More cleanup for Windows compilation

openmmapi/include/openmm/internal/AndersenThermostatImpl.h

@@ -45,7 +45,7 @@ class System;
  * This is the internal implementation of AndersenThermostat.
  */
 
-class AndersenThermostatImpl : public ForceImpl {
+class OPENMM_EXPORT AndersenThermostatImpl : public ForceImpl {
 public:
     AndersenThermostatImpl(AndersenThermostat& owner);
     void initialize(ContextImpl& context);

platforms/cuda/src/kernels/bbsort.h

@@ -10,6 +10,7 @@
  */
 #ifndef _BBSORT_H_
 #define _BBSORT_H_
+#include "windowsExportCuda.h"
 
 #define BLOCK_SIZE 512
 
@@ -18,6 +19,6 @@
 #define AUTO_EVALUATE 2
 
 template <typename T>
-void bbSort(T* dData,int number,int listOrder=AUTO_EVALUATE);
+void OPENMMCUDA_EXPORT bbSort(T* dData,int number,int listOrder=AUTO_EVALUATE);
 
 #endif // _BBSORT_H_

platforms/cuda/src/kernels/cudaKernels.h

@@ -97,7 +97,7 @@ extern void SetCalculateObcGbsaBornSumSim(gpuContext gpu);
 extern void GetCalculateObcGbsaBornSumSim(gpuContext gpu);
 extern void SetCalculateGBVIBornSumSim(gpuContext gpu);
 extern void GetCalculateGBVIBornSumSim(gpuContext gpu);
-extern void SetCalculateObcGbsaForces2Sim(gpuContext gpu);
+extern void OPENMMCUDA_EXPORT SetCalculateObcGbsaForces2Sim(gpuContext gpu);
 extern void GetCalculateObcGbsaForces2Sim(gpuContext gpu);
 extern void SetCalculateGBVIForces2Sim(gpuContext gpu);
 extern void GetCalculateGBVIForces2Sim(gpuContext gpu);

plugins/amoeba/openmmapi/include/internal/AmoebaMultipoleForceImpl.h

@@ -44,7 +44,7 @@ namespace OpenMM {
  * This is the internal implementation of AmoebaMultipoleForce.
  */
 
-class AmoebaMultipoleForceImpl : public ForceImpl {
+class OPENMM_EXPORT AmoebaMultipoleForceImpl : public ForceImpl {
 public:
     AmoebaMultipoleForceImpl(AmoebaMultipoleForce& owner);
     ~AmoebaMultipoleForceImpl();

plugins/amoeba/openmmapi/include/internal/AmoebaWcaDispersionForceImpl.h

@@ -45,7 +45,7 @@ namespace OpenMM {
  * This is the internal implementation of AmoebaWcaDispersionForce.
  */
 
-class AmoebaWcaDispersionForceImpl : public ForceImpl {
+class OPENMM_EXPORT AmoebaWcaDispersionForceImpl : public ForceImpl {
 public:
     AmoebaWcaDispersionForceImpl(AmoebaWcaDispersionForce& owner);
     ~AmoebaWcaDispersionForceImpl();

plugins/amoeba/platforms/cuda/tests/AmoebaTinkerParameterFile.cpp

@@ -40,8 +40,6 @@
 #include <sys/time.h>
 #endif
 
-extern int isNanOrInfinity( double number );
-
 using namespace std;
 
 
@@ -591,6 +589,19 @@ static int readIntVector( FILE* filePtr, const StringVector& tokens, int numberT
     return static_cast<int>(intVector.size());
 }
 
+/**---------------------------------------------------------------------------------------
+
+   Report whether a number is a nan or infinity
+
+   @param number               number to test
+   @return 1 if number is  nan or infinity; else return 0
+
+   --------------------------------------------------------------------------------------- */
+
+int isNan( double number ){
+    return (number != number || number == std::numeric_limits<double>::infinity() || number == -std::numeric_limits<double>::infinity()) ? 1 : 0; 
+}
+
 /**---------------------------------------------------------------------------------------
 
     Read particles count
@@ -3766,7 +3777,7 @@ void initializeForceMap( MapStringInt& forceMap, int initialValue ){
      return;
 
 }
-
+/*
 void checkIntermediateMultipoleQuantities( Context* context, MapStringVectorOfVectors& supplementary,
                                            int useOpenMMUnits, FILE* log ) {
 
@@ -3939,7 +3950,7 @@ void checkIntermediateMultipoleQuantities( Context* context, MapStringVectorOfVe
         (void) fflush( log );
     }
 
-}
+} */
 
 void calculateBorn1( System& amoebaSystem, std::vector<Vec3>& tinkerCoordinates, FILE* log ) {
 /*
@@ -4725,7 +4736,7 @@ void testUsingAmoebaTinkerParameterFile( const std::string& amoebaTinkerParamete
     if( gkIsActive == false ){
         isPresent = forceMap.find( AMOEBA_MULTIPOLE_FORCE );
         if( isPresent != forceMap.end() && isPresent->second != 0 ){
-             checkIntermediateMultipoleQuantities( context, supplementary, useOpenMMUnits, log );
+             //checkIntermediateMultipoleQuantities( context, supplementary, useOpenMMUnits, log );
         }
     }
 
@@ -4813,15 +4824,15 @@ void testEnergyForcesConsistent( std::string parameterFileName, MapStringInt& fo
  
     // check norm is not nan
  
-    if( isNanOrInfinity( forceNorm ) ){ 
+    if( isNan( forceNorm ) ){ 
         if( log ){
             (void) fprintf( log, "%s norm of force is nan -- aborting.\n", methodName.c_str() );
             unsigned int hitNan = 0;
             for( unsigned int ii = 0; (ii < forces.size()) && (hitNan < 10); ii++ ){
    
-               if( isNanOrInfinity( forces[ii][0] ) ||
-                   isNanOrInfinity( forces[ii][1] ) ||
-                   isNanOrInfinity( forces[ii][2] ) )hitNan++;
+               if( isNan( forces[ii][0] ) ||
+                   isNan( forces[ii][1] ) ||
+                   isNan( forces[ii][2] ) )hitNan++;
    
                 (void) fprintf( log, "%6u x[%15.7e %15.7e %15.7e] f[%15.7e %15.7e %15.7e]\n", ii,
                                 coordinates[ii][0], coordinates[ii][1], coordinates[ii][2],
@@ -4974,15 +4985,15 @@ void testEnergyForceByFiniteDifference( std::string parameterFileName, MapString
  
     // check norm is not nan
  
-    if( isNanOrInfinity( forceNorm ) ){ 
+    if( isNan( forceNorm ) ){ 
         if( log ){
             (void) fprintf( log, "%s norm of force is nan -- aborting.\n", methodName.c_str() );
             unsigned int hitNan = 0;
             for( unsigned int ii = 0; (ii < forces.size()) && (hitNan < 10); ii++ ){
    
-               if( isNanOrInfinity( forces[ii][0] ) ||
-                   isNanOrInfinity( forces[ii][1] ) ||
-                   isNanOrInfinity( forces[ii][2] ) )hitNan++;
+               if( isNan( forces[ii][0] ) ||
+                   isNan( forces[ii][1] ) ||
+                   isNan( forces[ii][2] ) )hitNan++;
    
                 (void) fprintf( log, "%6u x[%15.7e %15.7e %15.7e] f[%15.7e %15.7e %15.7e]\n", ii,
                                 coordinates[ii][0], coordinates[ii][1], coordinates[ii][2],
@@ -5696,7 +5707,7 @@ void testEnergyConservation( std::string parameterFileName, MapStringInt& forceM
             }
         }
   
-        if( isNanOrInfinity( totalEnergy ) ){
+        if( isNan( totalEnergy ) ){
             char buffer[1024];
             (void) sprintf( buffer, "%s nans detected at time %12.3f -- aborting.\n", methodName.c_str(), currentTime );
             throwException(__FILE__, __LINE__, buffer );