Updated to use new API

plugins/freeEnergy/platforms/cuda/src/CudaFreeEnergyKernels.cpp

@@ -294,7 +294,7 @@ void CudaFreeEnergyCalcNonbondedSoftcoreForceKernel::initialize(const System& sy
             exclusionList[exclusions[i].second].push_back(exclusions[i].first);
         }
         Vec3 boxVectors[3];
-        system.getPeriodicBoxVectors(boxVectors[0], boxVectors[1], boxVectors[2]);
+        system.getDefaultPeriodicBoxVectors(boxVectors[0], boxVectors[1], boxVectors[2]);
         gpuSetPeriodicBoxSize(gpu, static_cast<float>(boxVectors[0][0] ), static_cast<float>(boxVectors[1][1] ), static_cast<float>(boxVectors[2][2] ));
         CudaNonbondedMethod method = NO_CUTOFF;
         if (force.getNonbondedMethod() != NonbondedSoftcoreForce::NoCutoff) {

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

@@ -3321,9 +3321,9 @@ Integrator* readParameterFile( const std::string& inputParameterFile, MapStringI
                   boxIndex++;
                }
             }
-            system.setPeriodicBoxVectors( box[0], box[1], box[2] );
+            system.setDefaultPeriodicBoxVectors( box[0], box[1], box[2] );
             Vec3 a, b, c;
-            system.getPeriodicBoxVectors( a, b, c);
+            system.getDefaultPeriodicBoxVectors( a, b, c);
             if( log ){
                (void) fprintf( log, "Box [%14.7f %14.7f %14.7f]\n    [%14.7f %14.7f %14.7f]\n    [%14.7f %14.7f %14.7f]\n",
                                a[0], a[1], a[2], b[0], b[1], b[2], c[0], c[1], c[2] );

plugins/freeEnergy/platforms/reference/src/ReferenceFreeEnergyKernels.cpp

@@ -177,7 +177,7 @@ void ReferenceFreeEnergyCalcNonbondedSoftcoreForceKernel::initialize(const Syste
     //softCoreLJLambda = (RealOpenMM) force.getSoftCoreLJLambda();
 
     Vec3 boxVectors[3];
-    system.getPeriodicBoxVectors(boxVectors[0], boxVectors[1], boxVectors[2]);
+    system.getDefaultPeriodicBoxVectors(boxVectors[0], boxVectors[1], boxVectors[2]);
     periodicBoxSize[0] = (RealOpenMM) boxVectors[0][0];
     periodicBoxSize[1] = (RealOpenMM) boxVectors[1][1];
     periodicBoxSize[2] = (RealOpenMM) boxVectors[2][2];
@@ -351,7 +351,7 @@ void ReferenceFreeEnergyCalcGBSAOBCSoftcoreForceKernel::initialize(const System&
                 obcParameters->setUseCutoff(static_cast<RealOpenMM>(nonbonded->getCutoffDistance()));
             if (nonbonded->getNonbondedMethod() == NonbondedForce::CutoffPeriodic) {
                 Vec3 boxVectors[3];
-                system.getPeriodicBoxVectors(boxVectors[0], boxVectors[1], boxVectors[2]);
+                system.getDefaultPeriodicBoxVectors(boxVectors[0], boxVectors[1], boxVectors[2]);
                 RealOpenMM periodicBoxSize[3];
                 periodicBoxSize[0] = (RealOpenMM) boxVectors[0][0];
                 periodicBoxSize[1] = (RealOpenMM) boxVectors[1][1];
@@ -427,7 +427,7 @@ void ReferenceFreeEnergyCalcGBVISoftcoreForceKernel::initialize(const System& sy
         gBVIParameters->setUseCutoff(static_cast<RealOpenMM>(force.getCutoffDistance()));
     if (force.getNonbondedMethod() == GBVISoftcoreForce::CutoffPeriodic) {
         Vec3 boxVectors[3];
-        system.getPeriodicBoxVectors(boxVectors[0], boxVectors[1], boxVectors[2]);
+        system.getDefaultPeriodicBoxVectors(boxVectors[0], boxVectors[1], boxVectors[2]);
         RealOpenMM periodicBoxSize[3];
         periodicBoxSize[0] = (RealOpenMM) boxVectors[0][0];
         periodicBoxSize[1] = (RealOpenMM) boxVectors[1][1];