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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
invMass1[i] = 1.0f/mass[particle1Index];
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.
......@@ -438,7 +438,7 @@ void CudaIntegrateVerletStepKernel::execute(OpenMMContextImpl& context, const Ve
kVerletUpdatePart1(gpu);
kApplyFirstShake(gpu);
kApplyFirstSettle(gpu);
kApplyFirstCShake(gpu);
kApplyFirstCCMA(gpu);
if (data.removeCM) {
int step = (int) (context.getTime()/stepSize);
if (step%data.cmMotionFrequency == 0)
......@@ -477,7 +477,7 @@ void CudaIntegrateLangevinStepKernel::execute(OpenMMContextImpl& context, const
kUpdatePart1(gpu);
kApplyFirstShake(gpu);
kApplyFirstSettle(gpu);
kApplyFirstCShake(gpu);
kApplyFirstCCMA(gpu);
if (data.removeCM) {
int step = (int) (context.getTime()/stepSize);
if (step%data.cmMotionFrequency == 0)
......@@ -486,7 +486,7 @@ void CudaIntegrateLangevinStepKernel::execute(OpenMMContextImpl& context, const
kUpdatePart2(gpu);
kApplySecondShake(gpu);
kApplySecondSettle(gpu);
kApplySecondCShake(gpu);
kApplySecondCCMA(gpu);
}
CudaIntegrateBrownianStepKernel::~CudaIntegrateBrownianStepKernel() {
......@@ -519,7 +519,7 @@ void CudaIntegrateBrownianStepKernel::execute(OpenMMContextImpl& context, const
kBrownianUpdatePart1(gpu);
kApplyFirstShake(gpu);
kApplyFirstSettle(gpu);
kApplyFirstCShake(gpu);
kApplyFirstCCMA(gpu);
if (data.removeCM) {
int step = (int) (context.getTime()/stepSize);
if (step%data.cmMotionFrequency == 0)
......
platforms/cuda/src/kernels/cudaKernels.h
View file @ 05259f77
......@@ -42,14 +42,12 @@ extern void kCalculateAndersenThermostat(gpuContext gpu);
extern void kReduceBornSumAndForces(gpuContext gpu);
extern void kUpdatePart1(gpuContext gpu);
extern void kApplyFirstShake(gpuContext gpu);
extern void kApplyFirstCShake(gpuContext gpu);
extern void kApplyFirstCCMA(gpuContext gpu);
extern void kApplyFirstSettle(gpuContext gpu);
extern void kApplyFirstLincs(gpuContext gpu);
extern void kUpdatePart2(gpuContext gpu);
extern void kApplySecondShake(gpuContext gpu);
extern void kApplySecondCShake(gpuContext gpu);
extern void kApplySecondCCMA(gpuContext gpu);
extern void kApplySecondSettle(gpuContext gpu);
extern void kApplySecondLincs(gpuContext gpu);
extern void kVerletUpdatePart1(gpuContext gpu);
extern void kVerletUpdatePart2(gpuContext gpu);
extern void kBrownianUpdatePart1(gpuContext gpu);
......@@ -78,10 +76,8 @@ extern void SetUpdateShakeHSim(gpuContext gpu);
extern void GetUpdateShakeHSim(gpuContext gpu);
extern void SetSettleSim(gpuContext gpu);
extern void GetSettleSim(gpuContext gpu);
extern void SetCShakeSim(gpuContext gpu);
extern void GetCShakeSim(gpuContext gpu);
extern void SetLincsSim(gpuContext gpu);
extern void GetLincsSim(gpuContext gpu);
extern void SetCCMASim(gpuContext gpu);
extern void GetCCMASim(gpuContext gpu);
extern void SetVerletUpdateSim(gpuContext gpu);
extern void GetVerletUpdateSim(gpuContext gpu);
extern void SetBrownianUpdateSim(gpuContext gpu);
......
platforms/cuda/src/kernels/cudatypes.h
View file @ 05259f77
......@@ -258,7 +258,7 @@ struct cudaGmxSimulation {
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 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 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
......@@ -360,7 +360,7 @@ struct cudaGmxSimulation {
float inverseTotalMass; // Used in linear momentum removal
unsigned int ShakeConstraints; // Total number of Shake 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 maxRigidClusterSize; // The size of the largest rigid cluster
unsigned int clusterShakeBlockSize; // The number of threads to process each rigid cluster
......@@ -368,7 +368,6 @@ struct cudaGmxSimulation {
unsigned int maxShakeIterations; // Maximum shake iterations
unsigned int degreesOfFreedom; // Number of degrees of freedom in system
float shakeTolerance; // Shake tolerance
unsigned int lincsTerms; // Number of terms in the matrix expansion for LINCS
float InvMassJ; // Shake inverse mass for hydrogens
int* pNonShakeID; // Not Shaking atoms
int4* pShakeID; // Shake atoms and phase
......@@ -385,23 +384,15 @@ struct cudaGmxSimulation {
int* pAtomIndex; // The original index of each atom
float4* pGridBoundingBox; // The size of each grid cell
float4* pGridCenter; // The center of each grid cell
int2* pLincsAtoms; // The atoms connected by each LINCS constraint
float4* pLincsDistance; // The displacement vector (x, y, z) and constraint distance (w) for each LINCS constraint
int* pLincsConnections; // The indices of constraints that other constraints are connected to
int* pLincsNumConnections; // The number of other constraints that each constraint is linked to
float* pLincsS; // S matrix for LINCS
float* pLincsCoupling; // Coupling matrix for LINCS
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
int2* pCcmaAtoms; // The atoms connected by each CCMA constraint
float4* pCcmaDistance; // The displacement vector (x, y, z) and constraint distance (w) for each CCMA constraint
float* pCcmaDelta1; // Workspace for CCMA
float* pCcmaDelta2; // Workspace for CCMA
int* pCcmaAtomConstraints; // The indices of constraints involving each atom
int* pCcmaNumAtomConstraints; // The number of constraints involving each atom
short* pSyncCounter; // Used for global thread synchronization
unsigned int* pRequiredIterations; // Used by SHAKE to communicate whether iteration has converged
float* pShakeReducedMass; // The reduced mass for each SHAKE constraint
float* pRigidClusterMatrix; // The inverse constraint matrix for each rigid cluster
unsigned int* pRigidClusterConstraintIndex; // The index of each cluster in the stream containing cluster constraints.
unsigned int* pRigidClusterMatrixIndex; // The index of each cluster in the stream containing cluster matrices.
unsigned int* pRequiredIterations; // Used by CCMA to communicate whether iteration has converged
float* pCcmaReducedMass; // The reduced mass for each CCMA constraint
unsigned int* pConstraintMatrixColumn; // The column of each element in the constraint matrix.
float* pConstraintMatrixValue; // The value of each element in the constraint matrix.
......
platforms/cuda/src/kernels/gpu.cpp
View file @ 05259f77
This diff is collapsed.
platforms/cuda/src/kernels/gputypes.h
View file @ 05259f77
......@@ -127,20 +127,15 @@ struct _gpuContext {
CUDAStream<int>* psAtomIndex; // The original index of each atom
CUDAStream<float4>* psGridBoundingBox; // The size of 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<float4>* psLincsDistance; // The displacement vector (x, y, z) and constraint distance (w) for each LINCS constraint
CUDAStream<int>* psLincsConnections; // The indices of constraints that other constraints are connected to
CUDAStream<int>* psLincsNumConnections; // The number of other constraints that each constraint is linked to
CUDAStream<int>* psLincsAtomConstraints; // The indices of constraints involving each atom
CUDAStream<int>* psLincsNumAtomConstraints; // The number of constraints involving each atom
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<int2>* psCcmaAtoms; // The atoms connected by each CCMA constraint
CUDAStream<float4>* psCcmaDistance; // The displacement vector (x, y, z) and constraint distance (w) for each CCMA constraint
CUDAStream<int>* psCcmaAtomConstraints; // The indices of constraints involving each atom
CUDAStream<int>* psCcmaNumAtomConstraints; // The number of constraints involving each atom
CUDAStream<float>* psCcmaDelta1; // Workspace for CCMA
CUDAStream<float>* psCcmaDelta2; // Workspace for CCMA
CUDAStream<short>* psSyncCounter; // Used for global thread synchronization
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<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.
......@@ -192,7 +187,7 @@ void gpuSetObcParameters(gpuContext gpu, float innerDielectric, float solventDie
extern "C"
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"
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;
static __constant__ cudaGmxSimulation cSim;
void SetCShakeSim(gpuContext gpu)
void SetCCMASim(gpuContext gpu)
{
cudaError_t status;
status = cudaMemcpyToSymbol(cSim, &gpu->sim, sizeof(cudaGmxSimulation));
RTERROR(status, "cudaMemcpyToSymbol: SetSim copy to cSim failed");
}
void GetCShakeSim(gpuContext gpu)
void GetCCMASim(gpuContext gpu)
{
cudaError_t status;
status = cudaMemcpyFromSymbol(&gpu->sim, cSim, sizeof(cudaGmxSimulation));
......@@ -66,7 +66,7 @@ __device__ void kSyncAllThreads_kernel(short* syncCounter, short newCount)
__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.
......@@ -82,16 +82,16 @@ __global__ void kApplyCShake_kernel(float4* atomPositions, bool addOldPosition)
// Calculate the direction of each constraint.
unsigned int pos = threadIdx.x + blockIdx.x * blockDim.x;
while (pos < cSim.lincsConstraints)
while (pos < cSim.ccmaConstraints)
{
int2 atoms = cSim.pLincsAtoms[pos];
float4 dir = cSim.pLincsDistance[pos];
int2 atoms = cSim.pCcmaAtoms[pos];
float4 dir = cSim.pCcmaDistance[pos];
float4 oldPos1 = cSim.pOldPosq[atoms.x];
float4 oldPos2 = cSim.pOldPosq[atoms.y];
dir.x = oldPos1.x-oldPos2.x;
dir.y = oldPos1.y-oldPos2.y;
dir.z = oldPos1.z-oldPos2.z;
cSim.pLincsDistance[pos] = dir;
cSim.pCcmaDistance[pos] = dir;
pos += blockDim.x*gridDim.x;
}
__syncthreads();
......@@ -106,12 +106,12 @@ __global__ void kApplyCShake_kernel(float4* atomPositions, bool addOldPosition)
// Calculate the constraint force for each constraint.
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 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);
if (addOldPosition)
{
......@@ -124,8 +124,8 @@ __global__ void kApplyCShake_kernel(float4* atomPositions, bool addOldPosition)
float diff = dist2 - rp2;
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 reducedMass = cSim.pShakeReducedMass[pos];
cSim.pLincsRhs1[pos] = (rrpr > d_ij2*1e-6f ? reducedMass*diff/rrpr : 0.0f);
float reducedMass = cSim.pCcmaReducedMass[pos];
cSim.pCcmaDelta1[pos] = (rrpr > d_ij2*1e-6f ? reducedMass*diff/rrpr : 0.0f);
if (requiredIterations == iteration && (rp2 < lowerTol*dist2 || rp2 > upperTol*dist2))
requiredIterations = iteration+1;
pos += blockDim.x * gridDim.x;
......@@ -140,18 +140,18 @@ __global__ void kApplyCShake_kernel(float4* atomPositions, bool addOldPosition)
// Multiply by the inverse constraint matrix.
pos = threadIdx.x + blockIdx.x * blockDim.x;
while (pos < cSim.lincsConstraints)
while (pos < cSim.ccmaConstraints)
{
float sum = 0.0f;
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];
if (column >= cSim.lincsConstraints)
if (column >= cSim.ccmaConstraints)
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;
}
kSyncAllThreads_kernel(&cSim.pSyncCounter[gridDim.x], iteration);
......@@ -164,16 +164,16 @@ __global__ void kApplyCShake_kernel(float4* atomPositions, bool addOldPosition)
{
float4 atomPos = atomPositions[pos];
float invMass = cSim.pVelm4[pos].w;
int num = cSim.pLincsNumAtomConstraints[pos];
int num = cSim.pCcmaNumAtomConstraints[pos];
for (int i = 0; i < num; i++)
{
int index = pos+i*cSim.atoms;
int constraint = cSim.pLincsAtomConstraints[index];
int constraint = cSim.pCcmaAtomConstraints[index];
bool forward = (constraint > 0);
constraint = (forward ? constraint-1 : -constraint-1);
float constraintForce = damping*invMass*cSim.pLincsSolution[constraint];
float constraintForce = damping*invMass*cSim.pCcmaDelta2[constraint];
constraintForce = (forward ? constraintForce : -constraintForce);
float4 dir = cSim.pLincsDistance[constraint];
float4 dir = cSim.pCcmaDistance[constraint];
atomPos.x += constraintForce*dir.x;
atomPos.y += constraintForce*dir.y;
atomPos.z += constraintForce*dir.z;
......@@ -192,22 +192,22 @@ __global__ void kApplyCShake_kernel(float4* atomPositions, bool addOldPosition)
cSim.pSyncCounter[blockIdx.x] = -1;
}
void kApplyFirstCShake(gpuContext gpu)
void kApplyFirstCCMA(gpuContext gpu)
{
// printf("kApplyFirstCShake\n");
if (gpu->sim.lincsConstraints > 0)
// printf("kApplyFirstCCMA\n");
if (gpu->sim.ccmaConstraints > 0)
{
kApplyCShake_kernel<<<gpu->sim.blocks, gpu->sim.lincs_threads_per_block>>>(gpu->sim.pPosqP, true);
LAUNCHERROR("kApplyCShake");
kApplyCCMA_kernel<<<gpu->sim.blocks, gpu->sim.ccma_threads_per_block>>>(gpu->sim.pPosqP, true);
LAUNCHERROR("kApplyCCMA");
}
}
void kApplySecondCShake(gpuContext gpu)
void kApplySecondCCMA(gpuContext gpu)
{
// printf("kApplySecondCShake\n");
if (gpu->sim.lincsConstraints > 0)
// printf("kApplySecondCCMA\n");
if (gpu->sim.ccmaConstraints > 0)
{
kApplyCShake_kernel<<<gpu->sim.blocks, gpu->sim.lincs_threads_per_block>>>(gpu->sim.pPosq, false);
LAUNCHERROR("kApplyCShake");
kApplyCCMA_kernel<<<gpu->sim.blocks, gpu->sim.ccma_threads_per_block>>>(gpu->sim.pPosq, false);
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 @@
#include "SimTKReference/ReferenceBondForce.h"
#include "SimTKReference/ReferenceBrownianDynamics.h"
#include "SimTKReference/ReferenceHarmonicBondIxn.h"
#include "SimTKReference/ReferenceLincsAlgorithm.h"
#include "SimTKReference/ReferenceLJCoulomb14.h"
#include "SimTKReference/ReferenceLJCoulombIxn.h"
#include "SimTKReference/ReferenceProperDihedralBond.h"
#include "SimTKReference/ReferenceRbDihedralBond.h"
#include "SimTKReference/ReferenceStochasticDynamics.h"
#include "SimTKReference/ReferenceRigidShakeAlgorithm.h"
#include "SimTKReference/ReferenceShakeAlgorithm.h"
#include "SimTKReference/ReferenceCCMAAlgorithm.h"
#include "SimTKReference/ReferenceVerletDynamics.h"
#include "openmm/CMMotionRemover.h"
#include "openmm/System.h"
......@@ -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++) {
const HarmonicAngleForce* force = dynamic_cast<const HarmonicAngleForce*>(&system.getForce(i));
if (force != NULL) {
......@@ -116,7 +114,7 @@ static void findAnglesForShake(const System& system, vector<ReferenceRigidShakeA
int atom1, atom2, atom3;
double 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
delete constraints;
}
dynamics = new ReferenceVerletDynamics(context.getSystem().getNumParticles(), static_cast<RealOpenMM>(stepSize) );
vector<ReferenceRigidShakeAlgorithm::AngleInfo> angles;
findAnglesForShake(context.getSystem(), angles);
constraints = new ReferenceRigidShakeAlgorithm(context.getSystem().getNumParticles(), numConstraints, constraintIndices, constraintDistances, masses, angles, (RealOpenMM)integrator.getConstraintTolerance());
vector<ReferenceCCMAAlgorithm::AngleInfo> angles;
findAnglesForCCMA(context.getSystem(), angles);
constraints = new ReferenceCCMAAlgorithm(context.getSystem().getNumParticles(), numConstraints, constraintIndices, constraintDistances, masses, angles, (RealOpenMM)integrator.getConstraintTolerance());
dynamics->setReferenceConstraintAlgorithm(constraints);
prevStepSize = stepSize;
}
......@@ -684,9 +682,9 @@ void ReferenceIntegrateLangevinStepKernel::execute(OpenMMContextImpl& context, c
static_cast<RealOpenMM>(stepSize),
static_cast<RealOpenMM>(tau),
static_cast<RealOpenMM>(temperature) );
vector<ReferenceRigidShakeAlgorithm::AngleInfo> angles;
findAnglesForShake(context.getSystem(), angles);
constraints = new ReferenceRigidShakeAlgorithm(context.getSystem().getNumParticles(), numConstraints, constraintIndices, constraintDistances, masses, angles, (RealOpenMM)integrator.getConstraintTolerance());
vector<ReferenceCCMAAlgorithm::AngleInfo> angles;
findAnglesForCCMA(context.getSystem(), angles);
constraints = new ReferenceCCMAAlgorithm(context.getSystem().getNumParticles(), numConstraints, constraintIndices, constraintDistances, masses, angles, (RealOpenMM)integrator.getConstraintTolerance());
dynamics->setReferenceConstraintAlgorithm(constraints);
prevTemp = temperature;
prevFriction = friction;
......@@ -746,9 +744,9 @@ void ReferenceIntegrateBrownianStepKernel::execute(OpenMMContextImpl& context, c
static_cast<RealOpenMM>(stepSize),
static_cast<RealOpenMM>(friction),
static_cast<RealOpenMM>(temperature) );
vector<ReferenceRigidShakeAlgorithm::AngleInfo> angles;
findAnglesForShake(context.getSystem(), angles);
constraints = new ReferenceRigidShakeAlgorithm(context.getSystem().getNumParticles(), numConstraints, constraintIndices, constraintDistances, masses, angles, (RealOpenMM)integrator.getConstraintTolerance());
vector<ReferenceCCMAAlgorithm::AngleInfo> angles;
findAnglesForCCMA(context.getSystem(), angles);
constraints = new ReferenceCCMAAlgorithm(context.getSystem().getNumParticles(), numConstraints, constraintIndices, constraintDistances, masses, angles, (RealOpenMM)integrator.getConstraintTolerance());
dynamics->setReferenceConstraintAlgorithm(constraints);
prevTemp = temperature;
prevFriction = friction;
......
platforms/reference/src/SimTKReference/ReferenceRigidShakeAlgorithm.cpp → platforms/reference/src/SimTKReference/ReferenceCCMAAlgorithm.cpp
View file @ 05259f77
......@@ -28,9 +28,8 @@
#include "../SimTKUtilities/SimTKOpenMMCommon.h"
#include "../SimTKUtilities/SimTKOpenMMUtilities.h"
#include "../SimTKUtilities/SimTKOpenMMLog.h"
#include "ReferenceRigidShakeAlgorithm.h"
#include "ReferenceCCMAAlgorithm.h"
#include "ReferenceDynamics.h"
#include "jama_svd.h"
#include "quern.h"
#include "openmm/Vec3.h"
#include <map>
......@@ -40,22 +39,22 @@ using std::pair;
using std::vector;
using std::set;
using OpenMM::Vec3;
using TNT::Array2D;
using JAMA::SVD;
/**---------------------------------------------------------------------------------------
ReferenceQShakeAlgorithm constructor
ReferenceCCMAAlgorithm constructor
@param numberOfAtoms number of atoms
@param numberOfConstraints number of constraints
@param atomIndices block of atom indices
@param shakeParameters Shake parameters
@param atomIndices atom indices for contraints
@param distance distances for constraints
@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** atomIndices,
RealOpenMM* distance,
......@@ -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 one = 1.0;
......@@ -201,181 +200,26 @@ ReferenceRigidShakeAlgorithm::ReferenceRigidShakeAlgorithm( int numberOfAtoms,
QUERN_solve_with_r(numberOfConstraints, rRowStart, rColIndex, rValue, &rhs[0], &rhs[0]);
for (int j = 0; j < numberOfConstraints; 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));
}
}
QUERN_free_result(qRowStart, qColIndex, qValue);
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( ){
--------------------------------------------------------------------------------------- */
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 {
--------------------------------------------------------------------------------------- */
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 {
--------------------------------------------------------------------------------------- */
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
--------------------------------------------------------------------------------------- */
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 {
--------------------------------------------------------------------------------------- */
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 ){
/**---------------------------------------------------------------------------------------
Apply Shake algorithm
Apply CCMA algorithm
@param numberOfAtoms number of atoms
@param atomCoordinates atom coordinates
......@@ -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* inverseMasses ){
// ---------------------------------------------------------------------------------------
static const char* methodName = "\nReferenceQShakeAlgorithm::apply";
static const char* methodName = "\nReferenceCCMAAlgorithm::apply";
static const RealOpenMM zero = 0.0;
static const RealOpenMM one = 1.0;
......@@ -570,8 +414,8 @@ int ReferenceRigidShakeAlgorithm::apply( int numberOfAtoms, RealOpenMM** atomCoo
int iterations = 0;
int numberConverged = 0;
vector<RealOpenMM> constraintForce(_numberOfConstraints);
vector<RealOpenMM> tempForce(_numberOfConstraints);
vector<RealOpenMM> constraintDelta(_numberOfConstraints);
vector<RealOpenMM> tempDelta(_numberOfConstraints);
while (iterations < getMaximumNumberOfIterations()) {
numberConverged = 0;
for( int ii = 0; ii < _numberOfConstraints; ii++ ){
......@@ -586,14 +430,14 @@ int ReferenceRigidShakeAlgorithm::apply( int numberOfAtoms, RealOpenMM** atomCoo
RealOpenMM rp2 = DOT3( rp_ij, rp_ij );
RealOpenMM dist2= _distance[ii]*_distance[ii];
RealOpenMM diff = dist2 - rp2;
constraintForce[ii] = zero;
constraintDelta[ii] = zero;
RealOpenMM rrpr = DOT3( rp_ij, r_ij[ii] );
if( rrpr < d_ij2[ii]*epsilon6 ){
std::stringstream message;
message << iterations <<" "<<atomI<<" "<<atomJ<< " Error: sign of rrpr < 0?\n";
SimTKOpenMMLog::printMessage( message );
} else {
constraintForce[ii] = reducedMasses[ii]*diff/rrpr;
constraintDelta[ii] = reducedMasses[ii]*diff/rrpr;
}
if (rp2 >= lowerTol*dist2 && rp2 <= upperTol*dist2) {
numberConverged++;
......@@ -608,35 +452,18 @@ int ReferenceRigidShakeAlgorithm::apply( int numberOfAtoms, RealOpenMM** atomCoo
RealOpenMM sum = 0.0;
for (int j = 0; j < (int) _matrix[i].size(); j++) {
pair<int, RealOpenMM> element = _matrix[i][j];
sum += element.second*constraintForce[element.first];
}
tempForce[i] = sum;
}
constraintForce = tempForce;
}
// 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);
sum += element.second*constraintDelta[element.first];
}
tempDelta[i] = sum;
}
constraintDelta = tempDelta;
}
for( int ii = 0; ii < _numberOfConstraints; ii++ ){
int atomI = _atomIndices[ii][0];
int atomJ = _atomIndices[ii][1];
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[atomJ][jj] -= inverseMasses[atomJ]*dr;
}
......@@ -655,7 +482,7 @@ RealOpenMM damping = one;//(RealOpenMM) (iterations < 2 ? 0.5 : 1.0);
message << " FAILED";
}
message << "\n";
int errors = reportShake( numberOfAtoms, atomCoordinatesP, message );
int errors = reportCCMA( numberOfAtoms, atomCoordinatesP, message );
if( !errors ){
message << "*** no errors recorded in explicit check ***";
}
......@@ -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 ){
// ---------------------------------------------------------------------------------------
static const char* methodName = "\nReferenceQShakeAlgorithm::reportShake";
static const char* methodName = "\nReferenceCCMAAlgorithm::reportCCMA";
static const RealOpenMM zero = 0.0;
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 @@
* WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/
#ifndef __ReferenceQShakeAlgorithm_H__
#define __ReferenceQShakeAlgorithm_H__
#ifndef __ReferenceCCMAAlgorithm_H__
#define __ReferenceCCMAAlgorithm_H__
#include "ReferenceConstraintAlgorithm.h"
#include <utility>
......@@ -32,7 +32,7 @@
// ---------------------------------------------------------------------------------------
class ReferenceRigidShakeAlgorithm : public ReferenceConstraintAlgorithm {
class ReferenceCCMAAlgorithm : public ReferenceConstraintAlgorithm {
protected:
......@@ -48,8 +48,6 @@ class ReferenceRigidShakeAlgorithm : public ReferenceConstraintAlgorithm {
RealOpenMM* _distanceTolerance;
RealOpenMM* _reducedMasses;
bool _hasInitializedMasses;
// std::vector<std::vector<int> > _rigidClusters;
// std::vector<RealOpenMM**> _matrices;
std::vector<std::vector<std::pair<int, RealOpenMM> > > _matrix;
public:
......@@ -57,17 +55,19 @@ class ReferenceRigidShakeAlgorithm : public ReferenceConstraintAlgorithm {
/**---------------------------------------------------------------------------------------
ReferenceQShakeAlgorithm constructor
ReferenceCCMAAlgorithm constructor
@param numberOfAtoms number of atoms
@param numberOfConstraints number of constraints
@param atomIndices atom indices for contraints
@param distance distances for constraints
@param masses atom masses
@param angles angle force field terms
@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 {
--------------------------------------------------------------------------------------- */
~ReferenceRigidShakeAlgorithm( );
~ReferenceCCMAAlgorithm( );
/**---------------------------------------------------------------------------------------
......@@ -132,19 +132,7 @@ class ReferenceRigidShakeAlgorithm : public ReferenceConstraintAlgorithm {
/**---------------------------------------------------------------------------------------
Print parameters
@param message message
@return ReferenceQShakeAlgorithm::DefaultReturn
--------------------------------------------------------------------------------------- */
int printParameters( std::stringstream& message ) const;
/**---------------------------------------------------------------------------------------
Apply Shake algorithm
Apply CCMA algorithm
@param numberOfAtoms number of atoms
@param atomCoordinates atom coordinates
......@@ -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:
int atom1, atom2, atom3;
......@@ -187,4 +175,4 @@ public:
// ---------------------------------------------------------------------------------------
#endif // __ReferenceQShakeAlgorithm_H__
#endif // __ReferenceCCMAAlgorithm_H__
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