Base class for bonded/nonbonded classes

platforms/brook/src/BrookCommon.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: Mark Friedrichs                                                   *
+ * 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 <math.h>
+#include <sstream>
+#include "BrookCommon.h"
+#include "BrookPlatform.h"
+#include "BrookStreamFactory.h"
+#include "OpenMMException.h"
+
+using namespace OpenMM;
+using namespace std;
+
+/** 
+ * Constructor
+ * 
+ */
+
+BrookCommon::BrookCommon(  ){
+
+// ---------------------------------------------------------------------------------------
+
+   // static const std::string methodName      = "BrookCommon::BrookCommon";
+   // static const int debug                   = 1;
+
+// ---------------------------------------------------------------------------------------
+
+   _numberOfAtoms             = 0;
+   _atomSizeModified          = 0;
+
+   _atomStreamWidth           = -1;
+   _atomStreamHeight          = -1; 
+   _atomStreamSize            = -1;
+
+   _log                       = NULL;
+
+}   
+ 
+/** 
+ * Destructor
+ * 
+ */
+
+BrookCommon::~BrookCommon( ){
+
+// ---------------------------------------------------------------------------------------
+
+   //static const std::string methodName      = "BrookCommon::~BrookCommon";
+   //static const int debug                   = 1;
+
+// ---------------------------------------------------------------------------------------
+
+}
+
+/** 
+ * Get number of atoms
+ * 
+ * @return  number of atoms
+ *
+ */
+
+int BrookCommon::getNumberOfAtoms( void ) const {
+   return _numberOfAtoms;
+}
+
+/** 
+ * Get number of atoms
+ * 
+ * @param  numberOfAtoms number of atoms
+ * @return  number of atoms
+ *
+ */
+
+int BrookCommon::setNumberOfAtoms( int numberOfAtoms ){
+   if( numberOfAtoms != _numberOfAtoms ){
+      _atomSizeModified = numberOfAtoms;
+   }
+   _numberOfAtoms = numberOfAtoms;
+   return _numberOfAtoms;
+}
+
+/** 
+ * Get atom stream width
+ * 
+ * @param platform  platform
+ *
+ * @return  atom stream width
+ *
+ */
+
+int BrookCommon::getAtomStreamWidth( const Platform& platform ){
+
+// ---------------------------------------------------------------------------------------
+
+   // static const std::string methodName      = "BrookCommon::getAtomStreamWidth";
+   // static const int debug                   = 1;
+
+// ---------------------------------------------------------------------------------------
+
+   // get atom stream width
+
+   if( _atomStreamWidth < 0 ){
+      _getAtomStreamDimensions( platform );
+   }
+   return _atomStreamWidth;
+}
+
+/** 
+ * Get atom stream width
+ * 
+ * @return  atom stream width
+ *
+ */
+
+int BrookCommon::getAtomStreamWidth( void ) const {
+
+// ---------------------------------------------------------------------------------------
+
+   // static const std::string methodName      = "BrookCommon::getAtomStreamWidth";
+   // static const int debug                   = 1;
+
+// ---------------------------------------------------------------------------------------
+
+   return _atomStreamWidth;
+}
+
+/** 
+ * Get atom stream height
+ * 
+ * @param platform platform
+ *
+ * @return  atom stream height 
+ *
+ */
+
+int BrookCommon::getAtomStreamHeight( const Platform& platform ){
+
+// ---------------------------------------------------------------------------------------
+
+   // static const std::string methodName      = "BrookCommon::getAtomStreamHeight";
+   // static const int debug                   = 1;
+
+// ---------------------------------------------------------------------------------------
+
+   // get atom stream height
+
+   if( _atomStreamHeight < 0 ){
+      _getAtomStreamDimensions( platform );
+   }
+   return _atomStreamHeight;
+}
+
+/** 
+ * Get atom stream height
+ * 
+ * @return  atom stream height 
+ *
+ */
+
+int BrookCommon::getAtomStreamHeight( void ) const {
+
+// ---------------------------------------------------------------------------------------
+
+   // static const std::string methodName      = "BrookCommon::getAtomStreamHeight";
+   // static const int debug                   = 1;
+
+// ---------------------------------------------------------------------------------------
+
+   return _atomStreamHeight;
+}
+
+/** 
+ * Get atom stream size
+ * 
+ * @param platform  platform
+ *
+ * @return  atom stream size
+ *
+ */
+
+int BrookCommon::getAtomStreamSize( const Platform& platform ){
+
+// ---------------------------------------------------------------------------------------
+
+   // static const std::string methodName      = "BrookCommon::getAtomStreamSize";
+   // static const int debug                   = 1;
+
+// ---------------------------------------------------------------------------------------
+
+   // get atom stream size
+
+   if( _atomStreamSize < 0 ){
+      _getAtomStreamDimensions( platform );
+   }
+   return _atomStreamSize;
+}
+
+/** 
+ * Get atom stream size
+ * 
+ * @return  atom stream size
+ *
+ */
+
+int BrookCommon::getAtomStreamSize( void ) const {
+   return _atomStreamSize;
+}
+
+/** 
+ * Get atom stream dimensions
+ * 
+ * @param platform                  platform
+ *
+ */
+
+void BrookCommon::_getAtomStreamDimensions( const Platform& platform ){
+
+// ---------------------------------------------------------------------------------------
+
+   // static const std::string methodName      = "BrookCommon::_getAtomStreamDimensions";
+   // static const int debug                   = 1;
+
+// ---------------------------------------------------------------------------------------
+
+   // get atom stream size
+
+   const BrookPlatform brookPlatform            = dynamic_cast<const BrookPlatform&> (platform);
+   const BrookStreamFactory& brookStreamFactory = dynamic_cast<const BrookStreamFactory&> (platform.getDefaultStreamFactory() );
+   BrookStreamInfo* brookStreamInfo             = brookStreamFactory.getBrookStreamInfo( BrookStreamFactory::AtomPositions );
+   _atomStreamWidth                             = brookStreamInfo->getStreamWidth();
+   _atomStreamSize                              = brookPlatform.getStreamSize( getNumberOfAtoms(), _atomStreamWidth, NULL );
+   _atomStreamHeight                            = (int) ( ((float) _atomStreamSize)/( (float) _atomStreamWidth) + 0.001);
+
+   return;
+}
+
+/** 
+ * Get log file reference
+ * 
+ * @return  log file reference
+ *
+ */
+
+FILE* BrookCommon::getLog( void ) const {
+   return _log;
+}
+
+/** 
+ * Set log file reference
+ * 
+ * @param  log file reference
+ *
+ * @return  DefaultReturnValue
+ *
+ */
+
+int BrookCommon::setLog( FILE* log ){
+   _log = log;
+   return BrookCommon::DefaultReturnValue;
+}
+
+/* 
+ * Get contents of object
+ *
+ * @param tab         tab
+ * @param description description
+ * @param value       value
+ *
+ * @return string containing contents
+ *
+ * */
+
+std::string BrookCommon::_getLine( const std::string& tab, const std::string& description, const std::string& value ) const {
+
+// ---------------------------------------------------------------------------------------
+
+   static const std::string methodName      = "BrookCommon::_getLine";
+
+   static const unsigned int MAX_LINE_CHARS = 256;
+   char line[MAX_LINE_CHARS];
+
+// ---------------------------------------------------------------------------------------
+
+   std::stringstream message;
+   memset( line, ' ', MAX_LINE_CHARS ); 
+#ifdef WIN32
+   (void) sprintf_s( line, MAX_LINE_CHARS, "%s %-40s %s", tab.c_str(), description.c_str(), value.c_str() );
+#else
+   (void) sprintf( line, "%s %-40s %s", tab.c_str(), description.c_str(), value.c_str() );
+#endif
+   message << std::string( line ) << std::endl;
+
+   return message.str();
+
+}

platforms/brook/src/BrookCommon.h

+#ifndef BrookCommon_H_
+#define BrookCommon_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, Mark Friedrichs                                    *
+ * 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 <vector>
+#include <set>
+
+#include "BrookFloatStreamImpl.h"
+#include "BrookIntStreamImpl.h"
+#include "BrookPlatform.h"
+
+namespace OpenMM {
+
+/**
+ * This kernel is invoked by StandardMMForceField to calculate the forces acting on the system.
+ */
+class BrookCommon {
+
+   public:
+  
+      // return values
+
+      static const int DefaultReturnValue = 0;
+      static const int ErrorReturnValue   = -1;
+
+      BrookCommon( );
+  
+      ~BrookCommon();
+  
+      /**
+       * Return number of atoms
+       * 
+       * @return number of atoms
+       *
+       */
+
+      int getNumberOfAtoms( void ) const; 
+
+      /** 
+       * Get atom ceiling parameter
+       * 
+       * @return atom ceiling parameter
+       *
+       */
+      
+      int getAtomSizeCeiling( void ) const;
+      
+      /**
+       * Get atom stream width
+       *
+       * @param platform platform reference
+       *
+       * @return atom stream width
+       */
+
+      int getAtomStreamWidth( const Platform& platform ); 
+
+      /**
+       * Get atom stream width
+       *
+       * @return atom stream width
+       */
+
+      int getAtomStreamWidth( void ) const; 
+
+      /**
+       * Get atom stream height
+       *
+       * @param platform platform reference
+       *
+       * @return atom stream height
+       */
+
+      int getAtomStreamHeight( const Platform& platform ); 
+
+      /**
+       * Get atom stream height
+       *
+       * @return atom stream height
+       */
+
+      int getAtomStreamHeight( void ) const;
+
+      /**
+       * Get atom stream size
+       * 
+       * @param platform platform reference
+       *
+       * @return atom stream size
+       */
+
+      int getAtomStreamSize( const Platform& platform ); 
+
+      /**
+       * Get atom stream size
+       * 
+       * @return atom stream size
+       */
+
+      int getAtomStreamSize( void ) const; 
+
+      /** 
+       * Set log file reference
+       * 
+       * @param  log file reference
+       *
+       * @return DefaultReturnValue
+       *
+       */
+      
+      int setLog( FILE* log );
+
+      /* 
+       * Get contents of object
+       *
+       * @param level of dump
+       *
+       * @return string containing contents
+       *
+       * */
+      
+      std::string getContents( int level ) const;
+
+   protected:
+   
+      // number of atoms
+
+      int _numberOfAtoms;
+
+      // atom stream dimensions
+
+      int _atomStreamWidth;
+      int _atomStreamHeight;
+      int _atomStreamSize;
+
+      // atom size mod
+
+      int _atomSizeModified;
+
+      // log file reference
+
+      FILE* _log;
+
+      /**
+       * Set number of atoms
+       * 
+       * @param numberOfAtoms number of atoms
+       *
+       */
+
+      int setNumberOfAtoms( int numberOfAtoms ); 
+
+      /** 
+       * Get atom stream dimensions
+       * 
+       * @param platform                  platform
+       *
+       */
+      
+      void _getAtomStreamDimensions( const Platform& platform );
+      
+      /** 
+       * Get log file reference
+       * 
+       * @return  log file reference
+       *
+       */
+      
+      FILE* getLog( void ) const;
+      
+      /* 
+       * Get line
+       *
+       * @param tab         tab
+       * @param description description
+       * @param value       value
+       *
+       * @return string containing contents
+       *
+       * */
+      
+      std::string _getLine( const std::string& tab, const std::string& description, const std::string& value ) const;
+      
+};
+
+} // namespace OpenMM
+
+#endif /*OPENMM_BROOKKERNELS_H_*/