Package ffx.numerics.multipole

Class AmoebaPlusDampTensorGlobal

java.lang.Object

ffx.numerics.multipole.MultipoleTensor

ffx.numerics.multipole.CoulombTensorGlobal

ffx.numerics.multipole.AmoebaPlusDampTensorGlobal

public class AmoebaPlusDampTensorGlobal
extends CoulombTensorGlobal

The AmoebaPlusDampTensorGlobal class computes derivatives of damping via recursion to order <= 2 for Cartesian multipoles defined in AMOEBA+. These are the nuclear charge interactions with permanent multipoles. The zeroth order damp term is 1-exp(-alpha*r).

Since:

1.0

Author:

Matthew J. Speranza

See Also:

• Matt Challacombe, Eric Schwegler and Jan Almlof, Modern developments in Hartree-Fock theory: Fast methods for computing the Coulomb matrix. Computational Chemistry: Review of Current Trends. pp. 53-107, Ed. J. Leczszynski, World Scientifc, 1996.
• Rackers, Wang, Liu, Piquemal, Ren and Ponder, An optimized charge penetration model for use with the AMOEBA force field. Phys. Chem. Chem. Phys., 2017,19, 276-291.

Field Summary

Fields inherited from class ffx.numerics.multipole.MultipoleTensor

coordinates, coulombSource, il, im, in, o1, operator, order, R, r2, size, t000, T000, t001, t002, t003, t004, t005, t006, t010, t011, t012, t013, t014, t015, t020, t021, t022, t023, t024, t030, t031, t032, t033, t040, t041, t042, t050, t051, t060, t100, t101, t102, t103, t104, t105, t110, t111, t112, t113, t114, t120, t121, t122, t123, t130, t131, t132, t140, t141, t150, t200, t201, t202, t203, t204, t210, t211, t212, t213, t220, t221, t222, t230, t231, t240, t300, t301, t302, t303, t310, t311, t312, t320, t321, t330, t400, t401, t402, t410, t411, t420, t500, t501, t510, t600, work, x, y, z

Constructor Summary

Constructors

Constructor	Description
AmoebaPlusDampTensorGlobal(int order, double alpha1, double alpha2)	Constructor for CoulombTensorGlobal.
AmoebaPlusDampTensorGlobal(int order, double alpha1, double alpha2, double ewaldA)	Constructor for CoulombTensorGlobal.

Method Summary

Modifier and Type	Method	Description
double	coreInteraction(PolarizableMultipole mI, PolarizableMultipole mK)	Terms 1, 2, 3 in Eq. 5 of AMOEBA+ paper.
double	coreInteractionAndGradient(PolarizableMultipole mI, PolarizableMultipole mK, double[] Gi, double[] Gk)	Compute the core interaction and gradient between two sites.
protected static void	dampSource(double alpha, double R, double[] T000)	Generate source terms for the Challacombe et al. recursion.
protected void	source(double[] T000)	Generate source terms for the Challacombe et al. recursion.

Methods inherited from class ffx.numerics.multipole.CoulombTensorGlobal

chargeIPotentialAtK, chargeKPotentialAtI, codeTensorRecursion, codeVectorTensorRecursion, codeVectorTensorRecursion, dipoleIPotentialAtK, dipoleKPotentialAtI, getd2EdZ2, getdEdZ, multipoleIPotentialAtK, multipoleKPotentialAtI, noStorageRecursion, noStorageRecursion, order1, order2, order3, order4, order5, order6, quadrupoleIPotentialAtK, quadrupoleKPotentialAtI, recursion, recursion, setR, Tlmnj

Methods inherited from class ffx.numerics.multipole.MultipoleTensor

codePotentialMultipoleI, codePotentialMultipoleISIMD, codePotentialMultipoleK, codePotentialMultipoleKSIMD, contractMultipoleI, dipoleTorque, generateTensor, generateTensor, getTensor, log, multipoleEnergy, multipoleEnergy, multipoleEnergyAndGradient, multipoleGradient, multipoleTorque, polarizationEnergy, polarizationEnergy, polarizationEnergyAndGradient, polarizationEnergyS, potentialMultipoleI, quadrupoleTorque, setR, setTensor, ti, totalEnergy

Methods inherited from class java.lang.Object

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

Constructor Details

AmoebaPlusDampTensorGlobal

public AmoebaPlusDampTensorGlobal(int order,
 double alpha1,
 double alpha2)

Constructor for CoulombTensorGlobal.

Parameters:

order - The order of the tensor.

alpha1 - The first damping parameter.

alpha2 - The second damping parameter.

AmoebaPlusDampTensorGlobal

public AmoebaPlusDampTensorGlobal(int order,
 double alpha1,
 double alpha2,
 double ewaldA)

Constructor for CoulombTensorGlobal.

Parameters:

order - The order of the tensor.

alpha1 - The first damping parameter.

alpha2 - The second damping parameter.

ewaldA - The Ewald damping parameter.

Method Details

source

protected void source(double[] T000)

Generate source terms for the Challacombe et al. recursion.

Overrides:

source in class CoulombTensorGlobal

Parameters:

T000 - Location to store the source terms.

dampSource

protected static void dampSource(double alpha,
 double R,
 double[] T000)

Generate source terms for the Challacombe et al. recursion.

Parameters:

alpha - adjustable damping parameter

R - The separation distance.

T000 - Location to store the source terms.

coreInteraction

public double coreInteraction(PolarizableMultipole mI,
 PolarizableMultipole mK)

Terms 1, 2, 3 in Eq. 5 of AMOEBA+ paper. Uses a swap of alpha -> alpha2 that takes place in the first call to the source method to generate a new tensor with the second alpha.

Parameters:

mI - The multipole moment at site I.

mK - The multipole moment at site K.

Returns:

energy.

coreInteractionAndGradient

public double coreInteractionAndGradient(PolarizableMultipole mI,
 PolarizableMultipole mK,
 double[] Gi,
 double[] Gk)

Compute the core interaction and gradient between two sites.

Parameters:

mI - The multipole moment at site I.

mK - The multipole moment at site K.

Gi - The gradient at site I.

Gk - The gradient at site K.

Returns:

energy.