi Jun 26, 2019
0947a76
More PEP8 fixes
andrrizzi Jun 26, 2019
f02ed2b
Fix bug where exceptions where added to the reference force instead o…
andrrizzi Jun 26, 2019
675e7af
variables mis named
adw62 Jun 26, 2019
b988a8c
check for flatness criteria
Jul 8, 2019
d04d416
FIx module path
andrrizzi Jul 19, 2019
c16fc7d
Update releasehistory.rst
andrrizzi Jul 19, 2019
c641385
Temporarily allow macOS tests to fail
andrrizzi Jul 19, 2019
1cc66de
Temporarily allow macOS tests to fail
andrrizzi Jul 19, 2019
7712c07
Fix YAML dict -> list
andrrizzi Jul 19, 2019
c01b5b0
Fix #409: rename restart_attempts in docstring
andrrizzi Jul 19, 2019
0a39769
Fix #418: Fix tutorial comment
andrrizzi Jul 19, 2019
2ea991c
Merge pull request #430 from choderalab/fix-module-path
andrrizzi Jul 19, 2019
c831c14
Fix #408: Add util function to API sphinx docs
andrrizzi Jul 20, 2019
92fe2f2
Remove duplicate pyyaml requirement
andrrizzi Jul 20, 2019
3c30819
Fix #400: dummy cache cannot replace ContextCache
andrrizzi Jul 20, 2019
bc83976
PEP8
andrrizzi Jul 20, 2019
15bfeb1
Fix #422: Set chunksize=1 for iteration dimension
andrrizzi Jul 21, 2019
7a9dd32
Update releasehistory.rst
andrrizzi Jul 21, 2019
d1434ab
Merge branch 'master' into fix-docs
andrrizzi Jul 21, 2019
14adf7b
Update releasehistory.rst
andrrizzi Jul 21, 2019
6cf88cc
Merge pull request #432 from choderalab/fix-docs
andrrizzi Jul 21, 2019
a66b013
Corrections for current tests
adw62 Jul 25, 2019
56d2eba
Fix TolueneImplicitOBC2
adw62 Jul 25, 2019
3e44c94
remove print
adw62 Jul 25, 2019
11fda47
Compatabilty for MultiReg tests
adw62 Jul 26, 2019
cba7cc5
MultiReg TIP3P Box test
adw62 Jul 26, 2019
412e5ed
LennardJonesCluster and LennardJonesFluid
adw62 Jul 26, 2019
17dd9ba
make tests clearer
adw62 Aug 2, 2019
81755a9
make tests clearer
adw62 Aug 2, 2019
aeb45ee
tests working
adw62 Aug 9, 2019
a353409
tests working
adw62 Aug 9, 2019
eb032f1
remove extra lines
adw62 Aug 9, 2019
5ea2b1c
remove extra lines
adw62 Aug 9, 2019
d9fd743
fix single region tests
adw62 Aug 10, 2019
192a587
fix single region tests
adw62 Aug 10, 2019
ece15ea
compare_system_energies working
adw62 Aug 10, 2019
fcaacb9
all fast test working
adw62 Aug 12, 2019
8c4793b
all fast tests working
adw62 Aug 12, 2019
805ba45
fix for Long range correction did not converge
adw62 Sep 4, 2019
938a34b
correct typo
adw62 Sep 4, 2019
62fa036
All test working
adw62 Sep 11, 2019
793b6c4
all tests working
adw62 Sep 11, 2019
b11fc6a
ThermodynamicState support for more barostats
Olllom Sep 24, 2019
548e779
Add files via upload
adw62 Sep 25, 2019
25df3cf
Add files via upload
adw62 Sep 25, 2019
f26e55c
Correct mistaken push
adw62 Sep 25, 2019
25162ae
Add files via upload
adw62 Sep 25, 2019
37f4cf6
added ThermodynamicState support for non-zero surface tension
Olllom Sep 26, 2019
e75f212
removed old comment
Olllom Sep 26, 2019
a6f1f38
enable platform properties in ThermodynamicState.create_context
Olllom Sep 27, 2019
b6a60d6
enable platform properties in ContextCache
Olllom Sep 27, 2019
03158ef
added platform properties to ContextCache serialization
Olllom Sep 27, 2019
b7a9e7e
Avoid modifying reference nonbonded force and more docs
andrrizzi Oct 14, 2019
f5a6557
Style fixes
andrrizzi Oct 14, 2019
6d9c6e3
Comments from review #1
adw62 Oct 15, 2019
1b88dc9
Delete alchemy.py
adw62 Oct 15, 2019
315492a
Comments from review #1
adw62 Oct 15, 2019
03034c4
Small code simplification
andrrizzi Oct 15, 2019
eb7e305
remove one if in `Distribute exceptions contributions in appropriate …
adw62 Oct 15, 2019
02c9746
stop at_least_one_alchemical being treated multiple times
adw62 Oct 15, 2019
47e027b
rework _find_force_components
adw62 Oct 15, 2019
1212447
_find_force_components reworked
adw62 Oct 17, 2019
5879558
Test nightly and conda-forge openmm builds on travis
jchodera Oct 19, 2019
3b630f6
Update force-install of openmm
jchodera Oct 19, 2019
6ab23d5
Make sure to use 'latest' openmm for osx
jchodera Oct 19, 2019
e7090e0
Fix alchemy test that was previously trying to alchemically modify on…
jchodera Oct 19, 2019
debcf2b
Clean up contexts in test that is segfaulting
jchodera Oct 19, 2019
28a429d
Update releasehistory.rst
andrrizzi Oct 19, 2019
1f38908
Merge branch 'master' into alchemical-regions
andrrizzi Oct 19, 2019
048265d
Merge pull request #438 from choderalab/alchemical-regions
andrrizzi Oct 19, 2019
b500c6d
Fix reduced_potentials_at_states
andrrizzi Oct 19, 2019
4b8155f
Update releasehistory.rst
andrrizzi Oct 19, 2019
0704db1
Force removal of ocl-icd and ocl-icd-system to see if this prevents O…
Oct 19, 2019
861dfb6
Merge remote-tracking branch 'origin/master' into travis-test-conda-f…
jchodera Oct 19, 2019
1de5a17
Fix bug introduced in last commit
jchodera Oct 19, 2019
8ca9fb0
Merge pull request #442 from choderalab/travis-test-conda-forge
jchodera Oct 20, 2019
171d5b1
Merge branch 'master' into other_barostats
Olllom Oct 21, 2019
ba91110
Merge branch 'master' into other_barostats
Olllom Oct 21, 2019
e4b6b06
ContextCache refactoring
Olllom Oct 22, 2019
fb94572
ThermodynamicState refactoring for surface tension
Olllom Oct 23, 2019
101915a
ThermodynamicState._is_barostat_type_consistent
Olllom Oct 23, 2019
d1c1812
final cleanup of other barostats in ThermodynamicState
Olllom Oct 26, 2019
8f61441
Convert API warnings from warnings.warn() to logger.warn()
jchodera Oct 26, 2019
f25f6f6
Rework harmonic oscillator free energy tests with/without unsampled s…
jchodera Oct 26, 2019
6ad1427
Minor cleanup of comments
jchodera Oct 26, 2019
1934693
Update changelog
jchodera Oct 26, 2019
f89d318
Fix sphinx formatting in changelog
jchodera Oct 28, 2019
46308b0
attempted fix of surface tension test
Olllom Oct 29, 2019
21dee06
Merge pull request #446 from choderalab/sams-endpoint-tests
jchodera Oct 29, 2019
6e07232
Merge pull request #437 from Olllom/other_barostats
andrrizzi Oct 30, 2019
383a22a
Add test reduced_potential_at_states
andrrizzi Nov 5, 2019
110524b
Merge pull request #444 from choderalab/fix-reduced-potentials
andrrizzi Nov 6, 2019
b22711c
Merge branch 'master' into fix-mpi-mixing
andrrizzi Nov 7, 2019
2cd8310
Merge pull request #407 from choderalab/fix-mpi-mixing
andrrizzi Nov 8, 2019
e5a8f8f
Fix SEM in test
andrrizzi Nov 8, 2019
7980ea9
Better comment
andrrizzi Nov 8, 2019
acdcd8c
Fix release history
andrrizzi Nov 8, 2019
64dd4c7
Merge pull request #450 from choderalab/fix-release-notes
andrrizzi Nov 8, 2019
7de78f8
Fix release notes
andrrizzi Nov 8, 2019
82f14f0
Merge pull request #451 from choderalab/fix-release
andrrizzi Nov 8, 2019
9bd05c0
Fix restrained atom indices
andrrizzi Mar 21, 2020
9019ae9
Fix release history
andrrizzi Mar 21, 2020
c2b61c4
Merge pull request #462 from choderalab/fix-restrained-indices
jchodera Mar 22, 2020
61f6e00
add a loopy customintegrator
dominicrufa Apr 10, 2020
9eed89c
help example
dominicrufa Apr 10, 2020
bc21606
Update openmmtools/integrators.py
dominicrufa Apr 13, 2020
8f1a26f
deleting `x_annealing` as it is a redundant placeholder variable
dominicrufa Apr 13, 2020
dbc157f
Merge branch 'loopy_alchemical_customintegrator' of https://github.co…
dominicrufa Apr 13, 2020
b3bd3c3
Fix travis since miniconda changed location
jchodera Apr 14, 2020
a515540
Fix the fix
jchodera Apr 14, 2020
506c354
Merge pull request #465 from choderalab/fix-travis-2
jchodera Apr 14, 2020
aa14549
Merge remote-tracking branch 'origin/master' into loopy_alchemical_cu…
jchodera Apr 14, 2020
115d1fb
Remove accidentally committed C vile
jchodera Apr 15, 2020
fa871d1
Add PeriodicNonequilibriumIntegrator to docs
jchodera Apr 15, 2020
fe6042f
Add PeriodicNonequilibriumIntegrator (heavily based on loopy integrat…
jchodera Apr 15, 2020
88baad8
Update changelog
jchodera Apr 15, 2020
1585fdd
Add back C file
jchodera Apr 15, 2020
442fab2
Remove unused Jupyter
jchodera Apr 15, 2020
9924e5b
Address helpful comments from @dominicrufa
jchodera Apr 15, 2020
fa3fd80
fixing string syntax error and make 'cycle' variable consistent
dominicrufa Apr 17, 2020
9fa56df
Merge pull request #466 from choderalab/periodic-nonequilibrium-integ…
jchodera Apr 18, 2020
3cab265
Fix an issue with accidentally resetting PeriodicNonequilibriumIntegr…
jchodera Apr 21, 2020
141ac5f
Ensure alchemical parameters are correctly set at beginning of nonequ…
jchodera Apr 21, 2020
fb672f3
Use more robust scheme to initialize PeriodicNonequilibriumIntegrator
jchodera Apr 21, 2020
2a8537b
Merge pull request #467 from choderalab/fix-periodic-nonequilibrium
jchodera Apr 28, 2020
6f865a2
Update neq integrator tests to generate trajectory.
jchodera May 4, 2020
d409771
Merge pull request #469 from choderalab/update-neq-test
jchodera May 11, 2020
be5a0df
resolved merge conflict
Aug 20, 2020
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Fix bug in determining nonbonded lambda variables
  • Loading branch information
andrrizzi committed Jun 26, 2019
commit 97b8c77f90e59a8f71f9026d1e647e051e531b6a
5 changes: 4 additions & 1 deletion openmmtools/alchemy.py
Original file line number Diff line number Diff line change
@@ -1595,7 +1595,10 @@ def _alchemically_modify_NonbondedForce(self, reference_force, alchemical_region
# Make a list of region names for the alchemical regions interactions which are being built.
lambda_var_suffixes = []
for alchemical_region in alchemical_regions_pairs:
lambda_var_suffixes.append('_'+alchemical_region.name)
if alchemical_region.name is None:
lambda_var_suffixes.append('')
else:
lambda_var_suffixes.append('_' + alchemical_region.name)

# --------------------------------------------------
# Determine energy expression for all custom forces