Added index bounds checking to lots of methods

platforms/reference/tests/TestReferenceBrownianIntegrator.cpp

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

platforms/reference/tests/TestReferenceCMAPTorsionForce.cpp

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

platforms/reference/tests/TestReferenceCMMotionRemover.cpp

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

platforms/reference/tests/TestReferenceCustomAngleForce.cpp

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

platforms/reference/tests/TestReferenceCustomBondForce.cpp

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

platforms/reference/tests/TestReferenceCustomExternalForce.cpp

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

platforms/reference/tests/TestReferenceCustomGBForce.cpp

@@ -34,13 +34,14 @@
  * This tests all the different force terms in the reference implementation of CustomGBForce.
  */
 
-#include "../../../tests/AssertionUtilities.h"
+#include "openmm/internal/AssertionUtilities.h"
 #include "sfmt/SFMT.h"
 #include "openmm/Context.h"
 #include "ReferencePlatform.h"
 #include "openmm/CustomGBForce.h"
 #include "openmm/GBSAOBCForce.h"
 #include "openmm/GBVIForce.h"
+#include "openmm/OpenMMException.h"
 #include "openmm/System.h"
 #include "openmm/VerletIntegrator.h"
 #include <iostream>

platforms/reference/tests/TestReferenceCustomHbondForce.cpp

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

platforms/reference/tests/TestReferenceCustomIntegrator.cpp

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

platforms/reference/tests/TestReferenceCustomNonbondedForce.cpp

@@ -34,7 +34,7 @@
  * This tests all the different force terms in the reference implementation of CustomNonbondedForce.
  */
 
-#include "../../../tests/AssertionUtilities.h"
+#include "openmm/internal/AssertionUtilities.h"
 #include "sfmt/SFMT.h"
 #include "openmm/Context.h"
 #include "ReferencePlatform.h"

platforms/reference/tests/TestReferenceCustomTorsionForce.cpp

@@ -36,7 +36,7 @@
 #ifdef WIN32
   #define _USE_MATH_DEFINES // Needed to get M_PI
 #endif
-#include "../../../tests/AssertionUtilities.h"
+#include "openmm/internal/AssertionUtilities.h"
 #include "openmm/Context.h"
 #include "ReferencePlatform.h"
 #include "openmm/CustomTorsionForce.h"

platforms/reference/tests/TestReferenceEwald.cpp

@@ -33,7 +33,7 @@
  * This tests the Eewald summation method 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/TestReferenceGBSAOBCForce.cpp

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

platforms/reference/tests/TestReferenceGBVIForce.cpp

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

platforms/reference/tests/TestReferenceHarmonicAngleForce.cpp

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

platforms/reference/tests/TestReferenceHarmonicBondForce.cpp

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

platforms/reference/tests/TestReferenceKineticEnergy.cpp

@@ -33,7 +33,7 @@
  * This tests the reference implementation of the kernel to calculate kinetic energy.
  */
 
-#include "../../../tests/AssertionUtilities.h"
+#include "openmm/internal/AssertionUtilities.h"
 #include "openmm/Context.h"
 #include "ReferencePlatform.h"
 #include "openmm/System.h"

platforms/reference/tests/TestReferenceLangevinIntegrator.cpp

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

platforms/reference/tests/TestReferenceLocalEnergyMinimizer.cpp

@@ -30,7 +30,7 @@
  * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
  * -------------------------------------------------------------------------- */
 
-#include "../../../tests/AssertionUtilities.h"
+#include "openmm/internal/AssertionUtilities.h"
 #include "ReferencePlatform.h"
 #include "openmm/Context.h"
 #include "openmm/HarmonicBondForce.h"

platforms/reference/tests/TestReferenceMonteCarloBarostat.cpp

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