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Commit 05259f77 authored by Peter Eastman's avatar Peter Eastman
Browse files

Cleaned up constraint code and deleted obsolete constraint implementations

parent f62ba9d8
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Showing with 221 additions and 922 deletions
platforms/cuda/src/CudaKernels.cpp
View file @ 05259f77
...@@ -399,7 +399,7 @@ static void initializeIntegration(const System& system, CudaPlatform::PlatformDa ...@@ -399,7 +399,7 @@ static void initializeIntegration(const System& system, CudaPlatform::PlatformDa
invMass1[i] = 1.0f/mass[particle1Index]; invMass1[i] = 1.0f/mass[particle1Index];
invMass2[i] = 1.0f/mass[particle2Index]; invMass2[i] = 1.0f/mass[particle2Index];
} }
gpuSetConstraintParameters(gpu, particle1, particle2, distance, invMass1, invMass2, (float)integrator.getConstraintTolerance(), 4); gpuSetConstraintParameters(gpu, particle1, particle2, distance, invMass1, invMass2, (float)integrator.getConstraintTolerance());
// Finish initialization. // Finish initialization.
...@@ -438,7 +438,7 @@ void CudaIntegrateVerletStepKernel::execute(OpenMMContextImpl& context, const Ve ...@@ -438,7 +438,7 @@ void CudaIntegrateVerletStepKernel::execute(OpenMMContextImpl& context, const Ve
kVerletUpdatePart1(gpu); kVerletUpdatePart1(gpu);
kApplyFirstShake(gpu); kApplyFirstShake(gpu);
kApplyFirstSettle(gpu); kApplyFirstSettle(gpu);
kApplyFirstCShake(gpu); kApplyFirstCCMA(gpu);
if (data.removeCM) { if (data.removeCM) {
int step = (int) (context.getTime()/stepSize); int step = (int) (context.getTime()/stepSize);
if (step%data.cmMotionFrequency == 0) if (step%data.cmMotionFrequency == 0)
...@@ -477,7 +477,7 @@ void CudaIntegrateLangevinStepKernel::execute(OpenMMContextImpl& context, const ...@@ -477,7 +477,7 @@ void CudaIntegrateLangevinStepKernel::execute(OpenMMContextImpl& context, const
kUpdatePart1(gpu); kUpdatePart1(gpu);
kApplyFirstShake(gpu); kApplyFirstShake(gpu);
kApplyFirstSettle(gpu); kApplyFirstSettle(gpu);
kApplyFirstCShake(gpu); kApplyFirstCCMA(gpu);
if (data.removeCM) { if (data.removeCM) {
int step = (int) (context.getTime()/stepSize); int step = (int) (context.getTime()/stepSize);
if (step%data.cmMotionFrequency == 0) if (step%data.cmMotionFrequency == 0)
...@@ -486,7 +486,7 @@ void CudaIntegrateLangevinStepKernel::execute(OpenMMContextImpl& context, const ...@@ -486,7 +486,7 @@ void CudaIntegrateLangevinStepKernel::execute(OpenMMContextImpl& context, const
kUpdatePart2(gpu); kUpdatePart2(gpu);
kApplySecondShake(gpu); kApplySecondShake(gpu);
kApplySecondSettle(gpu); kApplySecondSettle(gpu);
kApplySecondCShake(gpu); kApplySecondCCMA(gpu);
} }
CudaIntegrateBrownianStepKernel::~CudaIntegrateBrownianStepKernel() { CudaIntegrateBrownianStepKernel::~CudaIntegrateBrownianStepKernel() {
...@@ -519,7 +519,7 @@ void CudaIntegrateBrownianStepKernel::execute(OpenMMContextImpl& context, const ...@@ -519,7 +519,7 @@ void CudaIntegrateBrownianStepKernel::execute(OpenMMContextImpl& context, const
kBrownianUpdatePart1(gpu); kBrownianUpdatePart1(gpu);
kApplyFirstShake(gpu); kApplyFirstShake(gpu);
kApplyFirstSettle(gpu); kApplyFirstSettle(gpu);
kApplyFirstCShake(gpu); kApplyFirstCCMA(gpu);
if (data.removeCM) { if (data.removeCM) {
int step = (int) (context.getTime()/stepSize); int step = (int) (context.getTime()/stepSize);
if (step%data.cmMotionFrequency == 0) if (step%data.cmMotionFrequency == 0)
......
platforms/cuda/src/kernels/cudaKernels.h
View file @ 05259f77
...@@ -42,14 +42,12 @@ extern void kCalculateAndersenThermostat(gpuContext gpu); ...@@ -42,14 +42,12 @@ extern void kCalculateAndersenThermostat(gpuContext gpu);
extern void kReduceBornSumAndForces(gpuContext gpu); extern void kReduceBornSumAndForces(gpuContext gpu);
extern void kUpdatePart1(gpuContext gpu); extern void kUpdatePart1(gpuContext gpu);
extern void kApplyFirstShake(gpuContext gpu); extern void kApplyFirstShake(gpuContext gpu);
extern void kApplyFirstCShake(gpuContext gpu); extern void kApplyFirstCCMA(gpuContext gpu);
extern void kApplyFirstSettle(gpuContext gpu); extern void kApplyFirstSettle(gpuContext gpu);
extern void kApplyFirstLincs(gpuContext gpu);
extern void kUpdatePart2(gpuContext gpu); extern void kUpdatePart2(gpuContext gpu);
extern void kApplySecondShake(gpuContext gpu); extern void kApplySecondShake(gpuContext gpu);
extern void kApplySecondCShake(gpuContext gpu); extern void kApplySecondCCMA(gpuContext gpu);
extern void kApplySecondSettle(gpuContext gpu); extern void kApplySecondSettle(gpuContext gpu);
extern void kApplySecondLincs(gpuContext gpu);
extern void kVerletUpdatePart1(gpuContext gpu); extern void kVerletUpdatePart1(gpuContext gpu);
extern void kVerletUpdatePart2(gpuContext gpu); extern void kVerletUpdatePart2(gpuContext gpu);
extern void kBrownianUpdatePart1(gpuContext gpu); extern void kBrownianUpdatePart1(gpuContext gpu);
...@@ -78,10 +76,8 @@ extern void SetUpdateShakeHSim(gpuContext gpu); ...@@ -78,10 +76,8 @@ extern void SetUpdateShakeHSim(gpuContext gpu);
extern void GetUpdateShakeHSim(gpuContext gpu); extern void GetUpdateShakeHSim(gpuContext gpu);
extern void SetSettleSim(gpuContext gpu); extern void SetSettleSim(gpuContext gpu);
extern void GetSettleSim(gpuContext gpu); extern void GetSettleSim(gpuContext gpu);
extern void SetCShakeSim(gpuContext gpu); extern void SetCCMASim(gpuContext gpu);
extern void GetCShakeSim(gpuContext gpu); extern void GetCCMASim(gpuContext gpu);
extern void SetLincsSim(gpuContext gpu);
extern void GetLincsSim(gpuContext gpu);
extern void SetVerletUpdateSim(gpuContext gpu); extern void SetVerletUpdateSim(gpuContext gpu);
extern void GetVerletUpdateSim(gpuContext gpu); extern void GetVerletUpdateSim(gpuContext gpu);
extern void SetBrownianUpdateSim(gpuContext gpu); extern void SetBrownianUpdateSim(gpuContext gpu);
......
platforms/cuda/src/kernels/cudatypes.h
View file @ 05259f77
...@@ -258,7 +258,7 @@ struct cudaGmxSimulation { ...@@ -258,7 +258,7 @@ struct cudaGmxSimulation {
unsigned int max_shake_threads_per_block; // Maximum threads per block in shake kernel calls unsigned int max_shake_threads_per_block; // Maximum threads per block in shake kernel calls
unsigned int shake_threads_per_block; // Threads per block in shake kernel calls unsigned int shake_threads_per_block; // Threads per block in shake kernel calls
unsigned int settle_threads_per_block; // Threads per block in SETTLE kernel calls unsigned int settle_threads_per_block; // Threads per block in SETTLE kernel calls
unsigned int lincs_threads_per_block; // Threads per block in LINCS kernel calls unsigned int ccma_threads_per_block; // Threads per block in CCMA kernel calls
unsigned int nonshake_threads_per_block; // Threads per block in nonshaking kernel call unsigned int nonshake_threads_per_block; // Threads per block in nonshaking kernel call
unsigned int max_localForces_threads_per_block; // Threads per block in local forces kernel calls unsigned int max_localForces_threads_per_block; // Threads per block in local forces kernel calls
unsigned int localForces_threads_per_block; // Threads per block in local forces kernel calls unsigned int localForces_threads_per_block; // Threads per block in local forces kernel calls
...@@ -360,7 +360,7 @@ struct cudaGmxSimulation { ...@@ -360,7 +360,7 @@ struct cudaGmxSimulation {
float inverseTotalMass; // Used in linear momentum removal float inverseTotalMass; // Used in linear momentum removal
unsigned int ShakeConstraints; // Total number of Shake constraints unsigned int ShakeConstraints; // Total number of Shake constraints
unsigned int settleConstraints; // Total number of Settle constraints unsigned int settleConstraints; // Total number of Settle constraints
unsigned int lincsConstraints; // Total number of LINCS constraints. unsigned int ccmaConstraints; // Total number of CCMA constraints.
unsigned int rigidClusters; // Total number of rigid clusters unsigned int rigidClusters; // Total number of rigid clusters
unsigned int maxRigidClusterSize; // The size of the largest rigid cluster unsigned int maxRigidClusterSize; // The size of the largest rigid cluster
unsigned int clusterShakeBlockSize; // The number of threads to process each rigid cluster unsigned int clusterShakeBlockSize; // The number of threads to process each rigid cluster
...@@ -368,7 +368,6 @@ struct cudaGmxSimulation { ...@@ -368,7 +368,6 @@ struct cudaGmxSimulation {
unsigned int maxShakeIterations; // Maximum shake iterations unsigned int maxShakeIterations; // Maximum shake iterations
unsigned int degreesOfFreedom; // Number of degrees of freedom in system unsigned int degreesOfFreedom; // Number of degrees of freedom in system
float shakeTolerance; // Shake tolerance float shakeTolerance; // Shake tolerance
unsigned int lincsTerms; // Number of terms in the matrix expansion for LINCS
float InvMassJ; // Shake inverse mass for hydrogens float InvMassJ; // Shake inverse mass for hydrogens
int* pNonShakeID; // Not Shaking atoms int* pNonShakeID; // Not Shaking atoms
int4* pShakeID; // Shake atoms and phase int4* pShakeID; // Shake atoms and phase
...@@ -385,25 +384,17 @@ struct cudaGmxSimulation { ...@@ -385,25 +384,17 @@ struct cudaGmxSimulation {
int* pAtomIndex; // The original index of each atom int* pAtomIndex; // The original index of each atom
float4* pGridBoundingBox; // The size of each grid cell float4* pGridBoundingBox; // The size of each grid cell
float4* pGridCenter; // The center of each grid cell float4* pGridCenter; // The center of each grid cell
int2* pLincsAtoms; // The atoms connected by each LINCS constraint int2* pCcmaAtoms; // The atoms connected by each CCMA constraint
float4* pLincsDistance; // The displacement vector (x, y, z) and constraint distance (w) for each LINCS constraint float4* pCcmaDistance; // The displacement vector (x, y, z) and constraint distance (w) for each CCMA constraint
int* pLincsConnections; // The indices of constraints that other constraints are connected to float* pCcmaDelta1; // Workspace for CCMA
int* pLincsNumConnections; // The number of other constraints that each constraint is linked to float* pCcmaDelta2; // Workspace for CCMA
float* pLincsS; // S matrix for LINCS int* pCcmaAtomConstraints; // The indices of constraints involving each atom
float* pLincsCoupling; // Coupling matrix for LINCS int* pCcmaNumAtomConstraints; // The number of constraints involving each atom
float* pLincsRhs1; // Workspace for LINCS
float* pLincsRhs2; // Workspace for LINCS
float* pLincsSolution; // Workspace for LINCS
int* pLincsAtomConstraints; // The indices of constraints involving each atom
int* pLincsNumAtomConstraints; // The number of constraints involving each atom
short* pSyncCounter; // Used for global thread synchronization short* pSyncCounter; // Used for global thread synchronization
unsigned int* pRequiredIterations; // Used by SHAKE to communicate whether iteration has converged unsigned int* pRequiredIterations; // Used by CCMA to communicate whether iteration has converged
float* pShakeReducedMass; // The reduced mass for each SHAKE constraint float* pCcmaReducedMass; // The reduced mass for each CCMA constraint
float* pRigidClusterMatrix; // The inverse constraint matrix for each rigid cluster unsigned int* pConstraintMatrixColumn; // The column of each element in the constraint matrix.
unsigned int* pRigidClusterConstraintIndex; // The index of each cluster in the stream containing cluster constraints. float* pConstraintMatrixValue; // The value of each element in the constraint matrix.
unsigned int* pRigidClusterMatrixIndex; // The index of each cluster in the stream containing cluster matrices.
unsigned int* pConstraintMatrixColumn; // The column of each element in the constraint matrix.
float* pConstraintMatrixValue; // The value of each element in the constraint matrix.
// Mutable stuff // Mutable stuff
float4* pPosq; // Pointer to atom positions and charges float4* pPosq; // Pointer to atom positions and charges
......
platforms/cuda/src/kernels/gpu.cpp
View file @ 05259f77
...@@ -48,12 +48,9 @@ using namespace std; ...@@ -48,12 +48,9 @@ using namespace std;
#include "cudaKernels.h" #include "cudaKernels.h"
#include "hilbert.h" #include "hilbert.h"
#include "openmm/OpenMMException.h" #include "openmm/OpenMMException.h"
#include "jama_svd.h"
#include "quern.h" #include "quern.h"
using OpenMM::OpenMMException; using OpenMM::OpenMMException;
using TNT::Array2D;
using JAMA::SVD;
struct ShakeCluster { struct ShakeCluster {
int centralID; int centralID;
...@@ -500,221 +497,9 @@ static void markShakeClusterInvalid(ShakeCluster& cluster, map<int, ShakeCluster ...@@ -500,221 +497,9 @@ static void markShakeClusterInvalid(ShakeCluster& cluster, map<int, ShakeCluster
} }
} }
static void findRigidClusters(gpuContext gpu, const vector<int>& firstAtom, const vector<int>& secondAtom, const vector<float>& invMass1, const vector<float>& invMass2, const vector<float>& distance, vector<int>& constraintIndices)
{
vector<map<int, int> > atomConstraints(firstAtom.size());
for (int i = 0; i < (int)constraintIndices.size(); i++) {
atomConstraints[firstAtom[i]][secondAtom[i]] = constraintIndices[i];
atomConstraints[secondAtom[i]][firstAtom[i]] = constraintIndices[i];
}
vector<vector<int> > rigidClusters;
int totalConstraints = 0;
int totalMatrixElements = 0;
for (int i = 0; i < (int)firstAtom.size(); i++) {
if (atomConstraints[i].size() < 2)
continue;
// Begin by looking for a triangle this atom is part of.
set<int> atoms;
atoms.insert(i);
for (map<int, int>::const_iterator atom1 = atomConstraints[i].begin(); atom1 != atomConstraints[i].end() && atoms.size() == 1; ++atom1) {
for (map<int, int>::const_iterator atom2 = atomConstraints[atom1->first].begin(); atom2 != atomConstraints[atom1->first].end(); ++atom2) {
if (atomConstraints[i].count(atom2->first) != 0) {
atoms.insert(atom1->first);
atoms.insert(atom2->first);
break;
}
}
}
if (atoms.size() == 1)
continue;
// We have three atoms that are part of a cluster, so look for other atoms we can add.
bool done = false;
while (!done) {
done = true;
for (set<int>::const_iterator atom1 = atoms.begin(); atom1 != atoms.end(); ++atom1) {
for (map<int, int>::const_iterator atom2 = atomConstraints[*atom1].begin(); atom2 != atomConstraints[*atom1].end(); ++atom2) {
if (atoms.find(atom2->first) != atoms.end())
continue; // This atom is already in the cluster.
// See if this atom is linked to three other atoms in the cluster.
int linkCount = 0;
for (map<int, int>::const_iterator atom3 = atomConstraints[atom2->first].begin(); atom3 != atomConstraints[atom2->first].end(); ++atom3)
if (atoms.find(atom3->first) != atoms.end())
linkCount++;
if (linkCount > 2) {
atoms.insert(atom2->first);
done = false;
}
}
}
}
// Record the cluster.
vector<int> constraints;
for (set<int>::const_iterator atom1 = atoms.begin(); atom1 != atoms.end(); ++atom1) {
for (map<int, int>::const_iterator atom2 = atomConstraints[*atom1].begin(); atom2 != atomConstraints[*atom1].end(); ++atom2) {
if (*atom1 < atom2->first && atoms.find(atom2->first) != atoms.end())
constraints.push_back(atom2->second);
}
}
rigidClusters.push_back(constraints);
totalConstraints += constraints.size();
totalMatrixElements += constraints.size()*constraints.size();
for (set<int>::const_iterator atom1 = atoms.begin(); atom1 != atoms.end(); ++atom1) {
for (map<int, int>::const_iterator atom2 = atomConstraints[*atom1].begin(); atom2 != atomConstraints[*atom1].end(); ++atom2)
atomConstraints[atom2->first].erase(*atom1);
atomConstraints[*atom1].clear();
}
}
// Reorder the constraints so those in a cluster are sequential.
// vector<int> constraintOrder(constraintIndices.size());
// vector<int> clusterStartIndex(rigidClusters.size());
// set<int> inCluster;
// int nextIndex = 0;
// for (int i = 0; i < (int) rigidClusters.size(); ++i) {
// clusterStartIndex[i] = nextIndex;
// for (int j = 0; j < (int) rigidClusters[i].size(); ++j) {
// int constraint = rigidClusters[i][j];
// constraintOrder[nextIndex++] = constraint;
// inCluster.insert(constraint);
// }
// }
// for (int i = 0; i < (int) constraintIndices.size(); ++i)
// if (inCluster.find(constraintIndices[i]) == inCluster.end())
// constraintOrder[nextIndex++] = constraintIndices[i];
// constraintIndices = constraintOrder;
// Build the CUDA streams.
CUDAStream<unsigned int>* psRigidClusterConstraintIndex = new CUDAStream<unsigned int>((int) rigidClusters.size()+1, 1, "RigidClusterConstraintIndex");
gpu->psRigidClusterConstraintIndex = psRigidClusterConstraintIndex;
gpu->sim.pRigidClusterConstraintIndex = psRigidClusterConstraintIndex->_pDevData;
CUDAStream<float>* psRigidClusterMatrix = new CUDAStream<float>(totalMatrixElements, 1, "RigidClusterMatrix");
gpu->psRigidClusterMatrix = psRigidClusterMatrix;
gpu->sim.pRigidClusterMatrix = psRigidClusterMatrix->_pDevData;
CUDAStream<unsigned int>* psRigidClusterMatrixIndex = new CUDAStream<unsigned int>((int) rigidClusters.size()+1, 1, "RigidClusterMatrixIndex");
gpu->psRigidClusterMatrixIndex = psRigidClusterMatrixIndex;
gpu->sim.pRigidClusterMatrixIndex = psRigidClusterMatrixIndex->_pDevData;
unsigned int constraintIndex = 0;
unsigned int maxClusterSize = 0;
for (unsigned int i = 0; i < rigidClusters.size(); i++) {
vector<int>& cluster = rigidClusters[i];
(*psRigidClusterConstraintIndex)[i] = constraintIndex;
constraintIndex += cluster.size();
if (cluster.size() > maxClusterSize)
maxClusterSize = cluster.size();
}
(*psRigidClusterConstraintIndex)[rigidClusters.size()] = constraintIndex;
gpu->sim.rigidClusters = rigidClusters.size();
gpu->sim.maxRigidClusterSize = maxClusterSize;
gpu->sim.clusterShakeBlockSize = 1;
while (gpu->sim.clusterShakeBlockSize < maxClusterSize)
gpu->sim.clusterShakeBlockSize *= 2;
psRigidClusterConstraintIndex->Upload();
// Build the inverse coupling matrix for each cluster.
unsigned int elementIndex = 0;
for (unsigned int i = 0; i < rigidClusters.size(); i++) {
// Compute the constraint coupling matrix for this cluster.
const vector<int>& cluster = rigidClusters[i];
unsigned int size = cluster.size();
Array2D<double> matrix(size, size);
for (int j = 0; j < (int)size; j++) {
for (int k = 0; k < (int)size; k++) {
if (j == k) {
matrix[j][j] = 1.0;
continue;
}
double scale;
int atomj0 = firstAtom[cluster[j]];
int atomj1 = secondAtom[cluster[j]];
int atomk0 = firstAtom[cluster[k]];
int atomk1 = secondAtom[cluster[k]];
int atoma, atomb;
if (atomj0 == atomk0) {
atoma = atomj1;
atomb = atomk1;
scale = invMass1[cluster[j]]/(invMass1[cluster[j]]+invMass2[cluster[j]]);
}
else if (atomj1 == atomk1) {
atoma = atomj0;
atomb = atomk0;
scale = invMass2[cluster[j]]/(invMass1[cluster[j]]+invMass2[cluster[j]]);
}
else if (atomj0 == atomk1) {
atoma = atomj1;
atomb = atomk0;
scale = invMass1[cluster[j]]/(invMass1[cluster[j]]+invMass2[cluster[j]]);
}
else if (atomj1 == atomk0) {
atoma = atomj0;
atomb = atomk1;
scale = invMass2[cluster[j]]/(invMass1[cluster[j]]+invMass2[cluster[j]]);
}
else {
matrix[j][k] = 0.0;
continue; // These constraints are not connected.
}
// Find the third constraint forming a triangle with these two.
for (int m = 0; m < size; m++) {
int other = cluster[m];
if ((firstAtom[other] == atoma && secondAtom[other] == atomb) || (firstAtom[other] == atomb && secondAtom[other] == atoma)) {
double d1 = distance[cluster[j]];
double d2 = distance[cluster[k]];
double d3 = distance[other];
matrix[j][k] = scale*(d1*d1+d2*d2-d3*d3)/(2.0*d1*d2);
break;
}
}
}
}
// Invert it using SVD.
Array2D<double> u, v;
Array1D<double> w;
SVD<double> svd(matrix);
svd.getU(u);
svd.getV(v);
svd.getSingularValues(w);
double singularValueCutoff = 0.01*w[0];
for (int j = 0; j < (int)size; j++)
w[j] = (w[j] < singularValueCutoff ? 0.0 : 1.0/w[j]);
for (int j = 0; j < (int)size; j++) {
for (int k = 0; k < (int)size; k++) {
matrix[j][k] = 0.0;
for (int m = 0; m < (int)size; m++)
matrix[j][k] += v[j][m]*w[m]*u[k][m];
}
}
// Record the inverted matrix.
(*gpu->psRigidClusterMatrixIndex)[i] = elementIndex;
for (int j = 0; j < (int)size; j++)
for (int k = 0; k < (int)size; k++)
(*gpu->psRigidClusterMatrix)[elementIndex++] = (float)(matrix[k][j]*distance[cluster[j]]/distance[cluster[k]]);
}
(*gpu->psRigidClusterMatrixIndex)[gpu->sim.rigidClusters] = elementIndex;
gpu->psRigidClusterMatrix->Upload();
gpu->psRigidClusterMatrixIndex->Upload();
}
extern "C" extern "C"
void gpuSetConstraintParameters(gpuContext gpu, const vector<int>& atom1, const vector<int>& atom2, const vector<float>& distance, 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) const vector<float>& invMass1, const vector<float>& invMass2, float constraintTolerance)
{ {
// Create a vector for recording which atoms are handled by SHAKE (or SETTLE). // Create a vector for recording which atoms are handled by SHAKE (or SETTLE).
...@@ -901,33 +686,29 @@ void gpuSetConstraintParameters(gpuContext gpu, const vector<int>& atom1, const ...@@ -901,33 +686,29 @@ void gpuSetConstraintParameters(gpuContext gpu, const vector<int>& atom1, const
} }
psShakeID->Upload(); psShakeID->Upload();
psShakeParameter->Upload(); psShakeParameter->Upload();
gpu->sim.shakeTolerance = shakeTolerance; gpu->sim.shakeTolerance = constraintTolerance;
gpu->sim.shake_threads_per_block = (gpu->sim.ShakeConstraints + gpu->sim.blocks - 1) / gpu->sim.blocks; 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) 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; gpu->sim.shake_threads_per_block = gpu->sim.max_shake_threads_per_block;
if (gpu->sim.shake_threads_per_block < 1) if (gpu->sim.shake_threads_per_block < 1)
gpu->sim.shake_threads_per_block = 1; gpu->sim.shake_threads_per_block = 1;
// Find connected constraints for LINCS. // Find connected constraints for CCMA.
vector<int> lincsConstraints; vector<int> ccmaConstraints;
for (unsigned i = 0; i < atom1.size(); i++) for (unsigned i = 0; i < atom1.size(); i++)
if (!isShakeAtom[atom1[i]]) if (!isShakeAtom[atom1[i]])
lincsConstraints.push_back(i); ccmaConstraints.push_back(i);
// Identify rigid clusters of atoms.
findRigidClusters(gpu, atom1, atom2, invMass1, invMass2, distance, lincsConstraints);
// Record the connections between constraints. // Record the connections between constraints.
int numLincs = (int) lincsConstraints.size(); int numCCMA = (int) ccmaConstraints.size();
vector<vector<int> > atomConstraints(gpu->natoms); vector<vector<int> > atomConstraints(gpu->natoms);
for (int i = 0; i < numLincs; i++) { for (int i = 0; i < numCCMA; i++) {
atomConstraints[atom1[lincsConstraints[i]]].push_back(i); atomConstraints[atom1[ccmaConstraints[i]]].push_back(i);
atomConstraints[atom2[lincsConstraints[i]]].push_back(i); atomConstraints[atom2[ccmaConstraints[i]]].push_back(i);
} }
vector<vector<int> > linkedConstraints(numLincs); vector<vector<int> > linkedConstraints(numCCMA);
for (unsigned atom = 0; atom < atomConstraints.size(); atom++) { for (unsigned atom = 0; atom < atomConstraints.size(); atom++) {
for (unsigned i = 0; i < atomConstraints[atom].size(); i++) for (unsigned i = 0; i < atomConstraints[atom].size(); i++)
for (unsigned j = 0; j < i; j++) { for (unsigned j = 0; j < i; j++) {
...@@ -949,17 +730,17 @@ void gpuSetConstraintParameters(gpuContext gpu, const vector<int>& atom1, const ...@@ -949,17 +730,17 @@ void gpuSetConstraintParameters(gpuContext gpu, const vector<int>& atom1, const
vector<vector<int> > atomAngles(gpu->natoms); vector<vector<int> > atomAngles(gpu->natoms);
for (int i = 0; i < gpu->sim.bond_angles; i++) for (int i = 0; i < gpu->sim.bond_angles; i++)
atomAngles[(*gpu->psBondAngleID1)[i].y].push_back(i); atomAngles[(*gpu->psBondAngleID1)[i].y].push_back(i);
vector<vector<pair<int, double> > > matrix(numLincs); vector<vector<pair<int, double> > > matrix(numCCMA);
if (numLincs > 0) { if (numCCMA > 0) {
for (int j = 0; j < numLincs; j++) { for (int j = 0; j < numCCMA; j++) {
for (int k = 0; k < numLincs; k++) { for (int k = 0; k < numCCMA; k++) {
if (j == k) { if (j == k) {
matrix[j].push_back(pair<int, double>(j, 1.0)); matrix[j].push_back(pair<int, double>(j, 1.0));
continue; continue;
} }
double scale; double scale;
int cj = lincsConstraints[j]; int cj = ccmaConstraints[j];
int ck = lincsConstraints[k]; int ck = ccmaConstraints[k];
int atomj0 = atom1[cj]; int atomj0 = atom1[cj];
int atomj1 = atom2[cj]; int atomj1 = atom2[cj];
int atomk0 = atom1[ck]; int atomk0 = atom1[ck];
...@@ -995,7 +776,7 @@ void gpuSetConstraintParameters(gpuContext gpu, const vector<int>& atom1, const ...@@ -995,7 +776,7 @@ void gpuSetConstraintParameters(gpuContext gpu, const vector<int>& atom1, const
// Look for a third constraint forming a triangle with these two. // Look for a third constraint forming a triangle with these two.
bool foundConstraint = false; bool foundConstraint = false;
for (int other = 0; other < numLincs; other++) { for (int other = 0; other < numCCMA; other++) {
if ((atom1[other] == atoma && atom2[other] == atomc) || (atom1[other] == atomc && atom2[other] == atoma)) { if ((atom1[other] == atoma && atom2[other] == atomc) || (atom1[other] == atomc && atom2[other] == atoma)) {
double d1 = distance[cj]; double d1 = distance[cj];
double d2 = distance[ck]; double d2 = distance[ck];
...@@ -1026,7 +807,7 @@ void gpuSetConstraintParameters(gpuContext gpu, const vector<int>& atom1, const ...@@ -1026,7 +807,7 @@ void gpuSetConstraintParameters(gpuContext gpu, const vector<int>& atom1, const
vector<int> matrixRowStart; vector<int> matrixRowStart;
vector<int> matrixColIndex; vector<int> matrixColIndex;
vector<double> matrixValue; vector<double> matrixValue;
for (int i = 0; i < numLincs; i++) { for (int i = 0; i < numCCMA; i++) {
matrixRowStart.push_back(matrixValue.size()); matrixRowStart.push_back(matrixValue.size());
for (int j = 0; j < (int) matrix[i].size(); j++) { for (int j = 0; j < (int) matrix[i].size(); j++) {
pair<int, double> element = matrix[i][j]; pair<int, double> element = matrix[i][j];
...@@ -1037,20 +818,20 @@ void gpuSetConstraintParameters(gpuContext gpu, const vector<int>& atom1, const ...@@ -1037,20 +818,20 @@ void gpuSetConstraintParameters(gpuContext gpu, const vector<int>& atom1, const
matrixRowStart.push_back(matrixValue.size()); matrixRowStart.push_back(matrixValue.size());
int *qRowStart, *qColIndex, *rRowStart, *rColIndex; int *qRowStart, *qColIndex, *rRowStart, *rColIndex;
double *qValue, *rValue; double *qValue, *rValue;
int result = QUERN_compute_qr(numLincs, numLincs, &matrixRowStart[0], &matrixColIndex[0], &matrixValue[0], NULL, int result = QUERN_compute_qr(numCCMA, numCCMA, &matrixRowStart[0], &matrixColIndex[0], &matrixValue[0], NULL,
&qRowStart, &qColIndex, &qValue, &rRowStart, &rColIndex, &rValue); &qRowStart, &qColIndex, &qValue, &rRowStart, &rColIndex, &rValue);
vector<double> rhs(numLincs); vector<double> rhs(numCCMA);
matrix.clear(); matrix.clear();
matrix.resize(numLincs); matrix.resize(numCCMA);
for (int i = 0; i < numLincs; i++) { for (int i = 0; i < numCCMA; i++) {
// Extract column i of the inverse matrix. // Extract column i of the inverse matrix.
for (int j = 0; j < numLincs; j++) for (int j = 0; j < numCCMA; j++)
rhs[j] = (i == j ? 1.0 : 0.0); rhs[j] = (i == j ? 1.0 : 0.0);
result = QUERN_multiply_with_q_transpose(numLincs, qRowStart, qColIndex, qValue, &rhs[0]); result = QUERN_multiply_with_q_transpose(numCCMA, qRowStart, qColIndex, qValue, &rhs[0]);
result = QUERN_solve_with_r(numLincs, rRowStart, rColIndex, rValue, &rhs[0], &rhs[0]); result = QUERN_solve_with_r(numCCMA, rRowStart, rColIndex, rValue, &rhs[0], &rhs[0]);
for (int j = 0; j < numLincs; j++) { for (int j = 0; j < numCCMA; j++) {
double value = rhs[j]*distance[lincsConstraints[i]]/distance[lincsConstraints[j]]; double value = rhs[j]*distance[ccmaConstraints[i]]/distance[ccmaConstraints[j]];
if (abs(value) > 0.1) if (abs(value) > 0.1)
matrix[j].push_back(pair<int, double>(i, value)); matrix[j].push_back(pair<int, double>(i, value));
} }
...@@ -1065,12 +846,12 @@ void gpuSetConstraintParameters(gpuContext gpu, const vector<int>& atom1, const ...@@ -1065,12 +846,12 @@ void gpuSetConstraintParameters(gpuContext gpu, const vector<int>& atom1, const
// Sort the constraints. // Sort the constraints.
vector<int> constraintOrder(numLincs); vector<int> constraintOrder(numCCMA);
for (int i = 0; i < numLincs; ++i) for (int i = 0; i < numCCMA; ++i)
constraintOrder[i] = i; constraintOrder[i] = i;
sort(constraintOrder.begin(), constraintOrder.end(), ConstraintOrderer(atom1, atom2)); sort(constraintOrder.begin(), constraintOrder.end(), ConstraintOrderer(atom1, atom2));
vector<int> inverseOrder(numLincs); vector<int> inverseOrder(numCCMA);
for (int i = 0; i < numLincs; ++i) for (int i = 0; i < numCCMA; ++i)
inverseOrder[constraintOrder[i]] = i; inverseOrder[constraintOrder[i]] = i;
for (int i = 0; i < matrix.size(); ++i) for (int i = 0; i < matrix.size(); ++i)
for (int j = 0; j < matrix[i].size(); ++j) for (int j = 0; j < matrix[i].size(); ++j)
...@@ -1078,100 +859,75 @@ void gpuSetConstraintParameters(gpuContext gpu, const vector<int>& atom1, const ...@@ -1078,100 +859,75 @@ void gpuSetConstraintParameters(gpuContext gpu, const vector<int>& atom1, const
// Fill in the CUDA streams. // Fill in the CUDA streams.
CUDAStream<int2>* psLincsAtoms = new CUDAStream<int2>(numLincs, 1, "LincsAtoms"); CUDAStream<int2>* psCcmaAtoms = new CUDAStream<int2>(numCCMA, 1, "CcmaAtoms");
gpu->psLincsAtoms = psLincsAtoms; gpu->psCcmaAtoms = psCcmaAtoms;
gpu->sim.pLincsAtoms = psLincsAtoms->_pDevData; gpu->sim.pCcmaAtoms = psCcmaAtoms->_pDevData;
CUDAStream<float4>* psLincsDistance = new CUDAStream<float4>(numLincs, 1, "LincsDistance"); CUDAStream<float4>* psCcmaDistance = new CUDAStream<float4>(numCCMA, 1, "CcmaDistance");
gpu->psLincsDistance = psLincsDistance; gpu->psCcmaDistance = psCcmaDistance;
gpu->sim.pLincsDistance = psLincsDistance->_pDevData; gpu->sim.pCcmaDistance = psCcmaDistance->_pDevData;
CUDAStream<int>* psLincsConnections = new CUDAStream<int>(numLincs*maxLinks, 1, "LincsConnections"); CUDAStream<int>* psCcmaAtomConstraints = new CUDAStream<int>(gpu->natoms*maxAtomConstraints, 1, "CcmaAtomConstraints");
gpu->psLincsConnections = psLincsConnections; gpu->psCcmaAtomConstraints = psCcmaAtomConstraints;
gpu->sim.pLincsConnections = psLincsConnections->_pDevData; gpu->sim.pCcmaAtomConstraints = psCcmaAtomConstraints->_pDevData;
CUDAStream<int>* psLincsNumConnections = new CUDAStream<int>(numLincs, 1, "LincsConnectionsIndex"); CUDAStream<int>* psCcmaNumAtomConstraints = new CUDAStream<int>(gpu->natoms, 1, "CcmaAtomConstraintsIndex");
gpu->psLincsNumConnections = psLincsNumConnections; gpu->psCcmaNumAtomConstraints = psCcmaNumAtomConstraints;
gpu->sim.pLincsNumConnections = psLincsNumConnections->_pDevData; gpu->sim.pCcmaNumAtomConstraints = psCcmaNumAtomConstraints->_pDevData;
CUDAStream<int>* psLincsAtomConstraints = new CUDAStream<int>(gpu->natoms*maxAtomConstraints, 1, "LincsAtomConstraints"); CUDAStream<float>* psCcmaDelta1 = new CUDAStream<float>(numCCMA, 1, "CcmaDelta1");
gpu->psLincsAtomConstraints = psLincsAtomConstraints; gpu->psCcmaDelta1 = psCcmaDelta1;
gpu->sim.pLincsAtomConstraints = psLincsAtomConstraints->_pDevData; gpu->sim.pCcmaDelta1 = psCcmaDelta1->_pDevData;
CUDAStream<int>* psLincsNumAtomConstraints = new CUDAStream<int>(gpu->natoms, 1, "LincsAtomConstraintsIndex"); CUDAStream<float>* psCcmaDelta2 = new CUDAStream<float>(numCCMA, 1, "CcmaDelta2");
gpu->psLincsNumAtomConstraints = psLincsNumAtomConstraints; gpu->psCcmaDelta2 = psCcmaDelta2;
gpu->sim.pLincsNumAtomConstraints = psLincsNumAtomConstraints->_pDevData; gpu->sim.pCcmaDelta2 = psCcmaDelta2->_pDevData;
CUDAStream<float>* psLincsS = new CUDAStream<float>(numLincs, 1, "LincsS");
gpu->psLincsS = psLincsS;
gpu->sim.pLincsS = psLincsS->_pDevData;
CUDAStream<float>* psLincsCoupling = new CUDAStream<float>(numLincs*maxLinks, 1, "LincsCoupling");
gpu->psLincsCoupling = psLincsCoupling;
gpu->sim.pLincsCoupling = psLincsCoupling->_pDevData;
CUDAStream<float>* psLincsRhs1 = new CUDAStream<float>(numLincs, 1, "LincsRhs1");
gpu->psLincsRhs1 = psLincsRhs1;
gpu->sim.pLincsRhs1 = psLincsRhs1->_pDevData;
CUDAStream<float>* psLincsRhs2 = new CUDAStream<float>(numLincs, 1, "LincsRhs2");
gpu->psLincsRhs2 = psLincsRhs2;
gpu->sim.pLincsRhs2 = psLincsRhs2->_pDevData;
CUDAStream<float>* psLincsSolution = new CUDAStream<float>(numLincs, 1, "LincsSolution");
gpu->psLincsSolution = psLincsSolution;
gpu->sim.pLincsSolution = psLincsSolution->_pDevData;
CUDAStream<short>* psSyncCounter = new CUDAStream<short>(3*gpu->sim.blocks, 1, "SyncCounter"); CUDAStream<short>* psSyncCounter = new CUDAStream<short>(3*gpu->sim.blocks, 1, "SyncCounter");
gpu->psSyncCounter = psSyncCounter; gpu->psSyncCounter = psSyncCounter;
gpu->sim.pSyncCounter = psSyncCounter->_pDevData; gpu->sim.pSyncCounter = psSyncCounter->_pDevData;
CUDAStream<unsigned int>* psRequiredIterations = new CUDAStream<unsigned int>(1, 1, "RequiredIterations"); CUDAStream<unsigned int>* psRequiredIterations = new CUDAStream<unsigned int>(1, 1, "RequiredIterations");
gpu->psRequiredIterations = psRequiredIterations; gpu->psRequiredIterations = psRequiredIterations;
gpu->sim.pRequiredIterations = psRequiredIterations->_pDevData; gpu->sim.pRequiredIterations = psRequiredIterations->_pDevData;
CUDAStream<float>* psShakeReducedMass = new CUDAStream<float>(numLincs, 1, "LincsSolution"); CUDAStream<float>* psCcmaReducedMass = new CUDAStream<float>(numCCMA, 1, "CcmaReducedMass");
gpu->psShakeReducedMass = psShakeReducedMass; gpu->psCcmaReducedMass = psCcmaReducedMass;
gpu->sim.pShakeReducedMass = psShakeReducedMass->_pDevData; gpu->sim.pCcmaReducedMass = psCcmaReducedMass->_pDevData;
CUDAStream<unsigned int>* psConstraintMatrixColumn = new CUDAStream<unsigned int>(numLincs*maxRowElements, 1, "ConstraintMatrixColumn"); CUDAStream<unsigned int>* psConstraintMatrixColumn = new CUDAStream<unsigned int>(numCCMA*maxRowElements, 1, "ConstraintMatrixColumn");
gpu->psConstraintMatrixColumn = psConstraintMatrixColumn; gpu->psConstraintMatrixColumn = psConstraintMatrixColumn;
gpu->sim.pConstraintMatrixColumn = psConstraintMatrixColumn->_pDevData; gpu->sim.pConstraintMatrixColumn = psConstraintMatrixColumn->_pDevData;
CUDAStream<float>* psConstraintMatrixValue = new CUDAStream<float>(numLincs*maxRowElements, 1, "ConstraintMatrixValue"); CUDAStream<float>* psConstraintMatrixValue = new CUDAStream<float>(numCCMA*maxRowElements, 1, "ConstraintMatrixValue");
gpu->psConstraintMatrixValue = psConstraintMatrixValue; gpu->psConstraintMatrixValue = psConstraintMatrixValue;
gpu->sim.pConstraintMatrixValue = psConstraintMatrixValue->_pDevData; gpu->sim.pConstraintMatrixValue = psConstraintMatrixValue->_pDevData;
gpu->sim.lincsConstraints = numLincs; gpu->sim.ccmaConstraints = numCCMA;
for (int i = 0; i < numLincs; i++) { for (int i = 0; i < numCCMA; i++) {
int index = constraintOrder[i]; int index = constraintOrder[i];
int c = lincsConstraints[index]; int c = ccmaConstraints[index];
(*psLincsAtoms)[i].x = atom1[c]; (*psCcmaAtoms)[i].x = atom1[c];
(*psLincsAtoms)[i].y = atom2[c]; (*psCcmaAtoms)[i].y = atom2[c];
(*psLincsDistance)[i].w = distance[c]; (*psCcmaDistance)[i].w = distance[c];
(*psLincsS)[i] = 1.0f/sqrt(invMass1[c]+invMass2[c]); (*psCcmaReducedMass)[i] = 0.5f/(invMass1[c]+invMass2[c]);
(*psShakeReducedMass)[i] = 0.5f/(invMass1[c]+invMass2[c]);
(*psLincsNumConnections)[i] = linkedConstraints[index].size();
for (unsigned int j = 0; j < linkedConstraints[index].size(); j++)
(*psLincsConnections)[i+j*numLincs] = linkedConstraints[index][j];
for (unsigned int j = 0; j < matrix[index].size(); j++) { for (unsigned int j = 0; j < matrix[index].size(); j++) {
(*psConstraintMatrixColumn)[i+j*numLincs] = matrix[index][j].first; (*psConstraintMatrixColumn)[i+j*numCCMA] = matrix[index][j].first;
(*psConstraintMatrixValue)[i+j*numLincs] = matrix[index][j].second; (*psConstraintMatrixValue)[i+j*numCCMA] = matrix[index][j].second;
} }
(*psConstraintMatrixColumn)[i+matrix[index].size()*numLincs] = numLincs; (*psConstraintMatrixColumn)[i+matrix[index].size()*numCCMA] = numCCMA;
} }
for (unsigned int i = 0; i < psSyncCounter->_length; i++) for (unsigned int i = 0; i < psSyncCounter->_length; i++)
(*psSyncCounter)[i] = -1; (*psSyncCounter)[i] = -1;
for (unsigned int i = 0; i < atomConstraints.size(); i++) { for (unsigned int i = 0; i < atomConstraints.size(); i++) {
(*psLincsNumAtomConstraints)[i] = atomConstraints[i].size(); (*psCcmaNumAtomConstraints)[i] = atomConstraints[i].size();
for (unsigned int j = 0; j < atomConstraints[i].size(); j++) { for (unsigned int j = 0; j < atomConstraints[i].size(); j++) {
bool forward = (atom1[lincsConstraints[atomConstraints[i][j]]] == i); bool forward = (atom1[ccmaConstraints[atomConstraints[i][j]]] == i);
(*psLincsAtomConstraints)[i+j*gpu->natoms] = (forward ? inverseOrder[atomConstraints[i][j]]+1 : -inverseOrder[atomConstraints[i][j]]-1); (*psCcmaAtomConstraints)[i+j*gpu->natoms] = (forward ? inverseOrder[atomConstraints[i][j]]+1 : -inverseOrder[atomConstraints[i][j]]-1);
} }
} }
psLincsAtoms->Upload(); psCcmaAtoms->Upload();
psLincsDistance->Upload(); psCcmaDistance->Upload();
psLincsS->Upload(); psCcmaReducedMass->Upload();
psShakeReducedMass->Upload(); psCcmaAtomConstraints->Upload();
psLincsConnections->Upload(); psCcmaNumAtomConstraints->Upload();
psLincsNumConnections->Upload();
psLincsAtomConstraints->Upload();
psLincsNumAtomConstraints->Upload();
psSyncCounter->Upload(); psSyncCounter->Upload();
psConstraintMatrixColumn->Upload(); psConstraintMatrixColumn->Upload();
psConstraintMatrixValue->Upload(); psConstraintMatrixValue->Upload();
gpu->sim.lincsTerms = lincsTerms; gpu->sim.ccma_threads_per_block = (gpu->sim.ccmaConstraints + gpu->sim.blocks - 1) / gpu->sim.blocks;
gpu->sim.lincs_threads_per_block = (gpu->sim.lincsConstraints + gpu->sim.blocks - 1) / gpu->sim.blocks; if (gpu->sim.ccma_threads_per_block > gpu->sim.threads_per_block)
if (gpu->sim.lincs_threads_per_block > gpu->sim.threads_per_block) gpu->sim.ccma_threads_per_block = gpu->sim.threads_per_block;
gpu->sim.lincs_threads_per_block = gpu->sim.threads_per_block; if (gpu->sim.ccma_threads_per_block < gpu->sim.blocks)
if (gpu->sim.lincs_threads_per_block < gpu->sim.blocks) gpu->sim.ccma_threads_per_block = gpu->sim.blocks;
gpu->sim.lincs_threads_per_block = gpu->sim.blocks;
if (gpu->sim.lincs_threads_per_block%gpu->sim.clusterShakeBlockSize != 0)
gpu->sim.lincs_threads_per_block += gpu->sim.clusterShakeBlockSize - gpu->sim.lincs_threads_per_block%gpu->sim.clusterShakeBlockSize;
// count number of atoms w/o constraint // count number of atoms w/o constraint
...@@ -1533,23 +1289,15 @@ void* gpuInit(int numAtoms) ...@@ -1533,23 +1289,15 @@ void* gpuInit(int numAtoms)
gpu->psInteractionCount = NULL; gpu->psInteractionCount = NULL;
gpu->psGridBoundingBox = NULL; gpu->psGridBoundingBox = NULL;
gpu->psGridCenter = NULL; gpu->psGridCenter = NULL;
gpu->psLincsAtoms = NULL; gpu->psCcmaAtoms = NULL;
gpu->psLincsDistance = NULL; gpu->psCcmaDistance = NULL;
gpu->psLincsConnections = NULL; gpu->psCcmaAtomConstraints = NULL;
gpu->psLincsNumConnections = NULL; gpu->psCcmaNumAtomConstraints = NULL;
gpu->psLincsAtomConstraints = NULL; gpu->psCcmaDelta1 = NULL;
gpu->psLincsNumAtomConstraints = NULL; gpu->psCcmaDelta2 = NULL;
gpu->psLincsS = NULL;
gpu->psLincsCoupling = NULL;
gpu->psLincsRhs1 = NULL;
gpu->psLincsRhs2 = NULL;
gpu->psLincsSolution = NULL;
gpu->psSyncCounter = NULL; gpu->psSyncCounter = NULL;
gpu->psRequiredIterations = NULL; gpu->psRequiredIterations = NULL;
gpu->psShakeReducedMass = NULL; gpu->psCcmaReducedMass = NULL;
gpu->psRigidClusterConstraintIndex = NULL;
gpu->psRigidClusterMatrix = NULL;
gpu->psRigidClusterMatrixIndex = NULL;
gpu->psConstraintMatrixColumn = NULL; gpu->psConstraintMatrixColumn = NULL;
gpu->psConstraintMatrixValue = NULL; gpu->psConstraintMatrixValue = NULL;
...@@ -1693,23 +1441,15 @@ void gpuShutDown(gpuContext gpu) ...@@ -1693,23 +1441,15 @@ void gpuShutDown(gpuContext gpu)
delete gpu->psAtomIndex; delete gpu->psAtomIndex;
delete gpu->psGridBoundingBox; delete gpu->psGridBoundingBox;
delete gpu->psGridCenter; delete gpu->psGridCenter;
delete gpu->psLincsAtoms; delete gpu->psCcmaAtoms;
delete gpu->psLincsDistance; delete gpu->psCcmaDistance;
delete gpu->psLincsConnections; delete gpu->psCcmaAtomConstraints;
delete gpu->psLincsNumConnections; delete gpu->psCcmaNumAtomConstraints;
delete gpu->psLincsAtomConstraints; delete gpu->psCcmaDelta1;
delete gpu->psLincsNumAtomConstraints; delete gpu->psCcmaDelta2;
delete gpu->psLincsS;
delete gpu->psLincsCoupling;
delete gpu->psLincsRhs1;
delete gpu->psLincsRhs2;
delete gpu->psLincsSolution;
delete gpu->psSyncCounter; delete gpu->psSyncCounter;
delete gpu->psRequiredIterations; delete gpu->psRequiredIterations;
delete gpu->psShakeReducedMass; delete gpu->psCcmaReducedMass;
delete gpu->psRigidClusterConstraintIndex;
delete gpu->psRigidClusterMatrix;
delete gpu->psRigidClusterMatrixIndex;
delete gpu->psConstraintMatrixColumn; delete gpu->psConstraintMatrixColumn;
delete gpu->psConstraintMatrixValue; delete gpu->psConstraintMatrixValue;
if (gpu->cudpp != 0) if (gpu->cudpp != 0)
...@@ -2021,8 +1761,7 @@ int gpuSetConstants(gpuContext gpu) ...@@ -2021,8 +1761,7 @@ int gpuSetConstants(gpuContext gpu)
SetVerletUpdateSim(gpu); SetVerletUpdateSim(gpu);
SetBrownianUpdateSim(gpu); SetBrownianUpdateSim(gpu);
SetSettleSim(gpu); SetSettleSim(gpu);
SetCShakeSim(gpu); SetCCMASim(gpu);
SetLincsSim(gpu);
SetRandomSim(gpu); SetRandomSim(gpu);
return 1; return 1;
} }
...@@ -2066,11 +1805,11 @@ static void findMoleculeGroups(gpuContext gpu) ...@@ -2066,11 +1805,11 @@ static void findMoleculeGroups(gpuContext gpu)
constraints.push_back(Constraint(atom1, atom3, distance12*distance12)); constraints.push_back(Constraint(atom1, atom3, distance12*distance12));
constraints.push_back(Constraint(atom2, atom3, distance23*distance23)); constraints.push_back(Constraint(atom2, atom3, distance23*distance23));
} }
for (int i = 0; i < (int)gpu->sim.lincsConstraints; i++) for (int i = 0; i < (int)gpu->sim.ccmaConstraints; i++)
{ {
int atom1 = (*gpu->psLincsAtoms)[i].x; int atom1 = (*gpu->psCcmaAtoms)[i].x;
int atom2 = (*gpu->psLincsAtoms)[i].y; int atom2 = (*gpu->psCcmaAtoms)[i].y;
float distance2 = (*gpu->psLincsDistance)[i].w; float distance2 = (*gpu->psCcmaDistance)[i].w;
constraints.push_back(Constraint(atom1, atom2, distance2)); constraints.push_back(Constraint(atom1, atom2, distance2));
} }
......
platforms/cuda/src/kernels/gputypes.h
View file @ 05259f77
...@@ -127,20 +127,15 @@ struct _gpuContext { ...@@ -127,20 +127,15 @@ struct _gpuContext {
CUDAStream<int>* psAtomIndex; // The original index of each atom CUDAStream<int>* psAtomIndex; // The original index of each atom
CUDAStream<float4>* psGridBoundingBox; // The size of each grid cell CUDAStream<float4>* psGridBoundingBox; // The size of each grid cell
CUDAStream<float4>* psGridCenter; // The center and radius for each grid cell CUDAStream<float4>* psGridCenter; // The center and radius for each grid cell
CUDAStream<int2>* psLincsAtoms; // The atoms connected by each LINCS constraint CUDAStream<int2>* psCcmaAtoms; // The atoms connected by each CCMA constraint
CUDAStream<float4>* psLincsDistance; // The displacement vector (x, y, z) and constraint distance (w) for each LINCS constraint CUDAStream<float4>* psCcmaDistance; // The displacement vector (x, y, z) and constraint distance (w) for each CCMA constraint
CUDAStream<int>* psLincsConnections; // The indices of constraints that other constraints are connected to CUDAStream<int>* psCcmaAtomConstraints; // The indices of constraints involving each atom
CUDAStream<int>* psLincsNumConnections; // The number of other constraints that each constraint is linked to CUDAStream<int>* psCcmaNumAtomConstraints; // The number of constraints involving each atom
CUDAStream<int>* psLincsAtomConstraints; // The indices of constraints involving each atom CUDAStream<float>* psCcmaDelta1; // Workspace for CCMA
CUDAStream<int>* psLincsNumAtomConstraints; // The number of constraints involving each atom CUDAStream<float>* psCcmaDelta2; // Workspace for CCMA
CUDAStream<float>* psLincsS; // S matrix for LINCS
CUDAStream<float>* psLincsCoupling; // Coupling matrix for LINCS
CUDAStream<float>* psLincsRhs1; // Workspace for LINCS
CUDAStream<float>* psLincsRhs2; // Workspace for LINCS
CUDAStream<float>* psLincsSolution; // Workspace for LINCS
CUDAStream<short>* psSyncCounter; // Used for global thread synchronization CUDAStream<short>* psSyncCounter; // Used for global thread synchronization
CUDAStream<unsigned int>* psRequiredIterations; // Used by SHAKE to communicate whether iteration has converged CUDAStream<unsigned int>* psRequiredIterations; // Used by SHAKE to communicate whether iteration has converged
CUDAStream<float>* psShakeReducedMass; // The reduced mass for each SHAKE constraint CUDAStream<float>* psCcmaReducedMass; // The reduced mass for each SHAKE constraint
CUDAStream<float>* psRigidClusterMatrix;// The inverse constraint matrix for each rigid cluster CUDAStream<float>* psRigidClusterMatrix;// The inverse constraint matrix for each rigid cluster
CUDAStream<unsigned int>* psRigidClusterConstraintIndex; // The index of each cluster in the stream containing cluster constraints. CUDAStream<unsigned int>* psRigidClusterConstraintIndex; // The index of each cluster in the stream containing cluster constraints.
CUDAStream<unsigned int>* psRigidClusterMatrixIndex; // The index of each cluster in the stream containing cluster matrices. CUDAStream<unsigned int>* psRigidClusterMatrixIndex; // The index of each cluster in the stream containing cluster matrices.
...@@ -192,7 +187,7 @@ void gpuSetObcParameters(gpuContext gpu, float innerDielectric, float solventDie ...@@ -192,7 +187,7 @@ void gpuSetObcParameters(gpuContext gpu, float innerDielectric, float solventDie
extern "C" extern "C"
void gpuSetConstraintParameters(gpuContext gpu, const std::vector<int>& atom1, const std::vector<int>& atom2, const std::vector<float>& distance, 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); const std::vector<float>& invMass1, const std::vector<float>& invMass2, float constraintTolerance);
extern "C" extern "C"
int gpuAllocateInitialBuffers(gpuContext gpu); int gpuAllocateInitialBuffers(gpuContext gpu);
......
platforms/cuda/src/kernels/kCShake.cu → platforms/cuda/src/kernels/kCCMA.cu
View file @ 05259f77
...@@ -34,14 +34,14 @@ using namespace std; ...@@ -34,14 +34,14 @@ using namespace std;
static __constant__ cudaGmxSimulation cSim; static __constant__ cudaGmxSimulation cSim;
void SetCShakeSim(gpuContext gpu) void SetCCMASim(gpuContext gpu)
{ {
cudaError_t status; cudaError_t status;
status = cudaMemcpyToSymbol(cSim, &gpu->sim, sizeof(cudaGmxSimulation)); status = cudaMemcpyToSymbol(cSim, &gpu->sim, sizeof(cudaGmxSimulation));
RTERROR(status, "cudaMemcpyToSymbol: SetSim copy to cSim failed"); RTERROR(status, "cudaMemcpyToSymbol: SetSim copy to cSim failed");
} }
void GetCShakeSim(gpuContext gpu) void GetCCMASim(gpuContext gpu)
{ {
cudaError_t status; cudaError_t status;
status = cudaMemcpyFromSymbol(&gpu->sim, cSim, sizeof(cudaGmxSimulation)); status = cudaMemcpyFromSymbol(&gpu->sim, cSim, sizeof(cudaGmxSimulation));
...@@ -66,7 +66,7 @@ __device__ void kSyncAllThreads_kernel(short* syncCounter, short newCount) ...@@ -66,7 +66,7 @@ __device__ void kSyncAllThreads_kernel(short* syncCounter, short newCount)
__syncthreads(); __syncthreads();
} }
__global__ void kApplyCShake_kernel(float4* atomPositions, bool addOldPosition) __global__ void kApplyCCMA_kernel(float4* atomPositions, bool addOldPosition)
{ {
// Initialize counters used for monitoring convergence and doing global thread synchronization. // Initialize counters used for monitoring convergence and doing global thread synchronization.
...@@ -82,16 +82,16 @@ __global__ void kApplyCShake_kernel(float4* atomPositions, bool addOldPosition) ...@@ -82,16 +82,16 @@ __global__ void kApplyCShake_kernel(float4* atomPositions, bool addOldPosition)
// Calculate the direction of each constraint. // Calculate the direction of each constraint.
unsigned int pos = threadIdx.x + blockIdx.x * blockDim.x; unsigned int pos = threadIdx.x + blockIdx.x * blockDim.x;
while (pos < cSim.lincsConstraints) while (pos < cSim.ccmaConstraints)
{ {
int2 atoms = cSim.pLincsAtoms[pos]; int2 atoms = cSim.pCcmaAtoms[pos];
float4 dir = cSim.pLincsDistance[pos]; float4 dir = cSim.pCcmaDistance[pos];
float4 oldPos1 = cSim.pOldPosq[atoms.x]; float4 oldPos1 = cSim.pOldPosq[atoms.x];
float4 oldPos2 = cSim.pOldPosq[atoms.y]; float4 oldPos2 = cSim.pOldPosq[atoms.y];
dir.x = oldPos1.x-oldPos2.x; dir.x = oldPos1.x-oldPos2.x;
dir.y = oldPos1.y-oldPos2.y; dir.y = oldPos1.y-oldPos2.y;
dir.z = oldPos1.z-oldPos2.z; dir.z = oldPos1.z-oldPos2.z;
cSim.pLincsDistance[pos] = dir; cSim.pCcmaDistance[pos] = dir;
pos += blockDim.x*gridDim.x; pos += blockDim.x*gridDim.x;
} }
__syncthreads(); __syncthreads();
...@@ -106,12 +106,12 @@ __global__ void kApplyCShake_kernel(float4* atomPositions, bool addOldPosition) ...@@ -106,12 +106,12 @@ __global__ void kApplyCShake_kernel(float4* atomPositions, bool addOldPosition)
// Calculate the constraint force for each constraint. // Calculate the constraint force for each constraint.
pos = threadIdx.x + blockIdx.x * blockDim.x; pos = threadIdx.x + blockIdx.x * blockDim.x;
while (pos < cSim.lincsConstraints) while (pos < cSim.ccmaConstraints)
{ {
int2 atoms = cSim.pLincsAtoms[pos]; int2 atoms = cSim.pCcmaAtoms[pos];
float4 delta1 = atomPositions[atoms.x]; float4 delta1 = atomPositions[atoms.x];
float4 delta2 = atomPositions[atoms.y]; float4 delta2 = atomPositions[atoms.y];
float4 dir = cSim.pLincsDistance[pos]; float4 dir = cSim.pCcmaDistance[pos];
float3 rp_ij = make_float3(delta1.x-delta2.x, delta1.y-delta2.y, delta1.z-delta2.z); float3 rp_ij = make_float3(delta1.x-delta2.x, delta1.y-delta2.y, delta1.z-delta2.z);
if (addOldPosition) if (addOldPosition)
{ {
...@@ -124,8 +124,8 @@ __global__ void kApplyCShake_kernel(float4* atomPositions, bool addOldPosition) ...@@ -124,8 +124,8 @@ __global__ void kApplyCShake_kernel(float4* atomPositions, bool addOldPosition)
float diff = dist2 - rp2; float diff = dist2 - rp2;
float rrpr = rp_ij.x*dir.x + rp_ij.y*dir.y + rp_ij.z*dir.z; float rrpr = rp_ij.x*dir.x + rp_ij.y*dir.y + rp_ij.z*dir.z;
float d_ij2 = dir.x*dir.x + dir.y*dir.y + dir.z*dir.z; float d_ij2 = dir.x*dir.x + dir.y*dir.y + dir.z*dir.z;
float reducedMass = cSim.pShakeReducedMass[pos]; float reducedMass = cSim.pCcmaReducedMass[pos];
cSim.pLincsRhs1[pos] = (rrpr > d_ij2*1e-6f ? reducedMass*diff/rrpr : 0.0f); cSim.pCcmaDelta1[pos] = (rrpr > d_ij2*1e-6f ? reducedMass*diff/rrpr : 0.0f);
if (requiredIterations == iteration && (rp2 < lowerTol*dist2 || rp2 > upperTol*dist2)) if (requiredIterations == iteration && (rp2 < lowerTol*dist2 || rp2 > upperTol*dist2))
requiredIterations = iteration+1; requiredIterations = iteration+1;
pos += blockDim.x * gridDim.x; pos += blockDim.x * gridDim.x;
...@@ -140,18 +140,18 @@ __global__ void kApplyCShake_kernel(float4* atomPositions, bool addOldPosition) ...@@ -140,18 +140,18 @@ __global__ void kApplyCShake_kernel(float4* atomPositions, bool addOldPosition)
// Multiply by the inverse constraint matrix. // Multiply by the inverse constraint matrix.
pos = threadIdx.x + blockIdx.x * blockDim.x; pos = threadIdx.x + blockIdx.x * blockDim.x;
while (pos < cSim.lincsConstraints) while (pos < cSim.ccmaConstraints)
{ {
float sum = 0.0f; float sum = 0.0f;
for (unsigned int i = 0; ; i++) for (unsigned int i = 0; ; i++)
{ {
unsigned int index = pos+i*cSim.lincsConstraints; unsigned int index = pos+i*cSim.ccmaConstraints;
unsigned int column = cSim.pConstraintMatrixColumn[index]; unsigned int column = cSim.pConstraintMatrixColumn[index];
if (column >= cSim.lincsConstraints) if (column >= cSim.ccmaConstraints)
break; break;
sum += cSim.pLincsRhs1[column]*cSim.pConstraintMatrixValue[index]; sum += cSim.pCcmaDelta1[column]*cSim.pConstraintMatrixValue[index];
} }
cSim.pLincsSolution[pos] = sum; cSim.pCcmaDelta2[pos] = sum;
pos += blockDim.x * gridDim.x; pos += blockDim.x * gridDim.x;
} }
kSyncAllThreads_kernel(&cSim.pSyncCounter[gridDim.x], iteration); kSyncAllThreads_kernel(&cSim.pSyncCounter[gridDim.x], iteration);
...@@ -164,16 +164,16 @@ __global__ void kApplyCShake_kernel(float4* atomPositions, bool addOldPosition) ...@@ -164,16 +164,16 @@ __global__ void kApplyCShake_kernel(float4* atomPositions, bool addOldPosition)
{ {
float4 atomPos = atomPositions[pos]; float4 atomPos = atomPositions[pos];
float invMass = cSim.pVelm4[pos].w; float invMass = cSim.pVelm4[pos].w;
int num = cSim.pLincsNumAtomConstraints[pos]; int num = cSim.pCcmaNumAtomConstraints[pos];
for (int i = 0; i < num; i++) for (int i = 0; i < num; i++)
{ {
int index = pos+i*cSim.atoms; int index = pos+i*cSim.atoms;
int constraint = cSim.pLincsAtomConstraints[index]; int constraint = cSim.pCcmaAtomConstraints[index];
bool forward = (constraint > 0); bool forward = (constraint > 0);
constraint = (forward ? constraint-1 : -constraint-1); constraint = (forward ? constraint-1 : -constraint-1);
float constraintForce = damping*invMass*cSim.pLincsSolution[constraint]; float constraintForce = damping*invMass*cSim.pCcmaDelta2[constraint];
constraintForce = (forward ? constraintForce : -constraintForce); constraintForce = (forward ? constraintForce : -constraintForce);
float4 dir = cSim.pLincsDistance[constraint]; float4 dir = cSim.pCcmaDistance[constraint];
atomPos.x += constraintForce*dir.x; atomPos.x += constraintForce*dir.x;
atomPos.y += constraintForce*dir.y; atomPos.y += constraintForce*dir.y;
atomPos.z += constraintForce*dir.z; atomPos.z += constraintForce*dir.z;
...@@ -192,22 +192,22 @@ __global__ void kApplyCShake_kernel(float4* atomPositions, bool addOldPosition) ...@@ -192,22 +192,22 @@ __global__ void kApplyCShake_kernel(float4* atomPositions, bool addOldPosition)
cSim.pSyncCounter[blockIdx.x] = -1; cSim.pSyncCounter[blockIdx.x] = -1;
} }
void kApplyFirstCShake(gpuContext gpu) void kApplyFirstCCMA(gpuContext gpu)
{ {
// printf("kApplyFirstCShake\n"); // printf("kApplyFirstCCMA\n");
if (gpu->sim.lincsConstraints > 0) if (gpu->sim.ccmaConstraints > 0)
{ {
kApplyCShake_kernel<<<gpu->sim.blocks, gpu->sim.lincs_threads_per_block>>>(gpu->sim.pPosqP, true); kApplyCCMA_kernel<<<gpu->sim.blocks, gpu->sim.ccma_threads_per_block>>>(gpu->sim.pPosqP, true);
LAUNCHERROR("kApplyCShake"); LAUNCHERROR("kApplyCCMA");
} }
} }
void kApplySecondCShake(gpuContext gpu) void kApplySecondCCMA(gpuContext gpu)
{ {
// printf("kApplySecondCShake\n"); // printf("kApplySecondCCMA\n");
if (gpu->sim.lincsConstraints > 0) if (gpu->sim.ccmaConstraints > 0)
{ {
kApplyCShake_kernel<<<gpu->sim.blocks, gpu->sim.lincs_threads_per_block>>>(gpu->sim.pPosq, false); kApplyCCMA_kernel<<<gpu->sim.blocks, gpu->sim.ccma_threads_per_block>>>(gpu->sim.pPosq, false);
LAUNCHERROR("kApplyCShake"); LAUNCHERROR("kApplyCCMA");
} }
} }
platforms/cuda/src/kernels/kLincs.cu deleted 100644 → 0
View file @ f62ba9d8
/* -------------------------------------------------------------------------- *
* OpenMM *
* -------------------------------------------------------------------------- *
* This is part of the OpenMM molecular simulation toolkit originating from *
* Simbios, the NIH National Center for Physics-Based Simulation of *
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2009 Stanford University and the Authors. *
* Authors: Scott Le Grand, Peter Eastman *
* Contributors: *
* *
* This program is free software: you can redistribute it and/or modify *
* it under the terms of the GNU Lesser General Public License as published *
* by the Free Software Foundation, either version 3 of the License, or *
* (at your option) any later version. *
* *
* This program is distributed in the hope that it will be useful, *
* but WITHOUT ANY WARRANTY; without even the implied warranty of *
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the *
* GNU Lesser General Public License for more details. *
* *
* You should have received a copy of the GNU Lesser General Public License *
* along with this program. If not, see <http://www.gnu.org/licenses/>. *
* -------------------------------------------------------------------------- */
#include <cuda.h>
#include <vector_functions.h>
using namespace std;
#include "gputypes.h"
static __constant__ cudaGmxSimulation cSim;
void SetLincsSim(gpuContext gpu)
{
cudaError_t status;
status = cudaMemcpyToSymbol(cSim, &gpu->sim, sizeof(cudaGmxSimulation));
RTERROR(status, "cudaMemcpyToSymbol: SetSim copy to cSim failed");
}
void GetLincsSim(gpuContext gpu)
{
cudaError_t status;
status = cudaMemcpyFromSymbol(&gpu->sim, cSim, sizeof(cudaGmxSimulation));
RTERROR(status, "cudaMemcpyFromSymbol: SetSim copy from cSim failed");
}
/**
* Synchronize all threads across all blocks.
*/
__device__ void kSyncAllThreads_kernel(short* syncCounter, short newCount)
{
// short* syncCounter = &cSim.pSyncCounter[newCount%2 == 0 ? 0 : gridDim.x];
__syncthreads();
if (threadIdx.x == 0)
syncCounter[blockIdx.x] = newCount;
if (threadIdx.x < gridDim.x)
{
volatile short* counter = &syncCounter[threadIdx.x];
do
{
} while (*counter != newCount);
}
__syncthreads();
}
__global__ void kSolveLincsMatrix_kernel(float4* atomPositions)
{
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;
while (pos < cSim.lincsConstraints)
{
float rhs = 0.0f;
int num = cSim.pLincsNumConnections[pos];
for (int i = 0; i < num; i++)
{
int index = pos+i*cSim.lincsConstraints;
int otherConstraint = cSim.pLincsConnections[index];
rhs += cSim.pLincsCoupling[index]*rhs1[otherConstraint];
}
rhs2[pos] = rhs;
cSim.pLincsSolution[pos] += rhs;
pos += blockDim.x * gridDim.x;
}
kSyncAllThreads_kernel(&cSim.pSyncCounter[iteration%2 == 0 ? 0 : gridDim.x], iteration);
}
// Update the atom positions based on the solution to the matrix equations.
unsigned int pos = threadIdx.x + blockIdx.x * blockDim.x;
while (pos < cSim.atoms)
{
float4 atomPos = atomPositions[pos];
float invMass = cSim.pVelm4[pos].w;
int num = cSim.pLincsNumAtomConstraints[pos];
for (int i = 0; i < num; i++)
{
int index = pos+i*cSim.atoms;
int constraint = cSim.pLincsAtomConstraints[index];
bool forward = (constraint > 0);
constraint = (forward ? constraint-1 : -constraint-1);
float4 dir = cSim.pLincsDistance[constraint];
float c = invMass*cSim.pLincsS[constraint]*cSim.pLincsSolution[constraint];
c = (forward ? -c : c);
atomPos.x += c*dir.x;
atomPos.y += c*dir.y;
atomPos.z += c*dir.z;
}
atomPositions[pos] = atomPos;
pos += blockDim.x * gridDim.x;
}
}
__global__ void kApplyLincsPart1_kernel(float4* atomPositions, bool addOldPosition)
{
// Calculate the direction of each constraint, along with the initial RHS and solution vectors.
unsigned int pos = threadIdx.x + blockIdx.x * blockDim.x;
while (pos < cSim.lincsConstraints)
{
int2 atoms = cSim.pLincsAtoms[pos];
float4 delta1 = atomPositions[atoms.x];
float4 delta2 = atomPositions[atoms.y];
float4 dir = cSim.pLincsDistance[pos];
if (addOldPosition)
{
float4 oldPos1 = cSim.pOldPosq[atoms.x];
float4 oldPos2 = cSim.pOldPosq[atoms.y];
dir.x = (oldPos1.x-oldPos2.x)+(delta1.x-delta2.x);
dir.y = (oldPos1.y-oldPos2.y)+(delta1.y-delta2.y);
dir.z = (oldPos1.z-oldPos2.z)+(delta1.z-delta2.z);
}
else
{
dir.x = delta1.x-delta2.x;
dir.y = delta1.y-delta2.y;
dir.z = delta1.z-delta2.z;
}
float invLength = 1.0f/sqrt(dir.x*dir.x + dir.y*dir.y + dir.z*dir.z);
dir.x *= invLength;
dir.y *= invLength;
dir.z *= invLength;
cSim.pLincsDistance[pos] = dir;
float diff = cSim.pLincsS[pos]*(1.0f/invLength-dir.w);
cSim.pLincsRhs1[pos] = diff;
cSim.pLincsSolution[pos] = diff;
pos += blockDim.x * gridDim.x;
}
kSyncAllThreads_kernel(cSim.pSyncCounter, cSim.lincsTerms+1);
// Build the coupling matrix.
pos = threadIdx.x + blockIdx.x * blockDim.x;
while (pos < cSim.lincsConstraints)
{
float4 dir1 = cSim.pLincsDistance[pos];
int2 atoms1 = cSim.pLincsAtoms[pos];
int num = cSim.pLincsNumConnections[pos];
float s = cSim.pLincsS[pos];
float invMass = cSim.pVelm4[atoms1.x].w;
for (int i = 0; i < num; i++)
{
int index = pos+i*cSim.lincsConstraints;
int otherConstraint = cSim.pLincsConnections[index];
float4 dir2 = cSim.pLincsDistance[otherConstraint];
int2 atoms2 = cSim.pLincsAtoms[otherConstraint];
float signedMass = (atoms1.x == atoms2.x || atoms1.y == atoms2.y ? -invMass : cSim.pVelm4[atoms1.y].w);
cSim.pLincsCoupling[index] = signedMass*s*(dir1.x*dir2.x+dir1.y*dir2.y+dir1.z*dir2.z)*cSim.pLincsS[otherConstraint];
}
pos += blockDim.x * gridDim.x;
}
}
__global__ void kApplyLincsPart2_kernel(float4* atomPositions, bool addOldPosition)
{
// Correct for rotational lengthening.
unsigned int pos = threadIdx.x + blockIdx.x * blockDim.x;
while (pos < cSim.lincsConstraints)
{
int2 atoms = cSim.pLincsAtoms[pos];
float4 delta1 = atomPositions[atoms.x];
float4 delta2 = atomPositions[atoms.y];
float3 delta;
if (addOldPosition)
{
float4 oldPos1 = cSim.pOldPosq[atoms.x];
float4 oldPos2 = cSim.pOldPosq[atoms.y];
delta = make_float3((oldPos1.x-oldPos2.x)+(delta1.x-delta2.x),
(oldPos1.y-oldPos2.y)+(delta1.y-delta2.y),
(oldPos1.z-oldPos2.z)+(delta1.z-delta2.z));
}
else
{
delta = make_float3(delta1.x-delta2.x, delta1.y-delta2.y, delta1.z-delta2.z);
}
float distance = cSim.pLincsDistance[pos].w;
float p2 = 2.0f*distance*distance-(delta.x*delta.x+delta.y*delta.y+delta.z*delta.z);
p2 = (p2 < 0.0f ? 0.0f : p2);
float diff = cSim.pLincsS[pos]*(distance-sqrt(p2));
cSim.pLincsRhs1[pos] = diff;
cSim.pLincsSolution[pos] = diff;
pos += blockDim.x * gridDim.x;
}
}
static void kApplyLincs(gpuContext gpu, float4* atomPositions, bool addOldPosition)
{
kApplyLincsPart1_kernel<<<gpu->sim.blocks, gpu->sim.lincs_threads_per_block>>>(atomPositions, addOldPosition);
LAUNCHERROR("kApplyLincsPart1");
kSolveLincsMatrix_kernel<<<gpu->sim.blocks, gpu->sim.lincs_threads_per_block>>>(atomPositions);
LAUNCHERROR("kSolveLincsMatrix_kernel");
kApplyLincsPart2_kernel<<<gpu->sim.blocks, gpu->sim.lincs_threads_per_block>>>(atomPositions, addOldPosition);
LAUNCHERROR("kApplyLincsPart2");
kSolveLincsMatrix_kernel<<<gpu->sim.blocks, gpu->sim.lincs_threads_per_block>>>(atomPositions);
LAUNCHERROR("kSolveLincsMatrix_kernel");
}
void kApplyFirstLincs(gpuContext gpu)
{
// printf("kApplyFirstLincs\n");
if (gpu->sim.lincsConstraints > 0)
kApplyLincs(gpu, gpu->sim.pPosqP, true);
}
void kApplySecondLincs(gpuContext gpu)
{
// printf("kApplySecondLincs\n");
if (gpu->sim.lincsConstraints > 0)
kApplyLincs(gpu, gpu->sim.pPosq, false);
}
platforms/reference/src/ReferenceKernels.cpp
View file @ 05259f77
...@@ -38,14 +38,12 @@ ...@@ -38,14 +38,12 @@
#include "SimTKReference/ReferenceBondForce.h" #include "SimTKReference/ReferenceBondForce.h"
#include "SimTKReference/ReferenceBrownianDynamics.h" #include "SimTKReference/ReferenceBrownianDynamics.h"
#include "SimTKReference/ReferenceHarmonicBondIxn.h" #include "SimTKReference/ReferenceHarmonicBondIxn.h"
#include "SimTKReference/ReferenceLincsAlgorithm.h"
#include "SimTKReference/ReferenceLJCoulomb14.h" #include "SimTKReference/ReferenceLJCoulomb14.h"
#include "SimTKReference/ReferenceLJCoulombIxn.h" #include "SimTKReference/ReferenceLJCoulombIxn.h"
#include "SimTKReference/ReferenceProperDihedralBond.h" #include "SimTKReference/ReferenceProperDihedralBond.h"
#include "SimTKReference/ReferenceRbDihedralBond.h" #include "SimTKReference/ReferenceRbDihedralBond.h"
#include "SimTKReference/ReferenceStochasticDynamics.h" #include "SimTKReference/ReferenceStochasticDynamics.h"
#include "SimTKReference/ReferenceRigidShakeAlgorithm.h" #include "SimTKReference/ReferenceCCMAAlgorithm.h"
#include "SimTKReference/ReferenceShakeAlgorithm.h"
#include "SimTKReference/ReferenceVerletDynamics.h" #include "SimTKReference/ReferenceVerletDynamics.h"
#include "openmm/CMMotionRemover.h" #include "openmm/CMMotionRemover.h"
#include "openmm/System.h" #include "openmm/System.h"
...@@ -108,7 +106,7 @@ static void disposeRealArray(RealOpenMM** array, int size) { ...@@ -108,7 +106,7 @@ static void disposeRealArray(RealOpenMM** array, int size) {
} }
} }
static void findAnglesForShake(const System& system, vector<ReferenceRigidShakeAlgorithm::AngleInfo>& angles) { static void findAnglesForCCMA(const System& system, vector<ReferenceCCMAAlgorithm::AngleInfo>& angles) {
for (int i = 0; i < system.getNumForces(); i++) { for (int i = 0; i < system.getNumForces(); i++) {
const HarmonicAngleForce* force = dynamic_cast<const HarmonicAngleForce*>(&system.getForce(i)); const HarmonicAngleForce* force = dynamic_cast<const HarmonicAngleForce*>(&system.getForce(i));
if (force != NULL) { if (force != NULL) {
...@@ -116,7 +114,7 @@ static void findAnglesForShake(const System& system, vector<ReferenceRigidShakeA ...@@ -116,7 +114,7 @@ static void findAnglesForShake(const System& system, vector<ReferenceRigidShakeA
int atom1, atom2, atom3; int atom1, atom2, atom3;
double angle, k; double angle, k;
force->getAngleParameters(j, atom1, atom2, atom3, angle, k); force->getAngleParameters(j, atom1, atom2, atom3, angle, k);
angles.push_back(ReferenceRigidShakeAlgorithm::AngleInfo(atom1, atom2, atom3, angle)); angles.push_back(ReferenceCCMAAlgorithm::AngleInfo(atom1, atom2, atom3, angle));
} }
} }
} }
...@@ -623,9 +621,9 @@ void ReferenceIntegrateVerletStepKernel::execute(OpenMMContextImpl& context, con ...@@ -623,9 +621,9 @@ void ReferenceIntegrateVerletStepKernel::execute(OpenMMContextImpl& context, con
delete constraints; delete constraints;
} }
dynamics = new ReferenceVerletDynamics(context.getSystem().getNumParticles(), static_cast<RealOpenMM>(stepSize) ); dynamics = new ReferenceVerletDynamics(context.getSystem().getNumParticles(), static_cast<RealOpenMM>(stepSize) );
vector<ReferenceRigidShakeAlgorithm::AngleInfo> angles; vector<ReferenceCCMAAlgorithm::AngleInfo> angles;
findAnglesForShake(context.getSystem(), angles); findAnglesForCCMA(context.getSystem(), angles);
constraints = new ReferenceRigidShakeAlgorithm(context.getSystem().getNumParticles(), numConstraints, constraintIndices, constraintDistances, masses, angles, (RealOpenMM)integrator.getConstraintTolerance()); constraints = new ReferenceCCMAAlgorithm(context.getSystem().getNumParticles(), numConstraints, constraintIndices, constraintDistances, masses, angles, (RealOpenMM)integrator.getConstraintTolerance());
dynamics->setReferenceConstraintAlgorithm(constraints); dynamics->setReferenceConstraintAlgorithm(constraints);
prevStepSize = stepSize; prevStepSize = stepSize;
} }
...@@ -684,9 +682,9 @@ void ReferenceIntegrateLangevinStepKernel::execute(OpenMMContextImpl& context, c ...@@ -684,9 +682,9 @@ void ReferenceIntegrateLangevinStepKernel::execute(OpenMMContextImpl& context, c
static_cast<RealOpenMM>(stepSize), static_cast<RealOpenMM>(stepSize),
static_cast<RealOpenMM>(tau), static_cast<RealOpenMM>(tau),
static_cast<RealOpenMM>(temperature) ); static_cast<RealOpenMM>(temperature) );
vector<ReferenceRigidShakeAlgorithm::AngleInfo> angles; vector<ReferenceCCMAAlgorithm::AngleInfo> angles;
findAnglesForShake(context.getSystem(), angles); findAnglesForCCMA(context.getSystem(), angles);
constraints = new ReferenceRigidShakeAlgorithm(context.getSystem().getNumParticles(), numConstraints, constraintIndices, constraintDistances, masses, angles, (RealOpenMM)integrator.getConstraintTolerance()); constraints = new ReferenceCCMAAlgorithm(context.getSystem().getNumParticles(), numConstraints, constraintIndices, constraintDistances, masses, angles, (RealOpenMM)integrator.getConstraintTolerance());
dynamics->setReferenceConstraintAlgorithm(constraints); dynamics->setReferenceConstraintAlgorithm(constraints);
prevTemp = temperature; prevTemp = temperature;
prevFriction = friction; prevFriction = friction;
...@@ -746,9 +744,9 @@ void ReferenceIntegrateBrownianStepKernel::execute(OpenMMContextImpl& context, c ...@@ -746,9 +744,9 @@ void ReferenceIntegrateBrownianStepKernel::execute(OpenMMContextImpl& context, c
static_cast<RealOpenMM>(stepSize), static_cast<RealOpenMM>(stepSize),
static_cast<RealOpenMM>(friction), static_cast<RealOpenMM>(friction),
static_cast<RealOpenMM>(temperature) ); static_cast<RealOpenMM>(temperature) );
vector<ReferenceRigidShakeAlgorithm::AngleInfo> angles; vector<ReferenceCCMAAlgorithm::AngleInfo> angles;
findAnglesForShake(context.getSystem(), angles); findAnglesForCCMA(context.getSystem(), angles);
constraints = new ReferenceRigidShakeAlgorithm(context.getSystem().getNumParticles(), numConstraints, constraintIndices, constraintDistances, masses, angles, (RealOpenMM)integrator.getConstraintTolerance()); constraints = new ReferenceCCMAAlgorithm(context.getSystem().getNumParticles(), numConstraints, constraintIndices, constraintDistances, masses, angles, (RealOpenMM)integrator.getConstraintTolerance());
dynamics->setReferenceConstraintAlgorithm(constraints); dynamics->setReferenceConstraintAlgorithm(constraints);
prevTemp = temperature; prevTemp = temperature;
prevFriction = friction; prevFriction = friction;
......
platforms/reference/src/SimTKReference/ReferenceRigidShakeAlgorithm.cpp → platforms/reference/src/SimTKReference/ReferenceCCMAAlgorithm.cpp
View file @ 05259f77
...@@ -28,9 +28,8 @@ ...@@ -28,9 +28,8 @@
#include "../SimTKUtilities/SimTKOpenMMCommon.h" #include "../SimTKUtilities/SimTKOpenMMCommon.h"
#include "../SimTKUtilities/SimTKOpenMMUtilities.h" #include "../SimTKUtilities/SimTKOpenMMUtilities.h"
#include "../SimTKUtilities/SimTKOpenMMLog.h" #include "../SimTKUtilities/SimTKOpenMMLog.h"
#include "ReferenceRigidShakeAlgorithm.h" #include "ReferenceCCMAAlgorithm.h"
#include "ReferenceDynamics.h" #include "ReferenceDynamics.h"
#include "jama_svd.h"
#include "quern.h" #include "quern.h"
#include "openmm/Vec3.h" #include "openmm/Vec3.h"
#include <map> #include <map>
...@@ -40,22 +39,22 @@ using std::pair; ...@@ -40,22 +39,22 @@ using std::pair;
using std::vector; using std::vector;
using std::set; using std::set;
using OpenMM::Vec3; using OpenMM::Vec3;
using TNT::Array2D;
using JAMA::SVD;
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
ReferenceQShakeAlgorithm constructor ReferenceCCMAAlgorithm constructor
@param numberOfAtoms number of atoms @param numberOfAtoms number of atoms
@param numberOfConstraints number of constraints @param numberOfConstraints number of constraints
@param atomIndices block of atom indices @param atomIndices atom indices for contraints
@param shakeParameters Shake parameters @param distance distances for constraints
@param tolerance constraint tolerance @param masses atom masses
@param angles angle force field terms
@param tolerance constraint tolerance
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
ReferenceRigidShakeAlgorithm::ReferenceRigidShakeAlgorithm( int numberOfAtoms, ReferenceCCMAAlgorithm::ReferenceCCMAAlgorithm( int numberOfAtoms,
int numberOfConstraints, int numberOfConstraints,
int** atomIndices, int** atomIndices,
RealOpenMM* distance, RealOpenMM* distance,
...@@ -65,7 +64,7 @@ ReferenceRigidShakeAlgorithm::ReferenceRigidShakeAlgorithm( int numberOfAtoms, ...@@ -65,7 +64,7 @@ ReferenceRigidShakeAlgorithm::ReferenceRigidShakeAlgorithm( int numberOfAtoms,
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
// static const char* methodName = "\nReferenceQShakeAlgorithm::ReferenceQShakeAlgorithm"; // static const char* methodName = "\nReferenceCCMAAlgorithm::ReferenceCCMAAlgorithm";
static const RealOpenMM zero = 0.0; static const RealOpenMM zero = 0.0;
static const RealOpenMM one = 1.0; static const RealOpenMM one = 1.0;
...@@ -201,181 +200,26 @@ ReferenceRigidShakeAlgorithm::ReferenceRigidShakeAlgorithm( int numberOfAtoms, ...@@ -201,181 +200,26 @@ ReferenceRigidShakeAlgorithm::ReferenceRigidShakeAlgorithm( int numberOfAtoms,
QUERN_solve_with_r(numberOfConstraints, rRowStart, rColIndex, rValue, &rhs[0], &rhs[0]); QUERN_solve_with_r(numberOfConstraints, rRowStart, rColIndex, rValue, &rhs[0], &rhs[0]);
for (int j = 0; j < numberOfConstraints; j++) { for (int j = 0; j < numberOfConstraints; j++) {
double value = rhs[j]*_distance[i]/_distance[j]; double value = rhs[j]*_distance[i]/_distance[j];
if (abs(value) > 0.02) if (FABS(value) > 0.02)
_matrix[j].push_back(pair<int, RealOpenMM>(i, (RealOpenMM) value)); _matrix[j].push_back(pair<int, RealOpenMM>(i, (RealOpenMM) value));
} }
} }
QUERN_free_result(qRowStart, qColIndex, qValue); QUERN_free_result(qRowStart, qColIndex, qValue);
QUERN_free_result(rRowStart, rColIndex, rValue); QUERN_free_result(rRowStart, rColIndex, rValue);
} }
// // Identify rigid clusters.
//
// vector<map<int, int> > atomConstraints(numberOfAtoms);
// for (int i = 0; i < numberOfConstraints; i++) {
// atomConstraints[atomIndices[i][0]][atomIndices[i][1]] = i;
// atomConstraints[atomIndices[i][1]][atomIndices[i][0]] = i;
// }
// for (int i = 0; i < numberOfAtoms; i++) {
// if (atomConstraints[i].size() < 2)
// continue;
//
// // Begin by looking for a triangle this atom is part of.
//
// set<int> atoms;
// atoms.insert(i);
// for (map<int, int>::const_iterator atom1 = atomConstraints[i].begin(); atom1 != atomConstraints[i].end() && atoms.size() == 1; ++atom1) {
// for (map<int, int>::const_iterator atom2 = atomConstraints[atom1->first].begin(); atom2 != atomConstraints[atom1->first].end(); ++atom2) {
// if (atomConstraints[i].count(atom2->first) != 0) {
// atoms.insert(atom1->first);
// atoms.insert(atom2->first);
// break;
// }
// }
// }
// if (atoms.size() == 1)
// continue;
//
// // We have three atoms that are part of a cluster, so look for other atoms we can add.
//
// bool done = false;
// while (!done) {
// done = true;
// for (set<int>::const_iterator atom1 = atoms.begin(); atom1 != atoms.end(); ++atom1) {
// for (map<int, int>::const_iterator atom2 = atomConstraints[*atom1].begin(); atom2 != atomConstraints[*atom1].end(); ++atom2) {
// if (atoms.find(atom2->first) != atoms.end())
// continue; // This atom is already in the cluster.
//
// // See if this atom is linked to three other atoms in the cluster.
//
// int linkCount = 0;
// for (map<int, int>::const_iterator atom3 = atomConstraints[atom2->first].begin(); atom3 != atomConstraints[atom2->first].end(); ++atom3)
// if (atoms.find(atom3->first) != atoms.end())
// linkCount++;
// if (linkCount > 2) {
// atoms.insert(atom2->first);
// done = false;
// }
// }
// }
// }
//
// // Record the cluster.
//
// vector<int> constraints;
// for (set<int>::const_iterator atom1 = atoms.begin(); atom1 != atoms.end(); ++atom1) {
// for (map<int, int>::const_iterator atom2 = atomConstraints[*atom1].begin(); atom2 != atomConstraints[*atom1].end(); ++atom2) {
// if (*atom1 < atom2->first && atoms.find(atom2->first) != atoms.end())
// constraints.push_back(atom2->second);
// }
// }
// _rigidClusters.push_back(constraints);
// for (set<int>::const_iterator atom1 = atoms.begin(); atom1 != atoms.end(); ++atom1) {
// for (map<int, int>::const_iterator atom2 = atomConstraints[*atom1].begin(); atom2 != atomConstraints[*atom1].end(); ++atom2)
// atomConstraints[atom2->first].erase(*atom1);
// atomConstraints[*atom1].clear();
// }
//
// // Compute the constraint coupling matrix for this cluster.
//
// const vector<int>& cluster = _rigidClusters[i];
// unsigned int size = cluster.size();
// Array2D<double> matrix(size, size);
// for (int j = 0; j < (int)size; j++) {
// for (int k = 0; k < (int)size; k++) {
// double scale;
// int atomj0 = _atomIndices[cluster[j]][0];
// int atomj1 = _atomIndices[cluster[j]][1];
// int atomk0 = _atomIndices[cluster[k]][0];
// int atomk1 = _atomIndices[cluster[k]][1];
// RealOpenMM invMass0 = one/masses[atomj0];
// RealOpenMM invMass1 = one/masses[atomj1];
// int atoma, atomb;
// if (atomj0 == atomk0) {
// atoma = atomj1;
// atomb = atomk1;
// scale = invMass0/(invMass0+invMass1);
// }
// else if (atomj1 == atomk1) {
// atoma = atomj0;
// atomb = atomk0;
// scale = invMass1/(invMass0+invMass1);
// }
// else if (atomj0 == atomk1) {
// atoma = atomj1;
// atomb = atomk0;
// scale = invMass0/(invMass0+invMass1);
// }
// else if (atomj1 == atomk0) {
// atoma = atomj0;
// atomb = atomk1;
// scale = invMass1/(invMass0+invMass1);
// }
// else {
// matrix[j][k] = 0.0;
// continue; // These constraints are not connected.
// }
//
// // Find the third constraint forming a triangle with these two.
//
// for (int m = 0; m < size; m++) {
// int other = cluster[m];
// if ((_atomIndices[other][0] == atoma && _atomIndices[other][1] == atomb) || (_atomIndices[other][0] == atomb && _atomIndices[other][1] == atoma)) {
// double d1 = _distance[cluster[j]];
// double d2 = _distance[cluster[k]];
// double d3 = _distance[other];
// matrix[j][k] = scale*(d1*d1+d2*d2-d3*d3)/(2.0*d1*d2);
// break;
// }
// }
// }
// matrix[j][j] = 1.0;
// }
//
// // Invert it using SVD.
//
// Array2D<double> u, v;
// Array1D<double> w;
// SVD<double> svd(matrix);
// svd.getU(u);
// svd.getV(v);
// svd.getSingularValues(w);
// double singularValueCutoff = 0.01*w[0];
// for (int j = 0; j < (int)size; j++)
// w[j] = (w[j] < singularValueCutoff ? 0.0 : 1.0/w[j]);
// for (int j = 0; j < (int)size; j++) {
// for (int k = 0; k < (int)size; k++) {
// matrix[j][k] = 0.0;
// for (int m = 0; m < (int)size; m++)
// matrix[j][k] += v[j][m]*w[m]*u[k][m];
// }
// }
//
// // Record the inverted matrix.
//
// _matrices.push_back(SimTKOpenMMUtilities::allocateTwoDRealOpenMMArray(constraints.size(), constraints.size(), NULL, false, 0.0, ""));
// for (int j = 0; j < (int)size; j++)
// for (int k = 0; k < (int)size; k++)
// _matrices[i][j][k] = (RealOpenMM)matrix[j][k]*_distance[cluster[k]]/_distance[cluster[j]];
// }
} }
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
ReferenceQShakeAlgorithm destructor ReferenceCCMAAlgorithm destructor
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
ReferenceRigidShakeAlgorithm::~ReferenceRigidShakeAlgorithm( ){ ReferenceCCMAAlgorithm::~ReferenceCCMAAlgorithm( ){
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
// static const char* methodName = "\nReferenceQShakeAlgorithm::~ReferenceQShakeAlgorithm"; // static const char* methodName = "\nReferenceCCMAAlgorithm::~ReferenceCCMAAlgorithm";
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
...@@ -398,11 +242,11 @@ ReferenceRigidShakeAlgorithm::~ReferenceRigidShakeAlgorithm( ){ ...@@ -398,11 +242,11 @@ ReferenceRigidShakeAlgorithm::~ReferenceRigidShakeAlgorithm( ){
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
int ReferenceRigidShakeAlgorithm::getNumberOfConstraints( void ) const { int ReferenceCCMAAlgorithm::getNumberOfConstraints( void ) const {
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
// static const char* methodName = "\nReferenceQShakeAlgorithm::getNumberOfConstraints"; // static const char* methodName = "\nReferenceCCMAAlgorithm::getNumberOfConstraints";
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
...@@ -417,11 +261,11 @@ int ReferenceRigidShakeAlgorithm::getNumberOfConstraints( void ) const { ...@@ -417,11 +261,11 @@ int ReferenceRigidShakeAlgorithm::getNumberOfConstraints( void ) const {
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
int ReferenceRigidShakeAlgorithm::getMaximumNumberOfIterations( void ) const { int ReferenceCCMAAlgorithm::getMaximumNumberOfIterations( void ) const {
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
// static const char* methodName = "\nReferenceQShakeAlgorithm::getMaximumNumberOfIterations"; // static const char* methodName = "\nReferenceCCMAAlgorithm::getMaximumNumberOfIterations";
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
...@@ -438,11 +282,11 @@ int ReferenceRigidShakeAlgorithm::getMaximumNumberOfIterations( void ) const { ...@@ -438,11 +282,11 @@ int ReferenceRigidShakeAlgorithm::getMaximumNumberOfIterations( void ) const {
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
int ReferenceRigidShakeAlgorithm::setMaximumNumberOfIterations( int maximumNumberOfIterations ){ int ReferenceCCMAAlgorithm::setMaximumNumberOfIterations( int maximumNumberOfIterations ){
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
// static const char* methodName = "\nReferenceQShakeAlgorithm::setMaximumNumberOfIterations"; // static const char* methodName = "\nReferenceCCMAAlgorithm::setMaximumNumberOfIterations";
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
...@@ -459,11 +303,11 @@ int ReferenceRigidShakeAlgorithm::setMaximumNumberOfIterations( int maximumNumbe ...@@ -459,11 +303,11 @@ int ReferenceRigidShakeAlgorithm::setMaximumNumberOfIterations( int maximumNumbe
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
RealOpenMM ReferenceRigidShakeAlgorithm::getTolerance( void ) const { RealOpenMM ReferenceCCMAAlgorithm::getTolerance( void ) const {
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
// static const char* methodName = "\nReferenceQShakeAlgorithm::getTolerance"; // static const char* methodName = "\nReferenceCCMAAlgorithm::getTolerance";
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
...@@ -480,12 +324,12 @@ RealOpenMM ReferenceRigidShakeAlgorithm::getTolerance( void ) const { ...@@ -480,12 +324,12 @@ RealOpenMM ReferenceRigidShakeAlgorithm::getTolerance( void ) const {
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
int ReferenceRigidShakeAlgorithm::setTolerance( RealOpenMM tolerance ){ int ReferenceCCMAAlgorithm::setTolerance( RealOpenMM tolerance ){
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
// static const char* methodName = "\nReferenceQShakeAlgorithm::setTolerance"; // static const char* methodName = "\nReferenceCCMAAlgorithm::setTolerance";
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
...@@ -497,7 +341,7 @@ int ReferenceRigidShakeAlgorithm::setTolerance( RealOpenMM tolerance ){ ...@@ -497,7 +341,7 @@ int ReferenceRigidShakeAlgorithm::setTolerance( RealOpenMM tolerance ){
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
Apply Shake algorithm Apply CCMA algorithm
@param numberOfAtoms number of atoms @param numberOfAtoms number of atoms
@param atomCoordinates atom coordinates @param atomCoordinates atom coordinates
...@@ -509,13 +353,13 @@ int ReferenceRigidShakeAlgorithm::setTolerance( RealOpenMM tolerance ){ ...@@ -509,13 +353,13 @@ int ReferenceRigidShakeAlgorithm::setTolerance( RealOpenMM tolerance ){
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
int ReferenceRigidShakeAlgorithm::apply( int numberOfAtoms, RealOpenMM** atomCoordinates, int ReferenceCCMAAlgorithm::apply( int numberOfAtoms, RealOpenMM** atomCoordinates,
RealOpenMM** atomCoordinatesP, RealOpenMM** atomCoordinatesP,
RealOpenMM* inverseMasses ){ RealOpenMM* inverseMasses ){
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
static const char* methodName = "\nReferenceQShakeAlgorithm::apply"; static const char* methodName = "\nReferenceCCMAAlgorithm::apply";
static const RealOpenMM zero = 0.0; static const RealOpenMM zero = 0.0;
static const RealOpenMM one = 1.0; static const RealOpenMM one = 1.0;
...@@ -570,8 +414,8 @@ int ReferenceRigidShakeAlgorithm::apply( int numberOfAtoms, RealOpenMM** atomCoo ...@@ -570,8 +414,8 @@ int ReferenceRigidShakeAlgorithm::apply( int numberOfAtoms, RealOpenMM** atomCoo
int iterations = 0; int iterations = 0;
int numberConverged = 0; int numberConverged = 0;
vector<RealOpenMM> constraintForce(_numberOfConstraints); vector<RealOpenMM> constraintDelta(_numberOfConstraints);
vector<RealOpenMM> tempForce(_numberOfConstraints); vector<RealOpenMM> tempDelta(_numberOfConstraints);
while (iterations < getMaximumNumberOfIterations()) { while (iterations < getMaximumNumberOfIterations()) {
numberConverged = 0; numberConverged = 0;
for( int ii = 0; ii < _numberOfConstraints; ii++ ){ for( int ii = 0; ii < _numberOfConstraints; ii++ ){
...@@ -586,14 +430,14 @@ int ReferenceRigidShakeAlgorithm::apply( int numberOfAtoms, RealOpenMM** atomCoo ...@@ -586,14 +430,14 @@ int ReferenceRigidShakeAlgorithm::apply( int numberOfAtoms, RealOpenMM** atomCoo
RealOpenMM rp2 = DOT3( rp_ij, rp_ij ); RealOpenMM rp2 = DOT3( rp_ij, rp_ij );
RealOpenMM dist2= _distance[ii]*_distance[ii]; RealOpenMM dist2= _distance[ii]*_distance[ii];
RealOpenMM diff = dist2 - rp2; RealOpenMM diff = dist2 - rp2;
constraintForce[ii] = zero; constraintDelta[ii] = zero;
RealOpenMM rrpr = DOT3( rp_ij, r_ij[ii] ); RealOpenMM rrpr = DOT3( rp_ij, r_ij[ii] );
if( rrpr < d_ij2[ii]*epsilon6 ){ if( rrpr < d_ij2[ii]*epsilon6 ){
std::stringstream message; std::stringstream message;
message << iterations <<" "<<atomI<<" "<<atomJ<< " Error: sign of rrpr < 0?\n"; message << iterations <<" "<<atomI<<" "<<atomJ<< " Error: sign of rrpr < 0?\n";
SimTKOpenMMLog::printMessage( message ); SimTKOpenMMLog::printMessage( message );
} else { } else {
constraintForce[ii] = reducedMasses[ii]*diff/rrpr; constraintDelta[ii] = reducedMasses[ii]*diff/rrpr;
} }
if (rp2 >= lowerTol*dist2 && rp2 <= upperTol*dist2) { if (rp2 >= lowerTol*dist2 && rp2 <= upperTol*dist2) {
numberConverged++; numberConverged++;
...@@ -608,35 +452,18 @@ int ReferenceRigidShakeAlgorithm::apply( int numberOfAtoms, RealOpenMM** atomCoo ...@@ -608,35 +452,18 @@ int ReferenceRigidShakeAlgorithm::apply( int numberOfAtoms, RealOpenMM** atomCoo
RealOpenMM sum = 0.0; RealOpenMM sum = 0.0;
for (int j = 0; j < (int) _matrix[i].size(); j++) { for (int j = 0; j < (int) _matrix[i].size(); j++) {
pair<int, RealOpenMM> element = _matrix[i][j]; pair<int, RealOpenMM> element = _matrix[i][j];
sum += element.second*constraintForce[element.first]; sum += element.second*constraintDelta[element.first];
} }
tempForce[i] = sum; tempDelta[i] = sum;
} }
constraintForce = tempForce; constraintDelta = tempDelta;
} }
// for (unsigned int i = 0; i < _rigidClusters.size(); i++) {
// const vector<int>& cluster = _rigidClusters[i];
// RealOpenMM** matrix = _matrices[i];
// unsigned int size = cluster.size();
// if (size > tempForce.size())
// tempForce.resize(size);
// for (unsigned int j = 0; j < size; j++) {
// tempForce[j] = zero;
// for (unsigned int k = 0; k < size; k++)
// tempForce[j] += matrix[j][k]*constraintForce[cluster[k]];
// }
// for (unsigned int j = 0; j < size; j++)
// constraintForce[cluster[j]] = tempForce[j];
//
// }
RealOpenMM damping = one;//(RealOpenMM) (iterations < 2 ? 0.5 : 1.0);
for( int ii = 0; ii < _numberOfConstraints; ii++ ){ for( int ii = 0; ii < _numberOfConstraints; ii++ ){
int atomI = _atomIndices[ii][0]; int atomI = _atomIndices[ii][0];
int atomJ = _atomIndices[ii][1]; int atomJ = _atomIndices[ii][1];
for( int jj = 0; jj < 3; jj++ ){ for( int jj = 0; jj < 3; jj++ ){
RealOpenMM dr = constraintForce[ii]*r_ij[ii][jj]*damping; RealOpenMM dr = constraintDelta[ii]*r_ij[ii][jj];
atomCoordinatesP[atomI][jj] += inverseMasses[atomI]*dr; atomCoordinatesP[atomI][jj] += inverseMasses[atomI]*dr;
atomCoordinatesP[atomJ][jj] -= inverseMasses[atomJ]*dr; atomCoordinatesP[atomJ][jj] -= inverseMasses[atomJ]*dr;
} }
...@@ -655,7 +482,7 @@ RealOpenMM damping = one;//(RealOpenMM) (iterations < 2 ? 0.5 : 1.0); ...@@ -655,7 +482,7 @@ RealOpenMM damping = one;//(RealOpenMM) (iterations < 2 ? 0.5 : 1.0);
message << " FAILED"; message << " FAILED";
} }
message << "\n"; message << "\n";
int errors = reportShake( numberOfAtoms, atomCoordinatesP, message ); int errors = reportCCMA( numberOfAtoms, atomCoordinatesP, message );
if( !errors ){ if( !errors ){
message << "*** no errors recorded in explicit check ***"; message << "*** no errors recorded in explicit check ***";
} }
...@@ -679,12 +506,12 @@ RealOpenMM damping = one;//(RealOpenMM) (iterations < 2 ? 0.5 : 1.0); ...@@ -679,12 +506,12 @@ RealOpenMM damping = one;//(RealOpenMM) (iterations < 2 ? 0.5 : 1.0);
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
int ReferenceRigidShakeAlgorithm::reportShake( int numberOfAtoms, RealOpenMM** atomCoordinates, int ReferenceCCMAAlgorithm::reportCCMA( int numberOfAtoms, RealOpenMM** atomCoordinates,
std::stringstream& message ){ std::stringstream& message ){
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
static const char* methodName = "\nReferenceQShakeAlgorithm::reportShake"; static const char* methodName = "\nReferenceCCMAAlgorithm::reportCCMA";
static const RealOpenMM zero = 0.0; static const RealOpenMM zero = 0.0;
static const RealOpenMM one = 1.0; static const RealOpenMM one = 1.0;
......
platforms/reference/src/SimTKReference/ReferenceRigidShakeAlgorithm.h → platforms/reference/src/SimTKReference/ReferenceCCMAAlgorithm.h
View file @ 05259f77
...@@ -22,8 +22,8 @@ ...@@ -22,8 +22,8 @@
* WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. * WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/ */
#ifndef __ReferenceQShakeAlgorithm_H__ #ifndef __ReferenceCCMAAlgorithm_H__
#define __ReferenceQShakeAlgorithm_H__ #define __ReferenceCCMAAlgorithm_H__
#include "ReferenceConstraintAlgorithm.h" #include "ReferenceConstraintAlgorithm.h"
#include <utility> #include <utility>
...@@ -32,7 +32,7 @@ ...@@ -32,7 +32,7 @@
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
class ReferenceRigidShakeAlgorithm : public ReferenceConstraintAlgorithm { class ReferenceCCMAAlgorithm : public ReferenceConstraintAlgorithm {
protected: protected:
...@@ -48,8 +48,6 @@ class ReferenceRigidShakeAlgorithm : public ReferenceConstraintAlgorithm { ...@@ -48,8 +48,6 @@ class ReferenceRigidShakeAlgorithm : public ReferenceConstraintAlgorithm {
RealOpenMM* _distanceTolerance; RealOpenMM* _distanceTolerance;
RealOpenMM* _reducedMasses; RealOpenMM* _reducedMasses;
bool _hasInitializedMasses; bool _hasInitializedMasses;
// std::vector<std::vector<int> > _rigidClusters;
// std::vector<RealOpenMM**> _matrices;
std::vector<std::vector<std::pair<int, RealOpenMM> > > _matrix; std::vector<std::vector<std::pair<int, RealOpenMM> > > _matrix;
public: public:
...@@ -57,17 +55,19 @@ class ReferenceRigidShakeAlgorithm : public ReferenceConstraintAlgorithm { ...@@ -57,17 +55,19 @@ class ReferenceRigidShakeAlgorithm : public ReferenceConstraintAlgorithm {
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
ReferenceQShakeAlgorithm constructor ReferenceCCMAAlgorithm constructor
@param numberOfAtoms number of atoms @param numberOfAtoms number of atoms
@param numberOfConstraints number of constraints @param numberOfConstraints number of constraints
@param atomIndices atom indices for contraints @param atomIndices atom indices for contraints
@param distance distances for constraints @param distance distances for constraints
@param masses atom masses
@param angles angle force field terms
@param tolerance constraint tolerance @param tolerance constraint tolerance
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
ReferenceRigidShakeAlgorithm( int numberOfAtoms, int numberOfConstraints, int** atomIndices, RealOpenMM* distance, RealOpenMM* masses, std::vector<AngleInfo>& angles, RealOpenMM tolerance ); ReferenceCCMAAlgorithm( int numberOfAtoms, int numberOfConstraints, int** atomIndices, RealOpenMM* distance, RealOpenMM* masses, std::vector<AngleInfo>& angles, RealOpenMM tolerance );
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
...@@ -75,7 +75,7 @@ class ReferenceRigidShakeAlgorithm : public ReferenceConstraintAlgorithm { ...@@ -75,7 +75,7 @@ class ReferenceRigidShakeAlgorithm : public ReferenceConstraintAlgorithm {
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
~ReferenceRigidShakeAlgorithm( ); ~ReferenceCCMAAlgorithm( );
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
...@@ -132,19 +132,7 @@ class ReferenceRigidShakeAlgorithm : public ReferenceConstraintAlgorithm { ...@@ -132,19 +132,7 @@ class ReferenceRigidShakeAlgorithm : public ReferenceConstraintAlgorithm {
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
Print parameters Apply CCMA algorithm
@param message message
@return ReferenceQShakeAlgorithm::DefaultReturn
--------------------------------------------------------------------------------------- */
int printParameters( std::stringstream& message ) const;
/**---------------------------------------------------------------------------------------
Apply Shake algorithm
@param numberOfAtoms number of atoms @param numberOfAtoms number of atoms
@param atomCoordinates atom coordinates @param atomCoordinates atom coordinates
...@@ -171,10 +159,10 @@ class ReferenceRigidShakeAlgorithm : public ReferenceConstraintAlgorithm { ...@@ -171,10 +159,10 @@ class ReferenceRigidShakeAlgorithm : public ReferenceConstraintAlgorithm {
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
int reportShake( int numberOfAtoms, RealOpenMM** atomCoordinates, std::stringstream& message ); int reportCCMA( int numberOfAtoms, RealOpenMM** atomCoordinates, std::stringstream& message );
}; };
class ReferenceRigidShakeAlgorithm::AngleInfo class ReferenceCCMAAlgorithm::AngleInfo
{ {
public: public:
int atom1, atom2, atom3; int atom1, atom2, atom3;
...@@ -187,4 +175,4 @@ public: ...@@ -187,4 +175,4 @@ public:
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
#endif // __ReferenceQShakeAlgorithm_H__ #endif // __ReferenceCCMAAlgorithm_H__
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