Merge pull request #63 from peastman/master

Fixed a bug in CustomIntegrator related to atom reordering

platforms/cuda/src/CudaKernels.cpp

@@ -5222,6 +5222,10 @@ void CudaIntegrateCustomStepKernel::execute(ContextImpl& context, CustomIntegrat
     cu.setTime(cu.getTime()+integrator.getStepSize());
     cu.setStepCount(cu.getStepCount()+1);
     cu.reorderAtoms();
+    if (cu.getAtomsWereReordered()) {
+        forcesAreValid = false;
+        validSavedForces.clear();
+    }
 }
 
 double CudaIntegrateCustomStepKernel::computeKineticEnergy(ContextImpl& context, CustomIntegrator& integrator, bool& forcesAreValid) {

platforms/opencl/src/OpenCLKernels.cpp

@@ -5444,6 +5444,10 @@ void OpenCLIntegrateCustomStepKernel::execute(ContextImpl& context, CustomIntegr
     cl.setTime(cl.getTime()+integrator.getStepSize());
     cl.setStepCount(cl.getStepCount()+1);
     cl.reorderAtoms();
+    if (cl.getAtomsWereReordered()) {
+        forcesAreValid = false;
+        validSavedForces.clear();
+    }
     
     // Reduce UI lag.