Merge pull request #155 from peastman/master

Ignore constraints that connect two massless particles (feature request 1915)

platforms/reference/tests/TestReferenceVariableVerletIntegrator.cpp

@@ -210,6 +210,38 @@ void testConstrainedClusters() {
     ASSERT(context.getState(State::Positions).getTime() > 0.1);
 }
 
+void testConstrainedMasslessParticles() {
+    ReferencePlatform platform;
+    System system;
+    system.addParticle(0.0);
+    system.addParticle(1.0);
+    system.addConstraint(0, 1, 1.5);
+    vector<Vec3> positions(2);
+    positions[0] = Vec3(-1, 0, 0);
+    positions[1] = Vec3(1, 0, 0);
+    VariableVerletIntegrator integrator(0.01);
+    bool failed = false;
+    try {
+        // This should throw an exception.
+        
+        Context context(system, integrator, platform);
+    }
+    catch (exception& ex) {
+        failed = true;
+    }
+    ASSERT(failed);
+    
+    // Now make both particles massless, which should work.
+    
+    system.setParticleMass(1, 0.0);
+    Context context(system, integrator, platform);
+    context.setPositions(positions);
+    context.setVelocitiesToTemperature(300.0);
+    integrator.step(1);
+    State state = context.getState(State::Velocities | State::Positions);
+    ASSERT_EQUAL(0.0, state.getVelocities()[0][0]);
+}
+
 void testArgonBox() {
     const int gridSize = 8;
     const double mass = 40.0;            // Ar atomic mass
@@ -272,6 +304,7 @@ int main() {
         testSingleBond();
         testConstraints();
         testConstrainedClusters();
+        testConstrainedMasslessParticles();
         testArgonBox();
     }
     catch(const exception& e) {

platforms/reference/tests/TestReferenceVerletIntegrator.cpp

@@ -200,11 +200,44 @@ void testConstrainedClusters() {
     }
 }
 
+void testConstrainedMasslessParticles() {
+    ReferencePlatform platform;
+    System system;
+    system.addParticle(0.0);
+    system.addParticle(1.0);
+    system.addConstraint(0, 1, 1.5);
+    vector<Vec3> positions(2);
+    positions[0] = Vec3(-1, 0, 0);
+    positions[1] = Vec3(1, 0, 0);
+    VerletIntegrator integrator(0.01);
+    bool failed = false;
+    try {
+        // This should throw an exception.
+        
+        Context context(system, integrator, platform);
+    }
+    catch (exception& ex) {
+        failed = true;
+    }
+    ASSERT(failed);
+    
+    // Now make both particles massless, which should work.
+    
+    system.setParticleMass(1, 0.0);
+    Context context(system, integrator, platform);
+    context.setPositions(positions);
+    context.setVelocitiesToTemperature(300.0);
+    integrator.step(1);
+    State state = context.getState(State::Velocities | State::Positions);
+    ASSERT_EQUAL(0.0, state.getVelocities()[0][0]);
+}
+
 int main() {
     try {
         testSingleBond();
         testConstraints();
         testConstrainedClusters();
+        testConstrainedMasslessParticles();
     }
     catch(const exception& e) {
         cout << "exception: " << e.what() << endl;

plugins/drude/platforms/reference/src/ReferenceDrudeKernels.cpp

@@ -271,18 +271,19 @@ void ReferenceIntegrateDrudeLangevinStepKernel::initialize(const System& system,
     
     // Prepare constraints.
     
-    int numConstraints = system.getNumConstraints();
-    if (numConstraints > 0) {
-        vector<pair<int, int> > constraintIndices(numConstraints);
-        vector<RealOpenMM> constraintDistances(numConstraints);
-        for (int i = 0; i < numConstraints; ++i) {
+    if (system.getNumConstraints() > 0) {
+        vector<pair<int, int> > constraintIndices;
+        vector<RealOpenMM> constraintDistances;
+        for (int i = 0; i < system.getNumConstraints(); ++i) {
             int particle1, particle2;
             double distance;
             system.getConstraintParameters(i, particle1, particle2, distance);
-            constraintIndices[i].first = particle1;
-            constraintIndices[i].second = particle2;
-            constraintDistances[i] = static_cast<RealOpenMM>(distance);
+            if (system.getParticleMass(particle1) != 0 || system.getParticleMass(particle2) != 0) {
+                constraintIndices.push_back(make_pair(particle1, particle2));
+                constraintDistances.push_back(distance);
             }
+        }
+        int numConstraints = constraintIndices.size();
         vector<ReferenceCCMAAlgorithm::AngleInfo> angles;
         findAnglesForCCMA(system, angles);
         constraints = new ReferenceCCMAAlgorithm(system.getNumParticles(), numConstraints, constraintIndices, constraintDistances, particleMass, angles, (RealOpenMM)integrator.getConstraintTolerance());
@@ -395,18 +396,19 @@ void ReferenceIntegrateDrudeSCFStepKernel::initialize(const System& system, cons
     
     // Prepare constraints.
     
-    int numConstraints = system.getNumConstraints();
-    if (numConstraints > 0) {
-        vector<pair<int, int> > constraintIndices(numConstraints);
-        vector<RealOpenMM> constraintDistances(numConstraints);
-        for (int i = 0; i < numConstraints; ++i) {
+    if (system.getNumConstraints() > 0) {
+        vector<pair<int, int> > constraintIndices;
+        vector<RealOpenMM> constraintDistances;
+        for (int i = 0; i < system.getNumConstraints(); ++i) {
             int particle1, particle2;
             double distance;
             system.getConstraintParameters(i, particle1, particle2, distance);
-            constraintIndices[i].first = particle1;
-            constraintIndices[i].second = particle2;
-            constraintDistances[i] = static_cast<RealOpenMM>(distance);
+            if (system.getParticleMass(particle1) != 0 || system.getParticleMass(particle2) != 0) {
+                constraintIndices.push_back(make_pair(particle1, particle2));
+                constraintDistances.push_back(distance);
+            }
         }
+        int numConstraints = constraintIndices.size();
         vector<ReferenceCCMAAlgorithm::AngleInfo> angles;
         findAnglesForCCMA(system, angles);
         constraints = new ReferenceCCMAAlgorithm(system.getNumParticles(), numConstraints, constraintIndices, constraintDistances, particleMass, angles, (RealOpenMM)integrator.getConstraintTolerance());