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Commit 047934e2 authored by Rafal P. Wiewiora's avatar Rafal P. Wiewiora
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Merge remote-tracking branch 'upstream/master'

parents ce3a5dc0 d12c9bd1
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Showing with 386 additions and 295 deletions
platforms/reference/tests/TestReferenceNeighborList.cpp
View file @ 047934e2
......@@ -41,14 +41,14 @@ using namespace OpenMM;
void testNeighborList()
{
vector<RealVec> particleList(2);
particleList[0] = RealVec(13.6, 0, 0);
particleList[1] = RealVec(0, 0, 0);
vector<Vec3> particleList(2);
particleList[0] = Vec3(13.6, 0, 0);
particleList[1] = Vec3(0, 0, 0);
vector<set<int> > exclusions(2);
NeighborList neighborList;
RealVec boxVectors[3];
Vec3 boxVectors[3];
computeNeighborListNaive(neighborList, 2, particleList, exclusions, boxVectors, false, 13.7, 0.01);
assert(neighborList.size() == 1);
......@@ -62,15 +62,15 @@ void testNeighborList()
assert(neighborList.size() == 0);
}
double distance2(RealVec& pos1, RealVec& pos2, const RealVec* periodicBoxVectors) {
RealVec diff = pos1-pos2;
double distance2(Vec3& pos1, Vec3& pos2, const Vec3* periodicBoxVectors) {
Vec3 diff = pos1-pos2;
diff -= periodicBoxVectors[2]*floor(diff[2]/periodicBoxVectors[2][2]+0.5);
diff -= periodicBoxVectors[1]*floor(diff[1]/periodicBoxVectors[1][1]+0.5);
diff -= periodicBoxVectors[0]*floor(diff[0]/periodicBoxVectors[0][0]+0.5);
return diff.dot(diff);
}
void verifyNeighborList(NeighborList& list, int numParticles, vector<RealVec>& positions, const RealVec* periodicBoxVectors, double cutoff) {
void verifyNeighborList(NeighborList& list, int numParticles, vector<Vec3>& positions, const Vec3* periodicBoxVectors, double cutoff) {
for (int i = 0; i < (int) list.size(); i++) {
int particle1 = list[i].first;
int particle2 = list[i].second;
......@@ -87,18 +87,18 @@ void verifyNeighborList(NeighborList& list, int numParticles, vector<RealVec>& p
void testPeriodic() {
const int numParticles = 100;
const double cutoff = 3.0;
RealVec periodicBoxVectors[3];
periodicBoxVectors[0] = RealVec(20, 0, 0);
periodicBoxVectors[1] = RealVec(0, 15, 0);
periodicBoxVectors[2] = RealVec(0, 0, 22);
vector<RealVec> particleList(numParticles);
Vec3 periodicBoxVectors[3];
periodicBoxVectors[0] = Vec3(20, 0, 0);
periodicBoxVectors[1] = Vec3(0, 15, 0);
periodicBoxVectors[2] = Vec3(0, 0, 22);
vector<Vec3> particleList(numParticles);
OpenMM_SFMT::SFMT sfmt;
init_gen_rand(0, sfmt);
for (int i = 0; i <numParticles; i++) {
particleList[i][0] = (RealOpenMM) (genrand_real2(sfmt)*periodicBoxVectors[0][0]*3);
particleList[i][1] = (RealOpenMM) (genrand_real2(sfmt)*periodicBoxVectors[1][1]*3);
particleList[i][2] = (RealOpenMM) (genrand_real2(sfmt)*periodicBoxVectors[2][2]*3);
particleList[i][0] = genrand_real2(sfmt)*periodicBoxVectors[0][0]*3;
particleList[i][1] = genrand_real2(sfmt)*periodicBoxVectors[1][1]*3;
particleList[i][2] = genrand_real2(sfmt)*periodicBoxVectors[2][2]*3;
}
vector<set<int> > exclusions(numParticles);
NeighborList neighborList;
......@@ -111,18 +111,18 @@ void testPeriodic() {
void testTriclinic() {
const int numParticles = 1000;
const double cutoff = 3.0;
RealVec periodicBoxVectors[3];
periodicBoxVectors[0] = RealVec(20, 0, 0);
periodicBoxVectors[1] = RealVec(5, 15, 0);
periodicBoxVectors[2] = RealVec(-3, -7, 22);
vector<RealVec> particleList(numParticles);
Vec3 periodicBoxVectors[3];
periodicBoxVectors[0] = Vec3(20, 0, 0);
periodicBoxVectors[1] = Vec3(5, 15, 0);
periodicBoxVectors[2] = Vec3(-3, -7, 22);
vector<Vec3> particleList(numParticles);
OpenMM_SFMT::SFMT sfmt;
init_gen_rand(0, sfmt);
for (int i = 0; i <numParticles; i++) {
particleList[i][0] = (RealOpenMM) (genrand_real2(sfmt)*periodicBoxVectors[0][0]*3);
particleList[i][1] = (RealOpenMM) (genrand_real2(sfmt)*periodicBoxVectors[1][1]*3);
particleList[i][2] = (RealOpenMM) (genrand_real2(sfmt)*periodicBoxVectors[2][2]*3);
particleList[i][0] = genrand_real2(sfmt)*periodicBoxVectors[0][0]*3;
particleList[i][1] = genrand_real2(sfmt)*periodicBoxVectors[1][1]*3;
particleList[i][2] = genrand_real2(sfmt)*periodicBoxVectors[2][2]*3;
}
vector<set<int> > exclusions(numParticles);
NeighborList neighborList;
......
plugins/amoeba/openmmapi/src/AmoebaAngleForceImpl.cpp
View file @ 047934e2
......@@ -64,4 +64,5 @@ std::vector<std::string> AmoebaAngleForceImpl::getKernelNames() {
void AmoebaAngleForceImpl::updateParametersInContext(ContextImpl& context) {
kernel.getAs<CalcAmoebaAngleForceKernel>().copyParametersToContext(context, owner);
context.systemChanged();
}
plugins/amoeba/openmmapi/src/AmoebaBondForceImpl.cpp
View file @ 047934e2
......@@ -75,4 +75,5 @@ vector<pair<int, int> > AmoebaBondForceImpl::getBondedParticles() const {
void AmoebaBondForceImpl::updateParametersInContext(ContextImpl& context) {
kernel.getAs<CalcAmoebaBondForceKernel>().copyParametersToContext(context, owner);
context.systemChanged();
}
plugins/amoeba/openmmapi/src/AmoebaGeneralizedKirkwoodForceImpl.cpp
View file @ 047934e2
......@@ -66,4 +66,5 @@ std::vector<std::string> AmoebaGeneralizedKirkwoodForceImpl::getKernelNames() {
void AmoebaGeneralizedKirkwoodForceImpl::updateParametersInContext(ContextImpl& context) {
kernel.getAs<CalcAmoebaGeneralizedKirkwoodForceKernel>().copyParametersToContext(context, owner);
context.systemChanged();
}
plugins/amoeba/openmmapi/src/AmoebaInPlaneAngleForceImpl.cpp
View file @ 047934e2
......@@ -64,4 +64,5 @@ std::vector<std::string> AmoebaInPlaneAngleForceImpl::getKernelNames() {
void AmoebaInPlaneAngleForceImpl::updateParametersInContext(ContextImpl& context) {
kernel.getAs<CalcAmoebaInPlaneAngleForceKernel>().copyParametersToContext(context, owner);
context.systemChanged();
}
plugins/amoeba/openmmapi/src/AmoebaMultipoleForceImpl.cpp
View file @ 047934e2
......@@ -50,7 +50,8 @@ AmoebaMultipoleForceImpl::~AmoebaMultipoleForceImpl() {
void AmoebaMultipoleForceImpl::initialize(ContextImpl& context) {
const System& system = context.getSystem();
if (owner.getNumMultipoles() != system.getNumParticles())
int numParticles = system.getNumParticles();
if (owner.getNumMultipoles() != numParticles)
throw OpenMMException("AmoebaMultipoleForce must have exactly as many particles as the System it belongs to.");
// check cutoff < 0.5*boxSize
......@@ -64,7 +65,7 @@ void AmoebaMultipoleForceImpl::initialize(ContextImpl& context) {
}
double quadrupoleValidationTolerance = 1.0e-05;
for (int ii = 0; ii < system.getNumParticles(); ii++) {
for (int ii = 0; ii < numParticles; ii++) {
int axisType, multipoleAtomZ, multipoleAtomX, multipoleAtomY;
double charge, thole, dampingFactor, polarity ;
......@@ -121,6 +122,23 @@ void AmoebaMultipoleForceImpl::initialize(ContextImpl& context) {
buffer << "] (ZThenX, Bisector, Z-Bisect, ThreeFold, NoAxisType) currently handled .";
throw OpenMMException(buffer.str());
}
if (axisType != AmoebaMultipoleForce::NoAxisType && (multipoleAtomZ < 0 || multipoleAtomZ >= numParticles)) {
std::stringstream buffer;
buffer << "AmoebaMultipoleForce: invalid z axis particle: " << multipoleAtomZ;
throw OpenMMException(buffer.str());
}
if (axisType != AmoebaMultipoleForce::NoAxisType && axisType != AmoebaMultipoleForce::ZOnly &&
(multipoleAtomX < 0 || multipoleAtomX >= numParticles)) {
std::stringstream buffer;
buffer << "AmoebaMultipoleForce: invalid x axis particle: " << multipoleAtomX;
throw OpenMMException(buffer.str());
}
if ((axisType == AmoebaMultipoleForce::ZBisect || axisType == AmoebaMultipoleForce::ThreeFold) &&
(multipoleAtomY < 0 || multipoleAtomY >= numParticles)) {
std::stringstream buffer;
buffer << "AmoebaMultipoleForce: invalid y axis particle: " << multipoleAtomY;
throw OpenMMException(buffer.str());
}
}
kernel = context.getPlatform().createKernel(CalcAmoebaMultipoleForceKernel::Name(), context);
kernel.getAs<CalcAmoebaMultipoleForceKernel>().initialize(context.getSystem(), owner);
......@@ -206,6 +224,7 @@ void AmoebaMultipoleForceImpl::getSystemMultipoleMoments(ContextImpl& context, s
void AmoebaMultipoleForceImpl::updateParametersInContext(ContextImpl& context) {
kernel.getAs<CalcAmoebaMultipoleForceKernel>().copyParametersToContext(context, owner);
context.systemChanged();
}
void AmoebaMultipoleForceImpl::getPMEParameters(double& alpha, int& nx, int& ny, int& nz) const {
......
plugins/amoeba/openmmapi/src/AmoebaOutOfPlaneBendForceImpl.cpp
View file @ 047934e2
......@@ -64,4 +64,5 @@ std::vector<std::string> AmoebaOutOfPlaneBendForceImpl::getKernelNames() {
void AmoebaOutOfPlaneBendForceImpl::updateParametersInContext(ContextImpl& context) {
kernel.getAs<CalcAmoebaOutOfPlaneBendForceKernel>().copyParametersToContext(context, owner);
context.systemChanged();
}
plugins/amoeba/openmmapi/src/AmoebaPiTorsionForceImpl.cpp
View file @ 047934e2
......@@ -64,4 +64,5 @@ std::vector<std::string> AmoebaPiTorsionForceImpl::getKernelNames() {
void AmoebaPiTorsionForceImpl::updateParametersInContext(ContextImpl& context) {
kernel.getAs<CalcAmoebaPiTorsionForceKernel>().copyParametersToContext(context, owner);
context.systemChanged();
}
plugins/amoeba/openmmapi/src/AmoebaStretchBendForceImpl.cpp
View file @ 047934e2
......@@ -64,4 +64,5 @@ std::vector<std::string> AmoebaStretchBendForceImpl::getKernelNames() {
void AmoebaStretchBendForceImpl::updateParametersInContext(ContextImpl& context) {
kernel.getAs<CalcAmoebaStretchBendForceKernel>().copyParametersToContext(context, owner);
context.systemChanged();
}
plugins/amoeba/platforms/cuda/CMakeLists.txt
View file @ 047934e2
......@@ -21,6 +21,7 @@ SET(OPENMM_SOURCE_SUBDIRS .)
SET(OPENMMAMOEBACUDA_LIBRARY_NAME OpenMMAmoebaCUDA)
SET(SHARED_TARGET ${OPENMMAMOEBACUDA_LIBRARY_NAME})
SET(STATIC_TARGET ${OPENMMAMOEBACUDA_LIBRARY_NAME}_static)
# These are all the places to search for header files which are
......@@ -85,17 +86,42 @@ ADD_CUSTOM_COMMAND(OUTPUT ${CUDA_KERNELS_CPP} ${CUDA_KERNELS_H}
DEPENDS ${CUDA_KERNELS}
)
SET_SOURCE_FILES_PROPERTIES(${CUDA_KERNELS_CPP} ${CUDA_KERNELS_H} PROPERTIES GENERATED TRUE)
ADD_LIBRARY(${SHARED_TARGET} SHARED ${SOURCE_FILES} ${SOURCE_INCLUDE_FILES} ${API_ABS_INCLUDE_FILES})
TARGET_LINK_LIBRARIES(${SHARED_TARGET} ${OPENMM_LIBRARY_NAME} ${PTHREADS_LIB})
TARGET_LINK_LIBRARIES(${SHARED_TARGET} ${OPENMM_LIBRARY_NAME}CUDA)
TARGET_LINK_LIBRARIES(${SHARED_TARGET} ${SHARED_AMOEBA_TARGET})
SET_TARGET_PROPERTIES(${SHARED_TARGET} PROPERTIES COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS} -DOPENMM_BUILDING_SHARED_LIBRARY")
IF (APPLE)
# Build the shared plugin library.
IF (OPENMM_BUILD_SHARED_LIB)
ADD_LIBRARY(${SHARED_TARGET} SHARED ${SOURCE_FILES} ${SOURCE_INCLUDE_FILES} ${API_ABS_INCLUDE_FILES})
TARGET_LINK_LIBRARIES(${SHARED_TARGET} ${OPENMM_LIBRARY_NAME} ${PTHREADS_LIB})
TARGET_LINK_LIBRARIES(${SHARED_TARGET} ${OPENMM_LIBRARY_NAME}CUDA)
TARGET_LINK_LIBRARIES(${SHARED_TARGET} ${SHARED_AMOEBA_TARGET})
SET_TARGET_PROPERTIES(${SHARED_TARGET} PROPERTIES COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS} -DOPENMM_BUILDING_SHARED_LIBRARY")
IF (APPLE)
SET_TARGET_PROPERTIES(${SHARED_TARGET} PROPERTIES LINK_FLAGS "${EXTRA_COMPILE_FLAGS} -F/Library/Frameworks -framework CUDA")
ELSE (APPLE)
ELSE (APPLE)
SET_TARGET_PROPERTIES(${SHARED_TARGET} PROPERTIES LINK_FLAGS "${EXTRA_LINK_FLAGS}")
ENDIF (APPLE)
ENDIF (APPLE)
INSTALL_TARGETS(/lib/plugins RUNTIME_DIRECTORY /lib/plugins ${SHARED_TARGET})
ENDIF (OPENMM_BUILD_SHARED_LIB)
# Build the static plugin library.
IF(OPENMM_BUILD_STATIC_LIB)
ADD_LIBRARY(${STATIC_TARGET} STATIC ${SOURCE_FILES} ${SOURCE_INCLUDE_FILES} ${API_ABS_INCLUDE_FILES})
TARGET_LINK_LIBRARIES(${STATIC_TARGET} ${OPENMM_LIBRARY_NAME} ${PTHREADS_LIB})
TARGET_LINK_LIBRARIES(${STATIC_TARGET} ${OPENMM_LIBRARY_NAME}CUDA)
TARGET_LINK_LIBRARIES(${STATIC_TARGET} ${STATIC_AMOEBA_TARGET})
SET_TARGET_PROPERTIES(${STATIC_TARGET} PROPERTIES COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS} -DOPENMM_BUILDING_STATIC_LIBRARY")
IF (APPLE)
SET_TARGET_PROPERTIES(${STATIC_TARGET} PROPERTIES LINK_FLAGS "${EXTRA_COMPILE_FLAGS} -F/Library/Frameworks -framework CUDA")
ELSE (APPLE)
SET_TARGET_PROPERTIES(${STATIC_TARGET} PROPERTIES LINK_FLAGS "${EXTRA_LINK_FLAGS}")
ENDIF (APPLE)
INSTALL_TARGETS(/lib/plugins RUNTIME_DIRECTORY /lib/plugins ${STATIC_TARGET})
ENDIF(OPENMM_BUILD_STATIC_LIB)
INSTALL(TARGETS ${SHARED_TARGET} DESTINATION ${CMAKE_INSTALL_PREFIX}/lib/plugins)
# Ensure that links to the main CUDA library will be resolved.
......
plugins/amoeba/platforms/cuda/src/AmoebaCudaKernelFactory.cpp
View file @ 047934e2
......@@ -6,7 +6,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2008-2012 Stanford University and the Authors. *
* Portions copyright (c) 2008-2016 Stanford University and the Authors. *
* Authors: Mark Friedrichs, Peter Eastman *
* Contributors: *
* *
......@@ -33,10 +33,18 @@
using namespace OpenMM;
#ifdef OPENMM_BUILDING_STATIC_LIBRARY
static void registerPlatforms() {
#else
extern "C" OPENMM_EXPORT void registerPlatforms() {
#endif
}
#ifdef OPENMM_BUILDING_STATIC_LIBRARY
static void registerKernelFactories() {
#else
extern "C" OPENMM_EXPORT void registerKernelFactories() {
#endif
try {
Platform& platform = Platform::getPlatformByName("CUDA");
AmoebaCudaKernelFactory* factory = new AmoebaCudaKernelFactory();
......
plugins/amoeba/platforms/cuda/src/AmoebaCudaKernels.cpp
View file @ 047934e2
......@@ -41,7 +41,7 @@
#include "CudaForceInfo.h"
#include "CudaKernelSources.h"
#include "CudaNonbondedUtilities.h"
#include "jama_svd.h"
#include "jama_lu.h"
#include <algorithm>
#include <cmath>
......@@ -52,10 +52,10 @@
using namespace OpenMM;
using namespace std;
#define CHECK_RESULT(result) \
#define CHECK_RESULT(result, prefix) \
if (result != CUDA_SUCCESS) { \
std::stringstream m; \
m<<errorMessage<<": "<<cu.getErrorString(result)<<" ("<<result<<")"<<" at "<<__FILE__<<":"<<__LINE__; \
m<<prefix<<": "<<cu.getErrorString(result)<<" ("<<result<<")"<<" at "<<__FILE__<<":"<<__LINE__; \
throw OpenMMException(m.str());\
}
......@@ -813,7 +813,7 @@ private:
};
CudaCalcAmoebaMultipoleForceKernel::CudaCalcAmoebaMultipoleForceKernel(std::string name, const Platform& platform, CudaContext& cu, const System& system) :
CalcAmoebaMultipoleForceKernel(name, platform), cu(cu), system(system), hasInitializedScaleFactors(false), hasInitializedFFT(false), multipolesAreValid(false),
CalcAmoebaMultipoleForceKernel(name, platform), cu(cu), system(system), hasInitializedScaleFactors(false), hasInitializedFFT(false), multipolesAreValid(false), hasCreatedEvent(false),
multipoleParticles(NULL), molecularDipoles(NULL), molecularQuadrupoles(NULL), labFrameDipoles(NULL), labFrameQuadrupoles(NULL), sphericalDipoles(NULL), sphericalQuadrupoles(NULL),
fracDipoles(NULL), fracQuadrupoles(NULL), field(NULL), fieldPolar(NULL), inducedField(NULL), inducedFieldPolar(NULL), torque(NULL), dampingAndThole(NULL), inducedDipole(NULL),
diisCoefficients(NULL), inducedDipolePolar(NULL), inducedDipoleErrors(NULL), prevDipoles(NULL), prevDipolesPolar(NULL), prevDipolesGk(NULL),
......@@ -822,7 +822,7 @@ CudaCalcAmoebaMultipoleForceKernel::CudaCalcAmoebaMultipoleForceKernel(std::stri
inducedDipoleFieldGradientGk(NULL), inducedDipoleFieldGradientGkPolar(NULL), extrapolatedDipoleFieldGradient(NULL), extrapolatedDipoleFieldGradientPolar(NULL),
extrapolatedDipoleFieldGradientGk(NULL), extrapolatedDipoleFieldGradientGkPolar(NULL), covalentFlags(NULL), polarizationGroupFlags(NULL),
pmeGrid(NULL), pmeBsplineModuliX(NULL), pmeBsplineModuliY(NULL), pmeBsplineModuliZ(NULL), pmeIgrid(NULL), pmePhi(NULL),
pmePhid(NULL), pmePhip(NULL), pmePhidp(NULL), pmeCphi(NULL), pmeAtomGridIndex(NULL), lastPositions(NULL), sort(NULL), gkKernel(NULL) {
pmePhid(NULL), pmePhip(NULL), pmePhidp(NULL), pmeCphi(NULL), lastPositions(NULL), sort(NULL), gkKernel(NULL) {
}
CudaCalcAmoebaMultipoleForceKernel::~CudaCalcAmoebaMultipoleForceKernel() {
......@@ -927,14 +927,14 @@ CudaCalcAmoebaMultipoleForceKernel::~CudaCalcAmoebaMultipoleForceKernel() {
delete pmePhidp;
if (pmeCphi != NULL)
delete pmeCphi;
if (pmeAtomGridIndex != NULL)
delete pmeAtomGridIndex;
if (lastPositions != NULL)
delete lastPositions;
if (sort != NULL)
delete sort;
if (hasInitializedFFT)
cufftDestroy(fft);
if (hasCreatedEvent)
cuEventDestroy(syncEvent);
}
void CudaCalcAmoebaMultipoleForceKernel::initialize(const System& system, const AmoebaMultipoleForce& force) {
......@@ -1021,6 +1021,8 @@ void CudaCalcAmoebaMultipoleForceKernel::initialize(const System& system, const
prevErrors = new CudaArray(cu, 3*numMultipoles*MaxPrevDIISDipoles, elementSize, "prevErrors");
diisMatrix = new CudaArray(cu, MaxPrevDIISDipoles*MaxPrevDIISDipoles, elementSize, "diisMatrix");
diisCoefficients = new CudaArray(cu, MaxPrevDIISDipoles+1, sizeof(float), "diisMatrix");
CHECK_RESULT(cuEventCreate(&syncEvent, CU_EVENT_DISABLE_TIMING), "Error creating event for AmoebaMultipoleForce");
hasCreatedEvent = true;
}
else if (polarizationType == AmoebaMultipoleForce::Extrapolated) {
int numOrders = force.getExtrapolationCoefficients().size();
......@@ -1153,7 +1155,7 @@ void CudaCalcAmoebaMultipoleForceKernel::initialize(const System& system, const
NonbondedForce nb;
nb.setEwaldErrorTolerance(force.getEwaldErrorTolerance());
nb.setCutoffDistance(force.getCutoffDistance());
NonbondedForceImpl::calcPMEParameters(system, nb, alpha, gridSizeX, gridSizeY, gridSizeZ);
NonbondedForceImpl::calcPMEParameters(system, nb, alpha, gridSizeX, gridSizeY, gridSizeZ, false);
gridSizeX = CudaFFT3D::findLegalDimension(gridSizeX);
gridSizeY = CudaFFT3D::findLegalDimension(gridSizeY);
gridSizeZ = CudaFFT3D::findLegalDimension(gridSizeZ);
......@@ -1212,6 +1214,7 @@ void CudaCalcAmoebaMultipoleForceKernel::initialize(const System& system, const
updateInducedFieldKernel = cu.getKernel(module, "updateInducedFieldByDIIS");
recordDIISDipolesKernel = cu.getKernel(module, "recordInducedDipolesForDIIS");
buildMatrixKernel = cu.getKernel(module, "computeDIISMatrix");
solveMatrixKernel = cu.getKernel(module, "solveDIISMatrix");
initExtrapolatedKernel = cu.getKernel(module, "initExtrapolatedDipoles");
iterateExtrapolatedKernel = cu.getKernel(module, "iterateExtrapolatedDipoles");
computeExtrapolatedKernel = cu.getKernel(module, "computeExtrapolatedDipoles");
......@@ -1253,7 +1256,6 @@ void CudaCalcAmoebaMultipoleForceKernel::initialize(const System& system, const
else if (polarizationType == AmoebaMultipoleForce::Extrapolated)
pmeDefines["EXTRAPOLATED_POLARIZATION"] = "";
CUmodule module = cu.createModule(CudaKernelSources::vectorOps+CudaAmoebaKernelSources::multipolePme, pmeDefines);
pmeGridIndexKernel = cu.getKernel(module, "findAtomGridIndex");
pmeTransformMultipolesKernel = cu.getKernel(module, "transformMultipolesToFractionalCoordinates");
pmeTransformPotentialKernel = cu.getKernel(module, "transformPotentialToCartesianCoordinates");
pmeSpreadFixedMultipolesKernel = cu.getKernel(module, "gridSpreadFixedMultipoles");
......@@ -1285,7 +1287,6 @@ void CudaCalcAmoebaMultipoleForceKernel::initialize(const System& system, const
pmePhidp = new CudaArray(cu, 20*numMultipoles, elementSize, "pmePhidp");
pmeCphi = new CudaArray(cu, 10*numMultipoles, elementSize, "pmeCphi");
pmeAtomRange = CudaArray::create<int>(cu, gridSizeX*gridSizeY*gridSizeZ+1, "pmeAtomRange");
pmeAtomGridIndex = CudaArray::create<int2>(cu, numMultipoles, "pmeAtomGridIndex");
sort = new CudaSort(cu, new SortTrait(), cu.getNumAtoms());
cufftResult result = cufftPlan3d(&fft, gridSizeX, gridSizeY, gridSizeZ, cu.getUseDoublePrecision() ? CUFFT_Z2Z : CUFFT_C2C);
if (result != CUFFT_SUCCESS)
......@@ -1569,16 +1570,11 @@ double CudaCalcAmoebaMultipoleForceKernel::execute(ContextImpl& context, bool in
// Reciprocal space calculation.
unsigned int maxTiles = nb.getInteractingTiles().getSize();
void* gridIndexArgs[] = {&cu.getPosq().getDevicePointer(), &pmeAtomGridIndex->getDevicePointer(),
cu.getPeriodicBoxVecXPointer(), cu.getPeriodicBoxVecYPointer(), cu.getPeriodicBoxVecZPointer(),
recipBoxVectorPointer[0], recipBoxVectorPointer[1], recipBoxVectorPointer[2]};
cu.executeKernel(pmeGridIndexKernel, gridIndexArgs, cu.getNumAtoms(), cu.ThreadBlockSize, cu.ThreadBlockSize*PmeOrder*PmeOrder*elementSize);
sort->sort(*pmeAtomGridIndex);
void* pmeTransformMultipolesArgs[] = {&labFrameDipoles->getDevicePointer(), &labFrameQuadrupoles->getDevicePointer(),
&fracDipoles->getDevicePointer(), &fracQuadrupoles->getDevicePointer(), recipBoxVectorPointer[0], recipBoxVectorPointer[1], recipBoxVectorPointer[2]};
cu.executeKernel(pmeTransformMultipolesKernel, pmeTransformMultipolesArgs, cu.getNumAtoms());
void* pmeSpreadFixedMultipolesArgs[] = {&cu.getPosq().getDevicePointer(), &fracDipoles->getDevicePointer(), &fracQuadrupoles->getDevicePointer(),
&pmeGrid->getDevicePointer(), &pmeAtomGridIndex->getDevicePointer(), cu.getPeriodicBoxVecXPointer(), cu.getPeriodicBoxVecYPointer(), cu.getPeriodicBoxVecZPointer(),
&pmeGrid->getDevicePointer(), cu.getPeriodicBoxVecXPointer(), cu.getPeriodicBoxVecYPointer(), cu.getPeriodicBoxVecZPointer(),
recipBoxVectorPointer[0], recipBoxVectorPointer[1], recipBoxVectorPointer[2]};
cu.executeKernel(pmeSpreadFixedMultipolesKernel, pmeSpreadFixedMultipolesArgs, cu.getNumAtoms());
void* finishSpreadArgs[] = {&pmeGrid->getDevicePointer()};
......@@ -1590,7 +1586,7 @@ double CudaCalcAmoebaMultipoleForceKernel::execute(ContextImpl& context, bool in
cufftExecC2C(fft, (float2*) pmeGrid->getDevicePointer(), (float2*) pmeGrid->getDevicePointer(), CUFFT_FORWARD);
void* pmeConvolutionArgs[] = {&pmeGrid->getDevicePointer(), &pmeBsplineModuliX->getDevicePointer(), &pmeBsplineModuliY->getDevicePointer(),
&pmeBsplineModuliZ->getDevicePointer(), cu.getPeriodicBoxSizePointer(), recipBoxVectorPointer[0], recipBoxVectorPointer[1], recipBoxVectorPointer[2]};
cu.executeKernel(pmeConvolutionKernel, pmeConvolutionArgs, cu.getNumAtoms());
cu.executeKernel(pmeConvolutionKernel, pmeConvolutionArgs, gridSizeX*gridSizeY*gridSizeZ, 256);
if (cu.getUseDoublePrecision())
cufftExecZ2Z(fft, (double2*) pmeGrid->getDevicePointer(), (double2*) pmeGrid->getDevicePointer(), CUFFT_INVERSE);
else
......@@ -1598,7 +1594,7 @@ double CudaCalcAmoebaMultipoleForceKernel::execute(ContextImpl& context, bool in
void* pmeFixedPotentialArgs[] = {&pmeGrid->getDevicePointer(), &pmePhi->getDevicePointer(), &field->getDevicePointer(),
&fieldPolar ->getDevicePointer(), &cu.getPosq().getDevicePointer(), &labFrameDipoles->getDevicePointer(),
cu.getPeriodicBoxVecXPointer(), cu.getPeriodicBoxVecYPointer(), cu.getPeriodicBoxVecZPointer(),
recipBoxVectorPointer[0], recipBoxVectorPointer[1], recipBoxVectorPointer[2], &pmeAtomGridIndex->getDevicePointer()};
recipBoxVectorPointer[0], recipBoxVectorPointer[1], recipBoxVectorPointer[2]};
cu.executeKernel(pmeFixedPotentialKernel, pmeFixedPotentialArgs, cu.getNumAtoms());
void* pmeTransformFixedPotentialArgs[] = {&pmePhi->getDevicePointer(), &pmeCphi->getDevicePointer(), recipBoxVectorPointer[0], recipBoxVectorPointer[1], recipBoxVectorPointer[2]};
cu.executeKernel(pmeTransformPotentialKernel, pmeTransformFixedPotentialArgs, cu.getNumAtoms());
......@@ -1625,7 +1621,7 @@ double CudaCalcAmoebaMultipoleForceKernel::execute(ContextImpl& context, bool in
cu.clearBuffer(*pmeGrid);
void* pmeSpreadInducedDipolesArgs[] = {&cu.getPosq().getDevicePointer(), &inducedDipole->getDevicePointer(), &inducedDipolePolar->getDevicePointer(),
&pmeGrid->getDevicePointer(), &pmeAtomGridIndex->getDevicePointer(), cu.getPeriodicBoxVecXPointer(), cu.getPeriodicBoxVecYPointer(), cu.getPeriodicBoxVecZPointer(),
&pmeGrid->getDevicePointer(), cu.getPeriodicBoxVecXPointer(), cu.getPeriodicBoxVecYPointer(), cu.getPeriodicBoxVecZPointer(),
recipBoxVectorPointer[0], recipBoxVectorPointer[1], recipBoxVectorPointer[2]};
cu.executeKernel(pmeSpreadInducedDipolesKernel, pmeSpreadInducedDipolesArgs, cu.getNumAtoms());
if (cu.getUseDoublePrecision())
......@@ -1634,15 +1630,14 @@ double CudaCalcAmoebaMultipoleForceKernel::execute(ContextImpl& context, bool in
cufftExecZ2Z(fft, (double2*) pmeGrid->getDevicePointer(), (double2*) pmeGrid->getDevicePointer(), CUFFT_FORWARD);
else
cufftExecC2C(fft, (float2*) pmeGrid->getDevicePointer(), (float2*) pmeGrid->getDevicePointer(), CUFFT_FORWARD);
cu.executeKernel(pmeConvolutionKernel, pmeConvolutionArgs, cu.getNumAtoms());
cu.executeKernel(pmeConvolutionKernel, pmeConvolutionArgs, gridSizeX*gridSizeY*gridSizeZ, 256);
if (cu.getUseDoublePrecision())
cufftExecZ2Z(fft, (double2*) pmeGrid->getDevicePointer(), (double2*) pmeGrid->getDevicePointer(), CUFFT_INVERSE);
else
cufftExecC2C(fft, (float2*) pmeGrid->getDevicePointer(), (float2*) pmeGrid->getDevicePointer(), CUFFT_INVERSE);
void* pmeInducedPotentialArgs[] = {&pmeGrid->getDevicePointer(), &pmePhid->getDevicePointer(), &pmePhip->getDevicePointer(),
&pmePhidp->getDevicePointer(), &cu.getPosq().getDevicePointer(), cu.getPeriodicBoxVecXPointer(), cu.getPeriodicBoxVecYPointer(),
cu.getPeriodicBoxVecZPointer(), recipBoxVectorPointer[0], recipBoxVectorPointer[1], recipBoxVectorPointer[2],
&pmeAtomGridIndex->getDevicePointer()};
cu.getPeriodicBoxVecZPointer(), recipBoxVectorPointer[0], recipBoxVectorPointer[1], recipBoxVectorPointer[2]};
cu.executeKernel(pmeInducedPotentialKernel, pmeInducedPotentialArgs, cu.getNumAtoms());
// Iterate until the dipoles converge.
......@@ -1771,7 +1766,7 @@ void CudaCalcAmoebaMultipoleForceKernel::computeInducedField(void** recipBoxVect
cu.executeKernel(computeInducedFieldKernel, &computeInducedFieldArgs[0], numForceThreadBlocks*inducedFieldThreads, inducedFieldThreads);
cu.clearBuffer(*pmeGrid);
void* pmeSpreadInducedDipolesArgs[] = {&cu.getPosq().getDevicePointer(), &inducedDipole->getDevicePointer(), &inducedDipolePolar->getDevicePointer(),
&pmeGrid->getDevicePointer(), &pmeAtomGridIndex->getDevicePointer(), cu.getPeriodicBoxVecXPointer(), cu.getPeriodicBoxVecYPointer(), cu.getPeriodicBoxVecZPointer(),
&pmeGrid->getDevicePointer(), cu.getPeriodicBoxVecXPointer(), cu.getPeriodicBoxVecYPointer(), cu.getPeriodicBoxVecZPointer(),
recipBoxVectorPointer[0], recipBoxVectorPointer[1], recipBoxVectorPointer[2]};
cu.executeKernel(pmeSpreadInducedDipolesKernel, pmeSpreadInducedDipolesArgs, cu.getNumAtoms());
if (cu.getUseDoublePrecision()) {
......@@ -1784,15 +1779,14 @@ void CudaCalcAmoebaMultipoleForceKernel::computeInducedField(void** recipBoxVect
cufftExecC2C(fft, (float2*) pmeGrid->getDevicePointer(), (float2*) pmeGrid->getDevicePointer(), CUFFT_FORWARD);
void* pmeConvolutionArgs[] = {&pmeGrid->getDevicePointer(), &pmeBsplineModuliX->getDevicePointer(), &pmeBsplineModuliY->getDevicePointer(),
&pmeBsplineModuliZ->getDevicePointer(), cu.getPeriodicBoxSizePointer(), recipBoxVectorPointer[0], recipBoxVectorPointer[1], recipBoxVectorPointer[2]};
cu.executeKernel(pmeConvolutionKernel, pmeConvolutionArgs, cu.getNumAtoms());
cu.executeKernel(pmeConvolutionKernel, pmeConvolutionArgs, gridSizeX*gridSizeY*gridSizeZ, 256);
if (cu.getUseDoublePrecision())
cufftExecZ2Z(fft, (double2*) pmeGrid->getDevicePointer(), (double2*) pmeGrid->getDevicePointer(), CUFFT_INVERSE);
else
cufftExecC2C(fft, (float2*) pmeGrid->getDevicePointer(), (float2*) pmeGrid->getDevicePointer(), CUFFT_INVERSE);
void* pmeInducedPotentialArgs[] = {&pmeGrid->getDevicePointer(), &pmePhid->getDevicePointer(), &pmePhip->getDevicePointer(),
&pmePhidp->getDevicePointer(), &cu.getPosq().getDevicePointer(), cu.getPeriodicBoxVecXPointer(), cu.getPeriodicBoxVecYPointer(),
cu.getPeriodicBoxVecZPointer(), recipBoxVectorPointer[0], recipBoxVectorPointer[1], recipBoxVectorPointer[2],
&pmeAtomGridIndex->getDevicePointer()};
cu.getPeriodicBoxVecZPointer(), recipBoxVectorPointer[0], recipBoxVectorPointer[1], recipBoxVectorPointer[2]};
cu.executeKernel(pmeInducedPotentialKernel, pmeInducedPotentialArgs, cu.getNumAtoms());
if (polarizationType == AmoebaMultipoleForce::Extrapolated) {
void* pmeRecordInducedFieldDipolesArgs[] = {&pmePhid->getDevicePointer(), &pmePhip->getDevicePointer(),
......@@ -1831,22 +1825,24 @@ bool CudaCalcAmoebaMultipoleForceKernel::iterateDipolesByDIIS(int iteration) {
cu.executeKernel(recordDIISDipolesKernel, recordDIISDipolesArgs, cu.getNumThreadBlocks()*cu.ThreadBlockSize, cu.ThreadBlockSize, cu.ThreadBlockSize*elementSize*2);
float2* errors = (float2*) cu.getPinnedBuffer();
inducedDipoleErrors->download(errors, false);
cuEventRecord(syncEvent, cu.getCurrentStream());
// Build the DIIS matrix.
int numPrev = (iteration+1 < MaxPrevDIISDipoles ? iteration+1 : MaxPrevDIISDipoles);
void* buildMatrixArgs[] = {&prevErrors->getDevicePointer(), &iteration, &diisMatrix->getDevicePointer()};
int threadBlocks = min(numPrev, cu.getNumThreadBlocks());
cu.executeKernel(buildMatrixKernel, buildMatrixArgs, threadBlocks*128, 128, 128*elementSize);
vector<float> matrixf;
vector<double> matrix;
if (cu.getUseDoublePrecision())
diisMatrix->download(matrix);
else
diisMatrix->download(matrixf);
int blockSize = 512;
cu.executeKernel(buildMatrixKernel, buildMatrixArgs, threadBlocks*blockSize, blockSize, blockSize*elementSize);
// Solve the matrix.
void* solveMatrixArgs[] = {&iteration, &diisMatrix->getDevicePointer(), &diisCoefficients->getDevicePointer()};
cu.executeKernel(solveMatrixKernel, solveMatrixArgs, 32, 32);
// Determine whether the iteration has converged.
cuEventSynchronize(syncEvent);
double total1 = 0.0, total2 = 0.0;
for (int j = 0; j < inducedDipoleErrors->getSize(); j++) {
total1 += errors[j].x;
......@@ -1855,55 +1851,15 @@ bool CudaCalcAmoebaMultipoleForceKernel::iterateDipolesByDIIS(int iteration) {
if (48.033324*sqrt(max(total1, total2)/cu.getNumAtoms()) < inducedEpsilon)
return true;
// Compute the coefficients for selecting the new dipoles.
float* coefficients = (float*) cu.getPinnedBuffer();
if (iteration == 0)
coefficients[0] = 1;
else {
int rank = numPrev+1;
Array2D<double> b(rank, rank);
b[0][0] = 0;
for (int i = 1; i < rank; i++)
b[i][0] = b[0][i] = -1;
if (cu.getUseDoublePrecision()) {
for (int i = 0; i < numPrev; i++)
for (int j = 0; j < numPrev; j++)
b[i+1][j+1] = matrix[i*MaxPrevDIISDipoles+j];
}
else {
for (int i = 0; i < numPrev; i++)
for (int j = 0; j < numPrev; j++)
b[i+1][j+1] = matrixf[i*MaxPrevDIISDipoles+j];
}
// Solve using SVD. Since the right hand side is (-1, 0, 0, 0, ...), this is simpler than the general case.
JAMA::SVD<double> svd(b);
Array2D<double> u, v;
svd.getU(u);
svd.getV(v);
Array1D<double> s;
svd.getSingularValues(s);
int effectiveRank = svd.rank();
for (int i = 1; i < rank; i++) {
double d = 0;
for (int j = 0; j < effectiveRank; j++)
d -= u[0][j]*v[i][j]/s[j];
coefficients[i-1] = d;
}
}
diisCoefficients->upload(coefficients, false);
// Compute the dipoles.
void* updateInducedFieldArgs[] = {&inducedDipole->getDevicePointer(), &inducedDipolePolar->getDevicePointer(),
&prevDipoles->getDevicePointer(), &prevDipolesPolar->getDevicePointer(), &diisCoefficients->getDevicePointer(), &numPrev};
cu.executeKernel(updateInducedFieldKernel, updateInducedFieldArgs, cu.getNumThreadBlocks()*cu.ThreadBlockSize);
cu.executeKernel(updateInducedFieldKernel, updateInducedFieldArgs, 3*cu.getNumAtoms(), 256);
if (gkKernel != NULL) {
void* updateInducedFieldGkArgs[] = {&gkKernel->getInducedDipoles()->getDevicePointer(), &gkKernel->getInducedDipolesPolar()->getDevicePointer(),
&prevDipolesGk->getDevicePointer(), &prevDipolesGkPolar->getDevicePointer(), &diisCoefficients->getDevicePointer(), &numPrev};
cu.executeKernel(updateInducedFieldKernel, updateInducedFieldGkArgs, cu.getNumThreadBlocks()*cu.ThreadBlockSize);
cu.executeKernel(updateInducedFieldKernel, updateInducedFieldGkArgs, 3*cu.getNumAtoms(), 256);
}
return false;
}
......
plugins/amoeba/platforms/cuda/src/AmoebaCudaKernels.h
View file @ 047934e2
......@@ -408,7 +408,7 @@ private:
int fixedFieldThreads, inducedFieldThreads, electrostaticsThreads;
int gridSizeX, gridSizeY, gridSizeZ;
double alpha, inducedEpsilon;
bool usePME, hasQuadrupoles, hasInitializedScaleFactors, hasInitializedFFT, multipolesAreValid;
bool usePME, hasQuadrupoles, hasInitializedScaleFactors, hasInitializedFFT, multipolesAreValid, hasCreatedEvent;
AmoebaMultipoleForce::PolarizationType polarizationType;
CudaContext& cu;
const System& system;
......@@ -465,16 +465,16 @@ private:
CudaArray* pmePhidp;
CudaArray* pmeCphi;
CudaArray* pmeAtomRange;
CudaArray* pmeAtomGridIndex;
CudaArray* lastPositions;
CudaSort* sort;
cufftHandle fft;
CUfunction computeMomentsKernel, recordInducedDipolesKernel, computeFixedFieldKernel, computeInducedFieldKernel, updateInducedFieldKernel, electrostaticsKernel, mapTorqueKernel;
CUfunction pmeGridIndexKernel, pmeSpreadFixedMultipolesKernel, pmeSpreadInducedDipolesKernel, pmeFinishSpreadChargeKernel, pmeConvolutionKernel;
CUfunction pmeSpreadFixedMultipolesKernel, pmeSpreadInducedDipolesKernel, pmeFinishSpreadChargeKernel, pmeConvolutionKernel;
CUfunction pmeFixedPotentialKernel, pmeInducedPotentialKernel, pmeFixedForceKernel, pmeInducedForceKernel, pmeRecordInducedFieldDipolesKernel, computePotentialKernel;
CUfunction recordDIISDipolesKernel, buildMatrixKernel;
CUfunction recordDIISDipolesKernel, buildMatrixKernel, solveMatrixKernel;
CUfunction initExtrapolatedKernel, iterateExtrapolatedKernel, computeExtrapolatedKernel, addExtrapolatedGradientKernel;
CUfunction pmeTransformMultipolesKernel, pmeTransformPotentialKernel;
CUevent syncEvent;
CudaCalcAmoebaGeneralizedKirkwoodForceKernel* gkKernel;
static const int PmeOrder = 5;
static const int MaxPrevDIISDipoles = 20;
......
plugins/amoeba/platforms/cuda/src/kernels/multipoleElectrostatics.cu
View file @ 047934e2
......@@ -107,9 +107,9 @@ __device__ void computeOneInteraction(AtomData& atom1, AtomData& atom2, bool has
real dmp = atom1.damp*atom2.damp;
real a = min(atom1.thole, atom2.thole);
real u = fabs(dmp) > 1.0e-5f ? r/dmp : 1e10f;
real au3 = a*u*u*u;
real expau3 = au3 < 50 ? EXP(-au3) : 0;
real u = r/dmp;
real au3 = fabs(dmp) > 1.0e-5f ? a*u*u*u : 0;
real expau3 = fabs(dmp) > 1.0e-5f ? EXP(-au3) : 0;
real a2u6 = au3*au3;
real a3u9 = a2u6*au3;
// Thole damping factors for energies
......@@ -336,7 +336,7 @@ __device__ void computeOneInteraction(AtomData& atom1, AtomData& atom2, bool has
iEIY -= eCoef*(qiUinpI.y*qiUindJ.x + qiUindI.y*qiUinpJ.x);
iEJY -= eCoef*(qiUinpJ.y*qiUindI.x + qiUindJ.y*qiUinpI.x);
fIZ += dCoef*(qiUinpI.x*qiUindJ.x + qiUindI.x*qiUinpJ.x);
fIZ += dCoef*(qiUinpJ.x*qiUindI.x + qiUindJ.x*qiUinpI.x);
fJZ += dCoef*(qiUinpJ.x*qiUindI.x + qiUindJ.x*qiUinpI.x);
// Uind-Uind terms (m=1)
eCoef = 2*rInvVec[3]*thole_d1;
dCoef = -3*rInvVec[4]*dthole_d1;
......@@ -345,7 +345,7 @@ __device__ void computeOneInteraction(AtomData& atom1, AtomData& atom2, bool has
iEIY += eCoef*(qiUinpI.x*qiUindJ.y + qiUindI.x*qiUinpJ.y);
iEJY += eCoef*(qiUinpJ.x*qiUindI.y + qiUindJ.x*qiUinpI.y);
fIZ += dCoef*(qiUinpI.y*qiUindJ.y + qiUindI.y*qiUinpJ.y + qiUinpI.z*qiUindJ.z + qiUindI.z*qiUinpJ.z);
fIZ += dCoef*(qiUinpJ.y*qiUindI.y + qiUindJ.y*qiUinpI.y + qiUinpJ.z*qiUindI.z + qiUindJ.z*qiUinpI.z);
fJZ += dCoef*(qiUinpJ.y*qiUindI.y + qiUindJ.y*qiUinpI.y + qiUinpJ.z*qiUindI.z + qiUindJ.z*qiUinpI.z);
#endif
// The quasi-internal frame forces and torques. Note that the induced torque intermediates are
......@@ -545,7 +545,7 @@ extern "C" __global__ void computeElectrostatics(
data.force = make_real3(0);
data.torque = make_real3(0);
#ifdef USE_CUTOFF
unsigned int j = (numTiles <= maxTiles ? interactingAtoms[pos*TILE_SIZE+tgx] : y*TILE_SIZE + tgx);
unsigned int j = interactingAtoms[pos*TILE_SIZE+tgx];
#else
unsigned int j = y*TILE_SIZE + tgx;
#endif
......
plugins/amoeba/platforms/cuda/src/kernels/multipoleFixedField.cu
View file @ 047934e2
......@@ -655,7 +655,7 @@ extern "C" __global__ void computeFixedField(
data.bornRadius = bornRadii[atom1];
#endif
#ifdef USE_CUTOFF
unsigned int j = (numTiles <= maxTiles ? interactingAtoms[pos*TILE_SIZE+tgx] : y*TILE_SIZE + tgx);
unsigned int j = interactingAtoms[pos*TILE_SIZE+tgx];
#else
unsigned int j = y*TILE_SIZE + tgx;
#endif
......
plugins/amoeba/platforms/cuda/src/kernels/multipoleInducedField.cu
View file @ 047934e2
......@@ -514,7 +514,7 @@ extern "C" __global__ void computeInducedField(
loadAtomData(data, atom1, posq, inducedDipole, inducedDipolePolar, dampingAndThole);
#endif
#ifdef USE_CUTOFF
unsigned int j = (numTiles <= maxTiles ? interactingAtoms[pos*TILE_SIZE+tgx] : y*TILE_SIZE + tgx);
unsigned int j = interactingAtoms[pos*TILE_SIZE+tgx];
#else
unsigned int j = y*TILE_SIZE + tgx;
#endif
......@@ -607,11 +607,6 @@ extern "C" __global__ void recordInducedDipolesForDIIS(const long long* __restri
const real* __restrict__ inducedDipole, const real* __restrict__ inducedDipolePolar, const float* __restrict__ polarizability, float2* __restrict__ errors,
real* __restrict__ prevDipoles, real* __restrict__ prevDipolesPolar, real* __restrict__ prevErrors, int iteration, bool recordPrevErrors, real* __restrict__ matrix) {
extern __shared__ real2 buffer[];
#ifdef USE_EWALD
const real ewaldScale = (4/(real) 3)*(EWALD_ALPHA*EWALD_ALPHA*EWALD_ALPHA)/SQRT_PI;
#else
const real ewaldScale = 0;
#endif
const real fieldScale = 1/(real) 0x100000000;
real sumErrors = 0;
real sumPolarErrors = 0;
......@@ -699,6 +694,126 @@ extern "C" __global__ void computeDIISMatrix(real* __restrict__ prevErrors, int
}
}
extern "C" __global__ void solveDIISMatrix(int iteration, const real* __restrict__ matrix, float* __restrict__ coefficients) {
__shared__ real b[MAX_PREV_DIIS_DIPOLES+1][MAX_PREV_DIIS_DIPOLES+1];
__shared__ real piv[MAX_PREV_DIIS_DIPOLES+1];
__shared__ real x[MAX_PREV_DIIS_DIPOLES+1];
// On the first iteration we don't need to do any calculation.
if (iteration == 0) {
if (threadIdx.x == 0)
coefficients[0] = 1;
return;
}
// Load the matrix.
int numPrev = min(iteration+1, MAX_PREV_DIIS_DIPOLES);
int rank = numPrev+1;
for (int index = threadIdx.x; index < numPrev*numPrev; index += blockDim.x) {
int i = index/numPrev;
int j = index-i*numPrev;
b[i+1][j+1] = matrix[i*MAX_PREV_DIIS_DIPOLES+j];
}
for (int i = threadIdx.x; i < rank; i += blockDim.x) {
b[i][0] = -1;
piv[i] = i;
}
__syncthreads();
// Compute the mean absolute value of the values we just loaded. We use that for preconditioning it,
// which is essential for doing the computation in single precision.
if (threadIdx.x == 0) {
real mean = 0;
for (int i = 0; i < numPrev; i++)
for (int j = 0; j < numPrev; j++)
mean += fabs(b[i+1][j+1]);
mean /= numPrev*numPrev;
b[0][0] = 0;
for (int i = 1; i < rank; i++)
b[0][i] = -mean;
// Compute the LU decomposition of the matrix. This code is adapted from JAMA.
int pivsign = 1;
for (int j = 0; j < rank; j++) {
// Apply previous transformations.
for (int i = 0; i < rank; i++) {
// Most of the time is spent in the following dot product.
int kmax = min(i, j);
real s = 0;
for (int k = 0; k < kmax; k++)
s += b[i][k] * b[k][j];
b[i][j] -= s;
}
// Find pivot and exchange if necessary.
int p = j;
for (int i = j+1; i < rank; i++)
if (abs(b[i][j]) > abs(b[p][j]))
p = i;
if (p != j) {
int k = 0;
for (k = 0; k < rank; k++) {
real t = b[p][k];
b[p][k] = b[j][k];
b[j][k] = t;
}
k = piv[p];
piv[p] = piv[j];
piv[j] = k;
pivsign = -pivsign;
}
// Compute multipliers.
if ((j < rank) && (b[j][j] != 0))
for (int i = j+1; i < rank; i++)
b[i][j] /= b[j][j];
}
for (int i = 0; i < rank; i++)
if (b[i][i] == 0) {
// The matrix is singular.
for (int j = 0; j < rank-1; j++)
coefficients[j] = 0;
coefficients[rank-1] = 1;
return;
}
// Solve b*Y = X(piv)
for (int i = 0; i < rank; i++)
x[i] = (piv[i] == 0 ? -1 : 0);
for (int k = 0; k < rank; k++)
for (int i = k+1; i < rank; i++)
x[i] -= x[k] * b[i][k];
// Solve U*X = Y;
for (int k = rank-1; k >= 0; k--) {
x[k] /= b[k][k];
for (int i = 0; i < k; i++)
x[i] -= x[k] * b[i][k];
}
// Record the coefficients.
real lastCoeff = 1;
for (int i = 0; i < rank-1; i++) {
real c = x[i+1]*mean;
coefficients[i] = c;
lastCoeff -= c;
}
coefficients[rank-1] = lastCoeff;
}
}
extern "C" __global__ void updateInducedFieldByDIIS(real* __restrict__ inducedDipole, real* __restrict__ inducedDipolePolar,
const real* __restrict__ prevDipoles, const real* __restrict__ prevDipolesPolar, const float* __restrict__ coefficients, int numPrev) {
for (int index = blockIdx.x*blockDim.x + threadIdx.x; index < 3*NUM_ATOMS; index += blockDim.x*gridDim.x) {
......
plugins/amoeba/platforms/cuda/src/kernels/multipolePme.cu
View file @ 047934e2
......@@ -69,47 +69,6 @@ __device__ void computeBSplinePoint(real4* thetai, real w, real* array) {
thetai[i-1] = make_real4(ARRAY(PME_ORDER,i), ARRAY(PME_ORDER-1,i), ARRAY(PME_ORDER-2,i), ARRAY(PME_ORDER-3,i));
}
/**
* Compute the index of the grid point each atom is associated with.
*/
extern "C" __global__ void findAtomGridIndex(const real4* __restrict__ posq, int2* __restrict__ pmeAtomGridIndex,
real4 periodicBoxVecX, real4 periodicBoxVecY, real4 periodicBoxVecZ, real3 recipBoxVecX, real3 recipBoxVecY, real3 recipBoxVecZ) {
for (int i = blockIdx.x*blockDim.x+threadIdx.x; i < NUM_ATOMS; i += blockDim.x*gridDim.x) {
real4 pos = posq[i];
pos -= periodicBoxVecZ*floor(pos.z*recipBoxVecZ.z+0.5f);
pos -= periodicBoxVecY*floor(pos.y*recipBoxVecY.z+0.5f);
pos -= periodicBoxVecX*floor(pos.x*recipBoxVecX.z+0.5f);
// First axis.
real w = pos.x*recipBoxVecX.x+pos.y*recipBoxVecY.x+pos.z*recipBoxVecZ.x;
real fr = GRID_SIZE_X*(w-(int)(w+0.5f)+0.5f);
int ifr = (int) fr;
int igrid1 = ifr-PME_ORDER+1;
// Second axis.
w = pos.y*recipBoxVecY.y+pos.z*recipBoxVecZ.y;
fr = GRID_SIZE_Y*(w-(int)(w+0.5f)+0.5f);
ifr = (int) fr;
int igrid2 = ifr-PME_ORDER+1;
// Third axis.
w = pos.z*recipBoxVecZ.z;
fr = GRID_SIZE_Z*(w-(int)(w+0.5f)+0.5f);
ifr = (int) fr;
int igrid3 = ifr-PME_ORDER+1;
// Record the grid point.
igrid1 += (igrid1 < 0 ? GRID_SIZE_X : 0);
igrid2 += (igrid2 < 0 ? GRID_SIZE_Y : 0);
igrid3 += (igrid3 < 0 ? GRID_SIZE_Z : 0);
pmeAtomGridIndex[i] = make_int2(i, igrid1*GRID_SIZE_Y*GRID_SIZE_Z+igrid2*GRID_SIZE_Z+igrid3);
}
}
/**
* Convert the fixed multipoles from Cartesian to fractional coordinates.
*/
......@@ -209,7 +168,7 @@ extern "C" __global__ void transformPotentialToCartesianCoordinates(const real*
}
extern "C" __global__ void gridSpreadFixedMultipoles(const real4* __restrict__ posq, const real* __restrict__ fracDipole,
const real* __restrict__ fracQuadrupole, real2* __restrict__ pmeGrid, int2* __restrict__ pmeAtomGridIndex,
const real* __restrict__ fracQuadrupole, real2* __restrict__ pmeGrid,
real4 periodicBoxVecX, real4 periodicBoxVecY, real4 periodicBoxVecZ, real3 recipBoxVecX, real3 recipBoxVecY, real3 recipBoxVecZ) {
#if __CUDA_ARCH__ < 500
real array[PME_ORDER*PME_ORDER];
......@@ -300,7 +259,7 @@ extern "C" __global__ void gridSpreadFixedMultipoles(const real4* __restrict__ p
}
extern "C" __global__ void gridSpreadInducedDipoles(const real4* __restrict__ posq, const real* __restrict__ inducedDipole,
const real* __restrict__ inducedDipolePolar, real2* __restrict__ pmeGrid, int2* __restrict__ pmeAtomGridIndex,
const real* __restrict__ inducedDipolePolar, real2* __restrict__ pmeGrid,
real4 periodicBoxVecX, real4 periodicBoxVecY, real4 periodicBoxVecZ, real3 recipBoxVecX, real3 recipBoxVecY, real3 recipBoxVecZ) {
#if __CUDA_ARCH__ < 500
real array[PME_ORDER*PME_ORDER];
......@@ -451,7 +410,7 @@ extern "C" __global__ void reciprocalConvolution(real2* __restrict__ pmeGrid, co
extern "C" __global__ void computeFixedPotentialFromGrid(const real2* __restrict__ pmeGrid, real* __restrict__ phi,
long long* __restrict__ fieldBuffers, long long* __restrict__ fieldPolarBuffers, const real4* __restrict__ posq,
const real* __restrict__ labFrameDipole, real4 periodicBoxVecX, real4 periodicBoxVecY, real4 periodicBoxVecZ,
real3 recipBoxVecX, real3 recipBoxVecY, real3 recipBoxVecZ, int2* __restrict__ pmeAtomGridIndex) {
real3 recipBoxVecX, real3 recipBoxVecY, real3 recipBoxVecZ) {
#if __CUDA_ARCH__ < 500
real array[PME_ORDER*PME_ORDER];
#else
......@@ -476,11 +435,7 @@ extern "C" __global__ void computeFixedPotentialFromGrid(const real2* __restrict
}
__syncthreads();
// Process the atoms in spatially sorted order. This improves cache performance when loading
// the grid values.
for (int i = blockIdx.x*blockDim.x+threadIdx.x; i < NUM_ATOMS; i += blockDim.x*gridDim.x) {
int m = pmeAtomGridIndex[i].x;
for (int m = blockIdx.x*blockDim.x+threadIdx.x; m < NUM_ATOMS; m += blockDim.x*gridDim.x) {
real4 pos = posq[m];
pos -= periodicBoxVecZ*floor(pos.z*recipBoxVecZ.z+0.5f);
pos -= periodicBoxVecY*floor(pos.y*recipBoxVecY.z+0.5f);
......@@ -533,9 +488,9 @@ extern "C" __global__ void computeFixedPotentialFromGrid(const real2* __restrict
real tuv102 = 0;
real tuv012 = 0;
real tuv111 = 0;
for (int iz = 0; iz < PME_ORDER; iz++) {
int k = igrid3+iz-(igrid3+iz >= GRID_SIZE_Z ? GRID_SIZE_Z : 0);
real4 v = theta3[iz];
for (int ix = 0; ix < PME_ORDER; ix++) {
int i = igrid1+ix-(igrid1+ix >= GRID_SIZE_X ? GRID_SIZE_X : 0);
real4 v = theta1[ix];
real tu00 = 0;
real tu10 = 0;
real tu01 = 0;
......@@ -550,47 +505,47 @@ extern "C" __global__ void computeFixedPotentialFromGrid(const real2* __restrict
int j = igrid2+iy-(igrid2+iy >= GRID_SIZE_Y ? GRID_SIZE_Y : 0);
real4 u = theta2[iy];
real4 t = make_real4(0, 0, 0, 0);
for (int ix = 0; ix < PME_ORDER; ix++) {
int i = igrid1+ix-(igrid1+ix >= GRID_SIZE_X ? GRID_SIZE_X : 0);
for (int iz = 0; iz < PME_ORDER; iz++) {
int k = igrid3+iz-(igrid3+iz >= GRID_SIZE_Z ? GRID_SIZE_Z : 0);
int gridIndex = i*GRID_SIZE_Y*GRID_SIZE_Z + j*GRID_SIZE_Z + k;
real tq = pmeGrid[gridIndex].x;
real4 tadd = theta1[ix];
real4 tadd = theta3[iz];
t.x += tq*tadd.x;
t.y += tq*tadd.y;
t.z += tq*tadd.z;
t.w += tq*tadd.w;
}
tu00 += t.x*u.x;
tu10 += t.y*u.x;
tu01 += t.x*u.y;
tu20 += t.z*u.x;
tu11 += t.y*u.y;
tu02 += t.x*u.z;
tu30 += t.w*u.x;
tu21 += t.z*u.y;
tu12 += t.y*u.z;
tu03 += t.x*u.w;
tu00 += u.x*t.x;
tu10 += u.y*t.x;
tu01 += u.x*t.y;
tu20 += u.z*t.x;
tu11 += u.y*t.y;
tu02 += u.x*t.z;
tu30 += u.w*t.x;
tu21 += u.z*t.y;
tu12 += u.y*t.z;
tu03 += u.x*t.w;
}
tuv000 += tu00*v.x;
tuv100 += tu10*v.x;
tuv010 += tu01*v.x;
tuv001 += tu00*v.y;
tuv200 += tu20*v.x;
tuv020 += tu02*v.x;
tuv002 += tu00*v.z;
tuv110 += tu11*v.x;
tuv101 += tu10*v.y;
tuv011 += tu01*v.y;
tuv300 += tu30*v.x;
tuv030 += tu03*v.x;
tuv003 += tu00*v.w;
tuv210 += tu21*v.x;
tuv201 += tu20*v.y;
tuv120 += tu12*v.x;
tuv021 += tu02*v.y;
tuv102 += tu10*v.z;
tuv012 += tu01*v.z;
tuv111 += tu11*v.y;
tuv000 += v.x*tu00;
tuv100 += v.y*tu00;
tuv010 += v.x*tu10;
tuv001 += v.x*tu01;
tuv200 += v.z*tu00;
tuv020 += v.x*tu20;
tuv002 += v.x*tu02;
tuv110 += v.y*tu10;
tuv101 += v.y*tu01;
tuv011 += v.x*tu11;
tuv300 += v.w*tu00;
tuv030 += v.x*tu30;
tuv003 += v.x*tu03;
tuv210 += v.z*tu10;
tuv201 += v.z*tu01;
tuv120 += v.y*tu20;
tuv021 += v.x*tu21;
tuv102 += v.y*tu02;
tuv012 += v.x*tu12;
tuv111 += v.y*tu11;
}
phi[m] = tuv000;
phi[m+NUM_ATOMS] = tuv100;
......@@ -628,7 +583,7 @@ extern "C" __global__ void computeFixedPotentialFromGrid(const real2* __restrict
extern "C" __global__ void computeInducedPotentialFromGrid(const real2* __restrict__ pmeGrid, real* __restrict__ phid,
real* __restrict__ phip, real* __restrict__ phidp, const real4* __restrict__ posq,
real4 periodicBoxVecX, real4 periodicBoxVecY, real4 periodicBoxVecZ, real3 recipBoxVecX,
real3 recipBoxVecY, real3 recipBoxVecZ, int2* __restrict__ pmeAtomGridIndex) {
real3 recipBoxVecY, real3 recipBoxVecZ) {
#if __CUDA_ARCH__ < 500
real array[PME_ORDER*PME_ORDER];
#else
......@@ -640,11 +595,7 @@ extern "C" __global__ void computeInducedPotentialFromGrid(const real2* __restri
real4 theta2[PME_ORDER];
real4 theta3[PME_ORDER];
// Process the atoms in spatially sorted order. This improves cache performance when loading
// the grid values.
for (int atom = blockIdx.x*blockDim.x+threadIdx.x; atom < NUM_ATOMS; atom += blockDim.x*gridDim.x) {
int m = pmeAtomGridIndex[atom].x;
for (int m = blockIdx.x*blockDim.x+threadIdx.x; m < NUM_ATOMS; m += blockDim.x*gridDim.x) {
real4 pos = posq[m];
pos -= periodicBoxVecZ*floor(pos.z*recipBoxVecZ.z+0.5f);
pos -= periodicBoxVecY*floor(pos.y*recipBoxVecY.z+0.5f);
......@@ -715,9 +666,9 @@ extern "C" __global__ void computeInducedPotentialFromGrid(const real2* __restri
real tuv102 = 0;
real tuv012 = 0;
real tuv111 = 0;
for (int iz = 0; iz < PME_ORDER; iz++) {
int k = igrid3+iz-(igrid3+iz >= GRID_SIZE_Z ? GRID_SIZE_Z : 0);
real4 v = theta3[iz];
for (int ix = 0; ix < PME_ORDER; ix++) {
int i = igrid1+ix-(igrid1+ix >= GRID_SIZE_X ? GRID_SIZE_X : 0);
real4 v = theta1[ix];
real tu00_1 = 0;
real tu01_1 = 0;
real tu10_1 = 0;
......@@ -750,11 +701,11 @@ extern "C" __global__ void computeInducedPotentialFromGrid(const real2* __restri
real t1_2 = 0;
real t2_2 = 0;
real t3 = 0;
for (int ix = 0; ix < PME_ORDER; ix++) {
int i = igrid1+ix-(igrid1+ix >= GRID_SIZE_X ? GRID_SIZE_X : 0);
for (int iz = 0; iz < PME_ORDER; iz++) {
int k = igrid3+iz-(igrid3+iz >= GRID_SIZE_Z ? GRID_SIZE_Z : 0);
int gridIndex = i*GRID_SIZE_Y*GRID_SIZE_Z + j*GRID_SIZE_Z + k;
real2 tq = pmeGrid[gridIndex];
real4 tadd = theta1[ix];
real4 tadd = theta3[iz];
t0_1 += tq.x*tadd.x;
t1_1 += tq.x*tadd.y;
t2_1 += tq.x*tadd.z;
......@@ -763,70 +714,70 @@ extern "C" __global__ void computeInducedPotentialFromGrid(const real2* __restri
t2_2 += tq.y*tadd.z;
t3 += (tq.x+tq.y)*tadd.w;
}
tu00_1 += t0_1*u.x;
tu10_1 += t1_1*u.x;
tu01_1 += t0_1*u.y;
tu20_1 += t2_1*u.x;
tu11_1 += t1_1*u.y;
tu02_1 += t0_1*u.z;
tu00_2 += t0_2*u.x;
tu10_2 += t1_2*u.x;
tu01_2 += t0_2*u.y;
tu20_2 += t2_2*u.x;
tu11_2 += t1_2*u.y;
tu02_2 += t0_2*u.z;
tu00_1 += u.x*t0_1;
tu10_1 += u.y*t0_1;
tu01_1 += u.x*t1_1;
tu20_1 += u.z*t0_1;
tu11_1 += u.y*t1_1;
tu02_1 += u.x*t2_1;
tu00_2 += u.x*t0_2;
tu10_2 += u.y*t0_2;
tu01_2 += u.x*t1_2;
tu20_2 += u.z*t0_2;
tu11_2 += u.y*t1_2;
tu02_2 += u.x*t2_2;
real t0 = t0_1 + t0_2;
real t1 = t1_1 + t1_2;
real t2 = t2_1 + t2_2;
tu00 += t0*u.x;
tu10 += t1*u.x;
tu01 += t0*u.y;
tu20 += t2*u.x;
tu11 += t1*u.y;
tu02 += t0*u.z;
tu30 += t3*u.x;
tu21 += t2*u.y;
tu12 += t1*u.z;
tu03 += t0*u.w;
tu00 += u.x*t0;
tu10 += u.y*t0;
tu01 += u.x*t1;
tu20 += u.z*t0;
tu11 += u.y*t1;
tu02 += u.x*t2;
tu30 += u.w*t0;
tu21 += u.z*t1;
tu12 += u.y*t2;
tu03 += u.x*t3;
}
tuv100_1 += tu10_1*v.x;
tuv010_1 += tu01_1*v.x;
tuv001_1 += tu00_1*v.y;
tuv200_1 += tu20_1*v.x;
tuv020_1 += tu02_1*v.x;
tuv002_1 += tu00_1*v.z;
tuv110_1 += tu11_1*v.x;
tuv101_1 += tu10_1*v.y;
tuv011_1 += tu01_1*v.y;
tuv100_2 += tu10_2*v.x;
tuv010_2 += tu01_2*v.x;
tuv001_2 += tu00_2*v.y;
tuv200_2 += tu20_2*v.x;
tuv020_2 += tu02_2*v.x;
tuv002_2 += tu00_2*v.z;
tuv110_2 += tu11_2*v.x;
tuv101_2 += tu10_2*v.y;
tuv011_2 += tu01_2*v.y;
tuv000 += tu00*v.x;
tuv100 += tu10*v.x;
tuv010 += tu01*v.x;
tuv001 += tu00*v.y;
tuv200 += tu20*v.x;
tuv020 += tu02*v.x;
tuv002 += tu00*v.z;
tuv110 += tu11*v.x;
tuv101 += tu10*v.y;
tuv011 += tu01*v.y;
tuv300 += tu30*v.x;
tuv030 += tu03*v.x;
tuv003 += tu00*v.w;
tuv210 += tu21*v.x;
tuv201 += tu20*v.y;
tuv120 += tu12*v.x;
tuv021 += tu02*v.y;
tuv102 += tu10*v.z;
tuv012 += tu01*v.z;
tuv111 += tu11*v.y;
tuv100_1 += v.y*tu00_1;
tuv010_1 += v.x*tu10_1;
tuv001_1 += v.x*tu01_1;
tuv200_1 += v.z*tu00_1;
tuv020_1 += v.x*tu20_1;
tuv002_1 += v.x*tu02_1;
tuv110_1 += v.y*tu10_1;
tuv101_1 += v.y*tu01_1;
tuv011_1 += v.x*tu11_1;
tuv100_2 += v.y*tu00_2;
tuv010_2 += v.x*tu10_2;
tuv001_2 += v.x*tu01_2;
tuv200_2 += v.z*tu00_2;
tuv020_2 += v.x*tu20_2;
tuv002_2 += v.x*tu02_2;
tuv110_2 += v.y*tu10_2;
tuv101_2 += v.y*tu01_2;
tuv011_2 += v.x*tu11_2;
tuv000 += v.x*tu00;
tuv100 += v.y*tu00;
tuv010 += v.x*tu10;
tuv001 += v.x*tu01;
tuv200 += v.z*tu00;
tuv020 += v.x*tu20;
tuv002 += v.x*tu02;
tuv110 += v.y*tu10;
tuv101 += v.y*tu01;
tuv011 += v.x*tu11;
tuv300 += v.w*tu00;
tuv030 += v.x*tu30;
tuv003 += v.x*tu03;
tuv210 += v.z*tu10;
tuv201 += v.z*tu01;
tuv120 += v.y*tu20;
tuv021 += v.x*tu21;
tuv102 += v.y*tu02;
tuv012 += v.x*tu12;
tuv111 += v.y*tu11;
}
phid[m] = 0;
phid[m+NUM_ATOMS] = tuv100_1;
......
plugins/amoeba/platforms/cuda/src/kernels/multipoles.cu
View file @ 047934e2
......@@ -24,13 +24,19 @@ extern "C" __global__ void computeLabFrameMoments(real4* __restrict__ posq, int4
// code common to ZThenX and Bisector
int4 particles = multipoleParticles[atom];
if (particles.x >= 0 && particles.z >= 0) {
if (particles.z >= 0) {
real4 thisParticlePos = posq[atom];
real4 posZ = posq[particles.z];
real3 vectorZ = make_real3(posZ.x-thisParticlePos.x, posZ.y-thisParticlePos.y, posZ.z-thisParticlePos.z);
real4 posX = posq[particles.x];
real3 vectorX = make_real3(posX.x-thisParticlePos.x, posX.y-thisParticlePos.y, posX.z-thisParticlePos.z);
int axisType = particles.w;
real4 posX;
real3 vectorX;
if (axisType >= 4)
vectorX = make_real3((real) 0.1f);
else {
posX = posq[particles.x];
vectorX = make_real3(posX.x-thisParticlePos.x, posX.y-thisParticlePos.y, posX.z-thisParticlePos.z);
}
/*
z-only
......@@ -108,8 +114,6 @@ extern "C" __global__ void computeLabFrameMoments(real4* __restrict__ posq, int4
}
}
else if (axisType >= 4)
vectorX = make_real3((real) 0.1f);
// x = x - (x.z)z
......@@ -137,7 +141,7 @@ extern "C" __global__ void computeLabFrameMoments(real4* __restrict__ posq, int4
// Check the chirality and see whether it needs to be reversed
bool reverse = false;
if (axisType != 0 && particles.x >= 0 && particles.y >=0 && particles.z >= 0) {
if (axisType == 0 && particles.x >= 0 && particles.y >=0 && particles.z >= 0) {
real4 posY = posq[particles.y];
real delta[4][3];
......
plugins/amoeba/platforms/cuda/src/kernels/pmeMultipoleElectrostatics.cu
View file @ 047934e2
......@@ -612,7 +612,7 @@ extern "C" __global__ void computeElectrostatics(
data.force = make_real3(0);
data.torque = make_real3(0);
#ifdef USE_CUTOFF
unsigned int j = (numTiles <= maxTiles ? interactingAtoms[pos*TILE_SIZE+tgx] : y*TILE_SIZE + tgx);
unsigned int j = interactingAtoms[pos*TILE_SIZE+tgx];
#else
unsigned int j = y*TILE_SIZE + tgx;
#endif
......
plugins/amoeba/platforms/cuda/tests/TestCudaAmoebaExtrapolatedPolarization.cpp
View file @ 047934e2
......@@ -284,8 +284,11 @@ vector<Vec3> setupWaterDimer(System& system, AmoebaMultipoleForce* amoebaMultip
static void check_finite_differences(vector<Vec3> analytic_forces, Context &context, vector<Vec3> positions)
{
// Take a small step in the direction of the energy gradient and see whether the potential energy changes by the expected amount.
double tol = 1e-5;
// We allow more permissive testing for single precision.
if(Platform::getPlatformByName("CUDA").getPropertyValue(context, "Precision") != "double") tol = 5e-4;
// Take a small step in the direction of the energy gradient and see whether the potential energy changes by the expected amount.
double norm = 0.0;
for (int i = 0; i < (int) analytic_forces.size(); ++i)
norm += analytic_forces[i].dot(analytic_forces[i]);
......@@ -303,7 +306,7 @@ static void check_finite_differences(vector<Vec3> analytic_forces, Context &cont
State state2 = context.getState(State::Energy);
context.setPositions(positions3);
State state3 = context.getState(State::Energy);
ASSERT_EQUAL_TOL(norm, (state2.getPotentialEnergy()-state3.getPotentialEnergy())/stepSize, 1e-4);
ASSERT_EQUAL_TOL(norm, (state2.getPotentialEnergy()-state3.getPotentialEnergy())/stepSize, tol);
}
......@@ -493,6 +496,8 @@ int main(int numberOfArguments, char* argv[]) {
try {
registerAmoebaCudaKernelFactories();
if (numberOfArguments > 1)
Platform::getPlatformByName("CUDA").setPropertyDefaultValue("Precision", std::string(argv[1]));
/*
* Water dimer energy / force tests under various conditions.
......
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