Interface  Description 

IPotential0Lrc 
Interface for a longrange correction potential.

IPotential0MoleculeLrc 
Interface for a longrange correction potential.

IPotentialAtomicMultibody 
Interface for an atomic nonadditive potential.

IPotentialMolecularSecondDerivative  
IPotentialMolecularTorque  
IPotentialTorque  
P1IntraMolecular  
P2SemiclassicalAtomic.AtomInfo  
P2SemiclassicalMolecular.MoleculeInfo  
Potential1.Intramolecular 
Marker interface indicating that a onebody potential is an intramolecular
potential, and not, e.g., a potential of interaction with an external field.

Potential2Soft 
Methods for properties obtained for a soft, differentiable pair potential.

Potential2Spherical 
interface for spherical 2body potentials

PotentialCalculation 
Class defining a particular action to be performed on a set of atoms using an
arbitrary potential.

PotentialCalculationMolecular 
Class defining a particular action to be performed on a set of atoms using an
arbitrary potential.

PotentialHard 
Interface for hard potentials, having impulsive forces.

PotentialMolecularSoft 
Methods for properties obtained for a soft, differentiable pair potential.

PotentialPolarizable 
Interface for a polarizable potential.

PotentialReactive 
Interface for potentials that change the bond state of an atom.

PotentialSoft 
Methods for properties obtained for a soft, differentiable pair potential.

PotentialTruncated 
Interface for a potential that is artificially truncated, and thus which can
provide a zerobody potential that (approximately) corrects for the
truncation.

Class  Description 

EwaldSummation 
Sabry

EwaldSummation.MyCharge  
EwaldSumMolecules 
basic Ewald Sum
U(coulomb) = U(realspace) + U(fourierspace) + U(selfcorrection)
Frenkel&Smit,

EwaldSumMolecules.MyCharge  
P1ExternalField  
P1HardBoundary 
Potential that places hard repulsive walls coinciding with the
boundary of the box, which is assumed to be rectangular in shape.

P1HardMovingBoundary 
Potential that places hard repulsive walls that move and
accelerate subject to an external force field (pressure).

P1HardPeriodic 
pseudopotential for a "collision" time to update colliders for periodic boundaries

P1Harmonic 
Potential in which attaches a harmonic spring between each affected atom and
the nearest boundary in each direction.

P1HarmonicSite 
Potential in which attaches a harmonic spring between each affected atom a
nominal site for that atom, as defined by an agent manager.

P1HydrogenMielke  
P1HydrogenMielke.P1HydrogenMielkeAtomic  
P1HydrogenMielke.P2HydrogenMielkeAtomic  
P1IntraSimple 
Generic intramolecular potential group, having one potential for bonded
atoms, and a different potential for unbonded ones.

P1SoftBoundary  
P22CLJQ 
Twocentered Lennard Jones molecule with a quadrupole.

P2Anharmonic 
Harmonic Well interatomic potential.

P2ArgonAziz1993 
Pair potential for argon from Aziz (1993) JCP 99(6): 4518.

P2ArgonSlavicekEtAl2003 
Ab initio pair potential for argon from Slavicek et al.

P2ArgonTangAndToennies2003 
Pair potential for argon from Tang and Toennies 2003.

P2CO2EMP 
3point potential for CO2.

P2CO2EMP1 
EPM model for CO2.

P2CO2EMP2 
EPM2 model for CO2

P2CO2TraPPE 
I used this original EPM2model to describe TraPPECO2 model
the two models are different in parameters.

P2DiscreteFeynmanHibbs 
Effective 2 body potential approximating the quantum behavior of atomic
interactions.

P2DiscreteFeynmanHibbs.P2HeEmpericalQuantum  
P2DLPOLY  
P2DoubleWell 
Doublewell potential.

P2Dreiding 
Dreiding potential.

P2EffectiveFeynmanHibbs 
Effective 2 body potential approximating the quantum behavior of atomic
interactions.

P2Electrostatic 
Simple electrostatic potential class.

P2ElectrostaticWithHardCore 
Simple electrostatic potential class.

P2Exp6 
Exponential6 atomatom repulsiondispersion potential.

P2Exp6Buckingham 
The Buckingham Exponential6 atomatom dispersion potential.

P2Fene 
Finite elastic nonlinear extensible (FENE) spring potential.

P2HardAssociation 
Purely attractive squarewell potential with no repulsive core.

P2HardAssociationCone 
LennardJones potential with a squarewell cone of attraction.

P2HardAssociationConeDoubleSites 
LennardJones potential with a squarewell cone of attraction.

P2HardAssociationConeFourSites 
LennardJones potential with a squarewell cone of attraction.

P2HardAssociationConeFourSitesSW 
SquareWell cone of attraction for associating fluid theory
Four association sites

P2HardAssociationConeOneSite 
LennardJones potential with a squarewell cone of attraction.

P2HardAssociationConeReference 
potential with a squarewell cone of attraction for reference system.

P2HardAssociationConeReferenceFourSites 
potential with a squarewell cone of attraction for reference system.

P2HardAssociationConeSW 
SquareWell cone of attraction for associating fluid theory
double association sites

P2HardBond 
Potential that acts like a hard string connecting the centers of two atoms.

P2HardBondedList 
Hard potential that wraps two others.

P2HardSphere 
Basic hard(rod/disk/sphere) potential.

P2HardWrapper 
Hard potential class that wraps another hard potential.

P2Harmonic 
Harmonic Well interatomic potential.

P2HePCKLJS 
Ab initio pair potential for helium from Przybytek et al.

P2HeSimplified 
Simplified pair potential for Helium.

P2HSDipole 
Hard sphere molecule with a dipole sitting at the center.

P2HydrogenHinde  
P2HydrogenHinde.P2HydrogenHindeAtomic  
P2HydrogenHinde.P2HydrogenHindeMolecular  
P2HydrogenHindeAtomic  
P2HydrogenHindePatkowski  
P2HydrogenHindePatkowski.P2HydrogenHindePatkowskiAtomic  
P2HydrogenHindePatkowski.P2HydrogenHindePatkowskiMolecular  
P2HydrogenHindePatkowskiAtomic  
P2HydrogenPatkowski  
P2HydrogenPatkowski.P2HydrogenPatkowskiAtomic  
P2HydrogenPatkowski.P2HydrogenPatkowskiMolecular  
P2HydrogenPatkowskiAtomic  
P2HydrogenPatkowskiIso  
P2Ideal 
Idealgas twobody potential, which defines no interactions and zero energy
for all pairs given to it.

P2LennardJones 
LennardJones interatomic potential.

P2LennardJonesDreiding 
Dreiding: LennardJones nonbonding potential.

P2LJDipole 
Lennard Jones molecule with a point dipole sitting in the center.

P2LJQ 
Lennard Jones molecule with a quadrupole.

P2LJQQ 
Lennard Jones molecule with a quadrupole.

P2ModifiedMorse  
P2MoleculeMonatomic  
P2MoleculeSoftTruncatedSwitched 
Wraps a softspherical potential to apply a truncation to it.

P2MoleculeTruncated 
Wraps a softspherical potential to apply a truncation to it.

P2Morse  
P2NitrogenHellmann  
P2O2Bartolomei  
P2PenetrableBond 
Potential with a well having a finite potential on either side.

P2PenetrableSphere 
Basic penetrablesphere potential.

P2PenetrableSquareWell 
Squarewell potential with a penetrable core.

P2QChem 
This class requires a bash script called ./runQChem to load the appropriate QChem module and run it.

P2QChemInterpolated 
Pair potential for argon interpolated from QChem results.

P2QChemInterpolated.DampingParams  
P2ReactionFieldDipole  
P2ReactionFieldDipole.P0ReactionField 
A 0body potential that should be added along with this potential.

P2ReactionFieldDipoleTruncated  
P2ReactionFieldDipoleTruncated.P0ReactionField 
A 0body potential that should be added along with this potential.

P2RoughSphere 
Basic hard(rod/disk/sphere) potential, with surface roughness to couple rotation and translational motions.

P2SemiclassicalAtomic 
Effective semiclassical molecular potential using the approach of
Takahashi and Imada
http://dx.doi.org/10.1143/JPSJ.53.3765
as described by Schenter
http://dx.doi.org/10.1063/1.1505441

P2SemiclassicalMolecular 
Effective semiclassical molecular potential using the approach of
Takahashi and Imada
http://dx.doi.org/10.1143/JPSJ.53.3765
as described by Schenter
http://dx.doi.org/10.1063/1.1505441

P2SemiclassicalMolecular.MoleculeInfoBrute  
P2SoftSphere 
Softsphere interatomic potential.

P2SoftSphericalTruncated 
Wraps a softspherical potential to apply a truncation to it.

P2SoftSphericalTruncated.P0Lrc 
Inner class that implements the longrange correction for this truncation scheme.

P2SoftSphericalTruncatedForceShifted 
Softspherical potential class that shifts both the potential energy and the
force such that both are 0 at the cutoff.

P2SoftSphericalTruncatedShifted 
Wraps a softspherical potential to apply a truncation to it.

P2SoftSphericalTruncatedSwitched 
Wraps a softspherical potential to apply a truncation to it.

P2SoftTruncated 
Wraps a softspherical potential to apply a truncation to it.

P2SpheroPolyhedron  
P2SquareWell 
Basic squarewell potential.

P2SquareWellRobust 
Basic squarewell potential.

P2Tether 
Potential that acts like a hard string connecting the centers of two atoms.

P2TriangleWell 
Hard core with an attractive tail that goes to zero linearly with r.

P2WaterPotentialsJankowski  
P2WCA 
WeeksChandlerAndersen potential.

P3AdditiveQChem  
P3AdditiveQChem.DampingParams  
P3AxilrodTeller 
AxilrodTeller potential.

P3AxilrodTeller.MyAgent  
P3BondAngle 
Simple 3body soft bondangle potential

P3BondAngleDreiding 
Simple 3body soft bondangle for Dreiding potential
* U(theta) = gamma * [ cos(theta)  cos(theta_e)]^2
where gamma is the potential's energy parameter
theta_e is the equilibrium bond angle

P3CPSNonAdditiveHe 
Ab initio nonadditive trimer potential for He developed by Cencek, Patkowski, and Szalewicz JCP 131 064105 2009.

P3CPSNonAdditiveHeLessSimplified 
Ab initio nonadditive trimer potential for He developed by Cencek, Patkowski, and Szalewicz JCP 131 064105 2009.

P3CPSNonAdditiveHeOrig 
Ab initio nonadditive trimer potential for He developed by Cencek, Patkowski, and Szalewicz JCP 131 064105 2009.

P3CPSNonAdditiveHeSimplified 
Simplified version of ab initio, nonadditive trimer potential for He developed by Cencek, Patkowski, and Szalewicz JCP 131 064105 2009.

P3HydrogenATM  
P3HydrogenATM.P3HydrogenAtomic  
P3HydrogenGarberoglioMolecular  
P3HydrogenManzhos  
P3HydrogenManzhos.P3HydrogenManzhosMolecular  
P3Induction 
3body induction potential based on form used by Oakley and Wheatley.

P3Induction.MyAgent  
P3NitrogenHellmannNonAdditive  
P3QChem  
P3QChem.DampingParams  
P4BondTorsion 
Torsion potential.

P4BondTorsionAlkaneXCCH 
slight modification from P4BondTorsion class(change energyAtAngle method)
Siepmann's Alkane TraPPEEH model, XCCH torsion potential, X can be H or C, H is for H on CH3 only
U(torsion) = Cx * (1 cos(3phi)); C(C):854K, C(H):717K

P4BondTorsionOPLS 
OPLS Torsion potential.

P4TorsionDreiding 
Simple 4body soft bondangle for Dreiding potential
U(phi) = (1/2) * Vjk * {1  cos [njk (phi  phiEq)]}
where Vjk is the rotation barrier (always +ve) [unit Kelvin]
njk is the periodicity (an integer)
phiEq is the equilibrium dihedral angle [unit radians]

Potential 
Superclass for all Potential classes, which define how the atoms in the
system interact with each other.

Potential0 
Potential that does not depend on any atom positions.

Potential0Lrc 
Zerobody potential implementing the longrange correction
that compensates for truncation of the potential.

Potential1 
Potential acting on a single atom or atom group.

Potential2 
Potential acting on 2 atoms or molecules.

Potential2HardSpherical 
Methods for a hard (impulsive), sphericallysymmetric pair potential.

Potential2SoftSpherical 
Methods for a soft (nonimpulsive), sphericallysymmetric pair potential.

Potential2SoftSphericalLS 
Methods for a soft (nonimpulsive), sphericallysymmetric pair potential.

PotentialArray 
Instances of this class are created by AtomType classes to
store the list of potentials and criteria that apply to
the atoms of that type.

PotentialArrayByType 
This class stores an array of Potentials and remembers the "other" IAtomType
that the IPotential applies to.

PotentialArrayMolecular 
Instances of this class are created by MoleculeType classes to
store the list of potentials and criteria that apply to
the molecules of that type.

PotentialAtomicSum 
Atomic potential class that simply sums up contributions from multiple
(atomic) potentials.

PotentialCalculationEnergySum 
Evaluates the energy summed over all iterated atoms.

PotentialCalculationEnergySumBigDecimal 
Mimics original PotentialEnergySum calculation, but uses a BigDecimal
representation for the sum.

PotentialCalculationForcePressureSum 
Sums the force on each iterated atom and adds it to the integrator agent
associated with the atom.

PotentialCalculationForceSum 
Sums the force on each iterated atom and adds it to the integrator agent
associated with the atom.

PotentialCalculationHyperVirialSum 
Evaluates the hypervirial summed over all iterated atoms.

PotentialCalculationMolecularVirialSum 
Evaluates the virial summed over all iterated molecules.

PotentialCalculationPhiSum  
PotentialCalculationPressureTensor 
Calculates the pressure tensor by calculating the force on each atom, along
with including the kinetic portion (from the velocities or an Integrator).

PotentialCalculationTorqueSum 
Sums the force and torque on each iterated atom or molecule and adds it to
the agent associated with the atom.

PotentialCalculationVirialSum 
Evaluates the virial summed over all iterated atoms.

PotentialDLPOLY  
PotentialEmul 
PotentialEmul class invokes the emul external program to compute energies
between molecules.

PotentialGroup 
Collection of potentials that act between the atoms contained in
one or more groups of atoms.

PotentialGroup.PotentialLinker  
PotentialGroupSoft 
include virial and gradient for a molecular potential

PotentialMaster 
Manager of all potentials in simulation.

PotentialMaster.AtomIterator0  
PotentialMaster.MoleculeIterator0  
PotentialMaster.PotentialLinker  
PotentialMasterLrc 
Collects potentials used for longrange correction.

PotentialMasterMonatomic 
PotentialMaster suitable for monatomic molecules without using neighbor
lists and avoids PotentialMaster's performance problems.

PotentialMolecular 
Superclass for all Potential classes, which define how the atoms in the
system interact with each other.

PotentialMolecularMonatomic 
Intermolecular potential that wraps an atomic potential.

PotentialMolecularSum 
Molecular potential class that simply sums up contributions from multiple
(molecular) potentials.

PotentialN  
PotentialReactive.BondChangeData 