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Commit 2ef05285 authored by Mark Friedrichs's avatar Mark Friedrichs
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Direct space PME

parent c22f00cf
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Showing with 546 additions and 452 deletions
plugins/amoeba/CMakeLists.txt
View file @ 2ef05285
......@@ -38,8 +38,7 @@ ENDIF(LOG)
# The source is organized into subdirectories, but we handle them all from
# this CMakeLists file rather than letting CMake visit them as SUBDIRS.
#SET(OPENMM_AMOEBA_PLUGIN_SOURCE_SUBDIRS . openmmapi platforms/reference)
SET(OPENMM_AMOEBA_PLUGIN_SOURCE_SUBDIRS . openmmapi )
SET(OPENMM_AMOEBA_PLUGIN_SOURCE_SUBDIRS . openmmapi platforms/reference)
# Collect up information about the version of the OpenMM library we're building
# and make it available to the code so it can be built into the binaries.
......@@ -103,8 +102,10 @@ FOREACH(subdir ${OPENMM_AMOEBA_PLUGIN_SOURCE_SUBDIRS})
INCLUDE_DIRECTORIES(BEFORE ${CMAKE_CURRENT_SOURCE_DIR}/${subdir}/include)
ENDFOREACH(subdir)
#INCLUDE_DIRECTORIES(BEFORE ${OPENMM_DIR}/platforms/reference/src)
#INCLUDE_DIRECTORIES(BEFORE ${OPENMM_DIR}/platforms/reference/src/SimTKReference)
INCLUDE_DIRECTORIES(BEFORE ${OPENMM_DIR}/platforms/reference/src)
INCLUDE_DIRECTORIES(BEFORE ${OPENMM_DIR}/platforms/reference/src/SimTKReference)
INCLUDE_DIRECTORIES(BEFORE ${CMAKE_CURRENT_SOURCE_DIR}/platforms/reference/src)
INCLUDE_DIRECTORIES(BEFORE ${CMAKE_CURRENT_SOURCE_DIR}/platforms/reference/src/SimTKReference)
# ----------------------------------------------------------------------------
IF(LOG)
......@@ -158,7 +159,7 @@ IF(OPENMM_BUILD_STATIC_LIB)
TARGET_LINK_LIBRARIES( ${STATIC_AMOEBA_TARGET} ${STATIC_TARGET} )
ENDIF(OPENMM_BUILD_STATIC_LIB)
#ADD_SUBDIRECTORY(platforms/reference/tests)
ADD_SUBDIRECTORY(platforms/reference/tests)
# Which hardware platforms to build
IF(CUDA_FOUND)
......
plugins/amoeba/openmmapi/include/AmoebaMultipoleForce.h
View file @ 2ef05285
......@@ -113,6 +113,20 @@ 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
*
......@@ -279,6 +293,7 @@ private:
AmoebaNonbondedMethod nonbondedMethod;
double cutoffDistance;
double aewald;
MutualInducedIterationMethod mutualInducedIterationMethod;
int mutualInducedMaxIterations;
double mutualInducedTargetEpsilon;
......
plugins/amoeba/openmmapi/src/AmoebaMultipoleForce.cpp
View file @ 2ef05285
......@@ -56,6 +56,14 @@ 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;
}
......
plugins/amoeba/platforms/cuda/src/AmoebaCudaKernels.cpp
View file @ 2ef05285
......@@ -589,6 +589,7 @@ 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;
......
plugins/amoeba/platforms/cuda/src/kernels/AmoebaGpu.cpp
View file @ 2ef05285
......@@ -350,6 +350,7 @@ void gpuPrintCudaAmoebaGmxSimulation(amoebaGpuContext amoebaGpu, FILE* log )
(void) fprintf( log, " pP_ScaleIndices %p\n", amoebaGpu->amoebaSim.pP_ScaleIndices );
(void) fprintf( log, " pM_ScaleIndices %p\n", amoebaGpu->amoebaSim.pM_ScaleIndices );
(void) fprintf( log, " sqrtPi %15.7e\n", amoebaGpu->amoebaSim.sqrtPi );
(void) fprintf( log, " alpha Ewald %15.7e\n", gpu->sim.alphaEwald );
(void) fprintf( log, " cutoffDistance2 %15.7e\n", amoebaGpu->amoebaSim.cutoffDistance2 );
(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);
......@@ -1463,7 +1464,7 @@ 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 electricConstant ){
int nonbondedMethod, float cutoffDistance, float alphaEwald, float electricConstant ){
// ---------------------------------------------------------------------------------------
......@@ -1565,9 +1566,8 @@ void gpuSetAmoebaMultipoleParameters(amoebaGpuContext amoebaGpu, const std::vect
amoebaGpu->amoebaSim.cutoffDistance2 = cutoffDistance*cutoffDistance;
amoebaGpu->amoebaSim.sqrtPi = sqrt( 3.1415926535897932384626433832795 );
amoebaGpu->amoebaSim.electric = electricConstant;
amoebaGpu->gpuContext->sim.alphaEwald = alphaEwald;
amoebaGpu->gpuContext->sim.nonbondedCutoff = cutoffDistance;
tabulateErfc(amoebaGpu->gpuContext);
if( amoebaGpu->amoebaSim.dielec < 1.0e-05 ){
amoebaGpu->amoebaSim.dielec = 1.0f;
......@@ -2766,7 +2766,7 @@ void amoebaGpuSetConstants(amoebaGpuContext amoebaGpu)
SetCalculateAmoebaCudaPmeMutualInducedFieldSim( amoebaGpu );
SetCalculateAmoebaCudaPmeFixedEFieldSim( amoebaGpu );
SetCalculateAmoebaElectrostaticSim( amoebaGpu );
SetCalculateAmoebaRealSpaceEwaldSim( amoebaGpu );
SetCalculateAmoebaPmeDirectElectrostaticSim( amoebaGpu );
SetCalculateAmoebaCudaMapTorquesSim( amoebaGpu );
SetCalculateAmoebaKirkwoodSim( amoebaGpu );
SetCalculateAmoebaKirkwoodEDiffSim( amoebaGpu );
......
plugins/amoeba/platforms/cuda/src/kernels/amoebaCudaKernels.h
View file @ 2ef05285
......@@ -106,9 +106,9 @@ extern void SetCalculateAmoebaElectrostaticSim( amoebaGpuContext amoebaGpu );
extern void GetCalculateAmoebaElectrostaticSim( amoebaGpuContext amoebaGpu );
extern void cudaComputeAmoebaElectrostatic( amoebaGpuContext amoebaGpu );
extern void SetCalculateAmoebaRealSpaceEwaldSim( amoebaGpuContext amoebaGpu );
extern void GetCalculateAmoebaRealSpaceEwaldSim( amoebaGpuContext amoebaGpu );
extern void cudaComputeAmoebaRealSpaceEwald( amoebaGpuContext amoebaGpu );
extern void SetCalculateAmoebaPmeDirectElectrostaticSim( amoebaGpuContext amoebaGpu );
extern void GetCalculateAmoebaPmeDirectElectrostaticSim( amoebaGpuContext amoebaGpu );
extern void cudaComputeAmoebaPmeElectrostatic( amoebaGpuContext amoebaGpu );
extern void SetCalculateAmoebaCudaMapTorquesSim(amoebaGpuContext gpu);
extern void GetCalculateAmoebaCudaMapTorquesSim(amoebaGpuContext gpu);
......
plugins/amoeba/platforms/cuda/src/kernels/amoebaGpuTypes.h
View file @ 2ef05285
......@@ -307,7 +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 electricConstant );
int nonbondedMethod, float cutoffDistance, float alphaEwald, float electricConstant );
extern "C"
......
plugins/amoeba/platforms/cuda/src/kernels/kCalculateAmoebaCudaPmeFixedEField.cu
View file @ 2ef05285
......@@ -322,7 +322,7 @@ __device__ void calculateFixedFieldRealSpacePairIxn_kernel( FixedFieldParticle&
--------------------------------------------------------------------------------------- */
void cudaComputeAmoebaPmeFixedEField( amoebaGpuContext amoebaGpu )
static void cudaComputeAmoebaPmeDirectFixedEField( amoebaGpuContext amoebaGpu )
{
// ---------------------------------------------------------------------------------------
......@@ -487,3 +487,9 @@ void cudaComputeAmoebaPmeFixedEField( amoebaGpuContext amoebaGpu )
}
}
void cudaComputeAmoebaPmeFixedEField( amoebaGpuContext amoebaGpu )
{
cudaComputeAmoebaPmeDirectFixedEField( amoebaGpu );
kCalculateAmoebaPMEFixedMultipoleField( amoebaGpu );
}
plugins/amoeba/platforms/cuda/src/kernels/kCalculateAmoebaCudaPmeMutualInducedField.cu
View file @ 2ef05285
......@@ -616,6 +616,7 @@ static void cudaComputeAmoebaPmeMutualInducedFieldBySOR( amoebaGpuContext amoeba
// matrix multiply
cudaComputeAmoebaPmeMutualInducedFieldMatrixMultiply( amoebaGpu, amoebaGpu->psWorkVector[0], amoebaGpu->psWorkVector[1] );
kCalculateAmoebaPMEInducedDipoleField( amoebaGpu );
LAUNCHERROR("cudaComputeAmoebaPmeMutualInducedFieldMatrixMultiply Loop\n");
......@@ -654,7 +655,7 @@ static void cudaComputeAmoebaPmeMutualInducedFieldBySOR( amoebaGpuContext amoeba
gpu->natoms, amoebaGpu->psPolarizability->_pDevStream[0],
amoebaGpu->psInducedDipole->_pDevStream[0], amoebaGpu->psInducedDipolePolar->_pDevStream[0],
amoebaGpu->psE_Field->_pDevStream[0], amoebaGpu->psE_FieldPolar->_pDevStream[0],
amoebaGpu->psWorkVector[0]->_pDevStream[0], amoebaGpu->psWorkVector[1]->_pDevStream[0] );
amoebaGpu->psWorkVector[0]->_pDevStream[0], amoebaGpu->psWorkVector[1]->_pDevStream[0] );
LAUNCHERROR("kSorUpdatePmeMutualInducedField");
// get total epsilon -- performing sums on gpu
......
plugins/amoeba/platforms/cuda/src/kernels/kCalculateAmoebaRotateFrame.cu
View file @ 2ef05285
......@@ -390,7 +390,7 @@ void kCalculateAmoebaMultipoleForces(amoebaGpuContext amoebaGpu, bool hasAmoebaG
if( amoebaGpu->multipoleNonbondedMethod == AMOEBA_NO_CUTOFF ){
cudaComputeAmoebaElectrostatic( amoebaGpu );
} else {
cudaComputeAmoebaRealSpaceEwald( amoebaGpu );
cudaComputeAmoebaPmeElectrostatic( amoebaGpu );
}
// map torques to forces
......
plugins/amoeba/platforms/cuda/tests/AmoebaTinkerParameterFile.cpp
View file @ 2ef05285
......@@ -2008,6 +2008,7 @@ static int readAmoebaMultipoleParameters( FILE* filePtr, int version, MapStringI
multipoleForce->setNonbondedMethod( AmoebaMultipoleForce::NoCutoff );
}
multipoleForce->setCutoffDistance( cutoffDistance );
multipoleForce->setAEwald( aewald );
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 ){
(void) fprintf( log, "%s number of MultipoleParameter terms=%d usePme=%d aewald=%15.7e cutoffDistance=%12.4f\n",
......@@ -2111,6 +2112,7 @@ 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 );
......@@ -2165,8 +2167,8 @@ 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 cutoff=%15.7e.\n", nonbondedMethod.c_str(),
multipoleForce->getCutoffDistance() );
(void) fprintf( log, "NonbondedMethod=%s aEwald=%15.7e cutoff=%15.7e.\n", nonbondedMethod.c_str(),
multipoleForce->getAEwald(), multipoleForce->getCutoffDistance() );
Vec3 a,b,c;
system.getDefaultPeriodicBoxVectors( a, b, c );
......
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