Fixes to make Windows happier

openmmapi/src/GBVIForceImpl.cpp

@@ -133,6 +133,7 @@ int GBVIForceImpl::getBondsFromForces(ContextImpl& context) {
         }
     }   
 
+    return 0;
 }
 
 #define GBVIDebug 0

platforms/cuda/tests/TstCudaUsingParameterFile.cpp

@@ -3936,7 +3936,7 @@ Context* _getContext( System* system, Context* inputContext, Integrator* inputIn
        if( log ){
           (void) fprintf( log, "OpenMM Platform: %s\n", context->getPlatform().getName().c_str() ); (void) fflush( log );
           const vector<string>& properties = gpuPlatform.getPropertyNames();
-          for (int i = 0; i < properties.size(); i++) {
+          for (unsigned int i = 0; i < properties.size(); i++) {
               fprintf( log, "%s: %s\n", properties[i].c_str(), gpuPlatform.getPropertyValue(*context, properties[i]).c_str());
           }    
        }    
@@ -4040,7 +4040,7 @@ static int getForceStrings( System& system, StringVector& forceStringArray, FILE
 
     // print active forces and relevant parameters
 
-    for( unsigned int ii = 0; ii < system.getNumForces(); ii++ ) {
+    for( int ii = 0; ii < system.getNumForces(); ii++ ) {
 
         int hit                 = 0;
         Force& force            = system.getForce(ii);
@@ -5989,62 +5989,69 @@ int main( int numberOfArguments, char* argv[] ){
    initializeForceMap( forceMap, 0 );
    int logFileNameIndex                     = -1;
    int summaryFileNameIndex                 = -1;
-   int forceEnum;
 
    // parse arguments
 
+#ifdef _MSC_VER
+#define STRCASECMP(X,Y)  stricmp(X,Y)
+#define STRNCASECMP(X,Y,Z)  strnicmp(X,Y,Z)
+#else
+#define STRCASECMP(X,Y)  strcasecmp(X,Y)
+#define STRNCASECMP(X,Y,Z)  strncasecmp(X,Y,Z)
+#endif
+
    for( int ii = 1; ii < numberOfArguments; ii++ ){
       int addToMap = 0;
-      if( strcasecmp( argv[ii], "-parameterFileName" ) == 0 ){
+      if( STRCASECMP( argv[ii], "-parameterFileName" ) == 0 ){
          parameterFileName          = argv[ii+1];
          ii++;
-      } else if( strcasecmp( argv[ii], "-logFileName" ) == 0 ){
+      } else if( STRCASECMP( argv[ii], "-logFileName" ) == 0 ){
          logFileNameIndex           = ii + 1;
          ii++;
-      } else if( strcasecmp( argv[ii], "-summaryFileName" ) == 0 ){ 
+      } else if( STRCASECMP( argv[ii], "-summaryFileName" ) == 0 ){ 
          summaryFileNameIndex       = ii + 1; 
          ii++;
-      } else if( strcasecmp( argv[ii], "-checkForces" ) == 0 ){
+      } else if( STRCASECMP( argv[ii], "-checkForces" ) == 0 ){
          checkForces                = atoi( argv[ii+1] );
          ii++;
-      } else if( strcasecmp( argv[ii], "-checkInputForces" ) == 0 ){
+      } else if( STRCASECMP( argv[ii], "-checkInputForces" ) == 0 ){
          checkInputForces           = atoi( argv[ii+1] );
          ii++;
-      } else if( strcasecmp( argv[ii], "-checkEnergyForceConsistent" ) == 0 ){
+      } else if( STRCASECMP( argv[ii], "-checkEnergyForceConsistent" ) == 0 ){
          checkEnergyForceConsistent = atoi( argv[ii+1] );
          ii++;
-      } else if( strcasecmp( argv[ii], "-checkEnergyConservation" ) == 0 ){
+      } else if( STRCASECMP( argv[ii], "-checkEnergyConservation" ) == 0 ){
          checkEnergyConservation = atoi( argv[ii+1] );;
          ii++;
-      } else if( strcasecmp( argv[ii], "-energyForceDelta" )     == 0    ||
-                 strcasecmp( argv[ii], "-energyForceTolerance" ) == 0    ||
-                 strcasecmp( argv[ii], "-cudaDeviceId" )         == 0    ||
-                 strcasecmp( argv[ii], "-platform" )             == 0    ||
-                 strcasecmp( argv[ii], "-applyAssertion" )       == 0 ){
+      } else if( STRCASECMP( argv[ii], "-energyForceDelta" )     == 0    ||
+                 STRCASECMP( argv[ii], "-energyForceTolerance" ) == 0    ||
+                 STRCASECMP( argv[ii], "-cudaDeviceId" )         == 0    ||
+                 STRCASECMP( argv[ii], "-platform" )             == 0    ||
+                 STRCASECMP( argv[ii], "-applyAssertion" )       == 0 ){
          addToMap                   = ii;
          ii++;
 
-      } else if( strcasecmp( argv[ii], "-allForces" ) == 0 ){
+      } else if( STRCASECMP( argv[ii], "-allForces" ) == 0 ){
          int flag = atoi( argv[ii+1] );
          ii++;
          initializeForceMap( forceMap, flag );
-      } else if( strcasecmp( argv[ii], "-log" ) == 0 ){
+      } else if( STRCASECMP( argv[ii], "-log" ) == 0 ){
          if( atoi( argv[ii+1] ) != 0 ){
             log = stderr;
          } else {
             log = NULL;
          }
          ii++;
-      } else if( strcasecmp( argv[ii], "-help" ) == 0 ){
+      } else if( STRCASECMP( argv[ii], "-help" ) == 0 ){
          printUsage( defaultParameterFileName );
 
       } else if( getForceOffset( ii, numberOfArguments, argv, forceMap ) ){
          ii++;
-      } else if( strncasecmp( argv[ii], "-equilibration", 14  ) == 0 ||
-                 strncasecmp( argv[ii], "-simulation",    11  ) == 0 ||
-                 strncasecmp( argv[ii], "-runId",          6  ) == 0 ||
-                 strncasecmp( argv[ii], "-nonbonded",     10  ) == 0 ||
-                 strncasecmp( argv[ii], "-readContext",   12  ) == 0 ){
+      } else if( STRNCASECMP( argv[ii], "-equilibration", 14  ) == 0 ||
+                 STRNCASECMP( argv[ii], "-simulation",    11  ) == 0 ||
+                 STRNCASECMP( argv[ii], "-runId",          6  ) == 0 ||
+                 STRNCASECMP( argv[ii], "-nonbonded",     10  ) == 0 ||
+                 STRNCASECMP( argv[ii], "-readContext",   12  ) == 0 ){
          addToMap = ii;
          ii++;
       } else {

plugins/freeEnergy/CMakeLists.txt

@@ -314,6 +314,14 @@ IF(DL_LIBRARY)
   TARGET_LINK_LIBRARIES(${STATIC_FREE_ENERGY_TARGET} ${DL_LIBRARY})
 ENDIF(DL_LIBRARY)
 
+SET( OpenMMLib OpenMM )
+# But on Unix or Cygwin we have to add the suffix manually
+IF (UNIX AND CMAKE_BUILD_TYPE MATCHES Debug)
+    SET(OpenMMLib ${OpenMMLib}_d)
+ENDIF (UNIX AND CMAKE_BUILD_TYPE MATCHES Debug)
+TARGET_LINK_LIBRARIES( ${SHARED_FREE_ENERGY_TARGET} ${SHARED_TARGET} )
+TARGET_LINK_LIBRARIES( ${STATIC_FREE_ENERGY_TARGET} ${STATIC_TARGET} )
+
 ADD_SUBDIRECTORY(platforms/reference/tests)
 
 # Which hardware platforms to build

plugins/freeEnergy/openmmapi/src/GBVISoftcoreForceImpl.cpp

@@ -149,6 +149,8 @@ int GBVISoftcoreForceImpl::getBondsFromForces(ContextImpl& context) {
         }
     }
 
+    return 0;
+
 }
 
 #define GBVIDebug 0

plugins/freeEnergy/platforms/cuda/src/kernels/GpuGBVISoftcore.cpp

@@ -24,8 +24,6 @@
  * along with this program.  If not, see <http://www.gnu.org/licenses/>.      *
  * -------------------------------------------------------------------------- */
 
-using namespace std;
-
 #include "GpuGBVISoftcore.h"
 #include "GpuFreeEnergyCudaKernels.h"
 
@@ -33,8 +31,8 @@ using namespace std;
 
 GpuGBVISoftcore::GpuGBVISoftcore( ){
     _bornRadiiScalingMethod   = 0;
-    _quinticLowerLimitFactor  = 0.8;
-    _quinticUpperLimit        = 0.008;
+    _quinticLowerLimitFactor  = 0.8f;
+    _quinticUpperLimit        = 0.008f;
     _psSwitchDerivative       = NULL;
 }
 

plugins/freeEnergy/platforms/cuda/src/kernels/GpuGBVISoftcore.h

@@ -28,7 +28,7 @@
 
 #include "gputypes.h"
 #include "cudatypes.h"
-#include "cudaKernels.h"
+//#include "cudaKernels.h"
 #include "openmm/OpenMMException.h"
 
 // info related to nonbonded softcore

plugins/freeEnergy/platforms/cuda/src/kernels/GpuLJ14Softcore.cpp

@@ -43,7 +43,7 @@ GpuLJ14Softcore::~GpuLJ14Softcore( ){
 
 int GpuLJ14Softcore::flipStrides( gpuContext gpu ){
     int flip = gpu->sim.outputBuffers - 1;
-    for (int ii = 0; ii < psLJ14SoftcoreID->_stride; ii++)
+    for (unsigned int ii = 0; ii < psLJ14SoftcoreID->_stride; ii++)
     {
         (*psLJ14SoftcoreID)[ii].z = flip - (*psLJ14SoftcoreID)[ii].z;
         (*psLJ14SoftcoreID)[ii].w = flip - (*psLJ14SoftcoreID)[ii].w;

plugins/freeEnergy/platforms/cuda/src/kernels/GpuNonbondedSoftcore.cpp

@@ -24,8 +24,6 @@
  * along with this program.  If not, see <http://www.gnu.org/licenses/>.      *
  * -------------------------------------------------------------------------- */
 
-using namespace std;
-
 #include "GpuNonbondedSoftcore.h"
 #include "GpuFreeEnergyCudaKernels.h"
 

plugins/freeEnergy/platforms/cuda/src/kernels/GpuObcGbsaSoftcore.cpp

@@ -24,8 +24,6 @@
  * along with this program.  If not, see <http://www.gnu.org/licenses/>.      *
  * -------------------------------------------------------------------------- */
 
-using namespace std;
-
 #include "GpuObcGbsaSoftcore.h"
 #include "GpuFreeEnergyCudaKernels.h"
 

plugins/freeEnergy/platforms/cuda/src/kernels/kCalculateCDLJObcGbsaSoftcoreForces1.cu

@@ -24,9 +24,9 @@
  * along with this program.  If not, see <http://www.gnu.org/licenses/>.      *
  * -------------------------------------------------------------------------- */
 
-#include "gputypes.h"
-#include "cudatypes.h"
-#include "cudaKernels.h"
+#include "kernels/gputypes.h"
+#include "kernels/cudatypes.h"
+#include "kernels/cudaKernels.h"
 #include "GpuFreeEnergyCudaKernels.h"
 
 #include <stdio.h>

plugins/freeEnergy/platforms/cuda/src/kernels/kCalculateGBVISoftcoreBornSum.cu

@@ -176,6 +176,20 @@ struct Atom {
     float bornRadiusScaleFactor;
 };
 
+__global__ void kClearGBVISoftcoreBornSum_kernel()
+{
+    unsigned int pos = blockIdx.x * blockDim.x + threadIdx.x;
+    while (pos < cSim.stride * cSim.nonbondOutputBuffers)
+    {   
+        ((float*)cSim.pBornSum)[pos] = 0.0f;
+        pos += gridDim.x * blockDim.x;
+    }   
+}
+
+void kClearGBVISoftcoreBornSum(gpuContext gpu) {
+    kClearGBVISoftcoreBornSum_kernel<<<gpu->sim.blocks, 384>>>();
+}
+
 // Include versions of the kernels for N^2 calculations.
 
 #define METHOD_NAME(a, b) a##N2##b
@@ -384,7 +398,7 @@ void kReduceGBVIBornForcesQuinticScaling(gpuContext gpu)
 void kCalculateGBVISoftcoreBornSum(gpuContext gpu)
 {
     //printf("kCalculateGBVIBornSum\n");
-    kClearGBVIBornSum( gpu );
+    kClearGBVISoftcoreBornSum( gpu );
     LAUNCHERROR("kClearGBVIBornSum from kCalculateGBVISoftcoreBornSum");
 
     size_t numWithInteractions;

plugins/freeEnergy/platforms/cuda/src/kernels/kCalculateObcGbsaSoftcoreBornSum.cu

@@ -25,7 +25,7 @@
  * -------------------------------------------------------------------------- */
 
 #include "gputypes.h"
-#include "cudaKernels.h"
+#include "kernels/cudaKernels.h"
 #include "GpuObcGbsaSoftcore.h"
 
 #include <cuda.h>

plugins/freeEnergy/platforms/cuda/src/kernels/kCalculateObcGbsaSoftcoreForces2.cu

@@ -34,7 +34,6 @@
 using namespace std;
 
 #include "gputypes.h"
-#include "cudaKernels.h"
 
 struct Atom {
     float x;

plugins/freeEnergy/platforms/reference/src/SimTKReference/ReferenceFreeEnergyLJCoulombSoftcoreIxn.cpp

@@ -36,6 +36,7 @@
 // In case we're using some primitive version of Visual Studio this will
 // make sure that erf() and erfc() are defined.
 //#include "MSVC_erfc.h"
+#include "openmm/internal/MSVC_erfc.h"
 
 using std::vector;