Merge pull request #959 from kyleabeauchamp/intsegfault

Add check for null context inside integrator.step()

openmmapi/src/BrownianIntegrator.cpp

@@ -72,6 +72,8 @@ double BrownianIntegrator::computeKineticEnergy() {
 }
 
 void BrownianIntegrator::step(int steps) {
+    if (context == NULL)
+        throw OpenMMException("This Integrator is not bound to a context!");  
     for (int i = 0; i < steps; ++i) {
         context->updateContextState();
         context->calcForcesAndEnergy(true, false);

openmmapi/src/CustomIntegrator.cpp

@@ -94,6 +94,8 @@ double CustomIntegrator::computeKineticEnergy() {
 }
 
 void CustomIntegrator::step(int steps) {
+    if (context == NULL)
+        throw OpenMMException("This Integrator is not bound to a context!");  
     globalsAreCurrent = false;
     for (int i = 0; i < steps; ++i) {
         kernel.getAs<IntegrateCustomStepKernel>().execute(*context, *this, forcesAreValid);

openmmapi/src/LangevinIntegrator.cpp

@@ -72,6 +72,8 @@ double LangevinIntegrator::computeKineticEnergy() {
 }
 
 void LangevinIntegrator::step(int steps) {
+    if (context == NULL)
+        throw OpenMMException("This Integrator is not bound to a context!");  
     for (int i = 0; i < steps; ++i) {
         context->updateContextState();
         context->calcForcesAndEnergy(true, false);

openmmapi/src/VariableLangevinIntegrator.cpp

@@ -75,6 +75,8 @@ double VariableLangevinIntegrator::computeKineticEnergy() {
 }
 
 void VariableLangevinIntegrator::step(int steps) {
+    if (context == NULL)
+        throw OpenMMException("This Integrator is not bound to a context!");  
     for (int i = 0; i < steps; ++i) {
         context->updateContextState();
         context->calcForcesAndEnergy(true, false);
@@ -83,6 +85,8 @@ void VariableLangevinIntegrator::step(int steps) {
 }
 
 void VariableLangevinIntegrator::stepTo(double time) {
+    if (context == NULL)
+        throw OpenMMException("This Integrator is not bound to a context!");
     while (time > context->getTime()) {
         context->updateContextState();
         context->calcForcesAndEnergy(true, false);

openmmapi/src/VariableVerletIntegrator.cpp

@@ -70,6 +70,8 @@ double VariableVerletIntegrator::computeKineticEnergy() {
 }
 
 void VariableVerletIntegrator::step(int steps) {
+    if (context == NULL)
+        throw OpenMMException("This Integrator is not bound to a context!");
     for (int i = 0; i < steps; ++i) {
         context->updateContextState();
         context->calcForcesAndEnergy(true, false);
@@ -78,6 +80,8 @@ void VariableVerletIntegrator::step(int steps) {
 }
 
 void VariableVerletIntegrator::stepTo(double time) {
+    if (context == NULL)
+        throw OpenMMException("This Integrator is not bound to a context!");  
     while (time > context->getTime()) {
         context->updateContextState();
         context->calcForcesAndEnergy(true, false);

openmmapi/src/VerletIntegrator.cpp

@@ -69,6 +69,8 @@ double VerletIntegrator::computeKineticEnergy() {
 }
 
 void VerletIntegrator::step(int steps) {
+    if (context == NULL)
+        throw OpenMMException("This Integrator is not bound to a context!");
     for (int i = 0; i < steps; ++i) {
         context->updateContextState();
         context->calcForcesAndEnergy(true, false);

plugins/drude/openmmapi/src/DrudeLangevinIntegrator.cpp

@@ -89,6 +89,8 @@ double DrudeLangevinIntegrator::computeKineticEnergy() {
 }
 
 void DrudeLangevinIntegrator::step(int steps) {
+    if (context == NULL)
+        throw OpenMMException("This Integrator is not bound to a context!");    
     for (int i = 0; i < steps; ++i) {
         context->updateContextState();
         context->calcForcesAndEnergy(true, false);

plugins/drude/openmmapi/src/DrudeSCFIntegrator.cpp

@@ -86,6 +86,8 @@ double DrudeSCFIntegrator::computeKineticEnergy() {
 }
 
 void DrudeSCFIntegrator::step(int steps) {
+    if (context == NULL)
+        throw OpenMMException("This Integrator is not bound to a context!");    
     for (int i = 0; i < steps; ++i) {
         context->updateContextState();
         context->calcForcesAndEnergy(true, false);

plugins/rpmd/openmmapi/src/RPMDIntegrator.cpp

@@ -100,7 +100,7 @@ State RPMDIntegrator::getState(int copy, int types, bool enforcePeriodicBox, int
         // Call setPositions() on the Context so it doesn't think the user is trying to
         // run a simulation without setting positions first.  These positions will
         // immediately get overwritten by the ones stored in this integrator.
-        
+
         vector<Vec3> p(context->getSystem().getNumParticles(), Vec3());
         context->getOwner().setPositions(p);
         isFirstStep = false;
@@ -110,7 +110,7 @@ State RPMDIntegrator::getState(int copy, int types, bool enforcePeriodicBox, int
     if (enforcePeriodicBox && copy > 0 && (types&State::Positions) != 0) {
         // Apply periodic boundary conditions based on copy 0.  Otherwise, molecules might end
         // up in different places for different copies.
-        
+
         kernel.getAs<IntegrateRPMDStepKernel>().copyToContext(0, *context);
         State state2 = context->getOwner().getState(State::Positions, false, groups);
         vector<Vec3> positions = state.getPositions();
@@ -144,9 +144,9 @@ State RPMDIntegrator::getState(int copy, int types, bool enforcePeriodicBox, int
                 pos[2] -= dz;
             }
         }
-        
+
         // Construct the new State.
-        
+
         State::StateBuilder builder(state.getTime());
         builder.setPositions(positions);
         builder.setPeriodicBoxVectors(periodicBoxSize[0], periodicBoxSize[1], periodicBoxSize[2]);
@@ -168,16 +168,18 @@ double RPMDIntegrator::computeKineticEnergy() {
 }
 
 void RPMDIntegrator::step(int steps) {
+    if (context == NULL)
+        throw OpenMMException("This Integrator is not bound to a context!");    
     if (!hasSetPosition) {
         // Initialize the positions from the context.
-        
+
         State s = context->getOwner().getState(State::Positions);
         for (int i = 0; i < numCopies; i++)
             setPositions(i, s.getPositions());
     }
     if (!hasSetVelocity) {
         // Initialize the velocities from the context.
-        
+
         State s = context->getOwner().getState(State::Velocities);
         for (int i = 0; i < numCopies; i++)
             setVelocities(i, s.getVelocities());
@@ -186,7 +188,7 @@ void RPMDIntegrator::step(int steps) {
         // Call setPositions() on the Context so it doesn't think the user is trying to
         // run a simulation without setting positions first.  These positions will
         // immediately get overwritten by the ones stored in this integrator.
-        
+
         vector<Vec3> p(context->getSystem().getNumParticles(), Vec3());
         context->getOwner().setPositions(p);
         isFirstStep = false;
@@ -212,12 +214,12 @@ double RPMDIntegrator::getTotalEnergy() {
     State prevState = getState(numCopies-1, State::Positions);
     for (int i = 0; i < numCopies; i++) {
         // Add the energy of this copy.
-        
+
         State state = getState(i, State::Positions | State::Energy);
         energy += state.getKineticEnergy()+state.getPotentialEnergy();
-        
+
         // Add the energy from the springs connecting it to the previous copy.
-        
+
         for (int j = 0; j < numParticles; j++) {
             Vec3 delta = state.getPositions()[j]-prevState.getPositions()[j];
             energy += 0.5*wn*wn*system.getParticleMass(j)*delta.dot(delta);