Package ffx.numerics.multipole

Class GKTensorGlobalSIMD

java.lang.Object

ffx.numerics.multipole.MultipoleTensorSIMD

ffx.numerics.multipole.CoulombTensorGlobalSIMD

ffx.numerics.multipole.GKTensorGlobalSIMD

public class GKTensorGlobalSIMD
extends CoulombTensorGlobalSIMD

The GeneralizedKirkwoodTensor class contains utilities for generated Generalized Kirkwood interaction tensors.

Since:

1.0

Author:

Michael J. Schnieders

Field Summary

Fields

Modifier and Type	Field	Description
protected final GKMultipoleOrder	multipoleOrder	The GK tensor can be constructed for monopoles (GB), dipoles or quadrupoles.

Fields inherited from class ffx.numerics.multipole.MultipoleTensorSIMD

coordinates, coulombSource, E000, E001, E002, E003, E010, E011, E012, E020, E021, E030, E100, E101, E102, E110, E111, E120, E200, E201, E210, E300, il, im, in, o1, operator, order, R, R000, R001, R002, R003, R004, R005, R006, R010, R011, R012, R013, R014, R015, R020, R021, R022, R023, R024, R030, R031, R032, R033, R040, R041, R042, R050, R051, R060, R100, R101, R102, R103, R104, R105, R110, R111, R112, R113, R114, R120, R121, R122, R123, R130, R131, R132, R140, R141, R150, r2, R200, R201, R202, R203, R204, R210, R211, R212, R213, R220, R221, R222, R230, R231, R240, R300, R301, R302, R303, R310, R311, R312, R320, R321, R330, R400, R401, R402, R410, R411, R420, R500, R501, R510, R600, size, 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
GKTensorGlobalSIMD(GKMultipoleOrder multipoleOrder, int order, GKSourceSIMD gkSource, double Eh, double Es)	Construct a new GKTensorGlobal object.

Method Summary

Modifier and Type	Method	Description
protected DoubleVector	dipoleEnergyAndGradient(PolarizableMultipoleSIMD mI, PolarizableMultipoleSIMD mK, DoubleVector[] Gi, DoubleVector[] Gk, DoubleVector[] Ti, DoubleVector[] Tk)	Permanent multipole energy and gradient using the GK dipole tensor.
DoubleVector	dipolePolarizationEnergyAndGradient(PolarizableMultipoleSIMD mI, PolarizableMultipoleSIMD mK, DoubleVector mutualMask, DoubleVector[] Gi, DoubleVector[] Ti, DoubleVector[] Tk)	Dipole Polarization Energy and Gradient.
protected DoubleVector	monopoleEnergyAndGradient(PolarizableMultipoleSIMD mI, PolarizableMultipoleSIMD mK, DoubleVector[] Gi, DoubleVector[] Gk, DoubleVector[] Ti, DoubleVector[] Tk)	Permanent multipole energy and gradient using the GK monopole tensor.
DoubleVector	monopolePolarizationEnergyAndGradient(PolarizableMultipoleSIMD mI, PolarizableMultipoleSIMD mK, DoubleVector[] Gi)	Monopole Polarization Energy and Gradient.
DoubleVector	multipoleEnergy(PolarizableMultipoleSIMD mI, PolarizableMultipoleSIMD mK)	GK Permanent multipole energy.
DoubleVector	multipoleEnergyAndGradient(PolarizableMultipoleSIMD mI, PolarizableMultipoleSIMD mK, DoubleVector[] Gi, DoubleVector[] Gk, DoubleVector[] Ti, DoubleVector[] Tk)	GK Permanent multipole energy and gradient.
DoubleVector	multipoleEnergyBornGrad(PolarizableMultipoleSIMD mI, PolarizableMultipoleSIMD mK)	GK Permanent multipole Born grad.
DoubleVector	mutualPolarizationEnergyBornGrad(PolarizableMultipoleSIMD mI, PolarizableMultipoleSIMD mK)	GK Mutual Polarization Contribution to the Born grad.
DoubleVector	polarizationEnergy(PolarizableMultipoleSIMD mI, PolarizableMultipoleSIMD mK)	GK Polarization Energy.
DoubleVector	polarizationEnergy(PolarizableMultipoleSIMD mI, PolarizableMultipoleSIMD mK, DoubleVector scaleEnergy)	GK Polarization Energy.
DoubleVector	polarizationEnergyAndGradient(PolarizableMultipoleSIMD mI, PolarizableMultipoleSIMD mK, DoubleVector inductionMask, DoubleVector energyMask, DoubleVector mutualMask, DoubleVector[] Gi, DoubleVector[] Ti, DoubleVector[] Tk)	Polarization Energy and Gradient.
DoubleVector	polarizationEnergyBorn(PolarizableMultipoleSIMD mI, PolarizableMultipoleSIMD mK)	GK Polarization Energy.
DoubleVector	polarizationEnergyBornGrad(PolarizableMultipoleSIMD mI, PolarizableMultipoleSIMD mK)	GK Direct Polarization Born grad.
protected DoubleVector	quadrupoleEnergyAndGradient(PolarizableMultipoleSIMD mI, PolarizableMultipoleSIMD mK, DoubleVector[] Gi, DoubleVector[] Gk, DoubleVector[] Ti, DoubleVector[] Tk)	Permanent multipole energy and gradient using the GK quadrupole tensor.
DoubleVector	quadrupolePolarizationEnergyAndGradient(PolarizableMultipoleSIMD mI, PolarizableMultipoleSIMD mK, DoubleVector[] Gi, DoubleVector[] Ti, DoubleVector[] Tk)	Quadrupole Polarization Energy and Gradient.
protected void	source(DoubleVector[] work)	Generate source terms for the Kirkwood version of the Challacombe et al. recursion.

Methods inherited from class ffx.numerics.multipole.CoulombTensorGlobalSIMD

chargeIPotentialAtK, chargeKPotentialAtI, dipoleIPotentialAtK, dipoleKPotentialAtI, multipoleIPotentialAtK, multipoleKPotentialAtI, order1, order2, order3, order4, order5, order6, quadrupoleIPotentialAtK, quadrupoleKPotentialAtI, setR

Methods inherited from class ffx.numerics.multipole.MultipoleTensorSIMD

dipoleTorque, generateTensor, getSource, multipoleEnergy, multipoleGradient, multipoleTorque, polarizationEnergy, polarizationEnergyS, quadrupoleTorque, setR, ti

Methods inherited from class java.lang.Object

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

Field Details

multipoleOrder

protected final GKMultipoleOrder multipoleOrder

The GK tensor can be constructed for monopoles (GB), dipoles or quadrupoles.

Constructor Details

GKTensorGlobalSIMD

public GKTensorGlobalSIMD(GKMultipoleOrder multipoleOrder,
 int order,
 GKSourceSIMD gkSource,
 double Eh,
 double Es)

Construct a new GKTensorGlobal object.

Parameters:

multipoleOrder - The multipole order.

order - The number of derivatives to complete.

gkSource - Generate the source terms for the GK recurrence.

Eh - Homogeneous dielectric constant.

Es - Solvent dielectric constant.

Method Details

multipoleEnergy

public DoubleVector multipoleEnergy(PolarizableMultipoleSIMD mI,
 PolarizableMultipoleSIMD mK)

GK Permanent multipole energy.

Overrides:

multipoleEnergy in class MultipoleTensorSIMD

Parameters:

mI - PolarizableMultipole at site I.

mK - PolarizableMultipole at site K.

Returns:

a double.

multipoleEnergyAndGradient

public DoubleVector multipoleEnergyAndGradient(PolarizableMultipoleSIMD mI,
 PolarizableMultipoleSIMD mK,
 DoubleVector[] Gi,
 DoubleVector[] Gk,
 DoubleVector[] Ti,
 DoubleVector[] Tk)

GK Permanent multipole energy and gradient.

Overrides:

multipoleEnergyAndGradient in class MultipoleTensorSIMD

Parameters:

mI - PolarizableMultipole at site I.

mK - PolarizableMultipole at site K.

Gi - Coordinate gradient at site I.

Gk - Coordinate gradient at site K.

Ti - Torque at site I.

Tk - Torque at site K.

Returns:

the permanent multipole GK energy.

monopoleEnergyAndGradient

protected DoubleVector monopoleEnergyAndGradient(PolarizableMultipoleSIMD mI,
 PolarizableMultipoleSIMD mK,
 DoubleVector[] Gi,
 DoubleVector[] Gk,
 DoubleVector[] Ti,
 DoubleVector[] Tk)

Permanent multipole energy and gradient using the GK monopole tensor.

Parameters:

mI - PolarizableMultipole at site I.

mK - PolarizableMultipole at site K.

Gi - Coordinate gradient at site I.

Gk - Coordinate gradient at site K.

Ti - Torque at site I.

Tk - Torque at site K.

Returns:

the permanent multipole GK energy.

dipoleEnergyAndGradient

protected DoubleVector dipoleEnergyAndGradient(PolarizableMultipoleSIMD mI,
 PolarizableMultipoleSIMD mK,
 DoubleVector[] Gi,
 DoubleVector[] Gk,
 DoubleVector[] Ti,
 DoubleVector[] Tk)

Permanent multipole energy and gradient using the GK dipole tensor.

Parameters:

mI - PolarizableMultipole at site I.

mK - PolarizableMultipole at site K.

Gi - Coordinate gradient at site I.

Gk - Coordinate gradient at site K.

Ti - Torque at site I.

Tk - Torque at site K.

Returns:

the permanent multipole GK energy.

quadrupoleEnergyAndGradient

protected DoubleVector quadrupoleEnergyAndGradient(PolarizableMultipoleSIMD mI,
 PolarizableMultipoleSIMD mK,
 DoubleVector[] Gi,
 DoubleVector[] Gk,
 DoubleVector[] Ti,
 DoubleVector[] Tk)

Permanent multipole energy and gradient using the GK quadrupole tensor.

Parameters:

mI - PolarizableMultipole at site I.

mK - PolarizableMultipole at site K.

Gi - Coordinate gradient at site I.

Gk - Coordinate gradient at site K.

Ti - Torque at site I.

Tk - Torque at site K.

Returns:

the permanent multipole GK energy.

multipoleEnergyBornGrad

public DoubleVector multipoleEnergyBornGrad(PolarizableMultipoleSIMD mI,
 PolarizableMultipoleSIMD mK)

GK Permanent multipole Born grad.

Parameters:

mI - PolarizableMultipole at site I.

mK - PolarizableMultipole at site K.

Returns:

a double.

polarizationEnergy

public DoubleVector polarizationEnergy(PolarizableMultipoleSIMD mI,
 PolarizableMultipoleSIMD mK,
 DoubleVector scaleEnergy)

GK Polarization Energy.

Parameters:

mI - PolarizableMultipole at site I.

mK - PolarizableMultipole at site K.

scaleEnergy - This is ignored, since masking/scaling is not applied to GK interactions (everything is intermolecular).

Returns:

a double.

polarizationEnergy

public DoubleVector polarizationEnergy(PolarizableMultipoleSIMD mI,
 PolarizableMultipoleSIMD mK)

GK Polarization Energy.

Parameters:

mI - PolarizableMultipole at site I.

mK - PolarizableMultipole at site K.

Returns:

a double.

polarizationEnergyBorn

public DoubleVector polarizationEnergyBorn(PolarizableMultipoleSIMD mI,
 PolarizableMultipoleSIMD mK)

GK Polarization Energy.

Parameters:

mI - PolarizableMultipole at site I.

mK - PolarizableMultipole at site K.

Returns:

a double.

polarizationEnergyAndGradient

public DoubleVector polarizationEnergyAndGradient(PolarizableMultipoleSIMD mI,
 PolarizableMultipoleSIMD mK,
 DoubleVector inductionMask,
 DoubleVector energyMask,
 DoubleVector mutualMask,
 DoubleVector[] Gi,
 DoubleVector[] Ti,
 DoubleVector[] Tk)

Polarization Energy and Gradient.

Overrides:

polarizationEnergyAndGradient in class MultipoleTensorSIMD

Parameters:

mI - PolarizableMultipole at site I.

mK - PolarizableMultipole at site K.

inductionMask - This is ignored, since masking/scaling is not applied to GK interactions (everything is intermolecular).

energyMask - This is ignored, since masking/scaling is not applied to GK interactions (everything is intermolecular).

mutualMask - This should be set to zero for direction polarization.

Gi - an array of

invalid reference

double

objects.

Ti - an array of

invalid reference

double

objects.

Tk - an array of

invalid reference

double

objects.

Returns:

a double.

monopolePolarizationEnergyAndGradient

public DoubleVector monopolePolarizationEnergyAndGradient(PolarizableMultipoleSIMD mI,
 PolarizableMultipoleSIMD mK,
 DoubleVector[] Gi)

Monopole Polarization Energy and Gradient.

Parameters:

mI - PolarizableMultipole at site I.

mK - PolarizableMultipole at site K.

Gi - an array of

invalid reference

double

objects.

Returns:

a double.

dipolePolarizationEnergyAndGradient

public DoubleVector dipolePolarizationEnergyAndGradient(PolarizableMultipoleSIMD mI,
 PolarizableMultipoleSIMD mK,
 DoubleVector mutualMask,
 DoubleVector[] Gi,
 DoubleVector[] Ti,
 DoubleVector[] Tk)

Dipole Polarization Energy and Gradient.

Parameters:

mI - PolarizableMultipole at site I.

mK - PolarizableMultipole at site K.

mutualMask - This should be set to zero for direction polarization.

Gi - an array of

invalid reference

double

objects.

Ti - an array of

invalid reference

double

objects.

Tk - an array of

invalid reference

double

objects.

Returns:

a double.

quadrupolePolarizationEnergyAndGradient

public DoubleVector quadrupolePolarizationEnergyAndGradient(PolarizableMultipoleSIMD mI,
 PolarizableMultipoleSIMD mK,
 DoubleVector[] Gi,
 DoubleVector[] Ti,
 DoubleVector[] Tk)

Quadrupole Polarization Energy and Gradient.

Parameters:

mI - PolarizableMultipole at site I.

mK - PolarizableMultipole at site K.

Gi - an array of

invalid reference

double

objects.

Ti - an array of

invalid reference

double

objects.

Tk - an array of

invalid reference

double

objects.

Returns:

a double.

polarizationEnergyBornGrad

public DoubleVector polarizationEnergyBornGrad(PolarizableMultipoleSIMD mI,
 PolarizableMultipoleSIMD mK)

GK Direct Polarization Born grad.

Parameters:

mI - PolarizableMultipole at site I.

mK - PolarizableMultipole at site K.

Returns:

Partial derivative of the Polarization energy with respect to a Born grad.

mutualPolarizationEnergyBornGrad

public DoubleVector mutualPolarizationEnergyBornGrad(PolarizableMultipoleSIMD mI,
 PolarizableMultipoleSIMD mK)

GK Mutual Polarization Contribution to the Born grad.

Parameters:

mI - PolarizableMultipole at site I.

mK - PolarizableMultipole at site K.

Returns:

Mutual Polarization contribution to the partial derivative with respect to a Born grad.

source

protected void source(DoubleVector[] work)

Generate source terms for the Kirkwood version of the Challacombe et al. recursion.

Overrides:

source in class CoulombTensorGlobalSIMD

Parameters:

work - Location to store the source terms.