Purpose

A Group is a collection of atoms, with an optional list of objects. These objects can be anything, e.g. rigid bodies, constraints, residues... etc. The idea is that different groups of atoms will require their equations of motion integrating in different ways, so currently AdvanceVerlet loops over all groups, checks the type of the group and integrates the equations of motion for the atoms in that group in the appropriate way.

Two examples:

• A methane molecule with all C-H bonds fixed would have all 5 of its atoms in one group, which would also contain (the indices of) four constraints. During AdvanceVerlet the RATTLE algorithm can find the correct constraint objects to enforce the fixed bond lengths

• A rigid ammonia molecule could be treated as a rigid body, in which case the group would contain the indices of all 4 of the atoms, and the index of 1 rigid body in the objects array. Then, during AdvanceVerlet, the NO_SQUISH algorithm would propagate these atoms rigidly all at the same time.

Initially, when a DynamicalSystem is initialised each atom is put into its own group. As constraints and rigid bodies are added the number of groups remains the same but some of them become empty. These empty groups can be used if extra atoms are added to the system, or they can be left without a problem. If more memory is needed then DS_Free_Groups can be called, which deletes all the empty groups and recreates the group_lookup array inside DynamicalSystem. This is most useful if all the constraints/rigid bodies are set up before a simulation and are known to never change.

A few notes:

• Groups aren't necessarily limited to the usage described here

• The atom and object arrays are self extensible, but are always exactly the right size (unlike a Table). This is based on the assumption that they will not change much (if at all) after they have been initially set up.

• Each group has a type, which defines how its atoms are integrated. Currently the types are TYPE_IGNORE (numerically zero, and atoms in it are not integrated, which could replace the move_mask variable(?)), TYPE_ATOM (a normal atom), TYPE_CONSTRAINED and TYPE_RIGID. The idea is that if other ways of integrating atoms is required (e.g. linear molecules, positional restraints, belly atoms, etc.) then an new type will be defined and the new will be added to the select case constructs in AdvanceVerlet.