Implemented parameter derivatives in OpenCL platform

platforms/opencl/include/OpenCLBondedUtilities.h

@@ -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) 2011-2015 Stanford University and the Authors.      *
+ * Portions copyright (c) 2011-2016 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -100,6 +100,15 @@ public:
      * refer to it by this name.
      */
     std::string addArgument(cl::Memory& data, const std::string& type);
+    /**
+     * Register that the interaction kernel will be computing the derivative of the potential energy
+     * with respect to a parameter.
+     * 
+     * @param param   the name of the parameter
+     * @return the variable that will be used to accumulate the derivative.  Any code you pass to addInteraction() should
+     * add its contributions to this variable.
+     */
+    std::string addEnergyParameterDerivative(const std::string& param);
     /**
      * Add some OpenCL code that should be included in the program, before the start of the kernel.
      * This can be used, for example, to define functions that will be called by the kernel.
@@ -137,6 +146,7 @@ private:
     std::vector<OpenCLArray*> atomIndices;
     std::vector<OpenCLArray*> bufferIndices;
     std::vector<std::string> prefixCode;
+    std::vector<std::string> energyParameterDerivatives;
     int numForceBuffers, maxBonds, allGroups;
     bool hasInitializedKernels;
 };

platforms/opencl/include/OpenCLContext.h

@@ -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) 2009-2015 Stanford University and the Authors.      *
+ * Portions copyright (c) 2009-2016 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -264,6 +264,12 @@ public:
     OpenCLArray& getEnergyBuffer() {
         return *energyBuffer;
     }
+    /**
+     * Get the array which contains the buffer in which derivatives of the energy with respect to parameters are computed.
+     */
+    OpenCLArray& getEnergyParamDerivBuffer() {
+        return *energyParamDerivBuffer;
+    }
     /**
      * Get a pointer to a block of pinned memory that can be used for efficient transfers between host and device.
      * This is guaranteed to be at least as large as any of the arrays returned by methods of this class.
@@ -659,6 +665,27 @@ public:
     std::vector<ForcePostComputation*>& getPostComputations() {
         return postComputations;
     }
+    /**
+     * Get the names of all parameters with respect to which energy derivatives are computed.
+     */
+    const std::vector<std::string>& getEnergyParamDerivNames() const {
+        return energyParamDerivNames;
+    }
+    /**
+     * Get a workspace data structure used for accumulating the values of derivatives of the energy
+     * with respect to parameters.
+     */
+    std::map<std::string, double>& getEnergyParamDerivWorkspace() {
+        return energyParamDerivWorkspace;
+    }
+    /**
+     * Register that the derivative of potential energy with respect to a context parameter
+     * will need to be calculated.  If this is called multiple times for a single parameter,
+     * it is only added to the list once.
+     * 
+     * @param param    the name of the parameter to add
+     */
+    void addEnergyParameterDerivative(const std::string& param);
     /**
      * Mark that the current molecule definitions (and hence the atom order) may be invalid.
      * This should be called whenever force field parameters change.  It will cause the definitions
@@ -725,7 +752,10 @@ private:
     OpenCLArray* forceBuffers;
     OpenCLArray* longForceBuffer;
     OpenCLArray* energyBuffer;
+    OpenCLArray* energyParamDerivBuffer;
     OpenCLArray* atomIndexDevice;
+    std::vector<std::string> energyParamDerivNames;
+    std::map<std::string, double> energyParamDerivWorkspace;
     std::vector<int> atomIndex;
     std::vector<cl::Memory*> autoclearBuffers;
     std::vector<int> autoclearBufferSizes;

platforms/opencl/include/OpenCLNonbondedUtilities.h

@@ -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) 2009-2013 Stanford University and the Authors.      *
+ * Portions copyright (c) 2009-2016 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -88,6 +88,15 @@ public:
      * Add an array (other than a per-atom parameter) that should be passed as an argument to the default interaction kernel.
      */
     void addArgument(const ParameterInfo& parameter);
+    /**
+     * Register that the interaction kernel will be computing the derivative of the potential energy
+     * with respect to a parameter.
+     * 
+     * @param param   the name of the parameter
+     * @return the variable that will be used to accumulate the derivative.  Any code you pass to addInteraction() should
+     * add its contributions to this variable.
+     */
+    std::string addEnergyParameterDerivative(const std::string& param);
     /**
      * Specify the list of exclusions that an interaction outside the default kernel will depend on.
      * 
@@ -287,6 +296,7 @@ private:
     std::vector<std::vector<int> > atomExclusions;
     std::vector<ParameterInfo> parameters;
     std::vector<ParameterInfo> arguments;
+    std::vector<std::string> energyParameterDerivatives;
     std::map<int, double> groupCutoff;
     std::map<int, std::string> groupKernelSource;
     double lastCutoff;

platforms/opencl/src/OpenCLBondedUtilities.cpp

@@ -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) 2011-2015 Stanford University and the Authors.      *
+ * Portions copyright (c) 2011-2016 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -56,12 +56,25 @@ void OpenCLBondedUtilities::addInteraction(const vector<vector<int> >& atoms, co
     }
 }
 
-std::string OpenCLBondedUtilities::addArgument(cl::Memory& data, const string& type) {
+string OpenCLBondedUtilities::addArgument(cl::Memory& data, const string& type) {
     arguments.push_back(&data);
     argTypes.push_back(type);
     return "customArg"+context.intToString(arguments.size());
 }
 
+string OpenCLBondedUtilities::addEnergyParameterDerivative(const string& param) {
+    // See if the parameter has already been added.
+    
+    int index;
+    for (index = 0; index < energyParameterDerivatives.size(); index++)
+        if (param == energyParameterDerivatives[index])
+            break;
+    if (index == energyParameterDerivatives.size())
+        energyParameterDerivatives.push_back(param);
+    context.addEnergyParameterDerivative(param);
+    return string("energyParamDeriv")+context.intToString(index);
+}
+
 void OpenCLBondedUtilities::addPrefixCode(const string& source) {
     for (int i = 0; i < (int) prefixCode.size(); i++)
         if (prefixCode[i] == source)
@@ -190,13 +203,23 @@ void OpenCLBondedUtilities::initialize(const System& system) {
         }
         for (int i = 0; i < (int) arguments.size(); i++)
             s<<", __global "<<argTypes[i]<<"* customArg"<<(i+1);
+        if (energyParameterDerivatives.size() > 0)
+            s<<", __global mixed* energyParamDerivs";
         s<<") {\n";
         s<<"mixed energy = 0;\n";
+        for (int i = 0; i < energyParameterDerivatives.size(); i++)
+            s<<"mixed energyParamDeriv"<<i<<" = 0;\n";
         for (int i = 0; i < setSize; i++) {
             int force = set[i];
             s<<createForceSource(i, forceAtoms[force].size(), forceAtoms[force][0].size(), forceGroup[force], forceSource[force]);
         }
         s<<"energyBuffer[get_global_id(0)] += energy;\n";
+        const vector<string>& allParamDerivNames = context.getEnergyParamDerivNames();
+        int numDerivs = allParamDerivNames.size();
+        for (int i = 0; i < energyParameterDerivatives.size(); i++)
+            for (int index = 0; index < numDerivs; index++)
+                if (allParamDerivNames[index] == energyParameterDerivatives[i])
+                    s<<"energyParamDerivs[get_global_id(0)*"<<numDerivs<<"+"<<i<<"] += energyParamDeriv"<<i<<";\n";
         s<<"}\n";
         map<string, string> defines;
         defines["PADDED_NUM_ATOMS"] = context.intToString(context.getPaddedNumAtoms());
@@ -274,6 +297,8 @@ void OpenCLBondedUtilities::computeInteractions(int groups) {
             }
             for (int j = 0; j < (int) arguments.size(); j++)
                 kernel.setArg<cl::Memory>(index++, *arguments[j]);
+            if (energyParameterDerivatives.size() > 0)
+                kernel.setArg<cl::Memory>(index++, context.getEnergyParamDerivBuffer().getDeviceBuffer());
         }
     }
     for (int i = 0; i < (int) kernels.size(); i++) {

platforms/opencl/src/OpenCLContext.cpp

@@ -69,7 +69,7 @@ static void CL_CALLBACK errorCallback(const char* errinfo, const void* private_i
 
 OpenCLContext::OpenCLContext(const System& system, int platformIndex, int deviceIndex, const string& precision, OpenCLPlatform::PlatformData& platformData) :
         system(system), time(0.0), platformData(platformData), stepCount(0), computeForceCount(0), stepsSinceReorder(99999), atomsWereReordered(false), posq(NULL),
-        posqCorrection(NULL), velm(NULL), forceBuffers(NULL), longForceBuffer(NULL), energyBuffer(NULL), atomIndexDevice(NULL), integration(NULL),
+        posqCorrection(NULL), velm(NULL), forceBuffers(NULL), longForceBuffer(NULL), energyBuffer(NULL), energyParamDerivBuffer(NULL), atomIndexDevice(NULL), integration(NULL),
         expression(NULL), bonded(NULL), nonbonded(NULL), thread(NULL) {
     if (precision == "single") {
         useDoublePrecision = false;
@@ -435,6 +435,8 @@ OpenCLContext::~OpenCLContext() {
         delete longForceBuffer;
     if (energyBuffer != NULL)
         delete energyBuffer;
+    if (energyParamDerivBuffer != NULL)
+        delete energyParamDerivBuffer;
     if (atomIndexDevice != NULL)
         delete atomIndexDevice;
     if (integration != NULL)
@@ -455,15 +457,16 @@ void OpenCLContext::initialize() {
     numForceBuffers = std::max(numForceBuffers, bonded->getNumForceBuffers());
     for (int i = 0; i < (int) forces.size(); i++)
         numForceBuffers = std::max(numForceBuffers, forces[i]->getRequiredForceBuffers());
+    int energyBufferSize = max(numThreadBlocks*ThreadBlockSize, nonbonded->getNumEnergyBuffers());
     if (useDoublePrecision) {
         forceBuffers = OpenCLArray::create<mm_double4>(*this, paddedNumAtoms*numForceBuffers, "forceBuffers");
         force = OpenCLArray::create<mm_double4>(*this, &forceBuffers->getDeviceBuffer(), paddedNumAtoms, "force");
-        energyBuffer = OpenCLArray::create<cl_double>(*this, max(numThreadBlocks*ThreadBlockSize, nonbonded->getNumEnergyBuffers()), "energyBuffer");
+        energyBuffer = OpenCLArray::create<cl_double>(*this, energyBufferSize, "energyBuffer");
     }
     else {
         forceBuffers = OpenCLArray::create<mm_float4>(*this, paddedNumAtoms*numForceBuffers, "forceBuffers");
         force = OpenCLArray::create<mm_float4>(*this, &forceBuffers->getDeviceBuffer(), paddedNumAtoms, "force");
-        energyBuffer = OpenCLArray::create<cl_double>(*this, max(numThreadBlocks*ThreadBlockSize, nonbonded->getNumEnergyBuffers()), "energyBuffer");
+        energyBuffer = OpenCLArray::create<cl_double>(*this, energyBufferSize, "energyBuffer");
     }
     if (supports64BitGlobalAtomics) {
         longForceBuffer = OpenCLArray::create<cl_long>(*this, 3*paddedNumAtoms, "longForceBuffer");
@@ -475,7 +478,15 @@ void OpenCLContext::initialize() {
     }
     addAutoclearBuffer(*forceBuffers);
     addAutoclearBuffer(*energyBuffer);
-    int bufferBytes = max(velm->getSize()*velm->getElementSize(), energyBuffer->getSize()*energyBuffer->getElementSize());
+    int numEnergyParamDerivs = energyParamDerivNames.size();
+    if (numEnergyParamDerivs > 0) {
+        if (useDoublePrecision || useMixedPrecision)
+            energyParamDerivBuffer = OpenCLArray::create<cl_double>(*this, numEnergyParamDerivs*energyBufferSize, "energyParamDerivBuffer");
+        else
+            energyParamDerivBuffer = OpenCLArray::create<cl_float>(*this, numEnergyParamDerivs*energyBufferSize, "energyParamDerivBuffer");
+        addAutoclearBuffer(*energyParamDerivBuffer);
+    }
+    int bufferBytes = max(velm->getSize()*velm->getElementSize(), energyBufferSize*energyBuffer->getElementSize());
     pinnedBuffer = new cl::Buffer(context, CL_MEM_ALLOC_HOST_PTR, bufferBytes);
     pinnedMemory = currentQueue.enqueueMapBuffer(*pinnedBuffer, CL_TRUE, CL_MAP_READ | CL_MAP_WRITE, 0, bufferBytes);
     for (int i = 0; i < numAtoms; i++) {
@@ -1229,6 +1240,15 @@ void OpenCLContext::addPostComputation(ForcePostComputation* computation) {
     postComputations.push_back(computation);
 }
 
+void OpenCLContext::addEnergyParameterDerivative(const string& param) {
+    // See if this parameter has already been registered.
+    
+    for (int i = 0; i < energyParamDerivNames.size(); i++)
+        if (param == energyParamDerivNames[i])
+            return;
+    energyParamDerivNames.push_back(param);
+}
+
 struct OpenCLContext::WorkThread::ThreadData {
     ThreadData(std::queue<OpenCLContext::WorkTask*>& tasks, bool& waiting,  bool& finished,
             pthread_mutex_t& queueLock, pthread_cond_t& waitForTaskCondition, pthread_cond_t& queueEmptyCondition) :

platforms/opencl/src/OpenCLKernels.cpp

@@ -125,6 +125,9 @@ void OpenCLCalcForcesAndEnergyKernel::beginComputation(ContextImpl& context, boo
     OpenCLNonbondedUtilities& nb = cl.getNonbondedUtilities();
     cl.setComputeForceCount(cl.getComputeForceCount()+1);
     nb.prepareInteractions(groups);
+    map<string, double>& derivs = cl.getEnergyParamDerivWorkspace();
+    for (map<string, double>::const_iterator iter = context.getParameters().begin(); iter != context.getParameters().end(); ++iter)
+        derivs[iter->first] = 0;
 }
 
 double OpenCLCalcForcesAndEnergyKernel::finishComputation(ContextImpl& context, bool includeForces, bool includeEnergy, int groups, bool& valid) {
@@ -369,7 +372,30 @@ void OpenCLUpdateStateDataKernel::getForces(ContextImpl& context, vector<Vec3>&
 }
 
 void OpenCLUpdateStateDataKernel::getEnergyParameterDerivatives(ContextImpl& context, map<string, double>& derivs) {
-    
+    const vector<string>& paramDerivNames = cl.getEnergyParamDerivNames();
+    int numDerivs = paramDerivNames.size();
+    if (numDerivs == 0)
+        return;
+    derivs = cl.getEnergyParamDerivWorkspace();
+    OpenCLArray& derivArray = cl.getEnergyParamDerivBuffer();
+    if (cl.getUseDoublePrecision() || cl.getUseMixedPrecision()) {
+        vector<double> derivBuffers;
+        derivArray.download(derivBuffers);
+        for (int i = numDerivs; i < derivArray.getSize(); i += numDerivs)
+            for (int j = 0; j < numDerivs; j++)
+                derivBuffers[j] += derivBuffers[i+j];
+        for (int i = 0; i < numDerivs; i++)
+            derivs[paramDerivNames[i]] += derivBuffers[i];
+    }
+    else {
+        vector<float> derivBuffers;
+        derivArray.download(derivBuffers);
+        for (int i = numDerivs; i < derivArray.getSize(); i += numDerivs)
+            for (int j = 0; j < numDerivs; j++)
+                derivBuffers[j] += derivBuffers[i+j];
+        for (int i = 0; i < numDerivs; i++)
+            derivs[paramDerivNames[i]] += derivBuffers[i];
+    }
 }
 
 void OpenCLUpdateStateDataKernel::getPeriodicBoxVectors(ContextImpl& context, Vec3& a, Vec3& b, Vec3& c) const {
@@ -675,6 +701,12 @@ void OpenCLCalcCustomBondForceKernel::initialize(const System& system, const Cus
             variables[name] = value;
         }
     }
+    for (int i = 0; i < force.getNumEnergyParameterDerivatives(); i++) {
+        string paramName = force.getEnergyParameterDerivativeName(i);
+        string derivVariable = cl.getBondedUtilities().addEnergyParameterDerivative(paramName);
+        Lepton::ParsedExpression derivExpression = energyExpression.differentiate(paramName).optimize();
+        expressions[derivVariable+" += "] = derivExpression;
+    }
     stringstream compute;
     for (int i = 0; i < (int) params->getBuffers().size(); i++) {
         const OpenCLNonbondedUtilities::ParameterInfo& buffer = params->getBuffers()[i];
@@ -907,6 +939,12 @@ void OpenCLCalcCustomAngleForceKernel::initialize(const System& system, const Cu
             variables[name] = value;
         }
     }
+    for (int i = 0; i < force.getNumEnergyParameterDerivatives(); i++) {
+        string paramName = force.getEnergyParameterDerivativeName(i);
+        string derivVariable = cl.getBondedUtilities().addEnergyParameterDerivative(paramName);
+        Lepton::ParsedExpression derivExpression = energyExpression.differentiate(paramName).optimize();
+        expressions[derivVariable+" += "] = derivExpression;
+    }
     stringstream compute;
     for (int i = 0; i < (int) params->getBuffers().size(); i++) {
         const OpenCLNonbondedUtilities::ParameterInfo& buffer = params->getBuffers()[i];
@@ -1359,6 +1397,12 @@ void OpenCLCalcCustomTorsionForceKernel::initialize(const System& system, const
             variables[name] = value;
         }
     }
+    for (int i = 0; i < force.getNumEnergyParameterDerivatives(); i++) {
+        string paramName = force.getEnergyParameterDerivativeName(i);
+        string derivVariable = cl.getBondedUtilities().addEnergyParameterDerivative(paramName);
+        Lepton::ParsedExpression derivExpression = energyExpression.differentiate(paramName).optimize();
+        expressions[derivVariable+" += "] = derivExpression;
+    }
     stringstream compute;
     for (int i = 0; i < (int) params->getBuffers().size(); i++) {
         const OpenCLNonbondedUtilities::ParameterInfo& buffer = params->getBuffers()[i];
@@ -2307,6 +2351,12 @@ void OpenCLCalcCustomNonbondedForceKernel::initialize(const System& system, cons
         string value = "globals["+cl.intToString(i)+"]";
         variables.push_back(makeVariable(name, prefix+value));
     }
+    for (int i = 0; i < force.getNumEnergyParameterDerivatives(); i++) {
+        string paramName = force.getEnergyParameterDerivativeName(i);
+        string derivVariable = cl.getNonbondedUtilities().addEnergyParameterDerivative(paramName);
+        Lepton::ParsedExpression derivExpression = energyExpression.differentiate(paramName).optimize();
+        forceExpressions[derivVariable+" += interactionScale*switchValue*"] = derivExpression;
+    }
     stringstream compute;
     compute << cl.getExpressionUtilities().createExpressions(forceExpressions, variables, functionList, functionDefinitions, prefix+"temp");
     map<string, string> replacements;
@@ -2639,7 +2689,11 @@ double OpenCLCalcCustomNonbondedForceKernel::execute(ContextImpl& context, bool
         cl.executeKernel(interactionGroupKernel, numGroupThreadBlocks*forceThreadBlockSize, forceThreadBlockSize);
     }
     mm_double4 boxSize = cl.getPeriodicBoxSizeDouble();
-    return longRangeCoefficient/(boxSize.x*boxSize.y*boxSize.z);
+    double volume = boxSize.x*boxSize.y*boxSize.z;
+    map<string, double>& derivs = cl.getEnergyParamDerivWorkspace();
+    for (int i = 0; i < longRangeCoefficientDerivs.size(); i++)
+        derivs[forceCopy->getEnergyParameterDerivativeName(i)] += longRangeCoefficientDerivs[i]/volume;
+    return longRangeCoefficient/volume;
 }
 
 void OpenCLCalcCustomNonbondedForceKernel::copyParametersToContext(ContextImpl& context, const CustomNonbondedForce& force) {

platforms/opencl/src/OpenCLNonbondedUtilities.cpp

@@ -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) 2009-2015 Stanford University and the Authors.      *
+ * Portions copyright (c) 2009-2016 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -162,6 +162,19 @@ void OpenCLNonbondedUtilities::addArgument(const ParameterInfo& parameter) {
     arguments.push_back(parameter);
 }
 
+string OpenCLNonbondedUtilities::addEnergyParameterDerivative(const string& param) {
+    // See if the parameter has already been added.
+    
+    int index;
+    for (index = 0; index < energyParameterDerivatives.size(); index++)
+        if (param == energyParameterDerivatives[index])
+            break;
+    if (index == energyParameterDerivatives.size())
+        energyParameterDerivatives.push_back(param);
+    context.addEnergyParameterDerivative(param);
+    return string("energyParamDeriv")+context.intToString(index);
+}
+
 void OpenCLNonbondedUtilities::requestExclusions(const vector<vector<int> >& exclusionList) {
     if (anyExclusions) {
         bool sameExclusions = (exclusionList.size() == atomExclusions.size());
@@ -591,6 +604,8 @@ cl::Kernel OpenCLNonbondedUtilities::createInteractionKernel(const string& sourc
             args << arguments[i].getName();
         }
     }
+    if (energyParameterDerivatives.size() > 0)
+        args << ", __global mixed* energyParamDerivs";
     replacements["PARAMETER_ARGUMENTS"] = args.str();
     stringstream loadLocal1;
     for (int i = 0; i < (int) params.size(); i++) {
@@ -641,6 +656,18 @@ cl::Kernel OpenCLNonbondedUtilities::createInteractionKernel(const string& sourc
         }
     }
     replacements["LOAD_ATOM2_PARAMETERS"] = load2j.str();
+    stringstream initDerivs;
+    for (int i = 0; i < energyParameterDerivatives.size(); i++)
+        initDerivs<<"mixed energyParamDeriv"<<i<<" = 0;\n";
+    replacements["INIT_DERIVATIVES"] = initDerivs.str();
+    stringstream saveDerivs;
+    const vector<string>& allParamDerivNames = context.getEnergyParamDerivNames();
+    int numDerivs = allParamDerivNames.size();
+    for (int i = 0; i < energyParameterDerivatives.size(); i++)
+        for (int index = 0; index < numDerivs; index++)
+            if (allParamDerivNames[index] == energyParameterDerivatives[i])
+                saveDerivs<<"energyParamDerivs[get_global_id(0)*"<<numDerivs<<"+"<<i<<"] += energyParamDeriv"<<i<<";\n";
+    replacements["SAVE_DERIVATIVES"] = saveDerivs.str();
     map<string, string> defines;
     if (useCutoff)
         defines["USE_CUTOFF"] = "1";
@@ -716,5 +743,7 @@ cl::Kernel OpenCLNonbondedUtilities::createInteractionKernel(const string& sourc
     for (int i = 0; i < (int) arguments.size(); i++) {
         kernel.setArg<cl::Memory>(index++, arguments[i].getMemory());
     }
+    if (energyParameterDerivatives.size() > 0)
+        kernel.setArg<cl::Memory>(index++, context.getEnergyParamDerivBuffer().getDeviceBuffer());
     return kernel;
 }

platforms/opencl/src/kernels/customNonbonded.cl

@@ -4,15 +4,18 @@ if (!isExcluded && r2 < CUTOFF_SQUARED) {
 if (!isExcluded) {
 #endif
     real tempForce = 0.0f;
-    COMPUTE_FORCE
+    real switchValue = 1, switchDeriv = 0;
 #if USE_SWITCH
     if (r > SWITCH_CUTOFF) {
         real x = r-SWITCH_CUTOFF;
-        real switchValue = 1+x*x*x*(SWITCH_C3+x*(SWITCH_C4+x*SWITCH_C5));
-        real switchDeriv = x*x*(3*SWITCH_C3+x*(4*SWITCH_C4+x*5*SWITCH_C5));
-        tempForce = tempForce*switchValue - tempEnergy*switchDeriv;
-        tempEnergy *= switchValue;
+        switchValue = 1+x*x*x*(SWITCH_C3+x*(SWITCH_C4+x*SWITCH_C5));
+        switchDeriv = x*x*(3*SWITCH_C3+x*(4*SWITCH_C4+x*5*SWITCH_C5));
     }
+#endif
+    COMPUTE_FORCE
+#if USE_SWITCH
+    tempForce = tempForce*switchValue - tempEnergy*switchDeriv;
+    tempEnergy *= switchValue;
 #endif
     dEdR += tempForce*invR;
 }

platforms/opencl/src/kernels/nonbonded.cl

@@ -35,6 +35,7 @@ __kernel void computeNonbonded(
     const unsigned int tgx = get_local_id(0) & (TILE_SIZE-1);
     const unsigned int tbx = get_local_id(0) - tgx;
     mixed energy = 0;
+    INIT_DERIVATIVES
     __local AtomData localData[FORCE_WORK_GROUP_SIZE];
 
     // First loop: process tiles that contain exclusions.
@@ -85,6 +86,7 @@ __kernel void computeNonbonded(
                 bool isExcluded = (atom1 >= NUM_ATOMS || atom2 >= NUM_ATOMS || !(excl & 0x1));
 #endif
                 real tempEnergy = 0;
+                const real interactionScale = 0.5f;
                 COMPUTE_INTERACTION
                 energy += 0.5f*tempEnergy;
 #ifdef INCLUDE_FORCES
@@ -144,6 +146,7 @@ __kernel void computeNonbonded(
                     bool isExcluded = (atom1 >= NUM_ATOMS || atom2 >= NUM_ATOMS || !(excl & 0x1));
 #endif
                     real tempEnergy = 0;
+                    const real interactionScale = 1.0f;
                     COMPUTE_INTERACTION
                     energy += tempEnergy;
 #ifdef INCLUDE_FORCES
@@ -320,6 +323,7 @@ __kernel void computeNonbonded(
                         bool isExcluded = (atom1 >= NUM_ATOMS || atom2 >= NUM_ATOMS);
 #endif
                         real tempEnergy = 0;
+                        const real interactionScale = 1.0f;
                         COMPUTE_INTERACTION
                         energy += tempEnergy;
 #ifdef INCLUDE_FORCES
@@ -374,6 +378,7 @@ __kernel void computeNonbonded(
                         bool isExcluded = (atom1 >= NUM_ATOMS || atom2 >= NUM_ATOMS);
 #endif
                         real tempEnergy = 0;
+                        const real interactionScale = 1.0f;
                         COMPUTE_INTERACTION
                         energy += tempEnergy;
 #ifdef INCLUDE_FORCES
@@ -429,4 +434,5 @@ __kernel void computeNonbonded(
 #ifdef INCLUDE_ENERGY
     energyBuffer[get_global_id(0)] += energy;
 #endif
+    SAVE_DERIVATIVES
 }