Code

july update #5

Code

Open

dominicrufa wants to merge 128 commits intochoderalab:masterchoderalab/timemachine_hydration_paper:masterfrom proteneer:masterproteneer/timemachine:masterCopy head branch name to clipboard

+27,355-24,768

Commits

Commits on May 23, 2024

• Test additional MCS pruning heuristics if connected_core = True (#1310)

  Show description for d211aaf
  

  proteneer

  and

  mcwitt

  authored
  d211aaf

  Copy full SHA for d211aaf

Commits on May 29, 2024

• Adds normalized kl divergence metric (#1314)

  Show description for 5bd58bb
  

  3 peopleauthored
  5bd58bb

  Copy full SHA for 5bd58bb

• Avoid reading in an invalid sample, triggering an invalid memory access (#1311)

  Show description for 847a1d9
  

  badisa

  and

  mcwitt

  authored
  847a1d9

  Copy full SHA for 847a1d9

• Add Potential::execute_batch_sparse (#1308)

  Show description for e16ab22
  mcwitt

  authored
  e16ab22

  Copy full SHA for e16ab22

• Adopt dummy values for segmented sumexp required to compile with latest cub (#1313)

  badisa

  authored
  1f8387e

  Copy full SHA for 1f8387e

Commits on May 30, 2024

• Use fast real to int64 conversion for all recent GPUs (#1312)

  Show description for 1791077
  badisa

  authored
  1791077

  Copy full SHA for 1791077

Commits on May 31, 2024

• Adds verify_chiral_consistency_of_core to verify cores quickly (#1315)

  Show description for a821ddc
  badisa

  authored
  a821ddc

  Copy full SHA for a821ddc

• Reduce cost of u_kl computation in HREX (#1309)

  mcwitt

  authored
  b90b37c

  Copy full SHA for b90b37c

• Improve performance of connected core MCS (#1317)

  Show description for be16478
  proteneer

  authored
  be16478

  Copy full SHA for be16478

• Fix nightly test (#1319)

  Show description for a4136a4
  mcwitt

  authored
  a4136a4

  Copy full SHA for a4136a4

Commits on Jun 4, 2024

• Remove HREX replica-state distribution convergence plot (#1316)

  Show description for 0ae3daf
  mcwitt

  authored
  0ae3daf

  Copy full SHA for 0ae3daf

Commits on Jun 5, 2024

• Fix off-by-one misalignment of permutations and frames in HREX output (#1321)

  Show description for c19de3a
  mcwitt

  authored
  c19de3a

  Copy full SHA for c19de3a

• Clean up DHFR nonbonded tests (#1322)

  Show description for 87cebc9
  badisa

  authored
  87cebc9

  Copy full SHA for 87cebc9

Commits on Jun 6, 2024

• Speed up energy decomposition (#1323)

  Show description for 55c3633
  

  badisa

  and

  mcwitt

  authored
  55c3633

  Copy full SHA for 55c3633

• Add convenience methods to extract ligand trajectories by replica (#1320)

  Show description for c30fffd
  mcwitt

  authored
  c30fffd

  Copy full SHA for c30fffd

Commits on Jun 7, 2024

• Hardcode n_frames_per_iter to 1 (#1325)

  mcwitt

  authored
  7109cd9

  Copy full SHA for 7109cd9

Commits on Jun 8, 2024

• Increment frame message to be one indexed (#1327)

  badisa

  authored
  c9191b5

  Copy full SHA for c9191b5

Commits on Jun 10, 2024

• Resolve inconsistency between bar_with_bootstrapped_uncertainty and df_and_err_from_u_kln (#1324)

  Show description for ff9cb5f
  

  3 peopleauthored
  ff9cb5f

  Copy full SHA for ff9cb5f

Commits on Jun 11, 2024

• Correct docstring in get_cores (#1328)

  Show description for 5a5b173
  badisa

  authored
  5a5b173

  Copy full SHA for 5a5b173

Commits on Jun 12, 2024

• Remove unnecessary array copy in extract_trajectories_by_replica (#1329)

  Show description for c63bc93
  mcwitt

  authored
  c63bc93

  Copy full SHA for c63bc93

Commits on Jun 20, 2024

• Log wall time per frame (#1330)

  mcwitt

  authored
  8240243

  Copy full SHA for 8240243

• Fixes Local MD HREX determinism (#1331)

  Show description for 02d5366
  badisa

  authored
  02d5366

  Copy full SHA for 02d5366

Commits on Jun 21, 2024

• Moves OpenMM imports to function calls (#1333)

  badisa

  authored
  6243305

  Copy full SHA for 6243305

Commits on Jun 25, 2024

• Add method to get samples from context without storing to disk (#1334)

  Show description for 2abb1c0
  

  badisa

  and

  mcwitt

  authored
  2abb1c0

  Copy full SHA for 2abb1c0

Commits on Jun 28, 2024

• update to 1.20.3-1ubuntu2.1 (#1335)

  Show description for b230ca7
  

  jkausrelay

  and

  badisa

  authored
  b230ca7

  Copy full SHA for b230ca7

Commits on Jul 1, 2024

• Minor improvements to optimize_coordinates (#1336)

  Show description for 1a726b1
  badisa

  authored
  1a726b1

  Copy full SHA for 1a726b1

• Remove redundant definition (#1337)

  Show description for 5e9d8c1
  mcwitt

  authored
  5e9d8c1

  Copy full SHA for 5e9d8c1

Commits on Jul 3, 2024

• Minimize InitialStates only considering fully interacting atoms for the min_cutoff threshold (#1338)

  Show description for b7d5550
  badisa

  authored
  b7d5550

  Copy full SHA for b7d5550

Commits on Jul 16, 2024

• Perf/verify_chiral_consistency_of_core (#1342)

  Show description for 8e2f36e
  maxentile

  authored
  8e2f36e

  Copy full SHA for 8e2f36e

• Fixes bar_with_pessimistic_uncertainty convergence error (#1344)

  Show description for ab3def7
  badisa

  authored
  ab3def7

  Copy full SHA for ab3def7

Commits on Jul 17, 2024

• Modify Minimization to avoid minimizing while mols are non-interacting (#1339)

  Show description for d7a3abb
  

  3 peopleauthored
  d7a3abb

  Copy full SHA for d7a3abb

• Revert "Modify Minimization to avoid minimizing while mols are non-interacting (#1339)" (#1345)

  Show description for 3c5a025
  badisa

  authored
  3c5a025

  Copy full SHA for 3c5a025

Commits on Jul 19, 2024

• Modified Minimization while keeping number of host atoms constant (#1346)

  Show description for 433e071
  

  3 peopleauthored
  433e071

  Copy full SHA for 433e071

Commits on Jul 22, 2024

• Fixes conditional that triggered warning incorrectly (#1348)

  Show description for b64ebd6
  badisa

  authored
  b64ebd6

  Copy full SHA for b64ebd6

Commits on Jul 23, 2024

• Improve nonbonded decoupling protocol for single topology transformations (#1340)

  Show description for 30e2a50
  mcwitt

  authored
  30e2a50

  Copy full SHA for 30e2a50

• Add support for specifying an initial mapping to get_cores (#1254)

  Show description for 3d18a73
  proteneer

  authored
  3d18a73

  Copy full SHA for 3d18a73

Commits on Jul 24, 2024

• Add atom mapping arguments to restrict the number of connected components in the core (#1349)

  mcwitt

  authored
  1e5b579

  Copy full SHA for 1e5b579

• Add utility to get trajectories by state (#1350)

  Show description for 5ea753f
  badisa

  authored
  5ea753f

  Copy full SHA for 5ea753f

Commits on Jul 25, 2024

• Add lambda schedule tuned to Bisection (#1347)

  Show description for 0790759
  

  badisa

  and

  maxentile

  authored
  0790759

  Copy full SHA for 0790759

• Move template instantiation to cu file instead of header (#1354)

  tkramer-motion

  authored
  bee0aea

  Copy full SHA for bee0aea

Commits on Jul 26, 2024

• Add failing test case of minimization (#1351)

  Show description for 85bbc90
  

  badisa

  and

  maxentile

  authored
  85bbc90

  Copy full SHA for 85bbc90

Commits on Jul 30, 2024

• Fixes Free Energy benchmarks (#1355)

  Show description for 3a174e6
  badisa

  authored
  3a174e6

  Copy full SHA for 3a174e6

Commits on Aug 6, 2024

• get_cores raises exception when total nodes visits exceed max_visits and no cores are generated (#1357)

  Show description for db56acb
  

  badisa

  and

  maxentile

  authored
  db56acb

  Copy full SHA for db56acb

• Add option disallowing atom mappings with no chirally-valid dummy anchor assignment (#1356)

  Show description for 1a8b412
  

  3 peopleauthored
  1a8b412

  Copy full SHA for 1a8b412

• Correctly report nodes visited (#1359)

  Show description for 51b6a5d
  badisa

  authored
  51b6a5d

  Copy full SHA for 51b6a5d

Commits on Aug 13, 2024

• Refactor chiral restraint setup to avoid repeated work (#1360)

  Show description for a743102
  

  mcwitt

  and

  badisa

  authored
  a743102

  Copy full SHA for a743102

Commits on Aug 15, 2024

• Clean up atom mapping code (#1362)

  Show description for 030faa2
  badisa

  authored
  030faa2

  Copy full SHA for 030faa2

Commits on Aug 20, 2024

• Remove guard threshold from local minimize (#1364)

  Show description for c5da44d
  

  badisa

  and

  mcwitt

  authored
  c5da44d

  Copy full SHA for c5da44d

Commits on Aug 26, 2024

• Removes Openeye conda channel from environment.yml (#1367)

  badisa

  authored
  ea7af89

  Copy full SHA for ea7af89

Commits on Sep 4, 2024

• Remove L-W ixn group and merge w/P-L group (#1372)

  Show description for 5478990
  jkausrelay

  authored
  5478990

  Copy full SHA for 5478990

Commits on Sep 9, 2024

• Assert that states differ only in their parameters (#1366)

  Show description for b4bd72b
  mcwitt

  authored
  b4bd72b

  Copy full SHA for b4bd72b

Commits on Sep 11, 2024

• Add plotting to benchmarks (#1375)

  Show description for b8e0589
  

  badisa

  and

  maxentile

  authored
  b8e0589

  Copy full SHA for b8e0589

• Adds test that verifies Neighborlist Tile Density (#1368)

  Show description for e7b319c
  badisa

  authored
  e7b319c

  Copy full SHA for e7b319c

• Removes code that assumes ordering of potentials (#1374)

  Show description for dcb69ea
  badisa

  authored
  dcb69ea

  Copy full SHA for dcb69ea

Commits on Sep 12, 2024

• Fixes failing nightly test (#1376)

  badisa

  authored
  aafe5cb

  Copy full SHA for aafe5cb

• Add test verify protein system waters are constant(#1378)

  Show description for f51ff35
  badisa

  authored
  f51ff35

  Copy full SHA for f51ff35

Commits on Sep 13, 2024

• Revert potential ordering introduced in #1374 (#1379)

  Show description for 39015e3
  badisa

  authored
  39015e3

  Copy full SHA for 39015e3

• Close Matplotlib figures after writing (#1377)

  Show description for 0430d50
  badisa

  authored
  0430d50

  Copy full SHA for 0430d50

Commits on Sep 16, 2024

• Updates docker and gitignore (#1381)

  Show description for 8e46cf8
  badisa

  authored
  8e46cf8

  Copy full SHA for 8e46cf8

• Release GIL on pybind calls to Context (#1370)

  Show description for edec138
  

  badisa

  and

  mcwitt

  authored
  edec138

  Copy full SHA for edec138

Commits on Sep 18, 2024

• remove extraneous summed potential now that the L-E ixn groups are merged (#1384)

  Show description for 60d8230
  jkausrelay

  authored
  60d8230

  Copy full SHA for 60d8230

Commits on Sep 20, 2024

• Revert "Release GIL on pybind calls to Context (#1370)" (#1386)

  Show description for 758725e
  badisa

  authored
  758725e

  Copy full SHA for 758725e

Commits on Sep 23, 2024

• Clean up HREX, BDExchangeMover and TIBDExchangeMover (#1391)

  Show description for 4624f03
  badisa

  authored
  4624f03

  Copy full SHA for 4624f03

• Allocate memory only once in multiple_step methods (#1389)

  Show description for 149dd0e
  badisa

  authored
  149dd0e

  Copy full SHA for 149dd0e

Commits on Sep 24, 2024

• Update jax to 0.4.28 to fix memory corruption issue (#1388)

  Show description for be389f9
  

  jkausrelay

  and

  badisa

  authored
  be389f9

  Copy full SHA for be389f9

• Perform shallow clones of Pybind/Eigen (#1392)

  Show description for e57b60a
  badisa

  authored
  e57b60a

  Copy full SHA for e57b60a

Commits on Sep 25, 2024

• Mark CPU only Chiral tests as nocuda (#1394)

  Show description for 3cd2a97
  badisa

  authored
  3cd2a97

  Copy full SHA for 3cd2a97

Commits on Sep 26, 2024

• Shallow clone of OpenMM (#1395)

  Show description for 303b7ec
  badisa

  authored
  303b7ec

  Copy full SHA for 303b7ec

• Fix Chiral restraint funcs when there are no chiral restraints (#1396)

  Show description for 3704756
  badisa

  authored
  3704756

  Copy full SHA for 3704756

Commits on Sep 27, 2024

• Updates to EnvironmentBCCHandler (#1390)

  Show description for dbb45e6
  jkausrelay

  authored
  dbb45e6

  Copy full SHA for dbb45e6

Commits on Oct 2, 2024

• Remove application code from rbfe module (#1398)

  Show description for 170759e
  mcwitt

  authored
  170759e

  Copy full SHA for 170759e

• Add InteractionGroupTraj (#1383)

  Show description for eda5a0d
  maxentile

  authored
  eda5a0d

  Copy full SHA for eda5a0d

Commits on Oct 3, 2024

• Fix 1-4 scaling factors for both ligand and protein. (#1399)

  Show description for 3237371
  proteneer

  authored
  3237371

  Copy full SHA for 3237371

• Perform restrained minimization on InitialStates (#1393)

  Show description for 80e4aae
  

  badisa

  and

  maxentile

  authored
  80e4aae

  Copy full SHA for 80e4aae

Commits on Oct 8, 2024

• Adds AM1BCC forcefields for Smirnoff 2.0 and 2.2 (#1400)

  Show description for 8982b81
  badisa

  authored
  8982b81

  Copy full SHA for 8982b81

Commits on Oct 9, 2024

• Ensure permutation equivariance of oe_assign_charges (#1397)

  Show description for 28a0866
  maxentile

  authored
  28a0866

  Copy full SHA for 28a0866

Commits on Oct 11, 2024

• Reduce MAX_FORCE_NORM by factor of 5 (#1403)

  Show description for 49a9da7
  badisa

  authored
  49a9da7

  Copy full SHA for 49a9da7

• Fixes Support for Disabling Optimizations (#1402)

  Show description for f6356ea
  badisa

  authored
  f6356ea

  Copy full SHA for f6356ea

• Raise exception on unstable simulations (#1401)

  Show description for 915cc7b
  badisa

  authored
  915cc7b

  Copy full SHA for 915cc7b

Commits on Oct 15, 2024

• Enable Serialization of PrecomputedChargeHandler (#1404)

  Show description for 78bab8a
  badisa

  authored
  78bab8a

  Copy full SHA for 78bab8a

Commits on Oct 22, 2024

• Adds support for different minimization schemes (#1405)

  Show description for 3d0ca7e
  

  badisa

  and

  mcwitt

  authored
  3d0ca7e

  Copy full SHA for 3d0ca7e

• Protocol overlap utils (#1387)

  Show description for 4a21620
  

  maxentile

  and

  mcwitt

  authored
  4a21620

  Copy full SHA for 4a21620

Commits on Oct 23, 2024

• Mark CPU only tests with nocuda (#1408)

  Show description for 8b07872
  badisa

  authored
  8b07872

  Copy full SHA for 8b07872

• Remove OpenMM imports from top level (#1409)

  Show description for eb7d8d7
  badisa

  authored
  eb7d8d7

  Copy full SHA for eb7d8d7

• Accept conformer id in utilities (#1407)

  Show description for 64f8e58
  mcwitt

  authored
  64f8e58

  Copy full SHA for 64f8e58

Commits on Oct 24, 2024

• Move more tests to nocuda (#1411)

  badisa

  authored
  5e80192

  Copy full SHA for 5e80192

Commits on Oct 31, 2024

• store bond elements in EnvironmentBCCHandler (#1410)

  Show description for cf67140
  jkausrelay

  authored
  cf67140

  Copy full SHA for cf67140

Commits on Nov 2, 2024

• Revert 1-4 charge scaling change (#1417)

  Show description for d859b55
  mcwitt

  authored
  d859b55

  Copy full SHA for d859b55

Commits on Nov 4, 2024

• Fixes incorrect print in minimizer (#1414)

  Show description for e7ff8ba
  badisa

  authored
  e7ff8ba

  Copy full SHA for e7ff8ba

Commits on Nov 5, 2024

• Best-first MCS search (#1415)

  Show description for be34fbf
  mcwitt

  authored
  be34fbf

  Copy full SHA for be34fbf

Commits on Nov 7, 2024

• Bugfix for improper parameterization and canonicalization. (#1418)

  Show description for 344f11c
  

  proteneer

  and

  maxentile

  authored
  344f11c

  Copy full SHA for 344f11c

• Add support for chiral volume conversions (#1406)

  Show description for 70bec1d
  proteneer

  authored
  70bec1d

  Copy full SHA for 70bec1d

Commits on Nov 8, 2024

• Fix nightly tests. (#1419)

  proteneer

  authored
  1e1ce2f

  Copy full SHA for 1e1ce2f

Commits on Nov 13, 2024

• Split of propers and impropers from torsions, add ST symmetry test. (#1422)

  proteneer

  authored
  205b1f0

  Copy full SHA for 205b1f0

• Stagger interpolation for core torsions that are turning on or off. (#1423)

  Show description for 374a2de
  proteneer

  authored
  374a2de

  Copy full SHA for 374a2de

Commits on Nov 15, 2024

• Enables minimizing systems with a subset of atoms restrained (#1421)

  Show description for ccc19fe
  badisa

  authored
  ccc19fe

  Copy full SHA for ccc19fe

Commits on Nov 19, 2024

• Add Titles and lambda labels to HREX plots (#1429)

  Show description for 49a1358
  

  badisa

  and

  mcwitt

  authored
  49a1358

  Copy full SHA for 49a1358

Commits on Dec 3, 2024

• Avoid uninitialized warning in newer GCC (#1432)

  Show description for 8bf96fc
  badisa

  authored
  8bf96fc

  Copy full SHA for 8bf96fc

• Upgrade to Cuda 12.4.1 (#1427)

  Show description for 97106b6
  badisa

  authored
  97106b6

  Copy full SHA for 97106b6

Commits on Dec 10, 2024

• Handle Water Sampling with AbsoluteFreeEnergy (#1431)

  Show description for e7e9223
  badisa

  authored
  e7e9223

  Copy full SHA for e7e9223

• Reduce Final Docker Image Size (#1435)

  Show description for 7f188b1
  badisa

  authored
  7f188b1

  Copy full SHA for 7f188b1

Commits on Dec 12, 2024

• Fixes failing nightly tests (#1436)

  Show description for c4eabfb
  badisa

  authored
  c4eabfb

  Copy full SHA for c4eabfb

Commits on Dec 16, 2024

• Env handler smirks (#1433)

  Show description for 5556d0e
  jkausrelay

  authored
  5556d0e

  Copy full SHA for 5556d0e

Commits on Dec 17, 2024

• Double Max Force Norm Threshold (#1438)

  Show description for f4721d9
  badisa

  authored
  f4721d9

  Copy full SHA for f4721d9

• Optimize Lambda Schedule Targeting Overlap Between Windows (#1426)

  Show description for 92e25e0
  

  badisa

  and

  maxentile

  authored
  92e25e0

  Copy full SHA for 92e25e0

• Pip install OpenMM (#1437)

  Show description for 4e2d769
  badisa

  authored
  4e2d769

  Copy full SHA for 4e2d769

Commits on Dec 18, 2024

• Switch to newer CMake API for finding python (#1439)

  Show description for 551b4b0
  badisa

  authored
  551b4b0

  Copy full SHA for 551b4b0

• Add option to enable REST in single-topology transformations with HREX (#1424)

  mcwitt

  authored
  abf5816

  Copy full SHA for abf5816

Commits on Jan 1, 2025

• Bumps Copyright for 2025 (#1444)

  Show description for 5f41936
  badisa

  authored
  5f41936

  Copy full SHA for 5f41936

Commits on Jan 2, 2025

• Improve Caching of CI Container (#1441)

  Show description for 69e9347
  badisa

  authored
  69e9347

  Copy full SHA for 69e9347

Commits on Jan 3, 2025

• Move pre-commit to CI requirements (#1447)

  Show description for eb4b79d
  badisa

  authored
  eb4b79d

  Copy full SHA for eb4b79d

Commits on Jan 6, 2025

• Enforce Existing C++ Conventions in Clang Format (#1442)

  Show description for ca26f07
  badisa

  authored
  ca26f07

  Copy full SHA for ca26f07

• Clean up SingleTopology code (#1445)

  Show description for 43b505f
  badisa

  authored
  43b505f

  Copy full SHA for 43b505f

Commits on Jan 7, 2025

• Moves linting Job to CPU instance (#1449)

  Show description for ffe4f31
  badisa

  authored
  ffe4f31

  Copy full SHA for ffe4f31

Commits on Jan 14, 2025

• Cache AM1BCC charges (#1451)

  Show description for b033807
  badisa

  authored
  b033807

  Copy full SHA for b033807

Commits on Jan 21, 2025

• Supports installing Timemachine from Tarball (#1443)

  Show description for e737b86
  badisa

  authored
  e737b86

  Copy full SHA for e737b86

• Convert uM to kJ using same temperature as simulations (#1452)

  Show description for 4657b53
  badisa

  authored
  4657b53

  Copy full SHA for 4657b53

Commits on Jan 22, 2025

• Remove legacy code related to chiral conversion (#1453)

  Show description for a0a452c
  mcwitt

  authored
  a0a452c

  Copy full SHA for a0a452c

Commits on Jan 23, 2025

• Update to use miniforge (#1455)

  Show description for a47e20e
  jkausrelay

  authored
  a47e20e

  Copy full SHA for a47e20e

• Add nn handlers (#1456)

  Show description for 8f524de
  jkausrelay

  authored
  8f524de

  Copy full SHA for 8f524de

Commits on Jan 24, 2025

• Bump to Python 3.12 (#1454)

  Show description for a319966
  

  badisa

  and

  mcwitt

  authored
  a319966

  Copy full SHA for a319966

• Purge attic (#1457)

  Show description for 82251f5
  mcwitt

  authored
  82251f5

  Copy full SHA for 82251f5

• Remove versioneer (#1460)

  Show description for e8afd79
  

  mcwitt

  and

  badisa

  authored
  e8afd79

  Copy full SHA for e8afd79

Commits on Jan 25, 2025

• Update packaging command in CI (#1461)

  Show description for 7bc394d
  mcwitt

  authored
  7bc394d

  Copy full SHA for 7bc394d

Commits on Jan 27, 2025

• Replace black, flake8, isort with ruff (#1459)

  Show description for 30d4806
  mcwitt

  authored
  30d4806

  Copy full SHA for 30d4806

Commits on Jan 28, 2025

• Fix Invalid Memory Write in TIBD Exchange Mover (#1464)

  Show description for 4d484d4
  

  badisa

  and

  mcwitt

  authored
  4d484d4

  Copy full SHA for 4d484d4

• Minor Clean up + Dead Code Removal (#1465)

  Show description for 8c60d83
  badisa

  authored
  8c60d83

  Copy full SHA for 8c60d83

Commits on Jan 29, 2025

• Consistently test with Compute-sanitizer (#1466)

  Show description for caaaad2
  badisa

  authored
  caaaad2

  Copy full SHA for caaaad2