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.