Cleaned up for Windows compile

plugins/amoeba/platforms/reference/src/SimTKReference/AmoebaReferenceMultipoleForce.cpp

@@ -182,7 +182,7 @@ void AmoebaReferenceMultipoleForce::logRealOpenMMVectors( const std::string& hea
 }
 
 void AmoebaReferenceMultipoleForce::logParticleData( const std::string& header, const std::vector<MultipoleParticleData>& particleData,
-                                                     unsigned int printFlag, FILE* log, int maxPrint ) const {
+                                                     unsigned int printFlag, FILE* log, unsigned int maxPrint ) const {
 
     (void) fprintf( log, "%s", header.c_str() );
 
@@ -224,7 +224,7 @@ void AmoebaReferenceMultipoleForce::logParticleData( const std::string& header,
  */ 
 void AmoebaReferenceMultipoleForce::showScaleMapForParticle( unsigned int particleI, FILE* log ) const {
 
-    (void) fprintf( log, "Scale map particle %5u maxIndex=%d\n", particleI, _maxScaleIndex[particleI] );
+    (void) fprintf( log, "Scale map particle %5u maxIndex=%u\n", particleI, _maxScaleIndex[particleI] );
 
     std::string scaleNames[LAST_SCALE_TYPE_INDEX] = { "D", "P", "M" }; 
     for( unsigned int ii = 0; ii < _scaleMaps[particleI].size(); ii++ ){
@@ -269,7 +269,7 @@ void AmoebaReferenceMultipoleForce::setupScaleMaps( const std::vector< std::vect
         for( unsigned jj = 0; jj < AmoebaMultipoleForce::PolarizationCovalent11; jj++ ){
             const std::vector<int> covalentList    = covalentInfo[jj];
             for( unsigned int kk = 0; kk < covalentList.size(); kk++ ){
-                int covalentIndex                      = covalentList[kk];
+                unsigned int covalentIndex             = static_cast<unsigned int>(covalentList[kk]);
                 if( covalentIndex < ii )continue;
 
                 // handle 0.5 factor for p14
@@ -293,7 +293,7 @@ void AmoebaReferenceMultipoleForce::setupScaleMaps( const std::vector< std::vect
         for( unsigned jj = AmoebaMultipoleForce::PolarizationCovalent11; jj < covalentInfo.size(); jj++ ){
             const std::vector<int> covalentList = covalentInfo[jj];
             for( unsigned int kk = 0; kk < covalentList.size(); kk++ ){
-                int covalentIndex                      = covalentList[kk];
+                unsigned int covalentIndex             = static_cast<unsigned int>(covalentList[kk]);
                 if( covalentIndex < ii )continue;
                 _scaleMaps[ii][D_SCALE][covalentIndex] = _dScale[jj-4];
                 _scaleMaps[ii][U_SCALE][covalentIndex] = _uScale[jj-4];
@@ -802,7 +802,7 @@ fprintf( stderr, "MIb %3u eps=%15.7e %15.7e %15.7e\n", iteration, epsilonDirect,
             setMutualInducedDipoleConverged( true );
             done = true;
         }
-        if( currentEpsilon < epsilon || iteration >= getMaximumMutualInducedDipoleIterations() ){
+        if( currentEpsilon < epsilon || static_cast<int>(iteration) >= getMaximumMutualInducedDipoleIterations() ){
             done = true;
         }
         currentEpsilon = epsilon;
@@ -848,7 +848,7 @@ off2
 
     // ---------------------------------------------------------------------------------------
 
-    RealOpenMM e,ei,fgrp,gfd;
+    RealOpenMM e,ei;
     RealOpenMM damp,expdamp;
     RealOpenMM pdi,pti,pgamma;
     RealOpenMM scale3,scale3i;
@@ -858,26 +858,28 @@ off2
     RealOpenMM psc3,psc5,psc7;
     RealOpenMM dsc3,dsc5,dsc7;
     RealOpenMM xr,yr,zr;
-    RealOpenMM xix,yix,zix;
-    RealOpenMM xiy,yiy,ziy;
-    RealOpenMM xiz,yiz,ziz;
-    RealOpenMM xkx,ykx,zkx;
-    RealOpenMM xky,yky,zky;
-    RealOpenMM xkz,ykz,zkz;
+    //RealOpenMM xix,yix,zix;
+    //RealOpenMM xiy,yiy,ziy;
+    //RealOpenMM xiz,yiz,ziz;
+    //RealOpenMM xkx,ykx,zkx;
+    //RealOpenMM xky,yky,zky;
+    //RealOpenMM xkz,ykz,zkz;
     RealOpenMM r,r2,rr1,rr3;
     RealOpenMM rr5,rr7,rr9,rr11;
-    RealOpenMM vxx,vyy,vzz;
-    RealOpenMM vyx,vzx,vzy;
+    //RealOpenMM vxx,vyy,vzz;
+    //RealOpenMM vyx,vzx,vzy;
     RealOpenMM qi[10];
-    RealOpenMM ck,qk[10];
+    RealOpenMM qk[10];
+/*
     RealOpenMM frcxi[4],frcxk[4];
     RealOpenMM frcyi[4],frcyk[4];
     RealOpenMM frczi[4],frczk[4];
+*/
     RealOpenMM fridmp[4],findmp[4];
     RealOpenMM ftm2[4],ftm2i[4];
     RealOpenMM ttm2[4],ttm3[4];
     RealOpenMM ttm2i[4],ttm3i[4];
-    RealOpenMM dixdk[4],fdir[4];
+    RealOpenMM dixdk[4];
     RealOpenMM dixuk[4],dkxui[4];
     RealOpenMM dixukp[4],dkxuip[4];
     RealOpenMM uixqkr[4],ukxqir[4];
@@ -1499,7 +1501,7 @@ RealOpenMM AmoebaReferenceMultipoleForce::calculateNoCutoffElectrostatic( std::v
     return energy;
 }
 
-RealOpenMM AmoebaReferenceMultipoleForce::calculateNoCutoffForceAndEnergy( int numParticles,
+RealOpenMM AmoebaReferenceMultipoleForce::calculateNoCutoffForceAndEnergy( unsigned int numParticles,
                                                                            RealOpenMM** particlePositions, 
                                                                            const std::vector<RealOpenMM>& charges,
                                                                            const std::vector<RealOpenMM>& dipoles,
@@ -1613,7 +1615,7 @@ RealOpenMM AmoebaReferenceMultipoleForce::calculateForceAndEnergy( int numPartic
     setupScaleMaps( multipoleParticleCovalentInfo );
     if( getNonbondedMethod() == NoCutoff || 1 ){
 
-        return calculateNoCutoffForceAndEnergy( numParticles, particlePositions, charges, dipoles, quadrupoles, tholes, dampingFactors,
+        return calculateNoCutoffForceAndEnergy( static_cast<unsigned int>(numParticles), particlePositions, charges, dipoles, quadrupoles, tholes, dampingFactors,
                                                 polarity, axisTypes, multipoleAtomId1s, multipoleAtomId2s, forces );
 
 

plugins/amoeba/platforms/reference/src/SimTKReference/AmoebaReferenceMultipoleForce.h

@@ -245,7 +245,7 @@ private:
 
     enum ScaleType { D_SCALE, P_SCALE, M_SCALE, U_SCALE, LAST_SCALE_TYPE_INDEX };
     std::vector<  std::vector< MapIntRealOpenMM > > _scaleMaps;
-    std::vector<int> _maxScaleIndex;
+    std::vector<unsigned int> _maxScaleIndex;
     RealOpenMM _dScale[5];
     RealOpenMM _pScale[5];
     RealOpenMM _mScale[5];
@@ -362,7 +362,7 @@ private:
                                FILE* log = stderr, unsigned int itemsPerVector = 1, int maxPrint = -1 ) const;
 
     void logParticleData( const std::string& header, const std::vector<MultipoleParticleData>& particleData,
-                          unsigned int printFlag, FILE* log, int maxPrint ) const;
+                          unsigned int printFlag, FILE* log, unsigned int maxPrint ) const;
 
     void showScaleMapForParticle( unsigned int particleI, FILE* log ) const;
 
@@ -462,7 +462,7 @@ private:
     
        --------------------------------------------------------------------------------------- */
     
-    RealOpenMM calculateNoCutoffForceAndEnergy( int numParticles, RealOpenMM** particlePositions,
+    RealOpenMM calculateNoCutoffForceAndEnergy( unsigned int numParticles, RealOpenMM** particlePositions,
                                                 const std::vector<RealOpenMM>& charges,
                                                 const std::vector<RealOpenMM>& dipoles,
                                                 const std::vector<RealOpenMM>& quadrupoles,

plugins/amoeba/platforms/reference/src/SimTKReference/AmoebaReferenceOutOfPlaneBendForce.cpp

@@ -205,7 +205,7 @@ RealOpenMM AmoebaReferenceOutOfPlaneBendForce::calculateForceAndEnergy( int numO
                                                                        RealOpenMM angleSextic,
                                                                        RealOpenMM** forceData) const {
     RealOpenMM energy      = 0.0; 
-    for (unsigned int ii = 0; ii < numOutOfPlaneBends; ii++) {
+    for (unsigned int ii = 0; ii < static_cast<unsigned int>(numOutOfPlaneBends); ii++) {
         int particle1Index      = particle1[ii];
         int particle2Index      = particle2[ii];
         int particle3Index      = particle3[ii];

plugins/amoeba/platforms/reference/src/SimTKReference/AmoebaReferencePiTorsionForce.cpp

@@ -193,7 +193,7 @@ RealOpenMM AmoebaReferencePiTorsionForce::calculateForceAndEnergy( int numPiTors
                                                                    const std::vector<RealOpenMM>& kTorsion,
                                                                    RealOpenMM** forceData ) const {
     RealOpenMM energy  = 0.0; 
-    for (unsigned int ii = 0; ii < numPiTorsions; ii++) {
+    for (unsigned int ii = 0; ii < static_cast<unsigned int>(numPiTorsions); ii++) {
 
         int particle1Index      = particle1[ii];
         int particle2Index      = particle2[ii];

plugins/amoeba/platforms/reference/src/SimTKReference/AmoebaReferenceStretchBendForce.cpp

@@ -154,7 +154,7 @@ RealOpenMM AmoebaReferenceStretchBendForce::calculateForceAndEnergy( int numStre
                                                                        const std::vector<RealOpenMM>&  kQuadratic,
                                                                        RealOpenMM** forceData) const {
     RealOpenMM energy      = 0.0; 
-    for (unsigned int ii = 0; ii < numStretchBends; ii++) {
+    for (unsigned int ii = 0; ii < static_cast<unsigned int>(numStretchBends); ii++) {
         int particle1Index      = particle1[ii];
         int particle2Index      = particle2[ii];
         int particle3Index      = particle3[ii];

plugins/amoeba/platforms/reference/src/SimTKReference/AmoebaReferenceTorsionForce.cpp

@@ -219,7 +219,7 @@ RealOpenMM AmoebaReferenceTorsionForce::calculateForceAndEnergy( int numTorsions
                                                                  const std::vector< std::vector<RealOpenMM> >& torsionParameters3,
                                                                  RealOpenMM** forceData ) const {
     RealOpenMM energy      = 0.0; 
-    for (unsigned int ii = 0; ii < numTorsions; ii++) {
+    for (unsigned int ii = 0; ii < static_cast<unsigned int>(numTorsions); ii++) {
         int particle1Index      = particle1[ii];
         int particle2Index      = particle2[ii];
         int particle3Index      = particle3[ii];

plugins/amoeba/platforms/reference/src/SimTKReference/AmoebaReferenceTorsionTorsionForce.cpp

@@ -560,7 +560,7 @@ RealOpenMM AmoebaReferenceTorsionTorsionForce::calculateForceAndEnergy( int numT
                                                                         const std::vector< std::vector< std::vector< std::vector<RealOpenMM> > > >& torsionTorsionGrids,
                                                                         RealOpenMM** forceData ) const {
     RealOpenMM energy  = 0.0; 
-    for (unsigned int ii = 0; ii < numTorsionTorsions; ii++) {
+    for (unsigned int ii = 0; ii < static_cast<unsigned int>(numTorsionTorsions); ii++) {
 
         int particle1Index       = particle1[ii];
         int particle2Index       = particle2[ii];

plugins/amoeba/platforms/reference/src/SimTKReference/AmoebaReferenceVdwForce.cpp

@@ -220,7 +220,7 @@ RealOpenMM AmoebaReferenceVdwForce::calculateNoCutoffForceAndEnergy( int numPart
 
     std::vector<Vec3> reducedPositions;
     reducedPositions.resize(numParticles);
-    for( unsigned int ii = 0; ii < numParticles; ii++ ){
+    for( unsigned int ii = 0; ii <  static_cast<unsigned int>(numParticles); ii++ ){
         if( reductions[ii] != zero ){
             int reductionIndex     = indexIVs[ii];
             reducedPositions[ii]   = Vec3( reductions[ii]*( particlePositions[ii][0] - particlePositions[reductionIndex][0] ) + particlePositions[reductionIndex][0], 
@@ -236,7 +236,7 @@ RealOpenMM AmoebaReferenceVdwForce::calculateNoCutoffForceAndEnergy( int numPart
 
     RealOpenMM energy = zero;
     std::vector<unsigned int> exclusions(numParticles, 0);
-    for( unsigned int ii = 0; ii < numParticles; ii++ ){
+    for( unsigned int ii = 0; ii < static_cast<unsigned int>(numParticles); ii++ ){
  
         RealOpenMM sigmaI      = sigmas[ii];
         RealOpenMM epsilonI    = epsilons[ii];
@@ -244,7 +244,7 @@ RealOpenMM AmoebaReferenceVdwForce::calculateNoCutoffForceAndEnergy( int numPart
             exclusions[allExclusions[ii][jj]] = 1;
         }
 
-        for( unsigned int jj = ii+1; jj < numParticles; jj++ ){
+        for( unsigned int jj = ii+1; jj < static_cast<unsigned int>(numParticles); jj++ ){
             if( exclusions[jj] == 0 ){
 
                 RealOpenMM combindedSigma   = (this->*_combineSigmas)(sigmaI, sigmas[jj] );

plugins/amoeba/platforms/reference/src/SimTKReference/AmoebaReferenceWcaDispersionForce.cpp

@@ -281,7 +281,7 @@ RealOpenMM AmoebaReferenceWcaDispersionForce::calculateForceAndEnergy( int numPa
 
     RealOpenMM intermediateValues[LastIntermediateValueIndex];
 
-    for( unsigned int ii = 0; ii < numParticles; ii++ ){
+    for( unsigned int ii = 0; ii < static_cast<unsigned int>(numParticles); ii++ ){
  
         RealOpenMM epsi              = epsilons[ii];
         RealOpenMM rmini             = radii[ii];
@@ -316,7 +316,7 @@ RealOpenMM AmoebaReferenceWcaDispersionForce::calculateForceAndEnergy( int numPa
 
         intermediateValues[AH]       = emixh*rmixh7;
 
-        for( unsigned int jj = 0; jj < numParticles; jj++ ){
+        for( unsigned int jj = 0; jj < static_cast<unsigned int>(numParticles); jj++ ){
 
             if( ii == jj )continue;