Many changes to build OpenMM on Windows:

1) Added DLL export macros to many classes; enough to get tests to compile
2) Cosmetic changes to reduce warnings in Visual Studio:
   a) change many "for (int i ="... to "for (size_t i ="... to avoid unsigned mismatch warnings
   b) included many explicit static_cast<OpenMMReal>() casts to document places where double->float conversion warnings occur

olla/include/Kernel.h

@@ -33,6 +33,7 @@
  * -------------------------------------------------------------------------- */
 
 #include "KernelImpl.h"
+#include "internal/windowsExport.h"
 
 namespace OpenMM {
 
@@ -54,7 +55,7 @@ namespace OpenMM {
  * </pre>
  */
 
-class Kernel {
+class OPENMM_EXPORT Kernel {
 public:
     Kernel();
     Kernel(const Kernel& copy);

olla/include/KernelImpl.h

@@ -35,6 +35,7 @@
 #include "Platform.h"
 #include <string>
 #include <cassert>
+#include "internal/windowsExport.h"
 
 namespace OpenMM {
 
@@ -44,7 +45,7 @@ namespace OpenMM {
  * will in turn subclass it and provide concrete implementations of the execute() method.
  */
 
-class KernelImpl {
+class OPENMM_EXPORT KernelImpl {
 public:
     /**
      * Create a KernelImpl.

olla/include/Platform.h

@@ -35,6 +35,7 @@
 #include "Stream.h"
 #include <map>
 #include <vector>
+#include "internal/windowsExport.h"
 
 namespace OpenMM {
 
@@ -60,7 +61,7 @@ class StreamFactory;
  * You can then call createKernel() and createStream() to construct particular kernels and streams as needed.
  */
 
-class Platform {
+class OPENMM_EXPORT Platform {
 public:
     virtual ~Platform();
     /**
@@ -168,9 +169,23 @@ public:
      */
     static Platform& findPlatform(std::vector<std::string> kernelNames);
 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;
     static std::vector<Platform*> platforms;
+
+#if defined(_MSC_VER)
+#pragma warning(pop)
+#endif
+
 };
 
 } // namespace OpenMM

olla/include/Stream.h

@@ -33,10 +33,11 @@
  * -------------------------------------------------------------------------- */
 
 #include <string>
+#include "internal/windowsExport.h"
 
 namespace OpenMM {
 
-class StreamImpl;
+class OPENMM_EXPORT StreamImpl;
 
 /**
  * A Stream encapsulates a particular implementation of a stream of data elements.  A Stream has three

olla/include/StreamFactory.h

@@ -33,6 +33,7 @@
  * -------------------------------------------------------------------------- */
 
 #include "StreamImpl.h"
+#include "internal/windowsExport.h"
 
 namespace OpenMM {
 
@@ -42,7 +43,7 @@ namespace OpenMM {
  * StreamImpls as needed.
  */
 
-class StreamFactory {
+class OPENMM_EXPORT StreamFactory {
 public:
     /**
      * Create a StreamImpl.

openmmapi/include/AndersenThermostat.h

@@ -34,6 +34,7 @@
 
 #include "Force.h"
 #include <string>
+#include "internal/windowsExport.h"
 
 namespace OpenMM {
 
@@ -41,7 +42,7 @@ namespace OpenMM {
  * This class uses the Andersen method to maintain constant temperature.
  */
 
-class AndersenThermostat : public Force {
+class OPENMM_EXPORT AndersenThermostat : public Force {
 public:
     /**
      * This is the name of the parameter which stores the current temperature of the

openmmapi/include/BrownianIntegrator.h

@@ -34,6 +34,7 @@
 
 #include "Integrator.h"
 #include "Kernel.h"
+#include "internal/windowsExport.h"
 
 namespace OpenMM {
 
@@ -41,7 +42,7 @@ namespace OpenMM {
  * This is an Integrator which simulates a System using Brownian dynamics.
  */
 
-class BrownianIntegrator : public Integrator {
+class OPENMM_EXPORT BrownianIntegrator : public Integrator {
 public:
     /**
      * Create a BrownianIntegrator.

openmmapi/include/CMMotionRemover.h

@@ -34,6 +34,7 @@
 
 #include "Force.h"
 #include <string>
+#include "internal/windowsExport.h"
 
 namespace OpenMM {
 
@@ -42,7 +43,7 @@ namespace OpenMM {
  * center of mass momentum, then adjusts the individual atom velocities to make it zero.
  */
 
-class CMMotionRemover : public Force {
+class OPENMM_EXPORT CMMotionRemover : public Force {
 public:
     /**
      * Create a CMMotionRemover.

openmmapi/include/Force.h

@@ -32,6 +32,8 @@
  * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
  * -------------------------------------------------------------------------- */
 
+#include "internal/windowsExport.h"
+
 namespace OpenMM {
 
 class ForceImpl;
@@ -51,7 +53,7 @@ class ForceImpl;
  * </ul>
  */
 
-class Force {
+class OPENMM_EXPORT Force {
 public:
 	Force() {}
     virtual ~Force() {

openmmapi/include/GBSAOBCForceField.h

@@ -34,6 +34,7 @@
 
 #include "Force.h"
 #include <vector>
+#include "internal/windowsExport.h"
 
 namespace OpenMM {
 
@@ -41,7 +42,7 @@ namespace OpenMM {
  * This class implements an implicit solvation force using the GBSA-OBC model.
  */
 
-class GBSAOBCForceField : public Force {
+class OPENMM_EXPORT GBSAOBCForceField : public Force {
 public:
     /*
      * Create a GBSAOBCForceField.
@@ -102,7 +103,21 @@ protected:
 private:
     class AtomInfo;
     double solventDielectric, soluteDielectric;
+
+// 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::vector<AtomInfo> atoms;
+
+#if defined(_MSC_VER)
+#pragma warning(pop)
+#endif
+
 };
 
 class GBSAOBCForceField::AtomInfo {

openmmapi/include/Integrator.h

@@ -35,6 +35,7 @@
 #include "Vec3.h"
 #include <map>
 #include <vector>
+#include "internal/windowsExport.h"
 
 namespace OpenMM {
 
@@ -49,7 +50,7 @@ class OpenMMContextImpl;
  * is specified by passing the Integrator as an argument to the constructor of the OpenMMContext.
  */
 
-class Integrator {
+class OPENMM_EXPORT Integrator {
 public:
     virtual ~Integrator() {
     }

openmmapi/include/LangevinIntegrator.h

@@ -34,6 +34,7 @@
 
 #include "Integrator.h"
 #include "Kernel.h"
+#include "internal/windowsExport.h"
 
 namespace OpenMM {
 
@@ -41,7 +42,7 @@ namespace OpenMM {
  * This is an Integrator which simulates a System using Langevin dynamics.
  */
 
-class LangevinIntegrator : public Integrator {
+class OPENMM_EXPORT LangevinIntegrator : public Integrator {
 public:
     /**
      * Create a LangevinIntegrator.

openmmapi/include/OpenMMContext.h

@@ -37,6 +37,7 @@
 #include "System.h"
 #include <string>
 #include <vector>
+#include "internal/windowsExport.h"
 
 namespace OpenMM {
 
@@ -60,7 +61,7 @@ class Platform;
  * atom and the current energy of the System.
  */
 
-class OpenMMContext {
+class OPENMM_EXPORT OpenMMContext {
 public:
     /**
      * Construct a new OpenMMContext in which to run a simulation.

openmmapi/include/StandardMMForceField.h

@@ -35,6 +35,7 @@
 #include "Force.h"
 #include <map>
 #include <vector>
+#include "internal/windowsExport.h"
 
 namespace OpenMM {
 
@@ -48,7 +49,7 @@ namespace OpenMM {
  * method to set the force field parameters for each one.
  */
 
-class StandardMMForceField : public Force {
+class OPENMM_EXPORT StandardMMForceField : public Force {
 public:
     /**
      * Create a StandardMMForceField.
@@ -216,11 +217,25 @@ private:
     class AngleInfo;
     class PeriodicTorsionInfo;
     class RBTorsionInfo;
+
+// 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::vector<AtomInfo> atoms;
     std::vector<BondInfo> bonds;
     std::vector<AngleInfo> angles;
     std::vector<PeriodicTorsionInfo> periodicTorsions;
     std::vector<RBTorsionInfo> rbTorsions;
+
+#if defined(_MSC_VER)
+#pragma warning(pop)
+#endif
+
 };
 
 class StandardMMForceField::AtomInfo {

openmmapi/include/State.h

@@ -35,6 +35,7 @@
 #include "Vec3.h"
 #include <map>
 #include <vector>
+#include "internal/windowsExport.h"
 
 namespace OpenMM {
 
@@ -49,7 +50,7 @@ namespace OpenMM {
  * when the State was created), it will throw an exception.
  */
 
-class State {
+class OPENMM_EXPORT State {
 public:
     /**
      * This is an enumeration of the types of data which may be stored in a State.  When you create
@@ -87,6 +88,15 @@ public:
 private:
     friend class OpenMMContext;
     State(double time, int numAtoms, DataType types);
+
+// 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::vector<Vec3>& updPositions();
     std::vector<Vec3>& updVelocities();
     std::vector<Vec3>& updForces();
@@ -98,6 +108,10 @@ private:
     std::vector<Vec3> velocities;
     std::vector<Vec3> forces;
     std::map<std::string, double> parameters;
+
+#if defined(_MSC_VER)
+#pragma warning(pop)
+#endif
     
 };
 

openmmapi/include/System.h

@@ -33,10 +33,11 @@
  * -------------------------------------------------------------------------- */
 
 #include <vector>
+#include "internal/windowsExport.h"
 
 namespace OpenMM {
 
-class Force;
+class OPENMM_EXPORT Force;
 
 /**
  * This class represents a molecular system.  The definition of a System involves
@@ -53,7 +54,7 @@ class Force;
  * stores a list of Force objects that determine the motion of the atoms.
  */
 
-class System {
+class OPENMM_EXPORT System {
 public:
     /**
      * Create a new System.
@@ -134,9 +135,23 @@ public:
     }
 private:
     class ConstraintInfo;
-    std::vector<double> masses;
+
+// 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::vector<double> masses;
     std::vector<ConstraintInfo> constraints;
     std::vector<Force*> forces;
+
+#if defined(_MSC_VER)
+#pragma warning(pop)
+#endif
+
 };
 
 class System::ConstraintInfo {

openmmapi/include/VerletIntegrator.h

@@ -34,6 +34,7 @@
 
 #include "Integrator.h"
 #include "Kernel.h"
+#include "internal/windowsExport.h"
 
 namespace OpenMM {
 
@@ -41,7 +42,7 @@ namespace OpenMM {
  * This is an Integrator which simulates a System using the leap-frog Verlet algorithm.
  */
 
-class VerletIntegrator : public Integrator {
+class OPENMM_EXPORT VerletIntegrator : public Integrator {
 public:
     /**
      * Create a VerletIntegrator.

openmmapi/include/internal/windowsExport.h

+#ifndef OPENMM_WINDOWSEXPORT_H_
+#define OPENMM_WINDOWSEXPORT_H_
+
+/*
+ * Shared libraries are messy in Visual Studio. We have to distinguish three
+ * cases:
+ *   (1) this header is being used to build the SimTKcommon shared library (dllexport)
+ *   (2) this header is being used by a *client* of the SimTKcommon shared
+ *       library (dllimport)
+ *   (3) we are building the SimTKcommon static library, or the client is
+ *       being compiled with the expectation of linking with the
+ *       SimTKcommon static library (nothing special needed)
+ * In the CMake script for building this library, we define one of the symbols
+ *     SimTK_SimTKCOMMON_BUILDING_{SHARED|STATIC}_LIBRARY
+ * Client code normally has no special symbol defined, in which case we'll
+ * assume it wants to use the shared library. However, if the client defines
+ * the symbol SimTK_USE_STATIC_LIBRARIES we'll suppress the dllimport so
+ * that the client code can be linked with static libraries. Note that
+ * the client symbol is not library dependent, while the library symbols
+ * affect only the SimTKcommon library, meaning that other libraries can
+ * be clients of this one. However, we are assuming all-static or all-shared.
+ */
+
+#ifdef _MSC_VER
+	#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
+		#define OPENMM_EXPORT __declspec(dllimport)   // i.e., a client of a shared library
+    #endif
+#else
+    #define OPENMM_EXPORT // Linux, Mac
+#endif
+
+#endif // OPENMM_WINDOWSEXPORT_H_

openmmapi/src/OpenMMContextImpl.cpp

@@ -45,7 +45,11 @@ using std::vector;
 using std::string;
 
 OpenMMContextImpl::OpenMMContextImpl(OpenMMContext& owner, System& system, Integrator& integrator, Platform* platform) :
-            owner(owner), system(system), integrator(integrator), platform(platform), platformData(NULL) {
+				owner(owner), system(system), 
+				integrator(integrator), platform(platform), 
+				platformData(NULL),
+				time(0)
+{
     vector<string> kernelNames;
     kernelNames.push_back(CalcKineticEnergyKernel::Name());
     for (int i = 0; i < system.getNumForces(); ++i) {
@@ -69,10 +73,10 @@ OpenMMContextImpl::OpenMMContextImpl(OpenMMContext& owner, System& system, Integ
     velocities.fillWithValue(&zero);
     kineticEnergyKernel = platform->createKernel(CalcKineticEnergyKernel::Name(), *this);
     vector<double> masses(system.getNumAtoms());
-    for (int i = 0; i < masses.size(); ++i)
+    for (size_t i = 0; i < masses.size(); ++i)
         masses[i] = system.getAtomMass(i);
     dynamic_cast<CalcKineticEnergyKernel&>(kineticEnergyKernel.getImpl()).initialize(masses);
-    for (int i = 0; i < forceImpls.size(); ++i)
+    for (size_t i = 0; i < forceImpls.size(); ++i)
         forceImpls[i]->initialize(*this);
     integrator.initialize(*this);
 }

openmmapi/src/State.cpp

@@ -69,8 +69,8 @@ const map<string, double>& State::getParameters() const {
     return parameters;
 }
 State::State(double time, int numAtoms, DataType types) : types(types), time(time), ke(0), pe(0),
-        positions(types&Positions == 0 ? 0 : numAtoms), velocities(types&Velocities== 0 ? 0 : numAtoms),
-        forces(types&Forces== 0 ? 0 : numAtoms) {
+        positions( (types & Positions) == 0 ? 0 : numAtoms), velocities( (types & Velocities) == 0 ? 0 : numAtoms),
+        forces( (types & Forces) == 0 ? 0 : numAtoms) {
 }
 vector<Vec3>& State::updPositions() {
     return positions;