Fixed periodic box changing from rectangular to triclinic (#4618)

platforms/common/src/CommonKernels.cpp

@@ -352,6 +352,9 @@ void CommonUpdateStateDataKernel::getPeriodicBoxVectors(ContextImpl& context, Ve
 }
 
 void CommonUpdateStateDataKernel::setPeriodicBoxVectors(ContextImpl& context, const Vec3& a, const Vec3& b, const Vec3& c) {
+    if (!cc.getBoxIsTriclinic() && (b[0] != 0 || c[0] != 0 || c[1] != 0))
+        throw OpenMMException("The box shape has changed from rectangular to triclinic.  To do this, you must call setDefaultPeriodicBoxVectors() on the System to specify a triclinic default box, then reinitialize the Context.");
+
     // If any particles have been wrapped to the first periodic box, we need to unwrap them
     // to avoid changing their positions.
 

platforms/cuda/src/CudaContext.cpp

@@ -6,7 +6,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2009-2023 Stanford University and the Authors.      *
+ * Portions copyright (c) 2009-2024 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -40,6 +40,7 @@
 #include "openmm/common/ComputeArray.h"
 #include "openmm/common/ContextSelector.h"
 #include "SHA1.h"
+#include "openmm/MonteCarloFlexibleBarostat.h"
 #include "openmm/Platform.h"
 #include "openmm/System.h"
 #include "openmm/VirtualSite.h"
@@ -292,6 +293,9 @@ CudaContext::CudaContext(const System& system, int deviceIndex, bool useBlocking
     boxIsTriclinic = (boxVectors[0][1] != 0.0 || boxVectors[0][2] != 0.0 ||
                       boxVectors[1][0] != 0.0 || boxVectors[1][2] != 0.0 ||
                       boxVectors[2][0] != 0.0 || boxVectors[2][1] != 0.0);
+    for (int i = 0; i < system.getNumForces(); i++)
+        if (dynamic_cast<const MonteCarloFlexibleBarostat*>(&system.getForce(i)) != NULL)
+            boxIsTriclinic = true;
     if (boxIsTriclinic) {
         compilationDefines["APPLY_PERIODIC_TO_DELTA(delta)"] =
             "{"

platforms/opencl/src/OpenCLContext.cpp

@@ -6,7 +6,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2009-2023 Stanford University and the Authors.      *
+ * Portions copyright (c) 2009-2024 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -38,6 +38,7 @@
 #include "OpenCLNonbondedUtilities.h"
 #include "OpenCLProgram.h"
 #include "openmm/common/ComputeArray.h"
+#include "openmm/MonteCarloFlexibleBarostat.h"
 #include "openmm/Platform.h"
 #include "openmm/System.h"
 #include "openmm/VirtualSite.h"
@@ -439,6 +440,9 @@ OpenCLContext::OpenCLContext(const System& system, int platformIndex, int device
     boxIsTriclinic = (boxVectors[0][1] != 0.0 || boxVectors[0][2] != 0.0 ||
                       boxVectors[1][0] != 0.0 || boxVectors[1][2] != 0.0 ||
                       boxVectors[2][0] != 0.0 || boxVectors[2][1] != 0.0);
+    for (int i = 0; i < system.getNumForces(); i++)
+        if (dynamic_cast<const MonteCarloFlexibleBarostat*>(&system.getForce(i)) != NULL)
+            boxIsTriclinic = true;
     if (boxIsTriclinic) {
         compilationDefines["APPLY_PERIODIC_TO_DELTA(delta)"] =
             "{"