Bonded & Nonbonded classes

platforms/brook/src/BrookBonded.h

+#ifndef BrookBonded_H_
+#define BrookBonded_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 "BrookFloatStreamImpl.h"
+#include "BrookIntStreamImpl.h"
+#include "BrookPlatform.h"
+#include "BrookCommon.h"
+#include "OpenMMContext.h"
+
+namespace OpenMM {
+
+/**
+ * This kernel is invoked by StandardMMForceField to calculate the forces acting on the system.
+ */
+class BrookBonded : public BrookCommon {
+
+   public:
+  
+      static const int DefaultReturnValue = 0;
+      static const int ErrorReturnValue   = -1; 
+
+      BrookBonded( );
+  
+      ~BrookBonded();
+  
+      /**
+       * Initialize the kernel, setting up the values of all the force field parameters.
+       * 
+       * @param bondIndices               the two atoms connected by each bond term
+       * @param bondParameters            the force parameters (length, k) for each bond term
+       * @param angleIndices              the three atoms connected by each angle term
+       * @param angleParameters           the force parameters (angle, k) for each angle term
+       * @param periodicTorsionIndices    the four atoms connected by each periodic torsion term
+       * @param periodicTorsionParameters the force parameters (k, phase, periodicity) for each periodic torsion term
+       * @param rbTorsionIndices          the four atoms connected by each Ryckaert-Bellemans torsion term
+       * @param rbTorsionParameters       the coefficients (in order of increasing powers) for each Ryckaert-Bellemans torsion term
+       * @param bonded14Indices           each element contains the indices of two atoms whose nonbonded interactions should be reduced since
+       *                                  they form a bonded 1-4 pair
+       * @param nonbondedParameters       the nonbonded force parameters (charge, sigma, epsilon) for each atom
+       * @param lj14Scale                 the factor by which van der Waals interactions should be reduced for bonded 1-4 pairs
+       * @param coulomb14Scale            the factor by which Coulomb interactions should be reduced for bonded 1-4 pairs
+       * @param log                       log reference
+       *
+       * @return nonzero value if error
+       *
+       */
+
+      int setup( int numberOfAtoms, 
+                 const std::vector<std::vector<int> >& bondIndices,            const std::vector<std::vector<double> >& bondParameters,
+                 const std::vector<std::vector<int> >& angleIndices,           const std::vector<std::vector<double> >& angleParameters,
+                 const std::vector<std::vector<int> >& periodicTorsionIndices, const std::vector<std::vector<double> >& periodicTorsionParameters,
+                 const std::vector<std::vector<int> >& rbTorsionIndices,       const std::vector<std::vector<double> >& rbTorsionParameters,
+                 const std::vector<std::vector<int> >& bonded14Indices,        const std::vector<std::vector<double> >& nonbondedParameters,
+                 double lj14Scale, double coulomb14Scale, const BrookPlatform& platform );
+
+      /**
+       * Return number of parameter streams
+       * 
+       * @return number of parameter streams
+       *
+       */
+
+      int getNumberOfParameterStreams( void ) const; 
+
+      /**
+       * Return number of force streams
+       * 
+       * @return number of force streams
+       *
+       */
+
+      int getNumberOfForceStreams( void ) const; 
+
+      /**
+       * Return stream count for specifed index (i, j, k, l)
+       * 
+       * @return stream count for specifed index
+       *
+       * @throw throws OpenMMException if index out of range
+       */
+
+      int getInverseMapStreamCount( int index ) const; 
+
+      /**
+       * Return max stream count
+       * 
+       * @return max stream count
+       */
+
+      int getMaxInverseMapStreamCount( void ) const; 
+
+      /**
+       * Return Brook stream handle
+       * 
+       * @return 
+       */
+
+      BrookFloatStreamImpl* getBrookAtomIndices( void ) const; 
+
+      /**
+       * Get LJ 14 scale factor
+       *
+       * @return  LJ 14 scaling (fudge) factor
+       * 
+       */
+
+       BrookOpenMMFloat getLJ_14Scale( void ) const;
+
+      /** 
+       * Get Coulomb factor
+       * 
+       * @return Coulomb factor
+       *
+       */
+      
+      BrookOpenMMFloat getCoulombFactor( void ) const;
+
+      /** 
+       * Get bonded atom indices stream
+       * 
+       * @return  atom indices stream
+       *
+       */
+      
+      BrookFloatStreamImpl* getAtomIndicesStream( void ) const;
+      
+      /** 
+       * Get array of bonded parameter streams
+       * 
+       * @return  array of bonded parameter streams
+       *
+       */
+      
+      BrookFloatStreamImpl** getBondedParameterStreams( void );
+      
+      /** 
+       * Get array of force streams
+       * 
+       * @return  array
+       *
+       */
+      
+      BrookFloatStreamImpl** getBondedForceStreams( void );
+      
+      /** 
+       * Get array of inverse map streams
+       * 
+       * @param index  array index 
+       *
+       * @return  array inverse map streams
+       *
+       */
+      
+      BrookFloatStreamImpl** getInverseStreamMapsStreams( int index );
+      
+      /** 
+       * Return true if force[index] stream is set
+       *
+       * @param    index into force stream
+       * @return   true if index is valid && force[index] stream is set; else false
+       *
+       */
+      
+      int isForceStreamSet( int index ) const;
+       
+      /** 
+       * Return true if paramsterSet[index] stream is set
+       *
+       * @param    index into parameter stream
+       *
+       * @return   true if index is valid && paramsterSet[index] stream is set; else false
+       *
+       */
+      
+      int isParameterStreamSet( int index ) const;
+          
+      /** 
+       * Return string showing if all inverse map streams are set
+       *
+       * @param    index into inverse map stream array
+       *
+       * @return   informative string
+       *
+       */
+      
+      std::string checkInverseMapStream( int index ) const;
+
+      /* 
+       * Get contents of object
+       *
+       *
+       * @param level   level of dump
+       *
+       * @return string containing contents
+       *
+       * */
+      
+      std::string getContents( int level ) const;
+
+   private:
+   
+      static const int NumberOfParameterStreams = 5;
+      static const int NumberOfForceStreams     = 4;
+      static const int MaxNumberOfInverseMaps   = 9;
+
+      enum { StreamI, StreamJ, StreamK, StreamL, StreamMax };
+
+      // inverse map stream width
+
+      int _invMapStreamWidth;
+
+      // actual max number of inverse maps 
+
+      int _maxNumberOfInverseMaps;
+
+      // scale factors for 1-4 ixn
+
+      BrookOpenMMFloat _ljScale;
+      BrookOpenMMFloat _coulombFactor;
+
+      // streams
+
+      BrookFloatStreamImpl* _atomIndicesStream;
+      BrookFloatStreamImpl* _bondedParameters[NumberOfParameterStreams];
+      BrookFloatStreamImpl* _bondedForceStreams[NumberOfForceStreams];
+      BrookFloatStreamImpl* _chargeStream;
+      BrookFloatStreamImpl* _inverseStreamMaps[NumberOfForceStreams][MaxNumberOfInverseMaps];
+
+      int _maxInverseMapStreamCount[NumberOfForceStreams];
+      int _inverseMapStreamCount[NumberOfForceStreams];
+
+      // helper methods in setup of parameters
+
+      void flipQuartet( int ibonded, int *atoms );
+      int matchTorsion( int i, int j, int k, int l, int nbondeds, int *atoms );
+      int matchAngle( int i, int j, int k, int nbondeds, int *atoms, int *flag );
+      int matchBond( int i, int j, int nbondeds, int *atoms, int *flag );
+      int matchPair( int i, int j, int nbondeds, int *atoms );
+
+      /**
+       * Setup Ryckaert-Bellemans parameters/atom indices
+       * 
+       * @param nbondeds                  number of bonded entries
+       * @param atoms                     array of atom indices
+       * @param params                    arrays of bond parameters
+       * @param rbTorsionIndices          the four atoms connected by each Ryckaert-Bellemans torsion term
+       * @param rbTorsionParameters       the coefficients (in order of increasing powers) for each Ryckaert-Bellemans torsion term
+       *
+       * @return nonzero value if error
+       *
+       */
+
+      int addRBDihedrals( int *nbondeds, int *atoms, BrookOpenMMFloat* params[], const std::vector<std::vector<int> >& rbTorsionIndices,  
+                          const std::vector<std::vector<double> >& rbTorsionParameters );
+
+      /**
+       * Setup periodic torsion parameters/atom indices
+       * 
+       * @param nbondeds                  number of bonded entries
+       * @param atoms                     array of atom indices
+       * @param params                    arrays of bond parameters
+       * @param periodicTorsionIndices    the four atoms connected by each periodic torsion term
+       * @param periodicTorsionParameters the force parameters (k, phase, periodicity) for each periodic torsion term
+       *
+       * @return nonzero value if error
+       *
+       */
+
+      int addPDihedrals( int *nbondeds, int *atoms, BrookOpenMMFloat* params[], const std::vector<std::vector<int> >& periodicTorsionIndices,  
+                          const std::vector<std::vector<double> >& periodicTorsionParameters );
+
+      /**
+       * Setup angle bond parameters/atom indices
+       * 
+       * @param nbondeds                  number of bonded entries
+       * @param atoms                     array of atom indices
+       * @param params                    arrays of bond parameters
+       * @param angleIndices              the angle bond atom indices
+       * @param angleParameters           the angle parameters (angle in radians, force constant)
+       *
+       * @return nonzero value if error
+       *
+       */
+
+      int addAngles( int *nbondeds, int *atoms, BrookOpenMMFloat* params[], const std::vector<std::vector<int> >& angleIndices,
+                     const std::vector<std::vector<double> >& angleParameters );
+
+      /**
+       * Setup harmonic bond parameters/atom indices
+       * 
+       * @param nbondeds                  number of bonded entries
+       * @param atoms                     array of atom indices
+       * @param params                    arrays of bond parameters
+       * @param bondIndices               two harmonic bond atom indices
+       * @param bondParameters            the force parameters (distance, k)
+       *
+       * @return nonzero value if error
+       *
+       */
+
+      int addBonds( int *nbondeds, int *atoms, BrookOpenMMFloat* params[], const std::vector<std::vector<int> >& bondIndices,
+                    const std::vector<std::vector<double> >& bondParameters );
+
+      /**
+       * Setup LJ/Coulomb 1-4 parameters/atom indices
+       * 
+       * @param nbondeds                  number of bonded entries
+       * @param atoms                     array of atom indices
+       * @param params                    arrays of bond parameters
+       * @param charges                   array of charges
+       * @param bonded14Indices           each element contains the indices of two atoms whose nonbonded interactions should be reduced since
+       *                                  they form a bonded 1-4 pair
+       * @param nonbondedParameters       the nonbonded force parameters (charge, sigma, epsilon) for each atom
+       * @param lj14Scale                 the factor by which van der Waals interactions should be reduced for bonded 1-4 pairs
+       *
+       * @return nonzero value if error
+       *
+       */
+
+      int addPairs( int *nbondeds, int *atoms, BrookOpenMMFloat* params[], BrookOpenMMFloat* charges,
+                    const std::vector<std::vector<int> >& bonded14Indices, const std::vector<std::vector<double> >& nonbondedParameters,
+                    double lj14Scale, double coulombScale );
+      
+      /**
+       * Create and load inverse maps for bonded ixns
+       * 
+       * @param nbondeds                  number of bonded entries
+       * @param natoms                    number of atoms
+       * @param atoms                     arrays of atom indices (atoms[numberOfBonds][4])
+       * @param platform                  BrookPlatform reference
+       * @param log                       log file reference (optional)
+       *
+       * @return nonzero value if error
+       *
+       */
+
+      int loadInvMaps( int nbondeds, int natoms, int *atoms, const BrookPlatform& platform );
+      
+      /**
+       * Get inverse amp stream width
+       * 
+       * @return stream width
+       *
+       */
+
+      int getInvMapStreamWidth( void ) const;
+      
+      /**
+       * Validate inverse map count
+       * 
+       * @param index index to check (1-4) 
+       * @param count count for index
+       *
+       * @return -1 if count invalid
+       *
+       * @tthrow OpenMMException exeception if count invalid
+       *
+       */
+
+      int validateInverseMapStreamCount( int index, int count ) const;
+      
+};
+
+} // namespace OpenMM
+
+#endif /*OPENMM_BROOKKERNELS_H_*/

platforms/brook/src/BrookNonBonded.h

+#ifndef BrookNonBonded_H_
+#define BrookNonBonded_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"
+#include "BrookCommon.h"
+
+namespace OpenMM {
+
+/**
+ * This kernel is invoked by StandardMMForceField to calculate the forces acting on the system.
+ */
+class BrookNonBonded : public BrookCommon {
+
+   public:
+  
+      // return values
+
+      static const int DefaultReturnValue = 0;
+      static const int ErrorReturnValue   = -1;
+
+      BrookNonBonded( );
+  
+      ~BrookNonBonded();
+  
+      /**
+       * Return number of force streams
+       * 
+       * @return number of force streams
+       *
+       */
+
+      int getNumberOfForceStreams( void ) const; 
+
+      /** 
+       * Get duplication factor
+       * 
+       * @return   duplication factor
+       *
+       */
+      
+      int getDuplicationFactor( void ) const;
+      
+      /** 
+       * Get atom ceiling parameter
+       * 
+       * @return atom ceiling parameter
+       *
+       */
+         
+      int getAtomSizeCeiling( void ) const;
+ 
+      /** 
+       * Get outer loop unroll
+       * 
+       * @return   outer loop unroll (fixed value)
+       *
+       */
+      
+      int getOuterLoopUnroll( void ) const;
+      
+      /** 
+       * Set outer loop unroll
+       * 
+       * @param  outer loop unroll (fixed value)
+       *
+       * @return updated outer loop unroll (fixed value)
+       *
+       */
+      
+      int setOuterLoopUnroll( int outerUnroll );
+      
+      /**
+       * Return unrolling for inner loops
+       * 
+       * @return outer loop unrolling
+       */
+
+      int getInnerLoopUnroll( void ) const; 
+
+      /**
+       * Get j-stream width
+       *
+       * @param platform platform reference
+       *
+       * @return j-stream width
+       */
+
+      int getJStreamWidth( const Platform& platform ); 
+
+      /**
+       * Get j-stream width
+       *
+       * @return j-stream width
+       */
+
+      int getJStreamWidth( void ) const; 
+
+      /**
+       * Get j-stream height
+       *
+       * @param platform platform reference
+       *
+       * @return j-stream height
+       */
+
+      int getJStreamHeight( const Platform& platform ); 
+
+      /**
+       * Get j-stream height
+       *
+       * @return j-stream height
+       */
+
+      int getJStreamHeight( void ) const;
+
+      /**
+       * Get j-stream size
+       * 
+       * @param platform platform reference
+       *
+       * @return j-stream size
+       */
+
+      int getJStreamSize( const Platform& platform ); 
+
+      /**
+       * Get j-stream size
+       * 
+       * @return j-stream size
+       */
+
+      int getJStreamSize( void ) const; 
+
+      /**
+       * Get partial force stream width
+       *
+       * @param platform platform reference
+       *
+       * @return partial force stream width
+       */
+
+      int getPartialForceStreamWidth( const Platform& platform ); 
+
+      /**
+       * Get partial force stream width
+       *
+       * @return partial force stream width
+       */
+
+      int getPartialForceStreamWidth( void ) const; 
+
+      /**
+       * Get partial force stream height
+       *
+       * @param platform platform reference
+       *
+       * @return partial force stream height
+       */
+
+      int getPartialForceStreamHeight( const Platform& platform ); 
+
+      /**
+       * Get partial force stream height
+       *
+       * @return partial force stream height
+       */
+
+      int getPartialForceStreamHeight( void ) const;
+
+      /**
+       * Get partial force stream size
+       * 
+       * @param platform platform reference
+       *
+       * @return partial force stream size
+       */
+
+      int getPartialForceStreamSize( const Platform& platform ); 
+
+      /**
+       * Get partial force stream size
+       * 
+       * @return partial force stream size
+       */
+
+      int getPartialForceStreamSize( void ) const; 
+
+      /**
+       * Get partial force stream size
+       * 
+       * @return partial force stream size
+       */
+
+      /**
+       * Get exclusion stream width
+       * 
+       * @return exclusion stream width
+       */
+
+      int getExclusionStreamWidth( void ) const; 
+
+      /**
+       * Get exclusion stream size
+       * 
+       * @return exclusion stream size
+       */
+
+      int getExclusionStreamSize( void ) const; 
+
+      /** 
+       * Get exclusion stream 
+       *
+       * @return  exclusion stream
+       *
+       */
+      
+      BrookFloatStreamImpl* getExclusionStream( void ) const;
+      
+      /** 
+       * Get vdw stream 
+       *
+       * @return  vdw stream
+       *
+       */
+      
+      BrookFloatStreamImpl* getVdwStream( void ) const;
+      
+      /** 
+       * Get charge stream 
+       *
+       * @return  charge stream
+       *
+       */
+      
+      BrookFloatStreamImpl* getChargeStream( void ) const;
+      
+      /** 
+       * Get sigma-eps stream 
+       *
+       * @return  sigma-eps stream
+       *
+       */
+      
+      BrookFloatStreamImpl* getSigmaStream( void ) const;
+      
+      /** 
+       * Get epsilon stream 
+       *
+       * @return  epsilon stream
+       *
+       */
+      
+      BrookFloatStreamImpl* getEpsilonStream( void ) const;
+      
+      /** 
+       * Get force streams 
+       *
+       * @return  force streams
+       *
+       */
+      
+      BrookFloatStreamImpl** getForceStreams( void );
+      
+      /** 
+       * Return true if force[index] stream is set 
+       *
+       * @return  true  if index is valid && force[index] stream is set; else false
+       *
+       */
+      
+      int isForceStreamSet( int index ) const;
+      
+      /* 
+       * Setup of nonbonded ixns
+       *
+       * @param numberOfAtoms         number of atoms
+       * @param nonbondedParameters   vector of nonbonded parameters [atomI][0=c6]
+       *                                                             [atomI][1=c12]
+       *                                                             [atomI][2=charge]
+       * @param platform              Brook platform
+       * @param log                   optional Log file reference
+       *
+       * @return nonzero value if error
+       * */
+      
+      int setup( int numberOfAtoms, const std::vector<std::vector<double> >& nonbondedParameters,
+                 const std::vector<std::set<int> >& exclusions,  const BrookPlatform& platform );
+      
+      /* 
+       * Get contents of object
+       *
+       * @param level of dump
+       *
+       * @return string containing contents
+       *
+       * */
+      
+      std::string getContents( int level ) const;
+
+   private:
+   
+      // fixed number of force streams
+
+      static const int NumberOfForceStreams     = 4;
+
+      // atom ceiling
+
+      int _atomSizeCeiling;
+
+      // unroll in i/j dimensions
+
+      int _outerUnroll;
+      int _innerUnroll;
+
+      // duplication factor
+
+      int _duplicationFactor;
+
+      // force stream width
+
+      int _partialForceStreamWidth;
+      int _partialForceStreamHeight;
+      int _partialForceStreamSize;
+
+      // exclusions stream dimensions
+
+      int _exclusionStreamWidth;
+      int _exclusionStreamHeight;
+      int _exclusionStreamSize;
+
+      // j-stream dimensions
+
+      int _jStreamWidth;
+      int _jStreamHeight;
+      int _jStreamSize;
+
+      // streams
+
+      BrookFloatStreamImpl* _exclusionStream;
+      BrookFloatStreamImpl* _vdwStream;
+      BrookFloatStreamImpl* _chargeStream;
+      BrookFloatStreamImpl* _sigmaStream;
+      BrookFloatStreamImpl* _epsilonStream;
+      BrookFloatStreamImpl* _nonbondedForceStreams[NumberOfForceStreams];
+
+      /** 
+       * Initialize exclusion stream dimensions and stream
+       * 
+       * @param platform                  platform
+       *
+       * @return nonzero value if error
+       *
+       */
+      
+      int initializeExclusionStream( const Platform& platform );
+            
+      /** 
+       * Set exclusion (4x4)
+       * 
+       * @param i                         atom i index
+       * @param j                         atom j index
+       * @param exclusionStreamWidth      exclusion stream width
+       * @param exclusion                 array of packed exclusions
+       *
+       * @return nonzero value if error
+       *
+       */
+      
+      int setExclusion( int i, int j, int exclusionStreamWidth, BrookOpenMMFloat* exclusion );
+      
+      /** 
+       * Initialize exclusions
+       * 
+       * @param exclusions                vector of sets containing exclusions (1 set entry for every atom)
+       * @param platform                  platform
+       *
+       * @return nonzero value if error
+       *
+       */
+      
+      int initializeExclusions( const std::vector<std::set<int> >& exclusionsVector, const Platform& platform );
+
+      /** 
+       * Initialize stream dimensions and streams
+       * 
+       * @param platform                  platform
+       *
+       * @return nonzero value if error
+       *
+       */
+      
+      int initializeStreams( int numberOfAtoms, const Platform& platform );
+      
+      /** 
+       * Set sigma & epsilon given c6 & c12 (geometric rule)
+       * 
+       * @param c6                        vdw c6
+       * @param c12                       vdw c12
+       * @param sigma                     massaged sigma
+       * @param epsilon                   massaged epsilon
+       *
+       * @return nonzero value if error
+       *
+       */
+      
+      int setSigmaEpsilon( double c6, double c12, double* sigma , double* epsilon );
+
+      /** 
+       * Initialize vdw & charge
+       * 
+       * @param exclusions                vector of sets containing exclusions (1 set entry for every atom)
+       * @param platform                  platform
+       *
+       * @return nonzero value if error
+       *
+       */
+      
+      int initializeVdwAndCharge( const std::vector<std::vector<double> >& nonbondedParameters, const Platform& platform );
+      
+};
+
+} // namespace OpenMM
+
+#endif /*OPENMM_BROOKKERNELS_H_*/