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Commit 99cebd08 authored by Peter Eastman's avatar Peter Eastman
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Implemented updateParametersInContext() for five more Force classes

parent 4bc723ab
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Showing with 617 additions and 29 deletions
openmmapi/src/CustomNonbondedForceImpl.cpp
View file @ 99cebd08
......@@ -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) 2008-2009 Stanford University and the Authors. *
* Portions copyright (c) 2008-2012 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -123,3 +123,7 @@ map<string, double> CustomNonbondedForceImpl::getDefaultParameters() {
parameters[owner.getGlobalParameterName(i)] = owner.getGlobalParameterDefaultValue(i);
return parameters;
}
void CustomNonbondedForceImpl::updateParametersInContext(ContextImpl& context) {
kernel.getAs<CalcCustomNonbondedForceKernel>().copyParametersToContext(context, owner);
}
platforms/cuda/src/CudaKernels.cpp
View file @ 99cebd08
......@@ -1033,6 +1033,10 @@ void CudaCalcCustomNonbondedForceKernel::updateGlobalParams(ContextImpl& context
SetCustomNonbondedGlobalParams(globalParamValues);
}
void CudaCalcCustomNonbondedForceKernel::copyParametersToContext(ContextImpl& context, const CustomNonbondedForce& force) {
throw OpenMMException("CudaPlatform does not support copyParametersToContext");
}
class CudaCalcGBSAOBCForceKernel::ForceInfo : public CudaForceInfo {
public:
ForceInfo(const GBSAOBCForce& force) : force(force) {
......@@ -1204,6 +1208,10 @@ void CudaCalcCustomExternalForceKernel::updateGlobalParams(ContextImpl& context)
SetCustomExternalGlobalParams(globalParamValues);
}
void CudaCalcCustomExternalForceKernel::copyParametersToContext(ContextImpl& context, const CustomExternalForce& force) {
throw OpenMMException("CudaPlatform does not support copyParametersToContext");
}
void OPENMMCUDA_EXPORT OpenMM::cudaOpenMMInitializeIntegration(const System& system, CudaPlatform::PlatformData& data, const Integrator& integrator) {
// Initialize any terms that haven't already been handled by a Force.
......
platforms/cuda/src/CudaKernels.h
View file @ 99cebd08
......@@ -596,6 +596,13 @@ public:
* @return the potential energy due to the force
*/
double execute(ContextImpl& context, bool includeForces, bool includeEnergy);
/**
* Copy changed parameters over to a context.
*
* @param context the context to copy parameters to
* @param force the CustomNonbondedForce to copy the parameters from
*/
void copyParametersToContext(ContextImpl& context, const CustomNonbondedForce& force);
private:
class ForceInfo;
void updateGlobalParams(ContextImpl& context);
......@@ -697,6 +704,13 @@ public:
* @return the potential energy due to the force
*/
double execute(ContextImpl& context, bool includeForces, bool includeEnergy);
/**
* Copy changed parameters over to a context.
*
* @param context the context to copy parameters to
* @param force the CustomNonbondedForce to copy the parameters from
*/
void copyParametersToContext(ContextImpl& context, const CustomExternalForce& force);
private:
class ForceInfo;
void updateGlobalParams(ContextImpl& context);
......
platforms/opencl/src/OpenCLKernels.cpp
View file @ 99cebd08
......@@ -98,11 +98,11 @@ void OpenCLCalcForcesAndEnergyKernel::beginComputation(ContextImpl& context, boo
OpenCLNonbondedUtilities& nb = cl.getNonbondedUtilities();
bool includeNonbonded = ((groups&(1<<nb.getForceGroup())) != 0);
cl.setAtomsWereReordered(false);
if (cl.getMoleculesAreInvalid() || (nb.getUseCutoff() && includeNonbonded && cl.getComputeForceCount()%100 == 0)) {
if (nb.getUseCutoff() && includeNonbonded && (cl.getMoleculesAreInvalid() || cl.getComputeForceCount()%100 == 0)) {
cl.reorderAtoms(!cl.getMoleculesAreInvalid());
nb.updateNeighborListSize();
cl.setComputeForceCount(cl.getComputeForceCount()+1);
}
cl.setComputeForceCount(cl.getComputeForceCount()+1);
cl.clearAutoclearBuffers();
if (includeNonbonded)
nb.prepareInteractions();
......@@ -1769,6 +1769,28 @@ double OpenCLCalcCustomNonbondedForceKernel::execute(ContextImpl& context, bool
return 0.0;
}
void OpenCLCalcCustomNonbondedForceKernel::copyParametersToContext(ContextImpl& context, const CustomNonbondedForce& force) {
int numParticles = force.getNumParticles();
if (numParticles != cl.getNumAtoms())
throw OpenMMException("updateParametersInContext: The number of particles has changed");
// Record the per-particle parameters.
vector<vector<cl_float> > paramVector(numParticles);
vector<double> parameters;
for (int i = 0; i < numParticles; i++) {
force.getParticleParameters(i, parameters);
paramVector[i].resize(parameters.size());
for (int j = 0; j < (int) parameters.size(); j++)
paramVector[i][j] = (cl_float) parameters[j];
}
params->setParameterValues(paramVector);
// Mark that the current reordering may be invalid.
cl.invalidateMolecules();
}
class OpenCLGBSAOBCForceInfo : public OpenCLForceInfo {
public:
OpenCLGBSAOBCForceInfo(int requiredBuffers, const GBSAOBCForce& force) : OpenCLForceInfo(requiredBuffers), force(force) {
......@@ -1946,7 +1968,7 @@ double OpenCLCalcGBSAOBCForceKernel::execute(ContextImpl& context, bool includeF
force1Kernel.setArg<mm_float4>(8, cl.getInvPeriodicBoxSize());
if (maxTiles < nb.getInteractingTiles().getSize()) {
maxTiles = nb.getInteractingTiles().getSize();
computeBornSumKernel.setArg<cl::Buffer>(4, nb.getInteractingTiles().getDeviceBuffer());
computeBornSumKernel.setArg<cl::Buffer>(3, nb.getInteractingTiles().getDeviceBuffer());
computeBornSumKernel.setArg<cl_uint>(7, maxTiles);
force1Kernel.setArg<cl::Buffer>(5, nb.getInteractingTiles().getDeviceBuffer());
force1Kernel.setArg<cl_uint>(9, maxTiles);
......@@ -2901,6 +2923,28 @@ double OpenCLCalcCustomGBForceKernel::execute(ContextImpl& context, bool include
return 0.0;
}
void OpenCLCalcCustomGBForceKernel::copyParametersToContext(ContextImpl& context, const CustomGBForce& force) {
int numParticles = force.getNumParticles();
if (numParticles != cl.getNumAtoms())
throw OpenMMException("updateParametersInContext: The number of particles has changed");
// Record the per-particle parameters.
vector<vector<cl_float> > paramVector(numParticles);
vector<double> parameters;
for (int i = 0; i < numParticles; i++) {
force.getParticleParameters(i, parameters);
paramVector[i].resize(parameters.size());
for (int j = 0; j < (int) parameters.size(); j++)
paramVector[i][j] = (cl_float) parameters[j];
}
params->setParameterValues(paramVector);
// Mark that the current reordering may be invalid.
cl.invalidateMolecules();
}
class OpenCLCustomExternalForceInfo : public OpenCLForceInfo {
public:
OpenCLCustomExternalForceInfo(const CustomExternalForce& force, int numParticles) : OpenCLForceInfo(0), force(force), indices(numParticles, -1) {
......@@ -3026,6 +3070,31 @@ double OpenCLCalcCustomExternalForceKernel::execute(ContextImpl& context, bool i
return 0.0;
}
void OpenCLCalcCustomExternalForceKernel::copyParametersToContext(ContextImpl& context, const CustomExternalForce& force) {
int numContexts = cl.getPlatformData().contexts.size();
int startIndex = cl.getContextIndex()*force.getNumParticles()/numContexts;
int endIndex = (cl.getContextIndex()+1)*force.getNumParticles()/numContexts;
if (numParticles != endIndex-startIndex)
throw OpenMMException("updateParametersInContext: The number of particles has changed");
// Record the per-particle parameters.
vector<vector<cl_float> > paramVector(numParticles);
vector<double> parameters;
for (int i = 0; i < numParticles; i++) {
int particle;
force.getParticleParameters(startIndex+i, particle, parameters);
paramVector[i].resize(parameters.size());
for (int j = 0; j < (int) parameters.size(); j++)
paramVector[i][j] = (cl_float) parameters[j];
}
params->setParameterValues(paramVector);
// Mark that the current reordering may be invalid.
cl.invalidateMolecules();
}
class OpenCLCustomHbondForceInfo : public OpenCLForceInfo {
public:
OpenCLCustomHbondForceInfo(int requiredBuffers, const CustomHbondForce& force) : OpenCLForceInfo(requiredBuffers), force(force) {
......@@ -3536,6 +3605,45 @@ double OpenCLCalcCustomHbondForceKernel::execute(ContextImpl& context, bool incl
return 0.0;
}
void OpenCLCalcCustomHbondForceKernel::copyParametersToContext(ContextImpl& context, const CustomHbondForce& force) {
int numContexts = cl.getPlatformData().contexts.size();
int startIndex = cl.getContextIndex()*force.getNumDonors()/numContexts;
int endIndex = (cl.getContextIndex()+1)*force.getNumDonors()/numContexts;
if (numDonors != endIndex-startIndex)
throw OpenMMException("updateParametersInContext: The number of donors has changed");
if (numAcceptors != force.getNumAcceptors())
throw OpenMMException("updateParametersInContext: The number of acceptors has changed");
// Record the per-donor parameters.
vector<vector<cl_float> > donorParamVector(numDonors);
vector<double> parameters;
for (int i = 0; i < numDonors; i++) {
int d1, d2, d3;
force.getDonorParameters(startIndex+i, d1, d2, d3, parameters);
donorParamVector[i].resize(parameters.size());
for (int j = 0; j < (int) parameters.size(); j++)
donorParamVector[i][j] = (cl_float) parameters[j];
}
donorParams->setParameterValues(donorParamVector);
// Record the per-acceptor parameters.
vector<vector<cl_float> > acceptorParamVector(numAcceptors);
for (int i = 0; i < numAcceptors; i++) {
int a1, a2, a3;
force.getAcceptorParameters(i, a1, a2, a3, parameters);
acceptorParamVector[i].resize(parameters.size());
for (int j = 0; j < (int) parameters.size(); j++)
acceptorParamVector[i][j] = (cl_float) parameters[j];
}
acceptorParams->setParameterValues(acceptorParamVector);
// Mark that the current reordering may be invalid.
cl.invalidateMolecules();
}
class OpenCLCustomCompoundBondForceInfo : public OpenCLForceInfo {
public:
OpenCLCustomCompoundBondForceInfo(const CustomCompoundBondForce& force) : OpenCLForceInfo(0), force(force) {
......@@ -3828,6 +3936,31 @@ double OpenCLCalcCustomCompoundBondForceKernel::execute(ContextImpl& context, bo
return 0.0;
}
void OpenCLCalcCustomCompoundBondForceKernel::copyParametersToContext(ContextImpl& context, const CustomCompoundBondForce& force) {
int numContexts = cl.getPlatformData().contexts.size();
int startIndex = cl.getContextIndex()*force.getNumBonds()/numContexts;
int endIndex = (cl.getContextIndex()+1)*force.getNumBonds()/numContexts;
if (numBonds != endIndex-startIndex)
throw OpenMMException("updateParametersInContext: The number of bonds has changed");
// Record the per-bond parameters.
vector<vector<cl_float> > paramVector(numBonds);
vector<int> particles;
vector<double> parameters;
for (int i = 0; i < numBonds; i++) {
force.getBondParameters(startIndex+i, particles, parameters);
paramVector[i].resize(parameters.size());
for (int j = 0; j < (int) parameters.size(); j++)
paramVector[i][j] = (cl_float) parameters[j];
}
params->setParameterValues(paramVector);
// Mark that the current reordering may be invalid.
cl.invalidateMolecules();
}
OpenCLIntegrateVerletStepKernel::~OpenCLIntegrateVerletStepKernel() {
}
......
platforms/opencl/src/OpenCLKernels.h
View file @ 99cebd08
......@@ -647,6 +647,13 @@ public:
* @return the potential energy due to the force
*/
double execute(ContextImpl& context, bool includeForces, bool includeEnergy);
/**
* Copy changed parameters over to a context.
*
* @param context the context to copy parameters to
* @param force the CustomNonbondedForce to copy the parameters from
*/
void copyParametersToContext(ContextImpl& context, const CustomNonbondedForce& force);
private:
bool hasInitializedKernel;
OpenCLContext& cl;
......@@ -736,6 +743,13 @@ public:
* @return the potential energy due to the force
*/
double execute(ContextImpl& context, bool includeForces, bool includeEnergy);
/**
* Copy changed parameters over to a context.
*
* @param context the context to copy parameters to
* @param force the CustomGBForce to copy the parameters from
*/
void copyParametersToContext(ContextImpl& context, const CustomGBForce& force);
private:
bool hasInitializedKernels, needParameterGradient;
int maxTiles, numComputedValues;
......@@ -781,6 +795,13 @@ public:
* @return the potential energy due to the force
*/
double execute(ContextImpl& context, bool includeForces, bool includeEnergy);
/**
* Copy changed parameters over to a context.
*
* @param context the context to copy parameters to
* @param force the CustomExternalForce to copy the parameters from
*/
void copyParametersToContext(ContextImpl& context, const CustomExternalForce& force);
private:
int numParticles;
bool hasInitializedKernel;
......@@ -819,6 +840,13 @@ public:
* @return the potential energy due to the force
*/
double execute(ContextImpl& context, bool includeForces, bool includeEnergy);
/**
* Copy changed parameters over to a context.
*
* @param context the context to copy parameters to
* @param force the CustomHbondForce to copy the parameters from
*/
void copyParametersToContext(ContextImpl& context, const CustomHbondForce& force);
private:
int numDonors, numAcceptors;
bool hasInitializedKernel;
......@@ -865,6 +893,14 @@ public:
* @return the potential energy due to the force
*/
double execute(ContextImpl& context, bool includeForces, bool includeEnergy);
/**
* Copy changed parameters over to a context.
*
* @param context the context to copy parameters to
* @param force the CustomCompoundBondForce to copy the parameters from
*/
void copyParametersToContext(ContextImpl& context, const CustomCompoundBondForce& force);
private:
int numBonds;
OpenCLContext& cl;
......
platforms/opencl/src/OpenCLParallelKernels.cpp
View file @ 99cebd08
......@@ -598,6 +598,11 @@ double OpenCLParallelCalcCustomNonbondedForceKernel::execute(ContextImpl& contex
return 0.0;
}
void OpenCLParallelCalcCustomNonbondedForceKernel::copyParametersToContext(ContextImpl& context, const CustomNonbondedForce& force) {
for (int i = 0; i < (int) kernels.size(); i++)
getKernel(i).copyParametersToContext(context, force);
}
class OpenCLParallelCalcCustomExternalForceKernel::Task : public OpenCLContext::WorkTask {
public:
Task(ContextImpl& context, OpenCLCalcCustomExternalForceKernel& kernel, bool includeForce,
......@@ -634,6 +639,11 @@ double OpenCLParallelCalcCustomExternalForceKernel::execute(ContextImpl& context
return 0.0;
}
void OpenCLParallelCalcCustomExternalForceKernel::copyParametersToContext(ContextImpl& context, const CustomExternalForce& force) {
for (int i = 0; i < (int) kernels.size(); i++)
getKernel(i).copyParametersToContext(context, force);
}
class OpenCLParallelCalcCustomHbondForceKernel::Task : public OpenCLContext::WorkTask {
public:
Task(ContextImpl& context, OpenCLCalcCustomHbondForceKernel& kernel, bool includeForce,
......@@ -670,6 +680,11 @@ double OpenCLParallelCalcCustomHbondForceKernel::execute(ContextImpl& context, b
return 0.0;
}
void OpenCLParallelCalcCustomHbondForceKernel::copyParametersToContext(ContextImpl& context, const CustomHbondForce& force) {
for (int i = 0; i < (int) kernels.size(); i++)
getKernel(i).copyParametersToContext(context, force);
}
class OpenCLParallelCalcCustomCompoundBondForceKernel::Task : public OpenCLContext::WorkTask {
public:
Task(ContextImpl& context, OpenCLCalcCustomCompoundBondForceKernel& kernel, bool includeForce,
......@@ -705,3 +720,8 @@ double OpenCLParallelCalcCustomCompoundBondForceKernel::execute(ContextImpl& con
}
return 0.0;
}
void OpenCLParallelCalcCustomCompoundBondForceKernel::copyParametersToContext(ContextImpl& context, const CustomCompoundBondForce& force) {
for (int i = 0; i < (int) kernels.size(); i++)
getKernel(i).copyParametersToContext(context, force);
}
platforms/opencl/src/OpenCLParallelKernels.h
View file @ 99cebd08
......@@ -450,6 +450,13 @@ public:
* @return the potential energy due to the force
*/
double execute(ContextImpl& context, bool includeForces, bool includeEnergy);
/**
* Copy changed parameters over to a context.
*
* @param context the context to copy parameters to
* @param force the CustomNonbondedForce to copy the parameters from
*/
void copyParametersToContext(ContextImpl& context, const CustomNonbondedForce& force);
private:
class Task;
OpenCLPlatform::PlatformData& data;
......@@ -481,6 +488,13 @@ public:
* @return the potential energy due to the force
*/
double execute(ContextImpl& context, bool includeForces, bool includeEnergy);
/**
* Copy changed parameters over to a context.
*
* @param context the context to copy parameters to
* @param force the CustomExternalForce to copy the parameters from
*/
void copyParametersToContext(ContextImpl& context, const CustomExternalForce& force);
private:
class Task;
OpenCLPlatform::PlatformData& data;
......@@ -512,6 +526,13 @@ public:
* @return the potential energy due to the force
*/
double execute(ContextImpl& context, bool includeForces, bool includeEnergy);
/**
* Copy changed parameters over to a context.
*
* @param context the context to copy parameters to
* @param force the CustomHbondForce to copy the parameters from
*/
void copyParametersToContext(ContextImpl& context, const CustomHbondForce& force);
private:
class Task;
OpenCLPlatform::PlatformData& data;
......@@ -543,6 +564,13 @@ public:
* @return the potential energy due to the force
*/
double execute(ContextImpl& context, bool includeForces, bool includeEnergy);
/**
* Copy changed parameters over to a context.
*
* @param context the context to copy parameters to
* @param force the CustomCompoundBondForce to copy the parameters from
*/
void copyParametersToContext(ContextImpl& context, const CustomCompoundBondForce& force);
private:
class Task;
OpenCLPlatform::PlatformData& data;
......
platforms/opencl/tests/TestOpenCLCustomCompoundBondForce.cpp
View file @ 99cebd08
......@@ -121,6 +121,24 @@ void testBond() {
ASSERT_EQUAL_VEC(s1.getForces()[i], s2.getForces()[i], TOL);
ASSERT_EQUAL_TOL(s1.getPotentialEnergy(), s2.getPotentialEnergy(), TOL);
}
// Try changing the bond parameters and make sure it's still correct.
parameters[0] = 1.6;
parameters[3] = 1.3;
custom->setBondParameters(0, particles, parameters);
custom->updateParametersInContext(c1);
bonds->setBondParameters(0, 0, 1, 1.3, 1.6);
bonds->setBondParameters(1, 1, 3, 1.3, 1.6);
bonds->updateParametersInContext(c2);
{
State s1 = c1.getState(State::Forces | State::Energy);
State s2 = c2.getState(State::Forces | State::Energy);
const vector<Vec3>& forces = s1.getForces();
for (int i = 0; i < customSystem.getNumParticles(); i++)
ASSERT_EQUAL_VEC(s1.getForces()[i], s2.getForces()[i], TOL);
ASSERT_EQUAL_TOL(s1.getPotentialEnergy(), s2.getPotentialEnergy(), TOL);
}
}
void testPositionDependence() {
......
platforms/opencl/tests/TestOpenCLCustomExternalForce.cpp
View file @ 99cebd08
......@@ -75,11 +75,28 @@ void testForce() {
positions[2] = Vec3(1, 0, 1);
context.setPositions(positions);
State state = context.getState(State::Forces | State::Energy);
const vector<Vec3>& forces = state.getForces();
ASSERT_EQUAL_VEC(Vec3(-0.5, -0.5*2.0*2.0*1.5, 0), forces[0], TOL);
ASSERT_EQUAL_VEC(Vec3(0, 0, 0), forces[1], TOL);
ASSERT_EQUAL_VEC(Vec3(-0.5, 0.5*3.0*2.0*1.5, 0), forces[2], TOL);
ASSERT_EQUAL_TOL(0.5*(1.0 + 2.0*1.5*1.5 + 3.0*1.5*1.5), state.getPotentialEnergy(), TOL);
{
const vector<Vec3>& forces = state.getForces();
ASSERT_EQUAL_VEC(Vec3(-0.5, -0.5*2.0*2.0*1.5, 0), forces[0], TOL);
ASSERT_EQUAL_VEC(Vec3(0, 0, 0), forces[1], TOL);
ASSERT_EQUAL_VEC(Vec3(-0.5, 0.5*3.0*2.0*1.5, 0), forces[2], TOL);
ASSERT_EQUAL_TOL(0.5*(1.0 + 2.0*1.5*1.5 + 3.0*1.5*1.5), state.getPotentialEnergy(), TOL);
}
// Try changing the parameters and make sure it's still correct.
parameters[0] = 1.4;
parameters[1] = 3.5;
forceField->setParticleParameters(1, 2, parameters);
forceField->updateParametersInContext(context);
state = context.getState(State::Forces | State::Energy);
{
const vector<Vec3>& forces = state.getForces();
ASSERT_EQUAL_VEC(Vec3(-0.5, -0.5*2.0*2.0*1.5, 0), forces[0], TOL);
ASSERT_EQUAL_VEC(Vec3(0, 0, 0), forces[1], TOL);
ASSERT_EQUAL_VEC(Vec3(-0.5, 0.5*3.5*2.0*1.4, 0), forces[2], TOL);
ASSERT_EQUAL_TOL(0.5*(1.0 + 2.0*1.5*1.5 + 3.5*1.4*1.4), state.getPotentialEnergy(), TOL);
}
}
void testManyParameters() {
......
platforms/opencl/tests/TestOpenCLCustomGBForce.cpp
View file @ 99cebd08
......@@ -7,7 +7,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2008-2009 Stanford University and the Authors. *
* Portions copyright (c) 2008-2012 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -139,6 +139,29 @@ void testOBC(GBSAOBCForce::NonbondedMethod obcMethod, CustomGBForce::NonbondedMe
for (int i = 0; i < numParticles; i++) {
ASSERT_EQUAL_VEC(state1.getForces()[i], state2.getForces()[i], 1e-4);
}
// Try changing the particle parameters and make sure it's still correct.
for (int i = 0; i < numMolecules/2; i++) {
obc->setParticleParameters(2*i, 1.1, 0.3, 0.6);
params[0] = 1.1;
params[1] = 0.3;
params[2] = 0.6;
custom->setParticleParameters(2*i, params);
obc->setParticleParameters(2*i+1, -1.1, 0.2, 0.4);
params[0] = -1.1;
params[1] = 0.2;
params[2] = 0.4;
custom->setParticleParameters(2*i+1, params);
}
obc->updateParametersInContext(context1);
custom->updateParametersInContext(context2);
state1 = context1.getState(State::Forces | State::Energy);
state2 = context2.getState(State::Forces | State::Energy);
ASSERT_EQUAL_TOL(state1.getPotentialEnergy(), state2.getPotentialEnergy(), 1e-4);
for (int i = 0; i < numParticles; i++) {
ASSERT_EQUAL_VEC(state1.getForces()[i], state2.getForces()[i], 1e-4);
}
}
void testMembrane() {
......
platforms/opencl/tests/TestOpenCLCustomHbondForce.cpp
View file @ 99cebd08
......@@ -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) 2008-2010 Stanford University and the Authors. *
* Portions copyright (c) 2008-2012 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -100,7 +100,7 @@ void testHbond() {
angle->addAngle(1, 2, 3, 1.9, 0.6);
standardSystem.addForce(angle);
PeriodicTorsionForce* torsion = new PeriodicTorsionForce();
torsion->addTorsion(1, 2, 3, 4, 2, 2.1, 0.7);;
torsion->addTorsion(1, 2, 3, 4, 2, 2.1, 0.7);
standardSystem.addForce(torsion);
// Set the atoms in various positions, and verify that both systems give identical forces and energy.
......@@ -109,11 +109,11 @@ void testHbond() {
init_gen_rand(0, sfmt);
vector<Vec3> positions(5);
VerletIntegrator integrator1(0.01);
VerletIntegrator integrator2(0.01);
Context c1(customSystem, integrator1, platform);
Context c2(standardSystem, integrator2, platform);
for (int i = 0; i < 10; i++) {
VerletIntegrator integrator1(0.01);
VerletIntegrator integrator2(0.01);
Context c1(customSystem, integrator1, platform);
Context c2(standardSystem, integrator2, platform);
for (int j = 0; j < (int) positions.size(); j++)
positions[j] = Vec3(2.0*genrand_real2(sfmt), 2.0*genrand_real2(sfmt), 2.0*genrand_real2(sfmt));
c1.setPositions(positions);
......@@ -124,6 +124,28 @@ void testHbond() {
ASSERT_EQUAL_VEC(s2.getForces()[i], s1.getForces()[i], TOL);
ASSERT_EQUAL_TOL(s2.getPotentialEnergy(), s1.getPotentialEnergy(), TOL);
}
// Try changing the parameters and make sure it's still correct.
parameters.resize(3);
parameters[0] = 1.4;
parameters[1] = 1.7;
parameters[2] = 1.9;
custom->setDonorParameters(0, 1, 0, -1, parameters);
parameters.resize(2);
parameters[0] = 2.2;
parameters[1] = 2;
custom->setAcceptorParameters(0, 2, 3, 4, parameters);
bond->setBondParameters(0, 1, 2, 1.4, 0.4);
torsion->setTorsionParameters(0, 1, 2, 3, 4, 2, 2.2, 0.7);
custom->updateParametersInContext(c1);
bond->updateParametersInContext(c2);
torsion->updateParametersInContext(c2);
State s1 = c1.getState(State::Forces | State::Energy);
State s2 = c2.getState(State::Forces | State::Energy);
for (int i = 0; i < customSystem.getNumParticles(); i++)
ASSERT_EQUAL_VEC(s2.getForces()[i], s1.getForces()[i], TOL);
ASSERT_EQUAL_TOL(s2.getPotentialEnergy(), s1.getPotentialEnergy(), TOL);
}
void testExclusions() {
......
platforms/opencl/tests/TestOpenCLCustomNonbondedForce.cpp
View file @ 99cebd08
......@@ -7,7 +7,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2008-2009 Stanford University and the Authors. *
* Portions copyright (c) 2008-2012 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -105,6 +105,9 @@ void testParameters() {
ASSERT_EQUAL_VEC(Vec3(-force, 0, 0), forces[0], TOL);
ASSERT_EQUAL_VEC(Vec3(force, 0, 0), forces[1], TOL);
ASSERT_EQUAL_TOL(3.0*(10*10*10), state.getPotentialEnergy(), TOL);
// Try changing the global parameters and make sure it's still correct.
context.setParameter("scale", 1.5);
context.setParameter("c", 1.0);
state = context.getState(State::Forces | State::Energy);
......@@ -113,6 +116,22 @@ void testParameters() {
ASSERT_EQUAL_VEC(Vec3(-force, 0, 0), forces[0], TOL);
ASSERT_EQUAL_VEC(Vec3(force, 0, 0), forces[1], TOL);
ASSERT_EQUAL_TOL(1.5*3.0*(12*12*12), state.getPotentialEnergy(), TOL);
// Try changing the per-particle parameters and make sure it's still correct.
params[0] = 1.6;
params[1] = 2.1;
forceField->setParticleParameters(0, params);
params[0] = 1.9;
params[1] = 2.8;
forceField->setParticleParameters(1, params);
forceField->updateParametersInContext(context);
state = context.getState(State::Forces | State::Energy);
forces = state.getForces();
force = -1.5*1.6*1.9*3*5.9*(11.8*11.8);
ASSERT_EQUAL_VEC(Vec3(-force, 0, 0), forces[0], TOL);
ASSERT_EQUAL_VEC(Vec3(force, 0, 0), forces[1], TOL);
ASSERT_EQUAL_TOL(1.5*1.6*1.9*(11.8*11.8*11.8), state.getPotentialEnergy(), TOL);
}
void testManyParameters() {
......
platforms/reference/src/ReferenceKernels.cpp
View file @ 99cebd08
......@@ -1041,6 +1041,22 @@ double ReferenceCalcCustomNonbondedForceKernel::execute(ContextImpl& context, bo
return energy;
}
void ReferenceCalcCustomNonbondedForceKernel::copyParametersToContext(ContextImpl& context, const CustomNonbondedForce& force) {
if (numParticles != force.getNumParticles())
throw OpenMMException("updateParametersInContext: The number of particles has changed");
// Record the values.
int numParameters = force.getNumPerParticleParameters();
vector<double> params;
for (int i = 0; i < numParticles; ++i) {
vector<double> parameters;
force.getParticleParameters(i, parameters);
for (int j = 0; j < numParameters; j++)
particleParamArray[i][j] = static_cast<RealOpenMM>(parameters[j]);
}
}
ReferenceCalcGBSAOBCForceKernel::~ReferenceCalcGBSAOBCForceKernel() {
if (obc) {
// delete obc->getObcParameters();
......@@ -1303,6 +1319,22 @@ double ReferenceCalcCustomGBForceKernel::execute(ContextImpl& context, bool incl
return energy;
}
void ReferenceCalcCustomGBForceKernel::copyParametersToContext(ContextImpl& context, const CustomGBForce& force) {
if (numParticles != force.getNumParticles())
throw OpenMMException("updateParametersInContext: The number of particles has changed");
// Record the values.
int numParameters = force.getNumPerParticleParameters();
vector<double> params;
for (int i = 0; i < numParticles; ++i) {
vector<double> parameters;
force.getParticleParameters(i, parameters);
for (int j = 0; j < numParameters; j++)
particleParamArray[i][j] = static_cast<RealOpenMM>(parameters[j]);
}
}
ReferenceCalcCustomExternalForceKernel::~ReferenceCalcCustomExternalForceKernel() {
disposeRealArray(particleParamArray, numParticles);
}
......@@ -1348,6 +1380,25 @@ double ReferenceCalcCustomExternalForceKernel::execute(ContextImpl& context, boo
return energy;
}
void ReferenceCalcCustomExternalForceKernel::copyParametersToContext(ContextImpl& context, const CustomExternalForce& force) {
if (numParticles != force.getNumParticles())
throw OpenMMException("updateParametersInContext: The number of particles has changed");
// Record the values.
int numParameters = force.getNumPerParticleParameters();
vector<double> params;
for (int i = 0; i < numParticles; ++i) {
int particle;
vector<double> parameters;
force.getParticleParameters(i, particle, parameters);
if (particle != particles[i])
throw OpenMMException("updateParametersInContext: A particle index has changed");
for (int j = 0; j < numParameters; j++)
particleParamArray[i][j] = static_cast<RealOpenMM>(parameters[j]);
}
}
ReferenceCalcCustomHbondForceKernel::~ReferenceCalcCustomHbondForceKernel() {
disposeRealArray(donorParamArray, numDonors);
disposeRealArray(acceptorParamArray, numAcceptors);
......@@ -1458,6 +1509,37 @@ double ReferenceCalcCustomHbondForceKernel::execute(ContextImpl& context, bool i
return energy;
}
void ReferenceCalcCustomHbondForceKernel::copyParametersToContext(ContextImpl& context, const CustomHbondForce& force) {
if (numDonors != force.getNumDonors())
throw OpenMMException("updateParametersInContext: The number of donors has changed");
if (numAcceptors != force.getNumAcceptors())
throw OpenMMException("updateParametersInContext: The number of acceptors has changed");
// Record the values.
vector<double> parameters;
int numDonorParameters = force.getNumPerDonorParameters();
const vector<vector<int> >& donorAtoms = ixn->getDonorAtoms();
for (int i = 0; i < numDonors; ++i) {
int d1, d2, d3;
force.getDonorParameters(i, d1, d2, d3, parameters);
if (d1 != donorAtoms[i][0] || d2 != donorAtoms[i][1] || d3 != donorAtoms[i][2])
throw OpenMMException("updateParametersInContext: The set of particles in a donor group has changed");
for (int j = 0; j < numDonorParameters; j++)
donorParamArray[i][j] = static_cast<RealOpenMM>(parameters[j]);
}
int numAcceptorParameters = force.getNumPerAcceptorParameters();
const vector<vector<int> >& acceptorAtoms = ixn->getAcceptorAtoms();
for (int i = 0; i < numAcceptors; ++i) {
int a1, a2, a3;
force.getAcceptorParameters(i, a1, a2, a3, parameters);
if (a1 != acceptorAtoms[i][0] || a2 != acceptorAtoms[i][1] || a3 != acceptorAtoms[i][2])
throw OpenMMException("updateParametersInContext: The set of particles in an acceptor group has changed");
for (int j = 0; j < numAcceptorParameters; j++)
acceptorParamArray[i][j] = static_cast<RealOpenMM>(parameters[j]);
}
}
ReferenceCalcCustomCompoundBondForceKernel::~ReferenceCalcCustomCompoundBondForceKernel() {
disposeRealArray(bondParamArray, numBonds);
if (ixn != NULL)
......@@ -1521,6 +1603,26 @@ double ReferenceCalcCustomCompoundBondForceKernel::execute(ContextImpl& context,
return energy;
}
void ReferenceCalcCustomCompoundBondForceKernel::copyParametersToContext(ContextImpl& context, const CustomCompoundBondForce& force) {
if (numBonds != force.getNumBonds())
throw OpenMMException("updateParametersInContext: The number of bonds has changed");
// Record the values.
int numParameters = force.getNumPerBondParameters();
const vector<vector<int> >& bondAtoms = ixn->getBondAtoms();
vector<int> particles;
vector<double> params;
for (int i = 0; i < numBonds; ++i) {
force.getBondParameters(i, particles, params);
for (int j = 0; j < numParticles; j++)
if (particles[j] != bondAtoms[i][j])
throw OpenMMException("updateParametersInContext: The set of particles in a bond has changed");
for (int j = 0; j < numParameters; j++)
bondParamArray[i][j] = (RealOpenMM) params[j];
}
}
ReferenceIntegrateVerletStepKernel::~ReferenceIntegrateVerletStepKernel() {
if (dynamics)
delete dynamics;
......
platforms/reference/src/ReferenceKernels.h
View file @ 99cebd08
......@@ -598,6 +598,13 @@ public:
* @return the potential energy due to the force
*/
double execute(ContextImpl& context, bool includeForces, bool includeEnergy);
/**
* Copy changed parameters over to a context.
*
* @param context the context to copy parameters to
* @param force the CustomNonbondedForce to copy the parameters from
*/
void copyParametersToContext(ContextImpl& context, const CustomNonbondedForce& force);
private:
int numParticles;
int **exclusionArray;
......@@ -702,6 +709,13 @@ public:
* @return the potential energy due to the force
*/
double execute(ContextImpl& context, bool includeForces, bool includeEnergy);
/**
* Copy changed parameters over to a context.
*
* @param context the context to copy parameters to
* @param force the CustomGBForce to copy the parameters from
*/
void copyParametersToContext(ContextImpl& context, const CustomGBForce& force);
private:
int numParticles;
bool isPeriodic;
......@@ -745,6 +759,13 @@ public:
* @return the potential energy due to the force
*/
double execute(ContextImpl& context, bool includeForces, bool includeEnergy);
/**
* Copy changed parameters over to a context.
*
* @param context the context to copy parameters to
* @param force the CustomExternalForce to copy the parameters from
*/
void copyParametersToContext(ContextImpl& context, const CustomExternalForce& force);
private:
int numParticles;
std::vector<int> particles;
......@@ -777,6 +798,13 @@ public:
* @return the potential energy due to the force
*/
double execute(ContextImpl& context, bool includeForces, bool includeEnergy);
/**
* Copy changed parameters over to a context.
*
* @param context the context to copy parameters to
* @param force the CustomHbondForce to copy the parameters from
*/
void copyParametersToContext(ContextImpl& context, const CustomHbondForce& force);
private:
int numDonors, numAcceptors, numParticles;
bool isPeriodic;
......@@ -812,6 +840,13 @@ public:
* @return the potential energy due to the force
*/
double execute(ContextImpl& context, bool includeForces, bool includeEnergy);
/**
* Copy changed parameters over to a context.
*
* @param context the context to copy parameters to
* @param force the CustomCompoundBondForce to copy the parameters from
*/
void copyParametersToContext(ContextImpl& context, const CustomCompoundBondForce& force);
private:
int numBonds, numParticles;
RealOpenMM **bondParamArray;
......
platforms/reference/src/SimTKReference/ReferenceCustomCompoundBondIxn.h
View file @ 99cebd08
......@@ -91,6 +91,15 @@ class ReferenceCustomCompoundBondIxn : public ReferenceBondIxn {
~ReferenceCustomCompoundBondIxn();
/**---------------------------------------------------------------------------------------
Get the list atoms in each bond.
--------------------------------------------------------------------------------------- */
const std::vector<std::vector<int> >& getBondAtoms() const {
return bondAtoms;
}
/**---------------------------------------------------------------------------------------
......
platforms/reference/src/SimTKReference/ReferenceCustomHbondIxn.h
View file @ 99cebd08
......@@ -116,6 +116,26 @@ class ReferenceCustomHbondIxn : public ReferenceBondIxn {
void setPeriodic(OpenMM::RealVec& boxSize);
/**---------------------------------------------------------------------------------------
Get the list of atoms for each donor group.
--------------------------------------------------------------------------------------- */
const std::vector<std::vector<int> >& getDonorAtoms() const {
return donorAtoms;
}
/**---------------------------------------------------------------------------------------
Get the list of atoms for each acceptor group.
--------------------------------------------------------------------------------------- */
const std::vector<std::vector<int> >& getAcceptorAtoms() const {
return acceptorAtoms;
}
/**---------------------------------------------------------------------------------------
Calculate custom hbond interaction
......
platforms/reference/tests/TestReferenceCustomCompoundBondForce.cpp
View file @ 99cebd08
......@@ -121,6 +121,24 @@ void testBond() {
ASSERT_EQUAL_VEC(s1.getForces()[i], s2.getForces()[i], TOL);
ASSERT_EQUAL_TOL(s1.getPotentialEnergy(), s2.getPotentialEnergy(), TOL);
}
// Try changing the bond parameters and make sure it's still correct.
parameters[0] = 1.6;
parameters[3] = 1.3;
custom->setBondParameters(0, particles, parameters);
custom->updateParametersInContext(c1);
bonds->setBondParameters(0, 0, 1, 1.3, 1.6);
bonds->setBondParameters(1, 1, 3, 1.3, 1.6);
bonds->updateParametersInContext(c2);
{
State s1 = c1.getState(State::Forces | State::Energy);
State s2 = c2.getState(State::Forces | State::Energy);
const vector<Vec3>& forces = s1.getForces();
for (int i = 0; i < customSystem.getNumParticles(); i++)
ASSERT_EQUAL_VEC(s1.getForces()[i], s2.getForces()[i], TOL);
ASSERT_EQUAL_TOL(s1.getPotentialEnergy(), s2.getPotentialEnergy(), TOL);
}
}
void testPositionDependence() {
......
platforms/reference/tests/TestReferenceCustomExternalForce.cpp
View file @ 99cebd08
......@@ -74,11 +74,28 @@ void testForce() {
positions[2] = Vec3(1, 0, 1);
context.setPositions(positions);
State state = context.getState(State::Forces | State::Energy);
const vector<Vec3>& forces = state.getForces();
ASSERT_EQUAL_VEC(Vec3(-0.5, -0.5*2.0*2.0*1.5, 0), forces[0], TOL);
ASSERT_EQUAL_VEC(Vec3(0, 0, 0), forces[1], TOL);
ASSERT_EQUAL_VEC(Vec3(-0.5, 0.5*3.0*2.0*1.5, 0), forces[2], TOL);
ASSERT_EQUAL_TOL(0.5*(1.0 + 2.0*1.5*1.5 + 3.0*1.5*1.5), state.getPotentialEnergy(), TOL);
{
const vector<Vec3>& forces = state.getForces();
ASSERT_EQUAL_VEC(Vec3(-0.5, -0.5*2.0*2.0*1.5, 0), forces[0], TOL);
ASSERT_EQUAL_VEC(Vec3(0, 0, 0), forces[1], TOL);
ASSERT_EQUAL_VEC(Vec3(-0.5, 0.5*3.0*2.0*1.5, 0), forces[2], TOL);
ASSERT_EQUAL_TOL(0.5*(1.0 + 2.0*1.5*1.5 + 3.0*1.5*1.5), state.getPotentialEnergy(), TOL);
}
// Try changing the parameters and make sure it's still correct.
parameters[0] = 1.4;
parameters[1] = 3.5;
forceField->setParticleParameters(1, 2, parameters);
forceField->updateParametersInContext(context);
state = context.getState(State::Forces | State::Energy);
{
const vector<Vec3>& forces = state.getForces();
ASSERT_EQUAL_VEC(Vec3(-0.5, -0.5*2.0*2.0*1.5, 0), forces[0], TOL);
ASSERT_EQUAL_VEC(Vec3(0, 0, 0), forces[1], TOL);
ASSERT_EQUAL_VEC(Vec3(-0.5, 0.5*3.5*2.0*1.4, 0), forces[2], TOL);
ASSERT_EQUAL_TOL(0.5*(1.0 + 2.0*1.5*1.5 + 3.5*1.4*1.4), state.getPotentialEnergy(), TOL);
}
}
int main() {
......
platforms/reference/tests/TestReferenceCustomGBForce.cpp
View file @ 99cebd08
......@@ -7,7 +7,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2008-2009 Stanford University and the Authors. *
* Portions copyright (c) 2008-2012 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -142,6 +142,29 @@ void testOBC(GBSAOBCForce::NonbondedMethod obcMethod, CustomGBForce::NonbondedMe
for (int i = 0; i < numParticles; i++) {
ASSERT_EQUAL_VEC(state1.getForces()[i], state2.getForces()[i], 1e-4);
}
// Try changing the particle parameters and make sure it's still correct.
for (int i = 0; i < numMolecules/2; i++) {
obc->setParticleParameters(2*i, 1.1, 0.3, 0.6);
params[0] = 1.1;
params[1] = 0.3;
params[2] = 0.6;
custom->setParticleParameters(2*i, params);
obc->setParticleParameters(2*i+1, -1.1, 0.2, 0.4);
params[0] = -1.1;
params[1] = 0.2;
params[2] = 0.4;
custom->setParticleParameters(2*i+1, params);
}
obc->updateParametersInContext(context1);
custom->updateParametersInContext(context2);
state1 = context1.getState(State::Forces | State::Energy);
state2 = context2.getState(State::Forces | State::Energy);
ASSERT_EQUAL_TOL(state1.getPotentialEnergy(), state2.getPotentialEnergy(), 1e-4);
for (int i = 0; i < numParticles; i++) {
ASSERT_EQUAL_VEC(state1.getForces()[i], state2.getForces()[i], 1e-4);
}
}
void testMembrane() {
......
platforms/reference/tests/TestReferenceCustomHbondForce.cpp
View file @ 99cebd08
......@@ -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) 2008-2010 Stanford University and the Authors. *
* Portions copyright (c) 2008-2012 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -100,7 +100,7 @@ void testHbond() {
angle->addAngle(1, 2, 3, 1.9, 0.6);
standardSystem.addForce(angle);
PeriodicTorsionForce* torsion = new PeriodicTorsionForce();
torsion->addTorsion(1, 2, 3, 4, 2, 2.1, 0.7);;
torsion->addTorsion(1, 2, 3, 4, 2, 2.1, 0.7);
standardSystem.addForce(torsion);
// Set the atoms in various positions, and verify that both systems give identical forces and energy.
......@@ -109,11 +109,11 @@ void testHbond() {
init_gen_rand(0, sfmt);
vector<Vec3> positions(5);
VerletIntegrator integrator1(0.01);
VerletIntegrator integrator2(0.01);
Context c1(customSystem, integrator1, platform);
Context c2(standardSystem, integrator2, platform);
for (int i = 0; i < 10; i++) {
VerletIntegrator integrator1(0.01);
VerletIntegrator integrator2(0.01);
Context c1(customSystem, integrator1, platform);
Context c2(standardSystem, integrator2, platform);
for (int j = 0; j < (int) positions.size(); j++)
positions[j] = Vec3(2.0*genrand_real2(sfmt), 2.0*genrand_real2(sfmt), 2.0*genrand_real2(sfmt));
c1.setPositions(positions);
......@@ -124,6 +124,28 @@ void testHbond() {
ASSERT_EQUAL_VEC(s2.getForces()[i], s1.getForces()[i], TOL);
ASSERT_EQUAL_TOL(s2.getPotentialEnergy(), s1.getPotentialEnergy(), TOL);
}
// Try changing the parameters and make sure it's still correct.
parameters.resize(3);
parameters[0] = 1.4;
parameters[1] = 1.7;
parameters[2] = 1.9;
custom->setDonorParameters(0, 1, 0, -1, parameters);
parameters.resize(2);
parameters[0] = 2.2;
parameters[1] = 2;
custom->setAcceptorParameters(0, 2, 3, 4, parameters);
bond->setBondParameters(0, 1, 2, 1.4, 0.4);
torsion->setTorsionParameters(0, 1, 2, 3, 4, 2, 2.2, 0.7);
custom->updateParametersInContext(c1);
bond->updateParametersInContext(c2);
torsion->updateParametersInContext(c2);
State s1 = c1.getState(State::Forces | State::Energy);
State s2 = c2.getState(State::Forces | State::Energy);
for (int i = 0; i < customSystem.getNumParticles(); i++)
ASSERT_EQUAL_VEC(s2.getForces()[i], s1.getForces()[i], TOL);
ASSERT_EQUAL_TOL(s2.getPotentialEnergy(), s1.getPotentialEnergy(), TOL);
}
void testExclusions() {
......
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