v0.22.0

The package is rewritten to use Enzyme.jl rather than Zygote.jl for differentiable simulations. This allows mutating code to be used, leading to better performance on CPU and GPU. In addition, faster CUDA kernels are added and support for other GPU backends is added via KernelAbstractions.jl.

Breaking changes

• CoordinateLogger, VelocityLogger and ForceLogger are renamed to CoordinatesLogger, VelocitiesLogger and ForcesLogger respectively for consistency.
• During system setup the gpu keyword argument is replaced by array_type, with CuArray giving the same behaviour as before. Use of other array types such as ROCArray is supported. The use_cell_list keyword argument is replaced with neighbor_finder_type, with the default depending on the backend.
• The second type parameter to System is changed from a Bool indicating whether the system is on the GPU to the array type of the system.
• Giving the force_units and energy_units is no longer required when constructing pairwise interactions such as LennardJones. In addition, mixing functions and shortcut functions can now be given to determine how to combine atomic parameters and when to skip the interaction respectively.
• The arguments to force and potential_energy for pairwise and specific interactions are changed to allow more flexible interaction definitions, depending for example on the velocities or step number.
• Differentiable simulations are no longer compatible with Zygote.jl, but can now be carried out using Enzyme.jl. This is faster and more memory-efficient.
• The solute field to Atom is removed and the atom_type field is added. weight_solute_solvent is no longer an option for LennardJones, though similar functionality is available with atom_type and mixing functions.
• box_volume is renamed to volume.
• run_loggers! is renamed to apply_loggers! to avoid confusion with the run_loggers function argument.
• The abstract types PairwiseInteraction and SpecificInteraction are removed. Custom interactions no longer need to sub-type anything.
• Extensions are added for code requiring Enzyme.jl, CUDA.jl and KernelDensity.jl, so relevant imports are now required before using those features.

Non-breaking changes

• Support for Julia versions before 1.10 is dropped.

New features

• Backends supported by KernelAbstractions.jl can be used to run simulations by using the appropriate array type or the array_type keyword argument during system setup.
• The Berendsen pressure coupling method is added as BerendsenBarostat.
• The density and dipole_moment functions are added.
• The AshbaughHatch and Yukawa potentials are added.
• VolumeLogger and DensityLogger are added.
• The rng keyword argument is added to place_atoms, place_diatomics and random_coord, allowing reproducible coordinate generation.
• The array_type function is added, giving the array type of a system or array.
• The step number can be given as a third argument with a default of 0 to forces, potential_energy and virial acting on a system. This allows time-dependent forces, with the caveat that the step number resets to 1 every time simulate! is called and can also be 0 to calculate forces before the first step.
• A method is added to random_velocities! which takes in and modifies the velocities as the first argument.

Performance improvements

• Better CUDA force and potential energy kernels significantly improve performance on CUDA compatible devices. The GPUNeighborFinder is added for this path but does not calculate neighbors, which are calculated each step in the kernels.
• Simulations are faster on both CPU and GPU due to mutating code leading to fewer memory allocations.
• System setup from a file is made much faster.
• The package is faster to load as a number of dependencies have been removed.
• The performance of implicit solvent on CPU is improved.

Bug fixes

• A bug when using more than two interactions on the GPU is fixed.
• A type conversion bug in CellListMapNeighborFinder construction is fixed.

v0.21.2

Non-breaking changes

• Updates are made for AtomsBase.jl 0.4. AtomsBase is no longer re-exported.

v0.21.1

Non-breaking changes

• Compatibility bounds are updated for various packages.

Bug fixes

• A bug in boundary gradient calculation is fixed.

v0.21.0

Breaking changes

• Observable functions for GeneralObservableLogger now need to accept arbitrary keyword arguments, for example by adding kwargs... to the function call. This allows the logging changes described below.

Non-breaking changes

• Support for Julia versions before 1.9 is dropped. A package extension, rather than Requires.jl, is used to provide visualize when GLMakie.jl is imported.

New features

• ASECalculator is added, allowing Python ASE calculators to be used in Molly. The code is in a package extension available when PythonCall.jl is imported. It is the user's responsibility to have the required Python packages installed. Examples of using MACE and psi4 are given.
• current_forces and current_potential_energy can be used in logging functions to reuse properties calculated in the simulation step. They default to nothing when the properties are not available.
• Interaction types are allowed to be different for each replica in a ReplicaSystem.

Performance improvements

• PotentialEnergyLogger, TotalEnergyLogger and ForceLogger avoid recomputation when the relevant properties are calculated in the simulation step.

Bug fixes

• MollyCalculator now works in two dimensions and for other floating point types.

v0.20.0

Breaking changes

• apply_constraints! and SHAKE are removed as part of the changes to constraints.
• The System constructor for AtomsBase.jl systems is changed to take force_units and energy_units as keyword arguments rather than positional arguments. The defaults are consistent with the rest of Molly.
• velocity_autocorr is removed since AutoCorrelationLogger provides a more general version of this functionality.

New features

• Support for constraints is improved and documented with SHAKE_RATTLE allowing the SHAKE and RATTLE algorithms to be applied as appropriate to most simulators. DistanceConstraint, disable_constrained_interactions!, apply_position_constraints!, apply_velocity_constraints!, check_position_constraints and check_velocity_constraints are all added. Constraints are not currently compatible with GPU simulation.
• Gradients with respect to the boundary can now be calculated in some contexts.

Community

• A logo is added to the project.

Bug fixes

• A bug in FENEBond potential energy calculation is fixed.

v0.19.0

Breaking changes

• General interactions are changed to use the AtomsCalculators.jl interface, allowing simulations to be run with calculators from other packages. A tuple of interactions compatible with the AtomsCalculators.jl interface should be given to general_inters when constructing a System. ImplicitSolventOBC, ImplicitSolventGBN2 and MullerBrown are changed to be calculators.
• The type parameters of System and ReplicaSystem are changed.

New features

• forces, accelerations, potential_energy, total_energy, virial and pressure now calculate the neighbors by default when called without neighbors. If they are being reused, neighbors should be pre-computed as before for performance.
• System and ReplicaSystem now have a data field, set with the data keyword argument to the constructors, that can be used to store arbitrary data. This data can be accessed inside simulators.
• LennardJonesSoftCore, CoulombSoftCore and custom atom types are now compatible with gradients.

v0.18.4

Bug fixes

• A bug that prevented system setup on Julia 1.7 is fixed.
• A type preservation bug in the rdf function is fixed.

v0.18.3

New features

• Compatibility with AtomsCalculators.jl is added via MollyCalculator.
• The documentation on setting up systems from structure files is improved.
• A list of relevant publications is added to the documentation.

Community

• The Contributor Covenant Code of Conduct is added to the project.

Bug fixes

• A bug in the NoseHoover simulator when not using units is fixed.

v0.18.2

Performance improvements

• The vector function for calculating the displacement between coordinates accounting for periodic boundary conditions is made faster, improving simulation performance on CPU and GPU.

v0.18.1

New features

• Simulation of overdamped Langevin dynamics is added as OverdampedLangevin.

Performance improvements

• The performance of force calculation without a neighbor list on the GPU is significantly improved.

Bug fixes

• A bug in compatibility with SimpleCrystals.jl is fixed.