Edits to remove some VC9 warnings

platforms/cuda/src/kernels/kCalculateGBVIBornSum.cu

@@ -259,7 +259,7 @@ void kPrintGBVI( gpuContext gpu, std::string callId, int call, FILE* log)
     int printOnlyOnNan = 1;
     int foundNan       = 0;
     if( printOnlyOnNan ){
-        for( int ii = 0; ii < gpu->sim.paddedNumberOfAtoms && foundNan == 0; ii++ ){
+        for( unsigned int ii = 0; ii < gpu->sim.paddedNumberOfAtoms && foundNan == 0; ii++ ){
             foundNan  += isNanOrInfinity( gpu->psBornRadii->_pSysData[ii] );
             foundNan  += isNanOrInfinity( gpu->psBornForce->_pSysData[ii] );
             foundNan  += isNanOrInfinity( gpu->psGBVISwitchDerivative->_pSysData[ii] );
@@ -267,7 +267,7 @@ void kPrintGBVI( gpuContext gpu, std::string callId, int call, FILE* log)
         if( foundNan ){
             log = stderr;
             (void) fprintf( log, "kPrintGBVI found nan \n", gpu->sim.paddedNumberOfAtoms );
-            for( int ii = 0; ii < gpu->sim.paddedNumberOfAtoms; ii++ ){
+            for( unsigned int ii = 0; ii < gpu->sim.paddedNumberOfAtoms; ii++ ){
                 (void) fprintf( log, "%6d %15.7e %15.7e %15.7e\n", ii,
                                 gpu->psPosq4->_pSysData[ii].x,
                                 gpu->psPosq4->_pSysData[ii].y,
@@ -281,7 +281,7 @@ void kPrintGBVI( gpuContext gpu, std::string callId, int call, FILE* log)
                         gpu->sim.nonbond_blocks, gpu->sim.nonbond_threads_per_block, gpu->sim.workUnits, gpu->psWorkUnit->_pSysStream[0][0],
                         sizeof(Atom)*gpu->sim.nonbond_threads_per_block );
         (void) fprintf( stderr, "bR bF swd r scR ...\n" );
-        for( int ii = 0; ii < gpu->sim.paddedNumberOfAtoms; ii++ ){
+        for( unsigned int ii = 0; ii < gpu->sim.paddedNumberOfAtoms; ii++ ){
             (void) fprintf( log, "%6d %15.7e %15.7e %15.7e %15.7e %15.7e %15.7e %15.7e %15.7e %15.7e\n", ii,
                         gpu->psBornRadii->_pSysData[ii],
                         gpu->psBornForce->_pSysData[ii],

platforms/cuda/src/kernels/kCalculateObcGbsaBornSum.cu

@@ -149,7 +149,7 @@ void kPrintObc( gpuContext gpu, std::string callId, int call, FILE* log)
     (void) fprintf( stderr, "bOutputWarp=%u blks=%u th/blk=%u wu=%u %u shrd=%u\n", gpu->bOutputBufferPerWarp,
                     gpu->sim.nonbond_blocks, gpu->sim.nonbond_threads_per_block, gpu->sim.workUnits, gpu->psWorkUnit->_pSysStream[0][0],
                     sizeof(Atom)*gpu->sim.nonbond_threads_per_block );
-    for( int ii = 0; ii < gpu->sim.paddedNumberOfAtoms; ii++ ){
+    for( unsigned int ii = 0; ii < gpu->sim.paddedNumberOfAtoms; ii++ ){
         (void) fprintf( log, "%6d %15.7e %15.7e %15.7e    %15.7e %15.7e   %15.7e %15.7e \n", ii, 
                         gpu->psObcChain->_pSysData[ii],
                         gpu->psBornRadii->_pSysData[ii],

platforms/cuda/src/kernels/kForces.cu

@@ -291,7 +291,7 @@ double kReduceEnergy(gpuContext gpu)
     //printf("kReduceEnergy\n");
     gpu->psEnergy->Download();
     double sum = 0.0;
-    for (int i = 0; i < gpu->sim.energyOutputBuffers; i++){
+    for (int i = 0; i < static_cast<int>(gpu->sim.energyOutputBuffers); i++){
         sum += (*gpu->psEnergy)[i];
     }
 

platforms/cuda/tests/TestCudaGBVIForce2.cpp

@@ -110,6 +110,7 @@ public:
      int _particle2;
      double _distance;
 };
+
 BondInfo_OpenMMTest::BondInfo_OpenMMTest( int particle1, int particle2, double distance ){
     _particle1 = particle1;
     _particle2 = particle2;
@@ -279,13 +280,14 @@ public:
      * @param boxDimensions             box dimensions
      * @param spacing                   spacing
      * @param sfmt                      input random number generator
+     * @param bondDistance              input bond distance
      * @param array                     output vector of grid values
      *
      * @return -1 if particles will not fit on grid; 0 if they do
      */
      
     int setParticlesOnGrid( const Vec3& origin, const Vec3& boxDimensions, const Vec3& spacing, 
-                            OpenMM_SFMT::SFMT& sfmt, std::vector<Vec3>& array ) const;
+                            OpenMM_SFMT::SFMT& sfmt, double bondDistance, std::vector<Vec3>& array ) const;
     
     /** 
      * Set bond distance
@@ -525,9 +527,9 @@ int PositionGenerator::setPositions( GenerationMethod method, OpenMM_SFMT::SFMT&
     int errorFlag = 0;
     positions.resize( _numParticles );
     if( method == Random ){
-        for( unsigned int ii = 0; ii < _numParticles; ii += _numParticlesPerMolecule ){ 
+        for( unsigned int ii = 0; ii < static_cast<unsigned int>(_numParticles); ii += _numParticlesPerMolecule ){ 
             positions[ii]    = Vec3(_boxSize*genrand_real2(sfmt), _boxSize*genrand_real2(sfmt), _boxSize*genrand_real2(sfmt));
-            for( unsigned int jj = 1; jj < _numParticlesPerMolecule; jj++) { 
+            for( unsigned int jj = 1; jj < static_cast<unsigned int>(_numParticlesPerMolecule); jj++) { 
                 positions[ii+jj]  = positions[ii] + Vec3(_bondDistance*genrand_real2(sfmt), _bondDistance*genrand_real2(sfmt), _bondDistance*genrand_real2(sfmt));
             }
         }
@@ -540,7 +542,7 @@ int PositionGenerator::setPositions( GenerationMethod method, OpenMM_SFMT::SFMT&
             double particlesPerDimension  = pow( static_cast<double>(_numMolecules), (1.0/3.0) ); 
             int particlesPerDimensionI    = static_cast<int>(particlesPerDimension+0.999999); 
             double boxSize                = _boxSize;
-            double spacingPerDimension    = boxSize/(particlesPerDimension+1.0);
+            double spacingPerDimension    = (boxSize-_bondDistance)/(particlesPerDimension+1.0);
             spacing                       = Vec3(spacingPerDimension, spacingPerDimension, spacingPerDimension );
             boxDimensions                 = Vec3(boxSize, boxSize, boxSize );
 
@@ -561,7 +563,7 @@ int PositionGenerator::setPositions( GenerationMethod method, OpenMM_SFMT::SFMT&
             (void) fprintf( _log, "SimpleGrid %s\n", msg.str().c_str() );
         }
 
-        errorFlag = setParticlesOnGrid( origin, boxDimensions, spacing, sfmt, positions );
+        errorFlag = setParticlesOnGrid( origin, boxDimensions, spacing, sfmt, _bondDistance, positions );
     }
 
     return errorFlag;
@@ -579,7 +581,7 @@ int PositionGenerator::setPositions( GenerationMethod method, OpenMM_SFMT::SFMT&
  */
  
 int PositionGenerator::setParticlesOnGrid( const Vec3& origin, const Vec3& boxDimensions, const Vec3& spacing, OpenMM_SFMT::SFMT& sfmt,
-                                           std::vector<Vec3>& array ) const {
+                                           double bondDistance, std::vector<Vec3>& array ) const {
 
     const double pi  = 3.14159265358979323846;
     const double pi2 = 2.0*pi;
@@ -595,12 +597,12 @@ int PositionGenerator::setParticlesOnGrid( const Vec3& origin, const Vec3& boxDi
 
     // place molecule centers on grid
 
-    for( unsigned int ii = 0; ii < _numParticles; ii += _numParticlesPerMolecule ){
+    for( unsigned int ii = 0; ii < static_cast<unsigned int>(_numParticles); ii += _numParticlesPerMolecule ){
         array[ii]  = Vec3(start);
         bool done  = false;
         for( unsigned int jj = 0; jj < 3 && !done; jj++ ){
             start[jj]  += spacing[jj];
-            if( start[jj] > boxDimensions[jj] ){
+            if( (start[jj]+4.0*bondDistance) > boxDimensions[jj] ){
                 start[jj] = origin[jj];
             } else {
                 done = true;
@@ -615,9 +617,9 @@ int PositionGenerator::setParticlesOnGrid( const Vec3& origin, const Vec3& boxDi
 
     // add molecule atoms
 
-    for( unsigned int ii = 0; ii < _numMolecules; ii++ ){
+    for( unsigned int ii = 0; ii < static_cast<unsigned int>(_numMolecules); ii++ ){
         int molecularIndex = ii*_numParticlesPerMolecule;
-        for( unsigned int jj = 1; jj < _numParticlesPerMolecule; jj++ ){
+        for( unsigned int jj = 1; jj < static_cast<unsigned int>(_numParticlesPerMolecule); jj++ ){
             double theta             = genrand_real2(sfmt)*pi2;
             double phi               = genrand_real2(sfmt)*pi;
             array[molecularIndex+jj] = array[molecularIndex] + Vec3(_bondDistance*cos(theta)*cos(phi), _bondDistance*cos(theta)*sin(phi), _bondDistance*sin(theta) );
@@ -688,12 +690,12 @@ void PositionGenerator::showMinMaxDistances( const std::vector<Vec3>& positions,
                     (box[1][0] - box[0][0]), (box[1][1] - box[0][1]), (box[1][2] - box[0][2]) );
 
     for( unsigned int ii = 0; ii < positionIndexVector.size(); ii++ ){
-        if( positionIndexVector[ii] < positions.size() ){
+        if( positionIndexVector[ii] < static_cast<int>(positions.size()) ){
             int positionIndex = positionIndexVector[ii];
             IntDoublePairVector sortVector;
             getSortedDistances( periodicBoundaryConditions, positionIndex, positions, sortVector );
             (void) fprintf( _log, "Min/max distance from %6d:\n    ", positionIndex );
-            for( unsigned int jj = 0; jj < sortVector.size() && jj < showIndex; jj++ ){
+            for( unsigned int jj = 0; jj < sortVector.size() && jj < static_cast<unsigned int>(showIndex); jj++ ){
                 IntDoublePair pair = sortVector[jj];
                 (void) fprintf( _log, "[%6d %15.7e] ", pair.first, pair.second);
             }   
@@ -748,7 +750,7 @@ void PositionGenerator::showMinMaxDistances( const std::vector<Vec3>& positions,
     std::sort( hitVector.begin(), hitVector.end(), TestIntDoublePair );
             
     (void) fprintf( _log, "Min distances pbc=%d\n", periodicBoundaryConditions );
-    for( unsigned int jj = 0; jj < hitVector.size() && jj < showIndex; jj++ ){
+    for( unsigned int jj = 0; jj < hitVector.size() && jj < static_cast<unsigned int>(showIndex); jj++ ){
         IntDoublePair pair  = hitVector[jj];
         int index           = pair.first;
         int iIndex          = static_cast<int>(index/positions.size());
@@ -798,7 +800,7 @@ void PositionGenerator::showParticlesWithinDistance( const std::vector<Vec3>& po
 void PositionGenerator::showDistances( const IntIntPairVector& pairs, const std::vector<Vec3>& positions ) const {
 
     for( IntIntPairVectorCI ii = pairs.begin(); ii != pairs.end(); ii++ ){
-        if( ii->first < positions.size() && ii->second < positions.size() ){
+        if( ii->first < static_cast<int>(positions.size()) && ii->second < static_cast<int>(positions.size()) ){
              double d = getDistance( ii->first, ii->second, positions );
              (void) fprintf( _log, "Distance %6d %6d  %15.7e d2=%15.7e\n", ii->first, ii->second,  d, d*d );
         }   
@@ -976,7 +978,6 @@ static int setDoubleFromMapStringToDouble( MapStringToDouble& argumentMap, std::
    return 0;
 }
 
-
 /**---------------------------------------------------------------------------------------
  *
  * Get relative difference between two forces
@@ -2128,7 +2129,7 @@ static void copySystem( const System& inputSystem, System& systemCopy, FILE* log
 
     // add particle/mass
 
-    for( unsigned int ii = 0; ii < inputSystem.getNumParticles(); ii++ ){
+    for( unsigned int ii = 0; ii < static_cast<unsigned int>(inputSystem.getNumParticles()); ii++ ){
         systemCopy.addParticle( inputSystem.getParticleMass( static_cast<int>(ii) ) );
     }
 
@@ -2142,8 +2143,7 @@ static void copySystem( const System& inputSystem, System& systemCopy, FILE* log
 
     // copy constraints
 
-    for( unsigned int ii = 0; ii < inputSystem.getNumConstraints(); ii++ ){
-        int index;
+    for( unsigned int ii = 0; ii < static_cast<unsigned int>(inputSystem.getNumConstraints()); ii++ ){
         int particle1, particle2;
         double distance;
         inputSystem.getConstraintParameters( ii, particle1, particle2, distance);
@@ -2152,7 +2152,7 @@ static void copySystem( const System& inputSystem, System& systemCopy, FILE* log
 
     // copy forces
 
-    for( unsigned int ii = 0; ii < inputSystem.getNumForces(); ii++ ){
+    for( unsigned int ii = 0; ii < static_cast<unsigned int>(inputSystem.getNumForces()); ii++ ){
         systemCopy.addForce( copyForce( inputSystem.getForce(ii), log) );
     }
 

platforms/opencl/tests/TestOpenCLGBSAOBCForce2.cpp

@@ -527,9 +527,9 @@ int PositionGenerator::setPositions( GenerationMethod method, OpenMM_SFMT::SFMT&
     int errorFlag = 0;
     positions.resize( _numParticles );
     if( method == Random ){
-        for( unsigned int ii = 0; ii < _numParticles; ii += _numParticlesPerMolecule ){ 
+        for( unsigned int ii = 0; ii < static_cast<unsigned int>(_numParticles); ii += _numParticlesPerMolecule ){ 
             positions[ii]    = Vec3(_boxSize*genrand_real2(sfmt), _boxSize*genrand_real2(sfmt), _boxSize*genrand_real2(sfmt));
-            for( unsigned int jj = 1; jj < _numParticlesPerMolecule; jj++) { 
+            for( unsigned int jj = 1; jj < static_cast<unsigned int>(_numParticlesPerMolecule); jj++) { 
                 positions[ii+jj]  = positions[ii] + Vec3(_bondDistance*genrand_real2(sfmt), _bondDistance*genrand_real2(sfmt), _bondDistance*genrand_real2(sfmt));
             }
         }
@@ -597,13 +597,12 @@ int PositionGenerator::setParticlesOnGrid( const Vec3& origin, const Vec3& boxDi
 
     // place molecule centers on grid
 
-    for( unsigned int ii = 0; ii < _numParticles; ii += _numParticlesPerMolecule ){
+    for( unsigned int ii = 0; ii < static_cast<unsigned int>(_numParticles); ii += _numParticlesPerMolecule ){
         array[ii]  = Vec3(start);
         bool done  = false;
         for( unsigned int jj = 0; jj < 3 && !done; jj++ ){
             start[jj]  += spacing[jj];
             if( (start[jj]+4.0*bondDistance) > boxDimensions[jj] ){
-//fprintf( stderr, "setParticlesOnGrid %6u %2u %15.7e %15.7e %15.7e\n", ii, jj, start[0], start[1], start[2] );
                 start[jj] = origin[jj];
             } else {
                 done = true;
@@ -618,9 +617,9 @@ int PositionGenerator::setParticlesOnGrid( const Vec3& origin, const Vec3& boxDi
 
     // add molecule atoms
 
-    for( unsigned int ii = 0; ii < _numMolecules; ii++ ){
+    for( unsigned int ii = 0; ii < static_cast<unsigned int>(_numMolecules); ii++ ){
         int molecularIndex = ii*_numParticlesPerMolecule;
-        for( unsigned int jj = 1; jj < _numParticlesPerMolecule; jj++ ){
+        for( unsigned int jj = 1; jj < static_cast<unsigned int>(_numParticlesPerMolecule); jj++ ){
             double theta             = genrand_real2(sfmt)*pi2;
             double phi               = genrand_real2(sfmt)*pi;
             array[molecularIndex+jj] = array[molecularIndex] + Vec3(_bondDistance*cos(theta)*cos(phi), _bondDistance*cos(theta)*sin(phi), _bondDistance*sin(theta) );
@@ -691,12 +690,12 @@ void PositionGenerator::showMinMaxDistances( const std::vector<Vec3>& positions,
                     (box[1][0] - box[0][0]), (box[1][1] - box[0][1]), (box[1][2] - box[0][2]) );
 
     for( unsigned int ii = 0; ii < positionIndexVector.size(); ii++ ){
-        if( positionIndexVector[ii] < positions.size() ){
+        if( positionIndexVector[ii] < static_cast<int>(positions.size()) ){
             int positionIndex = positionIndexVector[ii];
             IntDoublePairVector sortVector;
             getSortedDistances( periodicBoundaryConditions, positionIndex, positions, sortVector );
             (void) fprintf( _log, "Min/max distance from %6d:\n    ", positionIndex );
-            for( unsigned int jj = 0; jj < sortVector.size() && jj < showIndex; jj++ ){
+            for( unsigned int jj = 0; jj < sortVector.size() && jj < static_cast<unsigned int>(showIndex); jj++ ){
                 IntDoublePair pair = sortVector[jj];
                 (void) fprintf( _log, "[%6d %15.7e] ", pair.first, pair.second);
             }   
@@ -751,7 +750,7 @@ void PositionGenerator::showMinMaxDistances( const std::vector<Vec3>& positions,
     std::sort( hitVector.begin(), hitVector.end(), TestIntDoublePair );
             
     (void) fprintf( _log, "Min distances pbc=%d\n", periodicBoundaryConditions );
-    for( unsigned int jj = 0; jj < hitVector.size() && jj < showIndex; jj++ ){
+    for( unsigned int jj = 0; jj < hitVector.size() && jj < static_cast<unsigned int>(showIndex); jj++ ){
         IntDoublePair pair  = hitVector[jj];
         int index           = pair.first;
         int iIndex          = static_cast<int>(index/positions.size());
@@ -801,7 +800,7 @@ void PositionGenerator::showParticlesWithinDistance( const std::vector<Vec3>& po
 void PositionGenerator::showDistances( const IntIntPairVector& pairs, const std::vector<Vec3>& positions ) const {
 
     for( IntIntPairVectorCI ii = pairs.begin(); ii != pairs.end(); ii++ ){
-        if( ii->first < positions.size() && ii->second < positions.size() ){
+        if( ii->first < static_cast<int>(positions.size()) && ii->second < static_cast<int>(positions.size()) ){
              double d = getDistance( ii->first, ii->second, positions );
              (void) fprintf( _log, "Distance %6d %6d  %15.7e d2=%15.7e\n", ii->first, ii->second,  d, d*d );
         }   
@@ -1982,7 +1981,7 @@ static Force* copyForce( const Force& force, FILE* log ){
 
 #ifdef INCLUDE_AMOEBA_FORCES
 
-    if( forceCopy != NULL ){
+    if( forceCopy == NULL ){
 
         try {
            const AmoebaHarmonicBondForce& castForce = dynamic_cast<const AmoebaHarmonicBondForce&>(force);
@@ -1991,7 +1990,7 @@ static Force* copyForce( const Force& force, FILE* log ){
         }    
     }
 
-    if( forceCopy != NULL ){
+    if( forceCopy == NULL ){
 
         try {
            const AmoebaHarmonicAngleForce& castForce = dynamic_cast<const AmoebaHarmonicAngleForce&>(force);
@@ -2000,7 +1999,7 @@ static Force* copyForce( const Force& force, FILE* log ){
         }    
     }
 
-    if( forceCopy != NULL ){
+    if( forceCopy == NULL ){
 
         try {
            const AmoebaHarmonicInPlaneAngleForce& castForce = dynamic_cast<const AmoebaHarmonicInPlaneAngleForce&>(force);
@@ -2009,7 +2008,7 @@ static Force* copyForce( const Force& force, FILE* log ){
         }    
     }
 
-    if( forceCopy != NULL ){
+    if( forceCopy == NULL ){
 
         try {
            const AmoebaMultipoleForce& castForce = dynamic_cast<const AmoebaMultipoleForce&>(force);
@@ -2018,7 +2017,7 @@ static Force* copyForce( const Force& force, FILE* log ){
         }    
     }
 
-    if( forceCopy != NULL ){
+    if( forceCopy == NULL ){
 
         try {
            const AmoebaOutOfPlaneBendForce& castForce = dynamic_cast<const AmoebaOutOfPlaneBendForce&>(force);
@@ -2027,7 +2026,7 @@ static Force* copyForce( const Force& force, FILE* log ){
         }    
     }
 
-    if( forceCopy != NULL ){
+    if( forceCopy == NULL ){
 
         try {
            const AmoebaPiTorsionForce& castForce = dynamic_cast<const AmoebaPiTorsionForce&>(force);
@@ -2036,7 +2035,7 @@ static Force* copyForce( const Force& force, FILE* log ){
         }    
     }
 
-    if( forceCopy != NULL ){
+    if( forceCopy == NULL ){
 
         try {
            const AmoebaStretchBendForce& castForce = dynamic_cast<const AmoebaStretchBendForce&>(force);
@@ -2045,7 +2044,7 @@ static Force* copyForce( const Force& force, FILE* log ){
         }    
     }
 
-    if( forceCopy != NULL ){
+    if( forceCopy == NULL ){
 
         try {
            const AmoebaTorsionForce& castForce = dynamic_cast<const AmoebaTorsionForce&>(force);
@@ -2054,7 +2053,7 @@ static Force* copyForce( const Force& force, FILE* log ){
         }    
     }
 
-    if( forceCopy != NULL ){
+    if( forceCopy == NULL ){
 
         try {
            const AmoebaTorsionTorsionForce& castForce = dynamic_cast<const AmoebaTorsionTorsionForce&>(force);
@@ -2063,7 +2062,7 @@ static Force* copyForce( const Force& force, FILE* log ){
         }    
     }
 
-    if( forceCopy != NULL ){
+    if( forceCopy == NULL ){
 
         try {
            const AmoebaUreyBradleyForce& castForce = dynamic_cast<const AmoebaUreyBradleyForce&>(force);
@@ -2072,7 +2071,7 @@ static Force* copyForce( const Force& force, FILE* log ){
         }    
     }
 
-    if( forceCopy != NULL ){
+    if( forceCopy == NULL ){
 
         try {
            const AmoebaVdwForce& castForce = dynamic_cast<const AmoebaVdwForce&>(force);
@@ -2081,7 +2080,7 @@ static Force* copyForce( const Force& force, FILE* log ){
         }    
     }
 
-    if( forceCopy != NULL ){
+    if( forceCopy == NULL ){
 
         try {
            const AmoebaWcaDispersionForce& castForce = dynamic_cast<const AmoebaWcaDispersionForce&>(force);
@@ -2090,7 +2089,7 @@ static Force* copyForce( const Force& force, FILE* log ){
         }    
     }
 
-    if( forceCopy != NULL ){
+    if( forceCopy == NULL ){
 
         try {
            const AmoebaGeneralizedKirkwoodForce& castForce = dynamic_cast<const AmoebaGeneralizedKirkwoodForce&>(force);
@@ -2099,7 +2098,7 @@ static Force* copyForce( const Force& force, FILE* log ){
         }    
     }
 
-    if( forceCopy != NULL ){
+    if( forceCopy == NULL ){
 
         try {
            const AmoebaTorsionTorsionForce& castForce = dynamic_cast<const AmoebaTorsionTorsionForce&>(force);
@@ -2130,7 +2129,7 @@ static void copySystem( const System& inputSystem, System& systemCopy, FILE* log
 
     // add particle/mass
 
-    for( unsigned int ii = 0; ii < inputSystem.getNumParticles(); ii++ ){
+    for( unsigned int ii = 0; ii < static_cast<unsigned int>(inputSystem.getNumParticles()); ii++ ){
         systemCopy.addParticle( inputSystem.getParticleMass( static_cast<int>(ii) ) );
     }
 
@@ -2144,8 +2143,7 @@ static void copySystem( const System& inputSystem, System& systemCopy, FILE* log
 
     // copy constraints
 
-    for( unsigned int ii = 0; ii < inputSystem.getNumConstraints(); ii++ ){
-        int index;
+    for( unsigned int ii = 0; ii < static_cast<unsigned int>(inputSystem.getNumConstraints()); ii++ ){
         int particle1, particle2;
         double distance;
         inputSystem.getConstraintParameters( ii, particle1, particle2, distance);
@@ -2154,7 +2152,7 @@ static void copySystem( const System& inputSystem, System& systemCopy, FILE* log
 
     // copy forces
 
-    for( unsigned int ii = 0; ii < inputSystem.getNumForces(); ii++ ){
+    for( unsigned int ii = 0; ii < static_cast<unsigned int>(inputSystem.getNumForces()); ii++ ){
         systemCopy.addForce( copyForce( inputSystem.getForce(ii), log) );
     }
 
@@ -3361,8 +3359,8 @@ int main() {
 #endif
 
         DoubleVector numberOfMolecules;
-//        numberOfMolecules.push_back( 10 );
-//        numberOfMolecules.push_back( 100 );
+        numberOfMolecules.push_back( 10 );
+        numberOfMolecules.push_back( 100 );
         numberOfMolecules.push_back( 1000 );
         numberOfMolecules.push_back( 2000 );
         numberOfMolecules.push_back( 4000 );

plugins/amoeba/platforms/cuda/src/kernels/amoebaCudaGpu.cpp

@@ -1161,6 +1161,11 @@ static void testAmoebaTorsionTorsionGridLookup( amoebaGpuContext amoebaGpu, floa
     values[i++]   = grids[index++];
 }
 
+#if defined(_MSC_VER)
+#pragma warning(push)
+#pragma warning(disable: 4297)
+#endif
+
 extern "C"
 void gpuSetAmoebaTorsionTorsionGrids(amoebaGpuContext amoebaGpu, const std::vector< std::vector< std::vector< std::vector<float> > > >& floatGrids )
 {
@@ -1176,7 +1181,6 @@ void gpuSetAmoebaTorsionTorsionGrids(amoebaGpuContext amoebaGpu, const std::vect
         throw OpenMM::OpenMMException( message.str() );
     }
 
-    // 4 (grids) * (25 *25 grid)*(2 +4 a1, a2, f, f1,f2, f12) = 15000
 
     // assumming uniform spacing of grid angle values, set offset in to memory, beginning angle, angle spacing (delta), 
     // and number of y-angles
@@ -1779,7 +1783,7 @@ void gpuSetAmoebaMultipoleParameters(amoebaGpuContext amoebaGpu, const std::vect
     int maxTorqueBufferIndex         = 0;
 
     int chargeSize                   = static_cast<int>(charges.size());
-    for( int ii = 0; ii < chargeSize; ii++ ){
+    for( unsigned int ii = 0; ii < static_cast<unsigned int>(chargeSize); ii++ ){
 
         // axis type & multipole particles ids
  
@@ -2106,7 +2110,7 @@ void gpuSetAmoebaObcParameters( amoebaGpuContext amoebaGpu, float innerDielectri
     }    
 
     // Dummy out extra particles data
-    for (unsigned int i = particles; i < paddedNumberOfAtoms; i++) 
+    for (unsigned int i = particles; i < static_cast<unsigned int>(paddedNumberOfAtoms); i++) 
     {    
         (*gpu->psBornRadii)[i]     = 0.2f;
         (*gpu->psObcData)[i].x     = 0.01f;
@@ -2171,7 +2175,7 @@ void gpuSetAmoebaGrycukParameters( amoebaGpuContext amoebaGpu, float innerDielec
 
     // Dummy out extra particles data
 
-    for (unsigned int i = particles; i < paddedNumberOfAtoms; i++) 
+    for (unsigned int i = particles; i < static_cast<unsigned int>(paddedNumberOfAtoms); i++) 
     {    
         (*gpu->psBornRadii)[i]     = 0.2f;
         (*gpu->psObcData)[i].x     = 0.01f;
@@ -2398,7 +2402,7 @@ void gpuSetAmoebaVdwParameters( amoebaGpuContext amoebaGpu,
     psAmoebaVdwReduction->Upload();
 
     amoebaGpu->vdwExclusions.resize( gpu->natoms );
-    for( unsigned int ii = 0; ii < gpu->natoms; ii++ ){
+    for( unsigned int ii = 0; ii < static_cast<unsigned int>(gpu->natoms); ii++ ){
         for (unsigned int jj = 0; jj < allExclusions[ii].size(); jj++){ 
             amoebaGpu->vdwExclusions[ii].push_back( allExclusions[ii][jj] );
         }
@@ -2411,7 +2415,7 @@ void gpuSetAmoebaVdwParameters( amoebaGpuContext amoebaGpu,
         (void) fprintf( amoebaGpu->log, "%s particles=%d numberOfNonReductions=%d numberOfReductionsi=%d\n",
                         methodName, particles, numberOfNonReductions, numberOfReductions );
 #ifdef PARAMETER_PRINT
-        for( unsigned int ii = 0; ii < gpu->natoms; ii++ ){    
+        for( unsigned int ii = 0; ii < static_cast<unsigned int>(gpu->natoms); ii++ ){    
             (void) fprintf( amoebaGpu->log, "%5u %15.7e %15.7e %15.7e Ex[", ii, sigmas[ii], epsilons[ii], reductionFactors[ii] );
             for( unsigned int jj = 0; jj < allExclusions[ii].size(); jj++ ){ 
                 (void) fprintf( amoebaGpu->log, "%6d ", allExclusions[ii][jj] );
@@ -2850,7 +2854,7 @@ void gpuSetAmoebaWcaDispersionParameters( amoebaGpuContext amoebaGpu,
     
     // Dummy out extra particles data
 
-    for (unsigned int ii = particles; ii < paddedNumberOfAtoms; ii++) 
+    for (unsigned int ii = particles; ii < static_cast<unsigned int>(paddedNumberOfAtoms); ii++) 
     {    
         amoebaGpu->psWcaDispersionRadiusEpsilon->_pSysData[ii].x     = 1.0f;
         amoebaGpu->psWcaDispersionRadiusEpsilon->_pSysData[ii].y     = 0.0f;
@@ -2870,7 +2874,7 @@ void gpuSetAmoebaWcaDispersionParameters( amoebaGpuContext amoebaGpu,
         (void) fprintf( amoebaGpu->log, "%s particles=%u total max dispersion energy=%14.5e eps[%14.5e %14.5e] rmin[%14.5e %14.5e] awtr=%14.5e shctd=%14.5e dispoff=%14.5e\n",
                         methodName, static_cast<unsigned int>(radii.size()), totalMaxWcaDispersionEnergy, epso, epsh, rmino, rminh, awater, shctd, dispoff );
 #ifdef PARAMETER_PRINT
-        for( unsigned int ii = 0; ii < gpu->natoms; ii++ ){    
+        for( unsigned int ii = 0; ii < static_cast<unsigned int>(gpu->natoms); ii++ ){    
             (void) fprintf( amoebaGpu->log, "%5u %15.7e %15.7e\n", ii, radii[ii], epsilons[ii] );
             if( ii == maxPrint && ii < (paddedNumberOfAtoms - maxPrint) ){
                 (void) fprintf( amoebaGpu->log, "\n" );
@@ -3089,7 +3093,7 @@ void amoebaGpuBuildOutputBuffers( amoebaGpuContext amoebaGpu, int hasAmoebaGener
     // use the Cuda force output buffers for mapping torques onto forces, if max torque buffer count < number of buffers
 
      amoebaGpu->amoebaSim.maxTorqueBufferIndex++;
-    if( amoebaGpu->amoebaSim.maxTorqueBufferIndex > outputBuffers ){
+    if( static_cast<unsigned int>(amoebaGpu->amoebaSim.maxTorqueBufferIndex) > outputBuffers ){
         amoebaGpu->psTorqueMapForce4            = new CUDAStream<float4>(paddedNumberOfAtoms, amoebaGpu->amoebaSim.maxTorqueBufferIndex, "torqueMapForce");
         amoebaGpu->torqueMapForce4Delete        = 1;
     } else {
@@ -4714,7 +4718,7 @@ void initializeCudaFloatArray( int numberOfParticles, int entriesPerParticle,
 void zeroCUDAStreamFloat4( CUDAStream<float4>* streamToCopy )
 {
     for( unsigned int ii = 0; ii < streamToCopy->_stride; ii++ ){
-        for( int jj = 0; jj < streamToCopy->_subStreams; jj++ ){
+        for( unsigned int jj = 0; jj < streamToCopy->_subStreams; jj++ ){
             streamToCopy->_pSysStream[jj][ii].x = 0.0f;
             streamToCopy->_pSysStream[jj][ii].y = 0.0f;
             streamToCopy->_pSysStream[jj][ii].z = 0.0f;
@@ -4743,7 +4747,7 @@ void reduceAndCopyCUDAStreamFloat4( CUDAStream<float4>* streamToCopy, CUDAStream
         outputStream->_pSysData[indexOffset]    = streamToCopy->_pSysStream[0][ii].x;
         outputStream->_pSysData[indexOffset+1]  = streamToCopy->_pSysStream[0][ii].y;
         outputStream->_pSysData[indexOffset+2]  = streamToCopy->_pSysStream[0][ii].z;
-        for( int jj = 1; jj < streamToCopy->_subStreams; jj++ ){
+        for( unsigned int jj = 1; jj < streamToCopy->_subStreams; jj++ ){
             if(  streamToCopy->_pSysStream[jj][ii].x !=  streamToCopy->_pSysStream[jj][ii].x ||
                  streamToCopy->_pSysStream[jj][ii].y !=  streamToCopy->_pSysStream[jj][ii].y ||
                  streamToCopy->_pSysStream[jj][ii].z !=  streamToCopy->_pSysStream[jj][ii].z ){
@@ -4779,7 +4783,7 @@ void reduceAndCopyCUDAStreamFloat( CUDAStream<float>* streamToCopy, CUDAStream<f
     for( unsigned int ii = 0; ii < streamToCopy->_stride; ii++ ){
         outputStream->_pSysData[ii]    = streamToCopy->_pSysStream[0][ii];
 if( ii == 0 )(void) fprintf( stderr, "reduceAndCopyCUDAStreamFloat:%u %15.7e %u %u\n", ii, streamToCopy->_pSysStream[0][ii], streamToCopy->_stride, streamToCopy->_subStreams );
-        for( int jj = 1; jj < streamToCopy->_subStreams; jj++ ){
+        for( unsigned int jj = 1; jj < streamToCopy->_subStreams; jj++ ){
             if(  streamToCopy->_pSysStream[jj][ii] !=  streamToCopy->_pSysStream[jj][ii] ){
                 (void) fprintf( stderr, "Nan at particle=%d stream=%d\n", ii, jj );
             }
@@ -4828,3 +4832,8 @@ double getTimeOfDay( void ){
 #endif
 }
 
+#if defined(_MSC_VER)
+#pragma warning(pop)
+#endif
+
+    // 4 (grids) * (25 *25 grid)*(2 +4 a1, a2, f, f1,f2, f12) = 15000

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

@@ -439,7 +439,7 @@ void testOneOutOfPlaneBend2( FILE* log, int setId ) {
     Context context(system, integrator, Platform::getPlatformByName( "Reference"));
     std::vector<Vec3> positions(numberOfParticles);
 
-    for( unsigned int ii = 0; ii < numberOfParticles; ii++ ){
+    for( unsigned int ii = 0; ii < static_cast<unsigned int>(numberOfParticles); ii++ ){
         if( coordinates.find( particleIndices[ii] ) == coordinates.end() ){
 #ifdef AMOEBA_DEBUG
             if( log ){
@@ -480,7 +480,7 @@ void testOneOutOfPlaneBend2( FILE* log, int setId ) {
     computeAmoebaOutOfPlaneBendForce( 0, positions, *amoebaOutOfPlaneBendForce, forces, &energy, log );
 
     totalEnergy += energy;
-    for( unsigned int ii = 0; ii < numberOfParticles; ii++ ){
+    for( unsigned int ii = 0; ii < static_cast<unsigned int>(numberOfParticles); ii++ ){
         for( unsigned int jj = 0; jj < 3; jj++ ){
             totalForces[particleIndices[ii]][jj] += forces[ii][jj]; 
         }

plugins/amoeba/serialization/src/AmoebaGeneralizedKirkwoodForceProxy.cpp

@@ -53,7 +53,7 @@ void AmoebaGeneralizedKirkwoodForceProxy::serialize(const void* object, Serializ
     node.setIntProperty(   "GeneralizedKirkwoodIncludeCavityTerm", force.getIncludeCavityTerm() );
 
     SerializationNode& particles = node.createChildNode("GeneralizedKirkwoodParticles").setIntProperty( "size", force.getNumParticles() );
-    for (unsigned int ii = 0; ii < force.getNumParticles(); ii++) {
+    for (unsigned int ii = 0; ii < static_cast<unsigned int>(force.getNumParticles()); ii++) {
         double radius, charge, scalingFactor;
         force.getParticleParameters( ii, charge, radius, scalingFactor );
         particles.createChildNode("Particle").setIntProperty("index", ii).setDoubleProperty("charge", charge).setDoubleProperty("radius", radius).setDoubleProperty("scaleFactor", scalingFactor);

plugins/amoeba/serialization/src/AmoebaHarmonicAngleForceProxy.cpp

@@ -52,7 +52,7 @@ void AmoebaHarmonicAngleForceProxy::serialize(const void* object, SerializationN
     node.setDoubleProperty("HarmonicAngleSextic",  force.getAmoebaGlobalHarmonicAngleSextic());
 
     SerializationNode& bonds = node.createChildNode("Angles").setIntProperty( "size", force.getNumAngles() );
-    for (unsigned int ii = 0; ii < force.getNumAngles(); ii++) {
+    for (unsigned int ii = 0; ii < static_cast<unsigned int>(force.getNumAngles()); ii++) {
         int particle1, particle2, particle3;
         double distance, k;
         force.getAngleParameters(ii, particle1, particle2, particle3, distance, k);

plugins/amoeba/serialization/src/AmoebaHarmonicBondForceProxy.cpp

@@ -49,7 +49,7 @@ void AmoebaHarmonicBondForceProxy::serialize(const void* object, SerializationNo
     node.setDoubleProperty("HarmonicBondQuartic", force.getAmoebaGlobalHarmonicBondQuartic());
 
     SerializationNode& bonds = node.createChildNode("Bonds").setIntProperty( "size", force.getNumBonds() );
-    for (unsigned int ii = 0; ii < force.getNumBonds(); ii++) {
+    for (unsigned int ii = 0; ii < static_cast<unsigned int>(force.getNumBonds()); ii++) {
         int particle1, particle2;
         double distance, k;
         force.getBondParameters(ii, particle1, particle2, distance, k);

plugins/amoeba/serialization/src/AmoebaHarmonicInPlaneAngleForceProxy.cpp

@@ -52,7 +52,7 @@ void AmoebaHarmonicInPlaneAngleForceProxy::serialize(const void* object, Seriali
     node.setDoubleProperty("HarmonicInPlaneAngleSextic",     force.getAmoebaGlobalHarmonicInPlaneAngleSextic());
 
     SerializationNode& bonds = node.createChildNode("InPlaneAngles").setIntProperty( "size", force.getNumAngles() );
-    for ( unsigned int ii = 0; ii < force.getNumAngles(); ii++) {
+    for ( unsigned int ii = 0; ii < static_cast<unsigned int>(force.getNumAngles()); ii++) {
         int particle1, particle2, particle3, particle4;
         double distance, k;
         force.getAngleParameters(ii, particle1, particle2, particle3, particle4, distance, k);

plugins/amoeba/serialization/src/AmoebaMultipoleForceProxy.cpp

@@ -94,7 +94,7 @@ void AmoebaMultipoleForceProxy::serialize(const void* object, SerializationNode&
     getCovalentTypes( covalentTypes );
 
     SerializationNode& particles = node.createChildNode("MultipoleParticles").setIntProperty( "size", force.getNumMultipoles() );
-    for (unsigned int ii = 0; ii < force.getNumMultipoles(); ii++) {
+    for (unsigned int ii = 0; ii < static_cast<unsigned int>(force.getNumMultipoles()); ii++) {
 
         int axisType, multipoleAtomZ, multipoleAtomX, multipoleAtomY;
         double charge, thole, dampingFactor, polarity;

plugins/amoeba/serialization/src/AmoebaOutOfPlaneBendForceProxy.cpp

@@ -50,7 +50,7 @@ void AmoebaOutOfPlaneBendForceProxy::serialize(const void* object, Serialization
     node.setDoubleProperty("OutOfPlaneBendSextic",  force.getAmoebaGlobalOutOfPlaneBendSextic());
 
     SerializationNode& bonds = node.createChildNode("OutOfPlaneBend").setIntProperty( "size", force.getNumOutOfPlaneBends() );
-    for (unsigned int ii = 0; ii < force.getNumOutOfPlaneBends(); ii++) {
+    for (unsigned int ii = 0; ii < static_cast<unsigned int>(force.getNumOutOfPlaneBends()); ii++) {
         int particle1, particle2, particle3, particle4;
         double k;
         force.getOutOfPlaneBendParameters(ii, particle1, particle2, particle3, particle4, k);

plugins/amoeba/serialization/src/AmoebaPiTorsionForceProxy.cpp

@@ -45,7 +45,7 @@ void AmoebaPiTorsionForceProxy::serialize(const void* object, SerializationNode&
     node.setIntProperty("version", 1);
     const AmoebaPiTorsionForce& force = *reinterpret_cast<const AmoebaPiTorsionForce*>(object);
     SerializationNode& bonds = node.createChildNode("PiTorsion").setIntProperty( "size", force.getNumPiTorsions() );
-    for ( unsigned int ii = 0; ii < force.getNumPiTorsions(); ii++) {
+    for ( unsigned int ii = 0; ii < static_cast<unsigned int>(force.getNumPiTorsions()); ii++) {
         int particle1, particle2, particle3, particle4, particle5, particle6;
         double k;
         force.getPiTorsionParameters(ii, particle1, particle2, particle3, particle4, particle5, particle6, k);

plugins/amoeba/serialization/src/AmoebaStretchBendForceProxy.cpp

@@ -45,7 +45,7 @@ void AmoebaStretchBendForceProxy::serialize(const void* object, SerializationNod
     node.setIntProperty("version", 1);
     const AmoebaStretchBendForce& force = *reinterpret_cast<const AmoebaStretchBendForce*>(object);
     SerializationNode& bonds = node.createChildNode("StretchBendAngles").setIntProperty( "size", force.getNumStretchBends() );
-    for (unsigned int ii = 0; ii < force.getNumStretchBends(); ii++) {
+    for (unsigned int ii = 0; ii < static_cast<unsigned int>(force.getNumStretchBends()); ii++) {
         int particle1, particle2, particle3;
         double distanceAB, distanceCB, angle, k;
         force.getStretchBendParameters(ii, particle1, particle2, particle3, distanceAB, distanceCB, angle, k);

plugins/amoeba/serialization/src/AmoebaTorsionForceProxy.cpp

@@ -50,7 +50,7 @@ static void addTorsionValues( SerializationNode& torsion, const std::vector<doub
 static void loadTorsionValues( SerializationNode& torsion, std::vector<double>& torsionValues ){
     int size = torsion.getIntProperty("size");
     torsionValues.resize(size);
-    for (unsigned int jj = 0; jj < size; jj++) {
+    for (unsigned int jj = 0; jj < static_cast<unsigned int>(size); jj++) {
         torsionValues[jj] = ( torsion.getChildren()[jj].getDoubleProperty("v") );
     }
 }
@@ -60,7 +60,7 @@ void AmoebaTorsionForceProxy::serialize(const void* object, SerializationNode& n
     const AmoebaTorsionForce& force = *reinterpret_cast<const AmoebaTorsionForce*>(object);
 
     SerializationNode& bonds = node.createChildNode("Torsion").setIntProperty("size",  force.getNumTorsions() );
-    for (unsigned int ii = 0; ii < force.getNumTorsions(); ii++) {
+    for (unsigned int ii = 0; ii < static_cast<unsigned int>(force.getNumTorsions()); ii++) {
 
         int particle1, particle2, particle3, particle4;
         std::vector<double> torsion1;

plugins/amoeba/serialization/src/AmoebaTorsionTorsionForceProxy.cpp

@@ -77,7 +77,7 @@ void AmoebaTorsionTorsionForceProxy::serialize(const void* object, Serialization
 
     SerializationNode& grids = node.createChildNode("TorsionTorsionGrids");
     grids.setIntProperty("size", static_cast<int>(force.getNumTorsionTorsionGrids()));
-    for (unsigned int kk = 0; kk < force.getNumTorsionTorsionGrids(); kk++) {
+    for (unsigned int kk = 0; kk < static_cast<unsigned int>(force.getNumTorsionTorsionGrids()); kk++) {
 
         const std::vector< std::vector< std::vector<double> > > grid = force.getTorsionTorsionGrid( kk );
 
@@ -107,7 +107,7 @@ void AmoebaTorsionTorsionForceProxy::serialize(const void* object, Serialization
     }
 
     SerializationNode& bonds = node.createChildNode("TorsionTorsion");
-    for (unsigned int ii = 0; ii < force.getNumTorsionTorsions(); ii++) {
+    for (unsigned int ii = 0; ii < static_cast<unsigned int>(force.getNumTorsionTorsions()); ii++) {
         int particle1, particle2, particle3, particle4, particle5;
         int chiralCheckAtomIndex, gridIndex;
         force.getTorsionTorsionParameters(ii, particle1, particle2, particle3, particle4, particle5, chiralCheckAtomIndex, gridIndex );

plugins/amoeba/serialization/src/AmoebaUreyBradleyForceProxy.cpp

@@ -49,7 +49,7 @@ void AmoebaUreyBradleyForceProxy::serialize(const void* object, SerializationNod
     node.setDoubleProperty("UreyBradleyQuartic", force.getAmoebaGlobalUreyBradleyQuartic());
 
     SerializationNode& bonds = node.createChildNode("UreyBradley").setIntProperty( "size", force.getNumInteractions() );
-    for (unsigned int ii = 0; ii < force.getNumInteractions(); ii++) {
+    for (unsigned int ii = 0; ii < static_cast<unsigned int>(force.getNumInteractions()); ii++) {
         int particle1, particle2;
         double distance, k;
         force.getUreyBradleyParameters(ii, particle1, particle2, distance, k);

plugins/amoeba/serialization/src/AmoebaVdwForceProxy.cpp

@@ -53,7 +53,7 @@ void AmoebaVdwForceProxy::serialize(const void* object, SerializationNode& node)
     node.setIntProperty(   "VdwPBC",                 force.getPBC());
 
     SerializationNode& particles = node.createChildNode("VdwParticles").setIntProperty("size", force.getNumParticles() );
-    for (unsigned int ii = 0; ii < force.getNumParticles(); ii++) {
+    for (unsigned int ii = 0; ii < static_cast<unsigned int>(force.getNumParticles()); ii++) {
 
         int ivIndex, classIndex;
         double sigma, epsilon, reductionFactor;

plugins/amoeba/serialization/src/AmoebaWcaDispersionForceProxy.cpp

@@ -54,7 +54,7 @@ void AmoebaWcaDispersionForceProxy::serialize(const void* object, SerializationN
     node.setDoubleProperty("Slevy",   force.getSlevy());
 
     SerializationNode& particles = node.createChildNode("WcaDispersionParticles").setIntProperty( "size", force.getNumParticles() );
-    for (unsigned int ii = 0; ii < force.getNumParticles(); ii++) {
+    for (unsigned int ii = 0; ii < static_cast<unsigned int>(force.getNumParticles()); ii++) {
         double radius, epsilon;
         force.getParticleParameters( ii,  radius, epsilon );
         particles.createChildNode("Particle").setIntProperty("index", ii).setDoubleProperty("radius", radius).setDoubleProperty("epsilon", epsilon);