Package etomica.models.co2

Class PNGCPM

java.lang.Object

etomica.potential.PotentialMolecular

etomica.models.co2.PNGCPM

All Implemented Interfaces:

IPotential, IPotentialMolecular, PotentialPolarizable

Direct Known Subclasses:

PNGCPMX

public class PNGCPM
extends PotentialMolecular
implements PotentialPolarizable

Generic GCPM potential class, capable of handling both CO2 and water. The potential takes an AtomTypeAgentManager that is responsible for returning parameters for each atom. Cross-parameters are computing using mixing rules published in

http://dx.doi.org/10.1063/1.3519022

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static class	PNGCPM.Component
static class	PNGCPM.GCPMAgent
class	PNGCPM.P3GCPMAxilrodTeller
class	PNGCPM.PNGCPMCached

Field Summary

Fields

Modifier and Type	Field	Description
protected Boundary	boundary
protected PNGCPM.Component	component
protected double	coreFac
static boolean	debugme
protected Vector[][]	Ep
protected Vector[][]	Eq
protected Vector[][]	mu
protected int	nAtomTypes
protected Vector	oldMu
protected boolean	oops
protected MoleculePair	pair
protected PNGCPM.GCPMAgent[][]	pairAgents
protected double[][]	pairPolarization
protected Vector	rijVector
protected Vector	shift
protected java.util.Map<AtomType,PNGCPM.GCPMAgent>	typeManager
protected Vector	work

Fields inherited from class etomica.potential.PotentialMolecular

nBody, space

Constructor Summary

Constructors

Constructor	Description
PNGCPM(Space space, java.util.Map<AtomType,PNGCPM.GCPMAgent> typeManager, int nAtomTypes)
PNGCPM(Space space, java.util.Map<AtomType,PNGCPM.GCPMAgent> typeManager, int nAtomTypes, int nBody)

Method Summary

Modifier and Type	Method	Description
double	energy(IMoleculeList molecules)	Returns the interaction energy between the given molecules.
double	getLastPolarizationEnergy()	Returns the polarization energy from the last call to energy(AtomSet).
double	getNonPolarizationEnergy(IMoleculeList molecules)	This returns the pairwise-additive portion of the GCPM potential for a pair of atoms (dispersion + fixed-charge electrostatics)
PNGCPM.GCPMAgent	getPairAgent(AtomType type1, AtomType type2)
double	getPolarizationEnergy(IMoleculeList molecules)	This returns the polarizable portion of the GCPM potential for any number of atoms.
double	getRange()	Returns the range over which the potential applies.
static void	main(java.lang.String[] args)
static void	main2(java.lang.String[] args)
static void	mainCO2(java.lang.String[] args)
PNGCPM.P3GCPMAxilrodTeller	makeAxilrodTeller()
PNGCPM.PNGCPMCached	makeCachedPairPolarization()
void	setBox(Box box)	Informs the potential of the box on which it acts.
void	setComponent(PNGCPM.Component comp)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from class etomica.potential.PotentialMolecular

nBody

Field Detail

debugme

public static boolean debugme

pairPolarization

protected final double[][] pairPolarization

pair

protected final MoleculePair pair

coreFac

protected final double coreFac

rijVector

protected final Vector rijVector

work

protected final Vector work

shift

protected final Vector shift

typeManager

protected final java.util.Map<AtomType,PNGCPM.GCPMAgent> typeManager

nAtomTypes

protected final int nAtomTypes

pairAgents

protected final PNGCPM.GCPMAgent[][] pairAgents

oops

protected boolean oops

boundary

protected Boundary boundary

Eq

protected Vector[][] Eq

Ep

protected Vector[][] Ep

mu

protected Vector[][] mu

oldMu

protected Vector oldMu

component

protected PNGCPM.Component component

Constructor Detail

PNGCPM

public PNGCPM(Space space,
              java.util.Map<AtomType,PNGCPM.GCPMAgent> typeManager,
              int nAtomTypes)

PNGCPM

public PNGCPM(Space space,
              java.util.Map<AtomType,PNGCPM.GCPMAgent> typeManager,
              int nAtomTypes,
              int nBody)

Method Detail

main2

public static void main2(java.lang.String[] args)

mainCO2

public static void mainCO2(java.lang.String[] args)

main

public static void main(java.lang.String[] args)

setComponent

public void setComponent(PNGCPM.Component comp)

energy

public double energy(IMoleculeList molecules)

Description copied from class: PotentialMolecular

Returns the interaction energy between the given molecules. There might be 0, 1, 2 or more atoms in the IMoleculeList.

Specified by:

energy in interface IPotentialMolecular

Specified by:

energy in class PotentialMolecular

makeCachedPairPolarization

public PNGCPM.PNGCPMCached makeCachedPairPolarization()

getPairAgent

public PNGCPM.GCPMAgent getPairAgent(AtomType type1,
                                     AtomType type2)

getNonPolarizationEnergy

public double getNonPolarizationEnergy(IMoleculeList molecules)

This returns the pairwise-additive portion of the GCPM potential for a pair of atoms (dispersion + fixed-charge electrostatics)

getPolarizationEnergy

public double getPolarizationEnergy(IMoleculeList molecules)

This returns the polarizable portion of the GCPM potential for any number of atoms.

Specified by:

getPolarizationEnergy in interface PotentialPolarizable

getLastPolarizationEnergy

public double getLastPolarizationEnergy()

Description copied from interface: PotentialPolarizable

Returns the polarization energy from the last call to energy(AtomSet).

Specified by:

getLastPolarizationEnergy in interface PotentialPolarizable

Returns:

getRange

public final double getRange()

Description copied from interface: IPotential

Returns the range over which the potential applies. IAtoms with a greater separation do not interact.

Specified by:

getRange in interface IPotential

Specified by:

getRange in class PotentialMolecular

setBox

public void setBox(Box box)

Description copied from class: PotentialMolecular

Informs the potential of the box on which it acts. Typically this requires at least that it update the nearestImageTransformer of its coordinatePair (if it uses one), e.g.: cPair.setNearestImageTransformer(box.boundary());

Specified by:

setBox in interface IPotential

Specified by:

setBox in class PotentialMolecular

makeAxilrodTeller

public PNGCPM.P3GCPMAxilrodTeller makeAxilrodTeller()