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Commit bc71de2c authored by Peter Eastman's avatar Peter Eastman
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Bug fixes to BAOABLangevinIntegrator

parent a4bf00ee
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Showing with 76 additions and 26 deletions
platforms/cuda/include/CudaKernels.h
View file @ bc71de2c
......@@ -1437,7 +1437,7 @@ private:
CudaContext& cu;
double prevTemp, prevFriction, prevStepSize;
CudaArray params, oldDelta;
CUfunction kernel1, kernel2, kernel3;
CUfunction kernel1, kernel2, kernel3, kernel4;
};
/**
......
platforms/cuda/src/CudaKernels.cpp
View file @ bc71de2c
......@@ -7152,6 +7152,7 @@ void CudaIntegrateBAOABStepKernel::initialize(const System& system, const BAOABL
kernel1 = cu.getKernel(module, "integrateBAOABPart1");
kernel2 = cu.getKernel(module, "integrateBAOABPart2");
kernel3 = cu.getKernel(module, "integrateBAOABPart3");
kernel4 = cu.getKernel(module, "integrateBAOABPart4");
if (cu.getUseDoublePrecision() || cu.getUseMixedPrecision()) {
params.initialize<double>(cu, 3, "baoabParams");
oldDelta.initialize<double4>(cu, cu.getPaddedNumAtoms(), "oldDelta");
......@@ -7202,11 +7203,13 @@ void CudaIntegrateBAOABStepKernel::execute(ContextImpl& context, const BAOABLang
&oldDelta.getDevicePointer(), &params.getDevicePointer(), &integration.getStepSize().getDevicePointer(), &integration.getRandom().getDevicePointer(), &randomIndex};
cu.executeKernel(kernel2, args2, numAtoms, 128);
integration.applyConstraints(integrator.getConstraintTolerance());
context.calcForcesAndEnergy(true, false);
void* args3[] = {&numAtoms, &paddedNumAtoms, &cu.getPosq().getDevicePointer(), &posCorrection, &cu.getVelm().getDevicePointer(),
&cu.getForce().getDevicePointer(), &integration.getPosDelta().getDevicePointer(),
&oldDelta.getDevicePointer(), &integration.getStepSize().getDevicePointer()};
void* args3[] = {&numAtoms, &cu.getPosq().getDevicePointer(), &posCorrection, &cu.getVelm().getDevicePointer(),
&integration.getPosDelta().getDevicePointer(), &oldDelta.getDevicePointer(), &integration.getStepSize().getDevicePointer()};
cu.executeKernel(kernel3, args3, numAtoms, 128);
context.calcForcesAndEnergy(true, false);
void* args4[] = {&numAtoms, &paddedNumAtoms, &cu.getVelm().getDevicePointer(),
&cu.getForce().getDevicePointer(), &integration.getStepSize().getDevicePointer()};
cu.executeKernel(kernel4, args4, numAtoms, 128);
integration.applyVelocityConstraints(integrator.getConstraintTolerance());
integration.computeVirtualSites();
......@@ -7215,6 +7218,8 @@ void CudaIntegrateBAOABStepKernel::execute(ContextImpl& context, const BAOABLang
cu.setTime(cu.getTime()+stepSize);
cu.setStepCount(cu.getStepCount()+1);
cu.reorderAtoms();
if (cu.getAtomsWereReordered())
forcesAreValid = false;
// Reduce UI lag.
......
platforms/cuda/src/kernels/baoab.cu
View file @ bc71de2c
......@@ -75,18 +75,17 @@ extern "C" __global__ void integrateBAOABPart2(int numAtoms, real4* __restrict__
* Perform the third step of BAOAB integration.
*/
extern "C" __global__ void integrateBAOABPart3(int numAtoms, int paddedNumAtoms, real4* __restrict__ posq, real4* __restrict__ posqCorrection, mixed4* __restrict__ velm,
const long long* __restrict__ force, mixed4* __restrict__ posDelta, mixed4* __restrict__ oldDelta, const mixed2* __restrict__ dt) {
extern "C" __global__ void integrateBAOABPart3(int numAtoms, real4* __restrict__ posq, real4* __restrict__ posqCorrection, mixed4* __restrict__ velm,
mixed4* __restrict__ posDelta, mixed4* __restrict__ oldDelta, const mixed2* __restrict__ dt) {
mixed halfdt = 0.5*dt[0].y;
mixed invHalfdt = 1/halfdt;
mixed fscale = halfdt/(mixed) 0x100000000;
for (int index = blockIdx.x*blockDim.x+threadIdx.x; index < numAtoms; index += blockDim.x*gridDim.x) {
mixed4 velocity = velm[index];
if (velocity.w != 0.0) {
mixed4 delta = posDelta[index];
velocity.x += (delta.x-oldDelta[index].x)*invHalfdt + fscale*velocity.w*force[index];
velocity.y += (delta.y-oldDelta[index].y)*invHalfdt + fscale*velocity.w*force[index+paddedNumAtoms];
velocity.z += (delta.z-oldDelta[index].z)*invHalfdt + fscale*velocity.w*force[index+paddedNumAtoms*2];
velocity.x += (delta.x-oldDelta[index].x)*invHalfdt;
velocity.y += (delta.y-oldDelta[index].y)*invHalfdt;
velocity.z += (delta.z-oldDelta[index].z)*invHalfdt;
velm[index] = velocity;
#ifdef USE_MIXED_PRECISION
real4 pos1 = posq[index];
......@@ -107,3 +106,22 @@ extern "C" __global__ void integrateBAOABPart3(int numAtoms, int paddedNumAtoms,
}
}
}
/**
* Perform the fourth step of BAOAB integration.
*/
extern "C" __global__ void integrateBAOABPart4(int numAtoms, int paddedNumAtoms, mixed4* __restrict__ velm,
const long long* __restrict__ force, const mixed2* __restrict__ dt) {
mixed halfdt = 0.5*dt[0].y;
mixed fscale = halfdt/(mixed) 0x100000000;
for (int index = blockIdx.x*blockDim.x+threadIdx.x; index < numAtoms; index += blockDim.x*gridDim.x) {
mixed4 velocity = velm[index];
if (velocity.w != 0.0) {
velocity.x += fscale*velocity.w*force[index];
velocity.y += fscale*velocity.w*force[index+paddedNumAtoms];
velocity.z += fscale*velocity.w*force[index+paddedNumAtoms*2];
velm[index] = velocity;
}
}
}
platforms/opencl/include/OpenCLKernels.h
View file @ bc71de2c
......@@ -1421,7 +1421,7 @@ private:
double prevTemp, prevFriction, prevStepSize;
bool hasInitializedKernels;
OpenCLArray params, oldDelta;
cl::Kernel kernel1, kernel2, kernel3;
cl::Kernel kernel1, kernel2, kernel3, kernel4;
};
/**
......
platforms/opencl/src/OpenCLKernels.cpp
View file @ bc71de2c
......@@ -7483,6 +7483,7 @@ void OpenCLIntegrateBAOABStepKernel::initialize(const System& system, const BAOA
kernel1 = cl::Kernel(program, "integrateBAOABPart1");
kernel2 = cl::Kernel(program, "integrateBAOABPart2");
kernel3 = cl::Kernel(program, "integrateBAOABPart3");
kernel4 = cl::Kernel(program, "integrateBAOABPart4");
if (cl.getUseDoublePrecision() || cl.getUseMixedPrecision()) {
params.initialize<cl_double>(cl, 2, "baoabParams");
oldDelta.initialize<mm_double4>(cl, cl.getPaddedNumAtoms(), "oldDelta");
......@@ -7515,10 +7516,12 @@ void OpenCLIntegrateBAOABStepKernel::execute(ContextImpl& context, const BAOABLa
kernel3.setArg<cl::Buffer>(0, cl.getPosq().getDeviceBuffer());
setPosqCorrectionArg(cl, kernel3, 1);
kernel3.setArg<cl::Buffer>(2, cl.getVelm().getDeviceBuffer());
kernel3.setArg<cl::Buffer>(3, cl.getForce().getDeviceBuffer());
kernel3.setArg<cl::Buffer>(4, integration.getPosDelta().getDeviceBuffer());
kernel3.setArg<cl::Buffer>(5, oldDelta.getDeviceBuffer());
kernel3.setArg<cl::Buffer>(6, integration.getStepSize().getDeviceBuffer());
kernel3.setArg<cl::Buffer>(3, integration.getPosDelta().getDeviceBuffer());
kernel3.setArg<cl::Buffer>(4, oldDelta.getDeviceBuffer());
kernel3.setArg<cl::Buffer>(5, integration.getStepSize().getDeviceBuffer());
kernel4.setArg<cl::Buffer>(0, cl.getVelm().getDeviceBuffer());
kernel4.setArg<cl::Buffer>(1, cl.getForce().getDeviceBuffer());
kernel4.setArg<cl::Buffer>(2, integration.getStepSize().getDeviceBuffer());
}
if (!forcesAreValid) {
context.calcForcesAndEnergy(true, false);
......@@ -7550,8 +7553,9 @@ void OpenCLIntegrateBAOABStepKernel::execute(ContextImpl& context, const BAOABLa
integration.applyConstraints(integrator.getConstraintTolerance());
cl.executeKernel(kernel2, numAtoms);
integration.applyConstraints(integrator.getConstraintTolerance());
context.calcForcesAndEnergy(true, false);
cl.executeKernel(kernel3, numAtoms);
context.calcForcesAndEnergy(true, false);
cl.executeKernel(kernel4, numAtoms);
integration.applyVelocityConstraints(integrator.getConstraintTolerance());
integration.computeVirtualSites();
......@@ -7560,6 +7564,8 @@ void OpenCLIntegrateBAOABStepKernel::execute(ContextImpl& context, const BAOABLa
cl.setTime(cl.getTime()+stepSize);
cl.setStepCount(cl.getStepCount()+1);
cl.reorderAtoms();
if (cl.getAtomsWereReordered())
forcesAreValid = false;
// Reduce UI lag.
......
platforms/opencl/src/kernels/baoab.cl
View file @ bc71de2c
......@@ -71,16 +71,16 @@ __kernel void integrateBAOABPart2(__global real4* restrict posq, __global real4*
*/
__kernel void integrateBAOABPart3(__global real4* restrict posq, __global real4* restrict posqCorrection, __global mixed4* restrict velm,
__global const real4* restrict force, __global mixed4* restrict posDelta, __global mixed4* restrict oldDelta, __global const mixed2* restrict dt) {
__global mixed4* restrict posDelta, __global mixed4* restrict oldDelta, __global const mixed2* restrict dt) {
mixed halfdt = 0.5*dt[0].y;
mixed invHalfdt = 1/halfdt;
for (int index = get_global_id(0); index < NUM_ATOMS; index += get_global_size(0)) {
mixed4 velocity = velm[index];
if (velocity.w != 0.0) {
mixed4 delta = posDelta[index];
velocity.x += (delta.x-oldDelta[index].x)*invHalfdt + halfdt*velocity.w*force[index].x;
velocity.y += (delta.y-oldDelta[index].y)*invHalfdt + halfdt*velocity.w*force[index].y;
velocity.z += (delta.z-oldDelta[index].z)*invHalfdt + halfdt*velocity.w*force[index].z;
velocity.x += (delta.x-oldDelta[index].x)*invHalfdt;
velocity.y += (delta.y-oldDelta[index].y)*invHalfdt;
velocity.z += (delta.z-oldDelta[index].z)*invHalfdt;
velm[index] = velocity;
#ifdef USE_MIXED_PRECISION
real4 pos1 = posq[index];
......@@ -99,3 +99,20 @@ __kernel void integrateBAOABPart3(__global real4* restrict posq, __global real4*
}
}
}
/**
* Perform the fourth step of BAOAB integration.
*/
__kernel void integrateBAOABPart4(__global mixed4* restrict velm, __global const real4* restrict force, __global const mixed2* restrict dt) {
mixed halfdt = 0.5*dt[0].y;
for (int index = get_global_id(0); index < NUM_ATOMS; index += get_global_size(0)) {
mixed4 velocity = velm[index];
if (velocity.w != 0.0) {
velocity.x += halfdt*velocity.w*force[index].x;
velocity.y += halfdt*velocity.w*force[index].y;
velocity.z += halfdt*velocity.w*force[index].z;
velm[index] = velocity;
}
}
}
platforms/reference/include/ReferenceBAOABDynamics.h
View file @ bc71de2c
......@@ -121,6 +121,7 @@ class OPENMM_EXPORT ReferenceBAOABDynamics : public ReferenceDynamics {
Third update
@param context the context this integrator is updating
@param numberOfAtoms number of atoms
@param atomCoordinates atom coordinates
@param velocities velocities
......@@ -129,7 +130,7 @@ class OPENMM_EXPORT ReferenceBAOABDynamics : public ReferenceDynamics {
--------------------------------------------------------------------------------------- */
virtual void updatePart3(int numberOfAtoms, std::vector<OpenMM::Vec3>& atomCoordinates, std::vector<OpenMM::Vec3>& velocities,
virtual void updatePart3(OpenMM::ContextImpl& context, int numberOfAtoms, std::vector<OpenMM::Vec3>& atomCoordinates, std::vector<OpenMM::Vec3>& velocities,
std::vector<OpenMM::Vec3>& forces, std::vector<double>& masses, std::vector<OpenMM::Vec3>& xPrime);
};
......
platforms/reference/src/SimTKReference/ReferenceBAOABDynamics.cpp
View file @ bc71de2c
......@@ -87,17 +87,21 @@ void ReferenceBAOABDynamics::updatePart2(int numberOfAtoms, vector<Vec3>& atomCo
}
}
void ReferenceBAOABDynamics::updatePart3(int numberOfAtoms, vector<Vec3>& atomCoordinates,
void ReferenceBAOABDynamics::updatePart3(OpenMM::ContextImpl& context, int numberOfAtoms, vector<Vec3>& atomCoordinates,
vector<Vec3>& velocities, vector<Vec3>& forces, vector<double>& inverseMasses,
vector<Vec3>& xPrime) {
const double halfdt = 0.5*getDeltaT();
for (int i = 0; i < numberOfAtoms; i++) {
if (inverseMasses[i] != 0.0) {
velocities[i] += (xPrime[i]-oldx[i])/halfdt;
velocities[i] += (halfdt*inverseMasses[i])*forces[i];
atomCoordinates[i] = xPrime[i];
}
}
context.calcForcesAndEnergy(true, false);
for (int i = 0; i < numberOfAtoms; i++) {
if (inverseMasses[i] != 0.0)
velocities[i] += (halfdt*inverseMasses[i])*forces[i];
}
}
void ReferenceBAOABDynamics::update(ContextImpl& context, vector<Vec3>& atomCoordinates,
......@@ -135,8 +139,7 @@ void ReferenceBAOABDynamics::update(ContextImpl& context, vector<Vec3>& atomCoor
// 3rd update
context.calcForcesAndEnergy(true, false);
updatePart3(numberOfAtoms, atomCoordinates, velocities, forces, inverseMasses, xPrime);
updatePart3(context, numberOfAtoms, atomCoordinates, velocities, forces, inverseMasses, xPrime);
if (referenceConstraintAlgorithm)
referenceConstraintAlgorithm->applyToVelocities(atomCoordinates, velocities, inverseMasses, tolerance);
......
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