Merge pull request #2322 from peastman/cv

CustomCVForce applies ForceInfos from inner context to the outer one

platforms/cuda/include/CudaContext.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) 2009-2018 Stanford University and the Authors.      *
+ * Portions copyright (c) 2009-2019 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -86,9 +86,13 @@ public:
      */
     void initialize();
     /**
-     * Add a CudaForce to this context.
+     * Add a CudaForceInfo to this context.
      */
     void addForce(CudaForceInfo* force);
+    /**
+     * Get all CudaForceInfos that have been added to this context.
+     */
+    std::vector<CudaForceInfo*>& getForceInfos();
     /**
      * Get the CUcontext associated with this object.
      */

platforms/cuda/include/CudaKernels.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) 2008-2018 Stanford University and the Authors.      *
+ * Portions copyright (c) 2008-2019 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -1268,6 +1268,7 @@ public:
      */
     void copyParametersToContext(ContextImpl& context, const CustomCVForce& force);
 private:
+    class ForceInfo;
     class ReorderListener;
     CudaContext& cu;
     bool hasInitializedListeners;

platforms/cuda/src/CudaContext.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) 2009-2018 Stanford University and the Authors.      *
+ * Portions copyright (c) 2009-2019 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -488,6 +488,10 @@ void CudaContext::addForce(CudaForceInfo* force) {
     forces.push_back(force);
 }
 
+vector<CudaForceInfo*>& CudaContext::getForceInfos() {
+    return forces;
+}
+
 void CudaContext::setAsCurrent() {
     if (contextIsValid)
         cuCtxSetCurrent(context);

platforms/cuda/src/CudaKernels.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) 2008-2018 Stanford University and the Authors.      *
+ * Portions copyright (c) 2008-2019 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -6646,6 +6646,26 @@ void CudaCalcGayBerneForceKernel::sortAtoms() {
     exclusionStartIndex.upload(startIndexVec);
 }
 
+class CudaCalcCustomCVForceKernel::ForceInfo : public CudaForceInfo {
+public:
+    ForceInfo(CudaForceInfo& force) : force(force) {
+    }
+    bool areParticlesIdentical(int particle1, int particle2) {
+        return force.areParticlesIdentical(particle1, particle2);
+    }
+    int getNumParticleGroups() {
+        return force.getNumParticleGroups();
+    }
+    void getParticlesInGroup(int index, std::vector<int>& particles) {
+        force.getParticlesInGroup(index, particles);
+    }
+    bool areGroupsIdentical(int group1, int group2) {
+        return force.areGroupsIdentical(group1, group2);
+    }
+private:
+    CudaForceInfo& force;
+};
+
 class CudaCalcCustomCVForceKernel::ReorderListener : public CudaContext::ReorderListener {
 public:
     ReorderListener(CudaContext& cu, CudaArray& invAtomOrder) : cu(cu), invAtomOrder(invAtomOrder) {
@@ -6725,6 +6745,11 @@ void CudaCalcCustomCVForceKernel::initialize(const System& system, const CustomC
     copyStateKernel = cu.getKernel(module, "copyState");
     copyForcesKernel = cu.getKernel(module, "copyForces");
     addForcesKernel = cu.getKernel(module, "addForces");
+
+    // This context needs to respect all forces in the inner context when reordering atoms.
+
+    for (CudaForceInfo* info : cu2.getForceInfos())
+        cu.addForce(new ForceInfo(*info));
 }
 
 double CudaCalcCustomCVForceKernel::execute(ContextImpl& context, ContextImpl& innerContext, bool includeForces, bool includeEnergy) {

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) 2009-2018 Stanford University and the Authors.      *
+ * Portions copyright (c) 2009-2019 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -172,9 +172,13 @@ public:
      */
     void initialize();
     /**
-     * Add an OpenCLForce to this context.
+     * Add an OpenCLForceInfo to this context.
      */
     void addForce(OpenCLForceInfo* force);
+    /**
+     * Get all OpenCLForceInfos that have been added to this context.
+     */
+    std::vector<OpenCLForceInfo*>& getForceInfos();
     /**
      * Get the cl::Context associated with this object.
      */

platforms/opencl/include/OpenCLKernels.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) 2008-2018 Stanford University and the Authors.      *
+ * Portions copyright (c) 2008-2019 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -1245,6 +1245,7 @@ public:
      */
     void copyParametersToContext(ContextImpl& context, const CustomCVForce& force);
 private:
+    class ForceInfo;
     class ReorderListener;
     OpenCLContext& cl;
     bool hasInitializedKernels;

platforms/opencl/src/OpenCLContext.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) 2009-2018 Stanford University and the Authors.      *
+ * Portions copyright (c) 2009-2019 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -507,6 +507,10 @@ void OpenCLContext::addForce(OpenCLForceInfo* force) {
     forces.push_back(force);
 }
 
+vector<OpenCLForceInfo*>& OpenCLContext::getForceInfos() {
+    return forces;
+}
+
 string OpenCLContext::replaceStrings(const string& input, const std::map<std::string, std::string>& replacements) const {
     static set<char> symbolChars;
     if (symbolChars.size() == 0) {

platforms/opencl/src/OpenCLKernels.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) 2008-2018 Stanford University and the Authors.      *
+ * Portions copyright (c) 2008-2019 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -6925,6 +6925,26 @@ void OpenCLCalcGayBerneForceKernel::sortAtoms() {
     exclusionStartIndex.upload(startIndexVec);
 }
 
+class OpenCLCalcCustomCVForceKernel::ForceInfo : public OpenCLForceInfo {
+public:
+    ForceInfo(OpenCLForceInfo& force) : OpenCLForceInfo(0), force(force) {
+    }
+    bool areParticlesIdentical(int particle1, int particle2) {
+        return force.areParticlesIdentical(particle1, particle2);
+    }
+    int getNumParticleGroups() {
+        return force.getNumParticleGroups();
+    }
+    void getParticlesInGroup(int index, std::vector<int>& particles) {
+        force.getParticlesInGroup(index, particles);
+    }
+    bool areGroupsIdentical(int group1, int group2) {
+        return force.areGroupsIdentical(group1, group2);
+    }
+private:
+    OpenCLForceInfo& force;
+};
+
 class OpenCLCalcCustomCVForceKernel::ReorderListener : public OpenCLContext::ReorderListener {
 public:
     ReorderListener(OpenCLContext& cl, OpenCLArray& invAtomOrder) : cl(cl), invAtomOrder(invAtomOrder) {
@@ -7005,6 +7025,11 @@ void OpenCLCalcCustomCVForceKernel::initialize(const System& system, const Custo
     copyStateKernel = cl::Kernel(program, "copyState");
     copyForcesKernel = cl::Kernel(program, "copyForces");
     addForcesKernel = cl::Kernel(program, "addForces");
+
+    // This context needs to respect all forces in the inner context when reordering atoms.
+
+    for (OpenCLForceInfo* info : cl2.getForceInfos())
+        cl.addForce(new ForceInfo(*info));
 }
 
 double OpenCLCalcCustomCVForceKernel::execute(ContextImpl& context, ContextImpl& innerContext, bool includeForces, bool includeEnergy) {