Merge pull request #1547 from peastman/paramderivs

Energy derivatives with respect to global parameters

platforms/cuda/src/CudaContext.cpp

@@ -76,7 +76,7 @@ bool CudaContext::hasInitializedCuda = false;
 CudaContext::CudaContext(const System& system, int deviceIndex, bool useBlockingSync, const string& precision, const string& compiler,
         const string& tempDir, const std::string& hostCompiler, CudaPlatform::PlatformData& platformData) : system(system), currentStream(0),
         time(0.0), platformData(platformData), stepCount(0), computeForceCount(0), stepsSinceReorder(99999), contextIsValid(false), atomsWereReordered(false), hasCompilerKernel(false),
-        pinnedBuffer(NULL), posq(NULL), posqCorrection(NULL), velm(NULL), force(NULL), energyBuffer(NULL), atomIndexDevice(NULL), integration(NULL), expression(NULL), bonded(NULL), nonbonded(NULL), thread(NULL) {
+        pinnedBuffer(NULL), posq(NULL), posqCorrection(NULL), velm(NULL), force(NULL), energyBuffer(NULL), energyParamDerivBuffer(NULL), atomIndexDevice(NULL), integration(NULL), expression(NULL), bonded(NULL), nonbonded(NULL), thread(NULL) {
     this->compiler = "\""+compiler+"\"";
     if (platformData.context != NULL) {
         try {
@@ -339,6 +339,8 @@ CudaContext::~CudaContext() {
         delete force;
     if (energyBuffer != NULL)
         delete energyBuffer;
+    if (energyParamDerivBuffer != NULL)
+        delete energyParamDerivBuffer;
     if (atomIndexDevice != NULL)
         delete atomIndexDevice;
     if (integration != NULL)
@@ -390,6 +392,14 @@ void CudaContext::initialize() {
     force = CudaArray::create<long long>(*this, paddedNumAtoms*3, "force");
     addAutoclearBuffer(force->getDevicePointer(), force->getSize()*force->getElementSize());
     addAutoclearBuffer(energyBuffer->getDevicePointer(), energyBuffer->getSize()*energyBuffer->getElementSize());
+    int numEnergyParamDerivs = energyParamDerivNames.size();
+    if (numEnergyParamDerivs > 0) {
+        if (useDoublePrecision || useMixedPrecision)
+            energyParamDerivBuffer = CudaArray::create<double>(*this, numEnergyParamDerivs*numEnergyBuffers, "energyParamDerivBuffer");
+        else
+            energyParamDerivBuffer = CudaArray::create<float>(*this, numEnergyParamDerivs*numEnergyBuffers, "energyParamDerivBuffer");
+        addAutoclearBuffer(*energyParamDerivBuffer);
+    }
     atomIndexDevice = CudaArray::create<int>(*this, paddedNumAtoms, "atomIndex");
     atomIndex.resize(paddedNumAtoms);
     for (int i = 0; i < paddedNumAtoms; ++i)
@@ -1311,6 +1321,15 @@ void CudaContext::addPostComputation(ForcePostComputation* computation) {
     postComputations.push_back(computation);
 }
 
+void CudaContext::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 CudaContext::WorkThread::ThreadData {
     ThreadData(std::queue<CudaContext::WorkTask*>& tasks, bool& waiting,  bool& finished,
             pthread_mutex_t& queueLock, pthread_cond_t& waitForTaskCondition, pthread_cond_t& queueEmptyCondition) :

platforms/cuda/src/CudaNonbondedUtilities.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:                                                              *
  *                                                                            *
@@ -146,6 +146,19 @@ void CudaNonbondedUtilities::addArgument(const ParameterInfo& parameter) {
     arguments.push_back(parameter);
 }
 
+string CudaNonbondedUtilities::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 CudaNonbondedUtilities::requestExclusions(const vector<vector<int> >& exclusionList) {
     if (anyExclusions) {
         bool sameExclusions = (exclusionList.size() == atomExclusions.size());
@@ -308,6 +321,8 @@ void CudaNonbondedUtilities::initialize(const System& system) {
         forceArgs.push_back(&parameters[i].getMemory());
     for (int i = 0; i < (int) arguments.size(); i++)
         forceArgs.push_back(&arguments[i].getMemory());
+    if (energyParameterDerivatives.size() > 0)
+        forceArgs.push_back(&context.getEnergyParamDerivBuffer().getDevicePointer());
     if (useCutoff) {
         findBlockBoundsArgs.push_back(&numAtoms);
         findBlockBoundsArgs.push_back(context.getPeriodicBoxSizePointer());
@@ -515,6 +530,8 @@ CUfunction CudaNonbondedUtilities::createInteractionKernel(const string& source,
         args << "* __restrict__ ";
         args << arguments[i].getName();
     }
+    if (energyParameterDerivatives.size() > 0)
+        args << ", mixed* __restrict__ energyParamDerivs";
     replacements["PARAMETER_ARGUMENTS"] = args.str();
 
     stringstream load1;
@@ -623,6 +640,18 @@ CUfunction CudaNonbondedUtilities::createInteractionKernel(const string& source,
         }
     }
     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[(blockIdx.x*blockDim.x+threadIdx.x)*"<<numDerivs<<"+"<<index<<"] += energyParamDeriv"<<i<<";\n";
+    replacements["SAVE_DERIVATIVES"] = saveDerivs.str();
 
     stringstream shuffleWarpData;
     if(useShuffle) {

platforms/cuda/src/kernels/customCentroidBond.cu

@@ -111,10 +111,12 @@ extern "C" __global__ void computeGroupForces(unsigned long long* __restrict__ g
         const int* __restrict__ bondGroups, real4 periodicBoxSize, real4 invPeriodicBoxSize, real4 periodicBoxVecX, real4 periodicBoxVecY, real4 periodicBoxVecZ
         EXTRA_ARGS) {
     mixed energy = 0;
+    INIT_PARAM_DERIVS
     for (int index = blockIdx.x*blockDim.x+threadIdx.x; index < NUM_BONDS; index += blockDim.x*gridDim.x) {
         COMPUTE_FORCE
     }
     energyBuffer[blockIdx.x*blockDim.x+threadIdx.x] += energy;
+    SAVE_PARAM_DERIVS
 }
 
 /**

platforms/cuda/src/kernels/customGBEnergyN2.cu

@@ -28,6 +28,7 @@ extern "C" __global__ void computeN2Energy(unsigned long long* __restrict__ forc
     const unsigned int tgx = threadIdx.x & (TILE_SIZE-1);
     const unsigned int tbx = threadIdx.x - tgx;
     mixed energy = 0;
+    INIT_PARAM_DERIVS
     __shared__ AtomData localData[THREAD_BLOCK_SIZE];
 
     // First loop: process tiles that contain exclusions.
@@ -69,6 +70,7 @@ extern "C" __global__ void computeN2Energy(unsigned long long* __restrict__ forc
                     atom2 = y*TILE_SIZE+j;
                     real dEdR = 0;
                     real tempEnergy = 0;
+                    const real interactionScale = 0.5f;
 #ifdef USE_EXCLUSIONS
                     bool isExcluded = !(excl & 0x1);
 #endif
@@ -120,6 +122,7 @@ extern "C" __global__ void computeN2Energy(unsigned long long* __restrict__ forc
                     atom2 = y*TILE_SIZE+tj;
                     real dEdR = 0;
                     real tempEnergy = 0;
+                    const real interactionScale = 1;
 #ifdef USE_EXCLUSIONS
                     bool isExcluded = !(excl & 0x1);
 #endif
@@ -266,6 +269,7 @@ extern "C" __global__ void computeN2Energy(unsigned long long* __restrict__ forc
                         atom2 = atomIndices[tbx+tj];
                         real dEdR = 0;
                         real tempEnergy = 0;
+                        const real interactionScale = 1;
                         if (atom1 < NUM_ATOMS && atom2 < NUM_ATOMS) {
                             COMPUTE_INTERACTION
                             dEdR /= -r;
@@ -309,6 +313,7 @@ extern "C" __global__ void computeN2Energy(unsigned long long* __restrict__ forc
                         atom2 = atomIndices[tbx+tj];
                         real dEdR = 0;
                         real tempEnergy = 0;
+                        const real interactionScale = 1;
                         if (atom1 < NUM_ATOMS && atom2 < NUM_ATOMS) {
                             COMPUTE_INTERACTION
                             dEdR /= -r;
@@ -353,4 +358,5 @@ extern "C" __global__ void computeN2Energy(unsigned long long* __restrict__ forc
         pos++;
     }
     energyBuffer[blockIdx.x*blockDim.x+threadIdx.x] += energy;
+    SAVE_PARAM_DERIVS
 }

platforms/cuda/src/kernels/customGBEnergyPerParticle.cu

@@ -5,6 +5,7 @@
 extern "C" __global__ void computePerParticleEnergy(long long* __restrict__ forceBuffers, mixed* __restrict__ energyBuffer, const real4* __restrict__ posq
         PARAMETER_ARGUMENTS) {
     mixed energy = 0;
+    INIT_PARAM_DERIVS
     for (unsigned int index = blockIdx.x*blockDim.x+threadIdx.x; index < NUM_ATOMS; index += blockDim.x*gridDim.x) {
         // Load the derivatives
 
@@ -17,4 +18,5 @@ extern "C" __global__ void computePerParticleEnergy(long long* __restrict__ forc
         COMPUTE_ENERGY
     }
     energyBuffer[blockIdx.x*blockDim.x+threadIdx.x] += energy;
+    SAVE_PARAM_DERIVS
 }

platforms/cuda/src/kernels/customGBGradientChainRule.cu

@@ -4,6 +4,7 @@
 
 extern "C" __global__ void computeGradientChainRuleTerms(long long* __restrict__ forceBuffers, const real4* __restrict__ posq
         PARAMETER_ARGUMENTS) {
+    INIT_PARAM_DERIVS
     const real scale = RECIP((real) 0x100000000);
     for (unsigned int index = blockIdx.x*blockDim.x+threadIdx.x; index < NUM_ATOMS; index += blockDim.x*gridDim.x) {
         real4 pos = posq[index];
@@ -13,4 +14,5 @@ extern "C" __global__ void computeGradientChainRuleTerms(long long* __restrict__
         forceBuffers[index+PADDED_NUM_ATOMS] = (long long) (force.y*0x100000000);
         forceBuffers[index+PADDED_NUM_ATOMS*2] = (long long) (force.z*0x100000000);
     }
+    SAVE_PARAM_DERIVS
 }

platforms/cuda/src/kernels/customGBValueN2.cu

@@ -73,6 +73,7 @@ extern "C" __global__ void computeN2Value(const real4* __restrict__ posq, const
                         COMPUTE_VALUE
                     }
                     value += tempValue1;
+                    ADD_TEMP_DERIVS1
 #ifdef USE_CUTOFF
                 }
 #endif
@@ -121,6 +122,8 @@ extern "C" __global__ void computeN2Value(const real4* __restrict__ posq, const
                     }
                     value += tempValue1;
                     localData[tbx+tj].value += tempValue2;
+                    ADD_TEMP_DERIVS1
+                    ADD_TEMP_DERIVS2
 #ifdef USE_CUTOFF
                 }
 #endif
@@ -133,11 +136,13 @@ extern "C" __global__ void computeN2Value(const real4* __restrict__ posq, const
 
         // Write results.
 
-        unsigned int offset = x*TILE_SIZE + tgx;
-        atomicAdd(&global_value[offset], static_cast<unsigned long long>((long long) (value*0x100000000)));
+        unsigned int offset1 = x*TILE_SIZE + tgx;
+        atomicAdd(&global_value[offset1], static_cast<unsigned long long>((long long) (value*0x100000000)));
+        STORE_PARAM_DERIVS1
         if (x != y) {
-            offset = y*TILE_SIZE + tgx;
-            atomicAdd(&global_value[offset], static_cast<unsigned long long>((long long) (localData[threadIdx.x].value*0x100000000)));
+            unsigned int offset2 = y*TILE_SIZE + tgx;
+            atomicAdd(&global_value[offset2], static_cast<unsigned long long>((long long) (localData[threadIdx.x].value*0x100000000)));
+            STORE_PARAM_DERIVS2
         }
     }
 
@@ -244,6 +249,8 @@ extern "C" __global__ void computeN2Value(const real4* __restrict__ posq, const
                         }
                         value += tempValue1;
                         localData[tbx+tj].value += tempValue2;
+                        ADD_TEMP_DERIVS1
+                        ADD_TEMP_DERIVS2
                     }
                     tj = (tj + 1) & (TILE_SIZE - 1);
                 }
@@ -276,6 +283,8 @@ extern "C" __global__ void computeN2Value(const real4* __restrict__ posq, const
                         }
                         value += tempValue1;
                         localData[tbx+tj].value += tempValue2;
+                        ADD_TEMP_DERIVS1
+                        ADD_TEMP_DERIVS2
 #ifdef USE_CUTOFF
                     }
 #endif
@@ -285,14 +294,19 @@ extern "C" __global__ void computeN2Value(const real4* __restrict__ posq, const
         
             // Write results.
 
-            atomicAdd(&global_value[atom1], static_cast<unsigned long long>((long long) (value*0x100000000)));
+            unsigned int offset1 = atom1;
+            atomicAdd(&global_value[offset1], static_cast<unsigned long long>((long long) (value*0x100000000)));
+            STORE_PARAM_DERIVS1
 #ifdef USE_CUTOFF
             unsigned int atom2 = atomIndices[threadIdx.x];
 #else
             unsigned int atom2 = y*TILE_SIZE + tgx;
 #endif
-            if (atom2 < PADDED_NUM_ATOMS)
-                atomicAdd(&global_value[atom2], static_cast<unsigned long long>((long long) (localData[threadIdx.x].value*0x100000000)));
+            if (atom2 < PADDED_NUM_ATOMS) {
+                unsigned int offset2 = atom2;
+                atomicAdd(&global_value[offset2], static_cast<unsigned long long>((long long) (localData[threadIdx.x].value*0x100000000)));
+                STORE_PARAM_DERIVS2
+            }
         }
         pos++;
     }

platforms/cuda/src/kernels/customGBValuePerParticle.cu

@@ -8,6 +8,7 @@ extern "C" __global__ void computePerParticleValues(real4* posq, long long* valu
         // Load the pairwise value
 
         real sum = valueBuffers[index]/(real) 0x100000000;
+        REDUCE_PARAM0_DERIV
         
         // Now calculate other values
 

platforms/cuda/src/kernels/customIntegratorPerDof.cu

@@ -33,7 +33,8 @@ inline __device__ mixed4 convertFromDouble4(double4 a) {
 
 extern "C" __global__ void computePerDof(real4* __restrict__ posq, real4* __restrict__ posqCorrection, mixed4* __restrict__ posDelta,
         mixed4* __restrict__ velm, const long long* __restrict__ force, const mixed2* __restrict__ dt, const mixed* __restrict__ globals,
-        mixed* __restrict__ sum, const float4* __restrict__ gaussianValues, unsigned int gaussianBaseIndex, const float4* __restrict__ uniformValues, const real energy
+        mixed* __restrict__ sum, const float4* __restrict__ gaussianValues, unsigned int gaussianBaseIndex, const float4* __restrict__ uniformValues,
+        const real energy, mixed* __restrict__ energyParamDerivs
         PARAMETER_ARGUMENTS) {
     mixed stepSize = dt[0].y;
     int index = blockIdx.x*blockDim.x+threadIdx.x;

platforms/cuda/src/kernels/customNonbonded.cu

@@ -4,15 +4,18 @@ if (!isExcluded && r2 < CUTOFF_SQUARED) {
 if (!isExcluded) {
 #endif
     real tempForce = 0;
-    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/cuda/src/kernels/nonbonded.cu

@@ -113,6 +113,7 @@ extern "C" __global__ void computeNonbonded(
     const unsigned int tgx = threadIdx.x & (TILE_SIZE-1); // index within the warp
     const unsigned int tbx = threadIdx.x - tgx;           // block warpIndex
     mixed energy = 0;
+    INIT_DERIVATIVES
     // used shared memory if the device cannot shuffle
 #ifndef ENABLE_SHUFFLE
     __shared__ AtomData localData[THREAD_BLOCK_SIZE];
@@ -175,6 +176,7 @@ extern "C" __global__ void computeNonbonded(
                 bool isExcluded = (atom1 >= NUM_ATOMS || atom2 >= NUM_ATOMS || !(excl & 0x1));
 #endif
                 real tempEnergy = 0.0f;
+                const real interactionScale = 0.5f;
                 COMPUTE_INTERACTION
                 energy += 0.5f*tempEnergy;
 #ifdef INCLUDE_FORCES
@@ -243,6 +245,7 @@ extern "C" __global__ void computeNonbonded(
                 bool isExcluded = (atom1 >= NUM_ATOMS || atom2 >= NUM_ATOMS || !(excl & 0x1));
 #endif
                 real tempEnergy = 0.0f;
+                const real interactionScale = 1.0f;
                 COMPUTE_INTERACTION
                 energy += tempEnergy;
 #ifdef INCLUDE_FORCES
@@ -448,6 +451,7 @@ extern "C" __global__ void computeNonbonded(
                     bool isExcluded = (atom1 >= NUM_ATOMS || atom2 >= NUM_ATOMS);
 #endif
                     real tempEnergy = 0.0f;
+                    const real interactionScale = 1.0f;
                     COMPUTE_INTERACTION
                     energy += tempEnergy;
 #ifdef INCLUDE_FORCES
@@ -518,6 +522,7 @@ extern "C" __global__ void computeNonbonded(
                     bool isExcluded = (atom1 >= NUM_ATOMS || atom2 >= NUM_ATOMS);
 #endif
                     real tempEnergy = 0.0f;
+                    const real interactionScale = 1.0f;
                     COMPUTE_INTERACTION
                     energy += tempEnergy;
 #ifdef INCLUDE_FORCES
@@ -586,4 +591,5 @@ extern "C" __global__ void computeNonbonded(
 #ifdef INCLUDE_ENERGY
     energyBuffer[blockIdx.x*blockDim.x+threadIdx.x] += energy;
 #endif
+    SAVE_DERIVATIVES
 }
\ No newline at end of file

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/OpenCLKernels.h

@@ -141,6 +141,12 @@ public:
      * @param forces  on exit, this contains the forces
      */
     void getForces(ContextImpl& context, std::vector<Vec3>& forces);
+    /**
+     * Get the current derivatives of the energy with respect to context parameters.
+     *
+     * @param derivs  on exit, this contains the derivatives
+     */
+    void getEnergyParameterDerivatives(ContextImpl& context, std::map<std::string, double>& derivs);
     /**
      * Get the current periodic box vectors.
      *
@@ -709,6 +715,7 @@ private:
     std::vector<cl_float> globalParamValues;
     std::vector<OpenCLArray*> tabulatedFunctions;
     double longRangeCoefficient;
+    std::vector<double> longRangeCoefficientDerivs;
     bool hasInitializedLongRangeCorrection, hasInitializedKernel;
     int numGroupThreadBlocks;
     CustomNonbondedForce* forceCopy;
@@ -801,13 +808,15 @@ public:
     void copyParametersToContext(ContextImpl& context, const CustomGBForce& force);
 private:
     double cutoff;
-    bool hasInitializedKernels, needParameterGradient;
+    bool hasInitializedKernels, needParameterGradient, needEnergyParamDerivs;
     int maxTiles, numComputedValues;
     OpenCLContext& cl;
     OpenCLParameterSet* params;
     OpenCLParameterSet* computedValues;
     OpenCLParameterSet* energyDerivs;
     OpenCLParameterSet* energyDerivChain;
+    std::vector<OpenCLParameterSet*> dValuedParam;
+    std::vector<OpenCLArray*> dValue0dParam;
     OpenCLArray* longEnergyDerivs;
     OpenCLArray* globals;
     OpenCLArray* valueBuffers;
@@ -953,6 +962,7 @@ public:
 
 private:
     int numGroups, numBonds;
+    bool needEnergyParamDerivs;
     OpenCLContext& cl;
     OpenCLParameterSet* params;
     OpenCLArray* globals;
@@ -1273,7 +1283,7 @@ public:
     enum GlobalTargetType {DT, VARIABLE, PARAMETER};
     OpenCLIntegrateCustomStepKernel(std::string name, const Platform& platform, OpenCLContext& cl) : IntegrateCustomStepKernel(name, platform), cl(cl),
             hasInitializedKernels(false), localValuesAreCurrent(false), globalValues(NULL), sumBuffer(NULL), summedValue(NULL), uniformRandoms(NULL),
-            randomSeed(NULL), perDofValues(NULL) {
+            randomSeed(NULL), perDofEnergyParamDerivs(NULL), perDofValues(NULL), needsEnergyParamDerivs(false) {
     }
     ~OpenCLIntegrateCustomStepKernel();
     /**
@@ -1338,8 +1348,11 @@ public:
 private:
     class ReorderListener;
     class GlobalTarget;
+    class DerivFunction;
     std::string createPerDofComputation(const std::string& variable, const Lepton::ParsedExpression& expr, int component, CustomIntegrator& integrator, const std::string& forceName, const std::string& energyName);
     void prepareForComputation(ContextImpl& context, CustomIntegrator& integrator, bool& forcesAreValid);
+    Lepton::ExpressionTreeNode replaceDerivFunctions(const Lepton::ExpressionTreeNode& node, OpenMM::ContextImpl& context);
+    void findExpressionsForDerivs(const Lepton::ExpressionTreeNode& node, std::vector<std::pair<Lepton::ExpressionTreeNode, std::string> >& variableNodes);
     void recordGlobalValue(double value, GlobalTarget target);
     void recordChangedParameters(ContextImpl& context);
     bool evaluateCondition(int step);
@@ -1347,18 +1360,23 @@ private:
     double energy;
     float energyFloat;
     int numGlobalVariables;
-    bool hasInitializedKernels, deviceValuesAreCurrent, deviceGlobalsAreCurrent, modifiesParameters, keNeedsForce, hasAnyConstraints;
+    bool hasInitializedKernels, deviceValuesAreCurrent, deviceGlobalsAreCurrent, modifiesParameters, keNeedsForce, hasAnyConstraints, needsEnergyParamDerivs;
     mutable bool localValuesAreCurrent;
     OpenCLArray* globalValues;
     OpenCLArray* sumBuffer;
     OpenCLArray* summedValue;
     OpenCLArray* uniformRandoms;
     OpenCLArray* randomSeed;
+    OpenCLArray* perDofEnergyParamDerivs;
     std::map<int, OpenCLArray*> savedForces;
     std::set<int> validSavedForces;
     OpenCLParameterSet* perDofValues;
     mutable std::vector<std::vector<cl_float> > localPerDofValuesFloat;
     mutable std::vector<std::vector<cl_double> > localPerDofValuesDouble;
+    std::map<std::string, double> energyParamDerivs;
+    std::vector<std::string> perDofEnergyParamDerivNames;
+    std::vector<cl_float> localPerDofEnergyParamDerivsFloat;
+    std::vector<cl_double> localPerDofEnergyParamDerivsDouble;
     std::vector<float> globalValuesFloat;
     std::vector<double> globalValuesDouble;
     std::vector<double> initialGlobalVariables;

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* restrict 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<<"+"<<index<<"] += 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/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* restrict 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<<"+"<<index<<"] += 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;
 }