Merge remote-tracking branch 'upstream/master'

platforms/opencl/tests/TestOpenCLNonbondedForce.cpp

@@ -410,9 +410,9 @@ void testTriclinic() {
         }
         else {
             const Vec3 force = delta*ONE_4PI_EPS0*(-1.0/(distance*distance*distance)+2.0*krf);
-            ASSERT_EQUAL_TOL(ONE_4PI_EPS0*(1.0/distance+krf*distance*distance-crf), state.getPotentialEnergy(), TOL);
-            ASSERT_EQUAL_VEC(force, state.getForces()[0], TOL);
-            ASSERT_EQUAL_VEC(-force, state.getForces()[1], TOL);
+            ASSERT_EQUAL_TOL(ONE_4PI_EPS0*(1.0/distance+krf*distance*distance-crf), state.getPotentialEnergy(), 1e-4);
+            ASSERT_EQUAL_VEC(force, state.getForces()[0], 1e-4);
+            ASSERT_EQUAL_VEC(-force, state.getForces()[1], 1e-4);
         }
     }
 }

platforms/opencl/tests/TestOpenCLVirtualSites.cpp

@@ -413,7 +413,7 @@ void testConservationLaws() {
         if (i == 0)
             initialAngularMomentum = angularMomentum;
         else
-            ASSERT_EQUAL_VEC(initialAngularMomentum, angularMomentum, 0.03);
+            ASSERT_EQUAL_VEC(initialAngularMomentum, angularMomentum, 0.05);
         integrator.step(1);
     }
 }

platforms/reference/include/ReferenceCCMAAlgorithm.h

 
-/* Portions copyright (c) 2006-2013 Stanford University and Simbios.
+/* Portions copyright (c) 2006-2015 Stanford University and Simbios.
  * Contributors: Pande Group
  *
  * Permission is hereby granted, free of charge, to any person obtaining
@@ -37,6 +37,7 @@ class OPENMM_EXPORT ReferenceCCMAAlgorithm : public ReferenceConstraintAlgorithm
 protected:
 
     int _maximumNumberOfIterations;
+    RealOpenMM _elementCutoff;
 
     int _numberOfConstraints;
     std::vector<std::pair<int, int> > _atomIndices;
@@ -66,8 +67,9 @@ public:
      * @param distance                 distances for constraints
      * @param masses                   atom masses
      * @param angles                   angle force field terms
+     * @param elementCutoff            the cutoff for which elements of the inverse matrix to keep
      */
-    ReferenceCCMAAlgorithm(int numberOfAtoms, int numberOfConstraints, const std::vector<std::pair<int, int> >& atomIndices, const std::vector<RealOpenMM>& distance, std::vector<RealOpenMM>& masses, std::vector<AngleInfo>& angles);
+    ReferenceCCMAAlgorithm(int numberOfAtoms, int numberOfConstraints, const std::vector<std::pair<int, int> >& atomIndices, const std::vector<RealOpenMM>& distance, std::vector<RealOpenMM>& masses, std::vector<AngleInfo>& angles, RealOpenMM elementCutoff);
 
     ~ReferenceCCMAAlgorithm();
 
@@ -107,6 +109,13 @@ public:
      */
     void applyToVelocities(std::vector<OpenMM::RealVec>& atomCoordinates,
                      std::vector<OpenMM::RealVec>& velocities, std::vector<RealOpenMM>& inverseMasses, RealOpenMM tolerance);
+
+    /**
+     * Get the inverse constraint matrix.  Each element represents one column, and contains a list
+     * of all non-zero elements in the form (index, value).
+     */
+    const std::vector<std::vector<std::pair<int, RealOpenMM> > >& getMatrix() const;
+
 };
 
 class ReferenceCCMAAlgorithm::AngleInfo

platforms/reference/include/ReferenceKernels.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) 2008-2013 Stanford University and the Authors.      *
+ * Portions copyright (c) 2008-2015 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -493,6 +493,13 @@ public:
      * @return the potential energy due to the force
      */
     double execute(ContextImpl& context, bool includeForces, bool includeEnergy);
+    /**
+     * Copy changed parameters over to a context.
+     *
+     * @param context    the context to copy parameters to
+     * @param force      the CMAPTorsionForce to copy the parameters from
+     */
+    void copyParametersToContext(ContextImpl& context, const CMAPTorsionForce& force);
 private:
     std::vector<std::vector<std::vector<RealOpenMM> > > coeff;
     std::vector<int> torsionMaps;

platforms/reference/src/ReferenceKernels.cpp

@@ -6,7 +6,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2008-2013 Stanford University and the Authors.      *
+ * Portions copyright (c) 2008-2015 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -710,6 +710,40 @@ double ReferenceCalcCMAPTorsionForceKernel::execute(ContextImpl& context, bool i
     return totalEnergy;
 }
 
+void ReferenceCalcCMAPTorsionForceKernel::copyParametersToContext(ContextImpl& context, const CMAPTorsionForce& force) {
+    int numMaps = force.getNumMaps();
+    int numTorsions = force.getNumTorsions();
+    if (coeff.size() != numMaps)
+        throw OpenMMException("updateParametersInContext: The number of maps has changed");
+    if (torsionMaps.size() != numTorsions)
+        throw OpenMMException("updateParametersInContext: The number of CMAP torsions has changed");
+
+    // Update the maps.
+
+    vector<double> energy;
+    vector<vector<double> > c;
+    for (int i = 0; i < numMaps; i++) {
+        int size;
+        force.getMapParameters(i, size, energy);
+        if (coeff[i].size() != size*size)
+            throw OpenMMException("updateParametersInContext: The size of a map has changed");
+        CMAPTorsionForceImpl::calcMapDerivatives(size, energy, c);
+        for (int j = 0; j < size*size; j++)
+            for (int k = 0; k < 16; k++)
+                coeff[i][j][k] = c[j][k];
+    }
+
+    // Update the indices.
+
+    for (int i = 0; i < numTorsions; i++) {
+        int index[8];
+        force.getTorsionParameters(i, torsionMaps[i], index[0], index[1], index[2], index[3], index[4], index[5], index[6], index[7]);
+        for (int j = 0; j < 8; j++)
+            if (index[j] != torsionIndices[i][j])
+                throw OpenMMException("updateParametersInContext: The set of particles in a CMAP torsion has changed");
+    }
+}
+
 ReferenceCalcCustomTorsionForceKernel::~ReferenceCalcCustomTorsionForceKernel() {
     disposeIntArray(torsionIndexArray, numTorsions);
     disposeRealArray(torsionParamArray, numTorsions);

platforms/reference/src/SimTKReference/ObcParameters.cpp

@@ -382,9 +382,9 @@ void ObcParameters::setPeriodic(OpenMM::RealVec* vectors) {
 
     assert(_cutoff);
 
-    assert(boxSize[0][0] >= 2.0*_cutoffDistance);
-    assert(boxSize[1][1] >= 2.0*_cutoffDistance);
-    assert(boxSize[2][2] >= 2.0*_cutoffDistance);
+    assert(vectors[0][0] >= 2.0*_cutoffDistance);
+    assert(vectors[1][1] >= 2.0*_cutoffDistance);
+    assert(vectors[2][2] >= 2.0*_cutoffDistance);
 
     _periodic           = true;
     _periodicBoxVectors[0] = vectors[0];

platforms/reference/src/SimTKReference/ReferenceCCMAAlgorithm.cpp

 
-/* Portions copyright (c) 2006-2013 Stanford University and Simbios.
+/* Portions copyright (c) 2006-2015 Stanford University and Simbios.
  * Contributors: Peter Eastman, Pande Group
  *
  * Permission is hereby granted, free of charge, to any person obtaining
@@ -31,6 +31,7 @@
 #include "quern.h"
 #include "openmm/OpenMMException.h"
 #include "openmm/Vec3.h"
+#include "openmm/internal/ThreadPool.h"
 #include <map>
 
 using std::map;
@@ -39,13 +40,51 @@ using std::vector;
 using std::set;
 using namespace OpenMM;
 
+// This class extracts columns from the inverse matrix one at a time.  It is done in parallel,
+// since this can be very slow.
+
+class ExtractMatrixTask : public ThreadPool::Task {
+public:
+    ExtractMatrixTask(int numConstraints, vector<vector<pair<int, RealOpenMM> > >& matrix, const vector<RealOpenMM>& distance, RealOpenMM elementCutoff,
+                      const int* qRowStart, const int* qColIndex, const int* rRowStart, const int* rColIndex, const double* qValue, const double* rValue) :
+                numConstraints(numConstraints), matrix(matrix), distance(distance), elementCutoff(elementCutoff), qRowStart(qRowStart), qColIndex(qColIndex),
+                rRowStart(rRowStart), rColIndex(rColIndex), qValue(qValue), rValue(rValue) {
+    }
+    
+    void execute(ThreadPool& pool, int threadIndex) {
+        vector<double> rhs(numConstraints);
+        for (int i = threadIndex; i < numConstraints; i += pool.getNumThreads()) {
+            // Extract column i of the inverse matrix.
+
+            for (int j = 0; j < numConstraints; j++)
+                rhs[j] = (i == j ? 1.0 : 0.0);
+            QUERN_multiply_with_q_transpose(numConstraints, qRowStart, qColIndex, qValue, &rhs[0]);
+            QUERN_solve_with_r(numConstraints, rRowStart, rColIndex, rValue, &rhs[0], &rhs[0]);
+            for (int j = 0; j < numConstraints; j++) {
+                double value = rhs[j]*distance[j]/distance[i];
+                if (FABS((RealOpenMM) value) > elementCutoff)
+                    matrix[i].push_back(pair<int, RealOpenMM>(j, (RealOpenMM) value));
+            }
+        }
+    }
+private:
+    int numConstraints;
+    vector<vector<pair<int, RealOpenMM> > >& matrix;
+    const vector<RealOpenMM>& distance;
+    RealOpenMM elementCutoff;
+    const int *qRowStart, *qColIndex, *rRowStart, *rColIndex;
+    const double *qValue, *rValue;
+};
+
 ReferenceCCMAAlgorithm::ReferenceCCMAAlgorithm(int numberOfAtoms,
-                                                  int numberOfConstraints,
-                                                  const vector<pair<int, int> >& atomIndices,
-                                                  const vector<RealOpenMM>& distance,
-                                                  vector<RealOpenMM>& masses,
-                                                  vector<AngleInfo>& angles) {
+                                               int numberOfConstraints,
+                                               const vector<pair<int, int> >& atomIndices,
+                                               const vector<RealOpenMM>& distance,
+                                               vector<RealOpenMM>& masses,
+                                               vector<AngleInfo>& angles,
+                                               RealOpenMM elementCutoff) {
     _numberOfConstraints = numberOfConstraints;
+    _elementCutoff = elementCutoff;
     _atomIndices = atomIndices;
     _distance = distance;
 
@@ -157,19 +196,10 @@ ReferenceCCMAAlgorithm::ReferenceCCMAAlgorithm(int numberOfAtoms,
                 &qRowStart, &qColIndex, &qValue, &rRowStart, &rColIndex, &rValue);
         vector<double> rhs(numberOfConstraints);
         _matrix.resize(numberOfConstraints);
-        for (int i = 0; i < numberOfConstraints; i++) {
-            // Extract column i of the inverse matrix.
-
-            for (int j = 0; j < numberOfConstraints; j++)
-                rhs[j] = (i == j ? 1.0 : 0.0);
-            QUERN_multiply_with_q_transpose(numberOfConstraints, qRowStart, qColIndex, qValue, &rhs[0]);
-            QUERN_solve_with_r(numberOfConstraints, rRowStart, rColIndex, rValue, &rhs[0], &rhs[0]);
-            for (int j = 0; j < numberOfConstraints; j++) {
-                double value = rhs[j]*_distance[i]/_distance[j];
-                if (FABS((RealOpenMM)value) > 0.02)
-                    _matrix[j].push_back(pair<int, RealOpenMM>(i, (RealOpenMM) value));
-            }
-        }
+        ThreadPool threads;
+        ExtractMatrixTask task(numberOfConstraints, _matrix, _distance, _elementCutoff, qRowStart, qColIndex, rRowStart, rColIndex, qValue, rValue);
+        threads.execute(task);
+        threads.waitForThreads();
         QUERN_free_result(qRowStart, qColIndex, qValue);
         QUERN_free_result(rRowStart, rColIndex, rValue);
     }
@@ -290,3 +320,7 @@ void ReferenceCCMAAlgorithm::applyConstraints(vector<RealVec>& atomCoordinates,
         }
     }
 }
+
+const vector<vector<pair<int, RealOpenMM> > >& ReferenceCCMAAlgorithm::getMatrix() const {
+    return _matrix;
+}

platforms/reference/src/SimTKReference/ReferenceConstraints.cpp

@@ -180,7 +180,7 @@ ReferenceConstraints::ReferenceConstraints(const System& system) : ccma(NULL), s
         
         // Create the CCMA object.
         
-        ccma = new ReferenceCCMAAlgorithm(numParticles, numCCMA, ccmaIndices, ccmaDistance, masses, angles);
+        ccma = new ReferenceCCMAAlgorithm(numParticles, numCCMA, ccmaIndices, ccmaDistance, masses, angles, 0.02);
     }
 }
 

platforms/reference/tests/TestReferenceAndersenThermostat.cpp

@@ -48,12 +48,13 @@
 using namespace OpenMM;
 using namespace std;
 
+ReferencePlatform platform;
+
 void testTemperature() {
     const int numParticles = 8;
     const double temp = 100.0;
     const double collisionFreq = 10.0;
     const int numSteps = 5000;
-    ReferencePlatform platform;
     System system;
     VerletIntegrator integrator(0.003);
     NonbondedForce* forceField = new NonbondedForce();
@@ -94,7 +95,6 @@ void testConstraints() {
     const double temp = 100.0;
     const double collisionFreq = 10.0;
     const int numSteps = 15000;
-    ReferencePlatform platform;
     System system;
     VerletIntegrator integrator(0.004);
     NonbondedForce* forceField = new NonbondedForce();
@@ -147,7 +147,6 @@ void testRandomSeed() {
     const int numParticles = 8;
     const double temp = 100.0;
     const double collisionFreq = 10.0;
-    ReferencePlatform platform;
     System system;
     VerletIntegrator integrator(0.01);
     NonbondedForce* forceField = new NonbondedForce();

platforms/reference/tests/TestReferenceBrownianIntegrator.cpp

@@ -48,10 +48,11 @@
 using namespace OpenMM;
 using namespace std;
 
+ReferencePlatform platform;
+
 const double TOL = 1e-5;
 
 void testSingleBond() {
-    ReferencePlatform platform;
     System system;
     system.addParticle(2.0);
     system.addParticle(2.0);
@@ -88,7 +89,6 @@ void testTemperature() {
     const int numParticles = 8;
     const int numBonds = numParticles-1;
     const double temp = 10.0;
-    ReferencePlatform platform;
     System system;
     BrownianIntegrator integrator(temp, 2.0, 0.01);
     HarmonicBondForce* forceField = new HarmonicBondForce();
@@ -125,7 +125,6 @@ void testTemperature() {
 void testConstraints() {
     const int numParticles = 8;
     const double temp = 100.0;
-    ReferencePlatform platform;
     System system;
     BrownianIntegrator integrator(temp, 2.0, 0.001);
     integrator.setConstraintTolerance(1e-5);
@@ -165,7 +164,6 @@ void testConstraints() {
 }
 
 void testConstrainedMasslessParticles() {
-    ReferencePlatform platform;
     System system;
     system.addParticle(0.0);
     system.addParticle(1.0);
@@ -200,7 +198,6 @@ void testRandomSeed() {
     const int numParticles = 8;
     const double temp = 100.0;
     const double collisionFreq = 10.0;
-    ReferencePlatform platform;
     System system;
     BrownianIntegrator integrator(temp, 2.0, 0.001);
     NonbondedForce* forceField = new NonbondedForce();

platforms/reference/tests/TestReferenceCMAPTorsionForce.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) 2010 Stanford University and the Authors.           *
+ * Portions copyright (c) 2010-2015 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -48,6 +48,8 @@
 using namespace OpenMM;
 using namespace std;
 
+ReferencePlatform platform;
+
 const double TOL = 1e-5;
 
 void testCMAPTorsions() {
@@ -56,7 +58,6 @@ void testCMAPTorsions() {
     // Create two systems: one with a pair of periodic torsions, and one with a CMAP torsion
     // that approximates the same force.
 
-    ReferencePlatform platform;
     System system1;
     for (int i = 0; i < 5; i++)
         system1.addParticle(1.0);
@@ -108,9 +109,66 @@ void testCMAPTorsions() {
     }
 }
 
+void testChangingParameters() {
+    // Create a system with two maps and one torsion.
+
+    const int mapSize = 8;
+    System system;
+    for (int i = 0; i < 5; i++)
+        system.addParticle(1.0);
+    CMAPTorsionForce* cmap = new CMAPTorsionForce();
+    vector<double> mapEnergy1(mapSize*mapSize);
+    vector<double> mapEnergy2(mapSize*mapSize);
+    for (int i = 0; i < mapSize; i++) {
+        double angle1 = i*2*M_PI/mapSize;
+        double energy1 = cos(angle1);
+        for (int j = 0; j < mapSize; j++) {
+            double angle2 = j*2*M_PI/mapSize;
+            double energy2 = 10*sin(angle2);
+            mapEnergy1[i+j*mapSize] = energy1+energy2;
+            mapEnergy2[i+j*mapSize] = energy1-energy2;
+        }
+    }
+    cmap->addMap(mapSize, mapEnergy1);
+    cmap->addMap(mapSize, mapEnergy2);
+    cmap->addTorsion(0, 0, 1, 2, 3, 1, 2, 3, 4);
+    system.addForce(cmap);
+
+    // Set particle positions so angle1=0 and angle2=PI/4.
+
+    vector<Vec3> positions(5);
+    positions[0] = Vec3(0, 0, 1);
+    positions[1] = Vec3(0, 0, 0);
+    positions[2] = Vec3(1, 0, 0);
+    positions[3] = Vec3(1, 0, 1);
+    positions[4] = Vec3(0.5, -0.5, 1);
+    VerletIntegrator integrator(0.01);
+    Context context(system, integrator, platform);
+    context.setPositions(positions);
+
+    // Check that the energy is correct.
+
+    double energy = context.getState(State::Energy).getPotentialEnergy();
+    ASSERT_EQUAL_TOL(1+10*sin(M_PI/4), energy, 1e-5);
+
+    // Modify the parameters.
+
+    cmap->setTorsionParameters(0, 1, 0, 1, 2, 3, 1, 2, 3, 4);
+    for (int i = 0; i < mapSize*mapSize; i++)
+        mapEnergy2[i] *= 2.0;
+    cmap->setMapParameters(1, mapSize, mapEnergy2);
+    cmap->updateParametersInContext(context);
+
+    // See if the results are correct.
+
+    energy = context.getState(State::Energy).getPotentialEnergy();
+    ASSERT_EQUAL_TOL(2-20*sin(M_PI/4), energy, 1e-5);
+}
+
 int main() {
     try {
         testCMAPTorsions();
+        testChangingParameters();
     }
     catch(const exception& e) {
         cout << "exception: " << e.what() << endl;

platforms/reference/tests/TestReferenceCMMotionRemover.cpp

@@ -49,6 +49,8 @@
 using namespace OpenMM;
 using namespace std;
 
+ReferencePlatform platform;
+
 Vec3 calcCM(const vector<Vec3>& values, System& system) {
     Vec3 cm;
     for (int j = 0; j < system.getNumParticles(); ++j) {
@@ -63,7 +65,6 @@ void testMotionRemoval() {
     const int numParticles = 8;
     const double temp = 100.0;
     const double collisionFreq = 10.0;
-    ReferencePlatform platform;
     System system;
     VerletIntegrator integrator(0.01);
     HarmonicBondForce* bonds = new HarmonicBondForce();

platforms/reference/tests/TestReferenceCheckpoints.cpp

@@ -48,6 +48,8 @@
 using namespace OpenMM;
 using namespace std;
 
+ReferencePlatform platform;
+
 const double TOL = 1e-5;
 
 void compareStates(State& s1, State& s2) {
@@ -71,7 +73,6 @@ void testCheckpoint() {
     const int numParticles = 10;
     const double boxSize = 3.0;
     const double temperature = 200.0;
-    ReferencePlatform platform;
     System system;
     system.addForce(new AndersenThermostat(0.0, 100.0));
     NonbondedForce* nonbonded = new NonbondedForce();
@@ -125,7 +126,6 @@ void testSetState() {
     const int numParticles = 10;
     const double boxSize = 3.0;
     const double temperature = 200.0;
-    ReferencePlatform platform;
     System system;
     system.addForce(new AndersenThermostat(0.0, 100.0));
     NonbondedForce* nonbonded = new NonbondedForce();

platforms/reference/tests/TestReferenceCustomAngleForce.cpp

@@ -47,11 +47,11 @@
 using namespace OpenMM;
 using namespace std;
 
+ReferencePlatform platform;
+
 const double TOL = 1e-5;
 
 void testAngles() {
-    ReferencePlatform platform;
-
     // Create a system using a CustomAngleForce.
 
     System customSystem;

platforms/reference/tests/TestReferenceCustomBondForce.cpp

@@ -46,10 +46,11 @@
 using namespace OpenMM;
 using namespace std;
 
+ReferencePlatform platform;
+
 const double TOL = 1e-5;
 
 void testBonds() {
-    ReferencePlatform platform;
     System system;
     system.addParticle(1.0);
     system.addParticle(1.0);

platforms/reference/tests/TestReferenceCustomCompoundBondForce.cpp

@@ -52,11 +52,11 @@
 using namespace OpenMM;
 using namespace std;
 
+ReferencePlatform platform;
+
 const double TOL = 1e-5;
 
 void testBond() {
-    ReferencePlatform platform;
-
     // Create a system using a CustomCompoundBondForce.
 
     System customSystem;
@@ -147,7 +147,6 @@ void testBond() {
 }
 
 void testPositionDependence() {
-    ReferencePlatform platform;
     System customSystem;
     customSystem.addParticle(1.0);
     customSystem.addParticle(1.0);
@@ -179,7 +178,6 @@ void testContinuous2DFunction() {
     const double xmax = 1.1;
     const double ymin = 0.0;
     const double ymax = 0.9;
-    ReferencePlatform platform;
     System system;
     system.addParticle(1.0);
     VerletIntegrator integrator(0.01);
@@ -227,7 +225,6 @@ void testContinuous3DFunction() {
     const double ymax = 0.9;
     const double zmin = 0.2;
     const double zmax = 1.3;
-    ReferencePlatform platform;
     System system;
     system.addParticle(1.0);
     VerletIntegrator integrator(0.01);
@@ -273,7 +270,6 @@ void testContinuous3DFunction() {
 
 void testMultipleBonds() {
     // Two compound bonds using Urey-Bradley example from API doc
-    ReferencePlatform platform;
     System customSystem;
     customSystem.addParticle(1.0);
     customSystem.addParticle(1.0);

platforms/reference/tests/TestReferenceCustomExternalForce.cpp

@@ -46,10 +46,11 @@
 using namespace OpenMM;
 using namespace std;
 
+ReferencePlatform platform;
+
 const double TOL = 1e-5;
 
 void testForce() {
-    ReferencePlatform platform;
     System system;
     system.addParticle(1.0);
     system.addParticle(1.0);

platforms/reference/tests/TestReferenceCustomGBForce.cpp

@@ -51,6 +51,8 @@
 using namespace OpenMM;
 using namespace std;
 
+ReferencePlatform platform;
+
 const double TOL = 1e-5;
 
 void testOBC(GBSAOBCForce::NonbondedMethod obcMethod, CustomGBForce::NonbondedMethod customMethod) {
@@ -58,7 +60,6 @@ void testOBC(GBSAOBCForce::NonbondedMethod obcMethod, CustomGBForce::NonbondedMe
     const int numParticles = numMolecules*2;
     const double boxSize = 10.0;
     const double cutoff = 2.0;
-    ReferencePlatform platform;
 
     // Create two systems: one with a GBSAOBCForce, and one using a CustomGBForce to implement the same interaction.
 
@@ -190,7 +191,6 @@ void testMembrane() {
     const int numMolecules = 70;
     const int numParticles = numMolecules*2;
     const double boxSize = 10.0;
-    ReferencePlatform platform;
 
     // Create a system with an implicit membrane.
 
@@ -280,7 +280,6 @@ void testMembrane() {
 }
 
 void testTabulatedFunction() {
-    ReferencePlatform platform;
     System system;
     system.addParticle(1.0);
     system.addParticle(1.0);
@@ -313,7 +312,6 @@ void testTabulatedFunction() {
 }
 
 void testMultipleChainRules() {
-    ReferencePlatform platform;
     System system;
     system.addParticle(1.0);
     system.addParticle(1.0);
@@ -341,7 +339,6 @@ void testMultipleChainRules() {
 }
 
 void testPositionDependence() {
-    ReferencePlatform platform;
     System system;
     system.addParticle(1.0);
     system.addParticle(1.0);
@@ -405,7 +402,6 @@ void testPositionDependence() {
 }
 
 void testExclusions() {
-    ReferencePlatform platform;
     for (int i = 3; i < 4; i++) {
         System system;
         system.addParticle(1.0);
@@ -817,7 +813,6 @@ void testGBVI(GBVIForce::NonbondedMethod gbviMethod, CustomGBForce::NonbondedMet
 
     const int numMolecules = 1;
     const double boxSize   = 10.0;
-    ReferencePlatform platform;
 
     GBVIForce*        gbvi = new GBVIForce();
     std::vector<Vec3> positions;

platforms/reference/tests/TestReferenceCustomHbondForce.cpp

@@ -49,11 +49,11 @@
 using namespace OpenMM;
 using namespace std;
 
+ReferencePlatform platform;
+
 const double TOL = 1e-5;
 
 void testHbond() {
-    ReferencePlatform platform;
-
     // Create a system using a CustomHbondForce.
 
     System customSystem;
@@ -151,7 +151,6 @@ void testHbond() {
 }
 
 void testExclusions() {
-    ReferencePlatform platform;
     System system;
     system.addParticle(1.0);
     system.addParticle(1.0);
@@ -178,7 +177,6 @@ void testExclusions() {
 }
 
 void testCutoff() {
-    ReferencePlatform platform;
     System system;
     system.addParticle(1.0);
     system.addParticle(1.0);
@@ -206,7 +204,6 @@ void testCutoff() {
 }
 
 void testCustomFunctions() {
-    ReferencePlatform platform;
     System system;
     system.addParticle(1.0);
     system.addParticle(1.0);

platforms/reference/tests/TestReferenceCustomIntegrator.cpp

@@ -49,13 +49,14 @@
 using namespace OpenMM;
 using namespace std;
 
+ReferencePlatform platform;
+
 const double TOL = 1e-5;
 
 /**
  * Test a simple leapfrog integrator on a single bond.
  */
 void testSingleBond() {
-    ReferencePlatform platform;
     System system;
     system.addParticle(2.0);
     system.addParticle(2.0);
@@ -101,7 +102,6 @@ void testSingleBond() {
 void testConstraints() {
     const int numParticles = 8;
     const double temp = 500.0;
-    ReferencePlatform platform;
     System system;
     CustomIntegrator integrator(0.002);
     integrator.addPerDofVariable("oldx", 0);
@@ -160,7 +160,6 @@ void testConstraints() {
  */
 void testVelocityConstraints() {
     const int numParticles = 10;
-    ReferencePlatform platform;
     System system;
     CustomIntegrator integrator(0.002);
     integrator.addPerDofVariable("x1", 0);
@@ -236,7 +235,6 @@ void testVelocityConstraints() {
 }
 
 void testConstrainedMasslessParticles() {
-    ReferencePlatform platform;
     System system;
     system.addParticle(0.0);
     system.addParticle(1.0);
@@ -282,7 +280,6 @@ void testWithThermostat() {
     const double temp = 100.0;
     const double collisionFreq = 10.0;
     const int numSteps = 5000;
-    ReferencePlatform platform;
     System system;
     CustomIntegrator integrator(0.003);
     integrator.addUpdateContextState();
@@ -324,7 +321,6 @@ void testWithThermostat() {
  * Test a Monte Carlo integrator that uses global variables and depends on energy.
  */
 void testMonteCarlo() {
-    ReferencePlatform platform;
     System system;
     system.addParticle(1.0);
     system.addParticle(1.0);
@@ -379,7 +375,6 @@ void testMonteCarlo() {
 void testSum() {
     const int numParticles = 200;
     const double boxSize = 10;
-    ReferencePlatform platform;
     System system;
     system.setDefaultPeriodicBoxVectors(Vec3(boxSize, 0, 0), Vec3(0, boxSize, 0), Vec3(0, 0, boxSize));
     NonbondedForce* nb = new NonbondedForce();
@@ -422,7 +417,6 @@ void testSum() {
  * Test an integrator that both uses and modifies a context parameter.
  */
 void testParameter() {
-    ReferencePlatform platform;
     System system;
     system.addParticle(1.0);
     AndersenThermostat* thermostat = new AndersenThermostat(0.1, 0.1);
@@ -448,7 +442,6 @@ void testRandomDistributions() {
     const int numParticles = 100;
     const int numBins = 20;
     const int numSteps = 100;
-    ReferencePlatform platform;
     System system;
     for (int i = 0; i < numParticles; i++)
         system.addParticle(1.0);
@@ -516,7 +509,6 @@ void testRandomDistributions() {
 void testPerDofVariables() {
     const int numParticles = 200;
     const double boxSize = 10;
-    ReferencePlatform platform;
     System system;
     system.setDefaultPeriodicBoxVectors(Vec3(boxSize, 0, 0), Vec3(0, boxSize, 0), Vec3(0, 0, boxSize));
     NonbondedForce* nb = new NonbondedForce();
@@ -571,7 +563,6 @@ void testPerDofVariables() {
  * Test evaluating force groups separately.
  */
 void testForceGroups() {
-    ReferencePlatform platform;
     System system;
     system.addParticle(2.0);
     system.addParticle(2.0);
@@ -647,7 +638,6 @@ void testForceGroups() {
  */
 void testRespa() {
     const int numParticles = 8;
-    ReferencePlatform platform;
     System system;
     system.setDefaultPeriodicBoxVectors(Vec3(4, 0, 0), Vec3(0, 4, 0), Vec3(0, 0, 4));
     CustomIntegrator integrator(0.002);