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Commit f44890a4 authored by peastman's avatar peastman
Browse files

Fixed bug in CustomIntegrator's handling of massless particles (see bug 1871)

parent 0faa4852
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Showing with 24 additions and 26 deletions
platforms/cuda/src/CudaKernels.cpp
View file @ f44890a4
......@@ -4554,7 +4554,7 @@ void CudaIntegrateCustomStepKernel::initialize(const System& system, const Custo
numGlobalVariables = integrator.getNumGlobalVariables();
int elementSize = (cu.getUseDoublePrecision() || cu.getUseMixedPrecision() ? sizeof(double) : sizeof(float));
globalValues = new CudaArray(cu, max(1, numGlobalVariables), elementSize, "globalVariables");
sumBuffer = new CudaArray(cu, 3*system.getNumParticles(), elementSize, "sumBuffer");
sumBuffer = new CudaArray(cu, ((3*system.getNumParticles()+3)/4)*4, elementSize, "sumBuffer");
potentialEnergy = new CudaArray(cu, 1, cu.getEnergyBuffer().getElementSize(), "potentialEnergy");
kineticEnergy = new CudaArray(cu, 1, elementSize, "kineticEnergy");
perDofValues = new CudaParameterSet(cu, integrator.getNumPerDofVariables(), 3*system.getNumParticles(), "perDofVariables", false, cu.getUseDoublePrecision() || cu.getUseMixedPrecision());
......@@ -5103,6 +5103,7 @@ void CudaIntegrateCustomStepKernel::execute(ContextImpl& context, CustomIntegrat
kernelArgs[i][0][10] = &randomIndex;
if (requiredUniform[i] > 0)
cu.executeKernel(randomKernel, &randomArgs[0], numAtoms);
cu.clearBuffer(*sumBuffer);
cu.executeKernel(kernels[i][0], &kernelArgs[i][0][0], numAtoms);
cu.executeKernel(kernels[i][1], &kernelArgs[i][1][0], CudaContext::ThreadBlockSize, CudaContext::ThreadBlockSize);
}
......@@ -5150,6 +5151,7 @@ double CudaIntegrateCustomStepKernel::computeKineticEnergy(ContextImpl& context,
int randomIndex = 0;
kineticEnergyArgs[1] = &posCorrection;
kineticEnergyArgs[10] = &randomIndex;
cu.clearBuffer(*sumBuffer);
cu.executeKernel(kineticEnergyKernel, &kineticEnergyArgs[0], cu.getNumAtoms());
void* args[] = {&sumBuffer->getDevicePointer(), &kineticEnergy->getDevicePointer()};
cu.executeKernel(sumKineticEnergyKernel, args, CudaContext::ThreadBlockSize, CudaContext::ThreadBlockSize);
......
platforms/cuda/tests/TestCudaCustomIntegrator.cpp
View file @ f44890a4
......@@ -6,7 +6,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2008-2012 Stanford University and the Authors. *
* Portions copyright (c) 2008-2013 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -345,20 +345,20 @@ void testSum() {
OpenMM_SFMT::SFMT sfmt;
init_gen_rand(0, sfmt);
for (int i = 0; i < numParticles; i++) {
system.addParticle(1.5);
nb->addParticle(i%2 == 0 ? 1 : -1, 0.1, 1);
system.addParticle(i%10 == 0 ? 0.0 : 1.5);
nb->addParticle(i%2 == 0 ? 0.1 : -0.1, 0.1, 1);
bool close = true;
while (close) {
positions[i] = Vec3(boxSize*genrand_real2(sfmt), boxSize*genrand_real2(sfmt), boxSize*genrand_real2(sfmt));
close = false;
for (int j = 0; j < i; ++j) {
Vec3 delta = positions[i]-positions[j];
if (delta.dot(delta) < 0.1)
if (delta.dot(delta) < 1)
close = true;
}
}
}
CustomIntegrator integrator(0.01);
CustomIntegrator integrator(0.005);
integrator.addGlobalVariable("ke", 0);
integrator.addComputePerDof("v", "v+dt*f/m");
integrator.addComputePerDof("x", "x+dt*v");
......@@ -368,10 +368,8 @@ void testSum() {
// See if the sum is being computed correctly.
State state = context.getState(State::Energy);
const double initialEnergy = state.getKineticEnergy()+state.getPotentialEnergy();
for (int i = 0; i < 100; ++i) {
state = context.getState(State::Energy);
State state = context.getState(State::Energy);
ASSERT_EQUAL_TOL(state.getKineticEnergy(), integrator.getGlobalVariable(0), 1e-5);
integrator.step(1);
}
......
platforms/opencl/src/OpenCLKernels.cpp
View file @ f44890a4
......@@ -4786,7 +4786,7 @@ void OpenCLIntegrateCustomStepKernel::initialize(const System& system, const Cus
numGlobalVariables = integrator.getNumGlobalVariables();
int elementSize = (cl.getUseDoublePrecision() || cl.getUseMixedPrecision() ? sizeof(double) : sizeof(float));
globalValues = new OpenCLArray(cl, max(1, numGlobalVariables), elementSize, "globalVariables");
sumBuffer = new OpenCLArray(cl, 3*system.getNumParticles(), elementSize, "sumBuffer");
sumBuffer = new OpenCLArray(cl, ((3*system.getNumParticles()+3)/4)*4, elementSize, "sumBuffer");
potentialEnergy = new OpenCLArray(cl, 1, cl.getEnergyBuffer().getElementSize(), "potentialEnergy");
kineticEnergy = new OpenCLArray(cl, 1, elementSize, "kineticEnergy");
perDofValues = new OpenCLParameterSet(cl, integrator.getNumPerDofVariables(), 3*system.getNumParticles(), "perDofVariables", false, cl.getUseDoublePrecision() || cl.getUseMixedPrecision());
......@@ -5329,6 +5329,7 @@ void OpenCLIntegrateCustomStepKernel::execute(ContextImpl& context, CustomIntegr
kernels[i][0].setArg<cl_uint>(10, integration.prepareRandomNumbers(requiredGaussian[i]));
if (requiredUniform[i] > 0)
cl.executeKernel(randomKernel, numAtoms);
cl.clearBuffer(*sumBuffer);
cl.executeKernel(kernels[i][0], numAtoms);
cl.executeKernel(kernels[i][1], OpenCLContext::ThreadBlockSize, OpenCLContext::ThreadBlockSize);
}
......@@ -5375,6 +5376,7 @@ double OpenCLIntegrateCustomStepKernel::computeKineticEnergy(ContextImpl& contex
cl.executeKernel(sumPotentialEnergyKernel, OpenCLContext::ThreadBlockSize, OpenCLContext::ThreadBlockSize);
forcesAreValid = true;
}
cl.clearBuffer(*sumBuffer);
cl.executeKernel(kineticEnergyKernel, cl.getNumAtoms());
cl.executeKernel(sumKineticEnergyKernel, OpenCLContext::ThreadBlockSize, OpenCLContext::ThreadBlockSize);
if (cl.getUseDoublePrecision() || cl.getUseMixedPrecision()) {
......
platforms/opencl/tests/TestOpenCLCustomIntegrator.cpp
View file @ f44890a4
......@@ -6,7 +6,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2008-2011 Stanford University and the Authors. *
* Portions copyright (c) 2008-2013 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -345,20 +345,20 @@ void testSum() {
OpenMM_SFMT::SFMT sfmt;
init_gen_rand(0, sfmt);
for (int i = 0; i < numParticles; i++) {
system.addParticle(1.5);
nb->addParticle(i%2 == 0 ? 1 : -1, 0.1, 1);
system.addParticle(i%10 == 0 ? 0.0 : 1.5);
nb->addParticle(i%2 == 0 ? 0.1 : -0.1, 0.1, 1);
bool close = true;
while (close) {
positions[i] = Vec3(boxSize*genrand_real2(sfmt), boxSize*genrand_real2(sfmt), boxSize*genrand_real2(sfmt));
close = false;
for (int j = 0; j < i; ++j) {
Vec3 delta = positions[i]-positions[j];
if (delta.dot(delta) < 0.1)
if (delta.dot(delta) < 1)
close = true;
}
}
}
CustomIntegrator integrator(0.01);
CustomIntegrator integrator(0.005);
integrator.addGlobalVariable("ke", 0);
integrator.addComputePerDof("v", "v+dt*f/m");
integrator.addComputePerDof("x", "x+dt*v");
......@@ -368,10 +368,8 @@ void testSum() {
// See if the sum is being computed correctly.
State state = context.getState(State::Energy);
const double initialEnergy = state.getKineticEnergy()+state.getPotentialEnergy();
for (int i = 0; i < 100; ++i) {
state = context.getState(State::Energy);
State state = context.getState(State::Energy);
ASSERT_EQUAL_TOL(state.getKineticEnergy(), integrator.getGlobalVariable(0), 1e-5);
integrator.step(1);
}
......
platforms/reference/tests/TestReferenceCustomIntegrator.cpp
View file @ f44890a4
......@@ -6,7 +6,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2008-2011 Stanford University and the Authors. *
* Portions copyright (c) 2008-2013 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -336,20 +336,20 @@ void testSum() {
OpenMM_SFMT::SFMT sfmt;
init_gen_rand(0, sfmt);
for (int i = 0; i < numParticles; i++) {
system.addParticle(1.5);
nb->addParticle(i%2 == 0 ? 1 : -1, 0.1, 1);
system.addParticle(i%10 == 0 ? 0.0 : 1.5);
nb->addParticle(i%2 == 0 ? 0.1 : -0.1, 0.1, 1);
bool close = true;
while (close) {
positions[i] = Vec3(boxSize*genrand_real2(sfmt), boxSize*genrand_real2(sfmt), boxSize*genrand_real2(sfmt));
close = false;
for (int j = 0; j < i; ++j) {
Vec3 delta = positions[i]-positions[j];
if (delta.dot(delta) < 0.1)
if (delta.dot(delta) < 1)
close = true;
}
}
}
CustomIntegrator integrator(0.01);
CustomIntegrator integrator(0.005);
integrator.addGlobalVariable("ke", 0);
integrator.addComputePerDof("v", "v+dt*f/m");
integrator.addComputePerDof("x", "x+dt*v");
......@@ -359,10 +359,8 @@ void testSum() {
// See if the sum is being computed correctly.
State state = context.getState(State::Energy);
const double initialEnergy = state.getKineticEnergy()+state.getPotentialEnergy();
for (int i = 0; i < 100; ++i) {
state = context.getState(State::Energy);
State state = context.getState(State::Energy);
ASSERT_EQUAL_TOL(state.getKineticEnergy(), integrator.getGlobalVariable(0), 1e-5);
integrator.step(1);
}
......
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