Change Log¶
v1.0.2 (2020-8-14)¶
Bug fixes
- EDS Bias was not using mean for computing offset
- EDS Bias was not resetting statistics correctly
- Removed stale test-cc directory that caused cmake errors
v1.0.1 (2020-7-27)¶
Bug fixes
- Prevented CPU overflow when nlist is too small (and added unit test)
- Adding check on mapping validity
v1.0 (2020-7-20)¶
JOSS Review
Hoomd-TF has been published as a peer-reviewed article in the Journal of Open Source Software (JOSS)
New Features
- Added pre-built molecular features
- Added MDAnalysis style selection for defining mapping operators
Enhancements
- Docs can now be built without HTF install
- mol batching performance is much better
- Simplified variable saving
- More example notebooks and reduced file sizes of example trajectories
- Supports dynamic boxes
- Better EDS bias naming
- Prevents accidentally computing forces from positions, instead of nlist
- Added guards against compiler mismatch
- Added sanity tests to prevent unsupported CPU/GPU modes
- Added benchmarking script
- Added check for nlist overflows on GPU
- Added check for mismatch on saving variables/tensors
- Fixed all compiler warnings
- Added Dockerfile for containerized use
Bug Fixes
- Empty tensorboard summaries no longer crash
- Prevented import issues with name clashes between packages and classes
v0.6 (2020-02-21)¶
Enhancements
- Migrated documentation to sphinx
- Added Jupyter notebook examples
- Various documentation improvements
- Added CUDA 10 Support
v0.4 (2019-09-25)¶
New Features
- Added experiment directed simulation biasing to htf.
Enhancements
- Added box dimension to computation graph (graph.box and graph.box_size)
- Can now wrap position derived distances with graph.wrap_vector
- Made it possible to specify period for out_nodes
Bug Fixes
- Fixed dangling list element in rev_mol_indices
v0.3 (2019-07-03)¶
Enhancements
- Batching by molecule now has a atom id to mol id/atom id look-up (rev_mol_indices)
- Version string is visible in package
- Example models now take an argument specifying where to save them
- When batching, atom sorting is automatically disabled
- compute_pairwise_potential now outputs force as well as potential
Bug Fixes
- Computing nlist in TF now correctly sorts when requested
- Fixed Mac OS specific issues for compiling against existing HOOMD-blue install
- Running mean computation variables are now marked as untrainable
v0.2 (2019-06-03)¶
New Features
- Added attach batch_size argument enabling batching of TF calls
- Can now batch by molecule, enabling selection/exclusion of molecules
- Added XLA option to improve TF speed
- Now possible to compile the plugin after hoomd-blue install
- Changed name of package to htf instead of tensorflow_plugin
Enhancements
- Changed output logging to only output TF items to the tf_manager.log and
- Log-level is now consistent with hoomd
- Added C++ unit tests skeleton in the same format as HOOMD-blue. Compile with -DBUILD_TESTING=ON to use.
- Switched to hoomd-blue cuda error codes
- Added MPI tests with domain decomposition
- Improved style consistency with hoomd-blue
- Cmake now checks for TF and hoomd versions while building hoomd-tf.
v0.1 (2019-04-22)¶
- Made Python packages actual dependencies.
- Switched to using hoomd-blue cuda error codes.
- Removed TaskLock from C++ code.
- Documentation updates
- Included license.
- User can now use specific hoomd forces in the hoomd2tf force mode.
- Added the ability to create a custom nlist.
- Made unit tests stricter and fixed some cuda synchronization bugs.
- Fixed TF GPU Compiling bug.
- Fixed ordering/masking error in mapping nlist and type of neighbor particles in nlist.
- Fixed a bug which caused a seg fault in nonlist settings.