Edits to remove some VC9 warnings

plugins/amoeba/serialization/tests/TestSerializeAmoebaGeneralizedKirkwoodForce.cpp

@@ -77,7 +77,7 @@ void testSerialization() {
     ASSERT_EQUAL(force1.getIncludeCavityTerm(),    force2.getIncludeCavityTerm());
 
     ASSERT_EQUAL(force1.getNumParticles(), force2.getNumParticles());
-    for (unsigned int ii = 0; ii < force1.getNumParticles(); ii++) {
+    for (unsigned int ii = 0; ii < static_cast<unsigned int>(force1.getNumParticles()); ii++) {
 
         double radius1, charge1, scaleFactor1;
         double radius2, charge2, scaleFactor2;

plugins/amoeba/serialization/tests/TestSerializeAmoebaHarmonicAngleForce.cpp

@@ -64,7 +64,7 @@ void testSerialization() {
     ASSERT_EQUAL(force1.getAmoebaGlobalHarmonicAnglePentic(),  force2.getAmoebaGlobalHarmonicAnglePentic());
     ASSERT_EQUAL(force1.getAmoebaGlobalHarmonicAngleSextic(),  force2.getAmoebaGlobalHarmonicAngleSextic());
     ASSERT_EQUAL(force1.getNumAngles(),                        force2.getNumAngles());
-    for (unsigned int ii = 0; ii < force1.getNumAngles(); ii++) {
+    for (unsigned int ii = 0; ii < static_cast<unsigned int>(force1.getNumAngles()); ii++) {
         int a1, a2, a3, b1, b2, b3;
         double da, db, ka, kb;
         force1.getAngleParameters(ii, a1, a2, a3, da, ka);

plugins/amoeba/serialization/tests/TestSerializeAmoebaHarmonicBondForce.cpp

@@ -60,7 +60,7 @@ void testSerialization() {
     ASSERT_EQUAL(force1.getAmoebaGlobalHarmonicBondCubic(), force2.getAmoebaGlobalHarmonicBondCubic());
     ASSERT_EQUAL(force1.getAmoebaGlobalHarmonicBondQuartic(), force2.getAmoebaGlobalHarmonicBondQuartic());
     ASSERT_EQUAL(force1.getNumBonds(), force2.getNumBonds());
-    for (unsigned int ii = 0; ii < force1.getNumBonds(); ii++) {
+    for (unsigned int ii = 0; ii < static_cast<unsigned int>(force1.getNumBonds()); ii++) {
         int a1, a2, b1, b2;
         double da, db, ka, kb;
         force1.getBondParameters(ii, a1, a2, da, ka);

plugins/amoeba/serialization/tests/TestSerializeAmoebaHarmonicInPlaneAngleForce.cpp

@@ -68,7 +68,7 @@ void testSerialization() {
     ASSERT_EQUAL(force1.getAmoebaGlobalHarmonicInPlaneAngleSextic(),   force2.getAmoebaGlobalHarmonicInPlaneAngleSextic());
     ASSERT_EQUAL(force1.getNumAngles(),                                force2.getNumAngles());
 
-    for ( unsigned int ii = 0; ii < force1.getNumAngles(); ii++) {
+    for ( unsigned int ii = 0; ii < static_cast<unsigned int>(force1.getNumAngles()); ii++) {
         int a1, a2, a3, a4, b1, b2, b3, b4;
         double da, db, ka, kb;
         force1.getAngleParameters(ii, a1, a2, a3, a4, da, ka);

plugins/amoeba/serialization/tests/TestSerializeAmoebaMultipoleForce.cpp

@@ -130,7 +130,7 @@ void testSerialization() {
     }
     
     ASSERT_EQUAL(force1.getNumMultipoles(),  force2.getNumMultipoles());
-    for (unsigned int ii = 0; ii < force1.getNumMultipoles(); ii++) {
+    for (unsigned int ii = 0; ii < static_cast<unsigned int>(force1.getNumMultipoles()); ii++) {
 
         int axisType1, multipoleAtomZ1, multipoleAtomX1, multipoleAtomY1;
         int axisType2, multipoleAtomZ2, multipoleAtomX2, multipoleAtomY2;

plugins/amoeba/serialization/tests/TestSerializeAmoebaOutOfPlaneBendForce.cpp

@@ -68,7 +68,7 @@ void testSerialization() {
     ASSERT_EQUAL(force1.getAmoebaGlobalOutOfPlaneBendSextic(), force2.getAmoebaGlobalOutOfPlaneBendSextic());
     ASSERT_EQUAL(force1.getNumOutOfPlaneBends(), force2.getNumOutOfPlaneBends());
 
-    for (unsigned int ii = 0; ii < force1.getNumOutOfPlaneBends(); ii++) {
+    for (unsigned int ii = 0; ii < static_cast<unsigned int>(force1.getNumOutOfPlaneBends()); ii++) {
         int a1, a2, a3, a4, b1, b2, b3, b4;
         double ka, kb;
         force1.getOutOfPlaneBendParameters(ii, a1, a2, a3, a4, ka);

plugins/amoeba/serialization/tests/TestSerializeAmoebaPiTorsionForce.cpp

@@ -56,7 +56,7 @@ void testSerialization() {
     // Compare the two forces to see if they are identical.  
     AmoebaPiTorsionForce& force2 = *copy;
     ASSERT_EQUAL(force1.getNumPiTorsions(), force2.getNumPiTorsions());
-    for (unsigned int ii = 0; ii < force1.getNumPiTorsions(); ii++) {
+    for (unsigned int ii = 0; ii < static_cast<unsigned int>(force1.getNumPiTorsions()); ii++) {
         int a1, a2, a3, a4, a5, a6, b1, b2, b3, b4, b5, b6;
         double ka, kb;
         force1.getPiTorsionParameters(ii, a1, a2, a3, a4, a5, a6, ka);

plugins/amoeba/serialization/tests/TestSerializeAmoebaStretchBendForce.cpp

@@ -55,7 +55,7 @@ void testSerialization() {
     // Compare the two forces to see if they are identical.  
     AmoebaStretchBendForce& force2 = *copy;
     ASSERT_EQUAL(force1.getNumStretchBends(), force2.getNumStretchBends());
-    for (unsigned int ii = 0; ii < force1.getNumStretchBends(); ii++) {
+    for (unsigned int ii = 0; ii < static_cast<unsigned int>(force1.getNumStretchBends()); ii++) {
         int p11, p12, p13;
         int p21, p22, p23;
         double dAB1, dAB2;

plugins/amoeba/serialization/tests/TestSerializeAmoebaTorsionForce.cpp

@@ -85,7 +85,7 @@ void testSerialization() {
     // Compare the two forces to see if they are identical.  
     AmoebaTorsionForce& force2 = *copy;
     ASSERT_EQUAL(force1.getNumTorsions(), force2.getNumTorsions());
-    for (unsigned int ii = 0; ii < force1.getNumTorsions(); ii++) {
+    for (unsigned int ii = 0; ii < static_cast<unsigned int>(force1.getNumTorsions()); ii++) {
 
         int a1, a2, a3, a4, b1, b2, b3, b4;
 

plugins/amoeba/serialization/tests/TestSerializeAmoebaTorsionTorsionForce.cpp

@@ -64,9 +64,9 @@ static void compareGrids( const std::vector< std::vector< std::vector<double> >
     ASSERT_EQUAL(grid1.size(), grid2.size());
     for (unsigned int ii = 0; ii < grid1.size(); ii++) {
         ASSERT_EQUAL(grid1[ii].size(), grid2[ii].size());
-        for (int jj = 0; jj < grid1[ii].size(); jj++) {
+        for (unsigned int jj = 0; jj < grid1[ii].size(); jj++) {
             ASSERT_EQUAL(grid1[ii][jj].size(), grid2[ii][jj].size());
-            for (int kk = 0; kk < grid1[ii][jj].size(); kk++) {
+            for (unsigned int kk = 0; kk < grid1[ii][jj].size(); kk++) {
                 ASSERT_EQUAL(grid1[ii][jj][kk], grid2[ii][jj][kk]);
             }
         }
@@ -105,7 +105,7 @@ void testSerialization() {
 
     AmoebaTorsionTorsionForce & force2 = *copy;
     ASSERT_EQUAL(force1.getNumTorsionTorsions(), force2.getNumTorsionTorsions());
-    for (unsigned int ii = 0; ii < force1.getNumTorsionTorsions(); ii++) {
+    for (unsigned int ii = 0; ii < static_cast<unsigned int>(force1.getNumTorsionTorsions()); ii++) {
 
         int a1, a2, a3, a4, a5, aChiral, aGridIndex, b1, b2, b3, b4, b5, bChiral, bGridIndex;
 
@@ -122,7 +122,7 @@ void testSerialization() {
     }
 
     ASSERT_EQUAL(force1.getNumTorsionTorsionGrids(), force2.getNumTorsionTorsionGrids());
-    for (unsigned int ii = 0; ii < force1.getNumTorsionTorsionGrids(); ii++) {
+    for (unsigned int ii = 0; ii < static_cast<unsigned int>(force1.getNumTorsionTorsionGrids()); ii++) {
         const std::vector< std::vector< std::vector<double> > >& grid1 = force1.getTorsionTorsionGrid( ii );
         const std::vector< std::vector< std::vector<double> > >& grid2 = force2.getTorsionTorsionGrid( ii );
         compareGrids(grid1, grid2 );

plugins/amoeba/serialization/tests/TestSerializeAmoebaUreyBradleyForce.cpp

@@ -60,7 +60,7 @@ void testSerialization() {
     ASSERT_EQUAL(force1.getAmoebaGlobalUreyBradleyCubic(), force2.getAmoebaGlobalUreyBradleyCubic());
     ASSERT_EQUAL(force1.getAmoebaGlobalUreyBradleyQuartic(), force2.getAmoebaGlobalUreyBradleyQuartic());
     ASSERT_EQUAL(force1.getNumInteractions(), force2.getNumInteractions());
-    for (unsigned int ii = 0; ii < force1.getNumInteractions(); ii++) {
+    for (unsigned int ii = 0; ii < static_cast<unsigned int>(force1.getNumInteractions()); ii++) {
         int a1, a2, b1, b2;
         double da, db, ka, kb;
 

plugins/amoeba/serialization/tests/TestSerializeAmoebaVdwForce.cpp

@@ -84,7 +84,7 @@ void testSerialization() {
 
     ASSERT_EQUAL(force1.getNumParticles(),          force2.getNumParticles());
 
-    for (unsigned int ii = 0; ii < force1.getNumParticles(); ii++) {
+    for (unsigned int ii = 0; ii < static_cast<unsigned int>(force1.getNumParticles()); ii++) {
 
         int ivIndex1, classIndex1;
         int ivIndex2, classIndex2;
@@ -101,7 +101,7 @@ void testSerialization() {
         ASSERT_EQUAL(epsilon1,          epsilon2);
         ASSERT_EQUAL(reductionFactor1,  reductionFactor2);
     }
-    for (unsigned int ii = 0; ii < force1.getNumParticles(); ii++) {
+    for (unsigned int ii = 0; ii < static_cast<unsigned int>(force1.getNumParticles()); ii++) {
 
         std::vector< int > exclusions1;
         std::vector< int > exclusions2;

plugins/amoeba/serialization/tests/TestSerializeAmoebaWcaDispersionForce.cpp

@@ -83,7 +83,7 @@ void testSerialization() {
     ASSERT_EQUAL(force1.getSlevy(),   force2.getSlevy());
 
     ASSERT_EQUAL(force1.getNumParticles(), force2.getNumParticles());
-    for (unsigned int ii = 0; ii < force1.getNumParticles(); ii++) {
+    for (unsigned int ii = 0; ii < static_cast<unsigned int>(force1.getNumParticles()); ii++) {
 
         double radius1, epsilon1;
         double radius2, epsilon2;

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

@@ -356,8 +356,8 @@ void CudaFreeEnergyCalcNonbondedSoftcoreForceKernel::initialize(const System& sy
         for (int i = 0; i < numExceptions; i++) {
             double charge, sig, eps, softcoreLJLambda;
             force.getExceptionParameters(exceptions[i], particle1[i], particle2[i], charge, sig, eps, softcoreLJLambda);
-            c6[i]                    = static_cast<float>( (4.0f*eps*powf(sig, 6.0f)) );
-            c12[i]                   = static_cast<float>( (4.0f*eps*powf(sig, 12.0f)) );
+            c6[i]                    = static_cast<float>( (4.0*eps*pow(sig, 6.0)) );
+            c12[i]                   = static_cast<float>( (4.0*eps*pow(sig, 12.0)) );
             qProd[i]                 = static_cast<float>( charge );
             softcoreLJLambdaArray[i] = static_cast<float>( softcoreLJLambda );
         }

plugins/freeEnergy/platforms/cuda/src/kernels/freeEnergyCudaGpu.cpp

@@ -276,12 +276,17 @@ void freeEnergyGpuSetPeriodicBoxSize( freeEnergyGpuContext freeEnergyGpu, float
     gpuSetPeriodicBoxSize( freeEnergyGpu->gpuContext, xsize, ysize, zsize );
 }
 
+#if defined(_MSC_VER)
+#pragma warning(push)
+#pragma warning(disable: 4297)
+#endif
+
 extern "C"
 void gpuSetNonbondedSoftcoreParameters( freeEnergyGpuContext freeEnergyGpu, float epsfac, const std::vector<int>& atom, const std::vector<float>& c6,
                                         const std::vector<float>& c12, const std::vector<float>& q,
                                         const std::vector<float>& softcoreLJLambdaArray, const std::vector<char>& symbol,
                                         const std::vector<std::vector<int> >& exclusions, CudaFreeEnergyNonbondedMethod method,
-                                        float cutoffDistance, float solventDielectric ){
+                                        float cutoffDistance, float solventDielectric ) {
 
     unsigned int numberOfParticles                         = c6.size();
     gpuContext gpu                                         = freeEnergyGpu->gpuContext;
@@ -301,6 +306,10 @@ void gpuSetNonbondedSoftcoreParameters( freeEnergyGpuContext freeEnergyGpu, floa
         throw OpenMM::OpenMMException( msg.str() );
     }
 
+#if defined(_MSC_VER)
+#pragma warning(pop)
+#endif
+
     freeEnergyGpu->freeEnergySim.epsfac                    = epsfac;
     freeEnergyGpu->freeEnergySim.nonbondedMethod           = method;
 
@@ -349,7 +358,7 @@ void gpuSetNonbondedSoftcoreParameters( freeEnergyGpuContext freeEnergyGpu, floa
 
     // Dummy out extra atom data
 
-    for( unsigned int ii = numberOfParticles; ii < paddedNumberOfAtoms; ii++ ){
+    for( int ii = numberOfParticles; ii < paddedNumberOfAtoms; ii++ ){
 
         (*freeEnergyGpu->psSigEps4)[ii].x              = 1.0f;
         (*freeEnergyGpu->psSigEps4)[ii].y              = 0.0f;
@@ -380,7 +389,7 @@ void gpuSetNonbondedSoftcoreParameters( freeEnergyGpuContext freeEnergyGpu, floa
         if( offset > 0 ){
             if( offset > numberOfParticles ){
                 (void) fprintf( freeEnergyGpu->log,"Dummy padded entries\n" );
-                for (unsigned int ii = offset; ii < paddedNumberOfAtoms; ii++){
+                for (int ii = offset; ii < paddedNumberOfAtoms; ii++){
                     (void) fprintf( freeEnergyGpu->log,"%6u sig[%14.7e %14.7e] lambda=%10.3f q=%10.3f\n",
                                     ii, 
                                     (*freeEnergyGpu->psSigEps4)[ii].x, (*freeEnergyGpu->psSigEps4)[ii].y, (*freeEnergyGpu->psSigEps4)[ii].z, (*freeEnergyGpu->psSigEps4)[ii].w );

plugins/freeEnergy/platforms/reference/src/gbsa/CpuGBVISoftcore.cpp

@@ -793,7 +793,7 @@ void CpuGBVISoftcore::printGbvi( const std::vector<OpenMM::RealVec>& atomCoordin
                     gbviParameters->getBornRadiusScalingSoftcoreMethod(), GBVISoftcoreParameters::QuinticSpline );
     (void) fprintf( log, "    preFactor      %15.7e)\n", preFactor );
  
-    for( unsigned int atomI = 0; atomI < numberOfAtoms; atomI++ ){
+    for( unsigned int atomI = 0; atomI < static_cast<unsigned int>(numberOfAtoms); atomI++ ){
         (void) fprintf( log, "%6d r=%15.7e rSc=%15.7e swd=%15.7e lmda=%4.2f tau*gam=%15.7e q=%15.7e", atomI,
                         atomicRadii[atomI],    
                         scaledRadii[atomI],    

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

@@ -419,9 +419,9 @@ 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));
             }
         }
@@ -486,7 +486,7 @@ 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++ ){
@@ -507,9 +507,9 @@ int PositionGenerator::setParticlesOnGrid( const Vec3& origin, const Vec3& boxDi
     // add molecule atoms
 
     Vec3 bondOffset( 0.05, 0.05, 0.05 );
-    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++ ){
             array[molecularIndex+jj] = array[molecularIndex] + bondOffset + Vec3(_bondDistance*genrand_real2(sfmt), _bondDistance*genrand_real2(sfmt), _bondDistance*genrand_real2(sfmt));
         }
     }
@@ -1321,7 +1321,7 @@ static NonbondedForce* copyNonbondedForce( const NonbondedForce& nonbondedForce
  
 static void copySystem( const System& inputSystem, System& systemCopy ){
 
-    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) ) );
     }
 
@@ -1331,8 +1331,7 @@ static void copySystem( const System& inputSystem, System& systemCopy ){
     inputSystem.getDefaultPeriodicBoxVectors( a, b, c );
     systemCopy.setDefaultPeriodicBoxVectors( a, b, c );
 
-    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);
@@ -1698,7 +1697,7 @@ static CustomNonbondedForce* buildCustomNonbondedSoftcoreForce(  const Nonbonded
     customNonbonded->addPerParticleParameter("lambda");
 
     vector<double> nonbondedParams(4);
-    for( unsigned int ii = 0; ii < nonbondedSoftcoreForce.getNumParticles(); ii++ ){
+    for( unsigned int ii = 0; ii < static_cast<unsigned int>(nonbondedSoftcoreForce.getNumParticles()); ii++ ){
 
         double charge;
         double sigma;
@@ -1751,7 +1750,7 @@ CustomBondForce* buildCustomBondForceForNonbondedExceptions( const NonbondedSoft
     customBond->addPerBondParameter("eps");
     customBond->addPerBondParameter("lambda");
 
-    for( unsigned int ii = 0; ii < nonbondedSoftcoreForce.getNumExceptions(); ii++ ){
+    for( unsigned int ii = 0; ii < static_cast<unsigned int>(nonbondedSoftcoreForce.getNumExceptions()); ii++ ){
 
         int particle1, particle2;
         double chargeProd;