Feature GCMC - #79

Merged

lohedges merged 173 commits into

mainfrom

Oct 31, 2025

Commits on Feb 25, 2025

Add CLI entry-point for Boresch ghost atom modifications.
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3e2d734
Fix formatting of output name. (Prefix only.) [ci skip]
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40a5958
Add __all__ to CLI module. [ci skip]
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4827b56

Commits on Feb 26, 2025

Use input file name as base for output by default.
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4d9a991

Commits on May 14, 2025

Update environment for GCMC.
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56fc0d9

Commits on May 16, 2025

Commits on May 19, 2025

Set gcmc_kwargs to None if not performing GCMC.
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cba820e
Need unique GCMC log and ghost file for each lambda.
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d170705
Added GCMC implementation for replica exchange.
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62dce3b
Unable to decouple SOMD2 and GCMC loggers.
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99d951a
Log GCMC moves.
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a9bac0b
Write final ghost residue indices. [ci skip]
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1dfcdfc
Manually compute timings so they include GCMC sampling time.
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b5bbc42
Logging tweaks. [ci skip]
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fef2286
Add GCMC move to equilibration stage.
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00e7f95

Commits on May 20, 2025

Use PDB topology format for GCMC simulations.
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04c99f6
Use 'ratio' rather than 'scale' for clarity.
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cae9eba
Enable replica exchange to work with NVT.
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793017d
Pass GCMC specific kwargs to DynamicsCache constructor.
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6c746c3
Pass GCMC kwargs through to _create_dynamics method. [ci skip]
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5890c5b
Fix module name. [ci skip]
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2f1a45c
Pass output directory to DynamicsCache constructor.
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3d188ab
Create instance of GCMCSampler, then append to list.
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d977c10
Fix log messages. [ci skip]
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811d10a
Fix name clashes caused by manual timer.
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32e936f
No need to convert to int. [ci skip]
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95077e2
Requires manual context management via push and pop.
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da3cadb

Commits on May 21, 2025

PyCUDA context management now handled by GCMCSampler.
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d1043e0
Consolidate saving of end-state topology to single place.
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ac2487a
PyCUDA context needs to be pushed and popped by the thread.
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de3bd9c
Use d.context() for clarity.
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85921dd
Swap GCMC water state when mixing replicas.
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29c78f3
Call .context() on Dynamics not DynamicsData object.
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59746e1

Commits on May 22, 2025

Switch position of ghost residue writing.
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3596fc4
Use NumPy to find water indices where state differs between replicas.
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0da38fd
Make sure we store a copy of the water state array.
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a02eafe
Improve logging of water state swaps. [ci skip]
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7302e48
Rename attribute: self._gcmc --> self._gcmc_samplers.
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1bf1fdf
Grammar tweak. [ci skip]
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cc6210d

Commits on May 23, 2025

Commits on May 24, 2025

Initialise gcmc_sampler array with NoneType entries.
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e7c1469
Consolidate water state updates.
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7ca5216
Separate per-block and average timings.
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e5841f9
Report average speed correctly.
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7579bed
Fix indentation of return statement. [ci skip]
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701d55e
Fix variable names. [ci skip]
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5abd7e7
Remove unused variable. [ci skip]
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3a98b8c
Standardise variable name. [ci skip]
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8bb1b0b

Commits on May 27, 2025

Clarify performance logging. [ci skip]
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e1ca4e4
Add GCMC term to energy.
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00b367e
Pass through GCMC specific options to dynamics.run().
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b501770
Access list, not object directly. [ci skip]
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2f4359f
Pass excess chemical potential, not Adams value. [ci skip]
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a7f7581
Missing beta factor for GCMC term. [ci skip]
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d82606c
Energy now already includes pressure and GC term.
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f7e1043
No need to store volume. [ci skip]
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609a1a2
Add missing NumPy import. [ci skip]
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6c69768

Commits on May 28, 2025

Commits on Jun 2, 2025

Commits on Jun 3, 2025

Log the number of waters in the GCMC volume when checkpointing.
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22cf751
Fix method name [ci skip]
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edfd3d8

Commits on Jun 4, 2025

Log output formatting tweak. [ci skip]
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e451ef2
Need to push/pop the PyCUDA context when logging number of waters.
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af4f704

Commits on Jun 5, 2025

Allow GPU oversubscription for regular runner.
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5b6a2f7
Log the oversubscription factor. [ci skip]
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648fe36

Commits on Jun 6, 2025

Commits on Jun 9, 2025

Change GCMC parameter name. [ci skip]
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ecc1452
Don't evaluate timing statistics on error. [ci skip]
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0133994
Comment tweak. [ci skip]
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f98df3e
Set success to False if keyboard interrupt. [ci skip]
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f0d4a40
Return when exception is caught. [ci skip]
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df2b98e
Typo. [ci skip]
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06f9efa
Fix formatting of energy components output. [ci skip]
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1341dcc

Commits on Jun 13, 2025

No need to store lambda array in parquet metadata. [ci skip]
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b1dc921

Commits on Jun 17, 2025

Raise exception if dynamics cache context creation fails. [ci skip]
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fe607f2
Use sys.exit() rather than exit(). [ci skip]
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62f2218

Commits on Jun 18, 2025

Commits on Jun 19, 2025

Formatting tweak. [ci skip]
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8d53377

Commits on Jun 20, 2025

Commits on Jun 21, 2025

Reset water state when context is recreated. [ci skip]
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bd86e57
Merge branch 'main' into feature_gcmc [ci skip]
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fc4e764
Clarify reason for resetting the water state. [ci skip]
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d0b5a6b
Merge branch 'feature_ghostly' into feature_gcmc [ci skip]
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4dcb75d
Formatting tweaks. [ci skip]
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d756925
Add GCMC section to README. [ci skip]
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f083672
Add link to description of Parquet format. [ci skip]
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d0b3ea9
Use sys.exit() rather than exit(). [ci skip]
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708de44
Add note that GCMC is currently limited to the CUDA platform. [ci skip]
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a24ea0e

Commits on Jun 23, 2025

Commits on Jun 25, 2025

Don't reset the time to zero. [ref OpenBioSim/sire#320] [ci skip]
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160f8f8

Commits on Jun 26, 2025

Bind GCMC sampler to dynamics object to allow crash recovery. [ci skip]
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393c8d3
Fix storing of initial time.
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5e2f29a
Use a single GCMC based conditional block. [ci skip]
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92336d7
Fix post-equilibration time reset. [ci skip]
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da79206
Typo. [ci skip]
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e31a7a5
Fix accidental change to water state update during replica mixing.
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7dc652d

Commits on Jun 30, 2025

Decouple ghostly and add as an external dependency. [ci skip]
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258e1b6

Commits on Jul 1, 2025

Log ghost modifications. [ci skip]
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2d16a12

Commits on Jul 2, 2025

Set pressure based on the presence of solvent. [ci skip]
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3b01e2b

Commits on Jul 4, 2025

Timeout must be a float in seconds. [ci skip]
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938372f

Commits on Jul 9, 2025

Use no cutoff for vacuum. [ci skip]
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ed9fcb1
Save end-state topologies in base class constructor. [ci skip]
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9606076

Commits on Jul 10, 2025

Add support for OPC water. [ci skip]
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71e3c5d

Commits on Aug 15, 2025

Add link to ghostly repo. [ci skip]
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a36f0dc

Commits on Aug 29, 2025

Use spawn start method for multiprocessing processes. [closes #72]
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6731da8

Commits on Sep 3, 2025

Patch in fix from #73. [ci skip]
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1eef48b

Commits on Sep 4, 2025

Commits on Sep 8, 2025

Handle time rounding issues. [ci skip] [ref #74]
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1274802

Commits on Sep 22, 2025

Fix start time index. [ci skip]
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cc80924

Commits on Sep 23, 2025

Typos. [ci skip]
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f9f0d19

Commits on Sep 24, 2025

Save GCMC system topology to AMBER and PDB format. [ci skip]
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1037a70

Commits on Sep 25, 2025

Commits on Sep 26, 2025

Adjust default HMR factor. [ci skip]
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12cffec
Add option to restrict workers for checkpointing. [ci skip]
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20f9e5b

Commits on Sep 29, 2025

Move lock file operations outside of checkpoint function. [ci skip]
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573ca62
Pass dynamics kwargs to GCMC sampler constructor. [ci skip]
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c86ab10
Only pass required dynamics kwargs. [ci skip]
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86042a4
Decouple backup from checkpointing. [ci skip]
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21274ca
Rename previous trajectory file so it isn't cleaned up. [ci skip]
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2c9cfba
Fix backup method name. [ci skip]
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9b12054

Commits on Sep 30, 2025

Reset GCMC water state when restarting. [ci skip]
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d9d8ad0

Commits on Oct 1, 2025

Reset default HMR factor for now. [ci skip]
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70451d7

Commits on Oct 2, 2025

Fix missing format strings. [ci skip]
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4da4c20
Expose GCMC acceptance tolerance option. [ci skip]
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18f79fb

Commits on Oct 3, 2025

Commits on Oct 6, 2025

Remove redundant GCMC validation. [ci skip]
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68fa844
Reset logger attributes for spawned child processes. [ci skip]
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afc7571
Only run CI on default branches and for PRs.
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d8f8c22

Commits on Oct 7, 2025

Save GCMC topology for all indices for non-repex simulations.
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0905caf

Commits on Oct 8, 2025

Fix method name.
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bb89d20
Use new GCMCSampler.bind_dynamics() method.
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57c3173

Commits on Oct 9, 2025

Add support for multi-conformational seeding.
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d213ab0
Fix invalid variable name.
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42cdf2d
Simplify multiconformational seeding.
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8c5544d
Pad trajectory chunk file names.
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cad087b

Commits on Oct 21, 2025

Add note about temporary file limit issue. [ci skip]
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192d76e

Commits on Oct 23, 2025

Commits on Oct 25, 2025

Default to one frame per checkpoint.
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f34f4b4
Expose option to adjust the trajectory page size.
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13a3014

Commits on Oct 27, 2025

Docstring clarification. [ci skip]
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1851693

Commits on Oct 29, 2025

Update to recommended RBFE shift_delta value.
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fe2e20a
Add swap_end_states option to GCMC kwargs.
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f712e76
Always save GCMC system, but only at first checkpoint block.
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778d73d

Commits on Oct 30, 2025

Merge branch 'feature_gcmc' into merge_feature_gcmc
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e0a3166

Commits on Oct 31, 2025

Add macOS specific environment and handle missing loch package.
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c74e49b