CHANGELOG.rst

Release notes

v0.12.0

Released 1 Nov 2022

This will be the final minor release of azplugins to support HOOMD-blue v2.x. The next planned release of azplugins will be a major release to support HOOMD v3.x. This will be a breaking change because of the significant rewrite of HOOMD-blue's API. We plan to support bug fixes until this major release is ready, and we may support bug fixes targeted toward HOOMD-blue v2.x during a transition period.

New features

• Add shift parameter and allow sigma & epsilon to be zero in bond.fene.
• Add analyze.group_velocity to compute the center-of-mass velocity of a group.

Bug fixes

• Apply CUDA 11.5 thrust / CUB namespace wrap fix.

v0.11.0

Released 1 Feb 2022

New features

• flow.FlowProfiler is generalized to support multiple velocity components, mass averaged velocities, and to compute temperature.
• The documentation has been reorganized, and some tutorials have been added. The docs are now hosted on ReadTheDocs.
• Support is added for sinusoidal channels and expansion--constriction channels in integrate.sinusoidal_channel and integration.sinusoidal_expansion_constriction. Similar support is also available for the MPCD solvent.

Other changes

• Add a code of conduct for contributors.
• Update copyright. azplugins is now maintained as part of our work at Auburn University.
• The default git branch is renamed main. More information is available.
• CI testing has been moved to GitHub Actions.

v0.10.1

Released 12 Jan 2021

Bug fixes

• Fix normalization of velocity in flow.FlowProfiler.

v0.10.0

Released 27 Jul 2020

This is the first release of azplugins to include compilable documentation. The docs can be built using sphinx. Currently, only the APIs are thoroughly documented, but we will be expanding the rest of the documentation in future releases with examples and tutorials.

New features

• restrain.cylinder and restrain.sphere allow particles to be harmonically restrained by their distance relative to a cylinder or sphere, respectively. restrain.plane has been updated to share a condensed API using HOOMD walls.
• bond.double_well adds a new bond potential having two tunable minima.
• flow.FlowProfiler adds a python-level analyzer for averaging 1d density and velocity profiles for both HOOMD and MPCD systems.
• pair.hertz adds the Hertz pair potential.

Other changes

• The python unit tests have been updated to remove import *.

v0.9.2

Released 3 Mar 2020

Bug fixes

• Fix a compilation error on MacOS clang builds.

Other changes

• Update copyright to 2020.

v0.9.1

Released 18 Dec 2019

Bug fixes

• Fix a compilation error in CUDA-enabled builds.

v0.9.0

Released 15 Dec 2019

New features

• flow.constant implements a constant flow along a vector.
• variant.sphere_area adds a new variant that is physically motivated by a sphere shrinking with a constant rate of change in area. This may be useful with evaporate.implicit in the droplet geometry.

Other changes

• Support API changes in HOOMD 2.8.0. Backward compatibility is maintained through a new API header.
• The pair potential evaluators have been updated to support HOOMD 2.8.0. New pair potential evaluators should derive from one of the convenience base classes.
• CI testing has been added for HOOMD 2.8.0 in addition to 2.6.0.

v0.8.0

Released 5 Nov 2019

New features

• evaporate.implicit now supports evaporation in both film and droplet geometries. The default geometry remains the film.
• restrain.plane allows particles to be harmonically restrained by their distance relative to a plane.

v0.7.1

Released 20 Aug 2019

Bug fixes

• Silence a warning in CMake >= 3.12.
• Fix a link error in compiled unit tests.

v0.7.0

Released 24 Jun 2019

This version of the plugin requires HOOMD-blue v2.6.0 for compatibility with the new streaming geometries in its MPCD component. HOOMD-blue must be built with the MPCD component.

Bug fixes

• Fix compilation errors with HOOMD-blue v2.6.0.

Other changes

• random123 is used as the random number generator throughout azplugins. This API is more robust and stable than Saru, but sequences of random numbers drawn for a given seed will change. New features using random numbers should add a unique 32-bit identifier to RNGIdentifiers.h.

v0.6.2

Released 25 Apr 2019

All commits and pull requests are now automatically tested against HOOMD 2.5.1 on CircleCI. Unit tests are run for CPU-only build configurations. CUDA-enabled builds are tested for compilation, but their unit tests cannot be run on CircleCI. The CI test environment is available on Docker Hub (https://hub.docker.com/r/mphoward/ci), and tests for new code should be run locally on a GPU.

Bug fixes

• Fix import statements in azplugins modules for python3.
• Fix HOOMD version parsing in CMake for external builds.
• Fix CMake errors in testing for certain build configurations.

v0.6.1

Released 28 Mar 2019

Bug fixes

• Fix thrust template parameters in mpcd.reverse_perturbation for CUDA 9 & 10.

v0.6.0

Released 25 Feb 2019

This version of the plugin requires HOOMD-blue v2.3.0 for compatibility with the embedded pybind11 library. Be sure to update your git submodules when recompiling and installing HOOMD-blue.

azplugins is now maintained by Michael P. Howard and will be hosted on GitHub (https://github.com/mphoward/azplugins).

New features

• mpcd.reverse_perturbation implements the reverse perturbation method in the optional MPCD module to simulate shear flow.

Other changes

• The azplugins license and packaging has been updated to reflect the project continuation.
• FindHOOMD.cmake has been improved to support find_package and detect the installed version of HOOOMD.

v0.5.0

Released 11 Jun 2018

This version of the plugin requires HOOMD-blue v2.2.2 in order to ensure all necessary header files are available.

New features

• flow.reverse_perturbation implements the reverse perturbation method for generating shear flow. This implementation is significantly more stable than the HOOMD-blue release, but does not currently support MPI.
• integrate.slit supports NVE integration with bounce-back rules in the slit geometry. Other bounce back geometries can also be configured.
• dpd.general implements a generalized DPD potential where the exponent of the dissipative weight function can be adjusted. A framework is also implemented for adding other DPD potentials.
• flow.langevin and flow.brownian support Langevin and Brownian dynamics in external flow fields. Currently, the supported fields are flow.quiescent and flow.parabolic, but additional fields can be included by templating.

v0.4.0

Released 16 Nov 2017

This version of the plugin requires HOOMD-blue v2.2.1 in order to ensure all necessary header files are available.

New features

• A framework is configured for developing bond potentials.
• bond.fene implements a standard FENE potential that is cleaned up compared to the version found in HOOMD.
• bond.fene24 implements the FENE potential with the Ashbaugh-Hatch-style 48-24 Lennard-Jones potential repulsion.
• pair.ashbaugh24 implements a Ashbaugh-Hatch 48-24 Lennard-Jones potential.
• pair.spline implements a cubic spline potential.
• pair.two_patch_morse implements the two-patch Morse anisotropic potential.
• A framework is configured for developing special pair potentials from existing pair potentials.
• special_pair.lj96 implements the LJ 9-6 potential as a special pair.
• A framework is configured for writing and running compiled unit tests with upp11.
• All source code is now automatically validated for formatting.

Bug fixes

• Fix path to cub headers.
• Add missing status line prints.
• Fix possible linker errors for MPI libraries.
• Plugins now build when ENABLE_CUDA=OFF.
• CMake exits gracefully when the MD component is not available from hoomd.
• Plugins now compile with debug flags.

v0.3.0

Released 22 Aug 2017

This version of the plugin is now tested against HOOMD-blue v2.1.9. Users running older versions of HOOMD-blue are recommended to upgrade their installations in order to ensure compatibility and the latest bug fixes on the main code paths.

New features

• pair.lj124 implements the 12-4 Lennard-Jones potential.
• pair.lj96 implements the 9-6 Lennard-Jones potential.
• A framework is configured for developing anisotropic pair potentials.

Bug fixes

• Fix import hoomd.md error in analyze.rdf.
• Adds restraint module to ctest list and warns user about running with orientation restraints in single precision.
• Fix examples in contribution guidelines so that formatting of pull request checklist is OK.
• Remove unused include from particle evaporator which caused compilation errors with newer versions of hoomd where the header was removed.

v0.2.0

Released 28 Feb 2017

New features

• analyze.rdf implements a radial distribution function calculator between particle groups for small problem sizes.
• restrain.position implements position restraints for particles.
• restrain.orientation implements orientation restraints for particles.
• pair.slj implements a core-shifted Lennard-Jones potential that does not read from the particle diameters.

Other updates

• Source code guidelines and a pull request checklist are discussed in a new CONTRIBUTING.md.

v0.1.0

Released 9 Feb 2017

New features

• A framework is configured for developing pair potentials.
• pair.ashbaugh implements the Ashbaugh-Hatch (Lennard-Jones perturbation) potential.
• pair.colloid implements the colloid (integrated Lennard-Jones) potential for colloidal suspensions.
• A framework is configured for developing wall potentials.
• wall.colloid implements the integrated Lennard-Jones potential between a colloid and a half-plane wall.
• wall.lj93 implements the Lennard-Jones 9-3 potential between a point and a half-plane wall.
• update.types allows for swapping of particle types based on a slab region of the simulation box.
• evaporate.particles supports evaporation of single-particle fluids from a slab region of the simulation box.
• evaporate.implicit provides an implicit model for an evaporating solvent.