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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) ...@@ -38,8 +38,7 @@ ENDIF(LOG)
# The source is organized into subdirectories, but we handle them all from # The source is organized into subdirectories, but we handle them all from
# this CMakeLists file rather than letting CMake visit them as SUBDIRS. # 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 platforms/reference)
SET(OPENMM_AMOEBA_PLUGIN_SOURCE_SUBDIRS . openmmapi )
# Collect up information about the version of the OpenMM library we're building # 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. # 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}) ...@@ -103,8 +102,10 @@ FOREACH(subdir ${OPENMM_AMOEBA_PLUGIN_SOURCE_SUBDIRS})
INCLUDE_DIRECTORIES(BEFORE ${CMAKE_CURRENT_SOURCE_DIR}/${subdir}/include) INCLUDE_DIRECTORIES(BEFORE ${CMAKE_CURRENT_SOURCE_DIR}/${subdir}/include)
ENDFOREACH(subdir) ENDFOREACH(subdir)
#INCLUDE_DIRECTORIES(BEFORE ${OPENMM_DIR}/platforms/reference/src) 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/SimTKReference)
INCLUDE_DIRECTORIES(BEFORE ${CMAKE_CURRENT_SOURCE_DIR}/platforms/reference/src)
INCLUDE_DIRECTORIES(BEFORE ${CMAKE_CURRENT_SOURCE_DIR}/platforms/reference/src/SimTKReference)
# ---------------------------------------------------------------------------- # ----------------------------------------------------------------------------
IF(LOG) IF(LOG)
...@@ -158,7 +159,7 @@ IF(OPENMM_BUILD_STATIC_LIB) ...@@ -158,7 +159,7 @@ IF(OPENMM_BUILD_STATIC_LIB)
TARGET_LINK_LIBRARIES( ${STATIC_AMOEBA_TARGET} ${STATIC_TARGET} ) TARGET_LINK_LIBRARIES( ${STATIC_AMOEBA_TARGET} ${STATIC_TARGET} )
ENDIF(OPENMM_BUILD_STATIC_LIB) ENDIF(OPENMM_BUILD_STATIC_LIB)
#ADD_SUBDIRECTORY(platforms/reference/tests) ADD_SUBDIRECTORY(platforms/reference/tests)
# Which hardware platforms to build # Which hardware platforms to build
IF(CUDA_FOUND) IF(CUDA_FOUND)
......
plugins/amoeba/openmmapi/include/AmoebaMultipoleForce.h
View file @ 2ef05285
...@@ -113,6 +113,20 @@ public: ...@@ -113,6 +113,20 @@ public:
*/ */
void setCutoffDistance(double distance); 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 * Add multipole-related info for a particle
* *
...@@ -279,6 +293,7 @@ private: ...@@ -279,6 +293,7 @@ private:
AmoebaNonbondedMethod nonbondedMethod; AmoebaNonbondedMethod nonbondedMethod;
double cutoffDistance; double cutoffDistance;
double aewald;
MutualInducedIterationMethod mutualInducedIterationMethod; MutualInducedIterationMethod mutualInducedIterationMethod;
int mutualInducedMaxIterations; int mutualInducedMaxIterations;
double mutualInducedTargetEpsilon; double mutualInducedTargetEpsilon;
......
plugins/amoeba/openmmapi/src/AmoebaMultipoleForce.cpp
View file @ 2ef05285
...@@ -56,6 +56,14 @@ void AmoebaMultipoleForce::setCutoffDistance(double distance) { ...@@ -56,6 +56,14 @@ void AmoebaMultipoleForce::setCutoffDistance(double distance) {
cutoffDistance = distance; cutoffDistance = distance;
} }
double AmoebaMultipoleForce::getAEwald() const {
return aewald;
}
void AmoebaMultipoleForce::setAEwald(double inputAewald ) {
aewald = inputAewald;
}
AmoebaMultipoleForce::MutualInducedIterationMethod AmoebaMultipoleForce::getMutualInducedIterationMethod( void ) const { AmoebaMultipoleForce::MutualInducedIterationMethod AmoebaMultipoleForce::getMutualInducedIterationMethod( void ) const {
return mutualInducedIterationMethod; return mutualInducedIterationMethod;
} }
......
plugins/amoeba/platforms/cuda/src/AmoebaCudaKernels.cpp
View file @ 2ef05285
...@@ -589,6 +589,7 @@ void CudaCalcAmoebaMultipoleForceKernel::initialize(const System& system, const ...@@ -589,6 +589,7 @@ void CudaCalcAmoebaMultipoleForceKernel::initialize(const System& system, const
static_cast<float>( force.getMutualInducedTargetEpsilon()), static_cast<float>( force.getMutualInducedTargetEpsilon()),
nonbondedMethod, nonbondedMethod,
static_cast<float>( force.getCutoffDistance()), static_cast<float>( force.getCutoffDistance()),
static_cast<float>( force.getAEwald()),
static_cast<float>( force.getElectricConstant()) ); static_cast<float>( force.getElectricConstant()) );
if (nonbondedMethod == AmoebaMultipoleForce::PME) { if (nonbondedMethod == AmoebaMultipoleForce::PME) {
double alpha; double alpha;
......
plugins/amoeba/platforms/cuda/src/kernels/AmoebaGpu.cpp
View file @ 2ef05285
...@@ -350,6 +350,7 @@ void gpuPrintCudaAmoebaGmxSimulation(amoebaGpuContext amoebaGpu, FILE* log ) ...@@ -350,6 +350,7 @@ void gpuPrintCudaAmoebaGmxSimulation(amoebaGpuContext amoebaGpu, FILE* log )
(void) fprintf( log, " pP_ScaleIndices %p\n", amoebaGpu->amoebaSim.pP_ScaleIndices ); (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, " pM_ScaleIndices %p\n", amoebaGpu->amoebaSim.pM_ScaleIndices );
(void) fprintf( log, " sqrtPi %15.7e\n", amoebaGpu->amoebaSim.sqrtPi ); (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, " cutoffDistance2 %15.7e\n", amoebaGpu->amoebaSim.cutoffDistance2 );
(void) fprintf( log, " electric %15.7e\n", amoebaGpu->amoebaSim.electric ); (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, " 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 ...@@ -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< std::vector< std::vector<int> > >& multipoleParticleCovalentInfo, const std::vector<int>& covalentDegree,
const std::vector<int>& minCovalentIndices, const std::vector<int>& minCovalentPolarizationIndices, int maxCovalentRange, const std::vector<int>& minCovalentIndices, const std::vector<int>& minCovalentPolarizationIndices, int maxCovalentRange,
int mutualInducedIterativeMethod, int mutualInducedMaxIterations, float mutualInducedTargetEpsilon, 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 ...@@ -1565,9 +1566,8 @@ void gpuSetAmoebaMultipoleParameters(amoebaGpuContext amoebaGpu, const std::vect
amoebaGpu->amoebaSim.cutoffDistance2 = cutoffDistance*cutoffDistance; amoebaGpu->amoebaSim.cutoffDistance2 = cutoffDistance*cutoffDistance;
amoebaGpu->amoebaSim.sqrtPi = sqrt( 3.1415926535897932384626433832795 ); amoebaGpu->amoebaSim.sqrtPi = sqrt( 3.1415926535897932384626433832795 );
amoebaGpu->amoebaSim.electric = electricConstant; amoebaGpu->amoebaSim.electric = electricConstant;
amoebaGpu->gpuContext->sim.alphaEwald = alphaEwald;
amoebaGpu->gpuContext->sim.nonbondedCutoff = cutoffDistance; amoebaGpu->gpuContext->sim.nonbondedCutoff = cutoffDistance;
tabulateErfc(amoebaGpu->gpuContext);
if( amoebaGpu->amoebaSim.dielec < 1.0e-05 ){ if( amoebaGpu->amoebaSim.dielec < 1.0e-05 ){
amoebaGpu->amoebaSim.dielec = 1.0f; amoebaGpu->amoebaSim.dielec = 1.0f;
...@@ -2766,7 +2766,7 @@ void amoebaGpuSetConstants(amoebaGpuContext amoebaGpu) ...@@ -2766,7 +2766,7 @@ void amoebaGpuSetConstants(amoebaGpuContext amoebaGpu)
SetCalculateAmoebaCudaPmeMutualInducedFieldSim( amoebaGpu ); SetCalculateAmoebaCudaPmeMutualInducedFieldSim( amoebaGpu );
SetCalculateAmoebaCudaPmeFixedEFieldSim( amoebaGpu ); SetCalculateAmoebaCudaPmeFixedEFieldSim( amoebaGpu );
SetCalculateAmoebaElectrostaticSim( amoebaGpu ); SetCalculateAmoebaElectrostaticSim( amoebaGpu );
SetCalculateAmoebaRealSpaceEwaldSim( amoebaGpu ); SetCalculateAmoebaPmeDirectElectrostaticSim( amoebaGpu );
SetCalculateAmoebaCudaMapTorquesSim( amoebaGpu ); SetCalculateAmoebaCudaMapTorquesSim( amoebaGpu );
SetCalculateAmoebaKirkwoodSim( amoebaGpu ); SetCalculateAmoebaKirkwoodSim( amoebaGpu );
SetCalculateAmoebaKirkwoodEDiffSim( amoebaGpu ); SetCalculateAmoebaKirkwoodEDiffSim( amoebaGpu );
......
plugins/amoeba/platforms/cuda/src/kernels/amoebaCudaKernels.h
View file @ 2ef05285
...@@ -106,9 +106,9 @@ extern void SetCalculateAmoebaElectrostaticSim( amoebaGpuContext amoebaGpu ); ...@@ -106,9 +106,9 @@ extern void SetCalculateAmoebaElectrostaticSim( amoebaGpuContext amoebaGpu );
extern void GetCalculateAmoebaElectrostaticSim( amoebaGpuContext amoebaGpu ); extern void GetCalculateAmoebaElectrostaticSim( amoebaGpuContext amoebaGpu );
extern void cudaComputeAmoebaElectrostatic( amoebaGpuContext amoebaGpu ); extern void cudaComputeAmoebaElectrostatic( amoebaGpuContext amoebaGpu );
extern void SetCalculateAmoebaRealSpaceEwaldSim( amoebaGpuContext amoebaGpu ); extern void SetCalculateAmoebaPmeDirectElectrostaticSim( amoebaGpuContext amoebaGpu );
extern void GetCalculateAmoebaRealSpaceEwaldSim( amoebaGpuContext amoebaGpu ); extern void GetCalculateAmoebaPmeDirectElectrostaticSim( amoebaGpuContext amoebaGpu );
extern void cudaComputeAmoebaRealSpaceEwald( amoebaGpuContext amoebaGpu ); extern void cudaComputeAmoebaPmeElectrostatic( amoebaGpuContext amoebaGpu );
extern void SetCalculateAmoebaCudaMapTorquesSim(amoebaGpuContext gpu); extern void SetCalculateAmoebaCudaMapTorquesSim(amoebaGpuContext gpu);
extern void GetCalculateAmoebaCudaMapTorquesSim(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 ...@@ -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< std::vector< std::vector<int> > >& multipoleAtomCovalentInfo, const std::vector<int>& covalentDegree,
const std::vector<int>& minCovalentIndices, const std::vector<int>& minCovalentPolarizationIndices, int maxCovalentRange, const std::vector<int>& minCovalentIndices, const std::vector<int>& minCovalentPolarizationIndices, int maxCovalentRange,
int mutualInducedIterationMethod, int mutualInducedMaxIterations, float mutualInducedTargetEpsilon, int mutualInducedIterationMethod, int mutualInducedMaxIterations, float mutualInducedTargetEpsilon,
int nonbondedMethod, float cutoffDistance, float electricConstant ); int nonbondedMethod, float cutoffDistance, float alphaEwald, float electricConstant );
extern "C" extern "C"
......
plugins/amoeba/platforms/cuda/src/kernels/kCalculateAmoebaCudaRealSpaceEwald.h → plugins/amoeba/platforms/cuda/src/kernels/kCalculateAmoebaCudaPmeDirectElectrostatic.h
View file @ 2ef05285
...@@ -34,15 +34,8 @@ __launch_bounds__(128, 1) ...@@ -34,15 +34,8 @@ __launch_bounds__(128, 1)
#else #else
__launch_bounds__(64, 1) __launch_bounds__(64, 1)
#endif #endif
void METHOD_NAME(kCalculateAmoebaCudaRealSpaceEwald, Forces_kernel)( void METHOD_NAME(kCalculateAmoebaPmeDirectElectrostatic, Forces_kernel)(
unsigned int* workUnit, unsigned int* workUnit, float* outputForce, float* outputTorque
float4* atomCoord,
float* labFrameDipole,
float* labFrameQuadrupole,
float* inducedDipole,
float* inducedDipolePolar,
float* outputForce,
float* outputTorque
#ifdef AMOEBA_DEBUG #ifdef AMOEBA_DEBUG
, float4* debugArray, unsigned int targetAtom , float4* debugArray, unsigned int targetAtom
...@@ -50,10 +43,11 @@ void METHOD_NAME(kCalculateAmoebaCudaRealSpaceEwald, Forces_kernel)( ...@@ -50,10 +43,11 @@ void METHOD_NAME(kCalculateAmoebaCudaRealSpaceEwald, Forces_kernel)(
){ ){
#ifdef AMOEBA_DEBUG #ifdef AMOEBA_DEBUG
int pullIndexMax = 12;
float4 pullBack[20]; float4 pullBack[20];
#endif #endif
extern __shared__ RealSpaceEwaldParticle sA[]; extern __shared__ PmeDirectElectrostaticParticle sA[];
unsigned int totalWarps = gridDim.x*blockDim.x/GRID; unsigned int totalWarps = gridDim.x*blockDim.x/GRID;
unsigned int warp = (blockIdx.x*blockDim.x+threadIdx.x)/GRID; unsigned int warp = (blockIdx.x*blockDim.x+threadIdx.x)/GRID;
...@@ -80,12 +74,10 @@ void METHOD_NAME(kCalculateAmoebaCudaRealSpaceEwald, Forces_kernel)( ...@@ -80,12 +74,10 @@ void METHOD_NAME(kCalculateAmoebaCudaRealSpaceEwald, Forces_kernel)(
unsigned int tbx = threadIdx.x - tgx; unsigned int tbx = threadIdx.x - tgx;
unsigned int tj = tgx; unsigned int tj = tgx;
RealSpaceEwaldParticle* psA = &sA[tbx]; PmeDirectElectrostaticParticle* psA = &sA[tbx];
unsigned int atomI = x + tgx; unsigned int atomI = x + tgx;
RealSpaceEwaldParticle localParticle; PmeDirectElectrostaticParticle localParticle;
loadRealSpaceEwaldShared(&localParticle, atomI, loadPmeDirectElectrostaticShared(&localParticle, atomI );
atomCoord, labFrameDipole, labFrameQuadrupole,
inducedDipole, inducedDipolePolar, cAmoebaSim.pDampingFactorAndThole );
localParticle.force[0] = 0.0f; localParticle.force[0] = 0.0f;
localParticle.force[1] = 0.0f; localParticle.force[1] = 0.0f;
...@@ -105,9 +97,7 @@ void METHOD_NAME(kCalculateAmoebaCudaRealSpaceEwald, Forces_kernel)( ...@@ -105,9 +97,7 @@ void METHOD_NAME(kCalculateAmoebaCudaRealSpaceEwald, Forces_kernel)(
// load shared data // load shared data
loadRealSpaceEwaldShared( &(sA[threadIdx.x]), atomI, loadPmeDirectElectrostaticShared( &(sA[threadIdx.x]), atomI );
atomCoord, labFrameDipole, labFrameQuadrupole,
inducedDipole, inducedDipolePolar, cAmoebaSim.pDampingFactorAndThole );
if (!bExclusionFlag) if (!bExclusionFlag)
{ {
...@@ -122,9 +112,8 @@ void METHOD_NAME(kCalculateAmoebaCudaRealSpaceEwald, Forces_kernel)( ...@@ -122,9 +112,8 @@ void METHOD_NAME(kCalculateAmoebaCudaRealSpaceEwald, Forces_kernel)(
float torque[2][3]; float torque[2][3];
float energy; float energy;
calculateRealSpaceEwaldPairIxn_kernel( localParticle, psA[j], calculatePmeDirectElectrostaticPairIxn_kernel( localParticle, psA[j],
cAmoebaSim.scalingDistanceCutoff, scalingFactors, scalingFactors, force, torque, &energy
force, torque, &energy
#ifdef AMOEBA_DEBUG #ifdef AMOEBA_DEBUG
, pullBack , pullBack
#endif #endif
...@@ -171,9 +160,8 @@ void METHOD_NAME(kCalculateAmoebaCudaRealSpaceEwald, Forces_kernel)( ...@@ -171,9 +160,8 @@ void METHOD_NAME(kCalculateAmoebaCudaRealSpaceEwald, Forces_kernel)(
// force // force
float energy; float energy;
calculateRealSpaceEwaldPairIxn_kernel( localParticle, psA[j], calculatePmeDirectElectrostaticPairIxn_kernel( localParticle, psA[j],
cAmoebaSim.scalingDistanceCutoff, scalingFactors, scalingFactors, force, torque, &energy
force, torque, &energy
#ifdef AMOEBA_DEBUG #ifdef AMOEBA_DEBUG
, pullBack , pullBack
#endif #endif
...@@ -199,58 +187,54 @@ void METHOD_NAME(kCalculateAmoebaCudaRealSpaceEwald, Forces_kernel)( ...@@ -199,58 +187,54 @@ void METHOD_NAME(kCalculateAmoebaCudaRealSpaceEwald, Forces_kernel)(
#ifdef AMOEBA_DEBUG #ifdef AMOEBA_DEBUG
if( atomI == targetAtom ){ if( atomI == targetAtom ){
unsigned int index = (atomI == targetAtom) ? atomJ : atomI; unsigned int index = (atomI == targetAtom) ? atomJ : atomI;
float blockId = 1.0f;
debugArray[index].x = (float) atomI; debugArray[index].x = (float) atomI;
debugArray[index].y = (float) atomJ; debugArray[index].y = (float) atomJ;
debugArray[index].z = 1.0f; debugArray[index].z = (float) y;
debugArray[index].w = (float) y; debugArray[index].w = blockId;
/*
index += cAmoebaSim.paddedNumberOfAtoms; index += cAmoebaSim.paddedNumberOfAtoms;
debugArray[index].x = mask ? force[0] : 0.0f; debugArray[index].x = mask ? force[0] : 0.0f;
debugArray[index].y = mask ? force[1] : 0.0f; debugArray[index].y = mask ? force[1] : 0.0f;
debugArray[index].z = mask ? force[2] : 0.0f; debugArray[index].z = mask ? force[2] : 0.0f;
debugArray[index].w = blockId;
index += cAmoebaSim.paddedNumberOfAtoms; index += cAmoebaSim.paddedNumberOfAtoms;
debugArray[index].x = mask ? torque[0][0] : 0.0f; debugArray[index].x = mask ? torque[0][0] : 0.0f;
debugArray[index].y = mask ? torque[0][1] : 0.0f; debugArray[index].y = mask ? torque[0][1] : 0.0f;
debugArray[index].z = mask ? torque[0][2] : 0.0f; debugArray[index].z = mask ? torque[0][2] : 0.0f;
*/ debugArray[index].w = blockId;
index += cAmoebaSim.paddedNumberOfAtoms; index += cAmoebaSim.paddedNumberOfAtoms;
int pullIndex = 0; debugArray[index].x = mask ? torque[0][0] : 0.0f;
debugArray[index].x = pullBack[pullIndex].x; debugArray[index].y = mask ? torque[0][1] : 0.0f;
debugArray[index].y = pullBack[pullIndex].y; debugArray[index].z = mask ? torque[0][2] : 0.0f;
debugArray[index].z = pullBack[pullIndex].z; debugArray[index].w = blockId;
debugArray[index].w = pullBack[pullIndex].w;
index += cAmoebaSim.paddedNumberOfAtoms;
pullIndex++;
debugArray[index].x = pullBack[pullIndex].x;
debugArray[index].y = pullBack[pullIndex].y;
debugArray[index].z = pullBack[pullIndex].z;
debugArray[index].w = pullBack[pullIndex].w;
index += cAmoebaSim.paddedNumberOfAtoms;
pullIndex++;
debugArray[index].x = pullBack[pullIndex].x;
debugArray[index].y = pullBack[pullIndex].y;
debugArray[index].z = pullBack[pullIndex].z;
debugArray[index].w = pullBack[pullIndex].w;
for( int pullIndex = 0; pullIndex < pullIndexMax; pullIndex++ ){
index += cAmoebaSim.paddedNumberOfAtoms; index += cAmoebaSim.paddedNumberOfAtoms;
pullIndex++;
debugArray[index].x = pullBack[pullIndex].x; debugArray[index].x = pullBack[pullIndex].x;
debugArray[index].y = pullBack[pullIndex].y; debugArray[index].y = pullBack[pullIndex].y;
debugArray[index].z = pullBack[pullIndex].z; debugArray[index].z = pullBack[pullIndex].z;
debugArray[index].w = pullBack[pullIndex].w; debugArray[index].w = pullBack[pullIndex].w;
}
} }
#endif #endif
} }
} }
// include self energy and self torque
if( atomI < cAmoebaSim.numberOfAtoms ){
calculatePmeSelfTorqueElectrostaticPairIxn_kernel( localParticle );
//float energy;
//calculatePmeSelfEnergyElectrostaticPairIxn_kernel( localParticle, &energy );
//totalEnergy += energy;
}
// Write results // Write results
#ifdef USE_OUTPUT_BUFFER_PER_WARP #ifdef USE_OUTPUT_BUFFER_PER_WARP
...@@ -300,9 +284,7 @@ if( atomI == targetAtom ){ ...@@ -300,9 +284,7 @@ if( atomI == targetAtom ){
{ {
// load shared data // load shared data
loadRealSpaceEwaldShared( &(sA[threadIdx.x]), (y+tgx), loadPmeDirectElectrostaticShared( &(sA[threadIdx.x]), (y+tgx) );
atomCoord, labFrameDipole, labFrameQuadrupole,
inducedDipole, inducedDipolePolar, cAmoebaSim.pDampingFactorAndThole );
} }
...@@ -325,9 +307,8 @@ if( atomI == targetAtom ){ ...@@ -325,9 +307,8 @@ if( atomI == targetAtom ){
unsigned int atomJ = y + tj; unsigned int atomJ = y + tj;
float energy; float energy;
calculateRealSpaceEwaldPairIxn_kernel( localParticle, psA[tj], calculatePmeDirectElectrostaticPairIxn_kernel( localParticle, psA[tj],
cAmoebaSim.scalingDistanceCutoff, scalingFactors, scalingFactors, force, torque, &energy
force, torque, &energy
#ifdef AMOEBA_DEBUG #ifdef AMOEBA_DEBUG
, pullBack , pullBack
#endif #endif
...@@ -360,60 +341,44 @@ if( atomI == targetAtom ){ ...@@ -360,60 +341,44 @@ if( atomI == targetAtom ){
#ifdef AMOEBA_DEBUG #ifdef AMOEBA_DEBUG
if( atomI == targetAtom || atomJ == targetAtom ){ if( atomI == targetAtom || atomJ == targetAtom ){
unsigned int index = (atomI == targetAtom) ? atomJ : atomI; unsigned int index = (atomI == targetAtom) ? atomJ : atomI;
unsigned int indexI = (atomI == targetAtom) ? 0 : 1; unsigned int indexI = (atomI == targetAtom) ? 0 : 1;
unsigned int indexJ = (atomI == targetAtom) ? 1 : 0; unsigned int indexJ = (atomI == targetAtom) ? 1 : 0;
float forceSign = (atomI == targetAtom) ? 1.0f : -1.0f; float forceSign = (atomI == targetAtom) ? 1.0f : -1.0f;
float blockId = 2.0f;
debugArray[index].x = (float) atomI; debugArray[index].x = (float) atomI;
debugArray[index].y = (float) atomJ; debugArray[index].y = (float) atomJ;
debugArray[index].z = 2.0f; debugArray[index].z = (float) y;
debugArray[index].w = (float) y; debugArray[index].w = blockId;
/*
index += cAmoebaSim.paddedNumberOfAtoms; index += cAmoebaSim.paddedNumberOfAtoms;
debugArray[index].x = mask ? forceSign*force[0] : 0.0f; debugArray[index].x = mask ? forceSign*force[0] : 0.0f;
debugArray[index].y = mask ? forceSign*force[1] : 0.0f; debugArray[index].y = mask ? forceSign*force[1] : 0.0f;
debugArray[index].z = mask ? forceSign*force[2] : 0.0f; debugArray[index].z = mask ? forceSign*force[2] : 0.0f;
debugArray[index].w = blockId;
index += cAmoebaSim.paddedNumberOfAtoms; index += cAmoebaSim.paddedNumberOfAtoms;
debugArray[index].x = mask ? torque[indexI][0] : 0.0f; debugArray[index].x = mask ? torque[indexI][0] : 0.0f;
debugArray[index].y = mask ? torque[indexI][1] : 0.0f; debugArray[index].y = mask ? torque[indexI][1] : 0.0f;
debugArray[index].z = mask ? torque[indexI][2] : 0.0f; debugArray[index].z = mask ? torque[indexI][2] : 0.0f;
debugArray[index].w = blockId;
index += cAmoebaSim.paddedNumberOfAtoms; index += cAmoebaSim.paddedNumberOfAtoms;
debugArray[index].x = mask ? torque[indexJ][0] : 0.0f; debugArray[index].x = mask ? torque[indexJ][0] : 0.0f;
debugArray[index].y = mask ? torque[indexJ][1] : 0.0f; debugArray[index].y = mask ? torque[indexJ][1] : 0.0f;
debugArray[index].z = mask ? torque[indexJ][2] : 0.0f; debugArray[index].z = mask ? torque[indexJ][2] : 0.0f;
*/ debugArray[index].w = blockId;
index += cAmoebaSim.paddedNumberOfAtoms;
int pullIndex = 0;
debugArray[index].x = pullBack[pullIndex].x;
debugArray[index].y = pullBack[pullIndex].y;
debugArray[index].z = pullBack[pullIndex].z;
debugArray[index].w = pullBack[pullIndex].w;
for( int pullIndex = 0; pullIndex < pullIndexMax; pullIndex++ ){
index += cAmoebaSim.paddedNumberOfAtoms; index += cAmoebaSim.paddedNumberOfAtoms;
pullIndex++;
debugArray[index].x = pullBack[pullIndex].x; debugArray[index].x = pullBack[pullIndex].x;
debugArray[index].y = pullBack[pullIndex].y; debugArray[index].y = pullBack[pullIndex].y;
debugArray[index].z = pullBack[pullIndex].z; debugArray[index].z = pullBack[pullIndex].z;
debugArray[index].w = pullBack[pullIndex].w; debugArray[index].w = pullBack[pullIndex].w;
}
index += cAmoebaSim.paddedNumberOfAtoms;
pullIndex++;
debugArray[index].x = pullBack[pullIndex].x;
debugArray[index].y = pullBack[pullIndex].y;
debugArray[index].z = pullBack[pullIndex].z;
debugArray[index].w = pullBack[pullIndex].w;
index += cAmoebaSim.paddedNumberOfAtoms;
pullIndex++;
debugArray[index].x = pullBack[pullIndex].x;
debugArray[index].y = pullBack[pullIndex].y;
debugArray[index].z = pullBack[pullIndex].z;
debugArray[index].w = pullBack[pullIndex].w;
} }
#endif #endif
...@@ -449,9 +414,8 @@ if( atomI == targetAtom || atomJ == targetAtom ){ ...@@ -449,9 +414,8 @@ if( atomI == targetAtom || atomJ == targetAtom ){
// force // force
float energy; float energy;
calculateRealSpaceEwaldPairIxn_kernel( localParticle, psA[tj], calculatePmeDirectElectrostaticPairIxn_kernel( localParticle, psA[tj],
cAmoebaSim.scalingDistanceCutoff, scalingFactors, scalingFactors, force, torque, &energy
force, torque, &energy
#ifdef AMOEBA_DEBUG #ifdef AMOEBA_DEBUG
, pullBack , pullBack
#endif #endif
...@@ -490,55 +454,39 @@ if( atomI == targetAtom || atomJ == targetAtom ){ ...@@ -490,55 +454,39 @@ if( atomI == targetAtom || atomJ == targetAtom ){
unsigned int indexI = (atomI == targetAtom) ? 0 : 1; unsigned int indexI = (atomI == targetAtom) ? 0 : 1;
unsigned int indexJ = (atomI == targetAtom) ? 1 : 0; unsigned int indexJ = (atomI == targetAtom) ? 1 : 0;
float forceSign = (atomI == targetAtom) ? 1.0f : -1.0f; float forceSign = (atomI == targetAtom) ? 1.0f : -1.0f;
float blockId = 3.0f;
debugArray[index].x = (float) atomI; debugArray[index].x = (float) atomI;
debugArray[index].y = (float) atomJ; debugArray[index].y = (float) atomJ;
debugArray[index].z = 3.0f; debugArray[index].z = (float) y;
debugArray[index].w = (float) y; debugArray[index].w = blockId;
/*
index += cAmoebaSim.paddedNumberOfAtoms; index += cAmoebaSim.paddedNumberOfAtoms;
debugArray[index].x = mask ? forceSign*force[0] : 0.0f; debugArray[index].x = mask ? forceSign*force[0] : 0.0f;
debugArray[index].y = mask ? forceSign*force[1] : 0.0f; debugArray[index].y = mask ? forceSign*force[1] : 0.0f;
debugArray[index].z = mask ? forceSign*force[2] : 0.0f; debugArray[index].z = mask ? forceSign*force[2] : 0.0f;
debugArray[index].w = blockId;
index += cAmoebaSim.paddedNumberOfAtoms; index += cAmoebaSim.paddedNumberOfAtoms;
debugArray[index].x = mask ? torque[indexI][0] : 0.0f; debugArray[index].x = mask ? torque[indexI][0] : 0.0f;
debugArray[index].y = mask ? torque[indexI][1] : 0.0f; debugArray[index].y = mask ? torque[indexI][1] : 0.0f;
debugArray[index].z = mask ? torque[indexI][2] : 0.0f; debugArray[index].z = mask ? torque[indexI][2] : 0.0f;
debugArray[index].w = blockId;
index += cAmoebaSim.paddedNumberOfAtoms; index += cAmoebaSim.paddedNumberOfAtoms;
debugArray[index].x = mask ? torque[indexJ][0] : 0.0f; debugArray[index].x = mask ? torque[indexJ][0] : 0.0f;
debugArray[index].y = mask ? torque[indexJ][1] : 0.0f; debugArray[index].y = mask ? torque[indexJ][1] : 0.0f;
debugArray[index].z = mask ? torque[indexJ][2] : 0.0f; debugArray[index].z = mask ? torque[indexJ][2] : 0.0f;
*/ debugArray[index].w = blockId;
index += cAmoebaSim.paddedNumberOfAtoms;
int pullIndex = 0;
debugArray[index].x = pullBack[pullIndex].x;
debugArray[index].y = pullBack[pullIndex].y;
debugArray[index].z = pullBack[pullIndex].z;
debugArray[index].w = pullBack[pullIndex].w;
index += cAmoebaSim.paddedNumberOfAtoms;
pullIndex++;
debugArray[index].x = pullBack[pullIndex].x;
debugArray[index].y = pullBack[pullIndex].y;
debugArray[index].z = pullBack[pullIndex].z;
debugArray[index].w = pullBack[pullIndex].w;
index += cAmoebaSim.paddedNumberOfAtoms;
pullIndex++;
debugArray[index].x = pullBack[pullIndex].x;
debugArray[index].y = pullBack[pullIndex].y;
debugArray[index].z = pullBack[pullIndex].z;
debugArray[index].w = pullBack[pullIndex].w;
for( int pullIndex = 0; pullIndex < pullIndexMax; pullIndex++ ){
index += cAmoebaSim.paddedNumberOfAtoms; index += cAmoebaSim.paddedNumberOfAtoms;
pullIndex++;
debugArray[index].x = pullBack[pullIndex].x; debugArray[index].x = pullBack[pullIndex].x;
debugArray[index].y = pullBack[pullIndex].y; debugArray[index].y = pullBack[pullIndex].y;
debugArray[index].z = pullBack[pullIndex].z; debugArray[index].z = pullBack[pullIndex].z;
debugArray[index].w = pullBack[pullIndex].w; debugArray[index].w = pullBack[pullIndex].w;
}
#if 0 #if 0
index += cAmoebaSim.paddedNumberOfAtoms; index += cAmoebaSim.paddedNumberOfAtoms;
...@@ -550,13 +498,6 @@ if( atomI == targetAtom || atomJ == targetAtom ){ ...@@ -550,13 +498,6 @@ if( atomI == targetAtom || atomJ == targetAtom ){
index += cAmoebaSim.paddedNumberOfAtoms; index += cAmoebaSim.paddedNumberOfAtoms;
debugArray[index].x = scalingFactors[MScaleIndex]; debugArray[index].x = scalingFactors[MScaleIndex];
debugArray[index].y = mScaleVal; debugArray[index].y = mScaleVal;
for( int pIndex = 0; pIndex < 14; pIndex++ ){
index += cAmoebaSim.paddedNumberOfAtoms;
debugArray[index].x = pullBack[pIndex].x;
debugArray[index].y = pullBack[pIndex].y;
debugArray[index].z = pullBack[pIndex].z;
debugArray[index].w = pullBack[pIndex].w;
}
index += cAmoebaSim.paddedNumberOfAtoms; index += cAmoebaSim.paddedNumberOfAtoms;
debugArray[index].x = labFrameDipole[3*atomI]; debugArray[index].x = labFrameDipole[3*atomI];
......
plugins/amoeba/platforms/cuda/src/kernels/kCalculateAmoebaCudaPmeFixedEField.cu
View file @ 2ef05285
...@@ -322,7 +322,7 @@ __device__ void calculateFixedFieldRealSpacePairIxn_kernel( FixedFieldParticle& ...@@ -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 ) ...@@ -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 ...@@ -616,6 +616,7 @@ static void cudaComputeAmoebaPmeMutualInducedFieldBySOR( amoebaGpuContext amoeba
// matrix multiply // matrix multiply
cudaComputeAmoebaPmeMutualInducedFieldMatrixMultiply( amoebaGpu, amoebaGpu->psWorkVector[0], amoebaGpu->psWorkVector[1] ); cudaComputeAmoebaPmeMutualInducedFieldMatrixMultiply( amoebaGpu, amoebaGpu->psWorkVector[0], amoebaGpu->psWorkVector[1] );
kCalculateAmoebaPMEInducedDipoleField( amoebaGpu );
LAUNCHERROR("cudaComputeAmoebaPmeMutualInducedFieldMatrixMultiply Loop\n"); LAUNCHERROR("cudaComputeAmoebaPmeMutualInducedFieldMatrixMultiply Loop\n");
......
plugins/amoeba/platforms/cuda/src/kernels/kCalculateAmoebaRotateFrame.cu
View file @ 2ef05285
...@@ -390,7 +390,7 @@ void kCalculateAmoebaMultipoleForces(amoebaGpuContext amoebaGpu, bool hasAmoebaG ...@@ -390,7 +390,7 @@ void kCalculateAmoebaMultipoleForces(amoebaGpuContext amoebaGpu, bool hasAmoebaG
if( amoebaGpu->multipoleNonbondedMethod == AMOEBA_NO_CUTOFF ){ if( amoebaGpu->multipoleNonbondedMethod == AMOEBA_NO_CUTOFF ){
cudaComputeAmoebaElectrostatic( amoebaGpu ); cudaComputeAmoebaElectrostatic( amoebaGpu );
} else { } else {
cudaComputeAmoebaRealSpaceEwald( amoebaGpu ); cudaComputeAmoebaPmeElectrostatic( amoebaGpu );
} }
// map torques to forces // 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 ...@@ -2008,6 +2008,7 @@ static int readAmoebaMultipoleParameters( FILE* filePtr, int version, MapStringI
multipoleForce->setNonbondedMethod( AmoebaMultipoleForce::NoCutoff ); multipoleForce->setNonbondedMethod( AmoebaMultipoleForce::NoCutoff );
} }
multipoleForce->setCutoffDistance( cutoffDistance ); 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]) ); 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 ){ if( log ){
(void) fprintf( log, "%s number of MultipoleParameter terms=%d usePme=%d aewald=%15.7e cutoffDistance=%12.4f\n", (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 ...@@ -2111,6 +2112,7 @@ static int readAmoebaMultipoleParameters( FILE* filePtr, int version, MapStringI
double polarityConversion = AngstromToNm*AngstromToNm*AngstromToNm; double polarityConversion = AngstromToNm*AngstromToNm*AngstromToNm;
double dampingFactorConversion = sqrt( AngstromToNm ); double dampingFactorConversion = sqrt( AngstromToNm );
multipoleForce->setAEwald( multipoleForce->getAEwald()/AngstromToNm );
multipoleForce->setCutoffDistance( multipoleForce->getCutoffDistance()*AngstromToNm ); multipoleForce->setCutoffDistance( multipoleForce->getCutoffDistance()*AngstromToNm );
multipoleForce->setScalingDistanceCutoff( multipoleForce->getScalingDistanceCutoff()*AngstromToNm ); multipoleForce->setScalingDistanceCutoff( multipoleForce->getScalingDistanceCutoff()*AngstromToNm );
...@@ -2165,8 +2167,8 @@ static int readAmoebaMultipoleParameters( FILE* filePtr, int version, MapStringI ...@@ -2165,8 +2167,8 @@ static int readAmoebaMultipoleParameters( FILE* filePtr, int version, MapStringI
(useOpenMMUnits ? "OpenMM" : "Amoeba") ); (useOpenMMUnits ? "OpenMM" : "Amoeba") );
std::string nonbondedMethod = multipoleForce->getNonbondedMethod( ) == AmoebaMultipoleForce::PME ? "PME" : "NoCutoff"; std::string nonbondedMethod = multipoleForce->getNonbondedMethod( ) == AmoebaMultipoleForce::PME ? "PME" : "NoCutoff";
(void) fprintf( log, "NonbondedMethod=%s cutoff=%15.7e.\n", nonbondedMethod.c_str(), (void) fprintf( log, "NonbondedMethod=%s aEwald=%15.7e cutoff=%15.7e.\n", nonbondedMethod.c_str(),
multipoleForce->getCutoffDistance() ); multipoleForce->getAEwald(), multipoleForce->getCutoffDistance() );
Vec3 a,b,c; Vec3 a,b,c;
system.getDefaultPeriodicBoxVectors( a, b, c ); system.getDefaultPeriodicBoxVectors( a, b, c );
......
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