Merge remote-tracking branch 'origin'

platforms/cpu/include/CpuBondForce.h

+#ifndef OPENMM_CPUBONDFORCE_H_
+#define OPENMM_CPUBONDFORCE_H_
+
+/* -------------------------------------------------------------------------- *
+ *                                   OpenMM                                   *
+ * -------------------------------------------------------------------------- *
+ * This is part of the OpenMM molecular simulation toolkit originating from   *
+ * Simbios, the NIH National Center for Physics-Based Simulation of           *
+ * Biological Structures at Stanford, funded under the NIH Roadmap for        *
+ * Medical Research, grant U54 GM072970. See https://simtk.org.               *
+ *                                                                            *
+ * Portions copyright (c) 2014 Stanford University and the Authors.           *
+ * Authors: Peter Eastman                                                     *
+ * Contributors:                                                              *
+ *                                                                            *
+ * Permission is hereby granted, free of charge, to any person obtaining a    *
+ * copy of this software and associated documentation files (the "Software"), *
+ * to deal in the Software without restriction, including without limitation  *
+ * the rights to use, copy, modify, merge, publish, distribute, sublicense,   *
+ * and/or sell copies of the Software, and to permit persons to whom the      *
+ * Software is furnished to do so, subject to the following conditions:       *
+ *                                                                            *
+ * The above copyright notice and this permission notice shall be included in *
+ * all copies or substantial portions of the Software.                        *
+ *                                                                            *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
+ * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,   *
+ * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL    *
+ * THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,    *
+ * DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR      *
+ * OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE  *
+ * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
+ * -------------------------------------------------------------------------- */
+
+#include "ReferenceBondIxn.h"
+#include "windowsExportCpu.h"
+#include "openmm/internal/ThreadPool.h"
+#include <list>
+#include <set>
+#include <vector>
+
+namespace OpenMM {
+
+/**
+ * This class parallelizes the calculation of bonded forces.
+ */
+class OPENMM_EXPORT_CPU CpuBondForce {
+public:
+    class ComputeForceTask;
+    CpuBondForce();
+    /**
+     * Analyze the set of bonds and decide which to compute with each thread.
+     */
+    void initialize(int numAtoms, int numBonds, int numAtomsPerBond, int** bondAtoms, ThreadPool& threads);
+    /**
+     * Compute the forces from all bonds.
+     */
+    void calculateForce(std::vector<OpenMM::RealVec>& atomCoordinates, RealOpenMM** parameters, std::vector<OpenMM::RealVec>& forces, 
+            RealOpenMM* totalEnergy, ReferenceBondIxn& referenceBondIxn);
+    /**
+     * This routine contains the code executed by each thread.
+     */
+    void threadComputeForce(ThreadPool& threads, int threadIndex, std::vector<OpenMM::RealVec>& atomCoordinates, RealOpenMM** parameters,
+            std::vector<OpenMM::RealVec>& forces, RealOpenMM* totalEnergy, ReferenceBondIxn& referenceBondIxn);
+private:
+    bool canAssignBond(int bond, int thread, std::vector<int>& atomThread);
+    void assignBond(int bond, int thread, std::vector<int>& atomThread, std::vector<int>& bondThread, std::vector<std::set<int> >& atomBonds, std::list<int>& candidateBonds);
+    int numBonds, numAtomsPerBond;
+    int** bondAtoms;
+    ThreadPool* threads;
+    std::vector<std::vector<int> > threadBonds;
+    std::vector<int> extraBonds;
+};
+
+} // namespace OpenMM
+
+#endif /*OPENMM_CPUBONDFORCE_H_*/

platforms/cpu/include/CpuKernels.h

@@ -32,6 +32,7 @@
  * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
  * -------------------------------------------------------------------------- */
 
+#include "CpuBondForce.h"
 #include "CpuGBSAOBCForce.h"
 #include "CpuLangevinDynamics.h"
 #include "CpuNeighborList.h"
@@ -49,6 +50,7 @@ namespace OpenMM {
  */
 class CpuCalcForcesAndEnergyKernel : public CalcForcesAndEnergyKernel {
 public:
+    class InitForceTask;
     class SumForceTask;
     CpuCalcForcesAndEnergyKernel(std::string name, const Platform& platform, CpuPlatform::PlatformData& data, ContextImpl& context);
     /**
@@ -85,6 +87,86 @@ private:
     Kernel referenceKernel;
 };
 
+/**
+ * This kernel is invoked by PeriodicTorsionForce to calculate the forces acting on the system and the energy of the system.
+ */
+class CpuCalcPeriodicTorsionForceKernel : public CalcPeriodicTorsionForceKernel {
+public:
+    CpuCalcPeriodicTorsionForceKernel(std::string name, const Platform& platform, CpuPlatform::PlatformData& data) :
+            CalcPeriodicTorsionForceKernel(name, platform), data(data), torsionIndexArray(NULL), torsionParamArray(NULL) {
+    }
+    ~CpuCalcPeriodicTorsionForceKernel();
+    /**
+     * Initialize the kernel.
+     * 
+     * @param system     the System this kernel will be applied to
+     * @param force      the PeriodicTorsionForce this kernel will be used for
+     */
+    void initialize(const System& system, const PeriodicTorsionForce& force);
+    /**
+     * Execute the kernel to calculate the forces and/or energy.
+     *
+     * @param context        the context in which to execute this kernel
+     * @param includeForces  true if forces should be calculated
+     * @param includeEnergy  true if the energy should be calculated
+     * @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 PeriodicTorsionForce to copy the parameters from
+     */
+    void copyParametersToContext(ContextImpl& context, const PeriodicTorsionForce& force);
+private:
+    CpuPlatform::PlatformData& data;
+    int numTorsions;
+    int **torsionIndexArray;
+    RealOpenMM **torsionParamArray;
+    CpuBondForce bondForce;
+};
+
+/**
+ * This kernel is invoked by RBTorsionForce to calculate the forces acting on the system and the energy of the system.
+ */
+class CpuCalcRBTorsionForceKernel : public CalcRBTorsionForceKernel {
+public:
+    CpuCalcRBTorsionForceKernel(std::string name, const Platform& platform, CpuPlatform::PlatformData& data) :
+            CalcRBTorsionForceKernel(name, platform), data(data), torsionIndexArray(NULL), torsionParamArray(NULL) {
+    }
+    ~CpuCalcRBTorsionForceKernel();
+    /**
+     * Initialize the kernel.
+     * 
+     * @param system     the System this kernel will be applied to
+     * @param force      the RBTorsionForce this kernel will be used for
+     */
+    void initialize(const System& system, const RBTorsionForce& force);
+    /**
+     * Execute the kernel to calculate the forces and/or energy.
+     *
+     * @param context        the context in which to execute this kernel
+     * @param includeForces  true if forces should be calculated
+     * @param includeEnergy  true if the energy should be calculated
+     * @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 RBTorsionForce to copy the parameters from
+     */
+    void copyParametersToContext(ContextImpl& context, const RBTorsionForce& force);
+private:
+    CpuPlatform::PlatformData& data;
+    int numTorsions;
+    int **torsionIndexArray;
+    RealOpenMM **torsionParamArray;
+    CpuBondForce bondForce;
+};
+
 /**
  * This kernel is invoked by NonbondedForce to calculate the forces acting on the system.
  */

platforms/cpu/src/CpuBondForce.cpp

+/* -------------------------------------------------------------------------- *
+ *                                   OpenMM                                   *
+ * -------------------------------------------------------------------------- *
+ * This is part of the OpenMM molecular simulation toolkit originating from   *
+ * Simbios, the NIH National Center for Physics-Based Simulation of           *
+ * Biological Structures at Stanford, funded under the NIH Roadmap for        *
+ * Medical Research, grant U54 GM072970. See https://simtk.org.               *
+ *                                                                            *
+ * Portions copyright (c) 2014 Stanford University and the Authors.           *
+ * Authors: Peter Eastman                                                     *
+ * Contributors:                                                              *
+ *                                                                            *
+ * Permission is hereby granted, free of charge, to any person obtaining a    *
+ * copy of this software and associated documentation files (the "Software"), *
+ * to deal in the Software without restriction, including without limitation  *
+ * the rights to use, copy, modify, merge, publish, distribute, sublicense,   *
+ * and/or sell copies of the Software, and to permit persons to whom the      *
+ * Software is furnished to do so, subject to the following conditions:       *
+ *                                                                            *
+ * The above copyright notice and this permission notice shall be included in *
+ * all copies or substantial portions of the Software.                        *
+ *                                                                            *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
+ * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,   *
+ * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL    *
+ * THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,    *
+ * DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR      *
+ * OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE  *
+ * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
+ * -------------------------------------------------------------------------- */
+
+#include "CpuBondForce.h"
+#include "openmm/OpenMMException.h"
+
+using namespace OpenMM;
+using namespace std;
+
+class CpuBondForce::ComputeForceTask : public ThreadPool::Task {
+public:
+    ComputeForceTask(CpuBondForce& owner, vector<RealVec>& atomCoordinates, RealOpenMM** parameters, vector<RealVec>& forces, 
+        vector<RealOpenMM>& threadEnergy, RealOpenMM* totalEnergy, ReferenceBondIxn& referenceBondIxn) : owner(owner), atomCoordinates(atomCoordinates),
+        parameters(parameters), forces(forces), threadEnergy(threadEnergy), totalEnergy(totalEnergy), referenceBondIxn(referenceBondIxn) {
+    }
+    void execute(ThreadPool& threads, int threadIndex) {
+        RealOpenMM* energy = (totalEnergy == NULL ? NULL : &threadEnergy[threadIndex]);
+        owner.threadComputeForce(threads, threadIndex, atomCoordinates, parameters, forces, energy, referenceBondIxn);
+    }
+    CpuBondForce& owner;
+    vector<RealVec>& atomCoordinates;
+    RealOpenMM** parameters;
+    vector<RealVec>& forces;
+    vector<RealOpenMM>& threadEnergy;
+    RealOpenMM* totalEnergy;
+    ReferenceBondIxn& referenceBondIxn;
+};
+
+CpuBondForce::CpuBondForce() {
+}
+
+void CpuBondForce::initialize(int numAtoms, int numBonds, int numAtomsPerBond, int** bondAtoms, ThreadPool& threads) {
+    this->numBonds = numBonds;
+    this->numAtomsPerBond = numAtomsPerBond;
+    this->bondAtoms = bondAtoms;
+    this->threads = &threads;
+    int numThreads = threads.getNumThreads();
+    int targetBondsPerThread = numBonds/numThreads;
+    
+    // Record the bonds that include each atom.
+    
+    vector<set<int> > atomBonds(numAtoms);
+    for (int bond = 0; bond < numBonds; bond++) {
+        for (int i = 0; i < numAtomsPerBond; i++)
+            atomBonds[bondAtoms[bond][i]].insert(bond);
+    }
+    
+    // Divide bonds into groups.
+    
+    vector<int> atomThread(numAtoms, -1);
+    vector<int> bondThread(numBonds, -1);
+    threadBonds.resize(numThreads);
+    int numProcessed = 0;
+    int thread = 0;
+    list<int> candidateBonds;
+    while (thread < numThreads) {
+        // Find the next unassigned bond.
+        
+        while (numProcessed < numBonds && bondThread[numProcessed] != -1)
+            numProcessed++;
+        if (numProcessed == numBonds)
+            break; // We've gone through the whole list of bonds.
+        
+        // See if this bond can be assigned to this thread.
+        
+        if (!canAssignBond(numProcessed, thread, atomThread)) {
+            numProcessed++;
+            continue;
+        }
+        
+        // Assign this bond to the thread.
+        
+        assignBond(numProcessed++, thread, atomThread, bondThread, atomBonds, candidateBonds);
+        
+        // Assign additional bonds that have been identified as involving atoms assigned to this thread.
+        
+        while (!candidateBonds.empty() && threadBonds[thread].size() < targetBondsPerThread) {
+            int bond = *candidateBonds.begin();
+            if (bondThread[bond] == -1 && canAssignBond(bond, thread, atomThread))
+                assignBond(bond, thread, atomThread, bondThread, atomBonds, candidateBonds);
+            candidateBonds.pop_front();
+        }
+        
+        // If we have assigned enough bonds to this thread, move on to the next one.
+        
+        if (threadBonds[thread].size() >= targetBondsPerThread) {
+            candidateBonds.clear();
+            thread++;
+        }
+    }
+    
+    // Look through the remaining bonds and see whether any of them can be assigned.
+    
+    candidateBonds.clear();
+    for (int bond = 0; bond < numBonds; bond++) {
+        if (bondThread[bond] == -1) {
+            // See whether this bond can be assigned to a thread.
+            
+            bool canAssign = true;
+            int assignment = -1;
+            for (int i = 0; i < numAtomsPerBond; i++) {
+                int thread = atomThread[bondAtoms[bond][i]];
+                if (thread == -1 || thread == assignment)
+                    continue;
+                if (assignment == -1)
+                    assignment = thread;
+                else {
+                    canAssign = false;
+                    break;
+                }
+            }
+            if (canAssign) {
+                // Assign this bond to a thread.
+                
+                if (assignment == -1)
+                    assignment = numThreads-1;
+                assignBond(bond, assignment, atomThread, bondThread, atomBonds, candidateBonds);
+            }
+            else {
+                // Add it to the list of "extra" bonds.
+                
+                extraBonds.push_back(bond);
+            }
+        }
+    }
+}
+
+bool CpuBondForce::canAssignBond(int bond, int thread, vector<int>& atomThread) {
+    for (int i = 0; i < numAtomsPerBond; i++) {
+        int atom = bondAtoms[bond][i];
+        if (atomThread[atom] != -1 && atomThread[atom] != thread)
+            return false;
+    }
+    return true;
+}
+
+void CpuBondForce::assignBond(int bond, int thread, vector<int>& atomThread, vector<int>& bondThread, vector<set<int> >& atomBonds, list<int>& candidateBonds) {
+    // Assign the bond to a thread.
+    
+    bondThread[bond] = thread;
+    threadBonds[thread].push_back(bond);
+    
+    // Mark every atom in this bond as also belonging to the thread, and add all of their
+    // bonds to the list of candidates.
+    
+    for (int i = 0; i < numAtomsPerBond; i++) {
+        int& atom = atomThread[bondAtoms[bond][i]];
+        if (atom == thread)
+            continue;
+        if (atom != -1)
+            throw OpenMMException("CpuBondForce: Internal error: atoms assigned to threads incorrectly");
+        atom = thread;
+        for (set<int>::const_iterator iter = atomBonds[atom].begin(); iter != atomBonds[atom].end(); ++iter)
+            candidateBonds.push_back(*iter);
+    }
+}
+
+void CpuBondForce::calculateForce(vector<RealVec>& atomCoordinates, RealOpenMM** parameters, vector<RealVec>& forces, 
+        RealOpenMM* totalEnergy, ReferenceBondIxn& referenceBondIxn) {
+    // Have the worker threads compute their forces.
+    
+    vector<RealOpenMM> threadEnergy(threads->getNumThreads(), 0);
+    ComputeForceTask task(*this, atomCoordinates, parameters, forces, threadEnergy, totalEnergy, referenceBondIxn);
+    threads->execute(task);
+    threads->waitForThreads();
+    
+    // Compute any "extra" bonds.
+    
+    for (int i = 0; i < extraBonds.size(); i++) {
+        int bond = extraBonds[i];
+        referenceBondIxn.calculateBondIxn(bondAtoms[bond], atomCoordinates, parameters[bond], forces, totalEnergy);
+    }
+
+    // Compute the total energy.
+    
+    if (totalEnergy != NULL)
+        for (int i = 0; i < threads->getNumThreads(); i++)
+            *totalEnergy += threadEnergy[i];
+}
+
+void CpuBondForce::threadComputeForce(ThreadPool& threads, int threadIndex, vector<RealVec>& atomCoordinates, RealOpenMM** parameters, vector<RealVec>& forces, 
+            RealOpenMM* totalEnergy, ReferenceBondIxn& referenceBondIxn) {
+    vector<int>& bonds = threadBonds[threadIndex];
+    int numBonds = bonds.size();
+    for (int i = 0; i < numBonds; i++) {
+        int bond = bonds[i];
+        referenceBondIxn.calculateBondIxn(bondAtoms[bond], atomCoordinates, parameters[bond], forces, totalEnergy);
+    }
+}
\ No newline at end of file

platforms/cpu/src/CpuKernelFactory.cpp

@@ -41,6 +41,10 @@ KernelImpl* CpuKernelFactory::createKernelImpl(std::string name, const Platform&
     CpuPlatform::PlatformData& data = CpuPlatform::getPlatformData(context);
     if (name == CalcForcesAndEnergyKernel::Name())
         return new CpuCalcForcesAndEnergyKernel(name, platform, data, context);
+    if (name == CalcPeriodicTorsionForceKernel::Name())
+        return new CpuCalcPeriodicTorsionForceKernel(name, platform, data);
+    if (name == CalcRBTorsionForceKernel::Name())
+        return new CpuCalcRBTorsionForceKernel(name, platform, data);
     if (name == CalcNonbondedForceKernel::Name())
         return new CpuCalcNonbondedForceKernel(name, platform, data);
     if (name == CalcGBSAOBCForceKernel::Name())

platforms/cpu/src/CpuKernels.cpp

@@ -35,6 +35,8 @@
 #include "ReferenceKernelFactory.h"
 #include "ReferenceKernels.h"
 #include "ReferenceLJCoulomb14.h"
+#include "ReferenceProperDihedralBond.h"
+#include "ReferenceRbDihedralBond.h"
 #include "openmm/Context.h"
 #include "openmm/OpenMMException.h"
 #include "openmm/internal/ContextImpl.h"
@@ -130,6 +132,46 @@ public:
     CpuPlatform::PlatformData& data;
 };
 
+class CpuCalcForcesAndEnergyKernel::InitForceTask : public ThreadPool::Task {
+public:
+    InitForceTask(int numParticles, ContextImpl& context, CpuPlatform::PlatformData& data) : numParticles(numParticles), context(context), data(data) {
+    }
+    void execute(ThreadPool& threads, int threadIndex) {
+        // Convert the positions to single precision and apply periodic boundary conditions
+
+        AlignedArray<float>& posq = data.posq;
+        vector<RealVec>& posData = extractPositions(context);
+        RealVec boxSize = extractBoxSize(context);
+        double invBoxSize[3] = {1/boxSize[0], 1/boxSize[1], 1/boxSize[2]};
+        int numParticles = context.getSystem().getNumParticles();
+        int numThreads = threads.getNumThreads();
+        int start = threadIndex*numParticles/numThreads;
+        int end = (threadIndex+1)*numParticles/numThreads;
+        if (data.isPeriodic)
+            for (int i = start; i < end; i++)
+                for (int j = 0; j < 3; j++) {
+                    RealOpenMM x = posData[i][j];
+                    double base = floor(x*invBoxSize[j])*boxSize[j];
+                    posq[4*i+j] = (float) (x-base);
+                }
+        else
+            for (int i = start; i < end; i++) {
+                posq[4*i] = (float) posData[i][0];
+                posq[4*i+1] = (float) posData[i][1];
+                posq[4*i+2] = (float) posData[i][2];
+            }
+
+        // Clear the forces.
+
+        fvec4 zero(0.0f);
+        for (int j = 0; j < numParticles; j++)
+            zero.store(&data.threadForce[threadIndex][j*4]);
+    }
+    int numParticles;
+    ContextImpl& context;
+    CpuPlatform::PlatformData& data;
+};
+
 CpuCalcForcesAndEnergyKernel::CpuCalcForcesAndEnergyKernel(std::string name, const Platform& platform, CpuPlatform::PlatformData& data, ContextImpl& context) :
         CalcForcesAndEnergyKernel(name, platform), data(data) {
     // Create a Reference platform version of this kernel.
@@ -145,33 +187,11 @@ void CpuCalcForcesAndEnergyKernel::initialize(const System& system) {
 void CpuCalcForcesAndEnergyKernel::beginComputation(ContextImpl& context, bool includeForce, bool includeEnergy, int groups) {
     referenceKernel.getAs<ReferenceCalcForcesAndEnergyKernel>().beginComputation(context, includeForce, includeEnergy, groups);
     
-    // Convert the positions to single precision and apply periodic boundary conditions
+    // Convert positions to single precision and clear the forces.
     
-    AlignedArray<float>& posq = data.posq;
-    vector<RealVec>& posData = extractPositions(context);
-    RealVec boxSize = extractBoxSize(context);
-    double invBoxSize[3] = {1/boxSize[0], 1/boxSize[1], 1/boxSize[2]};
-    int numParticles = context.getSystem().getNumParticles();
-    if (data.isPeriodic)
-        for (int i = 0; i < numParticles; i++)
-            for (int j = 0; j < 3; j++) {
-                RealOpenMM x = posData[i][j];
-                double base = floor(x*invBoxSize[j])*boxSize[j];
-                posq[4*i+j] = (float) (x-base);
-            }
-    else
-        for (int i = 0; i < numParticles; i++) {
-            posq[4*i] = (float) posData[i][0];
-            posq[4*i+1] = (float) posData[i][1];
-            posq[4*i+2] = (float) posData[i][2];
-        }
-    
-    // Clear the forces.
-    
-    fvec4 zero(0.0f);
-    for (int i = 0; i < (int) data.threadForce.size(); i++)
-        for (int j = 0; j < numParticles; j++)
-            zero.store(&data.threadForce[i][j*4]);
+    InitForceTask task(context.getSystem().getNumParticles(), context, data);
+    data.threads.execute(task);
+    data.threads.waitForThreads();
 }
 
 double CpuCalcForcesAndEnergyKernel::finishComputation(ContextImpl& context, bool includeForce, bool includeEnergy, int groups) {
@@ -183,6 +203,134 @@ double CpuCalcForcesAndEnergyKernel::finishComputation(ContextImpl& context, boo
     return referenceKernel.getAs<ReferenceCalcForcesAndEnergyKernel>().finishComputation(context, includeForce, includeEnergy, groups);
 }
 
+CpuCalcPeriodicTorsionForceKernel::~CpuCalcPeriodicTorsionForceKernel() {
+    if (torsionIndexArray != NULL) {
+        for (int i = 0; i < numTorsions; i++) {
+            delete[] torsionIndexArray[i];
+            delete[] torsionParamArray[i];
+        }
+        delete[] torsionIndexArray;
+        delete[] torsionParamArray;
+    }
+}
+
+void CpuCalcPeriodicTorsionForceKernel::initialize(const System& system, const PeriodicTorsionForce& force) {
+    numTorsions = force.getNumTorsions();
+    torsionIndexArray = new int*[numTorsions];
+    for (int i = 0; i < numTorsions; i++)
+        torsionIndexArray[i] = new int[4];
+    torsionParamArray = new RealOpenMM*[numTorsions];
+    for (int i = 0; i < numTorsions; i++)
+        torsionParamArray[i] = new RealOpenMM[3];
+    for (int i = 0; i < numTorsions; ++i) {
+        int particle1, particle2, particle3, particle4, periodicity;
+        double phase, k;
+        force.getTorsionParameters(i, particle1, particle2, particle3, particle4, periodicity, phase, k);
+        torsionIndexArray[i][0] = particle1;
+        torsionIndexArray[i][1] = particle2;
+        torsionIndexArray[i][2] = particle3;
+        torsionIndexArray[i][3] = particle4;
+        torsionParamArray[i][0] = (RealOpenMM) k;
+        torsionParamArray[i][1] = (RealOpenMM) phase;
+        torsionParamArray[i][2] = (RealOpenMM) periodicity;
+    }
+    bondForce.initialize(system.getNumParticles(), numTorsions, 4, torsionIndexArray, data.threads);
+}
+
+double CpuCalcPeriodicTorsionForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
+    vector<RealVec>& posData = extractPositions(context);
+    vector<RealVec>& forceData = extractForces(context);
+    RealOpenMM energy = 0;
+    ReferenceProperDihedralBond periodicTorsionBond;
+    bondForce.calculateForce(posData, torsionParamArray, forceData, includeEnergy ? &energy : NULL, periodicTorsionBond);
+    return energy;
+}
+
+void CpuCalcPeriodicTorsionForceKernel::copyParametersToContext(ContextImpl& context, const PeriodicTorsionForce& force) {
+    if (numTorsions != force.getNumTorsions())
+        throw OpenMMException("updateParametersInContext: The number of torsions has changed");
+
+    // Record the values.
+
+    for (int i = 0; i < numTorsions; ++i) {
+        int particle1, particle2, particle3, particle4, periodicity;
+        double phase, k;
+        force.getTorsionParameters(i, particle1, particle2, particle3, particle4, periodicity, phase, k);
+        if (particle1 != torsionIndexArray[i][0] || particle2 != torsionIndexArray[i][1] || particle3 != torsionIndexArray[i][2] || particle4 != torsionIndexArray[i][3])
+            throw OpenMMException("updateParametersInContext: The set of particles in a torsion has changed");
+        torsionParamArray[i][0] = (RealOpenMM) k;
+        torsionParamArray[i][1] = (RealOpenMM) phase;
+        torsionParamArray[i][2] = (RealOpenMM) periodicity;
+    }
+}
+
+CpuCalcRBTorsionForceKernel::~CpuCalcRBTorsionForceKernel() {
+    if (torsionIndexArray != NULL) {
+        for (int i = 0; i < numTorsions; i++) {
+            delete[] torsionIndexArray[i];
+            delete[] torsionParamArray[i];
+        }
+        delete[] torsionIndexArray;
+        delete[] torsionParamArray;
+    }
+}
+
+void CpuCalcRBTorsionForceKernel::initialize(const System& system, const RBTorsionForce& force) {
+    numTorsions = force.getNumTorsions();
+    torsionIndexArray = new int*[numTorsions];
+    for (int i = 0; i < numTorsions; i++)
+        torsionIndexArray[i] = new int[4];
+    torsionParamArray = new RealOpenMM*[numTorsions];
+    for (int i = 0; i < numTorsions; i++)
+        torsionParamArray[i] = new RealOpenMM[6];
+    for (int i = 0; i < numTorsions; ++i) {
+        int particle1, particle2, particle3, particle4;
+        double c0, c1, c2, c3, c4, c5;
+        force.getTorsionParameters(i, particle1, particle2, particle3, particle4, c0, c1, c2, c3, c4, c5);
+        torsionIndexArray[i][0] = particle1;
+        torsionIndexArray[i][1] = particle2;
+        torsionIndexArray[i][2] = particle3;
+        torsionIndexArray[i][3] = particle4;
+        torsionParamArray[i][0] = (RealOpenMM) c0;
+        torsionParamArray[i][1] = (RealOpenMM) c1;
+        torsionParamArray[i][2] = (RealOpenMM) c2;
+        torsionParamArray[i][3] = (RealOpenMM) c3;
+        torsionParamArray[i][4] = (RealOpenMM) c4;
+        torsionParamArray[i][5] = (RealOpenMM) c5;
+    }
+    bondForce.initialize(system.getNumParticles(), numTorsions, 4, torsionIndexArray, data.threads);
+}
+
+double CpuCalcRBTorsionForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
+    vector<RealVec>& posData = extractPositions(context);
+    vector<RealVec>& forceData = extractForces(context);
+    RealOpenMM energy = 0;
+    ReferenceRbDihedralBond rbTorsionBond;
+    bondForce.calculateForce(posData, torsionParamArray, forceData, includeEnergy ? &energy : NULL, rbTorsionBond);
+    return energy;
+}
+
+void CpuCalcRBTorsionForceKernel::copyParametersToContext(ContextImpl& context, const RBTorsionForce& force) {
+    if (numTorsions != force.getNumTorsions())
+        throw OpenMMException("updateParametersInContext: The number of torsions has changed");
+
+    // Record the values.
+
+    for (int i = 0; i < numTorsions; ++i) {
+        int particle1, particle2, particle3, particle4;
+        double c0, c1, c2, c3, c4, c5;
+        force.getTorsionParameters(i, particle1, particle2, particle3, particle4, c0, c1, c2, c3, c4, c5);
+        if (particle1 != torsionIndexArray[i][0] || particle2 != torsionIndexArray[i][1] || particle3 != torsionIndexArray[i][2] || particle4 != torsionIndexArray[i][3])
+            throw OpenMMException("updateParametersInContext: The set of particles in a torsion has changed");
+        torsionParamArray[i][0] = (RealOpenMM) c0;
+        torsionParamArray[i][1] = (RealOpenMM) c1;
+        torsionParamArray[i][2] = (RealOpenMM) c2;
+        torsionParamArray[i][3] = (RealOpenMM) c3;
+        torsionParamArray[i][4] = (RealOpenMM) c4;
+        torsionParamArray[i][5] = (RealOpenMM) c5;
+    }
+}
+
 class CpuCalcNonbondedForceKernel::PmeIO : public CalcPmeReciprocalForceKernel::IO {
 public:
     PmeIO(float* posq, float* force, int numParticles) : posq(posq), force(force), numParticles(numParticles) {

platforms/cpu/src/CpuPlatform.cpp

@@ -51,6 +51,8 @@ map<ContextImpl*, CpuPlatform::PlatformData*> CpuPlatform::contextData;
 CpuPlatform::CpuPlatform() {
     CpuKernelFactory* factory = new CpuKernelFactory();
     registerKernelFactory(CalcForcesAndEnergyKernel::Name(), factory);
+    registerKernelFactory(CalcPeriodicTorsionForceKernel::Name(), factory);
+    registerKernelFactory(CalcRBTorsionForceKernel::Name(), factory);
     registerKernelFactory(CalcNonbondedForceKernel::Name(), factory);
     registerKernelFactory(CalcGBSAOBCForceKernel::Name(), factory);
     registerKernelFactory(IntegrateLangevinStepKernel::Name(), factory);

platforms/cpu/tests/TestCpuPeriodicTorsionForce.cpp

+/* -------------------------------------------------------------------------- *
+ *                                   OpenMM                                   *
+ * -------------------------------------------------------------------------- *
+ * This is part of the OpenMM molecular simulation toolkit originating from   *
+ * Simbios, the NIH National Center for Physics-Based Simulation of           *
+ * Biological Structures at Stanford, funded under the NIH Roadmap for        *
+ * Medical Research, grant U54 GM072970. See https://simtk.org.               *
+ *                                                                            *
+ * Portions copyright (c) 2008-2014 Stanford University and the Authors.      *
+ * Authors: Peter Eastman                                                     *
+ * Contributors:                                                              *
+ *                                                                            *
+ * Permission is hereby granted, free of charge, to any person obtaining a    *
+ * copy of this software and associated documentation files (the "Software"), *
+ * to deal in the Software without restriction, including without limitation  *
+ * the rights to use, copy, modify, merge, publish, distribute, sublicense,   *
+ * and/or sell copies of the Software, and to permit persons to whom the      *
+ * Software is furnished to do so, subject to the following conditions:       *
+ *                                                                            *
+ * The above copyright notice and this permission notice shall be included in *
+ * all copies or substantial portions of the Software.                        *
+ *                                                                            *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
+ * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,   *
+ * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL    *
+ * THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,    *
+ * DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR      *
+ * OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE  *
+ * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
+ * -------------------------------------------------------------------------- */
+
+/**
+ * This tests the CPU implementation of PeriodicTorsionForce.
+ */
+
+#include "openmm/internal/AssertionUtilities.h"
+#include "openmm/Context.h"
+#include "CpuPlatform.h"
+#include "openmm/PeriodicTorsionForce.h"
+#include "openmm/System.h"
+#include "openmm/VerletIntegrator.h"
+#include "SimTKOpenMMRealType.h"
+#include <iostream>
+#include <vector>
+
+using namespace OpenMM;
+using namespace std;
+
+CpuPlatform platform;
+
+const double TOL = 1e-5;
+
+void testPeriodicTorsions() {
+    System system;
+    system.addParticle(1.0);
+    system.addParticle(1.0);
+    system.addParticle(1.0);
+    system.addParticle(1.0);
+    VerletIntegrator integrator(0.01);
+    PeriodicTorsionForce* forceField = new PeriodicTorsionForce();
+    forceField->addTorsion(0, 1, 2, 3, 2, PI_M/3, 1.1);
+    system.addForce(forceField);
+    Context context(system, integrator, platform);
+    vector<Vec3> positions(4);
+    positions[0] = Vec3(0, 1, 0);
+    positions[1] = Vec3(0, 0, 0);
+    positions[2] = Vec3(1, 0, 0);
+    positions[3] = Vec3(1, 0, 2);
+    context.setPositions(positions);
+    State state = context.getState(State::Forces | State::Energy);
+    {
+        const vector<Vec3>& forces = state.getForces();
+        double torque = -2*1.1*std::sin(2*PI_M/3);
+        ASSERT_EQUAL_VEC(Vec3(0, 0, torque), forces[0], TOL);
+        ASSERT_EQUAL_VEC(Vec3(0, 0.5*torque, 0), forces[3], TOL);
+        ASSERT_EQUAL_VEC(Vec3(forces[0][0]+forces[1][0]+forces[2][0]+forces[3][0], forces[0][1]+forces[1][1]+forces[2][1]+forces[3][1], forces[0][2]+forces[1][2]+forces[2][2]+forces[3][2]), Vec3(0, 0, 0), TOL);
+        ASSERT_EQUAL_TOL(1.1*(1+std::cos(2*PI_M/3)), state.getPotentialEnergy(), TOL);
+    }
+    
+    // Try changing the torsion parameters and make sure it's still correct.
+    
+    forceField->setTorsionParameters(0, 0, 1, 2, 3, 3, PI_M/3.2, 1.3);
+    forceField->updateParametersInContext(context);
+    state = context.getState(State::Forces | State::Energy);
+    {
+        const vector<Vec3>& forces = state.getForces();
+        double dtheta = (3*PI_M/2)-(PI_M/3.2);
+        double torque = -3*1.3*std::sin(dtheta);
+        ASSERT_EQUAL_VEC(Vec3(0, 0, torque), forces[0], TOL);
+        ASSERT_EQUAL_VEC(Vec3(0, 0.5*torque, 0), forces[3], TOL);
+        ASSERT_EQUAL_VEC(Vec3(forces[0][0]+forces[1][0]+forces[2][0]+forces[3][0], forces[0][1]+forces[1][1]+forces[2][1]+forces[3][1], forces[0][2]+forces[1][2]+forces[2][2]+forces[3][2]), Vec3(0, 0, 0), TOL);
+        ASSERT_EQUAL_TOL(1.3*(1+std::cos(dtheta)), state.getPotentialEnergy(), TOL);
+    }
+}
+
+void testParallelComputation() {
+    System system;
+    const int numParticles = 200;
+    for (int i = 0; i < numParticles; i++)
+        system.addParticle(1.0);
+    PeriodicTorsionForce* force = new PeriodicTorsionForce();
+    for (int i = 3; i < numParticles; i++)
+        force->addTorsion(i-3, i-2, i-1, i, 2, 1.1, i);
+    system.addForce(force);
+    vector<Vec3> positions(numParticles);
+    for (int i = 0; i < numParticles; i++)
+        positions[i] = Vec3(i, i%2, i%3);
+    VerletIntegrator integrator1(0.01);
+    ReferencePlatform reference;
+    Context context1(system, integrator1, reference);
+    context1.setPositions(positions);
+    State state1 = context1.getState(State::Forces | State::Energy);
+    VerletIntegrator integrator2(0.01);
+    Context context2(system, integrator2, platform);
+    context2.setPositions(positions);
+    State state2 = context2.getState(State::Forces | State::Energy);
+    ASSERT_EQUAL_TOL(state1.getPotentialEnergy(), state2.getPotentialEnergy(), 1e-5);
+    for (int i = 0; i < numParticles; i++)
+        ASSERT_EQUAL_VEC(state1.getForces()[i], state2.getForces()[i], 1e-5);
+}
+
+int main(int argc, char* argv[]) {
+    try {
+        testPeriodicTorsions();
+        testParallelComputation();
+    }
+    catch(const exception& e) {
+        cout << "exception: " << e.what() << endl;
+        return 1;
+    }
+    cout << "Done" << endl;
+    return 0;
+}

platforms/cpu/tests/TestCpuRBTorsionForce.cpp

+/* -------------------------------------------------------------------------- *
+ *                                   OpenMM                                   *
+ * -------------------------------------------------------------------------- *
+ * This is part of the OpenMM molecular simulation toolkit originating from   *
+ * Simbios, the NIH National Center for Physics-Based Simulation of           *
+ * Biological Structures at Stanford, funded under the NIH Roadmap for        *
+ * Medical Research, grant U54 GM072970. See https://simtk.org.               *
+ *                                                                            *
+ * Portions copyright (c) 2008-2014 Stanford University and the Authors.      *
+ * Authors: Peter Eastman                                                     *
+ * Contributors:                                                              *
+ *                                                                            *
+ * Permission is hereby granted, free of charge, to any person obtaining a    *
+ * copy of this software and associated documentation files (the "Software"), *
+ * to deal in the Software without restriction, including without limitation  *
+ * the rights to use, copy, modify, merge, publish, distribute, sublicense,   *
+ * and/or sell copies of the Software, and to permit persons to whom the      *
+ * Software is furnished to do so, subject to the following conditions:       *
+ *                                                                            *
+ * The above copyright notice and this permission notice shall be included in *
+ * all copies or substantial portions of the Software.                        *
+ *                                                                            *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
+ * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,   *
+ * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL    *
+ * THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,    *
+ * DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR      *
+ * OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE  *
+ * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
+ * -------------------------------------------------------------------------- */
+
+/**
+ * This tests the CUDA implementation of RBTorsionForce.
+ */
+
+#include "openmm/internal/AssertionUtilities.h"
+#include "openmm/Context.h"
+#include "CpuPlatform.h"
+#include "openmm/RBTorsionForce.h"
+#include "openmm/System.h"
+#include "openmm/VerletIntegrator.h"
+#include "SimTKOpenMMRealType.h"
+#include <iostream>
+#include <vector>
+
+using namespace OpenMM;
+using namespace std;
+
+CpuPlatform platform;
+
+const double TOL = 1e-5;
+
+void testRBTorsions() {
+    System system;
+    system.addParticle(1.0);
+    system.addParticle(1.0);
+    system.addParticle(1.0);
+    system.addParticle(1.0);
+    VerletIntegrator integrator(0.01);
+    RBTorsionForce* forceField = new RBTorsionForce();
+    forceField->addTorsion(0, 1, 2, 3, 0.1, 0.2, 0.3, 0.4, 0.5, 0.6);
+    system.addForce(forceField);
+    Context context(system, integrator, platform);
+    vector<Vec3> positions(4);
+    positions[0] = Vec3(0, 1, 0);
+    positions[1] = Vec3(0, 0, 0);
+    positions[2] = Vec3(1, 0, 0);
+    positions[3] = Vec3(1, 1, 1);
+    context.setPositions(positions);
+    State state = context.getState(State::Forces | State::Energy);
+    {
+        const vector<Vec3>& forces = state.getForces();
+        double psi = 0.25*PI_M - PI_M;
+        double torque = 0.0;
+        for (int i = 1; i < 6; ++i) {
+            double c = 0.1*(i+1);
+            torque += -c*i*std::pow(std::cos(psi), i-1)*std::sin(psi);
+        }
+        ASSERT_EQUAL_VEC(Vec3(0, 0, torque), forces[0], TOL);
+        ASSERT_EQUAL_VEC(Vec3(0, 0.5*torque, -0.5*torque), forces[3], TOL);
+        ASSERT_EQUAL_VEC(Vec3(forces[0][0]+forces[1][0]+forces[2][0]+forces[3][0], forces[0][1]+forces[1][1]+forces[2][1]+forces[3][1], forces[0][2]+forces[1][2]+forces[2][2]+forces[3][2]), Vec3(0, 0, 0), TOL);
+        double energy = 0.0;
+        for (int i = 0; i < 6; ++i) {
+            double c = 0.1*(i+1);
+            energy += c*std::pow(std::cos(psi), i);
+        }
+        ASSERT_EQUAL_TOL(energy, state.getPotentialEnergy(), TOL);
+    }
+    
+    // Try changing the torsion parameters and make sure it's still correct.
+    
+    forceField->setTorsionParameters(0, 0, 1, 2, 3, 0.11, 0.22, 0.33, 0.44, 0.55, 0.66);
+    forceField->updateParametersInContext(context);
+    state = context.getState(State::Forces | State::Energy);
+    {
+        const vector<Vec3>& forces = state.getForces();
+        double psi = 0.25*PI_M - PI_M;
+        double torque = 0.0;
+        for (int i = 1; i < 6; ++i) {
+            double c = 0.11*(i+1);
+            torque += -c*i*std::pow(std::cos(psi), i-1)*std::sin(psi);
+        }
+        ASSERT_EQUAL_VEC(Vec3(0, 0, torque), forces[0], TOL);
+        ASSERT_EQUAL_VEC(Vec3(0, 0.5*torque, -0.5*torque), forces[3], TOL);
+        ASSERT_EQUAL_VEC(Vec3(forces[0][0]+forces[1][0]+forces[2][0]+forces[3][0], forces[0][1]+forces[1][1]+forces[2][1]+forces[3][1], forces[0][2]+forces[1][2]+forces[2][2]+forces[3][2]), Vec3(0, 0, 0), TOL);
+        double energy = 0.0;
+        for (int i = 0; i < 6; ++i) {
+            double c = 0.11*(i+1);
+            energy += c*std::pow(std::cos(psi), i);
+        }
+        ASSERT_EQUAL_TOL(energy, state.getPotentialEnergy(), TOL);
+    }
+}
+
+void testParallelComputation() {
+    System system;
+    const int numParticles = 200;
+    for (int i = 0; i < numParticles; i++)
+        system.addParticle(1.0);
+    RBTorsionForce* force = new RBTorsionForce();
+    for (int i = 3; i < numParticles; i++)
+        force->addTorsion(i-3, i-2, i-1, i, 2, 0.1*i, 0.5*i, i, 1, 1);
+    system.addForce(force);
+    vector<Vec3> positions(numParticles);
+    for (int i = 0; i < numParticles; i++)
+        positions[i] = Vec3(i, i%2, i%3);
+    VerletIntegrator integrator1(0.01);
+    ReferencePlatform reference;
+    Context context1(system, integrator1, reference);
+    context1.setPositions(positions);
+    State state1 = context1.getState(State::Forces | State::Energy);
+    VerletIntegrator integrator2(0.01);
+    Context context2(system, integrator2, platform);
+    context2.setPositions(positions);
+    State state2 = context2.getState(State::Forces | State::Energy);
+    ASSERT_EQUAL_TOL(state1.getPotentialEnergy(), state2.getPotentialEnergy(), 1e-5);
+    for (int i = 0; i < numParticles; i++)
+        ASSERT_EQUAL_VEC(state1.getForces()[i], state2.getForces()[i], 1e-5);
+}
+
+int main(int argc, char* argv[]) {
+    try {
+        testRBTorsions();
+        testParallelComputation();
+    }
+    catch(const exception& e) {
+        cout << "exception: " << e.what() << endl;
+        return 1;
+    }
+    cout << "Done" << endl;
+    return 0;
+}

platforms/opencl/src/OpenCLContext.cpp

@@ -107,8 +107,8 @@ OpenCLContext::OpenCLContext(const System& system, int platformIndex, int device
                 if (i != deviceIndex && deviceIndex >= 0 && deviceIndex < (int) devices.size())
                     continue;
 
-                if (platformVendor == "Apple" && devices[i].getInfo<CL_DEVICE_VENDOR>() == "AMD")
-                    continue; // Don't use AMD GPUs on OS X due to serious bugs.
+                if (platformVendor == "Apple" && (devices[i].getInfo<CL_DEVICE_TYPE>() == CL_DEVICE_TYPE_CPU || devices[i].getInfo<CL_DEVICE_VENDOR>() == "AMD"))
+                    continue; // The CPU device on OS X won't work correctly, and there are serious bugs using AMD GPUs.
                 int maxSize = devices[i].getInfo<CL_DEVICE_MAX_WORK_ITEM_SIZES>()[0];
                 int processingElementsPerComputeUnit = 8;
                 if (devices[i].getInfo<CL_DEVICE_TYPE>() != CL_DEVICE_TYPE_GPU) {

platforms/reference/include/ReferenceBondIxn.h

@@ -25,7 +25,9 @@
 #ifndef __ReferenceBondIxn_H__
 #define __ReferenceBondIxn_H__
 
-// #include "ReferenceIxn.h"
+#include "RealVec.h"
+#include "openmm/internal/windowsExport.h"
+#include <vector>
 
 // ---------------------------------------------------------------------------------------
 

plugins/amoeba/platforms/cuda/src/AmoebaCudaKernels.cpp

@@ -893,8 +893,9 @@ void CudaCalcAmoebaMultipoleForceKernel::initialize(const System& system, const
 
     numMultipoles = force.getNumMultipoles();
     CudaArray& posq = cu.getPosq();
-    float4* posqf = (float4*) cu.getPinnedBuffer();
-    double4* posqd = (double4*) cu.getPinnedBuffer();
+    vector<double4> temp(posq.getSize());
+    float4* posqf = (float4*) &temp[0];
+    double4* posqd = (double4*) &temp[0];
     vector<float2> dampingAndTholeVec;
     vector<float> polarizabilityVec;
     vector<float> molecularDipolesVec;
@@ -941,7 +942,7 @@ void CudaCalcAmoebaMultipoleForceKernel::initialize(const System& system, const
     multipoleParticles->upload(multipoleParticlesVec);
     molecularDipoles->upload(molecularDipolesVec);
     molecularQuadrupoles->upload(molecularQuadrupolesVec);
-    posq.upload(cu.getPinnedBuffer());
+    posq.upload(&temp[0]);
     
     // Create workspace arrays.
     

plugins/amoeba/wrappers/generateAmoebaWrappers.py

@@ -75,9 +75,10 @@ class WrapperGenerator:
         # Read all the XML files and merge them into a single document.
         self.doc = etree.ElementTree(etree.Element('root'))
         for file in os.listdir(inputDirname):
-            root = etree.parse(os.path.join(inputDirname, file)).getroot()
-            for node in root:
-                self.doc.getroot().append(node)
+            if file.lower().endswith('xml'):
+                root = etree.parse(os.path.join(inputDirname, file)).getroot()
+                for node in root:
+                    self.doc.getroot().append(node)
 
         self.out = output
 

wrappers/generateWrappers.py

@@ -75,9 +75,10 @@ class WrapperGenerator:
         # Read all the XML files and merge them into a single document.
         self.doc = etree.ElementTree(etree.Element('root'))
         for file in os.listdir(inputDirname):
-            root = etree.parse(os.path.join(inputDirname, file)).getroot()
-            for node in root:
-                self.doc.getroot().append(node)
+            if file.lower().endswith('xml'):
+                root = etree.parse(os.path.join(inputDirname, file)).getroot()
+                for node in root:
+                    self.doc.getroot().append(node)
 
         self.out = output
 

wrappers/python/src/swig_doxygen/swigInputBuilder.py

@@ -135,9 +135,10 @@ class SwigInputBuilder:
         # Read all the XML files and merge them into a single document.
         self.doc = etree.ElementTree(etree.Element('root'))
         for file in os.listdir(inputDirname):
-            root = etree.parse(os.path.join(inputDirname, file)).getroot()
-            for node in root:
-                self.doc.getroot().append(node)
+            if file.lower().endswith('xml'):
+                root = etree.parse(os.path.join(inputDirname, file)).getroot()
+                for node in root:
+                    self.doc.getroot().append(node)
 
         if outputFilename:
             self.fOut = open(outputFilename, 'w')