Fixed errors and warnings under Windows

examples/HelloArgon.cpp

@@ -11,11 +11,6 @@
 // other visualization tool to produce an animation of the resulting trajectory.
 // -----------------------------------------------------------------------------
 
-// Suppress irrelevant warning from Microsoft's compiler.
-#ifdef _MSC_VER
-    #pragma warning(disable:4251)   // no dll interface for some classes
-#endif
-
 #include "OpenMM.h"
 #include <cstdio>
 

examples/HelloEthane.cpp

@@ -202,7 +202,6 @@ int main() {
 // Suppress irrelevant warnings from Microsoft's compiler.
 #ifdef _MSC_VER
     #pragma warning(disable:4996)   // sprintf is unsafe 
-    #pragma warning(disable:4251)   // no dll interface for some classes
 #endif
 
 #include "OpenMM.h"

examples/HelloSodiumChloride.cpp

@@ -160,7 +160,6 @@ int main() {
 // Suppress irrelevant warnings from Microsoft's compiler.
 #ifdef _MSC_VER
     #pragma warning(disable:4996)   // sprintf is unsafe 
-    #pragma warning(disable:4251)   // no dll interface for some classes
 #endif
 
 #include "OpenMM.h"

examples/HelloWaterBox.cpp

@@ -170,7 +170,6 @@ int main() {
 // Suppress irrelevant warnings from Microsoft's compiler.
 #ifdef _MSC_VER
     #pragma warning(disable:4996)   // sprintf is unsafe 
-    #pragma warning(disable:4251)   // no dll interface for some classes
 #endif
 
 #include "OpenMM.h"

libraries/lepton/src/ExpressionProgram.cpp

@@ -42,7 +42,7 @@ ExpressionProgram::ExpressionProgram() : maxArgs(0), stackSize(0) {
 ExpressionProgram::ExpressionProgram(const ParsedExpression& expression) : maxArgs(0), stackSize(0) {
     buildProgram(expression.getRootNode());
     int currentStackSize = 0;
-    for (int i = 0; i < operations.size(); i++) {
+    for (int i = 0; i < (int) operations.size(); i++) {
         int args = operations[i]->getNumArguments();
         if (args > maxArgs)
             maxArgs = args;
@@ -53,7 +53,7 @@ ExpressionProgram::ExpressionProgram(const ParsedExpression& expression) : maxAr
 }
 
 ExpressionProgram::~ExpressionProgram() {
-    for (int i = 0; i < operations.size(); i++)
+    for (int i = 0; i < (int) operations.size(); i++)
         delete operations[i];
 }
 
@@ -65,7 +65,7 @@ ExpressionProgram& ExpressionProgram::operator=(const ExpressionProgram& program
     maxArgs = program.maxArgs;
     stackSize = program.stackSize;
     operations.resize(program.operations.size());
-    for (int i = 0; i < operations.size(); i++)
+    for (int i = 0; i < (int) operations.size(); i++)
         operations[i] = program.operations[i]->clone();
     return *this;
 }
@@ -93,10 +93,10 @@ double ExpressionProgram::evaluate() const {
 }
 
 double ExpressionProgram::evaluate(const std::map<std::string, double>& variables) const {
-    vector<double> args(maxArgs);
+    vector<double> args(max(maxArgs, 1));
     vector<double> stack(stackSize);
     int stackPointer = 0;
-    for (int i = 0; i < operations.size(); i++) {
+    for (int i = 0; i < (int) operations.size(); i++) {
         int numArgs = operations[i]->getNumArguments();
         for (int j = 0; j < numArgs; j++)
             args[j] = stack[--stackPointer];

libraries/lepton/src/ParsedExpression.cpp

@@ -54,8 +54,9 @@ double ParsedExpression::evaluate(const std::map<std::string, double>& variables
 }
 
 double ParsedExpression::evaluate(const ExpressionTreeNode& node, const map<string, double>& variables) {
-    vector<double> args(node.getChildren().size());
-    for (int i = 0; i < args.size(); i++)
+    int numArgs = node.getChildren().size();
+    vector<double> args(max(numArgs, 1));
+    for (int i = 0; i < numArgs; i++)
         args[i] = evaluate(node.getChildren()[i], variables);
     return node.getOperation().evaluate(&args[0], variables);
 }
@@ -84,19 +85,19 @@ ExpressionTreeNode ParsedExpression::preevaluateVariables(const ExpressionTreeNo
         return ExpressionTreeNode(new Operation::Constant(iter->second));
     }
     vector<ExpressionTreeNode> children(node.getChildren().size());
-    for (int i = 0; i < children.size(); i++)
+    for (int i = 0; i < (int) children.size(); i++)
         children[i] = preevaluateVariables(node.getChildren()[i], variables);
     return ExpressionTreeNode(node.getOperation().clone(), children);
 }
 
 ExpressionTreeNode ParsedExpression::precalculateConstantSubexpressions(const ExpressionTreeNode& node) {
     vector<ExpressionTreeNode> children(node.getChildren().size());
-    for (int i = 0; i < children.size(); i++)
+    for (int i = 0; i < (int) children.size(); i++)
         children[i] = precalculateConstantSubexpressions(node.getChildren()[i]);
     ExpressionTreeNode result = ExpressionTreeNode(node.getOperation().clone(), children);
     if (node.getOperation().getId() == Operation::VARIABLE)
         return result;
-    for (int i = 0; i < children.size(); i++)
+    for (int i = 0; i < (int) children.size(); i++)
         if (children[i].getOperation().getId() != Operation::CONSTANT)
             return result;
     return ExpressionTreeNode(new Operation::Constant(evaluate(result, map<string, double>())));
@@ -104,7 +105,7 @@ ExpressionTreeNode ParsedExpression::precalculateConstantSubexpressions(const Ex
 
 ExpressionTreeNode ParsedExpression::substituteSimplerExpression(const ExpressionTreeNode& node) {
     vector<ExpressionTreeNode> children(node.getChildren().size());
-    for (int i = 0; i < children.size(); i++)
+    for (int i = 0; i < (int) children.size(); i++)
         children[i] = substituteSimplerExpression(node.getChildren()[i]);
     switch (node.getOperation().getId()) {
         case Operation::ADD:
@@ -212,7 +213,7 @@ ParsedExpression ParsedExpression::differentiate(const std::string& variable) co
 
 ExpressionTreeNode ParsedExpression::differentiate(const ExpressionTreeNode& node, const std::string& variable) {
     vector<ExpressionTreeNode> childDerivs(node.getChildren().size());
-    for (int i = 0; i < childDerivs.size(); i++)
+    for (int i = 0; i < (int) childDerivs.size(); i++)
         childDerivs[i] = differentiate(node.getChildren()[i], variable);
     return node.getOperation().differentiate(node.getChildren(),childDerivs, variable);
 }
@@ -231,7 +232,7 @@ ostream& Lepton::operator<<(ostream& out, const ExpressionTreeNode& node) {
     out << node.getOperation().getName();
     if (node.getChildren().size() > 0) {
         out << "(";
-        for (int i = 0; i < node.getChildren().size(); i++) {
+        for (int i = 0; i < (int) node.getChildren().size(); i++) {
             if (i > 0)
                 out << ", ";
             out << node.getChildren()[i];

libraries/lepton/src/Parser.cpp

@@ -76,7 +76,7 @@ ParseToken Parser::getNextToken(string expression, int start) {
     if (c == ' ') {
         // White space
 
-        for (int pos = start+1; pos < expression.size(); pos++) {
+        for (int pos = start+1; pos < (int) expression.size(); pos++) {
             if (expression[pos] != ' ')
                 return ParseToken(expression.substr(start, pos-start), ParseToken::Whitespace);
         }
@@ -88,7 +88,7 @@ ParseToken Parser::getNextToken(string expression, int start) {
         bool foundDecimal = (c == '.');
         bool foundExp = false;
         int pos;
-        for (pos = start+1; pos < expression.size(); pos++) {
+        for (pos = start+1; pos < (int) expression.size(); pos++) {
             c = expression[pos];
             if (Digits.find(c) != string::npos)
                 continue;
@@ -98,7 +98,7 @@ ParseToken Parser::getNextToken(string expression, int start) {
             }
             if ((c == 'e' || c == 'E') && !foundExp) {
                 foundExp = true;
-                if (pos < expression.size()-1 && expression[pos+1] == '-')
+                if (pos < (int) expression.size()-1 && expression[pos+1] == '-')
                     pos++;
                 continue;
             }
@@ -109,7 +109,7 @@ ParseToken Parser::getNextToken(string expression, int start) {
 
     // A variable, function, or left parenthesis
 
-    for (int pos = start; pos < expression.size(); pos++) {
+    for (int pos = start; pos < (int) expression.size(); pos++) {
         c = expression[pos];
         if (c == '(')
             return ParseToken(expression.substr(start, pos-start+1), ParseToken::Function);
@@ -122,7 +122,7 @@ ParseToken Parser::getNextToken(string expression, int start) {
 vector<ParseToken> Parser::tokenize(string expression) {
     vector<ParseToken> tokens;
     int pos = 0;
-    while (pos < expression.size()) {
+    while (pos < (int) expression.size()) {
         ParseToken token = getNextToken(expression, pos);
         if (token.getType() != ParseToken::Whitespace)
             tokens.push_back(token);
@@ -176,7 +176,7 @@ ExpressionTreeNode Parser::parsePrecedence(const vector<ParseToken>& tokens, int
         bool moreArgs;
         do {
             args.push_back(parsePrecedence(tokens, pos, customFunctions, 0));
-            moreArgs = (pos < tokens.size() && tokens[pos].getType() == ParseToken::Comma);
+            moreArgs = (pos < (int) tokens.size() && tokens[pos].getType() == ParseToken::Comma);
             if (moreArgs)
                 pos++;
         } while (moreArgs);
@@ -195,7 +195,7 @@ ExpressionTreeNode Parser::parsePrecedence(const vector<ParseToken>& tokens, int
 
     // Now deal with the next binary operator.
 
-    while (pos < tokens.size() && tokens[pos].getType() == ParseToken::Operator) {
+    while (pos < (int) tokens.size() && tokens[pos].getType() == ParseToken::Operator) {
         token = tokens[pos];
         int op = Operators.find(token.getText());
         int opPrecedence = Precedence[op];

olla/include/openmm/Platform.h

@@ -248,24 +248,10 @@ protected:
     const ContextImpl& getContextImpl(const Context& context) const;
     std::vector<std::string> platformProperties;
 private:
-
-// Retarded visual studio compiler complains about being unable to 
-// export private stl class members.
-// This stanza explains that it should temporarily shut up.
-#if defined(_MSC_VER)
-#pragma warning(push)
-#pragma warning(disable:4251)
-#endif
-
     std::map<std::string, KernelFactory*> kernelFactories;
     std::map<std::string, StreamFactory*> streamFactories;
     std::map<std::string, std::string> defaultProperties;
     static std::vector<Platform*>& getPlatforms();
-
-#if defined(_MSC_VER)
-#pragma warning(pop)
-#endif
-
 };
 
 } // namespace OpenMM

openmmapi/include/openmm/internal/windowsExport.h

@@ -25,10 +25,10 @@
 #ifdef _MSC_VER
     // We don't want to hear about how sprintf is "unsafe".
     #pragma warning(disable:4996)
-    #if defined(OPENMM_BUILDING_SHARED_LIBRARY)
-        #define OPENMM_EXPORT __declspec(dllexport)
     // Keep MS VC++ quiet about lack of dll export of private members.
     #pragma warning(disable:4251)
+    #if defined(OPENMM_BUILDING_SHARED_LIBRARY)
+        #define OPENMM_EXPORT __declspec(dllexport)
     #elif defined(OPENMM_BUILDING_STATIC_LIBRARY) || defined(OPENMM_USE_STATIC_LIBRARIES)
 		#define OPENMM_EXPORT
     #else

platforms/reference/src/ReferenceKernels.cpp

@@ -565,7 +565,7 @@ void ReferenceCalcCustomNonbondedForceKernel::executeForces(ContextImpl& context
     if (periodic)
         ixn.setPeriodic(periodicBoxSize);
     map<string, double> globalParameters;
-    for (int i = 0; i < globalParameterNames.size(); i++)
+    for (int i = 0; i < (int) globalParameterNames.size(); i++)
         globalParameters[globalParameterNames[i]] = context.getParameter(globalParameterNames[i]);
     ixn.calculatePairIxn(numParticles, posData, particleParamArray, exclusionArray, 0, globalParameters, forceData, 0, 0);
     ixn.calculateExceptionIxn(numExceptions, exceptionIndexArray, posData, exceptionParamArray, globalParameters, forceData, 0, 0);
@@ -584,7 +584,7 @@ double ReferenceCalcCustomNonbondedForceKernel::executeEnergy(ContextImpl& conte
     if (periodic)
         ixn.setPeriodic(periodicBoxSize);
     map<string, double> globalParameters;
-    for (int i = 0; i < globalParameterNames.size(); i++)
+    for (int i = 0; i < (int) globalParameterNames.size(); i++)
         globalParameters[globalParameterNames[i]] = context.getParameter(globalParameterNames[i]);
     ixn.calculatePairIxn(numParticles, posData, particleParamArray, exclusionArray, 0, globalParameters, forceData, 0, &energy);
     ixn.calculateExceptionIxn(numExceptions, exceptionIndexArray, posData, exceptionParamArray, globalParameters, forceData, 0, &energy);

platforms/reference/src/SimTKReference/ReferenceCustomNonbondedIxn.cpp

@@ -53,7 +53,7 @@ ReferenceCustomNonbondedIxn::ReferenceCustomNonbondedIxn(const Lepton::Expressio
 
    // ---------------------------------------------------------------------------------------
 
-    for (int i = 0; i < paramNames.size(); i++) {
+    for (int i = 0; i < (int) paramNames.size(); i++) {
         for (int j = 1; j < 3; j++) {
             stringstream name;
             name << paramNames[i] << j;
@@ -159,11 +159,11 @@ int ReferenceCustomNonbondedIxn::calculatePairIxn( int numberOfAtoms, RealOpenMM
 
            // Apply the combining rules to compute the force field parameters.
 
-           for (int j = 0; j < combiningRules.size(); j++) {
+           for (int j = 0; j < (int) combiningRules.size(); j++) {
                variablesForParams[particleParamNames[j*2]] = atomParameters[pair.first][j];
                variablesForParams[particleParamNames[j*2+1]] = atomParameters[pair.second][j];
            }
-           for (int j = 0; j < combiningRules.size(); j++)
+           for (int j = 0; j < (int) combiningRules.size(); j++)
                variablesForForce[paramNames[j]] = combiningRules[j].evaluate(variablesForParams);
            calculateOneIxn(pair.first, pair.second, atomCoordinates, variablesForForce, forces, energyByAtom, totalEnergy);
        }
@@ -192,11 +192,11 @@ int ReferenceCustomNonbondedIxn::calculatePairIxn( int numberOfAtoms, RealOpenMM
 
                  // Apply the combining rules to compute the force field parameters.
 
-                 for (int j = 0; j < combiningRules.size(); j++) {
+                 for (int j = 0; j < (int) combiningRules.size(); j++) {
                      variablesForParams[particleParamNames[j*2]] = atomParameters[ii][j];
                      variablesForParams[particleParamNames[j*2+1]] = atomParameters[jj][j];
                  }
-                 for (int j = 0; j < combiningRules.size(); j++)
+                 for (int j = 0; j < (int) combiningRules.size(); j++)
                      variablesForForce[paramNames[j]] = combiningRules[j].evaluate(variablesForParams);
                  calculateOneIxn(ii, jj, atomCoordinates, variablesForForce, forces, energyByAtom, totalEnergy);
              }
@@ -229,7 +229,7 @@ void ReferenceCustomNonbondedIxn::calculateExceptionIxn( int numberOfExceptions,
 
     map<string, double> variables = globalParameters;
     for (int i = 0; i < numberOfExceptions; i++) {
-        for (int j = 0; j < combiningRules.size(); j++)
+        for (int j = 0; j < (int) combiningRules.size(); j++)
             variables[paramNames[j]] = parameters[i][j];
         calculateOneIxn(atomIndices[i][0], atomIndices[i][1], atomCoordinates, variables, forces, energyByAtom, totalEnergy);
     }
@@ -282,7 +282,7 @@ void ReferenceCustomNonbondedIxn::calculateOneIxn( int ii, int jj, RealOpenMM**
     // accumulate forces
 
     variables["r"] = deltaR[ReferenceForce::RIndex];
-    RealOpenMM dEdR = forceExpression.evaluate(variables)/(deltaR[ReferenceForce::RIndex]);
+    RealOpenMM dEdR = (RealOpenMM) (forceExpression.evaluate(variables)/(deltaR[ReferenceForce::RIndex]));
     for( int kk = 0; kk < 3; kk++ ){
        RealOpenMM force  = -dEdR*deltaR[kk];
        forces[ii][kk]   += force;
@@ -292,7 +292,7 @@ void ReferenceCustomNonbondedIxn::calculateOneIxn( int ii, int jj, RealOpenMM**
     // accumulate energies
 
     if( totalEnergy || energyByAtom ) {
-        RealOpenMM energy = energyExpression.evaluate(variables);
+        RealOpenMM energy = (RealOpenMM) energyExpression.evaluate(variables);
         if( totalEnergy )
            *totalEnergy += energy;
         if( energyByAtom ){

platforms/reference/src/SimTKReference/ReferenceLJCoulombIxn.cpp

@@ -445,7 +445,7 @@ int ReferenceLJCoulombIxn::calculateEwaldIxn( int numberOfAtoms, RealOpenMM** at
 
        // accumulate energies
 
-       realSpaceEwaldEnergy = atomParameters[ii][QIndex]*atomParameters[jj][QIndex]*inverseR*erfc(alphaR);
+       realSpaceEwaldEnergy = (RealOpenMM) (atomParameters[ii][QIndex]*atomParameters[jj][QIndex]*inverseR*erfc(alphaR));
        vdwEnergy = eps*(sig6-one)*sig6;
 
         if( totalEnergy )
@@ -484,7 +484,7 @@ int ReferenceLJCoulombIxn::calculateEwaldIxn( int numberOfAtoms, RealOpenMM** at
 
                // accumulate energies
 
-               realSpaceEwaldEnergy = atomParameters[ii][QIndex]*atomParameters[jj][QIndex]*inverseR*erf(alphaR);
+               realSpaceEwaldEnergy = (RealOpenMM) (atomParameters[ii][QIndex]*atomParameters[jj][QIndex]*inverseR*erf(alphaR));
 
                 if( totalEnergy )
                       *totalEnergy -= realSpaceEwaldEnergy;