Package ffx.potential.nonbonded

Class ParticleMeshEwald

java.lang.Object

ffx.potential.nonbonded.ParticleMeshEwald

All Implemented Interfaces:

LambdaInterface

public class ParticleMeshEwald
extends Object
implements LambdaInterface

This Particle Mesh Ewald class implements PME for the AMOEBA polarizable mutlipole force field in parallel using a NeighborList for any Crystal space group. The real space contribution is contained within this class and the reciprocal space contribution is delegated to the ReciprocalSpace class.

Author:

Michael J. Schnieders
derived from:
TINKER code by Jay Ponder, Pengyu Ren and Tom Darden.

See Also:

• 
  M. J. Schnieders, J. Baltrusaitis, Y. Shi, G. Chattree, L. Zheng, W. Yang and P. Ren, The Structure, Thermodynamics, and Solubility of Organic Crystals from Simulation with a Polarizable Force Field, Journal of Chemical Theory and Computation 8 (5), 1721-36 (2012)
• 
  M. J. Schnieders, T. D. Fenn and V. S. Pande, Polarizable atomic multipole X-ray refinement: Particle-mesh Ewald electrostatics for macromolecular crystals. Journal of Chemical Theory and Computation 7 (4), 1141-56 (2011)
• 
  C. Sagui, L. G. Pedersen, and T. A. Darden, Journal of Chemical Physics 120 (1), 73 (2004)
• 
  T. Darden, D. York, and L. Pedersen, Journal of Chemical Physics 98 (12), 10089 (1993)
• 
  W. Smith, "Point Multipoles in the Ewald Summation (Revisited)", CCP5 Newsletter, 46, 18-30 (1998)

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
class	ParticleMeshEwald.LambdaFactors	The setFactors(i,k,lambdaMode) method is called every time through the inner PME loops, avoiding an "if (esv)" branch statement.
class	ParticleMeshEwald.LambdaFactorsESV
class	ParticleMeshEwald.LambdaFactorsOST

Field Summary

Fields

Modifier and Type	Field	Description
protected Atom[]	atoms	An ordered array of atoms in the system.
double[][][]	coordinates	Dimensions of [nsymm][xyz][nAtoms].
double[][]	directDipole	Direct induced dipoles.
double[][]	directDipoleCR
double[][]	directField
double[][]	directFieldCR
double	electric	Coulomb constant in units of kcal*Ang/(mol*electron^2)
double[][][]	fractionalMultipole	Fractional multipoles in the global frame with dimensions of [nsymm][nAtoms][10]
double[][][]	globalMultipole	Cartesian multipoles in the global frame with dimensions of [nsymm][nAtoms][10]
double[][][]	inducedDipole	Dimensions of [nsymm][nAtoms][3]
double[][][]	inducedDipoleCR
protected double	inducedRealSpaceEnergy
protected double	inducedReciprocalEnergy
protected double	inducedSelfEnergy
protected int[][]	ip11	Polarization groups.
protected int[][]	ip12
protected int[][]	ip13
final ParticleMeshEwald.LambdaFactors	LambdaDefaults	The defaults are effectively final, as the implementation of setFactors in the base class is always a no-op.
protected int	nAtoms	The number of atoms in the system.
int[][][]	neighborLists	Neighbor lists, including atoms beyond the real space cutoff.
protected double	permanentMultipoleEnergy	Permanent multipole energy = permanentRealSpaceEnergy + permanentSelfEnergy + permanentReciprocalEnergy.
protected double	permanentRealSpaceEnergy
protected double	permanentReciprocalEnergy
protected double	permanentSelfEnergy
Polarization	polarization	Polarization modes include "direct", in which induced dipoles do not interact, and "mutual" that converges the self-consistent field to a tolerance specified by the "polar-eps" keyword.
protected double	polarizationEnergy	Polarization energy = inducedRealSpaceEnergy + inducedSelfEnergy + inducedReciprocalEnergy.
protected SCFAlgorithm	scfAlgorithm
double	soluteDielectric	The requested permittivity for the solute.
protected double	totalMultipoleEnergy	Total multipole energy = permanentMultipoleEnergy + polarizationEnergy.
double[][]	vacuumDirectDipole	Vacuum induced dipoles
double[][]	vacuumDirectDipoleCR
double[][][]	vacuumInducedDipole	Vacuum induced dipoles
double[][][]	vacuumInducedDipoleCR

Constructor Summary

Constructors

Constructor	Description
ParticleMeshEwald(Atom[] atoms, int[] molecule, ForceField forceField, Crystal crystal, NeighborList neighborList, ForceField.ELEC_FORM elecForm, double ewaldCutoff, double gkCutoff, ParallelTeam parallelTeam)	ParticleMeshEwald constructor.

Method Summary

Modifier and Type	Method	Description
protected void	assignPolarizationGroups()	AssignPolarizationGroups.
void	attachExtendedSystem(ExtendedSystem system)	Attach system with extended variable such as titrations.
void	computeInduceDipoleField()
void	computeMoments(Atom[] activeAtoms, boolean forceEnergy)	Compute multipole moments for an array of atoms.
void	destroy()
double	energy(boolean gradient, boolean print)	Calculate the PME electrostatic energy.
void	expandInducedDipoles()
AlchemicalParameters	getAlchemicalParameters()	Return the PME AlchemicalParameters.
int[][]	getAxisAtoms()
double	getCavitationEnergy()
double[][][]	getCoordinates()
double	getd2EdL2()	Get the 2nd partial derivative of the energy with respect to lambda.
double	getdEdL()	Get the partial derivative of the energy with respect to lambda.
void	getdEdXdL(double[] gradient)	Get the gradient of dEdL with respect to each parameter.
double	getDispersionEnergy()
ForceField.ELEC_FORM	getElecForm()	Returns the ELEC_FORM.
double	getEwaldCoefficient()
double	getEwaldCutoff()
GeneralizedKirkwood	getGK()
double	getGKEnergy()	getGeneralizedKirkwoodEnergy.
int	getGKInteractions()	getGKInteractions
double	getIndRealEnergy()	getIndRealEnergy.
double	getIndRecipEnergy()	getIndRecipEnergy.
double	getIndSelfEnergy()	getIndSelfEnergy.
int	getInteractions()	Getter for the field interactions.
double	getLambda()	Get the current value of the state variable.
boolean	getLambdaTerm()	If true, there are alchemical atoms impacted by the lambda state variable.
MultipoleType	getMultipoleType(int i)	Get the MultipoleType for Atom i.
double	getPermanentEnergy()
double	getPermRealEnergy()
double	getPermRecipEnergy()
double	getPermSelfEnergy()	getPermSelfEnergy.
double	getPolarEps()
int[][]	getPolarization11()
int[][]	getPolarization12()
int[][]	getPolarization13()
double	getPolarizationEnergy()	Getter for the field polarizationEnergy.
Polarization	getPolarizationType()
PolarizeType	getPolarizeType(int i)	Get the PolarizeType for Atom i.
ReciprocalSpace	getReciprocalSpace()
double	getScale14()
double	getSolvationEnergy()	getGKEnergy
double	getTotalMultipoleEnergy()	Getter for the field totalMultipoleEnergy.
void	setAtoms(Atom[] atoms, int[] molecule)
void	setCrystal(Crystal crystal)
void	setLambda(double lambda)	Set the current value of the state variable.
void	setPolarization(Polarization set)	Setter for the field polarization.

Methods inherited from class java.lang.Object

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

Methods inherited from interface ffx.potential.bonded.LambdaInterface

dEdLZeroAtEnds

Field Details

polarization

public Polarization polarization

Polarization modes include "direct", in which induced dipoles do not interact, and "mutual" that converges the self-consistent field to a tolerance specified by the "polar-eps" keyword.

coordinates

public double[][][] coordinates

Dimensions of [nsymm][xyz][nAtoms].

neighborLists

public int[][][] neighborLists

Neighbor lists, including atoms beyond the real space cutoff. [nsymm][nAtoms][nAllNeighbors]

globalMultipole

public double[][][] globalMultipole

Cartesian multipoles in the global frame with dimensions of [nsymm][nAtoms][10]

fractionalMultipole

public double[][][] fractionalMultipole

Fractional multipoles in the global frame with dimensions of [nsymm][nAtoms][10]

inducedDipole

public double[][][] inducedDipole

Dimensions of [nsymm][nAtoms][3]

inducedDipoleCR

public double[][][] inducedDipoleCR

directDipole

public double[][] directDipole

Direct induced dipoles.

directDipoleCR

public double[][] directDipoleCR

directField

public double[][] directField

directFieldCR

public double[][] directFieldCR

vacuumInducedDipole

public double[][][] vacuumInducedDipole

Vacuum induced dipoles

vacuumInducedDipoleCR

public double[][][] vacuumInducedDipoleCR

vacuumDirectDipole

public double[][] vacuumDirectDipole

Vacuum induced dipoles

vacuumDirectDipoleCR

public double[][] vacuumDirectDipoleCR

electric

@FFXProperty(name="electric",
             propertyGroup=LocalGeometryFunctionalForm,
             defaultValue="332.063713",
             description="Specifies a value for the so-called \"electric constant\" allowing conversion unit of electrostatic\npotential energy values from electrons^2/Angstrom to kcal/mol. Internally, FFX stores a default value\nfor this constant as 332.063713 based on CODATA reference values. Since different force fields are\nintended for use with slightly different values, this keyword allows overriding the default value.\n")
public double electric

Coulomb constant in units of kcal*Ang/(mol*electron^2)

soluteDielectric

public double soluteDielectric

The requested permittivity for the solute.

atoms

protected Atom[] atoms

An ordered array of atoms in the system.

nAtoms

protected int nAtoms

The number of atoms in the system.

ip11

protected int[][] ip11

Polarization groups.

ip12

protected int[][] ip12

ip13

protected int[][] ip13

totalMultipoleEnergy

protected double totalMultipoleEnergy

Total multipole energy = permanentMultipoleEnergy + polarizationEnergy.
This does not include GK.

permanentMultipoleEnergy

protected double permanentMultipoleEnergy

Permanent multipole energy = permanentRealSpaceEnergy + permanentSelfEnergy + permanentReciprocalEnergy.

permanentRealSpaceEnergy

protected double permanentRealSpaceEnergy

permanentSelfEnergy

protected double permanentSelfEnergy

permanentReciprocalEnergy

protected double permanentReciprocalEnergy

polarizationEnergy

protected double polarizationEnergy

Polarization energy = inducedRealSpaceEnergy + inducedSelfEnergy + inducedReciprocalEnergy.

inducedRealSpaceEnergy

protected double inducedRealSpaceEnergy

inducedSelfEnergy

protected double inducedSelfEnergy

inducedReciprocalEnergy

protected double inducedReciprocalEnergy

scfAlgorithm

protected SCFAlgorithm scfAlgorithm

LambdaDefaults

public final ParticleMeshEwald.LambdaFactors LambdaDefaults

The defaults are effectively final, as the implementation of setFactors in the base class is always a no-op.

Constructor Details

ParticleMeshEwald

public ParticleMeshEwald(Atom[] atoms,
 int[] molecule,
 ForceField forceField,
 Crystal crystal,
 NeighborList neighborList,
 ForceField.ELEC_FORM elecForm,
 double ewaldCutoff,
 double gkCutoff,
 ParallelTeam parallelTeam)

ParticleMeshEwald constructor.

Parameters:

atoms - the Atom array to do electrostatics on.

molecule - the molecule number for each atom.

forceField - the ForceField the defines the electrostatics parameters.

crystal - The boundary conditions.

neighborList - The NeighborList for both van der Waals and PME.

elecForm - The electrostatics functional form.

ewaldCutoff - The Ewald real space cutoff.

gkCutoff - The generalized Kirkwood cutoff.

parallelTeam - A ParallelTeam that delegates parallelization.

Method Details

getElecForm

public ForceField.ELEC_FORM getElecForm()

Returns the ELEC_FORM.

getLambdaTerm

public boolean getLambdaTerm()

If true, there are alchemical atoms impacted by the lambda state variable.

Returns:

True if there are alchemical atoms impacted by the lambda state variable.

getAlchemicalParameters

public AlchemicalParameters getAlchemicalParameters()

Return the PME AlchemicalParameters.

computeInduceDipoleField

public void computeInduceDipoleField()

destroy

public void destroy()

energy

public double energy(boolean gradient,
 boolean print)

Calculate the PME electrostatic energy.

Parameters:

gradient - If true, the gradient will be calculated.

print - If true, extra logging is enabled.

Returns:

return the total electrostatic energy (permanent + polarization).

expandInducedDipoles

public void expandInducedDipoles()

getAxisAtoms

public int[][] getAxisAtoms()

getCavitationEnergy

public double getCavitationEnergy()

getCoordinates

public double[][][] getCoordinates()

getDispersionEnergy

public double getDispersionEnergy()

getEwaldCoefficient

public double getEwaldCoefficient()

getEwaldCutoff

public double getEwaldCutoff()

getGK

public GeneralizedKirkwood getGK()

getGKEnergy

public double getGKEnergy()

getGeneralizedKirkwoodEnergy.

Returns:

a double.

getGKInteractions

public int getGKInteractions()

getGKInteractions

Returns:

The number of GK interactions.

getInteractions

public int getInteractions()

Getter for the field interactions.

Returns:

The number of PME interactions.

getLambda

public double getLambda()

Get the current value of the state variable.

Get the current lambda scale value.

Specified by:

getLambda in interface LambdaInterface

Returns:

state

setLambda

public void setLambda(double lambda)

Set the current value of the state variable. May be ignored if lambda is not being applied.

Set the electrostatic lambda scaling factor.

Specified by:

setLambda in interface LambdaInterface

Parameters:

lambda - a double.

getPermanentEnergy

public double getPermanentEnergy()

getIndRealEnergy

public double getIndRealEnergy()

getIndRealEnergy.

Returns:

a double.

getIndRecipEnergy

public double getIndRecipEnergy()

getIndRecipEnergy.

Returns:

a double.

getIndSelfEnergy

public double getIndSelfEnergy()

getIndSelfEnergy.

Returns:

a double.

getPermSelfEnergy

public double getPermSelfEnergy()

getPermSelfEnergy.

Returns:

a double.

getPermRealEnergy

public double getPermRealEnergy()

getPermRecipEnergy

public double getPermRecipEnergy()

getPolarEps

public double getPolarEps()

getPolarization11

public int[][] getPolarization11()

getPolarization12

public int[][] getPolarization12()

getPolarization13

public int[][] getPolarization13()

getPolarizationEnergy

public double getPolarizationEnergy()

Getter for the field polarizationEnergy.

Returns:

a double.

getPolarizationType

public Polarization getPolarizationType()

getReciprocalSpace

public ReciprocalSpace getReciprocalSpace()

getScale14

public double getScale14()

getSolvationEnergy

public double getSolvationEnergy()

getGKEnergy

Returns:

a double.

getMultipoleType

public MultipoleType getMultipoleType(int i)

Get the MultipoleType for Atom i.

Parameters:

i - The atom index.

Returns:

The MultipoleType.

getPolarizeType

public PolarizeType getPolarizeType(int i)

Get the PolarizeType for Atom i.

Parameters:

i - The atom index.

Returns:

The PolarizeType.

getd2EdL2

public double getd2EdL2()

Get the 2nd partial derivative of the energy with respect to lambda.

Specified by:

getd2EdL2 in interface LambdaInterface

Returns:

d2EdL2

getdEdL

public double getdEdL()

Get the partial derivative of the energy with respect to lambda.

Specified by:

getdEdL in interface LambdaInterface

Returns:

dEdL

getdEdXdL

public void getdEdXdL(double[] gradient)

Get the gradient of dEdL with respect to each parameter.

Specified by:

getdEdXdL in interface LambdaInterface

Parameters:

gradient - - A double array of length the number of parameters in the model (commonly 3 * number of atoms).

setAtoms

public void setAtoms(Atom[] atoms,
 int[] molecule)

setCrystal

public void setCrystal(Crystal crystal)

getTotalMultipoleEnergy

public double getTotalMultipoleEnergy()

Getter for the field totalMultipoleEnergy.

Returns:

a double.

setPolarization

public void setPolarization(Polarization set)

Setter for the field polarization.

Parameters:

set - a Polarization object.

assignPolarizationGroups

protected void assignPolarizationGroups()

AssignPolarizationGroups.

computeMoments

public void computeMoments(Atom[] activeAtoms,
 boolean forceEnergy)

Compute multipole moments for an array of atoms.

Parameters:

activeAtoms - Atom array to consider.

forceEnergy - Force calculation of the electrostatic energy (rotate multipoles, perform SCF).

attachExtendedSystem

public void attachExtendedSystem(ExtendedSystem system)

Attach system with extended variable such as titrations.

Parameters:

system - a ExtendedSystem object.