| Interface | Description |
|---|---|
| IPotential | |
| IPotential0Lrc |
Interface for a long-range correction potential.
|
| IPotential0MoleculeLrc |
Interface for a long-range correction potential.
|
| IPotentialAtomic | |
| IPotentialAtomicMultibody |
Interface for an atomic non-additive potential.
|
| IPotentialAtomicSecondDerivative | |
| IPotentialMolecular | |
| IPotentialMolecularSecondDerivative | |
| IPotentialMolecularTorque | |
| IPotentialTorque | |
| P1IntraMolecular | |
| P2SemiclassicalAtomic.AtomInfo | |
| P2SemiclassicalMolecular.MoleculeInfo | |
| Potential1.Intramolecular |
Marker interface indicating that a one-body 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 2-body 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 zero-body potential that (approximately) corrects for the
truncation.
|
| Class | Description |
|---|---|
| EwaldSummation |
Sabry
|
| EwaldSummation.MyCharge | |
| EwaldSumMolecules |
basic Ewald Sum
U(coulomb) = U(real-space) + U(fourier-space) + U(self-correction)
Frenkel&Smit,
|
| EwaldSumMolecules.MyCharge | |
| IteratorDirective |
Encapsulation of a set of instructions that an AtomsetIterator
uses to select the atoms it presents on iteration.
|
| 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 |
pseudo-potential 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 | |
| P22CLJmuQ |
Two-centered Lennard Jones heteronuclear molecule with a mu2 and quadrupole.
|
| P22CLJQ |
Two-centered 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 |
3-point 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 |
Double-well 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 |
Exponential-6 atom-atom repulsion-dispersion potential.
|
| P2Exp6Buckingham |
The Buckingham Exponential-6 atom-atom dispersion potential.
|
| P2Fene |
Finite elastic nonlinear extensible (FENE) spring potential.
|
| P2HardAssociation |
Purely attractive square-well potential with no repulsive core.
|
| P2HardAssociationCone |
Lennard-Jones potential with a square-well cone of attraction.
|
| P2HardAssociationConeDoubleSites |
Lennard-Jones potential with a square-well cone of attraction.
|
| P2HardAssociationConeFourSites |
Lennard-Jones potential with a square-well cone of attraction.
|
| P2HardAssociationConeFourSitesSW |
Square-Well cone of attraction for associating fluid theory
Four association sites
|
| P2HardAssociationConeOneSite |
Lennard-Jones potential with a square-well cone of attraction.
|
| P2HardAssociationConeReference |
potential with a square-well cone of attraction for reference system.
|
| P2HardAssociationConeReferenceFourSites |
potential with a square-well cone of attraction for reference system.
|
| P2HardAssociationConeSW |
Square-Well 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.
|
| P2HC2Yukawa |
Hard-core plus two Yukawa fluid (HC2Yukawa): A Lennard-Jones like potential.
|
| P2HePCJS |
pair potential for Helium Przybytek et al.
|
| 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 |
Ideal-gas two-body potential, which defines no interactions and zero energy
for all pairs given to it.
|
| P2LennardJones |
Lennard-Jones interatomic potential.
|
| P2LennardJonesDreiding |
Dreiding: Lennard-Jones non-bonding 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 soft-spherical potential to apply a truncation to it.
|
| P2MoleculeTruncated |
Wraps a soft-spherical potential to apply a truncation to it.
|
| P2Morse | |
| P2NitrogenHellmann | |
| P2O2Bartolomei | |
| P2PenetrableBond |
Potential with a well having a finite potential on either side.
|
| P2PenetrableSphere |
Basic penetrable-sphere potential.
|
| P2PenetrableSquareWell |
Square-well potential with a penetrable core.
|
| P2PotentialGroupBuilder |
Creates a two-body potential group using model parameters for 1 or 2 species.
|
| P2PotentialGroupBuilder.ModelParams | |
| P2QChem |
This class requires a bash script called ./runQChem to load the appropriate Q-Chem module and run it.
|
| P2QChemInterpolated |
Pair potential for argon interpolated from Q-Chem results.
|
| P2QChemInterpolated.DampingParams | |
| P2ReactionFieldDipole |
Potential to implement the reaction field treatment of electrostatic interactions.
|
| P2ReactionFieldDipoleTruncated | |
| P2ReactionFieldDipoleTruncated.P0ReactionField |
A 0-body 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
|
| 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 |
Soft-sphere interatomic potential.
|
| P2SoftSphericalTruncated |
Wraps a soft-spherical potential to apply a truncation to it.
|
| P2SoftSphericalTruncated.P0Lrc |
Inner class that implements the long-range correction for this truncation scheme.
|
| P2SoftSphericalTruncatedForceShifted |
Soft-spherical potential class that shifts both the potential energy and the
force such that both are 0 at the cutoff.
|
| P2SoftSphericalTruncatedShifted |
Wraps a soft-spherical potential to apply a truncation to it.
|
| P2SoftSphericalTruncatedSwitched |
Wraps a soft-spherical potential to apply a truncation to it.
|
| P2SoftTruncated |
Wraps a soft-spherical potential to apply a truncation to it.
|
| P2SpheroPolyhedron | |
| P2SquareWell |
Basic square-well potential.
|
| P2SquareWellRobust |
Basic square-well 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 |
Weeks-Chandler-Andersen potential.
|
| P2WCAP |
LJ potential minus WCA.
|
| P2Yukawa |
Yukawa interatomic potential.
|
| P3AdditiveQChem | |
| P3AdditiveQChem.DampingParams | |
| P3AxilrodTeller |
Axilrod-Teller potential.
|
| P3AxilrodTeller.MyAgent | |
| P3BondAngle |
Simple 3-body soft bond-angle potential
|
| P3BondAngleDreiding |
Simple 3-body soft bond-angle 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 non-additive trimer potential for He developed by Cencek, Patkowski, and Szalewicz JCP 131 064105 2009.
|
| P3CPSNonAdditiveHeLessSimplified |
Ab initio non-additive trimer potential for He developed by Cencek, Patkowski, and Szalewicz JCP 131 064105 2009.
|
| P3CPSNonAdditiveHeOrig |
Ab initio non-additive trimer potential for He developed by Cencek, Patkowski, and Szalewicz JCP 131 064105 2009.
|
| P3CPSNonAdditiveHeSimplified |
Simplified version of ab initio, non-additive trimer potential for He developed by Cencek, Patkowski, and Szalewicz JCP 131 064105 2009.
|
| P3HydrogenATM | |
| P3HydrogenATM.P3HydrogenAtomic | |
| P3HydrogenGarberoglioMolecular | |
| P3HydrogenManzhos | |
| P3HydrogenManzhos.P3HydrogenManzhosMolecular | |
| P3Induction |
3-body 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 TraPPE-EH 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 4-body soft bond-angle 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 |
Zero-body potential implementing the long-range 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), spherically-symmetric pair potential.
|
| Potential2SoftSpherical |
Methods for a soft (non-impulsive), spherically-symmetric pair potential.
|
| Potential2SoftSphericalLS |
Methods for a soft (non-impulsive), spherically-symmetric 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.
|
| PotentialCalculationFSum | |
| PotentialCalculationHyperVirialSum |
Evaluates the hypervirial summed over all iterated atoms.
|
| PotentialCalculationMolecularVirialSum |
Evaluates the virial summed over all iterated molecules.
|
| PotentialCalculationPhiSum | |
| PotentialCalculationPhiSumHeisenberg | |
| 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 long-range 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 | |
| PotentialNonAdditiveDifference | |
| PotentialReactive.BondChangeData |
| Enum | Description |
|---|---|
| IteratorDirective.Direction |