Changing box vectors does not change positions

olla/include/openmm/kernels.h

@@ -187,7 +187,7 @@ public:
      * @param b      the vector defining the second edge of the periodic box
      * @param c      the vector defining the third edge of the periodic box
      */
-    virtual void setPeriodicBoxVectors(ContextImpl& context, const Vec3& a, const Vec3& b, const Vec3& c) const = 0;
+    virtual void setPeriodicBoxVectors(ContextImpl& context, const Vec3& a, const Vec3& b, const Vec3& c) = 0;
     /**
      * Create a checkpoint recording the current state of the Context.
      * 

platforms/cuda/include/CudaKernels.h

@@ -178,7 +178,7 @@ public:
      * @param b      the vector defining the second edge of the periodic box
      * @param c      the vector defining the third edge of the periodic box
      */
-    void setPeriodicBoxVectors(ContextImpl& context, const Vec3& a, const Vec3& b, const Vec3& c) const;
+    void setPeriodicBoxVectors(ContextImpl& context, const Vec3& a, const Vec3& b, const Vec3& c);
     /**
      * Create a checkpoint recording the current state of the Context.
      * 

platforms/cuda/src/CudaKernels.cpp

@@ -340,10 +340,27 @@ void CudaUpdateStateDataKernel::getPeriodicBoxVectors(ContextImpl& context, Vec3
     cu.getPeriodicBoxVectors(a, b, c);
 }
 
-void CudaUpdateStateDataKernel::setPeriodicBoxVectors(ContextImpl& context, const Vec3& a, const Vec3& b, const Vec3& c) const {
+void CudaUpdateStateDataKernel::setPeriodicBoxVectors(ContextImpl& context, const Vec3& a, const Vec3& b, const Vec3& c) {
     vector<CudaContext*>& contexts = cu.getPlatformData().contexts;
+
+    // If any particles have been wrapped to the first periodic box, we need to unwrap them
+    // to avoid changing their positions.
+
+    vector<Vec3> positions;
+    for (int i = 0; i < (int) cu.getPosCellOffsets().size(); i++) {
+        int4& offset = cu.getPosCellOffsets()[i];
+        if (offset.x != 0 || offset.y != 0 || offset.z != 0) {
+            getPositions(context, positions);
+            break;
+        }
+    }
+    
+    // Update the vectors.
+
     for (int i = 0; i < (int) contexts.size(); i++)
         contexts[i]->setPeriodicBoxVectors(a, b, c);
+    if (positions.size() > 0)
+        setPositions(context, positions);
 }
 
 void CudaUpdateStateDataKernel::createCheckpoint(ContextImpl& context, ostream& stream) {

platforms/opencl/include/OpenCLKernels.h

@@ -156,7 +156,7 @@ public:
      * @param b      the vector defining the second edge of the periodic box
      * @param c      the vector defining the third edge of the periodic box
      */
-    void setPeriodicBoxVectors(ContextImpl& context, const Vec3& a, const Vec3& b, const Vec3& c) const;
+    void setPeriodicBoxVectors(ContextImpl& context, const Vec3& a, const Vec3& b, const Vec3& c);
     /**
      * Create a checkpoint recording the current state of the Context.
      * 

platforms/opencl/src/OpenCLKernels.cpp

@@ -369,10 +369,27 @@ void OpenCLUpdateStateDataKernel::getPeriodicBoxVectors(ContextImpl& context, Ve
     cl.getPeriodicBoxVectors(a, b, c);
 }
 
-void OpenCLUpdateStateDataKernel::setPeriodicBoxVectors(ContextImpl& context, const Vec3& a, const Vec3& b, const Vec3& c) const {
+void OpenCLUpdateStateDataKernel::setPeriodicBoxVectors(ContextImpl& context, const Vec3& a, const Vec3& b, const Vec3& c) {
     vector<OpenCLContext*>& contexts = cl.getPlatformData().contexts;
+
+    // If any particles have been wrapped to the first periodic box, we need to unwrap them
+    // to avoid changing their positions.
+
+    vector<Vec3> positions;
+    for (int i = 0; i < (int) cl.getPosCellOffsets().size(); i++) {
+        mm_int4& offset = cl.getPosCellOffsets()[i];
+        if (offset.x != 0 || offset.y != 0 || offset.z != 0) {
+            getPositions(context, positions);
+            break;
+        }
+    }
+    
+    // Update the vectors.
+
     for (int i = 0; i < (int) contexts.size(); i++)
         contexts[i]->setPeriodicBoxVectors(a, b, c);
+    if (positions.size() > 0)
+        setPositions(context, positions);
 }
 
 void OpenCLUpdateStateDataKernel::createCheckpoint(ContextImpl& context, ostream& stream) {

platforms/reference/include/ReferenceKernels.h

@@ -172,7 +172,7 @@ public:
      * @param b      the vector defining the second edge of the periodic box
      * @param c      the vector defining the third edge of the periodic box
      */
-    void setPeriodicBoxVectors(ContextImpl& context, const Vec3& a, const Vec3& b, const Vec3& c) const;
+    void setPeriodicBoxVectors(ContextImpl& context, const Vec3& a, const Vec3& b, const Vec3& c);
     /**
      * Create a checkpoint recording the current state of the Context.
      * 

platforms/reference/src/ReferenceKernels.cpp

@@ -280,7 +280,7 @@ void ReferenceUpdateStateDataKernel::getPeriodicBoxVectors(ContextImpl& context,
     c = vectors[2];
 }
 
-void ReferenceUpdateStateDataKernel::setPeriodicBoxVectors(ContextImpl& context, const Vec3& a, const Vec3& b, const Vec3& c) const {
+void ReferenceUpdateStateDataKernel::setPeriodicBoxVectors(ContextImpl& context, const Vec3& a, const Vec3& b, const Vec3& c) {
     RealVec& box = extractBoxSize(context);
     box[0] = (RealOpenMM) a[0];
     box[1] = (RealOpenMM) b[1];