HOOMD-TF - v2.4.0

New Features

• Can compute mapped nlists/positions while running a simulation

Enhancements

• Added benchmarking to CI and reporting
• Various documentation improvements

Scientific Software - Peer-reviewed - Python
Published by whitead almost 5 years ago

HOOMD-TF - v2.3.0

New Features

• Can generate HOOMD snapshot bonds group based on mapped exclusion lists

Enhancements

• Made it possible to have multiple molecule features

Bug Fixes

• Fixed bug in compute_nlist with types not masking out of cut nlists
• Fixed PBC error on molecular features
• Fixed bug on calls to model with 2 inputs

Scientific Software - Peer-reviewed - Python
Published by whitead about 5 years ago

HOOMD-TF - v2.2.0

Breaking Changes

• Removed sample_weight. Was not used by anyone and is an edge case.

New Features

• Can read molecules from GROAMCS topology
• Can compute one-hot encoding for different bead type interactions in CG systems
• Can generate mapped exclusion lists in CG systems

Enhancements

• Added jupyter notebook testing to continuous integration
• iter_from_trajectory can run in a user-defined time range
• Revised to work for TF 2.4
• Can add exclusion lists when computing nlists using htf

Scientific Software - Peer-reviewed - Python
Published by whitead over 5 years ago

HOOMD-TF - v2.1.0

New Features

• Added standard layers to code
• Can compute molecular features for CG models
• Can compute CG matrix given a molecule and bead mappings

Enhancements

• Added error checks on mapping shapes
• Added optional training flag to change behavior during training
• Added ability to retrace compute if self changes
• Can output type or index when computing nlist

Bug Fixes

• Removed unused cuda events which could cause segfault on destruction
• Fixed simulation box in iter_from_trajectory
• Fixed MDAnalysis universe based on atom group selection option in iter_from_trajectory

Scientific Software - Peer-reviewed - Python
Published by whitead over 5 years ago

HOOMD-TF - v1.0.2

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

Scientific Software - Peer-reviewed - Python
Published by whitead almost 6 years ago

HOOMD-TF - v2.0.1

Breaking Changes

• Hoomd 2.6 or above is now required for GPU-GPU Mode

Scientific Software - Peer-reviewed - Python
Published by whitead almost 6 years ago

HOOMD-TF - v2.0.0

New Features

• TensorFlow 2.0 now required
• Keras models replace computation graphs
• It is no longer required to save/load models for use
• Training is handled by Keras/TF functions now
• Getting values no longer requires save/load, instead everything is accessible in Python

Breaking Changes

• All code must be rewritten following new syntax
• feeddict is no longer supported
• graphbuilder is now SimModel, which must be subclassed
• Mol batching is now MolSimModel, which must be subclassed
• All graphbuilder methods (e.g., compute_rdf) are now functions
• Code that duplicates Keras functionality is removed:
  • checkpoint management, model save/load
  • saving values, computing means, other metrics
  • saving values over time is now done by tensorboard or other TF/Keras approaches
• How forces are computed must be explicit and virials are no longer implicit (use modify_virial flag)
• You can no longer save tensors, instead output what you would like to save in your model code
• EDS is now layer (EDSLayer)
• Running from a trajectory is now done via a generator

Enhancements

• There is no more multiprocessing required
• Benchmarks are significantly faster

Scientific Software - Peer-reviewed - Python
Published by whitead almost 6 years ago

HOOMD-TF - v1.0.1

Bug fixes

• Prevented CPU overflow when nlist is too small (and added unit test)
• Added check on mapping validity

Scientific Software - Peer-reviewed - Python
Published by whitead almost 6 years ago

HOOMD-TF - v1.0

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

Scientific Software - Peer-reviewed - Python
Published by whitead almost 6 years ago

HOOMD-TF - v0.6

Enhancements

• Migrated documentation to sphinx
• Added Jupyter notebook examples
• Various documentation improvements
• Added CUDA 10 Support

Scientific Software - Peer-reviewed - Python
Published by whitead over 6 years ago

HOOMD-TF - v0.5

Bug Fixes

• Types are now correctly translated to TF

Scientific Software - Peer-reviewed - Python
Published by whitead over 6 years ago

HOOMD-TF - v0.4

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

Scientific Software - Peer-reviewed - Python
Published by whitead over 6 years ago

HOOMD-TF - v0.3

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

Scientific Software - Peer-reviewed - Python
Published by whitead almost 7 years ago

HOOMD-TF - v0.2

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.

Scientific Software - Peer-reviewed - Python
Published by whitead about 7 years ago