Fixed some portability problems that show up in

- MingW, where "WIN32" is set by CMake but the compiler is not Microsoft's (should use _MSC_VER) in that case, and 
- in gcc 4.4 which is fussy about some issues that earlier versions were silent about, such as passing a string constant to a "char*" rather than a "const char*".
I also fixed a syntax error in CMakeLists that showed up in the OpenMM workshop for some unknown reason.

Brook is not currently building correctly; I think it has not yet been fully converted to the getTime() interface needed for variable step integrators.

examples/CMakeLists.txt

@@ -46,7 +46,7 @@ FOREACH(EX_ROOT ${CPP_EXAMPLES})
 
     INSTALL(FILES ${EX_ROOT}.cpp DESTINATION examples)
 
-ENDFOREACH(EX_PROG ${CPP_EXAMPLES})
+ENDFOREACH(EX_ROOT ${CPP_EXAMPLES})
 
 FOREACH(EX_ROOT ${C_EXAMPLES})
     IF (BUILD_TESTING_SHARED)
@@ -71,11 +71,11 @@ FOREACH(EX_ROOT ${C_EXAMPLES})
 
     INSTALL(FILES ${EX_ROOT}.c DESTINATION examples)
 
-ENDFOREACH(EX_PROG ${C_EXAMPLES})
+ENDFOREACH(EX_ROOT ${C_EXAMPLES})
 
 FOREACH(EX_ROOT ${F_EXAMPLES})
     INSTALL(FILES ${EX_ROOT}.f90 DESTINATION examples)
-ENDFOREACH(EX_PROG ${F_EXAMPLES})
+ENDFOREACH(EX_ROOT ${F_EXAMPLES})
 
 INSTALL(FILES ${OpenMM_CWRAPPER}.h ${OpenMM_CWRAPPER}.cpp DESTINATION examples)
 INSTALL(FILES ${OpenMM_FMODULE}.f90 DESTINATION examples)

examples/HelloWaterBox.cpp

@@ -17,6 +17,7 @@
 #include <cstdio>
 #include <string>
 #include <vector>
+#include <cstdlib>
 
 // -----------------------------------------------------------------------------
 //                                 MOCK MD CODE

openmmapi/src/GBVIForceImpl.cpp

@@ -34,7 +34,8 @@
 #include "openmm/OpenMMException.h"
 #include "openmm/kernels.h"
 #include <vector>
-#include <math.h>
+#include <cmath>
+#include <cstdio>
 
 using namespace OpenMM;
 using std::vector;

platforms/brook/src/BrookIntegrateLangevinStepKernel.cpp

@@ -250,5 +250,5 @@ void BrookIntegrateLangevinStepKernel::execute( OpenMMContextImpl& context, cons
 
    _brookLangevinDynamics->update( *(_openMMBrookInterface.getParticlePositions()), *(_openMMBrookInterface.getParticleVelocities()), 
                                    *(_openMMBrookInterface.getParticleForces()), *_brookShakeAlgorithm, *_brookRandomNumberGenerator );
-   _openMMBrookInterface->setTime(_openMMBrookInterface->getTime(integrator.getStepSize()));
+   _openMMBrookInterface.setTime(_openMMBrookInterface.getTime(integrator.getStepSize()));
 }

platforms/brook/src/BrookIntegrateVerletStepKernel.cpp

@@ -202,5 +202,5 @@ void BrookIntegrateVerletStepKernel::execute( OpenMMContextImpl& context, const
 
    _brookVerletDynamics->update( *(_openMMBrookInterface.getParticlePositions()), *(_openMMBrookInterface.getParticleVelocities()),
                                  *(_openMMBrookInterface.getParticleForces()), *_brookShakeAlgorithm );
-   _openMMBrookInterface->setTime(_openMMBrookInterface->getTime(stepSize));
+   _openMMBrookInterface.setTime(_openMMBrookInterface.getTime(stepSize));
 }

platforms/cuda/src/kernels/gpu.cpp

@@ -428,9 +428,9 @@ void gpuSetEwaldParameters(gpuContext gpu)//, float alphaEwald, int kmax )
 {
 
     // hard coded alphaEwald and kmax, no interface yet
-    float alpha            = 3.123413;
+    float alpha            = 3.123413f;
     float PI               = 3.14159265358979323846f;
-    float TWO_PI           = 2.0 * PI;
+    float TWO_PI           = 2.0f * PI;
 
     gpu->sim.recipBoxSizeX = TWO_PI / gpu->sim.periodicBoxSizeX ;
     gpu->sim.recipBoxSizeY = TWO_PI / gpu->sim.periodicBoxSizeY ;
@@ -728,7 +728,7 @@ void gpuSetConstraintParameters(gpuContext gpu, const vector<int>& atom1, const
     // Compute the constraint coupling matrix
 
     vector<vector<int> > atomAngles(gpu->natoms);
-    for (int i = 0; i < gpu->sim.bond_angles; i++)
+    for (int i = 0; i < (int)gpu->sim.bond_angles; i++)
         atomAngles[(*gpu->psBondAngleID1)[i].y].push_back(i);
     vector<vector<pair<int, double> > > matrix(numCCMA);
     if (numCCMA > 0) {
@@ -853,8 +853,8 @@ void gpuSetConstraintParameters(gpuContext gpu, const vector<int>& atom1, const
     vector<int> inverseOrder(numCCMA);
     for (int i = 0; i < numCCMA; ++i)
         inverseOrder[constraintOrder[i]] = i;
-    for (int i = 0; i < matrix.size(); ++i)
-        for (int j = 0; j < matrix[i].size(); ++j)
+    for (int i = 0; i < (int)matrix.size(); ++i)
+        for (int j = 0; j < (int)matrix[i].size(); ++j)
             matrix[i][j].first = inverseOrder[matrix[i][j].first];
 
     // Fill in the CUDA streams.
@@ -902,7 +902,7 @@ void gpuSetConstraintParameters(gpuContext gpu, const vector<int>& atom1, const
         (*psCcmaReducedMass)[i] = 0.5f/(invMass1[c]+invMass2[c]);
         for (unsigned int j = 0; j < matrix[index].size(); j++) {
             (*psConstraintMatrixColumn)[i+j*numCCMA] = matrix[index][j].first;
-            (*psConstraintMatrixValue)[i+j*numCCMA] = matrix[index][j].second;
+            (*psConstraintMatrixValue)[i+j*numCCMA] = (float)matrix[index][j].second;
         }
         (*psConstraintMatrixColumn)[i+matrix[index].size()*numCCMA] = numCCMA;
     }

platforms/reference/src/SimTKReference/ReferenceBrownianDynamics.cpp

@@ -22,7 +22,7 @@
  * WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
  */
 
-#include <string.h>
+#include <cstring>
 #include <sstream>
 
 #include "../SimTKUtilities/SimTKOpenMMCommon.h"
@@ -30,6 +30,8 @@
 #include "../SimTKUtilities/SimTKOpenMMUtilities.h"
 #include "ReferenceBrownianDynamics.h"
 
+#include <cstdio>
+
 /**---------------------------------------------------------------------------------------
 
    ReferenceBrownianDynamics constructor
@@ -266,7 +268,7 @@ int ReferenceBrownianDynamics::writeState( int numberOfAtoms, RealOpenMM** atomC
    // open file -- return if unsuccessful
 
    FILE* stateFile = NULL;
-#ifdef WIN32
+#ifdef _MSC_VER
    fopen_s( &stateFile, stateFileName.str().c_str(), "w" );
 #else
    stateFile = fopen( stateFileName.str().c_str(), "w" );

platforms/reference/src/SimTKReference/ReferenceDynamics.cpp

@@ -22,7 +22,7 @@
  * WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
  */
 
-#include <string.h>
+#include <cstring>
 #include <sstream>
 
 #include "../SimTKUtilities/SimTKOpenMMCommon.h"
@@ -30,6 +30,8 @@
 #include "../SimTKUtilities/SimTKOpenMMUtilities.h"
 #include "ReferenceDynamics.h"
 
+#include <cstdio>
+
 const int ReferenceDynamics::DefaultReturn      = 0;
 const int ReferenceDynamics::ErrorReturn        = -1;
 
@@ -656,7 +658,7 @@ int ReferenceDynamics::writeState( int numberOfAtoms, RealOpenMM** atomCoordinat
    // open file -- return if unsuccessful
 
    FILE* stateFile = NULL;
-#ifdef WIN32
+#ifdef _MSC_VER
    fopen_s( &stateFile, stateFileName.str().c_str(), "w" );
 #else
    stateFile = fopen( stateFileName.str().c_str(), "w" );

platforms/reference/src/SimTKReference/ReferenceForce.cpp

@@ -22,7 +22,7 @@
  * WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
  */
 
-#include <string.h>
+#include <cstring>
 #include <sstream>
 
 #include "../SimTKUtilities/SimTKOpenMMCommon.h"
@@ -30,6 +30,8 @@
 #include "../SimTKUtilities/SimTKOpenMMUtilities.h"
 #include "ReferenceForce.h"
 
+#include <cstdio>
+
 /**---------------------------------------------------------------------------------------
 
    ReferenceForce constructor
@@ -208,7 +210,7 @@ int ReferenceForce::writeForces( int numberOfAtoms, int atomsPerBond,
    // open file -- return if unsuccessful
 
    FILE* resultsFile = NULL;
-#ifdef WIN32
+#ifdef _MSC_VER
    fopen_s( &resultsFile, resultsFileName.c_str(), "w" );
 #else
    resultsFile = fopen( resultsFileName.c_str(), "w" );

platforms/reference/src/SimTKReference/ReferenceStochasticDynamics.cpp

@@ -22,7 +22,7 @@
  * WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
  */
 
-#include <string.h>
+#include <cstring>
 #include <sstream>
 
 #include "../SimTKUtilities/SimTKOpenMMCommon.h"
@@ -30,6 +30,8 @@
 #include "../SimTKUtilities/SimTKOpenMMUtilities.h"
 #include "ReferenceStochasticDynamics.h"
 
+#include <cstdio>
+
 /**---------------------------------------------------------------------------------------
 
    ReferenceStochasticDynamics constructor
@@ -626,7 +628,7 @@ int ReferenceStochasticDynamics::writeState( int numberOfAtoms, RealOpenMM** ato
    // open file -- return if unsuccessful
 
    FILE* stateFile = NULL;
-#ifdef WIN32
+#ifdef _MSC_VER
    fopen_s( &stateFile, stateFileName.str().c_str(), "w" );
 #else
    stateFile = fopen( stateFileName.str().c_str(), "w" );

platforms/reference/src/SimTKReference/ReferenceVerletDynamics.cpp

@@ -22,7 +22,7 @@
  * WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
  */
 
-#include <string.h>
+#include <cstring>
 #include <sstream>
 
 #include "../SimTKUtilities/SimTKOpenMMCommon.h"
@@ -30,6 +30,8 @@
 #include "../SimTKUtilities/SimTKOpenMMUtilities.h"
 #include "ReferenceVerletDynamics.h"
 
+#include <cstdio>
+
 /**---------------------------------------------------------------------------------------
 
    ReferenceVerletDynamics constructor
@@ -233,7 +235,7 @@ int ReferenceVerletDynamics::writeState( int numberOfAtoms, RealOpenMM** atomCoo
    // open file -- return if unsuccessful
 
    FILE* stateFile = NULL;
-#ifdef WIN32
+#ifdef _MSC_VER
    fopen_s( &stateFile, stateFileName.str().c_str(), "w" );
 #else
    stateFile = fopen( stateFileName.str().c_str(), "w" );

platforms/reference/src/SimTKUtilities/SimTKOpenMMUtilities.cpp

@@ -30,7 +30,8 @@
 
 // fabs(), ...
 
-#include <math.h>
+#include <cmath>
+#include <cstdio>
 
 uint32_t SimTKOpenMMUtilities::_randomNumberSeed = 0;
 bool SimTKOpenMMUtilities::_randomInitialized = false;
@@ -320,7 +321,7 @@ FILE* SimTKOpenMMUtilities::writeDebugFile( int numberOfFields, const RealOpenMM
 
    // open file
 
-#ifdef WIN32
+#ifdef _MSC_VER
       fopen_s( &debugFile, debugFileName, "w" );
 #else
       debugFile = fopen( debugFileName, "w" );
@@ -800,7 +801,7 @@ void SimTKOpenMMUtilities::matrixCrossProductMatrix3( RealOpenMM* matrixX,
 
    --------------------------------------------------------------------------------------- */
      
-void* SimTKOpenMMUtilities::Xmalloc( const char* name, char* fileName, int line, unsigned int size ){
+void* SimTKOpenMMUtilities::Xmalloc( const char* name, const char* fileName, int line, unsigned int size ){
 
    // ---------------------------------------------------------------------------------------
 
@@ -827,7 +828,7 @@ void* SimTKOpenMMUtilities::Xmalloc( const char* name, char* fileName, int line,
 
    --------------------------------------------------------------------------------------- */
      
-void SimTKOpenMMUtilities::Xfree( const char* name, char* fileName, int line, void* ptr ){
+void SimTKOpenMMUtilities::Xfree( const char* name, const char* fileName, int line, void* ptr ){
 
    // ---------------------------------------------------------------------------------------
 
@@ -1017,7 +1018,7 @@ int SimTKOpenMMUtilities::readFileIntoStringVector( const std::string& fileName,
    // open file
 
    FILE* file = NULL;
-#ifdef WIN32
+#ifdef _MSC_VER
    fopen_s( &file, fileName.c_str(), "r" );
 #else
    file = fopen( fileName.c_str(), "r" );
@@ -1167,7 +1168,7 @@ int SimTKOpenMMUtilities::tokenizeString( const std::string& line, StringVector&
       lineBuffer = (char*) malloc( bufferSz*sizeof( char ) );
    }
 
-#ifdef WIN32
+#ifdef _MSC_VER
    (void) sprintf_s( lineBuffer, bufferSz, "%s", line.c_str() );
 #else
    (void) sprintf( lineBuffer, "%s", line.c_str() );
@@ -1280,7 +1281,7 @@ int SimTKOpenMMUtilities::writeFile( const StringVector& lineVector, const std::
    // open file
 
    FILE* file = NULL;
-#ifdef WIN32
+#ifdef _MSC_VER
    fopen_s( &file, fileName.c_str(), "w" );
 #else
    file = fopen( fileName.c_str(), "w" );

platforms/reference/src/SimTKUtilities/SimTKOpenMMUtilities.h

@@ -386,7 +386,7 @@ class OPENMM_EXPORT SimTKOpenMMUtilities {
       
          --------------------------------------------------------------------------------------- */
                
-      static void* Xmalloc( const char* name, char* fileName, int line, unsigned int size );
+      static void* Xmalloc( const char* name, const char* fileName, int line, unsigned int size );
       
       /* ---------------------------------------------------------------------------------------
       
@@ -399,7 +399,7 @@ class OPENMM_EXPORT SimTKOpenMMUtilities {
       
          --------------------------------------------------------------------------------------- */
       
-      static void Xfree( const char* name, char* fileName, int line, void* ptr );
+      static void Xfree( const char* name, const char* fileName, int line, void* ptr );
       
       /* ---------------------------------------------------------------------------------------
       

platforms/reference/src/gbsa/CpuImplicitSolvent.cpp

@@ -27,6 +27,8 @@
 #include "../SimTKUtilities/SimTKOpenMMUtilities.h"
 #include "CpuImplicitSolvent.h"
 
+#include <cstdio>
+
 //#define UseGromacsMalloc 1
 
 // Replacement new/delete w/ Gromac's smalloc() and sfree()
@@ -862,7 +864,7 @@ int CpuImplicitSolvent::writeBornEnergyForces( RealOpenMM** atomCoordinates,
    // open file -- return if unsuccessful
 
    FILE* implicitSolventResultsFile = NULL;
-#ifdef WIN32
+#ifdef _MSC_VER
    fopen_s( &implicitSolventResultsFile, resultsFileName.c_str(), "w" );
 #else
    implicitSolventResultsFile = fopen( resultsFileName.c_str(), "w" );
@@ -1023,7 +1025,7 @@ int CpuImplicitSolvent::readInfoFile( const std::string infoFileName ){
    // ---------------------------------------------------------------------------------------
 
    FILE* infoFile = NULL;
-#ifdef WIN32
+#ifdef _MSC_VER
    fopen_s( &infoFile, infoFileName.c_str(), "r" );
 #else
    infoFile = fopen( infoFileName.c_str(), "r" );
@@ -1031,7 +1033,7 @@ int CpuImplicitSolvent::readInfoFile( const std::string infoFileName ){
 
    if( infoFile == NULL ){
 
-#ifdef WIN32
+#ifdef _MSC_VER
       fopen_s( &infoFile, _defaultInfoFileName.c_str(), "r" );
 #else
       infoFile = fopen( _defaultInfoFileName.c_str(), "r" );

platforms/reference/src/gbsa/CpuObc.cpp

@@ -30,7 +30,8 @@
 #include "../SimTKUtilities/SimTKOpenMMUtilities.h"
 #include "CpuObc.h"
 #include "../SimTKReference/ReferenceForce.h"
-#include <math.h>
+#include <cmath>
+#include <cstdio>
 
 /**---------------------------------------------------------------------------------------
 
@@ -694,7 +695,7 @@ int CpuObc::writeBornEnergyForces( RealOpenMM** atomCoordinates,
    // open file -- return if unsuccessful
 
    FILE* implicitSolventResultsFile = NULL;
-#ifdef WIN32
+#ifdef _MSC_VER
    fopen_s( &implicitSolventResultsFile, resultsFileName.c_str(), "w" );
 #else
    implicitSolventResultsFile = fopen( resultsFileName.c_str(), "w" );