Dev

[JosePereiraUA]

Since last Master commit: (23 Oct 2018)

• Added ILSRR Driver
• Added eSol and eH energy components as part of Forcefield.CoarseGrain
• Added eContacts and eDihedralFBR energy components as part of Forcefield.Restraints
• Added Blockrot Mutator
• Added Sidechain Mutator
• Optimized all Forcefield evaluators
• Bug fixes, documentation updates, etc

[JosePereiraUA]

As of 0d594d4d57a050770e9a185b301684338a5d325a (17 May 2019): Available to merge

Updates:

• Major efficiency and speed improvements;
• Changed main function names: drivers = run!; evaluators = evaluate!; mutators = apply!;
• Drivers now have a DriverConfig and a DriverState. The DriverConfig holds all immutable information defining the functioning of the Drive, while the DriverState is updated with the current state of the simulation;
• Callbacks are defined in the DriverConfig only, and retrieve 2 arguments from the simulation: the current State and current DriverState. Callbacks should now input information to the system (should be "read-only"). For this reason, Drivers now are cleared of "hard-coded" prints.
• ProtoSyn now supports Samplers, who are aggregators of Mutators (and possibly certain Drivers such as SteepestDescent). Samplers have an apply! function that can be customized by the user. By default, this function is automatically creates and simply applies all mutators in the Sampler in a for loop. Moreover, Samplers have a tune! function that is called in certain Drivers. The objetive is to adjust the parameters of the mutators (such as step size, for example) in accordance to the simulation state.
• ProtoSyn now supports Evaluators, who are aggregators of ForcefieldComponents. In analogy to Samplers, the default evaluate! function simply sums all components in a for loop, and can be overloaded by the user.
• Common.State now supports NonBondedList, limiting the number of atoms required for the calculations of non bonded interactions. This list is updated every N steps in certain Drivers, such as SteepestDescent.