Added index bounds checking to lots of methods

platforms/reference/tests/TestReferenceNeighborList.cpp

@@ -29,7 +29,7 @@
  * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
  * -------------------------------------------------------------------------- */
 
-#include "../../../tests/AssertionUtilities.h"
+#include "openmm/internal/AssertionUtilities.h"
 #include "../src/SimTKReference/ReferenceNeighborList.h"
 #include "sfmt/SFMT.h"
 #include <cassert>

platforms/reference/tests/TestReferenceNonbondedForce.cpp

@@ -33,7 +33,7 @@
  * This tests all the different force terms in the reference implementation of NonbondedForce.
  */
 
-#include "../../../tests/AssertionUtilities.h"
+#include "openmm/internal/AssertionUtilities.h"
 #include "openmm/Context.h"
 #include "ReferencePlatform.h"
 #include "openmm/NonbondedForce.h"

platforms/reference/tests/TestReferencePeriodicTorsionForce.cpp

@@ -33,7 +33,7 @@
  * This tests all the different force terms in the reference implementation of PeriodicTorsionForce.
  */
 
-#include "../../../tests/AssertionUtilities.h"
+#include "openmm/internal/AssertionUtilities.h"
 #include "openmm/Context.h"
 #include "ReferencePlatform.h"
 #include "openmm/PeriodicTorsionForce.h"

platforms/reference/tests/TestReferenceRBTorsionForce.cpp

@@ -33,7 +33,7 @@
  * This tests all the different force terms in the reference implementation of RBTorsionForce.
  */
 
-#include "../../../tests/AssertionUtilities.h"
+#include "openmm/internal/AssertionUtilities.h"
 #include "openmm/Context.h"
 #include "ReferencePlatform.h"
 #include "openmm/RBTorsionForce.h"

platforms/reference/tests/TestReferenceRandom.cpp

@@ -33,7 +33,7 @@
  * This tests the reference implementation of random number generation.
  */
 
-#include "../../../tests/AssertionUtilities.h"
+#include "openmm/internal/AssertionUtilities.h"
 #include "../src/SimTKUtilities/SimTKOpenMMUtilities.h"
 #include <iostream>
 

platforms/reference/tests/TestReferenceVariableLangevinIntegrator.cpp

@@ -33,7 +33,7 @@
  * This tests the reference implementation of VariableLangevinIntegrator.
  */
 
-#include "../../../tests/AssertionUtilities.h"
+#include "openmm/internal/AssertionUtilities.h"
 #include "openmm/Context.h"
 #include "ReferencePlatform.h"
 #include "openmm/HarmonicBondForce.h"

platforms/reference/tests/TestReferenceVariableVerletIntegrator.cpp

@@ -33,7 +33,7 @@
  * This tests the reference implementation of VariableVerletIntegrator.
  */
 
-#include "../../../tests/AssertionUtilities.h"
+#include "openmm/internal/AssertionUtilities.h"
 #include "openmm/Context.h"
 #include "ReferencePlatform.h"
 #include "openmm/HarmonicBondForce.h"

platforms/reference/tests/TestReferenceVerletIntegrator.cpp

@@ -33,7 +33,7 @@
  * This tests the reference implementation of VerletIntegrator.
  */
 
-#include "../../../tests/AssertionUtilities.h"
+#include "openmm/internal/AssertionUtilities.h"
 #include "openmm/Context.h"
 #include "ReferencePlatform.h"
 #include "openmm/HarmonicBondForce.h"

platforms/reference/tests/TestReferenceVirtualSites.cpp

@@ -33,7 +33,7 @@
  * This tests the reference implementation of virtual sites.
  */
 
-#include "../../../tests/AssertionUtilities.h"
+#include "openmm/internal/AssertionUtilities.h"
 #include "openmm/Context.h"
 #include "ReferencePlatform.h"
 #include "openmm/CustomBondForce.h"

plugins/amoeba/platforms/cuda/tests/AmoebaTinkerParameterFile.h

@@ -24,7 +24,7 @@
  * along with this program.  If not, see <http://www.gnu.org/licenses/>.      *
  * -------------------------------------------------------------------------- */
 
-#include "../../../tests/AssertionUtilities.h"
+#include "openmm/internal/AssertionUtilities.h"
 
 #include "openmm/CMMotionRemover.h"
 #include "openmm/System.h"

plugins/amoeba/platforms/cuda/tests/TestCudaAmoebaHarmonicAngleForce.cpp

@@ -33,7 +33,7 @@
  * This tests the Cuda implementation of CudaAmoebaHarmonicAngleForce.
  */
 
-#include "../../../tests/AssertionUtilities.h"
+#include "openmm/internal/AssertionUtilities.h"
 #include "AmoebaTinkerParameterFile.h"
 #include "openmm/Context.h"
 #include "OpenMMAmoeba.h"

plugins/amoeba/platforms/cuda/tests/TestCudaAmoebaHarmonicBondForce.cpp

@@ -33,7 +33,7 @@
  * This tests the Cuda implementation of HarmonicBondForce.
  */
 
-#include "../../../tests/AssertionUtilities.h"
+#include "openmm/internal/AssertionUtilities.h"
 #include "CudaPlatform.h"
 #include "AmoebaTinkerParameterFile.h"
 #include "openmm/Context.h"

plugins/amoeba/platforms/cuda/tests/TestCudaAmoebaHarmonicInPlaneAngleForce.cpp

@@ -33,7 +33,7 @@
  * This tests the Cuda implementation of CudaAmoebaHarmonicInPlaneAngleForce.
  */
 
-#include "../../../tests/AssertionUtilities.h"
+#include "openmm/internal/AssertionUtilities.h"
 #include "AmoebaTinkerParameterFile.h"
 #include "openmm/Context.h"
 #include "OpenMMAmoeba.h"

plugins/amoeba/platforms/cuda/tests/TestCudaAmoebaOutOfPlaneBendForce.cpp

@@ -33,7 +33,7 @@
  * This tests the Cuda implementation of CudaAmoebaOutOfPlaneBendForce.
  */
 
-#include "../../../tests/AssertionUtilities.h"
+#include "openmm/internal/AssertionUtilities.h"
 #include "AmoebaTinkerParameterFile.h"
 #include "openmm/Context.h"
 #include "OpenMMAmoeba.h"

plugins/amoeba/platforms/cuda/tests/TestCudaAmoebaPME.cpp

@@ -33,7 +33,7 @@
  * This tests the Ewald summation method cuda implementation of NonbondedForce.
  */
 
-#include "../../../tests/AssertionUtilities.h"
+#include "openmm/internal/AssertionUtilities.h"
 #include "AmoebaTinkerParameterFile.h"
 #include "openmm/Context.h"
 #include "CudaPlatform.h"

plugins/amoeba/platforms/cuda/tests/TestCudaAmoebaPiTorsionForce.cpp

@@ -33,7 +33,7 @@
  * This tests the Cuda implementation of CudaAmoebaPiTorsionForce.
  */
 
-#include "../../../tests/AssertionUtilities.h"
+#include "openmm/internal/AssertionUtilities.h"
 #include "AmoebaTinkerParameterFile.h"
 #include "openmm/Context.h"
 #include "OpenMMAmoeba.h"

plugins/amoeba/platforms/cuda/tests/TestCudaAmoebaStretchBendForce.cpp

@@ -33,7 +33,7 @@
  * This tests the Cuda implementation of CudaAmoebaStretchBendForce.
  */
 
-#include "../../../tests/AssertionUtilities.h"
+#include "openmm/internal/AssertionUtilities.h"
 #include "AmoebaTinkerParameterFile.h"
 #include "openmm/Context.h"
 #include "OpenMMAmoeba.h"

plugins/amoeba/platforms/cuda/tests/TestCudaAmoebaTorsionForce.cpp

@@ -33,7 +33,7 @@
  * This tests the Cuda implementation of CudaAmoebaTorsionForce.
  */
 
-#include "../../../tests/AssertionUtilities.h"
+#include "openmm/internal/AssertionUtilities.h"
 #include "AmoebaTinkerParameterFile.h"
 #include "openmm/Context.h"
 #include "OpenMMAmoeba.h"

plugins/amoeba/platforms/cuda/tests/TestCudaAmoebaTorsionTorsionForce.cpp

@@ -33,7 +33,7 @@
  * This tests the Cuda implementation of CudaAmoebaTorsionTorsionForce.
  */
 
-#include "../../../tests/AssertionUtilities.h"
+#include "openmm/internal/AssertionUtilities.h"
 #include "openmm/Context.h"
 #include "OpenMMAmoeba.h"
 #include "openmm/System.h"

plugins/amoeba/platforms/cuda/tests/TestCudaAmoebaUreyBradleyForce.cpp

@@ -33,7 +33,7 @@
  * This tests the Cuda implementation of UreyBradleyForce.
  */
 
-#include "../../../tests/AssertionUtilities.h"
+#include "openmm/internal/AssertionUtilities.h"
 #include "AmoebaTinkerParameterFile.h"
 #include "openmm/Context.h"
 #include "OpenMMAmoeba.h"