Added index bounds checking to lots of methods

plugins/amoeba/serialization/tests/TestSerializeAmoebaTorsionTorsionForce.cpp

@@ -29,7 +29,7 @@
  * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
  * -------------------------------------------------------------------------- */
 
-#include "../../../tests/AssertionUtilities.h"
+#include "openmm/internal/AssertionUtilities.h"
 #include "openmm/AmoebaTorsionTorsionForce.h"
 #include "openmm/serialization/XmlSerializer.h"
 #include <iostream>

plugins/amoeba/serialization/tests/TestSerializeAmoebaUreyBradleyForce.cpp

@@ -29,7 +29,7 @@
  * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
  * -------------------------------------------------------------------------- */
 
-#include "../../../tests/AssertionUtilities.h"
+#include "openmm/internal/AssertionUtilities.h"
 #include "openmm/AmoebaUreyBradleyForce.h"
 #include "openmm/serialization/XmlSerializer.h"
 #include <iostream>

plugins/amoeba/serialization/tests/TestSerializeAmoebaVdwForce.cpp

@@ -29,7 +29,7 @@
  * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
  * -------------------------------------------------------------------------- */
 
-#include "../../../tests/AssertionUtilities.h"
+#include "openmm/internal/AssertionUtilities.h"
 #include "openmm/AmoebaVdwForce.h"
 #include "openmm/serialization/XmlSerializer.h"
 #include <iostream>

plugins/amoeba/serialization/tests/TestSerializeAmoebaWcaDispersionForce.cpp

@@ -29,7 +29,7 @@
  * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
  * -------------------------------------------------------------------------- */
 
-#include "../../../tests/AssertionUtilities.h"
+#include "openmm/internal/AssertionUtilities.h"
 #include "openmm/AmoebaWcaDispersionForce.h"
 #include "openmm/serialization/XmlSerializer.h"
 #include <iostream>

plugins/freeEnergy/platforms/cuda/tests/TestCudaGBVISoftcoreForce.cpp

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

plugins/freeEnergy/platforms/cuda/tests/TestCudaLJSoftcoreForce.cpp

@@ -33,7 +33,7 @@
  * 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"

plugins/freeEnergy/platforms/cuda/tests/TestCudaOBCSoftcoreForce.cpp

@@ -34,7 +34,7 @@
  */
 
 #include "openmm/System.h"
-#include "../../../tests/AssertionUtilities.h"
+#include "openmm/internal/AssertionUtilities.h"
 
 #include "sfmt/SFMT.h"
 #include "openmm/Context.h"

plugins/freeEnergy/platforms/reference/tests/TestReferenceGBVISoftcoreForce.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/GBVISoftcoreForce.h"

plugins/freeEnergy/platforms/reference/tests/TestReferenceLJSoftcoreForce.cpp

@@ -33,7 +33,7 @@
  * 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"

plugins/freeEnergy/platforms/reference/tests/TestReferenceOBCSoftcoreForce.cpp

@@ -33,7 +33,7 @@
  * 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"

plugins/freeEnergy/platforms/reference/tests/TestReferenceSoftcoreForce.h

@@ -36,7 +36,7 @@
  * Utility methods shared across unit tests
  */
 
-#include "../../../tests/AssertionUtilities.h"
+#include "openmm/internal/AssertionUtilities.h"
 #include "openmm/Context.h"
 #include "openmm/System.h"
 #include "../src/SimTKUtilities/SimTKOpenMMRealType.h"

plugins/freeEnergy/serialization/tests/TestSerializeFreeEnergyGBSAOBCSoftcoreForce.cpp

@@ -29,7 +29,7 @@
  * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
  * -------------------------------------------------------------------------- */
 
-#include "../../../tests/AssertionUtilities.h"
+#include "openmm/internal/AssertionUtilities.h"
 #include "openmm/GBSAOBCSoftcoreForce.h"
 #include "openmm/serialization/XmlSerializer.h"
 #include <iostream>

plugins/freeEnergy/serialization/tests/TestSerializeFreeEnergyGBVISoftcoreForce.cpp

@@ -29,7 +29,7 @@
  * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
  * -------------------------------------------------------------------------- */
 
-#include "../../../tests/AssertionUtilities.h"
+#include "openmm/internal/AssertionUtilities.h"
 #include "openmm/GBVISoftcoreForce.h"
 #include "openmm/serialization/XmlSerializer.h"
 #include <iostream>

plugins/freeEnergy/serialization/tests/TestSerializeFreeEnergyNonbondedSoftcoreForce.cpp

@@ -29,7 +29,7 @@
  * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
  * -------------------------------------------------------------------------- */
 
-#include "../../../tests/AssertionUtilities.h"
+#include "openmm/internal/AssertionUtilities.h"
 #include "openmm/NonbondedSoftcoreForce.h"
 #include "openmm/serialization/XmlSerializer.h"
 #include <iostream>

plugins/rpmd/platforms/opencl/tests/TestOpenCLRpmd.cpp

@@ -33,7 +33,7 @@
  * This tests the OpenCL implementation of RPMDIntegrator.
  */
 
-#include "../../../tests/AssertionUtilities.h"
+#include "openmm/internal/AssertionUtilities.h"
 #include "openmm/Context.h"
 #include "openmm/CustomNonbondedForce.h"
 #include "openmm/HarmonicBondForce.h"
@@ -73,7 +73,6 @@ void testFreeParticles() {
     vector<double> ke(numCopies, 0.0);
     vector<double> rg(numParticles, 0.0);
     const RealOpenMM hbar = 1.054571628e-34*AVOGADRO/(1000*1e-12);
-    const double wn = numCopies*BOLTZ*temperature/hbar;
     for (int i = 0; i < numSteps; i++) {
         integ.step(1);
         vector<State> state(numCopies);
@@ -167,7 +166,6 @@ void testParaHydrogen() {
     const double invBoxSize = 1.0/boxSize;
     double meanKE = 0.0;
     const RealOpenMM hbar = 1.054571628e-34*AVOGADRO/(1000*1e-12);
-    const double wn = numCopies*BOLTZ*temperature/hbar;
     for (int step = 0; step < numSteps; step++) {
         integ.step(20);
         vector<State> states(numCopies);

plugins/rpmd/platforms/reference/tests/TestReferenceRpmd.cpp

@@ -33,7 +33,7 @@
  * This tests the Reference implementation of RPMDIntegrator.
  */
 
-#include "../../../tests/AssertionUtilities.h"
+#include "openmm/internal/AssertionUtilities.h"
 #include "openmm/Context.h"
 #include "openmm/HarmonicBondForce.h"
 #include "openmm/Platform.h"

serialization/tests/TestSerializationNode.cpp

@@ -29,7 +29,7 @@
  * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
  * -------------------------------------------------------------------------- */
 
-#include "../../../tests/AssertionUtilities.h"
+#include "openmm/internal/AssertionUtilities.h"
 #include "openmm/serialization/SerializationNode.h"
 #include <iostream>
 

serialization/tests/TestSerializeAndersenThermostat.cpp

@@ -29,7 +29,7 @@
  * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
  * -------------------------------------------------------------------------- */
 
-#include "../../../tests/AssertionUtilities.h"
+#include "openmm/internal/AssertionUtilities.h"
 #include "openmm/AndersenThermostat.h"
 #include "openmm/serialization/XmlSerializer.h"
 #include <iostream>

serialization/tests/TestSerializeCMAPTorsion.cpp

@@ -29,7 +29,7 @@
  * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
  * -------------------------------------------------------------------------- */
 
-#include "../../../tests/AssertionUtilities.h"
+#include "openmm/internal/AssertionUtilities.h"
 #include "openmm/CMAPTorsionForce.h"
 #include "openmm/serialization/XmlSerializer.h"
 #include <iostream>

serialization/tests/TestSerializeCMMotionRemover.cpp

@@ -29,7 +29,7 @@
  * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
  * -------------------------------------------------------------------------- */
 
-#include "../../../tests/AssertionUtilities.h"
+#include "openmm/internal/AssertionUtilities.h"
 #include "openmm/CMMotionRemover.h"
 #include "openmm/serialization/XmlSerializer.h"
 #include <iostream>