Minor fixes to some recent changes that prevented compilation (Mark looked at...

Minor fixes to some recent changes that prevented compilation (Mark looked at these). This code still has never been tested, at least on Windows.

platforms/brook/src/BrookCalcNonbondedForceKernel.cpp

@@ -176,7 +176,7 @@ void BrookCalcNonbondedForceKernel::initialize( const System& system, const Nonb
 
    // Go through the exclusions.
 
-   std::vector<std::set<int> >& exclusions(_numberOfParticles);
+   std::vector<std::set<int> > exclusions(_numberOfParticles);
    std::vector<int> nb14s;
    for (int i = 0; i < force.getNumExceptions(); i++) {
         int particle1, particle2;
@@ -184,7 +184,6 @@ void BrookCalcNonbondedForceKernel::initialize( const System& system, const Nonb
         force.getExceptionParameters(i, particle1, particle2, chargeProd, sigma, epsilon);
         exclusions[particle1].insert(particle2);
         exclusions[particle2].insert(particle1);
-        exclusions.push_back(pair<int, int>(particle1, particle2));
         if (chargeProd != 0.0 || epsilon != 0.0)
             nb14s.push_back(i);
    }
@@ -212,7 +211,7 @@ void BrookCalcNonbondedForceKernel::initialize( const System& system, const Nonb
  * 
  * @param system                    System reference
  * @param force                     HarmonicLJ14Force reference
- *
+ * @param nb14s                     which of the exceptions need to be calculated
  */
 
 void BrookCalcNonbondedForceKernel::initialize14Interactions( const System& system, const NonbondedForce& force, const std::vector<int>& nb14s ){

platforms/brook/src/BrookCalcNonbondedForceKernel.h

@@ -63,9 +63,10 @@ class BrookCalcNonbondedForceKernel : public CalcNonbondedForceKernel {
        * 
        * @param system     the System this kernel will be applied to
        * @param force      the NonbondedForce this kernel will be used for
+       * @param nb14s      which of the exceptions need to be calculated
        */
 
-      void initialize14Interactions( const System& system, const NonbondedForce& force );
+      void initialize14Interactions( const System& system, const NonbondedForce& force, const std::vector<int>& nb14s );
   
       /**
        * Execute the kernel to calculate the forces.

platforms/brook/tests/TestBrookNonbondedForce.cpp

@@ -215,7 +215,7 @@ void testBrookExclusionsAnd14( FILE* log ){
    NonbondedForce* nonbonded = new NonbondedForce();
    for (int i = 0; i < numberOfParticles; i++) {
        system.addParticle(1.0);
-       nonbonded->addParticle(0, 1.5, 0)
+       nonbonded->addParticle(0, 1.5, 0);
    }
    vector<pair<int, int> > bonds;
    bonds.push_back(pair<int, int>(0, 1));

platforms/brook/tests/TstBrookGBSAOBCForce.cpp

@@ -156,7 +156,7 @@ static OpenMMContext* testObcForceSetup( int numParticles, int brookContext, FIL
 
    System* system                 = new System();
    for (int i = 0; i < numParticles; i++)
-       system.addParticle(1.0);
+       system->addParticle(1.0);
    LangevinIntegrator* integrator = new LangevinIntegrator(0, 0.1, 0.01);
    GBSAOBCForce* forceField  = new GBSAOBCForce();
 
@@ -284,7 +284,7 @@ static OpenMMContext* testObcForceFileSetup( std::string fileName, int brookCont
 
    System* system                 = new System();
    for (int i = 0; i < numberOfParticles; i++)
-       system.addParticle(1.0);
+       system->addParticle(1.0);
    GBSAOBCForce* forceField       = new GBSAOBCForce();
 
    vector<Vec3> positions(numberOfParticles);