Molly.jl Files

Breaking changes

• pressure and virial now return tensor quantities, e.g. 3x3 in 3D. The virial now takes into account all pairwise and specific interaction terms automatically. The virial is also supported for the Ewald and PME methods, but not constraints or implicit solvent methods. Custom general interactions can define a virial term if required. The scalar values can be calcuated with scalar_pressure and scalar_virial, with the corresponding loggers ScalarPressureLogger and ScalarVirialLogger. The new forces_virial function allows calculation of both the forces and the virial at the same time, which can save computation. The kinetic_energy_tensor function allows the kinetic energy of a system in its tensorial form to be calculated. The needs_virial function should be defined for couplers that require virial computation.
• All pairwise interactions should be a subtype of the abstract type PairwiseInteraction. This was previously removed but has been added back to allow dispatch to be used in the future.
• General interactions should now define AtomsCalculators.forces! rather than AtomsCalculators.forces and should mutate the input forces, leading to fewer allocations. This means that the order of general interactions can matter and that general interactions can be used to modify forces directly.
• LennardJonesSoftCore and CoulombSoftCore are removed and replaced with LennardJonesSoftCoreBeutler/LennardJonesSoftCoreGapsys and CoulombSoftCoreBeutler/CoulombSoftCoreGapsys, two popular soft core implementations.
• MonteCarloAnisotropicBarostat and MonteCarloMembraneBarostat are removed as their functionality is now available using MonteCarloBarostat with the coupling_type keyword argument.
• TrajectoryWriter and write_structure now keep molecules connected over the periodic boundaries by default. The correction keyword argument allows this to be controlled, with :wrap providing the previous behaviour.
• StructureWriter, which wrote to the PDB format, is removed. TrajectoryWriter should be used to write to all file formats including PDB.
• RescaleThermostat is renamed to ImmediateThermostat to better reflect what it does and to avoid confusion with the new VelocityRescaleThermostat.
• The implicit_solvent keyword argument when setting up a system from a file now takes symbols rather than strings, e.g. :gbn2 instead of "gbn2", to increase consistency across the package.
• The default nonbonded_method during setup is now :none, i.e. short range interactions, compared to the reaction field approximation used before (now available with :cutoff).
• The dist_neighbors keyword argument during setup from a file is replaced with dist_buffer, a buffer distance added to dist_cutoff. This means that dist_cutoff can be changed without having to also update dist_buffer.
• The arguments of apply_loggers! and apply_couplers! are changed.
• AbstractGBSA, ResidueType, AtomType, PeriodicTorsionType, born_radii_and_grad, extract_parameters, inject_gradients and molecule_centers are no longer exported.
• The type parameters of CubicBoundary, RectangularBoundary and TriclinicBoundary are changed.

New features

• Ewald and particle mesh Ewald (PME) electrostatic summation methods are added as the Ewald and PME general interactions respectively, which should be used alongside the corresponding CoulombEwald pairwise interaction. PME runs on all backends and is compatible with Enzyme when the grad_safe option is given during system setup from a file. The nonbonded_method keyword argument during system setup from a file allows the electrostatic summation approach to be selected. The ewald_error_tol and approximate_pme keyword arguments are also added.
• Constraints now work on the GPU and the documentation is improved. The constraints and rigid_water keyword arguments during system setup from a file allow different constraint options to be selected. The check_constraints function is added to check both position and velocity constraints.
• The stochastic velocity rescaling thermostat is added as VelocityRescaleThermostat.
• The stochastic cell rescaling barostat is added as CRescaleBarostat.
• Non-isotropic pressure coupling is now available for the BerendsenBarostat with the coupling_type keyword argument.
• The cutoff interface is now available for custom pairwise interactions with the use of force_cutoff and pe_cutoff. Documentation for custom cutoff methods is added.
• Functions and documentation for calculating free energies with the Multistate Bennett Acceptance Ratio (MBAR) method are added.
• The EnsembleSystem struct and read_frame! function are added to help with loading trajectory data into a System.
• The DisplacementsLogger, useful for calculating properties such as mean squared displacements, is added.
• The replica_boundaries keyword argument is added for ReplicaSystem.
• The cutoff keyword argument is added for Gravity.
• More informative errors are given during setup for incompatible arguments.

Performance improvements

• GPU simulation is made faster.

Bug fixes

• A bug when applying cutoffs is fixed.
• A bug when using a TriclinicBoundary with CUDA is fixed.
• A bug when using custom atom types with CUDA is fixed.
• A rare bug in force calculation with CUDA is fixed.
• Bugs when setting up a TriclinicBoundary with certain values are fixed.
• A bug when using CellListMapNeighborFinder in 2D is fixed.