CudaCalcMeldForceKernel::CudaCalcMeldForceKernel(std::string name, const Platform& platform, CudaContext& cu,
const System& system) :
CalcMeldForceKernel(name, platform), cu(cu), system(system)
{
if (cu.getUseDoublePrecision()) {
cout << "***\n";
cout << "*** MeldForce does not support double precision.\n";
cout << "***" << endl;
throw OpenMMException("MeldForce does not support double precision");
}
numDistRestraints = 0;
numTorsionRestraints = 0;
numDistProfileRestraints = 0;
numRestraints = 0;
numGroups = 0;
numCollections = 0;
distanceRestRParams = NULL;
distanceRestKParams = NULL;
distanceRestAtomIndices = NULL;
distanceRestGlobalIndices = NULL;
distanceRestForces = NULL;
torsionRestParams = NULL;
torsionRestAtomIndices = NULL;
torsionRestGlobalIndices = NULL;
torsionRestForces = NULL;
distProfileRestAtomIndices = NULL;
distProfileRestDistRanges = NULL;
distProfileRestNumBins = NULL;
distProfileRestParamBounds = NULL;
distProfileRestParams = NULL;
distProfileRestScaleFactor = NULL;
distProfileRestGlobalIndices = NULL;
distProfileRestForces = NULL;
torsProfileRestAtomIndices0 = NULL;
torsProfileRestAtomIndices1 = NULL;
torsProfileRestNumBins = NULL;
torsProfileRestParamBounds = NULL;
torsProfileRestParams0 = NULL;
torsProfileRestParams1 = NULL;
torsProfileRestParams2 = NULL;
torsProfileRestParams3 = NULL;
torsProfileRestScaleFactor = NULL;
torsProfileRestGlobalIndices = NULL;
torsProfileRestForces = NULL;
restraintEnergies = NULL;
restraintActive = NULL;
groupRestraintIndices = NULL;
groupRestraintIndicesTemp = NULL;
groupEnergies = NULL;
groupActive = NULL;
groupBounds = NULL;
groupNumActive = NULL;
collectionGroupIndices = NULL;
collectionBounds = NULL;
collectionNumActive = NULL;
collectionEnergies = NULL;
}
CudaCalcRdcForceKernel::CudaCalcRdcForceKernel(std::string name, const Platform& platform,
CudaContext& cu, const System& system) :
CalcRdcForceKernel(name, platform), cu(cu), system(system) {
if (cu.getUseDoublePrecision()) {
cout << "***\n";
cout << "*** RdcForce does not support double precision.\n";
cout << "***" << endl;
throw OpenMMException("RdcForce does not support double precision");
}
int numExperiments = 0;
int numRdcRestraints = 0;
r = NULL;
atomExptIndices = NULL;
lhs = NULL;
rhs = NULL;
S = NULL;
kappa = NULL;
tolerance = NULL;
force_const = NULL;
weight = NULL;
}
CudaIntegrationUtilities::CudaIntegrationUtilities(CudaContext& context, const System& system) : context(context),
randomPos(0) {
// Create workspace arrays.
lastStepSize = make_double2(0.0, 0.0);
if (context.getUseDoublePrecision() || context.getUseMixedPrecision()) {
posDelta.initialize<double4>(context, context.getPaddedNumAtoms(), "posDelta");
vector<double4> deltas(posDelta.getSize(), make_double4(0.0, 0.0, 0.0, 0.0));
posDelta.upload(deltas);
stepSize.initialize<double2>(context, 1, "stepSize");
stepSize.upload(&lastStepSize);
}
else {
posDelta.initialize<float4>(context, context.getPaddedNumAtoms(), "posDelta");
vector<float4> deltas(posDelta.getSize(), make_float4(0.0f, 0.0f, 0.0f, 0.0f));
posDelta.upload(deltas);
stepSize.initialize<float2>(context, 1, "stepSize");
float2 lastStepSizeFloat = make_float2(0.0f, 0.0f);
stepSize.upload(&lastStepSizeFloat);
}
// Record the set of constraints and how many constraints each atom is involved in.
vector<int> atom1;
vector<int> atom2;
vector<double> distance;
vector<int> constraintCount(context.getNumAtoms(), 0);
for (int i = 0; i < system.getNumConstraints(); i++) {
int p1, p2;
double d;
system.getConstraintParameters(i, p1, p2, d);
if (system.getParticleMass(p1) != 0 || system.getParticleMass(p2) != 0) {
atom1.push_back(p1);
atom2.push_back(p2);
distance.push_back(d);
constraintCount[p1]++;
constraintCount[p2]++;
}
}
// Identify clusters of three atoms that can be treated with SETTLE. First, for every
// atom that might be part of such a cluster, make a list of the two other atoms it is
// connected to.
int numAtoms = system.getNumParticles();
vector<map<int, float> > settleConstraints(numAtoms);
for (int i = 0; i < (int)atom1.size(); i++) {
if (constraintCount[atom1[i]] == 2 && constraintCount[atom2[i]] == 2) {
settleConstraints[atom1[i]][atom2[i]] = (float) distance[i];
settleConstraints[atom2[i]][atom1[i]] = (float) distance[i];
}
}
// Now remove the ones that don't actually form closed loops of three atoms.
vector<int> settleClusters;
for (int i = 0; i < (int)settleConstraints.size(); i++) {
if (settleConstraints[i].size() == 2) {
int partner1 = settleConstraints[i].begin()->first;
int partner2 = (++settleConstraints[i].begin())->first;
if (settleConstraints[partner1].size() != 2 || settleConstraints[partner2].size() != 2 ||
settleConstraints[partner1].find(partner2) == settleConstraints[partner1].end())
settleConstraints[i].clear();
else if (i < partner1 && i < partner2)
settleClusters.push_back(i);
}
else
settleConstraints[i].clear();
}
// Record the SETTLE clusters.
vector<bool> isShakeAtom(numAtoms, false);
if (settleClusters.size() > 0) {
vector<int4> atoms;
vector<float2> params;
for (int i = 0; i < (int) settleClusters.size(); i++) {
int atom1 = settleClusters[i];
int atom2 = settleConstraints[atom1].begin()->first;
int atom3 = (++settleConstraints[atom1].begin())->first;
float dist12 = settleConstraints[atom1].find(atom2)->second;
float dist13 = settleConstraints[atom1].find(atom3)->second;
float dist23 = settleConstraints[atom2].find(atom3)->second;
if (dist12 == dist13) {
// atom1 is the central atom
atoms.push_back(make_int4(atom1, atom2, atom3, 0));
params.push_back(make_float2(dist12, dist23));
}
else if (dist12 == dist23) {
// atom2 is the central atom
atoms.push_back(make_int4(atom2, atom1, atom3, 0));
params.push_back(make_float2(dist12, dist13));
}
else if (dist13 == dist23) {
// atom3 is the central atom
atoms.push_back(make_int4(atom3, atom1, atom2, 0));
params.push_back(make_float2(dist13, dist12));
}
else
continue; // We can't handle this with SETTLE
isShakeAtom[atom1] = true;
isShakeAtom[atom2] = true;
isShakeAtom[atom3] = true;
}
if (atoms.size() > 0) {
settleAtoms.initialize<int4>(context, atoms.size(), "settleAtoms");
settleParams.initialize<float2>(context, params.size(), "settleParams");
settleAtoms.upload(atoms);
settleParams.upload(params);
}
}
// Find clusters consisting of a central atom with up to three peripheral atoms.
map<int, ShakeCluster> clusters;
vector<bool> invalidForShake(numAtoms, false);
for (int i = 0; i < (int) atom1.size(); i++) {
if (isShakeAtom[atom1[i]])
continue; // This is being taken care of with SETTLE.
// Determine which is the central atom.
bool firstIsCentral;
if (constraintCount[atom1[i]] > 1)
firstIsCentral = true;
else if (constraintCount[atom2[i]] > 1)
firstIsCentral = false;
else if (atom1[i] < atom2[i])
firstIsCentral = true;
else
firstIsCentral = false;
int centralID, peripheralID;
if (firstIsCentral) {
centralID = atom1[i];
peripheralID = atom2[i];
}
else {
centralID = atom2[i];
peripheralID = atom1[i];
}
// Add it to the cluster.
if (clusters.find(centralID) == clusters.end()) {
clusters[centralID] = ShakeCluster(centralID, 1.0/system.getParticleMass(centralID));
}
ShakeCluster& cluster = clusters[centralID];
cluster.addAtom(peripheralID, distance[i], 1.0/system.getParticleMass(peripheralID));
if (constraintCount[peripheralID] != 1 || invalidForShake[atom1[i]] || invalidForShake[atom2[i]]) {
cluster.markInvalid(clusters, invalidForShake);
map<int, ShakeCluster>::iterator otherCluster = clusters.find(peripheralID);
if (otherCluster != clusters.end() && otherCluster->second.valid)
otherCluster->second.markInvalid(clusters, invalidForShake);
}
}
int validShakeClusters = 0;
for (map<int, ShakeCluster>::iterator iter = clusters.begin(); iter != clusters.end(); ++iter) {
ShakeCluster& cluster = iter->second;
if (cluster.valid) {
cluster.valid = !invalidForShake[cluster.centralID] && cluster.size == constraintCount[cluster.centralID];
for (int i = 0; i < cluster.size; i++)
if (invalidForShake[cluster.peripheralID[i]])
cluster.valid = false;
if (cluster.valid)
++validShakeClusters;
}
}
// Record the SHAKE clusters.
if (validShakeClusters > 0) {
vector<int4> atoms;
vector<float4> params;
int index = 0;
for (map<int, ShakeCluster>::const_iterator iter = clusters.begin(); iter != clusters.end(); ++iter) {
const ShakeCluster& cluster = iter->second;
if (!cluster.valid)
continue;
atoms.push_back(make_int4(cluster.centralID, cluster.peripheralID[0], (cluster.size > 1 ? cluster.peripheralID[1] : -1), (cluster.size > 2 ? cluster.peripheralID[2] : -1)));
params.push_back(make_float4((float) cluster.centralInvMass, (float) (0.5/(cluster.centralInvMass+cluster.peripheralInvMass)), (float) (cluster.distance*cluster.distance), (float) cluster.peripheralInvMass));
isShakeAtom[cluster.centralID] = true;
isShakeAtom[cluster.peripheralID[0]] = true;
if (cluster.size > 1)
isShakeAtom[cluster.peripheralID[1]] = true;
if (cluster.size > 2)
isShakeAtom[cluster.peripheralID[2]] = true;
++index;
}
shakeAtoms.initialize<int4>(context, atoms.size(), "shakeAtoms");
shakeParams.initialize<float4>(context, params.size(), "shakeParams");
shakeAtoms.upload(atoms);
shakeParams.upload(params);
}
// Find connected constraints for CCMA.
vector<int> ccmaConstraints;
for (unsigned i = 0; i < atom1.size(); i++)
if (!isShakeAtom[atom1[i]])
ccmaConstraints.push_back(i);
// Record the connections between constraints.
int numCCMA = (int) ccmaConstraints.size();
if (numCCMA > 0) {
// Record information needed by ReferenceCCMAAlgorithm.
vector<pair<int, int> > refIndices(numCCMA);
vector<double> refDistance(numCCMA);
for (int i = 0; i < numCCMA; i++) {
int index = ccmaConstraints[i];
refIndices[i] = make_pair(atom1[index], atom2[index]);
refDistance[i] = distance[index];
}
vector<double> refMasses(numAtoms);
for (int i = 0; i < numAtoms; ++i)
refMasses[i] = system.getParticleMass(i);
// Look up angles for CCMA.
vector<ReferenceCCMAAlgorithm::AngleInfo> angles;
for (int i = 0; i < system.getNumForces(); i++) {
const HarmonicAngleForce* force = dynamic_cast<const HarmonicAngleForce*>(&system.getForce(i));
if (force != NULL) {
for (int j = 0; j < force->getNumAngles(); j++) {
int atom1, atom2, atom3;
double angle, k;
force->getAngleParameters(j, atom1, atom2, atom3, angle, k);
angles.push_back(ReferenceCCMAAlgorithm::AngleInfo(atom1, atom2, atom3, angle));
}
}
}
// Create a ReferenceCCMAAlgorithm. It will build and invert the constraint matrix for us.
ReferenceCCMAAlgorithm ccma(numAtoms, numCCMA, refIndices, refDistance, refMasses, angles, 0.1);
vector<vector<pair<int, double> > > matrix = ccma.getMatrix();
int maxRowElements = 0;
for (unsigned i = 0; i < matrix.size(); i++)
maxRowElements = max(maxRowElements, (int) matrix[i].size());
maxRowElements++;
// Build the list of constraints for each atom.
vector<vector<int> > atomConstraints(context.getNumAtoms());
for (int i = 0; i < numCCMA; i++) {
atomConstraints[atom1[ccmaConstraints[i]]].push_back(i);
atomConstraints[atom2[ccmaConstraints[i]]].push_back(i);
}
int maxAtomConstraints = 0;
for (unsigned i = 0; i < atomConstraints.size(); i++)
maxAtomConstraints = max(maxAtomConstraints, (int) atomConstraints[i].size());
// Sort the constraints.
vector<int> constraintOrder(numCCMA);
for (int i = 0; i < numCCMA; ++i)
constraintOrder[i] = i;
sort(constraintOrder.begin(), constraintOrder.end(), ConstraintOrderer(atom1, atom2, ccmaConstraints));
vector<int> inverseOrder(numCCMA);
for (int i = 0; i < numCCMA; ++i)
inverseOrder[constraintOrder[i]] = i;
for (int i = 0; i < (int)matrix.size(); ++i)
for (int j = 0; j < (int)matrix[i].size(); ++j)
matrix[i][j].first = inverseOrder[matrix[i][j].first];
// Record the CCMA data structures.
ccmaAtoms.initialize<int2>(context, numCCMA, "CcmaAtoms");
ccmaAtomConstraints.initialize<int>(context, numAtoms*maxAtomConstraints, "CcmaAtomConstraints");
ccmaNumAtomConstraints.initialize<int>(context, numAtoms, "CcmaAtomConstraintsIndex");
ccmaConstraintMatrixColumn.initialize<int>(context, numCCMA*maxRowElements, "ConstraintMatrixColumn");
ccmaConverged.initialize<int>(context, 2, "ccmaConverged");
CHECK_RESULT2(cuMemHostAlloc((void**) &ccmaConvergedMemory, sizeof(int), CU_MEMHOSTALLOC_DEVICEMAP), "Error allocating pinned memory");
CHECK_RESULT2(cuMemHostGetDevicePointer(&ccmaConvergedDeviceMemory, ccmaConvergedMemory, 0), "Error getting device address for pinned memory");
vector<int2> atomsVec(ccmaAtoms.getSize());
vector<int> atomConstraintsVec(ccmaAtomConstraints.getSize());
vector<int> numAtomConstraintsVec(ccmaNumAtomConstraints.getSize());
vector<int> constraintMatrixColumnVec(ccmaConstraintMatrixColumn.getSize());
int elementSize = (context.getUseDoublePrecision() || context.getUseMixedPrecision() ? sizeof(double) : sizeof(float));
ccmaDistance.initialize(context, numCCMA, 4*elementSize, "CcmaDistance");
ccmaDelta1.initialize(context, numCCMA, elementSize, "CcmaDelta1");
ccmaDelta2.initialize(context, numCCMA, elementSize, "CcmaDelta2");
ccmaReducedMass.initialize(context, numCCMA, elementSize, "CcmaReducedMass");
ccmaConstraintMatrixValue.initialize(context, numCCMA*maxRowElements, elementSize, "ConstraintMatrixValue");
vector<double4> distanceVec(ccmaDistance.getSize());
vector<double> reducedMassVec(ccmaReducedMass.getSize());
vector<double> constraintMatrixValueVec(ccmaConstraintMatrixValue.getSize());
for (int i = 0; i < numCCMA; i++) {
int index = constraintOrder[i];
int c = ccmaConstraints[index];
atomsVec[i].x = atom1[c];
atomsVec[i].y = atom2[c];
distanceVec[i].w = distance[c];
reducedMassVec[i] = (0.5/(1.0/system.getParticleMass(atom1[c])+1.0/system.getParticleMass(atom2[c])));
for (unsigned int j = 0; j < matrix[index].size(); j++) {
constraintMatrixColumnVec[i+j*numCCMA] = matrix[index][j].first;
constraintMatrixValueVec[i+j*numCCMA] = matrix[index][j].second;
}
constraintMatrixColumnVec[i+matrix[index].size()*numCCMA] = numCCMA;
}
ccmaDistance.upload(distanceVec, true);
ccmaReducedMass.upload(reducedMassVec, true);
ccmaConstraintMatrixValue.upload(constraintMatrixValueVec, true);
for (unsigned int i = 0; i < atomConstraints.size(); i++) {
numAtomConstraintsVec[i] = atomConstraints[i].size();
for (unsigned int j = 0; j < atomConstraints[i].size(); j++) {
bool forward = (atom1[ccmaConstraints[atomConstraints[i][j]]] == i);
atomConstraintsVec[i+j*numAtoms] = (forward ? inverseOrder[atomConstraints[i][j]]+1 : -inverseOrder[atomConstraints[i][j]]-1);
}
}
ccmaAtoms.upload(atomsVec);
ccmaAtomConstraints.upload(atomConstraintsVec);
ccmaNumAtomConstraints.upload(numAtomConstraintsVec);
ccmaConstraintMatrixColumn.upload(constraintMatrixColumnVec);
}
// Build the list of virtual sites.
vector<int4> vsite2AvgAtomVec;
vector<double2> vsite2AvgWeightVec;
vector<int4> vsite3AvgAtomVec;
vector<double4> vsite3AvgWeightVec;
vector<int4> vsiteOutOfPlaneAtomVec;
vector<double4> vsiteOutOfPlaneWeightVec;
vector<int> vsiteLocalCoordsIndexVec;
vector<int> vsiteLocalCoordsAtomVec;
vector<int> vsiteLocalCoordsStartVec;
vector<double> vsiteLocalCoordsWeightVec;
vector<double4> vsiteLocalCoordsPosVec;
for (int i = 0; i < numAtoms; i++) {
if (system.isVirtualSite(i)) {
if (dynamic_cast<const TwoParticleAverageSite*>(&system.getVirtualSite(i)) != NULL) {
// A two particle average.
const TwoParticleAverageSite& site = dynamic_cast<const TwoParticleAverageSite&>(system.getVirtualSite(i));
vsite2AvgAtomVec.push_back(make_int4(i, site.getParticle(0), site.getParticle(1), 0));
vsite2AvgWeightVec.push_back(make_double2(site.getWeight(0), site.getWeight(1)));
}
else if (dynamic_cast<const ThreeParticleAverageSite*>(&system.getVirtualSite(i)) != NULL) {
// A three particle average.
const ThreeParticleAverageSite& site = dynamic_cast<const ThreeParticleAverageSite&>(system.getVirtualSite(i));
vsite3AvgAtomVec.push_back(make_int4(i, site.getParticle(0), site.getParticle(1), site.getParticle(2)));
vsite3AvgWeightVec.push_back(make_double4(site.getWeight(0), site.getWeight(1), site.getWeight(2), 0.0));
}
else if (dynamic_cast<const OutOfPlaneSite*>(&system.getVirtualSite(i)) != NULL) {
// An out of plane site.
const OutOfPlaneSite& site = dynamic_cast<const OutOfPlaneSite&>(system.getVirtualSite(i));
vsiteOutOfPlaneAtomVec.push_back(make_int4(i, site.getParticle(0), site.getParticle(1), site.getParticle(2)));
vsiteOutOfPlaneWeightVec.push_back(make_double4(site.getWeight12(), site.getWeight13(), site.getWeightCross(), 0.0));
}
else if (dynamic_cast<const LocalCoordinatesSite*>(&system.getVirtualSite(i)) != NULL) {
// A local coordinates site.
const LocalCoordinatesSite& site = dynamic_cast<const LocalCoordinatesSite&>(system.getVirtualSite(i));
int numParticles = site.getNumParticles();
vector<double> origin, x, y;
site.getOriginWeights(origin);
site.getXWeights(x);
site.getYWeights(y);
vsiteLocalCoordsIndexVec.push_back(i);
vsiteLocalCoordsStartVec.push_back(vsiteLocalCoordsAtomVec.size());
for (int j = 0; j < numParticles; j++) {
vsiteLocalCoordsAtomVec.push_back(site.getParticle(j));
vsiteLocalCoordsWeightVec.push_back(origin[j]);
vsiteLocalCoordsWeightVec.push_back(x[j]);
vsiteLocalCoordsWeightVec.push_back(y[j]);
}
Vec3 pos = site.getLocalPosition();
vsiteLocalCoordsPosVec.push_back(make_double4(pos[0], pos[1], pos[2], 0.0));
}
}
}
vsiteLocalCoordsStartVec.push_back(vsiteLocalCoordsAtomVec.size());
int num2Avg = vsite2AvgAtomVec.size();
int num3Avg = vsite3AvgAtomVec.size();
int numOutOfPlane = vsiteOutOfPlaneAtomVec.size();
int numLocalCoords = vsiteLocalCoordsPosVec.size();
vsite2AvgAtoms.initialize<int4>(context, max(1, num2Avg), "vsite2AvgAtoms");
vsite3AvgAtoms.initialize<int4>(context, max(1, num3Avg), "vsite3AvgAtoms");
vsiteOutOfPlaneAtoms.initialize<int4>(context, max(1, numOutOfPlane), "vsiteOutOfPlaneAtoms");
vsiteLocalCoordsIndex.initialize<int>(context, max(1, (int) vsiteLocalCoordsIndexVec.size()), "vsiteLocalCoordsIndex");
vsiteLocalCoordsAtoms.initialize<int>(context, max(1, (int) vsiteLocalCoordsAtomVec.size()), "vsiteLocalCoordsAtoms");
vsiteLocalCoordsStartIndex.initialize<int>(context, max(1, (int) vsiteLocalCoordsStartVec.size()), "vsiteLocalCoordsStartIndex");
if (num2Avg > 0)
vsite2AvgAtoms.upload(vsite2AvgAtomVec);
if (num3Avg > 0)
vsite3AvgAtoms.upload(vsite3AvgAtomVec);
if (numOutOfPlane > 0)
vsiteOutOfPlaneAtoms.upload(vsiteOutOfPlaneAtomVec);
if (numLocalCoords > 0) {
vsiteLocalCoordsIndex.upload(vsiteLocalCoordsIndexVec);
vsiteLocalCoordsAtoms.upload(vsiteLocalCoordsAtomVec);
vsiteLocalCoordsStartIndex.upload(vsiteLocalCoordsStartVec);
}
int elementSize = (context.getUseDoublePrecision() ? sizeof(double) : sizeof(float));
vsite2AvgWeights.initialize(context, max(1, num2Avg), 2*elementSize, "vsite2AvgWeights");
vsite3AvgWeights.initialize(context, max(1, num3Avg), 4*elementSize, "vsite3AvgWeights");
vsiteOutOfPlaneWeights.initialize(context, max(1, numOutOfPlane), 4*elementSize, "vsiteOutOfPlaneWeights");
vsiteLocalCoordsWeights.initialize(context, max(1, (int) vsiteLocalCoordsWeightVec.size()), elementSize, "vsiteLocalCoordsWeights");
vsiteLocalCoordsPos.initialize(context, max(1, (int) vsiteLocalCoordsPosVec.size()), 4*elementSize, "vsiteLocalCoordsPos");
if (num2Avg > 0)
vsite2AvgWeights.upload(vsite2AvgWeightVec, true);
if (num3Avg > 0)
vsite3AvgWeights.upload(vsite3AvgWeightVec, true);
if (numOutOfPlane > 0)
vsiteOutOfPlaneWeights.upload(vsiteOutOfPlaneWeightVec, true);
if (numLocalCoords > 0) {
vsiteLocalCoordsWeights.upload(vsiteLocalCoordsWeightVec, true);
vsiteLocalCoordsPos.upload(vsiteLocalCoordsPosVec, true);
}
// Create the kernels used by this class.
map<string, string> defines;
defines["NUM_CCMA_CONSTRAINTS"] = context.intToString(numCCMA);
defines["NUM_ATOMS"] = context.intToString(numAtoms);
defines["NUM_2_AVERAGE"] = context.intToString(num2Avg);
defines["NUM_3_AVERAGE"] = context.intToString(num3Avg);
defines["NUM_OUT_OF_PLANE"] = context.intToString(numOutOfPlane);
defines["NUM_LOCAL_COORDS"] = context.intToString(numLocalCoords);
defines["PADDED_NUM_ATOMS"] = context.intToString(context.getPaddedNumAtoms());
CUmodule module = context.createModule(CudaKernelSources::vectorOps+CudaKernelSources::integrationUtilities, defines);
settlePosKernel = context.getKernel(module, "applySettleToPositions");
settleVelKernel = context.getKernel(module, "applySettleToVelocities");
shakePosKernel = context.getKernel(module, "applyShakeToPositions");
shakeVelKernel = context.getKernel(module, "applyShakeToVelocities");
ccmaDirectionsKernel = context.getKernel(module, "computeCCMAConstraintDirections");
ccmaPosForceKernel = context.getKernel(module, "computeCCMAPositionConstraintForce");
ccmaVelForceKernel = context.getKernel(module, "computeCCMAVelocityConstraintForce");
ccmaMultiplyKernel = context.getKernel(module, "multiplyByCCMAConstraintMatrix");
ccmaUpdateKernel = context.getKernel(module, "updateCCMAAtomPositions");
CHECK_RESULT2(cuEventCreate(&ccmaEvent, CU_EVENT_DISABLE_TIMING), "Error creating event for CCMA");
vsitePositionKernel = context.getKernel(module, "computeVirtualSites");
vsiteForceKernel = context.getKernel(module, "distributeVirtualSiteForces");
numVsites = num2Avg+num3Avg+numOutOfPlane+numLocalCoords;
randomKernel = context.getKernel(module, "generateRandomNumbers");
timeShiftKernel = context.getKernel(module, "timeShiftVelocities");
}