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Commit 2762adf4 authored by peastman's avatar peastman
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Merge pull request #854 from peastman/cmap 

CMAPTorsionForce implements updateParametersInContext()
parents 1cb9c795 6dc2f9a8
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Showing with 383 additions and 18 deletions
olla/include/openmm/kernels.h
View file @ 2762adf4
......@@ -9,7 +9,7 @@
* 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) 2008-2015 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -494,6 +494,13 @@ public:
* @return the potential energy due to the force
*/
virtual double execute(ContextImpl& context, bool includeForces, bool includeEnergy) = 0;
/**
* Copy changed parameters over to a context.
*
* @param context the context to copy parameters to
* @param force the CMAPTorsionForce to copy the parameters from
*/
virtual void copyParametersToContext(ContextImpl& context, const CMAPTorsionForce& force) = 0;
};
/**
......
openmmapi/include/openmm/CMAPTorsionForce.h
View file @ 2762adf4
......@@ -9,7 +9,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2010 Stanford University and the Authors. *
* Portions copyright (c) 2010-2015 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -148,6 +148,17 @@ public:
* @param b4 the index of the fourth particle forming the second torsion
*/
void setTorsionParameters(int index, int map, int a1, int a2, int a3, int a4, int b1, int b2, int b3, int b4);
/**
* Update the map and torsion parameters in a Context to match those stored in this Force object. This method provides
* an efficient method to update certain parameters in an existing Context without needing to reinitialize it.
* Simply call setMapParameters() and setTorsionParameters() to modify this object's parameters, then call updateParametersInContext()
* to copy them over to the Context.
*
* The only information that can be updated with this method is the energy values for a map, and the map index
* for a torsion. The size of a map and the set of particles involved in a torsion cannot be changed. Also,
* new bonds and torsions cannot be added.
*/
void updateParametersInContext(Context& context);
/**
* Returns whether or not this force makes use of periodic boundary
* conditions.
......
openmmapi/include/openmm/internal/CMAPTorsionForceImpl.h
View file @ 2762adf4
......@@ -9,7 +9,7 @@
* 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) 2008-2015 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -60,6 +60,7 @@ public:
return std::map<std::string, double>(); // This force field doesn't define any parameters.
}
std::vector<std::string> getKernelNames();
void updateParametersInContext(ContextImpl& context);
/**
* Given the energy values for a map, compute the spline coefficients at each point of the map.
*/
......
openmmapi/src/CMAPTorsionForce.cpp
View file @ 2762adf4
......@@ -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) 2010 Stanford University and the Authors. *
* Portions copyright (c) 2010-2015 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -96,3 +96,6 @@ ForceImpl* CMAPTorsionForce::createImpl() const {
return new CMAPTorsionForceImpl(*this);
}
void CMAPTorsionForce::updateParametersInContext(Context& context) {
dynamic_cast<CMAPTorsionForceImpl&>(getImplInContext(context)).updateParametersInContext(getContextImpl(context));
}
openmmapi/src/CMAPTorsionForceImpl.cpp
View file @ 2762adf4
......@@ -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) 2010 Stanford University and the Authors. *
* Portions copyright (c) 2010-2015 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -155,3 +155,7 @@ void CMAPTorsionForceImpl::calcMapDerivatives(int size, const vector<double>& en
}
}
}
void CMAPTorsionForceImpl::updateParametersInContext(ContextImpl& context) {
kernel.getAs<CalcCMAPTorsionForceKernel>().copyParametersToContext(context, owner);
}
platforms/cuda/include/CudaKernels.h
View file @ 2762adf4
......@@ -9,7 +9,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2008-2013 Stanford University and the Authors. *
* Portions copyright (c) 2008-2015 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -520,11 +520,19 @@ 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 CMAPTorsionForce to copy the parameters from
*/
void copyParametersToContext(ContextImpl& context, const CMAPTorsionForce& force);
private:
int numTorsions;
bool hasInitializedKernel;
CudaContext& cu;
const System& system;
std::vector<int2> mapPositionsVec;
CudaArray* coefficients;
CudaArray* mapPositions;
CudaArray* torsionMaps;
......
platforms/cuda/include/CudaParallelKernels.h
View file @ 2762adf4
......@@ -9,7 +9,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2011-2013 Stanford University and the Authors. *
* Portions copyright (c) 2011-2015 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -345,6 +345,13 @@ 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 CMAPTorsionForce to copy the parameters from
*/
void copyParametersToContext(ContextImpl& context, const CMAPTorsionForce& force);
private:
class Task;
CudaPlatform::PlatformData& data;
......
platforms/cuda/src/CudaKernels.cpp
View file @ 2762adf4
......@@ -1127,7 +1127,7 @@ void CudaCalcCMAPTorsionForceKernel::initialize(const System& system, const CMAP
return;
int numMaps = force.getNumMaps();
vector<float4> coeffVec;
vector<int2> mapPositionsVec(numMaps);
mapPositionsVec.resize(numMaps);
vector<double> energy;
vector<vector<double> > c;
int currentPosition = 0;
......@@ -1166,6 +1166,49 @@ double CudaCalcCMAPTorsionForceKernel::execute(ContextImpl& context, bool includ
return 0.0;
}
void CudaCalcCMAPTorsionForceKernel::copyParametersToContext(ContextImpl& context, const CMAPTorsionForce& force) {
int numMaps = force.getNumMaps();
int numContexts = cu.getPlatformData().contexts.size();
int startIndex = cu.getContextIndex()*force.getNumTorsions()/numContexts;
int endIndex = (cu.getContextIndex()+1)*force.getNumTorsions()/numContexts;
numTorsions = endIndex-startIndex;
if (mapPositions->getSize() != numMaps)
throw OpenMMException("updateParametersInContext: The number of maps has changed");
if (torsionMaps->getSize() != numTorsions)
throw OpenMMException("updateParametersInContext: The number of CMAP torsions has changed");
// Update the maps.
vector<float4> coeffVec;
vector<double> energy;
vector<vector<double> > c;
int currentPosition = 0;
for (int i = 0; i < numMaps; i++) {
int size;
force.getMapParameters(i, size, energy);
if (size != mapPositionsVec[i].y)
throw OpenMMException("updateParametersInContext: The size of a map has changed");
CMAPTorsionForceImpl::calcMapDerivatives(size, energy, c);
currentPosition += 4*size*size;
for (int j = 0; j < size*size; j++) {
coeffVec.push_back(make_float4((float) c[j][0], (float) c[j][1], (float) c[j][2], (float) c[j][3]));
coeffVec.push_back(make_float4((float) c[j][4], (float) c[j][5], (float) c[j][6], (float) c[j][7]));
coeffVec.push_back(make_float4((float) c[j][8], (float) c[j][9], (float) c[j][10], (float) c[j][11]));
coeffVec.push_back(make_float4((float) c[j][12], (float) c[j][13], (float) c[j][14], (float) c[j][15]));
}
}
coefficients->upload(coeffVec);
// Update the indices.
vector<int> torsionMapsVec(numTorsions);
for (int i = 0; i < numTorsions; i++) {
int index[8];
force.getTorsionParameters(i, torsionMapsVec[i], index[0], index[1], index[2], index[3], index[4], index[5], index[6], index[7]);
}
torsionMaps->upload(torsionMapsVec);
}
class CudaCustomTorsionForceInfo : public CudaForceInfo {
public:
CudaCustomTorsionForceInfo(const CustomTorsionForce& force) : force(force) {
......
platforms/cuda/src/CudaParallelKernels.cpp
View file @ 2762adf4
......@@ -536,6 +536,11 @@ double CudaParallelCalcCMAPTorsionForceKernel::execute(ContextImpl& context, boo
return 0.0;
}
void CudaParallelCalcCMAPTorsionForceKernel::copyParametersToContext(ContextImpl& context, const CMAPTorsionForce& force) {
for (int i = 0; i < (int) kernels.size(); i++)
getKernel(i).copyParametersToContext(context, force);
}
class CudaParallelCalcCustomTorsionForceKernel::Task : public CudaContext::WorkTask {
public:
Task(ContextImpl& context, CudaCalcCustomTorsionForceKernel& kernel, bool includeForce,
......
platforms/cuda/tests/TestCudaCMAPTorsionForce.cpp
View file @ 2762adf4
......@@ -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) 2010-2012 Stanford University and the Authors. *
* Portions copyright (c) 2010-2015 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -105,11 +105,68 @@ void testCMAPTorsions() {
}
}
void testChangingParameters() {
// Create a system with two maps and one torsion.
const int mapSize = 8;
System system;
for (int i = 0; i < 5; i++)
system.addParticle(1.0);
CMAPTorsionForce* cmap = new CMAPTorsionForce();
vector<double> mapEnergy1(mapSize*mapSize);
vector<double> mapEnergy2(mapSize*mapSize);
for (int i = 0; i < mapSize; i++) {
double angle1 = i*2*M_PI/mapSize;
double energy1 = cos(angle1);
for (int j = 0; j < mapSize; j++) {
double angle2 = j*2*M_PI/mapSize;
double energy2 = 10*sin(angle2);
mapEnergy1[i+j*mapSize] = energy1+energy2;
mapEnergy2[i+j*mapSize] = energy1-energy2;
}
}
cmap->addMap(mapSize, mapEnergy1);
cmap->addMap(mapSize, mapEnergy2);
cmap->addTorsion(0, 0, 1, 2, 3, 1, 2, 3, 4);
system.addForce(cmap);
// Set particle positions so angle1=0 and angle2=PI/4.
vector<Vec3> positions(5);
positions[0] = Vec3(0, 0, 1);
positions[1] = Vec3(0, 0, 0);
positions[2] = Vec3(1, 0, 0);
positions[3] = Vec3(1, 0, 1);
positions[4] = Vec3(0.5, -0.5, 1);
VerletIntegrator integrator(0.01);
Context context(system, integrator, platform);
context.setPositions(positions);
// Check that the energy is correct.
double energy = context.getState(State::Energy).getPotentialEnergy();
ASSERT_EQUAL_TOL(1+10*sin(M_PI/4), energy, 1e-5);
// Modify the parameters.
cmap->setTorsionParameters(0, 1, 0, 1, 2, 3, 1, 2, 3, 4);
for (int i = 0; i < mapSize*mapSize; i++)
mapEnergy2[i] *= 2.0;
cmap->setMapParameters(1, mapSize, mapEnergy2);
cmap->updateParametersInContext(context);
// See if the results are correct.
energy = context.getState(State::Energy).getPotentialEnergy();
ASSERT_EQUAL_TOL(2-20*sin(M_PI/4), energy, 1e-5);
}
int main(int argc, char* argv[]) {
try {
if (argc > 1)
platform.setPropertyDefaultValue("CudaPrecision", string(argv[1]));
testCMAPTorsions();
testChangingParameters();
}
catch(const exception& e) {
cout << "exception: " << e.what() << endl;
......
platforms/opencl/include/OpenCLKernels.h
View file @ 2762adf4
......@@ -9,7 +9,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2008-2013 Stanford University and the Authors. *
* Portions copyright (c) 2008-2015 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -498,11 +498,19 @@ 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 CMAPTorsionForce to copy the parameters from
*/
void copyParametersToContext(ContextImpl& context, const CMAPTorsionForce& force);
private:
int numTorsions;
bool hasInitializedKernel;
OpenCLContext& cl;
const System& system;
std::vector<mm_int2> mapPositionsVec;
OpenCLArray* coefficients;
OpenCLArray* mapPositions;
OpenCLArray* torsionMaps;
......
platforms/opencl/include/OpenCLParallelKernels.h
View file @ 2762adf4
......@@ -9,7 +9,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2011-2013 Stanford University and the Authors. *
* Portions copyright (c) 2011-2015 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -344,6 +344,13 @@ 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 CMAPTorsionForce to copy the parameters from
*/
void copyParametersToContext(ContextImpl& context, const CMAPTorsionForce& force);
private:
class Task;
OpenCLPlatform::PlatformData& data;
......
platforms/opencl/src/OpenCLKernels.cpp
View file @ 2762adf4
......@@ -1125,7 +1125,7 @@ void OpenCLCalcCMAPTorsionForceKernel::initialize(const System& system, const CM
return;
int numMaps = force.getNumMaps();
vector<mm_float4> coeffVec;
vector<mm_int2> mapPositionsVec(numMaps);
mapPositionsVec.resize(numMaps);
vector<double> energy;
vector<vector<double> > c;
int currentPosition = 0;
......@@ -1164,6 +1164,49 @@ double OpenCLCalcCMAPTorsionForceKernel::execute(ContextImpl& context, bool incl
return 0.0;
}
void OpenCLCalcCMAPTorsionForceKernel::copyParametersToContext(ContextImpl& context, const CMAPTorsionForce& force) {
int numMaps = force.getNumMaps();
int numContexts = cl.getPlatformData().contexts.size();
int startIndex = cl.getContextIndex()*force.getNumTorsions()/numContexts;
int endIndex = (cl.getContextIndex()+1)*force.getNumTorsions()/numContexts;
numTorsions = endIndex-startIndex;
if (mapPositions->getSize() != numMaps)
throw OpenMMException("updateParametersInContext: The number of maps has changed");
if (torsionMaps->getSize() != numTorsions)
throw OpenMMException("updateParametersInContext: The number of CMAP torsions has changed");
// Update the maps.
vector<mm_float4> coeffVec;
vector<double> energy;
vector<vector<double> > c;
int currentPosition = 0;
for (int i = 0; i < numMaps; i++) {
int size;
force.getMapParameters(i, size, energy);
if (size != mapPositionsVec[i].y)
throw OpenMMException("updateParametersInContext: The size of a map has changed");
CMAPTorsionForceImpl::calcMapDerivatives(size, energy, c);
currentPosition += 4*size*size;
for (int j = 0; j < size*size; j++) {
coeffVec.push_back(mm_float4((float) c[j][0], (float) c[j][1], (float) c[j][2], (float) c[j][3]));
coeffVec.push_back(mm_float4((float) c[j][4], (float) c[j][5], (float) c[j][6], (float) c[j][7]));
coeffVec.push_back(mm_float4((float) c[j][8], (float) c[j][9], (float) c[j][10], (float) c[j][11]));
coeffVec.push_back(mm_float4((float) c[j][12], (float) c[j][13], (float) c[j][14], (float) c[j][15]));
}
}
coefficients->upload(coeffVec);
// Update the indices.
vector<int> torsionMapsVec(numTorsions);
for (int i = 0; i < numTorsions; i++) {
int index[8];
force.getTorsionParameters(i, torsionMapsVec[i], index[0], index[1], index[2], index[3], index[4], index[5], index[6], index[7]);
}
torsionMaps->upload(torsionMapsVec);
}
class OpenCLCustomTorsionForceInfo : public OpenCLForceInfo {
public:
OpenCLCustomTorsionForceInfo(const CustomTorsionForce& force) : OpenCLForceInfo(0), force(force) {
......
platforms/opencl/src/OpenCLParallelKernels.cpp
View file @ 2762adf4
......@@ -492,6 +492,11 @@ double OpenCLParallelCalcCMAPTorsionForceKernel::execute(ContextImpl& context, b
return 0.0;
}
void OpenCLParallelCalcCMAPTorsionForceKernel::copyParametersToContext(ContextImpl& context, const CMAPTorsionForce& force) {
for (int i = 0; i < (int) kernels.size(); i++)
getKernel(i).copyParametersToContext(context, force);
}
class OpenCLParallelCalcCustomTorsionForceKernel::Task : public OpenCLContext::WorkTask {
public:
Task(ContextImpl& context, OpenCLCalcCustomTorsionForceKernel& kernel, bool includeForce,
......
platforms/opencl/tests/TestOpenCLCMAPTorsionForce.cpp
View file @ 2762adf4
......@@ -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) 2010 Stanford University and the Authors. *
* Portions copyright (c) 2010-2015 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -105,11 +105,68 @@ void testCMAPTorsions() {
}
}
void testChangingParameters() {
// Create a system with two maps and one torsion.
const int mapSize = 8;
System system;
for (int i = 0; i < 5; i++)
system.addParticle(1.0);
CMAPTorsionForce* cmap = new CMAPTorsionForce();
vector<double> mapEnergy1(mapSize*mapSize);
vector<double> mapEnergy2(mapSize*mapSize);
for (int i = 0; i < mapSize; i++) {
double angle1 = i*2*M_PI/mapSize;
double energy1 = cos(angle1);
for (int j = 0; j < mapSize; j++) {
double angle2 = j*2*M_PI/mapSize;
double energy2 = 10*sin(angle2);
mapEnergy1[i+j*mapSize] = energy1+energy2;
mapEnergy2[i+j*mapSize] = energy1-energy2;
}
}
cmap->addMap(mapSize, mapEnergy1);
cmap->addMap(mapSize, mapEnergy2);
cmap->addTorsion(0, 0, 1, 2, 3, 1, 2, 3, 4);
system.addForce(cmap);
// Set particle positions so angle1=0 and angle2=PI/4.
vector<Vec3> positions(5);
positions[0] = Vec3(0, 0, 1);
positions[1] = Vec3(0, 0, 0);
positions[2] = Vec3(1, 0, 0);
positions[3] = Vec3(1, 0, 1);
positions[4] = Vec3(0.5, -0.5, 1);
VerletIntegrator integrator(0.01);
Context context(system, integrator, platform);
context.setPositions(positions);
// Check that the energy is correct.
double energy = context.getState(State::Energy).getPotentialEnergy();
ASSERT_EQUAL_TOL(1+10*sin(M_PI/4), energy, 1e-5);
// Modify the parameters.
cmap->setTorsionParameters(0, 1, 0, 1, 2, 3, 1, 2, 3, 4);
for (int i = 0; i < mapSize*mapSize; i++)
mapEnergy2[i] *= 2.0;
cmap->setMapParameters(1, mapSize, mapEnergy2);
cmap->updateParametersInContext(context);
// See if the results are correct.
energy = context.getState(State::Energy).getPotentialEnergy();
ASSERT_EQUAL_TOL(2-20*sin(M_PI/4), energy, 1e-5);
}
int main(int argc, char* argv[]) {
try {
if (argc > 1)
platform.setPropertyDefaultValue("OpenCLPrecision", string(argv[1]));
testCMAPTorsions();
testChangingParameters();
}
catch(const exception& e) {
cout << "exception: " << e.what() << endl;
......
platforms/reference/include/ReferenceKernels.h
View file @ 2762adf4
......@@ -9,7 +9,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2008-2013 Stanford University and the Authors. *
* Portions copyright (c) 2008-2015 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -493,6 +493,13 @@ 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 CMAPTorsionForce to copy the parameters from
*/
void copyParametersToContext(ContextImpl& context, const CMAPTorsionForce& force);
private:
std::vector<std::vector<std::vector<RealOpenMM> > > coeff;
std::vector<int> torsionMaps;
......
platforms/reference/src/ReferenceKernels.cpp
View file @ 2762adf4
......@@ -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) 2008-2013 Stanford University and the Authors. *
* Portions copyright (c) 2008-2015 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -710,6 +710,40 @@ double ReferenceCalcCMAPTorsionForceKernel::execute(ContextImpl& context, bool i
return totalEnergy;
}
void ReferenceCalcCMAPTorsionForceKernel::copyParametersToContext(ContextImpl& context, const CMAPTorsionForce& force) {
int numMaps = force.getNumMaps();
int numTorsions = force.getNumTorsions();
if (coeff.size() != numMaps)
throw OpenMMException("updateParametersInContext: The number of maps has changed");
if (torsionMaps.size() != numTorsions)
throw OpenMMException("updateParametersInContext: The number of CMAP torsions has changed");
// Update the maps.
vector<double> energy;
vector<vector<double> > c;
for (int i = 0; i < numMaps; i++) {
int size;
force.getMapParameters(i, size, energy);
if (coeff[i].size() != size*size)
throw OpenMMException("updateParametersInContext: The size of a map has changed");
CMAPTorsionForceImpl::calcMapDerivatives(size, energy, c);
for (int j = 0; j < size*size; j++)
for (int k = 0; k < 16; k++)
coeff[i][j][k] = c[j][k];
}
// Update the indices.
for (int i = 0; i < numTorsions; i++) {
int index[8];
force.getTorsionParameters(i, torsionMaps[i], index[0], index[1], index[2], index[3], index[4], index[5], index[6], index[7]);
for (int j = 0; j < 8; j++)
if (index[j] != torsionIndices[i][j])
throw OpenMMException("updateParametersInContext: The set of particles in a CMAP torsion has changed");
}
}
ReferenceCalcCustomTorsionForceKernel::~ReferenceCalcCustomTorsionForceKernel() {
disposeIntArray(torsionIndexArray, numTorsions);
disposeRealArray(torsionParamArray, numTorsions);
......
platforms/reference/tests/TestReferenceCMAPTorsionForce.cpp
View file @ 2762adf4
......@@ -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) 2010 Stanford University and the Authors. *
* Portions copyright (c) 2010-2015 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -48,6 +48,8 @@
using namespace OpenMM;
using namespace std;
ReferencePlatform platform;
const double TOL = 1e-5;
void testCMAPTorsions() {
......@@ -56,7 +58,6 @@ void testCMAPTorsions() {
// Create two systems: one with a pair of periodic torsions, and one with a CMAP torsion
// that approximates the same force.
ReferencePlatform platform;
System system1;
for (int i = 0; i < 5; i++)
system1.addParticle(1.0);
......@@ -108,9 +109,66 @@ void testCMAPTorsions() {
}
}
void testChangingParameters() {
// Create a system with two maps and one torsion.
const int mapSize = 8;
System system;
for (int i = 0; i < 5; i++)
system.addParticle(1.0);
CMAPTorsionForce* cmap = new CMAPTorsionForce();
vector<double> mapEnergy1(mapSize*mapSize);
vector<double> mapEnergy2(mapSize*mapSize);
for (int i = 0; i < mapSize; i++) {
double angle1 = i*2*M_PI/mapSize;
double energy1 = cos(angle1);
for (int j = 0; j < mapSize; j++) {
double angle2 = j*2*M_PI/mapSize;
double energy2 = 10*sin(angle2);
mapEnergy1[i+j*mapSize] = energy1+energy2;
mapEnergy2[i+j*mapSize] = energy1-energy2;
}
}
cmap->addMap(mapSize, mapEnergy1);
cmap->addMap(mapSize, mapEnergy2);
cmap->addTorsion(0, 0, 1, 2, 3, 1, 2, 3, 4);
system.addForce(cmap);
// Set particle positions so angle1=0 and angle2=PI/4.
vector<Vec3> positions(5);
positions[0] = Vec3(0, 0, 1);
positions[1] = Vec3(0, 0, 0);
positions[2] = Vec3(1, 0, 0);
positions[3] = Vec3(1, 0, 1);
positions[4] = Vec3(0.5, -0.5, 1);
VerletIntegrator integrator(0.01);
Context context(system, integrator, platform);
context.setPositions(positions);
// Check that the energy is correct.
double energy = context.getState(State::Energy).getPotentialEnergy();
ASSERT_EQUAL_TOL(1+10*sin(M_PI/4), energy, 1e-5);
// Modify the parameters.
cmap->setTorsionParameters(0, 1, 0, 1, 2, 3, 1, 2, 3, 4);
for (int i = 0; i < mapSize*mapSize; i++)
mapEnergy2[i] *= 2.0;
cmap->setMapParameters(1, mapSize, mapEnergy2);
cmap->updateParametersInContext(context);
// See if the results are correct.
energy = context.getState(State::Energy).getPotentialEnergy();
ASSERT_EQUAL_TOL(2-20*sin(M_PI/4), energy, 1e-5);
}
int main() {
try {
testCMAPTorsions();
testChangingParameters();
}
catch(const exception& e) {
cout << "exception: " << e.what() << endl;
......
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