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Commit cf99c386 authored by Peter Eastman's avatar Peter Eastman
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Continuing implementation of PME reciprocal space calculation

parent 7b3072df
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Showing with 153 additions and 56 deletions
plugins/amoeba/openmmapi/include/AmoebaMultipoleForce.h
View file @ cf99c386
......@@ -113,20 +113,6 @@ public:
*/
void setCutoffDistance(double distance);
/**
* Get the aEwald parameter
*
* @return the Ewald parameter
*/
double getAEwald() const;
/**
* Set the aEwald parameter
*
* @param Ewald parameter
*/
void setAEwald(double aewald);
/**
* Add multipole-related info for a particle
*
......@@ -272,6 +258,20 @@ public:
* @param the electric constant
*/
void setElectricConstant( double inputElectricConstant );
/**
* Get the error tolerance for Ewald summation. This corresponds to the fractional error in the forces
* which is acceptable. This value is used to select the reciprocal space cutoff and separation
* parameter so that the average error level will be less than the tolerance. There is not a
* rigorous guarantee that all forces on all atoms will be less than the tolerance, however.
*/
double getEwaldErrorTolerance() const;
/**
* Get the error tolerance for Ewald summation. This corresponds to the fractional error in the forces
* which is acceptable. This value is used to select the reciprocal space cutoff and separation
* parameter so that the average error level will be less than the tolerance. There is not a
* rigorous guarantee that all forces on all atoms will be less than the tolerance, however.
*/
void setEwaldErrorTolerance(double tol);
protected:
ForceImpl* createImpl();
......@@ -279,27 +279,15 @@ private:
AmoebaNonbondedMethod nonbondedMethod;
double cutoffDistance;
double aewald;
MutualInducedIterationMethod mutualInducedIterationMethod;
int mutualInducedMaxIterations;
double mutualInducedTargetEpsilon;
double scalingDistanceCutoff;
double electricConstant;
double ewaldErrorTol;
class MultipoleInfo;
// Retarded visual studio compiler complains about being unable to
// export private stl class members.
// This stanza explains that it should temporarily shut up.
#if defined(_MSC_VER)
#pragma warning(push)
#pragma warning(disable:4251)
#endif
std::vector<MultipoleInfo> multipoles;
#if defined(_MSC_VER)
#pragma warning(pop)
#endif
};
class AmoebaMultipoleForce::MultipoleInfo {
......
plugins/amoeba/openmmapi/src/AmoebaMultipoleForce.cpp
View file @ cf99c386
......@@ -36,7 +36,7 @@
using namespace OpenMM;
AmoebaMultipoleForce::AmoebaMultipoleForce() : nonbondedMethod(NoCutoff), cutoffDistance(1.0), aewald(0.0), mutualInducedIterationMethod(SOR), mutualInducedMaxIterations(60),
AmoebaMultipoleForce::AmoebaMultipoleForce() : nonbondedMethod(NoCutoff), cutoffDistance(1.0), ewaldErrorTol(5e-4), mutualInducedIterationMethod(SOR), mutualInducedMaxIterations(60),
mutualInducedTargetEpsilon(1.0e-05), scalingDistanceCutoff(100.0), electricConstant(138.9354558456) {
}
......@@ -56,14 +56,6 @@ void AmoebaMultipoleForce::setCutoffDistance(double distance) {
cutoffDistance = distance;
}
double AmoebaMultipoleForce::getAEwald() const {
return aewald;
}
void AmoebaMultipoleForce::setAEwald(double inputAewald ) {
aewald = inputAewald;
}
AmoebaMultipoleForce::MutualInducedIterationMethod AmoebaMultipoleForce::getMutualInducedIterationMethod( void ) const {
return mutualInducedIterationMethod;
}
......@@ -104,6 +96,14 @@ void AmoebaMultipoleForce::setElectricConstant( double inputElectricConstant ) {
electricConstant = inputElectricConstant;
}
double AmoebaMultipoleForce::getEwaldErrorTolerance() const {
return ewaldErrorTol;
}
void AmoebaMultipoleForce::setEwaldErrorTolerance(double tol) {
ewaldErrorTol = tol;
}
int AmoebaMultipoleForce::addParticle( double charge, std::vector<double>& molecularDipole, std::vector<double>& molecularQuadrupole, int axisType,
int multipoleAtomId1, int multipoleAtomId2, double thole, double dampingFactor, double polarity) {
multipoles.push_back(MultipoleInfo( charge, molecularDipole, molecularQuadrupole, axisType, multipoleAtomId1, multipoleAtomId2, thole, dampingFactor, polarity));
......
plugins/amoeba/platforms/cuda/src/AmoebaCudaKernels.cpp
View file @ cf99c386
......@@ -31,6 +31,7 @@
#include "kernels/amoebaCudaKernels.h"
#include "internal/AmoebaMultipoleForceImpl.h"
#include "internal/AmoebaWcaDispersionForceImpl.h"
#include "openmm/internal/NonbondedForceImpl.h"
#include <cmath>
#ifdef _MSC_VER
......@@ -588,8 +589,16 @@ void CudaCalcAmoebaMultipoleForceKernel::initialize(const System& system, const
static_cast<float>( force.getMutualInducedTargetEpsilon()),
nonbondedMethod,
static_cast<float>( force.getCutoffDistance()),
static_cast<float>( force.getAEwald()),
static_cast<float>( force.getElectricConstant()) );
if (nonbondedMethod == AmoebaMultipoleForce::PME) {
double alpha;
int xsize, ysize, zsize;
NonbondedForce nb;
nb.setEwaldErrorTolerance(force.getEwaldErrorTolerance());
nb.setCutoffDistance(force.getCutoffDistance());
NonbondedForceImpl::calcPMEParameters(system, nb, alpha, xsize, ysize, zsize);
gpuSetAmoebaPMEParameters(data.getAmoebaGpu(), (float) alpha, xsize, ysize, zsize);
}
}
......
plugins/amoeba/platforms/cuda/src/kernels/AmoebaGpu.cpp
View file @ cf99c386
......@@ -351,7 +351,6 @@ void gpuPrintCudaAmoebaGmxSimulation(amoebaGpuContext amoebaGpu, FILE* log )
(void) fprintf( log, " pM_ScaleIndices %p\n", amoebaGpu->amoebaSim.pM_ScaleIndices );
(void) fprintf( log, " sqrtPi %15.7e\n", amoebaGpu->amoebaSim.sqrtPi );
(void) fprintf( log, " cutoffDistance2 %15.7e\n", amoebaGpu->amoebaSim.cutoffDistance2 );
(void) fprintf( log, " aewald %15.7e\n", amoebaGpu->amoebaSim.aewald );
(void) fprintf( log, " electric %15.7e\n", amoebaGpu->amoebaSim.electric );
(void) fprintf( log, " box %15.7e %15.7e %15.7e\n", gpu->sim.periodicBoxSizeX, gpu->sim.periodicBoxSizeY, gpu->sim.periodicBoxSizeZ);
(void) fprintf( log, " gkc %15.7e\n", amoebaGpu->amoebaSim.gkc );
......@@ -1464,7 +1463,7 @@ void gpuSetAmoebaMultipoleParameters(amoebaGpuContext amoebaGpu, const std::vect
const std::vector< std::vector< std::vector<int> > >& multipoleParticleCovalentInfo, const std::vector<int>& covalentDegree,
const std::vector<int>& minCovalentIndices, const std::vector<int>& minCovalentPolarizationIndices, int maxCovalentRange,
int mutualInducedIterativeMethod, int mutualInducedMaxIterations, float mutualInducedTargetEpsilon,
int nonbondedMethod, float cutoffDistance, float aewald, float electricConstant ){
int nonbondedMethod, float cutoffDistance, float electricConstant ){
// ---------------------------------------------------------------------------------------
......@@ -1565,10 +1564,8 @@ void gpuSetAmoebaMultipoleParameters(amoebaGpuContext amoebaGpu, const std::vect
}
amoebaGpu->amoebaSim.cutoffDistance2 = cutoffDistance*cutoffDistance;
amoebaGpu->amoebaSim.sqrtPi = sqrt( 3.1415926535897932384626433832795 );
amoebaGpu->amoebaSim.aewald = aewald;
amoebaGpu->amoebaSim.electric = electricConstant;
amoebaGpu->gpuContext->sim.alphaEwald = aewald;
amoebaGpu->gpuContext->sim.nonbondedCutoff = cutoffDistance;
tabulateErfc(amoebaGpu->gpuContext);
......
plugins/amoeba/platforms/cuda/src/kernels/amoebaCudaTypes.h
View file @ cf99c386
......@@ -128,7 +128,6 @@ struct cudaAmoebaGmxSimulation {
unsigned int paddedNumberOfAtoms; // padded number of atoms
float cutoffDistance2; // cutoff distance squared for PME
float sqrtPi; // sqrt(PI)
float aewald; // aewald parameter
float scalingDistanceCutoff; // scaling cutoff
float2* pDampingFactorAndThole; // Thole & damping factors
......
plugins/amoeba/platforms/cuda/src/kernels/amoebaGpuTypes.h
View file @ cf99c386
......@@ -154,7 +154,6 @@ struct _amoebaGpuContext {
int multipoleNonbondedMethod;
double cutoffDistance;
double aewald;
// mutual induced field
......@@ -308,7 +307,7 @@ void gpuSetAmoebaMultipoleParameters(amoebaGpuContext amoebaGpu, const std::vect
const std::vector< std::vector< std::vector<int> > >& multipoleAtomCovalentInfo, const std::vector<int>& covalentDegree,
const std::vector<int>& minCovalentIndices, const std::vector<int>& minCovalentPolarizationIndices, int maxCovalentRange,
int mutualInducedIterationMethod, int mutualInducedMaxIterations, float mutualInducedTargetEpsilon,
int nonbondedMethod, float cutoffDistance, float aewald, float electricConstant );
int nonbondedMethod, float cutoffDistance, float electricConstant );
extern "C"
......@@ -326,6 +325,9 @@ void gpuSetAmoebaVdwParameters( amoebaGpuContext amoebaGpu,
const std::string& sigmaCombiningRule,
const std::string& epsilonCombiningRule,
const std::vector< std::vector<int> >& allExclusions );
extern "C"
void gpuSetAmoebaPMEParameters(amoebaGpuContext amoebaGpu, float alpha, int gridSizeX, int gridSizeY, int gridSizeZ);
extern "C"
void amoebaGpuBuildVdwExclusionList( amoebaGpuContext amoebaGpu, const std::vector< std::vector<int> >& exclusions );
......
plugins/amoeba/platforms/cuda/src/kernels/kCalculateAmoebaCudaPmeFixedEField.cu
View file @ cf99c386
......@@ -45,7 +45,7 @@ void kReduceDirectSelfFields_kernel( unsigned int fieldComponents, unsigned int
// Reduce field
const float term = (4.0f/3.0f)*(cAmoebaSim.aewald*cAmoebaSim.aewald*cAmoebaSim.aewald)/cAmoebaSim.sqrtPi;
const float term = (4.0f/3.0f)*(cSim.alphaEwald*cSim.alphaEwald*cSim.alphaEwald)/cAmoebaSim.sqrtPi;
while (pos < fieldComponents)
{
......@@ -123,12 +123,12 @@ __device__ void calculateFixedFieldRealSpacePairIxn_kernel( FixedFieldParticle&
// calculate the error function damping terms
float ralpha = cAmoebaSim.aewald*r;
float ralpha = cSim.alphaEwald*r;
float bn[4];
bn[0] = erfc(ralpha)/r;
float alsq2 = 2.0f*cAmoebaSim.aewald*cAmoebaSim.aewald;
float alsq2n = 1.0f/(cAmoebaSim.sqrtPi*cAmoebaSim.aewald);
float alsq2 = 2.0f*cSim.alphaEwald*cSim.alphaEwald;
float alsq2n = 1.0f/(cAmoebaSim.sqrtPi*cSim.alphaEwald);
float exp2a = exp(-(ralpha*ralpha));
alsq2n *= alsq2;
bn[1] = (bn[0]+alsq2n*exp2a)/r2;
......
plugins/amoeba/platforms/cuda/src/kernels/kCalculateAmoebaCudaRealSpaceEwald.cu
View file @ cf99c386
......@@ -212,14 +212,14 @@ __device__ void calculateRealSpaceEwaldPairIxn_kernel( RealSpaceEwaldParticle& a
// calculate the real space error function terms;
float ralpha = cAmoebaSim.aewald*r;
float ralpha = cSim.alphaEwald*r;
bn[0] = fastErfc(ralpha)/r;
float alsq2 = 2.0f*cAmoebaSim.aewald*cAmoebaSim.aewald;
float alsq2 = 2.0f*cSim.alphaEwald*cSim.alphaEwald;
float alsq2n = 0.0f;
if( cAmoebaSim.aewald > 0.0f){
alsq2n = 1.0f/(cAmoebaSim.sqrtPi*cAmoebaSim.aewald);
if( cSim.alphaEwald > 0.0f){
alsq2n = 1.0f/(cAmoebaSim.sqrtPi*cSim.alphaEwald);
}
float exp2a = exp(-(ralpha*ralpha));
......
plugins/amoeba/platforms/cuda/tests/AmoebaTinkerParameterFile.cpp
View file @ cf99c386
......@@ -2007,7 +2007,6 @@ static int readAmoebaMultipoleParameters( FILE* filePtr, int version, MapStringI
} else {
multipoleForce->setNonbondedMethod( AmoebaMultipoleForce::NoCutoff );
}
multipoleForce->setAEwald( aewald );
multipoleForce->setCutoffDistance( cutoffDistance );
system.setDefaultPeriodicBoxVectors( Vec3(box[0], 0.0, 0.0), Vec3(0.0, box[1], 0.0), Vec3(0.0, 0.0, box[2]) );
if( log ){
......@@ -2112,7 +2111,6 @@ static int readAmoebaMultipoleParameters( FILE* filePtr, int version, MapStringI
double polarityConversion = AngstromToNm*AngstromToNm*AngstromToNm;
double dampingFactorConversion = sqrt( AngstromToNm );
multipoleForce->setAEwald( multipoleForce->getAEwald()/AngstromToNm);
multipoleForce->setCutoffDistance( multipoleForce->getCutoffDistance()*AngstromToNm );
multipoleForce->setScalingDistanceCutoff( multipoleForce->getScalingDistanceCutoff()*AngstromToNm );
......@@ -2167,8 +2165,8 @@ static int readAmoebaMultipoleParameters( FILE* filePtr, int version, MapStringI
(useOpenMMUnits ? "OpenMM" : "Amoeba") );
std::string nonbondedMethod = multipoleForce->getNonbondedMethod( ) == AmoebaMultipoleForce::PME ? "PME" : "NoCutoff";
(void) fprintf( log, "NonbondedMethod=%s aEwald=%15.7e cutoff=%15.7e.\n", nonbondedMethod.c_str(),
multipoleForce->getAEwald(), multipoleForce->getCutoffDistance() );
(void) fprintf( log, "NonbondedMethod=%s cutoff=%15.7e.\n", nonbondedMethod.c_str(),
multipoleForce->getCutoffDistance() );
Vec3 a,b,c;
system.getDefaultPeriodicBoxVectors( a, b, c );
......
plugins/amoeba/platforms/cuda/tests/TestCudaAmoebaPME.cpp 0 → 100644
View file @ cf99c386
/* -------------------------------------------------------------------------- *
* OpenMM *
* -------------------------------------------------------------------------- *
* This is part of the OpenMM molecular simulation toolkit originating from *
* Simbios, the NIH National Center for Physics-Based Simulation of *
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2008-2010 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
* 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. *
* -------------------------------------------------------------------------- */
/**
* This tests the Ewald summation method cuda implementation of NonbondedForce.
*/
#include "../../../tests/AssertionUtilities.h"
#include "openmm/Context.h"
#include "CudaPlatform.h"
#include "AmoebaMultipoleForce.h"
#include "openmm/System.h"
#include "openmm/VerletIntegrator.h"
#include "../src/SimTKUtilities/SimTKOpenMMRealType.h"
#include <iostream>
#include <vector>
using namespace OpenMM;
using namespace std;
const double TOL = 1e-5;
void testPMEWater() {
Platform& platform = Platform::getPlatformByName("Cuda");
System system;
system.addParticle(16);
system.addParticle(1);
system.addParticle(1);
VerletIntegrator integrator(0.01);
AmoebaMultipoleForce* mp = new AmoebaMultipoleForce();
mp->setNonbondedMethod(AmoebaMultipoleForce::PME);
vector<double> dipole(3, 0.0);
dipole[2] = 7.556121361e-2;
vector<double> quadrupole(9, 0.0);
quadrupole[0] = 3.540307211e-2;
quadrupole[4] = -3.902570771e-2;
quadrupole[8] = 3.622635596e-3;
mp->addParticle(-0.51966, dipole, quadrupole, 1, 1, 2, 0.39, 9.707801995e-1, 0.837);
dipole[0] = -2.042094848e-2;
dipole[2] = -3.078753000e-2;
quadrupole[0] = -3.428482490e-3;
quadrupole[2] = -1.894859639e-4;
quadrupole[4] = -1.002408752e-2;
quadrupole[6] = -1.894859639e-4;
quadrupole[8] = 1.345257001e-2;
mp->addParticle(0.25983, dipole, quadrupole, 0, 0, 2, 0.39, 8.897068742e-1, 0.496);
mp->addParticle(0.25983, dipole, quadrupole, 0, 0, 1, 0.39, 8.897068742e-1, 0.496);
mp->setCutoffDistance(1.0);
// nonbonded->setEwaldErrorTolerance(TOL);
system.setDefaultPeriodicBoxVectors(Vec3(2, 0, 0), Vec3(0, 2, 0), Vec3(0, 0, 2));
system.addForce(mp);
Context context(system, integrator, platform);
vector<Vec3> positions(3);
const double angle = 109.47*M_PI/180;
const double dOH = 0.1;
positions[0] = Vec3();
positions[1] = Vec3(dOH, 0, 0);
positions[2] = Vec3(dOH*std::cos(angle), dOH*std::sin(angle), 0);
context.setPositions(positions);
State state = context.getState(State::Forces | State::Energy);
const vector<Vec3>& forces = state.getForces();
}
int main() {
try {
Platform::loadPluginsFromDirectory(Platform::getDefaultPluginsDirectory());
testPMEWater();
}
catch(const exception& e) {
cout << "exception: " << e.what() << endl;
return 1;
}
cout << "Done" << endl;
return 0;
}
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