| Interface | Description |
|---|---|
| AssociationDefinition |
Interface for a method that defines whether two atoms are considered associated.
|
| AssociationDefinitionMolecule |
Interface for a method that defines whether two molecules are considered associated.
|
| IAssociationHelper |
Interface for a class that is capable of populating a list of atoms in an
smer as well as checking the validity of the bonding
|
| IAssociationHelperMolecule |
Interface for a class that is capable of populating a list of molecules in an
smer as well as checking the validity of the bonding
|
| Class | Description |
|---|---|
| AssociationHelperBranched |
AssociationHelperBranched is capable of populating a list of atoms in an smer
within a simulation with multiple association sites per atom.
|
| AssociationHelperDouble |
AssociationHelperDouble is capable of populating a list of atoms in an smer
within a simulation with double-bonding (two bonding sites per atom).
|
| AssociationHelperMolecule |
AssociationHelperBranched is capable of populating a list of molecules in an smer
within a simulation with multiple association sites per molecule.
|
| AssociationHelperSingle |
AssociationHelperSingle is capable of populating a list of atoms in an smer
within a simulation with single-bonding (one bonding site per atom).
|
| AssociationManager |
Class to define and track atom associations.
|
| AssociationManagerMolecule |
Class to define and track molecule associations.
|
| AtomSourceRandomDimer | |
| AtomSourceRandomMonomer | |
| AtomSourceRandomSmer | |
| BiasVolume | |
| BiasVolume2SiteAceticAcid | |
| BiasVolumeAceticAcid | |
| BiasVolumeCube | |
| BiasVolumeMolecule | |
| BiasVolumeSphere | |
| BiasVolumeSphereOriented | |
| BiasVolumeSphereOrientedDoubleSites | |
| ColorSchemeSmer |
Color scheme for smer association.
|
| ColorSchemeSmer.ColorAgent | |
| ColorSchemeSmerByLength |
Color scheme for smer association.
|
| MCMoveAtomDimer | |
| MCMoveAtomMonomer | |
| MCMoveAtomNoSmer | |
| MCMoveAtomSmer | |
| MCMoveBiasUB | |
| MCMoveBiasUBMolecule | |
| MCMoveDimer |
Standard Monte Carlo atom-displacement trial move of dimer
|
| MCMoveDimerRotate |
Standard Monte Carlo atom-displacement trial move.
|
| MCMoveMoleculeMonomer |
Monte Carlo molecule-displacement trial move for monomer molecules
|
| MCMoveMoleculeRotateAssociated |
Performs a rotation of a molecule that has an orientation coordinate.
|
| MCMoveMoleculeSmer |
Monte Carlo molecule-displacement trial move for a molecule in smer
|
| MCMoveRotateAssociated |
Performs a rotation of an atom (not a molecule) that has an orientation coordinate.
|
| MCMoveRotateNoSmer | |
| MCMoveSmer |
Standard Monte Carlo atom-displacement trial move of Trimer
|
| MCMoveSmerRotate |
Standard Monte Carlo atom-displacement trial move.
|
| MCMoveVolumeAssociated |
Standard Monte Carlo volume-change move for simulations in the NPT ensemble.
|
| MCMoveVolumeAssociated.Agent | |
| MCMoveVolumeAssociatedMolecule |
Monte Carlo volume-change move for associating fluids simulations in the NPT ensemble.
|
| MCMoveVolumeAssociatedMolecule.Agent | |
| MeterDimerMoleFraction |
Meter for measurement of species mole fraction within a specified subvolume
|
| MoleculeSourceRandomDimer | |
| MoleculeSourceRandomMonomer | |
| TestIGAssociationMC3D_NPT_DoubleSites |
Simple ideal gas + S-W Association Monte Carlo NPT simulation in 3D.
|
| TestIGAssociationMC3D_NPT_DoubleSites.VirialAssociatingFluidParam | |
| TestLJAssociationMC3D_NPT |
Simple Lennard-Jones + S-W Association Monte Carlo NPT simulation in 3D.
|
| TestLJAssociationMC3D_NPT_DoubleSites |
Simple Lennard-Jones + S-W Association Monte Carlo NPT simulation in 3D.
|
| TestLJAssociationMC3D_NPT_DoubleSites.VirialAssociatingFluidParam | |
| TestLJAssociationMC3D_NPT.VirialAssociatingFluidParam | |
| TestLJAssociationMC3D_NVTOld |
Simple Lennard-Jones + S-W Association Monte Carlo NPT simulation in 3D.
|
| TestLJAssociationMC3D_NVTOld.VirialAssociatingFluidParam |