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Commit 968cb132 authored by Peter Eastman's avatar Peter Eastman
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Continuing implementation of LINCS for Cuda platform

parent 1b9ab82b
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Showing with 186 additions and 132 deletions
platforms/cuda/src/CudaKernels.cpp
View file @ 968cb132
......@@ -372,7 +372,7 @@ static void initializeIntegration(const System& system, CudaPlatform::PlatformDa
invMass1[i] = 1.0f/mass[particle1Index];
invMass2[i] = 1.0f/mass[particle2Index];
}
gpuSetShakeParameters(gpu, particle1, particle2, distance, invMass1, invMass2, integrator.getConstraintTolerance());
gpuSetConstraintParameters(gpu, particle1, particle2, distance, invMass1, invMass2, integrator.getConstraintTolerance(), 4);
// Initialize any terms that haven't already been handled by a Force.
......
platforms/cuda/src/kernels/cudatypes.h
View file @ 968cb132
......@@ -352,6 +352,7 @@ struct cudaGmxSimulation {
unsigned int maxShakeIterations; // Maximum shake iterations
unsigned int degreesOfFreedom; // Number of degrees of freedom in system
float shakeTolerance; // Shake tolerance
unsigned int lincsTerms; // Number of terms in the matrix expansion for LINCS
float InvMassJ; // Shake inverse mass for hydrogens
int* pNonShakeID; // Not Shaking atoms
int4* pShakeID; // Shake atoms and phase
......
platforms/cuda/src/kernels/gpu.cpp
View file @ 968cb132
......@@ -59,23 +59,22 @@ struct ShakeCluster {
int centralID;
int peripheralID[3];
int size;
bool valid;
float distance;
float centralInvMass, peripheralInvMass;
ShakeCluster() {
ShakeCluster() : valid(true) {
}
ShakeCluster(int centralID, float invMass) : centralID(centralID), centralInvMass(invMass), size(0) {
ShakeCluster(int centralID, float invMass) : centralID(centralID), centralInvMass(invMass), size(0), valid(true) {
}
void addAtom(int id, float dist, float invMass) {
if (size == 3)
throw OpenMMException("A single atom may only have three constraints");
if (size > 0 && dist != distance)
throw OpenMMException("All constraints for a central atom must have the same distance");
if (size > 0 && invMass != peripheralInvMass)
throw OpenMMException("All constraints for a central atom must have the same mass");
if (size == 3 || (size > 0 && dist != distance) || (size > 0 && invMass != peripheralInvMass))
valid = false;
else {
peripheralID[size++] = id;
distance = dist;
peripheralInvMass = invMass;
}
}
};
struct Constraint
......@@ -457,10 +456,26 @@ void gpuSetObcParameters(gpuContext gpu, float innerDielectric, float solventDie
gpu->sim.preFactor = 2.0f*electricConstant*((1.0f/innerDielectric)-(1.0f/solventDielectric))*gpu->sim.forceConversionFactor;
}
void markShakeClusterInvalid(ShakeCluster& cluster, map<int, ShakeCluster>& allClusters, vector<bool>& invalidForShake)
{
cluster.valid = false;
invalidForShake[cluster.centralID] = true;
for (int i = 0; i < cluster.size; i++) {
invalidForShake[cluster.peripheralID[i]] = true;
map<int, ShakeCluster>::iterator otherCluster = allClusters.find(cluster.peripheralID[i]);
if (otherCluster != allClusters.end() && otherCluster->second.valid)
markShakeClusterInvalid(otherCluster->second, allClusters, invalidForShake);
}
}
extern "C"
void gpuSetShakeParameters(gpuContext gpu, const vector<int>& atom1, const vector<int>& atom2, const vector<float>& distance,
const vector<float>& invMass1, const vector<float>& invMass2, float tolerance)
void gpuSetConstraintParameters(gpuContext gpu, const vector<int>& atom1, const vector<int>& atom2, const vector<float>& distance,
const vector<float>& invMass1, const vector<float>& invMass2, float shakeTolerance, unsigned int lincsTerms)
{
// Create a vector for recording which atoms are handled by SHAKE (or SETTLE).
vector<bool> isShakeAtom(gpu->natoms, false);
// Find how many constraints each atom is involved in.
vector<int> constraintCount(gpu->natoms, 0);
......@@ -537,6 +552,9 @@ void gpuSetShakeParameters(gpuContext gpu, const vector<int>& atom1, const vecto
}
else
throw OpenMMException("Two of the three distances constrained with SETTLE must be the same.");
isShakeAtom[atom1] = true;
isShakeAtom[atom2] = true;
isShakeAtom[atom3] = true;
}
psSettleID->Upload();
psSettleParameter->Upload();
......@@ -546,11 +564,111 @@ void gpuSetShakeParameters(gpuContext gpu, const vector<int>& atom1, const vecto
if (gpu->sim.settle_threads_per_block < 1)
gpu->sim.settle_threads_per_block = 1;
// Find clusters consisting of a central atom with up to three peripheral atoms.
map<int, ShakeCluster> clusters;
vector<bool> invalidForShake(gpu->natoms, false);
for (int i = 0; i < 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;
float centralInvMass, peripheralInvMass;
if (firstIsCentral) {
centralID = atom1[i];
peripheralID = atom2[i];
centralInvMass = invMass1[i];
peripheralInvMass = invMass2[i];
}
else {
centralID = atom2[i];
peripheralID = atom1[i];
centralInvMass = invMass2[i];
peripheralInvMass = invMass1[i];
}
// Add it to the cluster.
if (clusters.find(centralID) == clusters.end()) {
clusters[centralID] = ShakeCluster(centralID, centralInvMass);
}
ShakeCluster& cluster = clusters[centralID];
cluster.addAtom(peripheralID, distance[i], peripheralInvMass);
if (constraintCount[peripheralID] != 1 || invalidForShake[atom1[i]] || invalidForShake[atom2[i]]) {
markShakeClusterInvalid(cluster, clusters, invalidForShake);
map<int, ShakeCluster>::iterator otherCluster = clusters.find(peripheralID);
if (otherCluster != clusters.end() && otherCluster->second.valid)
markShakeClusterInvalid(otherCluster->second, 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];
for (int i = 0; i < cluster.size; i++)
if (invalidForShake[cluster.peripheralID[i]])
cluster.valid = false;
if (cluster.valid)
++validShakeClusters;
}
}
// Fill in the Cuda streams.
CUDAStream<int4>* psShakeID = new CUDAStream<int4>(validShakeClusters, 1);
gpu->psShakeID = psShakeID;
gpu->sim.pShakeID = psShakeID->_pDevStream[0];
CUDAStream<float4>* psShakeParameter = new CUDAStream<float4>(validShakeClusters, 1);
gpu->psShakeParameter = psShakeParameter;
gpu->sim.pShakeParameter = psShakeParameter->_pDevStream[0];
gpu->sim.ShakeConstraints = validShakeClusters;
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;
psShakeID->_pSysStream[0][index].x = cluster.centralID;
psShakeID->_pSysStream[0][index].y = cluster.peripheralID[0];
psShakeID->_pSysStream[0][index].z = cluster.size > 1 ? cluster.peripheralID[1] : -1;
psShakeID->_pSysStream[0][index].w = cluster.size > 2 ? cluster.peripheralID[2] : -1;
psShakeParameter->_pSysStream[0][index].x = cluster.centralInvMass;
psShakeParameter->_pSysStream[0][index].y = 0.5f/(cluster.centralInvMass+cluster.peripheralInvMass);
psShakeParameter->_pSysStream[0][index].z = cluster.distance*cluster.distance;
psShakeParameter->_pSysStream[0][index].w = 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;
}
psShakeID->Upload();
psShakeParameter->Upload();
gpu->sim.shakeTolerance = shakeTolerance;
gpu->sim.shake_threads_per_block = (gpu->sim.ShakeConstraints + gpu->sim.blocks - 1) / gpu->sim.blocks;
if (gpu->sim.shake_threads_per_block > gpu->sim.max_shake_threads_per_block)
gpu->sim.shake_threads_per_block = gpu->sim.max_shake_threads_per_block;
if (gpu->sim.shake_threads_per_block < 1)
gpu->sim.shake_threads_per_block = 1;
// Find connected constraints for LINCS.
vector<int> lincsConstraints;
for (unsigned int i = 0; i < atom1.size(); i++)
if (settleConstraints[atom1[i]].size() != 2)
if (!isShakeAtom[atom1[i]])
lincsConstraints.push_back(i);
vector<vector<int> > atomConstraints(gpu->natoms);
for (unsigned int i = 0; i < lincsConstraints.size(); i++) {
......@@ -606,11 +724,11 @@ void gpuSetShakeParameters(gpuContext gpu, const vector<int>& atom1, const vecto
CUDAStream<float>* psLincsSolution = new CUDAStream<float>((int) lincsConstraints.size(), 1);
gpu->psLincsSolution = psLincsSolution;
gpu->sim.pLincsSolution = psLincsSolution->_pDevData;
CUDAStream<unsigned int>* psSyncCounter = new CUDAStream<unsigned int>(100, 1);
CUDAStream<unsigned int>* psSyncCounter = new CUDAStream<unsigned int>(2*lincsTerms+2, 1);
gpu->psSyncCounter = psSyncCounter;
gpu->sim.pSyncCounter = psSyncCounter->_pDevData;
gpu->sim.lincsConstraints = lincsConstraints.size();
int index = 0;
index = 0;
for (unsigned int i = 0; i < lincsConstraints.size(); i++) {
int c = lincsConstraints[i];
psLincsAtoms->_pSysData[i].x = atom1[c];
......@@ -639,92 +757,19 @@ void gpuSetShakeParameters(gpuContext gpu, const vector<int>& atom1, const vecto
psLincsAtomConstraints->Upload();
psLincsAtomConstraintsIndex->Upload();
psSyncCounter->Upload();
gpu->sim.lincsTerms = lincsTerms;
gpu->sim.lincs_threads_per_block = (gpu->sim.lincsConstraints + gpu->sim.blocks - 1) / gpu->sim.blocks;
if (gpu->sim.lincs_threads_per_block > gpu->sim.max_shake_threads_per_block)
gpu->sim.lincs_threads_per_block = gpu->sim.max_shake_threads_per_block;
if (gpu->sim.lincs_threads_per_block < 1)
gpu->sim.lincs_threads_per_block = 1;
/*
// Find clusters consisting of a central atom with up to three peripheral atoms.
map<int, ShakeCluster> clusters;
for (int i = 0; i < atom1.size(); i++) {
if (settleConstraints[atom1[i]].size() == 2)
continue; // This is being taken care of with SETTLE.
gpu->psLincsConnectionsIndex->Download();
gpu->psLincsConnections->Download();
gpu->psLincsCoupling->Download();
// 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;
float centralInvMass, peripheralInvMass;
if (firstIsCentral) {
centralID = atom1[i];
peripheralID = atom2[i];
centralInvMass = invMass1[i];
peripheralInvMass = invMass2[i];
}
else {
centralID = atom2[i];
peripheralID = atom1[i];
centralInvMass = invMass2[i];
peripheralInvMass = invMass1[i];
}
if (constraintCount[peripheralID] != 1)
throw OpenMMException("Only bonds to hydrogens may be constrained");
// Add it to the cluster.
if (clusters.find(centralID) == clusters.end()) {
clusters[centralID] = ShakeCluster(centralID, centralInvMass);
}
clusters[centralID].addAtom(peripheralID, distance[i], peripheralInvMass);
}
// Fill in the Cuda streams.
CUDAStream<int4>* psShakeID = new CUDAStream<int4>((int) clusters.size(), 1);
gpu->psShakeID = psShakeID;
gpu->sim.pShakeID = psShakeID->_pDevStream[0];
CUDAStream<float4>* psShakeParameter = new CUDAStream<float4>((int) clusters.size(), 1);
gpu->psShakeParameter = psShakeParameter;
gpu->sim.pShakeParameter = psShakeParameter->_pDevStream[0];
gpu->sim.ShakeConstraints = clusters.size();
int index = 0;
for (map<int, ShakeCluster>::const_iterator iter = clusters.begin(); iter != clusters.end(); ++iter) {
const ShakeCluster& cluster = iter->second;
psShakeID->_pSysStream[0][index].x = cluster.centralID;
psShakeID->_pSysStream[0][index].y = cluster.peripheralID[0];
psShakeID->_pSysStream[0][index].z = cluster.size > 1 ? cluster.peripheralID[1] : -1;
psShakeID->_pSysStream[0][index].w = cluster.size > 2 ? cluster.peripheralID[2] : -1;
psShakeParameter->_pSysStream[0][index].x = cluster.centralInvMass;
psShakeParameter->_pSysStream[0][index].y = 0.5f/(cluster.centralInvMass+cluster.peripheralInvMass);
psShakeParameter->_pSysStream[0][index].z = cluster.distance*cluster.distance;
psShakeParameter->_pSysStream[0][index].w = cluster.peripheralInvMass;
++index;
}
psShakeID->Upload();
psShakeParameter->Upload();
gpu->sim.shakeTolerance = tolerance;
*/
gpu->sim.ShakeConstraints = 0;
gpu->sim.shake_threads_per_block = (gpu->sim.ShakeConstraints + gpu->sim.blocks - 1) / gpu->sim.blocks;
if (gpu->sim.shake_threads_per_block > gpu->sim.max_shake_threads_per_block)
gpu->sim.shake_threads_per_block = gpu->sim.max_shake_threads_per_block;
if (gpu->sim.shake_threads_per_block < 1)
gpu->sim.shake_threads_per_block = 1;
#ifdef DeltaShake
......@@ -732,7 +777,7 @@ void gpuSetShakeParameters(gpuContext gpu, const vector<int>& atom1, const vecto
int count = 0;
for (int i = 0; i < gpu->natoms; i++)
// if (constraintCount[i] == 0)
if (!isShakeAtom[i])
count++;
// Allocate NonShake parameters
......@@ -756,9 +801,9 @@ void gpuSetShakeParameters(gpuContext gpu, const vector<int>& atom1, const vecto
count = 0;
for (int i = 0; i < gpu->natoms; i++){
// if (constraintCount[i] == 0){
if (!isShakeAtom[i]){
psNonShakeID->_pSysStream[0][count++] = i;
// }
}
}
psNonShakeID->Upload();
......
platforms/cuda/src/kernels/gputypes.h
View file @ 968cb132
......@@ -183,8 +183,8 @@ extern "C"
void gpuSetObcParameters(gpuContext gpu, float innerDielectric, float solventDielectric, const std::vector<int>& atom, const std::vector<float>& radius, const std::vector<float>& scale);
extern "C"
void gpuSetShakeParameters(gpuContext gpu, const std::vector<int>& atom1, const std::vector<int>& atom2, const std::vector<float>& distance,
const std::vector<float>& invMass1, const std::vector<float>& invMass2, float tolerance);
void gpuSetConstraintParameters(gpuContext gpu, const std::vector<int>& atom1, const std::vector<int>& atom2, const std::vector<float>& distance,
const std::vector<float>& invMass1, const std::vector<float>& invMass2, float shakeTolerance, unsigned int lincsTerms);
extern "C"
int gpuAllocateInitialBuffers(gpuContext gpu);
......
platforms/cuda/src/kernels/kLincs.cu
View file @ 968cb132
......@@ -73,9 +73,9 @@ __device__ void kSyncAllThreads_kernel(unsigned int* syncCounter)
} while (counterValue > 0);
}
__device__ void kSolveMatrix_kernel(unsigned int numTerms, unsigned int* syncCounter)
__device__ void kSolveMatrix_kernel(unsigned int* syncCounter)
{
for (unsigned int iteration = 0; iteration < numTerms; iteration++) {
for (unsigned int iteration = 0; iteration < cSim.lincsTerms; iteration++) {
float* rhs1 = (iteration%2 == 0 ? cSim.pLincsRhs1 : cSim.pLincsRhs2);
float* rhs2 = (iteration%2 == 0 ? cSim.pLincsRhs2 : cSim.pLincsRhs1);
unsigned int pos = threadIdx.x + blockIdx.x * blockDim.x;
......@@ -121,7 +121,7 @@ __device__ void kUpdateAtomPositions_kernel(float4* atomPositions)
}
}
__global__ void kApplyLincs_kernel(unsigned int numTerms, float4* atomPositions, bool addOldPosition)
__global__ void kApplyLincs_kernel(float4* atomPositions, bool addOldPosition)
{
// Calculate the direction of each constraint, along with the initial RHS and solution vectors.
......@@ -174,15 +174,15 @@ __global__ void kApplyLincs_kernel(unsigned int numTerms, float4* atomPositions,
int otherConstraint = cSim.pLincsConnections[i];
float4 dir2 = cSim.pLincsDistance[otherConstraint];
int2 atoms2 = cSim.pLincsAtoms[otherConstraint];
float sign = (atoms1.x == atoms2.x || atoms1.y == atoms2.y ? -1.0f : 1.0f);
cSim.pLincsCoupling[i] = sign*invMass*s*(dir1.x*dir2.x+dir1.y*dir2.y+dir1.z*dir2.z)*cSim.pLincsS[otherConstraint]; // ***** Is this the correct mass? *****
float signedMass = (atoms1.x == atoms2.x || atoms1.y == atoms2.y ? -invMass : cSim.pVelm4[atoms1.y].w);
cSim.pLincsCoupling[i] = signedMass*s*(dir1.x*dir2.x+dir1.y*dir2.y+dir1.z*dir2.z)*cSim.pLincsS[otherConstraint];
}
pos += blockDim.x * gridDim.x;
}
// Solve the matrix equation and update the atom positions.
kSolveMatrix_kernel(numTerms, cSim.pSyncCounter+1);
kSolveMatrix_kernel(cSim.pSyncCounter+1);
kUpdateAtomPositions_kernel(atomPositions);
// Correct for rotational lengthening.
......@@ -217,7 +217,7 @@ __global__ void kApplyLincs_kernel(unsigned int numTerms, float4* atomPositions,
// Solve the matrix equation and update the atom positions.
kSolveMatrix_kernel(numTerms, cSim.pSyncCounter+numTerms+1);
kSolveMatrix_kernel(cSim.pSyncCounter+cSim.lincsTerms+1);
kUpdateAtomPositions_kernel(atomPositions);
}
......@@ -226,7 +226,7 @@ void kApplyFirstLincs(gpuContext gpu)
// printf("kApplyFirstLincs\n");
if (gpu->sim.lincsConstraints > 0)
{
kApplyLincs_kernel<<<gpu->sim.blocks, gpu->sim.lincs_threads_per_block>>>(4, gpu->sim.pPosqP, true);
kApplyLincs_kernel<<<gpu->sim.blocks, gpu->sim.lincs_threads_per_block>>>(gpu->sim.pPosqP, true);
LAUNCHERROR("kApplyFirstLincs");
}
}
......@@ -236,7 +236,7 @@ void kApplySecondLincs(gpuContext gpu)
// printf("kApplySecondLincs\n");
if (gpu->sim.lincsConstraints > 0)
{
kApplyLincs_kernel<<<gpu->sim.blocks, gpu->sim.lincs_threads_per_block>>>(4, gpu->sim.pPosq, false);
kApplyLincs_kernel<<<gpu->sim.blocks, gpu->sim.lincs_threads_per_block>>>(gpu->sim.pPosq, false);
LAUNCHERROR("kApplySecondLincs");
}
}
platforms/cuda/tests/TestCudaBrownianIntegrator.cpp
View file @ 968cb132
......@@ -126,7 +126,7 @@ void testTemperature() {
void testConstraints() {
const int numParticles = 8;
const int numConstraints = numParticles/2;
const int numConstraints = 5;
const double temp = 20.0;
CudaPlatform platform;
System system(numParticles, numConstraints);
......@@ -137,8 +137,11 @@ void testConstraints() {
system.setParticleMass(i, 10.0);
forceField->setParticleParameters(i, (i%2 == 0 ? 0.2 : -0.2), 0.5, 5.0);
}
for (int i = 0; i < numConstraints; ++i)
system.setConstraintParameters(i, 2*i, 2*i+1, 1.0);
system.setConstraintParameters(0, 0, 1, 1.0);
system.setConstraintParameters(1, 1, 2, 1.0);
system.setConstraintParameters(2, 2, 3, 1.0);
system.setConstraintParameters(3, 4, 5, 1.0);
system.setConstraintParameters(4, 6, 7, 1.0);
system.addForce(forceField);
OpenMMContext context(system, integrator, platform);
vector<Vec3> positions(numParticles);
......
platforms/cuda/tests/TestCudaLangevinIntegrator.cpp
View file @ 968cb132
......@@ -131,7 +131,7 @@ void testTemperature() {
void testConstraints() {
const int numParticles = 8;
const int numConstraints = 7;
const int numConstraints = 5;
const double temp = 100.0;
CudaPlatform platform;
System system(numParticles, numConstraints);
......@@ -142,8 +142,11 @@ void testConstraints() {
system.setParticleMass(i, 10.0);
forceField->setParticleParameters(i, (i%2 == 0 ? 0.2 : -0.2), 0.5, 5.0);
}
for (int i = 0; i < numConstraints; ++i)
system.setConstraintParameters(i, i, i+1, 1.0);
system.setConstraintParameters(0, 0, 1, 1.0);
system.setConstraintParameters(1, 1, 2, 1.0);
system.setConstraintParameters(2, 2, 3, 1.0);
system.setConstraintParameters(3, 4, 5, 1.0);
system.setConstraintParameters(4, 6, 7, 1.0);
system.addForce(forceField);
OpenMMContext context(system, integrator, platform);
vector<Vec3> positions(numParticles);
......@@ -241,7 +244,7 @@ int main() {
}
catch(const exception& e) {
cout << "exception: " << e.what() << endl;
// return 1;
return 1;
}
cout << "Done" << endl;
return 0;
......
platforms/cuda/tests/TestCudaVerletIntegrator.cpp
View file @ 968cb132
......@@ -87,7 +87,7 @@ void testSingleBond() {
void testConstraints() {
const int numParticles = 8;
const int numConstraints = numParticles/2;
const int numConstraints = 5;
const double temp = 100.0;
CudaPlatform platform;
System system(numParticles, numConstraints);
......@@ -98,8 +98,11 @@ void testConstraints() {
system.setParticleMass(i, 10.0);
forceField->setParticleParameters(i, (i%2 == 0 ? 0.2 : -0.2), 0.5, 5.0);
}
for (int i = 0; i < numConstraints; ++i)
system.setConstraintParameters(i, 2*i, 2*i+1, 1.0);
system.setConstraintParameters(0, 0, 1, 1.0);
system.setConstraintParameters(1, 1, 2, 1.0);
system.setConstraintParameters(2, 2, 3, 1.0);
system.setConstraintParameters(3, 4, 5, 1.0);
system.setConstraintParameters(4, 6, 7, 1.0);
system.addForce(forceField);
OpenMMContext context(system, integrator, platform);
vector<Vec3> positions(numParticles);
......
platforms/reference/src/ReferenceKernels.cpp
View file @ 968cb132
......@@ -517,11 +517,10 @@ void ReferenceIntegrateVerletStepKernel::execute(OpenMMContextImpl& context, con
delete constraints;
}
dynamics = new ReferenceVerletDynamics(context.getSystem().getNumParticles(), static_cast<RealOpenMM>(stepSize) );
constraints = new ReferenceShakeAlgorithm(numConstraints, constraintIndices, constraintDistances);
constraints = new ReferenceShakeAlgorithm(numConstraints, constraintIndices, constraintDistances, integrator.getConstraintTolerance());
dynamics->setReferenceConstraintAlgorithm(constraints);
prevStepSize = stepSize;
}
// shake->setTolerance(integrator.getConstraintTolerance());
dynamics->update(context.getSystem().getNumParticles(), posData, velData, forceData, masses);
}
......@@ -577,14 +576,12 @@ void ReferenceIntegrateLangevinStepKernel::execute(OpenMMContextImpl& context, c
static_cast<RealOpenMM>(stepSize),
static_cast<RealOpenMM>(tau),
static_cast<RealOpenMM>(temperature) );
constraints = new ReferenceLincsAlgorithm(numConstraints, constraintIndices, constraintDistances);
// shake = new ReferenceShakeAlgorithm(numConstraints, constraintIndices, shakeParameters);
constraints = new ReferenceShakeAlgorithm(numConstraints, constraintIndices, constraintDistances, integrator.getConstraintTolerance());
dynamics->setReferenceConstraintAlgorithm(constraints);
prevTemp = temperature;
prevFriction = friction;
prevStepSize = stepSize;
}
// shake->setTolerance(integrator.getConstraintTolerance());
dynamics->update(context.getSystem().getNumParticles(), posData, velData, forceData, masses);
}
......@@ -639,13 +636,12 @@ void ReferenceIntegrateBrownianStepKernel::execute(OpenMMContextImpl& context, c
static_cast<RealOpenMM>(stepSize),
static_cast<RealOpenMM>(friction),
static_cast<RealOpenMM>(temperature) );
constraints = new ReferenceShakeAlgorithm(numConstraints, constraintIndices, constraintDistances);
constraints = new ReferenceShakeAlgorithm(numConstraints, constraintIndices, constraintDistances, integrator.getConstraintTolerance());
dynamics->setReferenceConstraintAlgorithm(constraints);
prevTemp = temperature;
prevFriction = friction;
prevStepSize = stepSize;
}
// shake->setTolerance(integrator.getConstraintTolerance());
dynamics->update(context.getSystem().getNumParticles(), posData, velData, forceData, masses);
}
......
platforms/reference/src/SimTKReference/ReferenceLincsAlgorithm.cpp
View file @ 968cb132
......@@ -57,7 +57,7 @@ ReferenceLincsAlgorithm::ReferenceLincsAlgorithm( int numberOfConstraints,
_atomIndices = atomIndices;
_distance = distance;
_numTerms = 8;
_numTerms = 4;
_hasInitialized = false;
}
......
platforms/reference/src/SimTKReference/ReferenceShakeAlgorithm.cpp
View file @ 968cb132
/* Portions copyright (c) 2006 Stanford University and Simbios.
/* Portions copyright (c) 2006-2009 Stanford University and Simbios.
* Contributors: Pande Group
*
* Permission is hereby granted, free of charge, to any person obtaining
......@@ -38,12 +38,14 @@
@param numberOfConstraints number of constraints
@param atomIndices block of atom indices
@param shakeParameters Shake parameters
@param tolerance constraint tolerance
--------------------------------------------------------------------------------------- */
ReferenceShakeAlgorithm::ReferenceShakeAlgorithm( int numberOfConstraints,
int** atomIndices,
RealOpenMM* distance ){
RealOpenMM* distance,
RealOpenMM tolerance){
// ---------------------------------------------------------------------------------------
......@@ -64,7 +66,7 @@ ReferenceShakeAlgorithm::ReferenceShakeAlgorithm( int numberOfConstraints,
_distance = distance;
_maximumNumberOfIterations = 15;
_tolerance = (RealOpenMM) 1.0e-04;
_tolerance = tolerance;
_hasInitializedMasses = false;
// work arrays
......
platforms/reference/src/SimTKReference/ReferenceShakeAlgorithm.h
View file @ 968cb132
/* Portions copyright (c) 2006 Stanford University and Simbios.
/* Portions copyright (c) 2006-2009 Stanford University and Simbios.
* Contributors: Pande Group
*
* Permission is hereby granted, free of charge, to any person obtaining
......@@ -55,10 +55,11 @@ class ReferenceShakeAlgorithm : public ReferenceConstraintAlgorithm {
@param numberOfConstraints number of constraints
@param atomIndices atom indices for contraints
@param distance distances for constraints
@param tolerance constraint tolerance
--------------------------------------------------------------------------------------- */
ReferenceShakeAlgorithm( int numberOfConstraints, int** atomIndices, RealOpenMM* distance );
ReferenceShakeAlgorithm( int numberOfConstraints, int** atomIndices, RealOpenMM* distance, RealOpenMM tolerance );
/**---------------------------------------------------------------------------------------
......
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