Added ReferenceFreeEnergyPlatform & CudaFreeEnergyPlatform

plugins/freeEnergy/platforms/cuda/include/CudaFreeEnergyPlatform.h

+#ifndef OPENMM_CUDA_FREE_ENERGY_PLATFORM_H_
+#define OPENMM_CUDA_FREE_ENERGY_PLATFORM_H_
+
+/* -------------------------------------------------------------------------- *
+ *                                   OpenMM                                   *
+ * -------------------------------------------------------------------------- *
+ * This is part of the OpenMM molecular simulation toolkit originating from   *
+ * Simbios, the NIH National Center for Physics-Based Simulation of           *
+ * Biological Structures at Stanford, funded under the NIH Roadmap for        *
+ * Medical Research, grant U54 GM072970. See https://simtk.org.               *
+ *                                                                            *
+ * Portions copyright (c) 2008 Stanford University and the Authors.           *
+ * Authors: Peter Eastman                                                     *
+ * Contributors:                                                              *
+ *                                                                            *
+ * This program is free software: you can redistribute it and/or modify       *
+ * it under the terms of the GNU Lesser General Public License as published   *
+ * by the Free Software Foundation, either version 3 of the License, or       *
+ * (at your option) any later version.                                        *
+ *                                                                            *
+ * This program is distributed in the hope that it will be useful,            *
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of             *
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the              *
+ * GNU Lesser General Public License for more details.                        *
+ *                                                                            *
+ * You should have received a copy of the GNU Lesser General Public License   *
+ * along with this program.  If not, see <http://www.gnu.org/licenses/>.      *
+ * -------------------------------------------------------------------------- */
+
+#include "CudaPlatform.h"
+
+struct _gpuContext;
+
+namespace OpenMM {
+
+/**
+ * This Platform subclass uses CUDA implementations of the OpenMM kernels to run on NVidia GPUs.
+ */
+
+class OPENMM_EXPORT CudaFreeEnergyPlatform : public CudaPlatform {
+public:
+
+    //class PlatformData;
+
+    CudaFreeEnergyPlatform();
+    const std::string& getName() const {
+        static const std::string name = "CudaFreeEnergy";
+        return name;
+    }
+
+#if 0
+    double getSpeed() const {
+        return 100;
+    }
+    bool supportsDoublePrecision() const;
+    const std::string& getPropertyValue(const Context& context, const std::string& property) const;
+    void setPropertyValue(Context& context, const std::string& property, const std::string& value) const;
+    void contextCreated(ContextImpl& context) const;
+    void contextDestroyed(ContextImpl& context) const;
+    /**
+     * This is the name of the parameter for selecting which CUDA device to use.
+     */
+    static const std::string& CudaDevice() {
+        static const std::string key = "CudaDevice";
+        return key;
+    }
+    /**
+     * This is the name of the parameter for selecting whether CUDA should sync or spin loop while waiting for results.
+     */
+    static const std::string& CudaUseBlockingSync() {
+        static const std::string key = "CudaUseBlockingSync";
+        return key;
+    }
+#endif
+};
+
+#if 0
+class CudaPlatform::PlatformData {
+public:
+    PlatformData(_gpuContext* gpu);
+    _gpuContext* gpu;
+    bool removeCM;
+    bool hasBonds, hasAngles, hasPeriodicTorsions, hasRB, hasNonbonded, hasCustomNonbonded;
+    int nonbondedMethod, customNonbondedMethod;
+    int cmMotionFrequency;
+    int stepCount, computeForceCount;
+    double time, ewaldSelfEnergy;
+    std::map<std::string, std::string> propertyValues;
+};
+#endif
+
+} // namespace OpenMM
+
+#endif /*OPENMM_CUDA_FREE_ENERGY_PLATFORM_H_*/

plugins/freeEnergy/platforms/cuda/src/CudaFreeEnergyKernelFactory.cpp

@@ -30,39 +30,8 @@
 #include "openmm/internal/ContextImpl.h"
 #include "openmm/OpenMMException.h"
 
-#if defined(OPENMM_BUILDING_SHARED_LIBRARY)
-    #if defined(WIN32)
-      #include <windows.h>
-        extern "C" void initOpenMMCudaFreeEnergyPlugin();
-        BOOL WINAPI DllMain(HANDLE hModule, DWORD  ul_reason_for_call, LPVOID lpReserved) {
-            if (ul_reason_for_call == DLL_PROCESS_ATTACH)
-                initOpenMMCudaFreeEnergyPlugin();
-            return TRUE;
-        }   
-    #else
-        extern "C" void __attribute__((constructor)) initOpenMMCudaFreeEnergyPlugin();
-    #endif
-#endif
-
 using namespace OpenMM;
 
-extern "C" void initOpenMMCudaFreeEnergyPlugin() {
-
-//(void) fprintf( stderr, "initOpenMMCudaFreeEnergyPlugin called ");
-    if ( gpuIsAvailable() ){
-        CudaPlatform* cudaPlatform            = new CudaPlatform();
-        CudaFreeEnergyKernelFactory* factory  = new CudaFreeEnergyKernelFactory();
-    
-//(void) fprintf( stderr, "gpu is available platform=%p", cudaPlatform);
-        cudaPlatform->registerKernelFactory(CalcNonbondedSoftcoreForceKernel::Name(), factory);
-        cudaPlatform->registerKernelFactory(CalcGBSAOBCSoftcoreForceKernel::Name(), factory);
-        cudaPlatform->registerKernelFactory(CalcGBVISoftcoreForceKernel::Name(), factory);
-    
-        Platform::registerPlatform(cudaPlatform);
-    }
-//(void) fprintf( stderr, "\n");
-}
-
 KernelImpl* CudaFreeEnergyKernelFactory::createKernelImpl(std::string name, const Platform& platform, ContextImpl& context) const {
 
     CudaPlatform::PlatformData& data = *static_cast<CudaPlatform::PlatformData*>(context.getPlatformData());

plugins/freeEnergy/platforms/cuda/src/CudaFreeEnergyKernels.cpp

@@ -193,7 +193,7 @@ static void getForceMap(const System& system, MapStringInt& forceMap, FILE* log)
         }
 
         if( log ){
-            (void) fprintf( stderr, "Map: Force %d %s\n", i, forceName.c_str() );
+            (void) fprintf( log, "Map: Force %d %s\n", i, forceName.c_str() );
         }
      }
 }

plugins/freeEnergy/platforms/cuda/src/CudaFreeEnergyPlatform.cpp

+/* -------------------------------------------------------------------------- *
+ *                                   OpenMM                                   *
+ * -------------------------------------------------------------------------- *
+ * This is part of the OpenMM molecular simulation toolkit originating from   *
+ * Simbios, the NIH National Center for Physics-Based Simulation of           *
+ * Biological Structures at Stanford, funded under the NIH Roadmap for        *
+ * Medical Research, grant U54 GM072970. See https://simtk.org.               *
+ *                                                                            *
+ * Portions copyright (c) 2008 Stanford University and the Authors.           *
+ * Authors: Peter Eastman                                                     *
+ * Contributors:                                                              *
+ *                                                                            *
+ * This program is free software: you can redistribute it and/or modify       *
+ * it under the terms of the GNU Lesser General Public License as published   *
+ * by the Free Software Foundation, either version 3 of the License, or       *
+ * (at your option) any later version.                                        *
+ *                                                                            *
+ * This program is distributed in the hope that it will be useful,            *
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of             *
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the              *
+ * GNU Lesser General Public License for more details.                        *
+ *                                                                            *
+ * You should have received a copy of the GNU Lesser General Public License   *
+ * along with this program.  If not, see <http://www.gnu.org/licenses/>.      *
+ * -------------------------------------------------------------------------- */
+
+#include "CudaFreeEnergyPlatform.h"
+#include "CudaFreeEnergyKernelFactory.h"
+#include "openmm/freeEnergyKernels.h"
+#include "kernels/gputypes.h"
+
+using namespace OpenMM;
+
+#if defined(OPENMM_BUILDING_SHARED_LIBRARY)
+    #if defined(WIN32)
+      #include <windows.h>
+        extern "C" void initOpenMMCudaFreeEnergyPlugin();
+        BOOL WINAPI DllMain(HANDLE hModule, DWORD  ul_reason_for_call, LPVOID lpReserved) {
+            if (ul_reason_for_call == DLL_PROCESS_ATTACH)
+                initOpenMMCudaFreeEnergyPlugin();
+            return TRUE;
+        }
+    #else
+        extern "C" void __attribute__((constructor)) initOpenMMCudaFreeEnergyPlugin();
+    #endif
+#endif
+
+using namespace OpenMM;
+
+extern "C" void initOpenMMCudaFreeEnergyPlugin() {
+
+//(void) fprintf( stderr, "initOpenMMCudaFreeEnergyPlugin called\n");
+    if ( gpuIsAvailable() ){
+        Platform::registerPlatform(new CudaFreeEnergyPlatform());
+    }   
+}
+
+CudaFreeEnergyPlatform::CudaFreeEnergyPlatform( void ){
+    CudaFreeEnergyKernelFactory* factory = new CudaFreeEnergyKernelFactory();
+    registerKernelFactory(CalcNonbondedSoftcoreForceKernel::Name(), factory);
+    registerKernelFactory(CalcGBSAOBCSoftcoreForceKernel::Name(), factory);
+    registerKernelFactory(CalcGBVISoftcoreForceKernel::Name(), factory);
+}
+

plugins/freeEnergy/platforms/reference/include/ReferenceFreeEnergyPlatform.h

+#ifndef OPENMM_REFERENCE_FREE_ENERGY_PLATFORM_H_
+#define OPENMM_REFERENCE_FREE_ENERGY_PLATFORM_H_
+
+/* -------------------------------------------------------------------------- *
+ *                                   OpenMM                                   *
+ * -------------------------------------------------------------------------- *
+ * This is part of the OpenMM molecular simulation toolkit originating from   *
+ * Simbios, the NIH National Center for Physics-Based Simulation of           *
+ * Biological Structures at Stanford, funded under the NIH Roadmap for        *
+ * Medical Research, grant U54 GM072970. See https://simtk.org.               *
+ *                                                                            *
+ * Portions copyright (c) 2008 Stanford University and the Authors.           *
+ * Authors: Peter Eastman                                                     *
+ * Contributors:                                                              *
+ *                                                                            *
+ * Permission is hereby granted, free of charge, to any person obtaining a    *
+ * copy of this software and associated documentation files (the "Software"), *
+ * to deal in the Software without restriction, including without limitation  *
+ * the rights to use, copy, modify, merge, publish, distribute, sublicense,   *
+ * and/or sell copies of the Software, and to permit persons to whom the      *
+ * Software is furnished to do so, subject to the following conditions:       *
+ *                                                                            *
+ * The above copyright notice and this permission notice shall be included in *
+ * all copies or substantial portions of the Software.                        *
+ *                                                                            *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
+ * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,   *
+ * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL    *
+ * THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,    *
+ * DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR      *
+ * OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE  *
+ * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
+ * -------------------------------------------------------------------------- */
+
+#include "ReferencePlatform.h"
+
+namespace OpenMM {
+
+/**
+ * This Platform subclass uses the reference implementations of all the OpenMM kernels.
+ */
+
+class OPENMM_EXPORT  ReferenceFreeEnergyPlatform : public ReferencePlatform {
+public:
+//    class PlatformData;
+    ReferenceFreeEnergyPlatform();
+    const std::string& getName() const {
+        static const std::string name = "ReferenceFreeEnergyPlatform";
+        return name;
+    }
+#if 0
+    double getSpeed() const {
+        return 1;
+    }
+    bool supportsDoublePrecision() const;
+    void contextCreated(ContextImpl& context) const;
+    void contextDestroyed(ContextImpl& context) const;
+#endif
+};
+
+#if 0
+class ReferencePlatform::PlatformData {
+public:
+    PlatformData(int numParticles);
+    ~PlatformData();
+    int numParticles, stepCount;
+    double time;
+    void* positions;
+    void* velocities;
+    void* forces;
+};
+#endif
+} // namespace OpenMM
+
+#endif /*OPENMM_REFERENCE_FREE_ENERGY_PLATFORM_H_*/

plugins/freeEnergy/platforms/reference/src/ReferenceFreeEnergyKernelFactory.cpp

@@ -34,38 +34,8 @@
 #include "openmm/internal/ContextImpl.h"
 #include "openmm/OpenMMException.h"
 
-// using PluginInitializer.h and initOpenMMPlugin() does not seem to work
-//#include "openmm/PluginInitializer.h"
-
-#if defined(OPENMM_BUILDING_SHARED_LIBRARY)
-    #if defined(WIN32)
-      #include <windows.h>
-        extern "C" void initOpenMMReferenceFreeEnergyPlugin();
-        BOOL WINAPI DllMain(HANDLE hModule, DWORD  ul_reason_for_call, LPVOID lpReserved) {
-            if (ul_reason_for_call == DLL_PROCESS_ATTACH)
-                initOpenMMReferenceFreeEnergyPlugin();
-            return TRUE;
-        }
-    #else
-        extern "C" void __attribute__((constructor)) initOpenMMReferenceFreeEnergyPlugin();
-    #endif
-#endif
-
 using namespace OpenMM;
 
-extern "C" void initOpenMMReferenceFreeEnergyPlugin() {
-    ReferencePlatform* referencePlatform       = new ReferencePlatform();
-
-//(void) fprintf( stderr, "In initOpenMMReferenceFreeEnergyPlugin platform=%p\n", referencePlatform );
-    ReferenceFreeEnergyKernelFactory* factory  = new ReferenceFreeEnergyKernelFactory();
-    referencePlatform->registerKernelFactory(CalcNonbondedSoftcoreForceKernel::Name(), factory);
-    referencePlatform->registerKernelFactory(CalcGBSAOBCSoftcoreForceKernel::Name(), factory);
-    referencePlatform->registerKernelFactory(CalcGBVISoftcoreForceKernel::Name(), factory);
-
-    Platform::registerPlatform(referencePlatform);
-   
-}
-
 KernelImpl* ReferenceFreeEnergyKernelFactory::createKernelImpl(std::string name, const Platform& platform, ContextImpl& context) const {
     ReferencePlatform::PlatformData& data = *static_cast<ReferencePlatform::PlatformData*>(context.getPlatformData());
 

plugins/freeEnergy/platforms/reference/src/ReferenceFreeEnergyPlatform.cpp

+/* -------------------------------------------------------------------------- *
+ *                                   OpenMM                                   *
+ * -------------------------------------------------------------------------- *
+ * This is part of the OpenMM molecular simulation toolkit originating from   *
+ * Simbios, the NIH National Center for Physics-Based Simulation of           *
+ * Biological Structures at Stanford, funded under the NIH Roadmap for        *
+ * Medical Research, grant U54 GM072970. See https://simtk.org.               *
+ *                                                                            *
+ * Portions copyright (c) 2008 Stanford University and the Authors.           *
+ * Authors: Peter Eastman                                                     *
+ * Contributors:                                                              *
+ *                                                                            *
+ * Permission is hereby granted, free of charge, to any person obtaining a    *
+ * copy of this software and associated documentation files (the "Software"), *
+ * to deal in the Software without restriction, including without limitation  *
+ * the rights to use, copy, modify, merge, publish, distribute, sublicense,   *
+ * and/or sell copies of the Software, and to permit persons to whom the      *
+ * Software is furnished to do so, subject to the following conditions:       *
+ *                                                                            *
+ * The above copyright notice and this permission notice shall be included in *
+ * all copies or substantial portions of the Software.                        *
+ *                                                                            *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
+ * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,   *
+ * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL    *
+ * THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,    *
+ * DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR      *
+ * OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE  *
+ * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
+ * -------------------------------------------------------------------------- */
+
+#include "ReferenceFreeEnergyPlatform.h"
+#include "openmm/freeEnergyKernels.h"
+#include "ReferenceFreeEnergyKernelFactory.h"
+
+// using PluginInitializer.h and initOpenMMPlugin() does not seem to work
+//#include "openmm/PluginInitializer.h"
+
+#if defined(OPENMM_BUILDING_SHARED_LIBRARY)
+    #if defined(WIN32)
+      #include <windows.h>
+        extern "C" void initOpenMMReferenceFreeEnergyPlugin();
+        BOOL WINAPI DllMain(HANDLE hModule, DWORD  ul_reason_for_call, LPVOID lpReserved) {
+            if (ul_reason_for_call == DLL_PROCESS_ATTACH)
+                initOpenMMReferenceFreeEnergyPlugin();
+            return TRUE;
+        }
+    #else
+        extern "C" void __attribute__((constructor)) initOpenMMReferenceFreeEnergyPlugin();
+    #endif
+#endif
+
+using namespace OpenMM;
+
+extern "C" void initOpenMMReferenceFreeEnergyPlugin() {
+    Platform::registerPlatform( new ReferenceFreeEnergyPlatform() );
+}
+
+ReferenceFreeEnergyPlatform::ReferenceFreeEnergyPlatform( void ){
+
+    ReferenceFreeEnergyKernelFactory* factory  = new ReferenceFreeEnergyKernelFactory();
+    registerKernelFactory(CalcNonbondedSoftcoreForceKernel::Name(), factory);
+    registerKernelFactory(CalcGBSAOBCSoftcoreForceKernel::Name(), factory);
+    registerKernelFactory(CalcGBVISoftcoreForceKernel::Name(), factory);
+}