Package ffx.potential.nonbonded
@ParametersAreNonnullByDefault
package ffx.potential.nonbonded
The Nonbonded package implements nonbonded molecular mechanics terms such as van der Waals and
Particle Mesh Ewald electrostastics.
- Since:
- 1.0
- Author:
- Michael J. Schnieders
-
ClassDescriptionRestrain molecules to their center of mass.This Generalized Kirkwood class implements GK for the AMOEBA polarizable atomic multipole force field in parallel using a
NeighborList.By implementing the MaskingInterface interface, interaction pairs can be excluded duringNeighborListconstruction.Given unit cell parameters and symmetry operators, NCS copies are restrained to the asymmetric unit atoms.The NeighborList class builds Verlet lists in parallel via a spatial decomposition.Hold the atom index and its symmetry operator.Hold the atoms in each cell.This class contains fields and methods for maintaining details of non-bonded cutoffs.A fixed schedule that balances pairwise work across threads.This Particle Mesh Ewald class implements PME for the AMOEBA polarizable mutlipole force field in parallel using aNeighborListfor anyCrystalspace group.The Reciprocal Space class computes the reciprocal space contribution toParticleMeshEwaldfor the AMOEBA force field.Apply a restraint between groups.Restrain the position of atoms to their initial coordinates.The RowLoop class is used to parallelize placing onto a 3D gridThe RowRegion class is used to parallelize placing onto a 3D gridPredict Mutual Induced Dipoles based on previous steps.The SliceLoop class is used to parallelize placing onto a 3D gridThe SliceLoop class is used to parallelize placing onto a 3D gridLoop over a list of atoms and assign their density to a grid.This class implements a spatial decomposition based on partitioning a grid into octants.A fixed schedule that load balances work chunks across threads.The Van der Waals class computes Van der Waals interaction in parallel using aNeighborListfor anyCrystal.The trick: The setFactors(i,k) method is called every time through the inner VdW loop, avoiding an "if (esv)" branch statement.This class contains fields and methods for maintaining details of the van der Waals functional form.Epsilon combining rule.Radius combining rule.Radius size in the parameter file (radius or diameter).Radius type in the parameter file (R-Min or Sigma).VDW Type.The Van der Waals class computes Van der Waals interaction in parallel using aNeighborListfor P1 (no symmetry)Crystalsystems.