Add test to the Amoeba plugin for the new usesPeriodicBoundaryConditions

function call.

plugins/amoeba/platforms/reference/tests/TestReferenceAmoebaAngleForce.cpp

@@ -286,6 +286,8 @@ void testOneAngle( FILE* log ) {
     amoebaAngleForce->setAmoebaGlobalAngleSextic(sexticK);
 
     system.addForce(amoebaAngleForce);
+    ASSERT(!amoebaAngleForce->usesPeriodicBoundaryConditions());
+    ASSERT(!system.usesPeriodicBoundaryConditions());
     Context context(system, integrator, Platform::getPlatformByName( "Reference"));
 
     std::vector<Vec3> positions(numberOfParticles);

plugins/amoeba/platforms/reference/tests/TestReferenceAmoebaBondForce.cpp

@@ -193,6 +193,8 @@ void testTwoBond( FILE* log ) {
     amoebaBondForce->addBond(1, 2, bondLength, quadraticK);
 
     system.addForce(amoebaBondForce);
+    ASSERT(!amoebaBondForce->usesPeriodicBoundaryConditions());
+    ASSERT(!system.usesPeriodicBoundaryConditions());
     Context context(system, integrator, Platform::getPlatformByName( "Reference"));
     std::vector<Vec3> positions(3);
 

plugins/amoeba/platforms/reference/tests/TestReferenceAmoebaGeneralizedKirkwoodForce.cpp

@@ -7176,6 +7176,8 @@ static void testGeneralizedKirkwoodAmmoniaMutualPolarizationWithCavityTerm( FILE
     System system;
     AmoebaGeneralizedKirkwoodForce* amoebaGeneralizedKirkwoodForce  = new AmoebaGeneralizedKirkwoodForce();
     setupMultipoleAmmonia(system, amoebaGeneralizedKirkwoodForce, AmoebaMultipoleForce::Mutual, 1);
+    ASSERT(!amoebaGeneralizedKirkwoodForce->usesPeriodicBoundaryConditions());
+    ASSERT(!system.usesPeriodicBoundaryConditions());
     LangevinIntegrator integrator(0.0, 0.1, 0.01);
     Context context(system, integrator, Platform::getPlatformByName("Reference"));
     getForcesEnergyMultipoleAmmonia(context, forces, energy, log );

plugins/amoeba/platforms/reference/tests/TestReferenceAmoebaInPlaneAngleForce.cpp

@@ -361,6 +361,8 @@ void testOneAngle( FILE* log ) {
     amoebaInPlaneAngleForce->setAmoebaGlobalInPlaneAngleSextic(sexticK);
 
     system.addForce(amoebaInPlaneAngleForce);
+    ASSERT(!amoebaInPlaneAngleForce->usesPeriodicBoundaryConditions());
+    ASSERT(!system.usesPeriodicBoundaryConditions());
     Context context(system, integrator, Platform::getPlatformByName( "Reference"));
 
     std::vector<Vec3> positions(numberOfParticles);

plugins/amoeba/platforms/reference/tests/TestReferenceAmoebaMultipoleForce.cpp

@@ -460,6 +460,8 @@ static void testMultipoleAmmoniaMutualPolarization( FILE* log ) {
     AmoebaMultipoleForce* amoebaMultipoleForce = new AmoebaMultipoleForce();;
     setupMultipoleAmmonia(system, amoebaMultipoleForce, AmoebaMultipoleForce::NoCutoff, AmoebaMultipoleForce::Mutual, 
                                              cutoff, inputPmeGridDimension);
+    ASSERT(!amoebaMultipoleForce->usesPeriodicBoundaryConditions());
+    ASSERT(!system.usesPeriodicBoundaryConditions());
     LangevinIntegrator integrator(0.0, 0.1, 0.01);
     Context context(system, integrator, Platform::getPlatformByName("Reference"));
     getForcesEnergyMultipoleAmmonia(context, forces, energy);
@@ -639,6 +641,8 @@ static void setupAndGetForcesEnergyMultipoleWater( AmoebaMultipoleForce::Nonbond
     positions[11]             = Vec3(   5.0590640e-01,   1.8880920e-01,   -6.8813470e-01 );
 
     system.addForce(amoebaMultipoleForce);
+    ASSERT(amoebaMultipoleForce->usesPeriodicBoundaryConditions());
+    ASSERT(system.usesPeriodicBoundaryConditions());
 
     std::string platformName;
     platformName = "Reference";

plugins/amoeba/platforms/reference/tests/TestReferenceAmoebaOutOfPlaneBendForce.cpp

@@ -321,6 +321,8 @@ void testOneOutOfPlaneBend( FILE* log ) {
     amoebaOutOfPlaneBendForce->addOutOfPlaneBend(0, 1, 2, 3, kOutOfPlaneBend );
 
     system.addForce(amoebaOutOfPlaneBendForce);
+    ASSERT(!amoebaOutOfPlaneBendForce->usesPeriodicBoundaryConditions());
+    ASSERT(!system.usesPeriodicBoundaryConditions());
     Context context(system, integrator, Platform::getPlatformByName( "Reference"));
 
     std::vector<Vec3> positions(numberOfParticles);

plugins/amoeba/platforms/reference/tests/TestReferenceAmoebaPiTorsionForce.cpp

@@ -285,6 +285,8 @@ void testOnePiTorsion( FILE* log ) {
     amoebaPiTorsionForce->addPiTorsion(0, 1, 2, 3, 4, 5, kTorsion );
 
     system.addForce(amoebaPiTorsionForce);
+    ASSERT(!amoebaPiTorsionForce->usesPeriodicBoundaryConditions());
+    ASSERT(!system.usesPeriodicBoundaryConditions());
     Context context(system, integrator, Platform::getPlatformByName( "Reference"));
 
     std::vector<Vec3> positions(numberOfParticles);

plugins/amoeba/platforms/reference/tests/TestReferenceAmoebaStretchBendForce.cpp

@@ -275,6 +275,8 @@ void testOneStretchBend( FILE* log ) {
     amoebaStretchBendForce->addStretchBend(0, 1, 2, abLength, cbLength, angleStretchBend, kStretchBend );
 
     system.addForce(amoebaStretchBendForce);
+    ASSERT(!amoebaStretchBendForce->usesPeriodicBoundaryConditions());
+    ASSERT(!system.usesPeriodicBoundaryConditions());
     Context context(system, integrator, Platform::getPlatformByName( "Reference"));
 
     std::vector<Vec3> positions(numberOfParticles);

plugins/amoeba/platforms/reference/tests/TestReferenceAmoebaTorsionTorsionForce.cpp

@@ -2646,6 +2646,8 @@ void testTorsionTorsion(int systemId, bool includeDerivs) {
     amoebaTorsionTorsionForce->setTorsionTorsionGrid(0, getTorsionGrid(gridIndex, includeDerivs));
     
     system.addForce(amoebaTorsionTorsionForce);
+    ASSERT(!amoebaTorsionTorsionForce->usesPeriodicBoundaryConditions());
+    ASSERT(!system.usesPeriodicBoundaryConditions());
     Context context(system, integrator, Platform::getPlatformByName("Reference"));
 
     context.setPositions(positions);

plugins/amoeba/platforms/reference/tests/TestReferenceAmoebaVdwForce.cpp

@@ -328,6 +328,12 @@ void setupAndGetForcesEnergyVdwAmmonia( const std::string& sigmaCombiningRule, c
 
     system.addForce(amoebaVdwForce);
 
+    if( boxDimension > 0.0 ){
+        ASSERT(amoebaVdwForce->usesPeriodicBoundaryConditions());
+    } else {
+        ASSERT(!amoebaVdwForce->usesPeriodicBoundaryConditions());
+    }
+
     std::string platformName;
     platformName = "Reference";
     LangevinIntegrator integrator(0.0, 0.1, 0.01);

plugins/amoeba/platforms/reference/tests/TestReferenceWcaDispersionForce.cpp

@@ -116,6 +116,8 @@ void testWcaDispersionAmmonia( FILE* log ) {
     positions[7]              = Vec3(  -2.0426290e-01,  -8.1231400e-02,    4.1033500e-02 );
 
     system.addForce(amoebaWcaDispersionForce);
+    ASSERT(!amoebaWcaDispersionForce->usesPeriodicBoundaryConditions());
+    ASSERT(!system.usesPeriodicBoundaryConditions());
 
     std::string platformName;
     platformName = "Reference";