Skip to content

GitLab

"vscode:/vscode.git/clone" did not exist on "65e2a700f0330f3fb1c26f49a0250d1f9d0ac1e3"
Commit 967968ad authored by Mark Friedrichs's avatar Mark Friedrichs
Browse files

Code for AmoebaReferenceHarmonicInPlaneAngleForce

parent 4868314a
Show whitespace changes
Inline Side-by-side
Showing with 450 additions and 91 deletions
plugins/amoeba/platforms/reference/src/AmoebaReferenceKernelFactory.cpp
View file @ 967968ad
......@@ -41,8 +41,8 @@ fprintf( stderr,"In registerKernelFactories AmoebaReferenceKernelFactory\n" ); f
AmoebaReferenceKernelFactory* factory = new AmoebaReferenceKernelFactory();
platform.registerKernelFactory(CalcAmoebaHarmonicBondForceKernel::Name(), factory);
platform.registerKernelFactory(CalcAmoebaHarmonicAngleForceKernel::Name(), factory);
/*
platform.registerKernelFactory(CalcAmoebaHarmonicInPlaneAngleForceKernel::Name(), factory);
/*
platform.registerKernelFactory(CalcAmoebaTorsionForceKernel::Name(), factory);
platform.registerKernelFactory(CalcAmoebaPiTorsionForceKernel::Name(), factory);
platform.registerKernelFactory(CalcAmoebaStretchBendForceKernel::Name(), factory);
......@@ -68,10 +68,10 @@ KernelImpl* AmoebaReferenceKernelFactory::createKernelImpl(std::string name, con
if (name == CalcAmoebaHarmonicAngleForceKernel::Name())
return new ReferenceCalcAmoebaHarmonicAngleForceKernel(name, platform, context.getSystem());
/*
if (name == CalcAmoebaHarmonicInPlaneAngleForceKernel::Name())
return new ReferenceCalcAmoebaHarmonicInPlaneAngleForceKernel(name, platform, context.getSystem());
/*
if (name == CalcAmoebaTorsionForceKernel::Name())
return new ReferenceCalcAmoebaTorsionForceKernel(name, platform, context.getSystem());
......
plugins/amoeba/platforms/reference/src/AmoebaReferenceKernels.cpp
View file @ 967968ad
......@@ -27,6 +27,7 @@
#include "AmoebaReferenceKernels.h"
#include "AmoebaReferenceHarmonicBondForce.h"
#include "AmoebaReferenceHarmonicAngleForce.h"
#include "AmoebaReferenceHarmonicInPlaneAngleForce.h"
#include "ReferencePlatform.h"
#include "openmm/internal/ContextImpl.h"
//#include "internal/AmoebaMultipoleForceImpl.h"
......@@ -155,48 +156,57 @@ double ReferenceCalcAmoebaHarmonicAngleForceKernel::execute(ContextImpl& context
return static_cast<double>(energy);
}
//ReferenceCalcAmoebaHarmonicInPlaneAngleForceKernel::ReferenceCalcAmoebaHarmonicInPlaneAngleForceKernel(std::string name, const Platform& platform, System& system) :
// CalcAmoebaHarmonicInPlaneAngleForceKernel(name, platform), system(system) {
//}
//
//ReferenceCalcAmoebaHarmonicInPlaneAngleForceKernel::~ReferenceCalcAmoebaHarmonicInPlaneAngleForceKernel() {
//}
//
//void ReferenceCalcAmoebaHarmonicInPlaneAngleForceKernel::initialize(const System& system, const AmoebaHarmonicInPlaneAngleForce& force) {
//
// numAngles = force.getNumAngles();
//
// std::vector<int> particle1(numAngles);
// std::vector<int> particle2(numAngles);
// std::vector<int> particle3(numAngles);
// std::vector<int> particle4(numAngles);
// std::vector<RealOpenMM> angle(numAngles);
// std::vector<RealOpenMM> k(numAngles);
//
// for (int i = 0; i < numAngles; i++) {
// double angleValue, kQuadratic;
// force.getAngleParameters(i, particle1[i], particle2[i], particle3[i], particle4[i], angleValue, kQuadratic);
// //angle[i] = static_cast<RealOpenMM>( (angleValue*RadiansToDegrees) );
// angle[i] = static_cast<RealOpenMM>( angleValue );
// k[i] = static_cast<RealOpenMM>( kQuadratic );
// }
///*
// gpuSetAmoebaInPlaneAngleParameters(data.getAmoebaGpu(), particle1, particle2, particle3, particle4, angle, k,
// static_cast<RealOpenMM>( force.getAmoebaGlobalHarmonicInPlaneAngleCubic()),
// static_cast<RealOpenMM>( force.getAmoebaGlobalHarmonicInPlaneAngleQuartic()),
// static_cast<RealOpenMM>( force.getAmoebaGlobalHarmonicInPlaneAnglePentic()),
// static_cast<RealOpenMM>( force.getAmoebaGlobalHarmonicInPlaneAngleSextic() ) );
//*/
//
//}
//
//double ReferenceCalcAmoebaHarmonicInPlaneAngleForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
// if( data.getAmoebaLocalForcesKernel() == this ){
// computeAmoebaLocalForces( data );
// }
// return 0.0;
//}
//
ReferenceCalcAmoebaHarmonicInPlaneAngleForceKernel::ReferenceCalcAmoebaHarmonicInPlaneAngleForceKernel(std::string name, const Platform& platform, System& system) :
CalcAmoebaHarmonicInPlaneAngleForceKernel(name, platform), system(system) {
}
ReferenceCalcAmoebaHarmonicInPlaneAngleForceKernel::~ReferenceCalcAmoebaHarmonicInPlaneAngleForceKernel() {
}
void ReferenceCalcAmoebaHarmonicInPlaneAngleForceKernel::initialize(const System& system, const AmoebaHarmonicInPlaneAngleForce& force) {
numAngles = force.getNumAngles();
for (int ii = 0; ii < numAngles; ii++) {
int particle1Index, particle2Index, particle3Index, particle4Index;
double angleValue, k;
force.getAngleParameters(ii, particle1Index, particle2Index, particle3Index, particle4Index, angleValue, k);
particle1.push_back( particle1Index );
particle2.push_back( particle2Index );
particle3.push_back( particle3Index );
particle4.push_back( particle4Index );
angle.push_back( static_cast<RealOpenMM>( angleValue ) );
kQuadratic.push_back( static_cast<RealOpenMM>( k ) );
}
globalHarmonicInPlaneAngleCubic = static_cast<RealOpenMM>(force.getAmoebaGlobalHarmonicInPlaneAngleCubic());
globalHarmonicInPlaneAngleQuartic = static_cast<RealOpenMM>(force.getAmoebaGlobalHarmonicInPlaneAngleQuartic());
globalHarmonicInPlaneAnglePentic = static_cast<RealOpenMM>(force.getAmoebaGlobalHarmonicInPlaneAnglePentic());
globalHarmonicInPlaneAngleSextic = static_cast<RealOpenMM>(force.getAmoebaGlobalHarmonicInPlaneAngleSextic());
}
double ReferenceCalcAmoebaHarmonicInPlaneAngleForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
RealOpenMM** posData = extractPositions(context);
RealOpenMM** forceData = extractForces(context);
RealOpenMM energy = 0.0;
for (unsigned int ii = 0; ii < numAngles; ii++) {
int particle1Index = particle1[ii];
int particle2Index = particle2[ii];
int particle3Index = particle3[ii];
int particle4Index = particle4[ii];
RealOpenMM idealAngle = angle[ii];
RealOpenMM angleK = kQuadratic[ii];
RealOpenMM* forces[4];
forces[0] = forceData[particle1Index];
forces[1] = forceData[particle2Index];
forces[2] = forceData[particle3Index];
forces[3] = forceData[particle4Index];
energy += AmoebaReferenceHarmonicInPlaneAngleForce::calculateForceAndEnergy(
posData[particle1Index], posData[particle2Index], posData[particle3Index], posData[particle4Index],
idealAngle, angleK, globalHarmonicInPlaneAngleCubic, globalHarmonicInPlaneAngleQuartic,
globalHarmonicInPlaneAnglePentic, globalHarmonicInPlaneAngleSextic, forces );
}
return static_cast<double>(energy);
}
//ReferenceCalcAmoebaTorsionForceKernel::ReferenceCalcAmoebaTorsionForceKernel(std::string name, const Platform& platform, System& system) :
// CalcAmoebaTorsionForceKernel(name, platform), system(system) {
// data.incrementKernelCount();
......
plugins/amoeba/platforms/reference/src/AmoebaReferenceKernels.h
View file @ 967968ad
......@@ -106,41 +106,50 @@ private:
System& system;
};
// /**
// * This kernel is invoked by AmoebaHarmonicInPlaneAngleForce to calculate the forces acting on the system and the energy of the system.
// */
// class ReferenceCalcAmoebaHarmonicInPlaneAngleForceKernel : public CalcAmoebaHarmonicInPlaneAngleForceKernel {
// public:
// ReferenceCalcAmoebaHarmonicInPlaneAngleForceKernel(std::string name, const Platform& platform, AmoebaReferenceData& data, System& system);
// ~ReferenceCalcAmoebaHarmonicInPlaneAngleForceKernel();
// /**
// * Initialize the kernel.
// *
// * @param system the System this kernel will be applied to
// * @param force the AmoebaHarmonicInPlaneAngleForce this kernel will be used for
// */
// void initialize(const System& system, const AmoebaHarmonicInPlaneAngleForce& force);
// /**
// * Execute the kernel to calculate the forces and/or energy.
// *
// * @param context the context in which to execute this kernel
// * @param includeForces true if forces should be calculated
// * @param includeEnergy true if the energy should be calculated
// * @return the potential energy due to the force
// */
// double execute(ContextImpl& context, bool includeForces, bool includeEnergy);
// private:
// int numAngles;
// AmoebaReferenceData& data;
// System& system;
// };
//
/**
* This kernel is invoked by AmoebaHarmonicInPlaneAngleForce to calculate the forces acting on the system and the energy of the system.
*/
class ReferenceCalcAmoebaHarmonicInPlaneAngleForceKernel : public CalcAmoebaHarmonicInPlaneAngleForceKernel {
public:
ReferenceCalcAmoebaHarmonicInPlaneAngleForceKernel(std::string name, const Platform& platform, System& system);
~ReferenceCalcAmoebaHarmonicInPlaneAngleForceKernel();
/**
* Initialize the kernel.
*
* @param system the System this kernel will be applied to
* @param force the AmoebaHarmonicInPlaneAngleForce this kernel will be used for
*/
void initialize(const System& system, const AmoebaHarmonicInPlaneAngleForce& force);
/**
* Execute the kernel to calculate the forces and/or energy.
*
* @param context the context in which to execute this kernel
* @param includeForces true if forces should be calculated
* @param includeEnergy true if the energy should be calculated
* @return the potential energy due to the force
*/
double execute(ContextImpl& context, bool includeForces, bool includeEnergy);
private:
int numAngles;
std::vector<int> particle1;
std::vector<int> particle2;
std::vector<int> particle3;
std::vector<int> particle4;
std::vector<RealOpenMM> angle;
std::vector<RealOpenMM> kQuadratic;
RealOpenMM globalHarmonicInPlaneAngleCubic;
RealOpenMM globalHarmonicInPlaneAngleQuartic;
RealOpenMM globalHarmonicInPlaneAnglePentic;
RealOpenMM globalHarmonicInPlaneAngleSextic;
System& system;
};
// /**
// * This kernel is invoked by AmoebaTorsionForce to calculate the forces acting on the system and the energy of the system.
// */
// class ReferenceCalcAmoebaTorsionForceKernel : public CalcAmoebaTorsionForceKernel {
// public:
// ReferenceCalcAmoebaTorsionForceKernel(std::string name, const Platform& platform, AmoebaReferenceData& data, System& system);
// ReferenceCalcAmoebaTorsionForceKernel(std::string name, const Platform& platform, System& system);
// ~ReferenceCalcAmoebaTorsionForceKernel();
// /**
// * Initialize the kernel.
......@@ -160,7 +169,6 @@ private:
// double execute(ContextImpl& context, bool includeForces, bool includeEnergy);
// private:
// int numTorsions;
// AmoebaReferenceData& data;
// System& system;
// };
//
......@@ -169,7 +177,7 @@ private:
// */
// class ReferenceCalcAmoebaPiTorsionForceKernel : public CalcAmoebaPiTorsionForceKernel {
// public:
// ReferenceCalcAmoebaPiTorsionForceKernel(std::string name, const Platform& platform, AmoebaReferenceData& data, System& system);
// ReferenceCalcAmoebaPiTorsionForceKernel(std::string name, const Platform& platform, System& system);
// ~ReferenceCalcAmoebaPiTorsionForceKernel();
// /**
// * Initialize the kernel.
......@@ -189,7 +197,6 @@ private:
// double execute(ContextImpl& context, bool includeForces, bool includeEnergy);
// private:
// int numPiTorsions;
// AmoebaReferenceData& data;
// System& system;
// };
//
......@@ -198,7 +205,7 @@ private:
// */
// class ReferenceCalcAmoebaStretchBendForceKernel : public CalcAmoebaStretchBendForceKernel {
// public:
// ReferenceCalcAmoebaStretchBendForceKernel(std::string name, const Platform& platform, AmoebaReferenceData& data, System& system);
// ReferenceCalcAmoebaStretchBendForceKernel(std::string name, const Platform& platform, System& system);
// ~ReferenceCalcAmoebaStretchBendForceKernel();
// /**
// * Initialize the kernel.
......@@ -218,7 +225,6 @@ private:
// double execute(ContextImpl& context, bool includeForces, bool includeEnergy);
// private:
// int numStretchBends;
// AmoebaReferenceData& data;
// System& system;
// };
//
......@@ -227,7 +233,7 @@ private:
// */
// class ReferenceCalcAmoebaOutOfPlaneBendForceKernel : public CalcAmoebaOutOfPlaneBendForceKernel {
// public:
// ReferenceCalcAmoebaOutOfPlaneBendForceKernel(std::string name, const Platform& platform, AmoebaReferenceData& data, System& system);
// ReferenceCalcAmoebaOutOfPlaneBendForceKernel(std::string name, const Platform& platform, System& system);
// ~ReferenceCalcAmoebaOutOfPlaneBendForceKernel();
// /**
// * Initialize the kernel.
......@@ -247,7 +253,6 @@ private:
// double execute(ContextImpl& context, bool includeForces, bool includeEnergy);
// private:
// int numOutOfPlaneBends;
// AmoebaReferenceData& data;
// System& system;
// };
//
......@@ -256,7 +261,7 @@ private:
// */
// class ReferenceCalcAmoebaTorsionTorsionForceKernel : public CalcAmoebaTorsionTorsionForceKernel {
// public:
// ReferenceCalcAmoebaTorsionTorsionForceKernel(std::string name, const Platform& platform, AmoebaReferenceData& data, System& system);
// ReferenceCalcAmoebaTorsionTorsionForceKernel(std::string name, const Platform& platform, System& system);
// ~ReferenceCalcAmoebaTorsionTorsionForceKernel();
// /**
// * Initialize the kernel.
......@@ -277,7 +282,6 @@ private:
// private:
// int numTorsionTorsions;
// int numTorsionTorsionGrids;
// AmoebaReferenceData& data;
// System& system;
// };
//
......@@ -286,7 +290,7 @@ private:
// */
// class ReferenceCalcAmoebaMultipoleForceKernel : public CalcAmoebaMultipoleForceKernel {
// public:
// ReferenceCalcAmoebaMultipoleForceKernel(std::string name, const Platform& platform, AmoebaReferenceData& data, System& system);
// ReferenceCalcAmoebaMultipoleForceKernel(std::string name, const Platform& platform, System& system);
// ~ReferenceCalcAmoebaMultipoleForceKernel();
// /**
// * Initialize the kernel.
......@@ -306,7 +310,6 @@ private:
// double execute(ContextImpl& context, bool includeForces, bool includeEnergy);
// private:
// int numMultipoles;
// AmoebaReferenceData& data;
// System& system;
// };
//
......@@ -315,7 +318,7 @@ private:
// */
// class ReferenceCalcAmoebaGeneralizedKirkwoodForceKernel : public CalcAmoebaGeneralizedKirkwoodForceKernel {
// public:
// ReferenceCalcAmoebaGeneralizedKirkwoodForceKernel(std::string name, const Platform& platform, AmoebaReferenceData& data, System& system);
// ReferenceCalcAmoebaGeneralizedKirkwoodForceKernel(std::string name, const Platform& platform, System& system);
// ~ReferenceCalcAmoebaGeneralizedKirkwoodForceKernel();
// /**
// * Initialize the kernel.
......@@ -334,7 +337,6 @@ private:
// */
// double execute(ContextImpl& context, bool includeForces, bool includeEnergy);
// private:
// AmoebaReferenceData& data;
// System& system;
// };
//
......@@ -343,7 +345,7 @@ private:
// */
// class ReferenceCalcAmoebaVdwForceKernel : public CalcAmoebaVdwForceKernel {
// public:
// ReferenceCalcAmoebaVdwForceKernel(std::string name, const Platform& platform, AmoebaReferenceData& data, System& system);
// ReferenceCalcAmoebaVdwForceKernel(std::string name, const Platform& platform, System& system);
// ~ReferenceCalcAmoebaVdwForceKernel();
// /**
// * Initialize the kernel.
......@@ -362,7 +364,6 @@ private:
// */
// double execute(ContextImpl& context, bool includeForces, bool includeEnergy);
// private:
// AmoebaReferenceData& data;
// System& system;
// };
//
......@@ -371,7 +372,7 @@ private:
// */
// class ReferenceCalcAmoebaWcaDispersionForceKernel : public CalcAmoebaWcaDispersionForceKernel {
// public:
// ReferenceCalcAmoebaWcaDispersionForceKernel(std::string name, const Platform& platform, AmoebaReferenceData& data, System& system);
// ReferenceCalcAmoebaWcaDispersionForceKernel(std::string name, const Platform& platform, System& system);
// ~ReferenceCalcAmoebaWcaDispersionForceKernel();
// /**
// * Initialize the kernel.
......@@ -390,7 +391,6 @@ private:
// */
// double execute(ContextImpl& context, bool includeForces, bool includeEnergy);
// private:
// AmoebaReferenceData& data;
// System& system;
// };
......
plugins/amoeba/platforms/reference/src/SimTKReference/AmoebaReferenceHarmonicInPlaneAngleForce.cpp 0 → 100644
View file @ 967968ad
/* Portions copyright (c) 2006 Stanford University and Simbios.
* Contributors: Pande Group
*
* Permission is hereby granted, free of charge, to any person obtaining
* a copy of this software and associated documentation files (the
* "Software"), to deal in the Software without restriction, including
* without limitation the rights to use, copy, modify, merge, publish,
* distribute, sublicense, and/or sell copies of the Software, and to
* permit persons to whom the Software is furnished to do so, subject
* to the following conditions:
*
* The above copyright notice and this permission notice shall be included
* in all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
* OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
* MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
* IN NO EVENT SHALL THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE
* LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
* OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
* WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/
#include "AmoebaReferenceForce.h"
#include "AmoebaReferenceHarmonicInPlaneAngleForce.h"
#include <vector>
/**---------------------------------------------------------------------------------------
Get dEdT and energy prefactor given cosine of angle :: the calculation for different
the force types is identical
@param cosine cosine of angle
@param idealAngle ideal angle
@param angleK angle k (quadratic prefactor)
@param angleCubic cubic prefactor
@param angleQuartic quartiic prefactor
@param anglePentic pentic prefactor
@param angleSextic sextic prefactor
@param dEdR dEdR
@return energy
--------------------------------------------------------------------------------------- */
RealOpenMM AmoebaReferenceHarmonicInPlaneAngleForce::getPrefactorsGivenAngleCosine( RealOpenMM cosine,
RealOpenMM idealAngle, RealOpenMM angleK,
RealOpenMM angleCubic, RealOpenMM angleQuartic,
RealOpenMM anglePentic, RealOpenMM angleSextic,
RealOpenMM* dEdR ){
// ---------------------------------------------------------------------------------------
static const RealOpenMM zero = 0.0;
static const RealOpenMM one = 1.0;
static const RealOpenMM two = 2.0;
static const RealOpenMM three = 3.0;
static const RealOpenMM four = 4.0;
static const RealOpenMM five = 5.0;
static const RealOpenMM six = 6.0;
// static const std::string methodName = "AmoebaReferenceHarmonicInPlaneAngleForce::getPrefactorsGivenAngleCosine";
// ---------------------------------------------------------------------------------------
RealOpenMM angle;
if( cosine >= one ){
angle = zero;
} else if( cosine <= -one ){
angle = RADIAN*PI_M;
} else {
angle = RADIAN*ACOS(cosine);
}
RealOpenMM deltaIdeal = angle - idealAngle;
RealOpenMM deltaIdeal2 = deltaIdeal*deltaIdeal;
RealOpenMM deltaIdeal3 = deltaIdeal*deltaIdeal2;
RealOpenMM deltaIdeal4 = deltaIdeal2*deltaIdeal2;
*dEdR = ( two + three*angleCubic*deltaIdeal +
four*angleQuartic*deltaIdeal2 +
five*anglePentic*deltaIdeal3 +
six*angleSextic*deltaIdeal4 );
*dEdR *= RADIAN*angleK*deltaIdeal;
RealOpenMM energy = 1.0f + angleCubic*deltaIdeal + angleQuartic*deltaIdeal2 +
anglePentic*deltaIdeal3 + angleSextic*deltaIdeal4;
energy *= angleK*deltaIdeal2;
return energy;
}
/**---------------------------------------------------------------------------------------
Calculate Amoeba harmonic angle ixn (force and energy)
@param positionAtomA Cartesian coordinates of atom A
@param positionAtomB Cartesian coordinates of atom B
@param positionAtomC Cartesian coordinates of atom C
@param positionAtomD Cartesian coordinates of atom D
@param angleLength angle
@param angleK quadratic angle force
@param angleCubic cubic angle force parameter
@param angleQuartic quartic angle force parameter
@param anglePentic pentic angle force parameter
@param angleSextic sextic angle force parameter
@param forces force vector
@return energy
--------------------------------------------------------------------------------------- */
RealOpenMM AmoebaReferenceHarmonicInPlaneAngleForce::calculateForceAndEnergy( RealOpenMM* positionAtomA, RealOpenMM* positionAtomB,
RealOpenMM* positionAtomC, RealOpenMM* positionAtomD,
RealOpenMM angle, RealOpenMM angleK,
RealOpenMM angleCubic, RealOpenMM angleQuartic,
RealOpenMM anglePentic, RealOpenMM angleSextic,
RealOpenMM** forces ){
// ---------------------------------------------------------------------------------------
//static const std::string methodName = "AmoebaReferenceHarmonicInPlaneAngleForce::calculateHarmonicForce";
static const RealOpenMM zero = 0.0;
static const RealOpenMM one = 1.0;
static const RealOpenMM two = 2.0;
// ---------------------------------------------------------------------------------------
// T = AD x CD
// P = B + T*delta
// AP = A - P
// CP = A - P
// M = CP x AP
enum { AD, BD, CD, T, AP, P, CP, M, APxM, CPxM, ADxBD, BDxCD, TxCD, ADxT, dBxAD, CDxdB, LastDeltaAtomIndex };
std::vector<RealOpenMM> deltaR[LastDeltaAtomIndex];
for( int ii = 0; ii < LastDeltaAtomIndex; ii++ ){
deltaR[ii].resize(3);
}
AmoebaReferenceForce::loadDeltaR( positionAtomD, positionAtomA, deltaR[AD] );
AmoebaReferenceForce::loadDeltaR( positionAtomD, positionAtomB, deltaR[BD] );
AmoebaReferenceForce::loadDeltaR( positionAtomD, positionAtomC, deltaR[CD] );
AmoebaReferenceForce::getCrossProduct( deltaR[AD], deltaR[CD], deltaR[T] );
RealOpenMM rT2 = AmoebaReferenceForce::getNormSquared3( deltaR[T] );
RealOpenMM delta = AmoebaReferenceForce::getDotProduct3( deltaR[T], deltaR[BD] )/rT2;
delta *= -one;
for( int ii = 0; ii < 3; ii++ ){
deltaR[P][ii] = positionAtomB[ii] + deltaR[T][ii]*delta;
deltaR[AP][ii] = positionAtomA[ii] - deltaR[P][ii];
deltaR[CP][ii] = positionAtomC[ii] - deltaR[P][ii];
}
RealOpenMM rAp2 = AmoebaReferenceForce::getNormSquared3( deltaR[AP] );
RealOpenMM rCp2 = AmoebaReferenceForce::getNormSquared3( deltaR[CP] );
if( rAp2 <= zero && rCp2 <= zero ){
return zero;
}
AmoebaReferenceForce::getCrossProduct( deltaR[CP], deltaR[AP], deltaR[M] );
RealOpenMM rm = AmoebaReferenceForce::getNorm3( deltaR[M] );
if( rm < 1.0e-06 ){
rm = 1.0e-06;
}
RealOpenMM dot = AmoebaReferenceForce::getDotProduct3( deltaR[AP], deltaR[CP] );
RealOpenMM cosine = dot/SQRT( rAp2*rCp2 );
RealOpenMM dEdR;
RealOpenMM energy = getPrefactorsGivenAngleCosine( cosine, angle, angleK, angleCubic, angleQuartic,
anglePentic, angleSextic, &dEdR );
RealOpenMM termA = -dEdR/(rAp2*rm);
RealOpenMM termC = dEdR/(rCp2*rm);
AmoebaReferenceForce::getCrossProduct( deltaR[AP], deltaR[M], deltaR[APxM] );
AmoebaReferenceForce::getCrossProduct( deltaR[CP], deltaR[M], deltaR[CPxM] );
// forces will be gathered here
enum { dA, dB, dC, dD, LastDIndex };
std::vector<RealOpenMM> forceTerm[LastDIndex];
for( int ii = 0; ii < LastDIndex; ii++ ){
forceTerm[ii].resize(3);
}
for( int ii = 0; ii < 3; ii++ ){
forceTerm[dA][ii] = deltaR[APxM][ii]*termA;
forceTerm[dC][ii] = deltaR[CPxM][ii]*termC;
forceTerm[dB][ii] = -one*( forceTerm[dA][ii] + forceTerm[dC][ii] );
}
RealOpenMM pTrT2 = AmoebaReferenceForce::getDotProduct3( forceTerm[dB], deltaR[T] );
pTrT2 /= rT2;
AmoebaReferenceForce::getCrossProduct( deltaR[CD], forceTerm[dB], deltaR[CDxdB] );
AmoebaReferenceForce::getCrossProduct( forceTerm[dB], deltaR[AD], deltaR[dBxAD] );
if( FABS( pTrT2 ) > 1.0e-08 ){
RealOpenMM delta2 = delta*two;
AmoebaReferenceForce::getCrossProduct( deltaR[BD], deltaR[CD], deltaR[BDxCD] );
AmoebaReferenceForce::getCrossProduct( deltaR[T], deltaR[CD], deltaR[TxCD] );
AmoebaReferenceForce::getCrossProduct( deltaR[AD], deltaR[BD], deltaR[ADxBD] );
AmoebaReferenceForce::getCrossProduct( deltaR[AD], deltaR[T], deltaR[ADxT] );
for( int ii = 0; ii < 3; ii++ ){
RealOpenMM term = deltaR[BDxCD][ii] + delta2*deltaR[TxCD][ii];
forceTerm[dA][ii] += delta*deltaR[CDxdB][ii] + term*pTrT2;
term = deltaR[ADxBD][ii] + delta2*deltaR[ADxT][ii];
forceTerm[dC][ii] += delta*deltaR[dBxAD][ii] + term*pTrT2;
forceTerm[dD][ii] = -( forceTerm[dA][ii] + forceTerm[dB][ii] + forceTerm[dC][ii] );
}
} else {
for( int ii = 0; ii < 3; ii++ ){
forceTerm[dA][ii] += delta*deltaR[CDxdB][ii];
forceTerm[dC][ii] += delta*deltaR[dBxAD][ii];
forceTerm[dD][ii] = -( forceTerm[dA][ii] + forceTerm[dB][ii] + forceTerm[dC][ii] );
}
}
// accumulate forces
for( int jj = 0; jj < 4; jj++ ){
forces[jj][0] -= forceTerm[jj][0];
forces[jj][1] -= forceTerm[jj][1];
forces[jj][2] -= forceTerm[jj][2];
}
return energy;
}
plugins/amoeba/platforms/reference/src/SimTKReference/AmoebaReferenceHarmonicInPlaneAngleForce.h 0 → 100644
View file @ 967968ad
/* Portions copyright (c) 2006 Stanford University and Simbios.
* Contributors: Pande Group
*
* Permission is hereby granted, free of charge, to any person obtaining
* a copy of this software and associated documentation files (the
* "Software"), to deal in the Software without restriction, including
* without limitation the rights to use, copy, modify, merge, publish,
* distribute, sublicense, and/or sell copies of the Software, and to
* permit persons to whom the Software is furnished to do so, subject
* to the following conditions:
*
* The above copyright notice and this permission notice shall be included
* in all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
* OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
* MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
* IN NO EVENT SHALL THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE
* LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
* OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
* WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/
#ifndef __AmoebaReferenceHarmonicInPlaneAngleForce_H__
#define __AmoebaReferenceHarmonicInPlaneAngleForce_H__
#include "SimTKUtilities/SimTKOpenMMRealType.h"
// ---------------------------------------------------------------------------------------
class AmoebaReferenceHarmonicInPlaneAngleForce {
public:
/**---------------------------------------------------------------------------------------
Constructor
--------------------------------------------------------------------------------------- */
AmoebaReferenceHarmonicInPlaneAngleForce( );
/**---------------------------------------------------------------------------------------
Destructor
--------------------------------------------------------------------------------------- */
~AmoebaReferenceHarmonicInPlaneAngleForce( );
/**---------------------------------------------------------------------------------------
Get dEdT and energy prefactor given cosine of angle :: the calculation for different
the force types is identical
@param cosine cosine of angle
@param idealAngle ideal angle
@param angleK angle k (quadratic prefactor)
@param angleCubic cubic prefactor
@param angleQuartic quartiic prefactor
@param anglePentic pentic prefactor
@param angleSextic sextic prefactor
@param dEdR dEdR
@return energy
--------------------------------------------------------------------------------------- */
static RealOpenMM getPrefactorsGivenAngleCosine( RealOpenMM cosine, RealOpenMM idealAngle, RealOpenMM angleK,
RealOpenMM angleCubic, RealOpenMM angleQuartic,
RealOpenMM anglePentic, RealOpenMM angleSextic,
RealOpenMM* dEdR );
/**---------------------------------------------------------------------------------------
Calculate Amoeba harmonic angle ixn (force and energy)
@param positionAtomA Cartesian coordinates of atom A
@param positionAtomB Cartesian coordinates of atom B
@param positionAtomC Cartesian coordinates of atom C
@param positionAtomD Cartesian coordinates of atom D
@param angleLength angle
@param angleK quadratic angle force
@param angleCubic cubic angle force parameter
@param angleQuartic quartic angle force parameter
@param anglePentic pentic angle force parameter
@param angleSextic sextic angle force parameter
@param forces force vector
@return energy
--------------------------------------------------------------------------------------- */
static RealOpenMM calculateForceAndEnergy( RealOpenMM* positionAtomA, RealOpenMM* positionAtomB,
RealOpenMM* positionAtomC, RealOpenMM* positionAtomD,
RealOpenMM angle, RealOpenMM angleK,
RealOpenMM angleCubic, RealOpenMM angleQuartic,
RealOpenMM anglePentic, RealOpenMM angleSextic,
RealOpenMM** forces );
};
// ---------------------------------------------------------------------------------------
#endif // _AmoebaReferenceHarmonicInPlaneAngleForce___
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment