Fixed various bugs that caused energy to come out wrong after per-particle parameters were changed

platforms/opencl/src/OpenCLContext.cpp

@@ -796,9 +796,11 @@ void OpenCLContext::validateMolecules() {
     velm->upload();
     atomIndex->upload();
     findMoleculeGroups();
+    for (int i = 0; i < (int) reorderListeners.size(); i++)
+        reorderListeners[i]->execute();
 }
 
-void OpenCLContext::reorderAtoms() {
+void OpenCLContext::reorderAtoms(bool enforcePeriodic) {
     if (numAtoms == 0 || nonbonded == NULL || !nonbonded->getUseCutoff())
         return;
     if (moleculesInvalid)
@@ -873,16 +875,18 @@ void OpenCLContext::reorderAtoms() {
                     molPos[i].x -= dx;
                     molPos[i].y -= dy;
                     molPos[i].z -= dz;
-                    for (int j = 0; j < (int) atoms.size(); j++) {
-                        int atom = atoms[j]+mol.offsets[i];
-                        mm_float4 p = posq->get(atom);
-                        p.x -= dx;
-                        p.y -= dy;
-                        p.z -= dz;
-                        posq->set(atom, p);
-                        posCellOffsets[atom].x -= xcell;
-                        posCellOffsets[atom].y -= ycell;
-                        posCellOffsets[atom].z -= zcell;
+                    if (enforcePeriodic) {
+                        for (int j = 0; j < (int) atoms.size(); j++) {
+                            int atom = atoms[j]+mol.offsets[i];
+                            mm_float4 p = posq->get(atom);
+                            p.x -= dx;
+                            p.y -= dy;
+                            p.z -= dz;
+                            posq->set(atom, p);
+                            posCellOffsets[atom].x -= xcell;
+                            posCellOffsets[atom].y -= ycell;
+                            posCellOffsets[atom].z -= zcell;
+                        }
                     }
                 }
             }

platforms/opencl/src/OpenCLContext.h

@@ -466,8 +466,10 @@ public:
     /**
      * Reorder the internal arrays of atoms to try to keep spatially contiguous atoms close
      * together in the arrays.
+     * 
+     * @param enforcePeriodic    if true, the atom positions may be altered to enforce periodic boundary conditions
      */
-    void reorderAtoms();
+    void reorderAtoms(bool enforcePeriodic);
     /**
      * Add a listener that should be called whenever atoms get reordered.  The OpenCLContext
      * assumes ownership of the object, and deletes it when the context itself is deleted.

platforms/opencl/src/OpenCLKernels.cpp

@@ -98,8 +98,8 @@ void OpenCLCalcForcesAndEnergyKernel::beginComputation(ContextImpl& context, boo
     OpenCLNonbondedUtilities& nb = cl.getNonbondedUtilities();
     bool includeNonbonded = ((groups&(1<<nb.getForceGroup())) != 0);
     cl.setAtomsWereReordered(false);
-    if (nb.getUseCutoff() && includeNonbonded && (cl.getComputeForceCount()%100 == 0 || cl.getMoleculesAreInvalid())) {
-        cl.reorderAtoms();
+    if (cl.getMoleculesAreInvalid() || (nb.getUseCutoff() && includeNonbonded && cl.getComputeForceCount()%100 == 0)) {
+        cl.reorderAtoms(!cl.getMoleculesAreInvalid());
         nb.updateNeighborListSize();
         cl.setComputeForceCount(cl.getComputeForceCount()+1);
     }
@@ -4645,9 +4645,10 @@ double OpenCLCalcKineticEnergyKernel::execute(ContextImpl& context) {
     OpenCLArray<mm_float4>& velm = cl.getVelm();
     velm.download();
     double energy = 0.0;
+    OpenCLArray<cl_int>& order = cl.getAtomIndex();
     for (size_t i = 0; i < masses.size(); ++i) {
         mm_float4 v = velm[i];
-        energy += masses[i]*(v.x*v.x+v.y*v.y+v.z*v.z);
+        energy += masses[order[i]]*(v.x*v.x+v.y*v.y+v.z*v.z);
     }
     return 0.5*energy;
 }