New

platforms/brook/src/BrookCalcProperDihedralBondForceKernel.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, 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 "OpenMMException.h"
+#include <sstream>
+#include "BrookCalcProperDihedralForceKernel.h"
+
+using namespace OpenMM;
+using namespace std;
+
+const std::string BrookCalcProperDihedralForceKernel::BondName = "ProperDihedral";
+
+/** 
+ * BrookCalcProperDihedralForceKernel constructor
+ * 
+ * @param name                      kernel name
+ * @param platform                  platform
+ * @param OpenMMBrookInterface      OpenMM-Brook interface
+ * @param System                    System reference
+ *
+ */
+
+BrookCalcProperDihedralForceKernel::BrookCalcProperDihedralForceKernel( std::string name, const Platform& platform,
+                                                                      OpenMMBrookInterface& openMMBrookInterface, System& system ) :
+                     CalcProperDihedralForceKernel( name, platform ), _openMMBrookInterface( openMMBrookInterface ), _system( system ){
+
+// ---------------------------------------------------------------------------------------
+
+   // static const std::string methodName      = "BrookCalcProperDihedralForceKernel::BrookCalcProperDihedralForceKernel";
+   // static const int debug                   = 1;
+
+// ---------------------------------------------------------------------------------------
+
+   _brookBondParameters              = NULL;
+   _log                              = NULL;
+
+   const BrookPlatform brookPlatform = dynamic_cast<const BrookPlatform&> (platform);
+   if( brookPlatform.getLog() != NULL ){
+      setLog( brookPlatform.getLog() );
+   }
+      
+}   
+
+/** 
+ * BrookCalcProperDihedralForceKernel destructor
+ * 
+ */
+
+BrookCalcProperDihedralForceKernel::~BrookCalcProperDihedralForceKernel( ){
+
+// ---------------------------------------------------------------------------------------
+
+   // static const std::string methodName      = "BrookCalcProperDihedralForceKernel::BrookCalcProperDihedralForceKernel";
+   // static const int debug                   = 1;
+
+// ---------------------------------------------------------------------------------------
+
+   delete _brookBondParameters;
+}
+
+/** 
+ * Get log file reference
+ * 
+ * @return  log file reference
+ *
+ */
+
+FILE* BrookCalcProperDihedralForceKernel::getLog( void ) const {
+   return _log;
+}
+
+/** 
+ * Set log file reference
+ * 
+ * @param  log file reference
+ *
+ * @return  DefaultReturnValue
+ *
+ */
+
+int BrookCalcProperDihedralForceKernel::setLog( FILE* log ){
+   _log = log;
+   return BrookCommon::DefaultReturnValue;
+}
+
+/** 
+ * Initialize the kernel, setting up the values of all the force field parameters.
+ * 
+ * @param system                    System reference
+ * @param force                     ProperDihedralForce reference
+ *
+ */
+
+void BrookCalcProperDihedralForceKernel::initialize( const System& system, const ProperDihedralForce& force ){
+
+// ---------------------------------------------------------------------------------------
+
+   static const std::string methodName      = "BrookCalcProperDihedralForceKernel::initialize";
+
+// ---------------------------------------------------------------------------------------
+
+   FILE* log                 = getLog();
+
+   // ---------------------------------------------------------------------------------------
+
+   // create _brookBondParameters object containing atom indices/parameters
+
+   int numberOfBonds         = force.getNumAngles();
+
+   if( _brookBondParameters ){
+      delete _brookBondParameters;
+   }
+   _brookBondParameters = new BrookBondParameters( BondName, NumberOfAtomsInBond, NumberOfParametersInBond, numberOfBonds, getLog() );
+
+   for( int ii = 0; ii < numberOfBonds; ii++ ){
+
+      int particle1, particle2, particle3;
+      double angle, k;
+
+      int particles[NumberOfAtomsInBond];
+      double parameters[NumberOfParametersInBond];
+
+      force.getAngleParameters( ii, particle1, particle2, particle3, angle, k ); 
+      particles[0]    = particle1;
+      particles[1]    = particle2;
+      particles[2]    = particle3;
+ 
+      parameters[0]   = angle;
+      parameters[1]   = k;
+
+      _brookBondParameters->setBond( ii, particles, parameters );
+   }   
+   _openMMBrookInterface.setProperDihedralForceParameters( _brookBondParameters );
+   _openMMBrookInterface.setTriggerForceKernel( this );
+   _openMMBrookInterface.setTriggerEnergyKernel( this );
+
+   if( log ){
+      std::string contents = _brookBondParameters->getContentsString( ); 
+      (void) fprintf( log, "%s brookGbsa::contents\n%s", methodName.c_str(), contents.c_str() );
+      (void) fflush( log );
+   }
+
+   // ---------------------------------------------------------------------------------------
+    
+}
+
+/** 
+ * Compute forces given atom coordinates
+ * 
+ * @param context OpenMMContextImpl context
+ *
+ */
+
+void BrookCalcProperDihedralForceKernel::executeForces( OpenMMContextImpl& context ){
+
+// ---------------------------------------------------------------------------------------
+
+   //static const std::string methodName   = "BrookCalcProperDihedralForceKernel::executeForces";
+
+// ---------------------------------------------------------------------------------------
+
+   if( _openMMBrookInterface.getTriggerForceKernel() == this ){
+      _openMMBrookInterface.computeForces( context );
+   }
+
+   return;
+
+   // ---------------------------------------------------------------------------------------
+}
+
+/**
+ * Execute the kernel to calculate the energy
+ * 
+ * @param context OpenMMContextImpl context
+ *
+ * @return  potential energy
+ *
+ */
+
+double BrookCalcProperDihedralForceKernel::executeEnergy( OpenMMContextImpl& context ){
+
+// ---------------------------------------------------------------------------------------
+
+   //static const std::string methodName      = "BrookCalcProperDihedralForceKernel::executeEnergy";
+
+// ---------------------------------------------------------------------------------------
+
+   if( _openMMBrookInterface.getTriggerEnergyKernel() == this ){
+      return (double) _openMMBrookInterface.computeEnergy( context );
+   } else {
+      return 0.0;
+   }
+
+}

platforms/brook/src/BrookCalcProperDihedralBondForceKernel.h

+#ifndef OPENMM_BROOK_CALC_PROPER_DIHEDRAL_FORCE_KERNEL_H_
+#define OPENMM_BROOK_CALC_PROPER_DIHEDRAL_FORCE_KERNEL_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 "kernels.h"
+#include "BrookPlatform.h"
+#include "BrookBondParameters.h"
+#include "OpenMMBrookInterface.h"
+
+namespace OpenMM {
+
+/**
+ * This kernel is invoked to calculate the harmonic angle forces acting on the system.
+ */
+
+class BrookCalcProperDihedralForceKernel : public CalcProperDihedralForceKernel {
+
+   public:
+  
+      /**
+       * BrookCalcProperDihedralForceKernel constructor
+       */
+
+      BrookCalcProperDihedralForceKernel( std::string name, const Platform& platform, OpenMMBrookInterface& openMMBrookInterface, System& system );
+  
+      /**
+       * BrookCalcProperDihedralForceKernel destructor
+       */
+
+      ~BrookCalcProperDihedralForceKernel();
+  
+      /**
+       * Initialize the kernel, setting up the values to calculate harmonic bond force & energy
+       * 
+       * @param system                    System reference
+       * @param force                     ProperDihedralForce reference
+       *
+       */
+
+      void initialize( const System& system, const ProperDihedralForce& force );
+  
+      /**
+       * Execute the kernel to calculate the forces.
+       * 
+       * @param positions   atom coordiantes
+       * @param forces      output forces
+       *
+       */
+
+      void executeForces( OpenMMContextImpl& context );
+  
+      /**
+       * Execute the kernel to calculate the energy.
+       * 
+       * @param context    the context in which to execute this kernel
+       *
+       * @return  potential energy associated with the harmonic angle force
+       *
+       */
+
+      double executeEnergy( OpenMMContextImpl& context );
+
+      /** 
+       * 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;
+
+      /** 
+       * Get log file reference
+       * 
+       * @return  log file reference
+       *
+       */
+      
+      FILE* getLog( void ) const;
+      
+      /** 
+       * Get number of bonds
+       * 
+       * @return  number of bonds
+       *
+       */
+      
+      int getNumberOfBonds( void ) const;
+      
+      /** 
+       * Get indices/parameters
+       * 
+       * @return  BrookBondParameters containing atom indices/parameters
+       *
+       */
+      
+      BrookBondParameters* getBrookBondParameters( void ) const;
+      
+   private:
+   
+      static const int NumberOfAtomsInBond      = 3;
+      static const int NumberOfParametersInBond = 2;
+
+      // bond name
+
+      static const std::string BondName;
+
+      // log file reference
+
+      FILE* _log;
+
+
+      // Brook bond parameters
+
+      BrookBondParameters* _brookBondParameters;
+
+      // interface
+
+      OpenMMBrookInterface& _openMMBrookInterface;
+
+      // System reference
+
+      System& _system;
+
+};
+
+} // namespace OpenMM
+
+#endif /* OPENMM_BROOK_CALC_PROPER_DIHEDRAL_FORCE_KERNEL_H_ */