Moving the reference code into the platforms folder

platforms/reference/src/ReferenceAngleBondIxn.cpp

+
+/* Portions copyright (c) 2006 Stanford University and Simbios.
+ * Contributors: Pande Group
+ *
+ * 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 <string.h>
+#include <sstream>
+
+#include "SimTKOpenMMCommon.h"
+#include "SimTKOpenMMLog.h"
+#include "SimTKOpenMMUtilities.h"
+#include "ReferenceAngleBondIxn.h"
+#include "ReferenceForce.h"
+
+/**---------------------------------------------------------------------------------------
+
+   ReferenceAngleBondIxn constructor
+
+   --------------------------------------------------------------------------------------- */
+
+ReferenceAngleBondIxn::ReferenceAngleBondIxn( ){
+
+   // ---------------------------------------------------------------------------------------
+
+   // static const char* methodName = "\nReferenceAngleBondIxn::ReferenceAngleBondIxn";
+
+   // ---------------------------------------------------------------------------------------
+
+}
+
+/**---------------------------------------------------------------------------------------
+
+   ReferenceAngleBondIxn destructor
+
+   --------------------------------------------------------------------------------------- */
+
+ReferenceAngleBondIxn::~ReferenceAngleBondIxn( ){
+
+   // ---------------------------------------------------------------------------------------
+
+   // static const char* methodName = "\nReferenceAngleBondIxn::~ReferenceAngleBondIxn";
+
+   // ---------------------------------------------------------------------------------------
+
+}
+
+/**---------------------------------------------------------------------------------------
+
+   Get dEdR and energy term for angle bond
+
+   @param  cosine               cosine of angle
+   @param  angleParameters      angleParameters: angleParameters[0] = angle in degrees
+                                                 angleParameters[1] = k (force constant)
+   @param  dEdR                 output dEdR
+   @param  energyTerm           output energyTerm
+
+   @return ReferenceForce::DefaultReturn
+
+   --------------------------------------------------------------------------------------- */
+
+int ReferenceAngleBondIxn::getPrefactorsGivenAngleCosine( RealOpenMM cosine, RealOpenMM* angleParameters,
+                                                          RealOpenMM* dEdR, RealOpenMM* energyTerm ) const {
+
+   // ---------------------------------------------------------------------------------------
+
+   // static const std::string methodName = "\nReferenceAngleBondIxn::getPrefactorsGivenAngleCosine";
+
+   static const RealOpenMM zero        = 0.0;
+   static const RealOpenMM one         = 1.0;
+   static const RealOpenMM half        = 0.5;
+
+   // ---------------------------------------------------------------------------------------
+
+   RealOpenMM angle;
+   if( cosine >= one ){
+      angle = zero;
+   } else if( cosine <= -one ){
+      angle = PI_M;
+   } else {
+      angle = ACOS(cosine);
+   }
+   RealOpenMM deltaIdeal         = angle - (angleParameters[0]*DEGREE_TO_RADIAN);
+   RealOpenMM deltaIdeal2        = deltaIdeal*deltaIdeal;
+
+  *dEdR                          = angleParameters[1]*deltaIdeal;
+  *energyTerm                    = half*angleParameters[1]*deltaIdeal2;
+
+   return ReferenceForce::DefaultReturn;
+
+}
+
+/**---------------------------------------------------------------------------------------
+
+   Calculate Angle Bond ixn
+
+   @param atomIndices      two bond indices
+   @param atomCoordinates  atom coordinates
+   @param parameters       parameters: parameters[0] = ideal bond length
+                                       parameters[1] = bond k (includes factor of 2)
+   @param forces           force array (forces added)
+   @param energiesByBond   energies by bond: energiesByBond[bondIndex]
+   @param energiesByAtom   energies by atom: energiesByAtom[atomIndex]
+
+   @return ReferenceForce::DefaultReturn
+
+   --------------------------------------------------------------------------------------- */
+
+int ReferenceAngleBondIxn::calculateBondIxn( int* atomIndices,
+                                             RealOpenMM** atomCoordinates,
+                                             RealOpenMM* parameters,
+                                             RealOpenMM** forces,
+                                             RealOpenMM* energiesByBond,
+                                             RealOpenMM* energiesByAtom ) const {
+
+   // ---------------------------------------------------------------------------------------
+
+   // static const char* methodName = "\nReferenceAngleBondIxn::calculateBondIxn";
+
+   // ---------------------------------------------------------------------------------------
+
+   static const std::string methodName = "\nReferenceAngleBondIxn::calculateBondIxn";
+
+   // constants -- reduce Visual Studio warnings regarding conversions between float & double
+
+   static const RealOpenMM zero        =  0.0;
+   static const RealOpenMM one         =  1.0;
+   static const RealOpenMM two         =  2.0;
+   static const RealOpenMM three       =  3.0;
+   static const RealOpenMM oneM        = -1.0;
+
+   static const int threeI             = 3;
+
+   // debug flag
+
+   static const int debug              = 0;
+
+   static const int LastAtomIndex      = 3;
+
+   RealOpenMM deltaR[2][ReferenceForce::LastDeltaRIndex];
+
+   // ---------------------------------------------------------------------------------------
+
+   // get deltaR, R2, and R between 2 atoms
+
+   int atomAIndex = atomIndices[0];
+   int atomBIndex = atomIndices[1];
+   int atomCIndex = atomIndices[2];
+   ReferenceForce::getDeltaR( atomCoordinates[atomAIndex], atomCoordinates[atomBIndex], deltaR[0] );  
+   ReferenceForce::getDeltaR( atomCoordinates[atomCIndex], atomCoordinates[atomBIndex], deltaR[1] );  
+
+   RealOpenMM pVector[threeI];
+   SimTKOpenMMUtilities::crossProductVector3( deltaR[0], deltaR[1], pVector );
+   RealOpenMM rp              = DOT3( pVector, pVector );
+   rp                         = SQRT( rp );
+   if( rp < 1.0e-06 ){
+      rp = (RealOpenMM) 1.0e-06;
+   }   
+   RealOpenMM dot             = DOT3( deltaR[0], deltaR[1] );
+   RealOpenMM cosine          = dot/SQRT( (deltaR[0][ReferenceForce::R2Index]*deltaR[1][ReferenceForce::R2Index]) );
+
+   RealOpenMM dEdR;
+   RealOpenMM energy;
+   getPrefactorsGivenAngleCosine( cosine, parameters, &dEdR, &energy );
+
+   RealOpenMM termA           =  dEdR/(deltaR[0][ReferenceForce::R2Index]*rp);
+   RealOpenMM termC           = -dEdR/(deltaR[1][ReferenceForce::R2Index]*rp);
+
+   RealOpenMM deltaCrossP[LastAtomIndex][threeI];
+   SimTKOpenMMUtilities::crossProductVector3( deltaR[0], pVector, deltaCrossP[0] );
+   SimTKOpenMMUtilities::crossProductVector3( deltaR[1], pVector, deltaCrossP[2] );
+
+   for( int ii = 0; ii < threeI; ii++ ){
+      deltaCrossP[0][ii] *= termA;
+      deltaCrossP[2][ii] *= termC;
+      deltaCrossP[1][ii]  = oneM*(deltaCrossP[0][ii] + deltaCrossP[2][ii]);
+   }   
+
+   // accumulate forces
+ 
+   for( int jj = 0; jj < LastAtomIndex; jj++ ){
+      for( int ii = 0; ii < threeI; ii++ ){
+         forces[atomIndices[jj]][ii] += deltaCrossP[jj][ii];
+      }   
+   }   
+
+   // accumulate energies
+
+   updateEnergy( energy, energiesByBond, LastAtomIndex, atomIndices, energiesByAtom );
+
+   // debug 
+
+   if( debug ){
+      static bool printHeader = false;
+      std::stringstream message;
+      message << methodName;
+      message << std::endl;
+      if( !printHeader  ){  
+         printHeader = true;
+         message << std::endl;
+         message << methodName.c_str() << " a0 k [c q p s] r1 r2  angle dt rp p[] dot cosine angle dEdR*r F[]" << std::endl;
+      }   
+
+      message << std::endl;
+      for( int ii = 0; ii < 3; ii++ ){
+         message << " Atm " << atomIndices[ii] << " [" << atomCoordinates[ii][0] << " " << atomCoordinates[ii][1] << " " << atomCoordinates[ii][2] << "] ";
+      }
+      message << std::endl << " Delta:";
+      for( int ii = 0; ii < 2; ii++ ){
+         message << " [";
+         for( int jj = 0; jj < ReferenceForce::LastDeltaRIndex; jj++ ){
+            message << deltaR[ii][jj] << " ";
+         }
+         message << "]";
+      }
+      message << std::endl;
+
+      message << " a0="     << parameters[0];
+      message << " k="      << parameters[1];
+      message << " rab2="  << deltaR[0][ReferenceForce::R2Index];
+      message << " rcb2="  << deltaR[1][ReferenceForce::R2Index];
+      message << std::endl << "            ";
+      message << " rp="    << rp; 
+      message << " p[";
+      SimTKOpenMMUtilities::formatRealStringStream( message, pVector );
+      message << "] dot="   << dot;
+      message << " cos="   << cosine;
+
+      message << std::endl << "            ";
+      message << " dEdr=" << dEdR;
+      message << " trmA=" << termA;
+      message << " trmC=" << termC;
+
+      message << " E=" << energy << " F=compute force; f=cumulative force";
+
+      message << std::endl << "            ";
+      for( int ii = 0; ii < 3; ii++ ){
+         message << " F" << (ii+1) << "[";
+         SimTKOpenMMUtilities::formatRealStringStream( message, deltaCrossP[ii], threeI );
+         message << "]";
+      }   
+      message << std::endl << "            ";
+
+      for( int ii = 0; ii < LastAtomIndex; ii++ ){
+         message << " f" << (ii+1) << "[";
+         SimTKOpenMMUtilities::formatRealStringStream( message, forces[atomIndices[ii]], threeI );
+         message << "]";
+      }
+
+      SimTKOpenMMLog::printMessage( message );
+   }   
+
+   return ReferenceForce::DefaultReturn;
+}

platforms/reference/src/ReferenceAngleBondIxn.h

+
+/* Portions copyright (c) 2006 Stanford University and Simbios.
+ * Contributors: Pande Group
+ *
+ * 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.
+ */
+
+#ifndef __ReferenceAngleBondIxn_H__
+#define __ReferenceAngleBondIxn_H__
+
+#include "ReferenceBondIxn.h"
+
+// ---------------------------------------------------------------------------------------
+
+class ReferenceAngleBondIxn : public ReferenceBondIxn {
+
+   private:
+
+   public:
+
+      /**---------------------------------------------------------------------------------------
+      
+         Constructor
+      
+         --------------------------------------------------------------------------------------- */
+
+       ReferenceAngleBondIxn( );
+
+      /**---------------------------------------------------------------------------------------
+      
+         Destructor
+      
+         --------------------------------------------------------------------------------------- */
+
+       ~ReferenceAngleBondIxn( );
+
+      /**---------------------------------------------------------------------------------------
+
+         Get dEdR and energy term for angle bond
+      
+         @param  cosine               cosine of angle
+         @param  angleParameters      angleParameters: angleParameters[0] = angle in degrees
+                                                       angleParameters[1] = k (force constant)
+         @param  dEdR                 output dEdR
+         @param  energyTerm           output energyTerm
+      
+         @return ReferenceForce::DefaultReturn
+      
+         --------------------------------------------------------------------------------------- */
+      
+      int getPrefactorsGivenAngleCosine( RealOpenMM cosine, RealOpenMM* angleParameters,
+                                         RealOpenMM* dEdR, RealOpenMM* energyTerm ) const;
+      
+      /**---------------------------------------------------------------------------------------
+
+         Calculate Angle Bond ixn
+      
+         @param atomIndices      two bond indices
+         @param atomCoordinates  atom coordinates
+         @param parameters       parameters: parameters[0] = ideal bond length
+                                             parameters[1] = bond k (includes factor of 2)
+         @param forces           force array (forces added)
+         @param energiesByBond   energies by bond: energiesByBond[bondIndex]
+         @param energiesByAtom   energies by atom: energiesByAtom[atomIndex]
+      
+         @return ReferenceForce::DefaultReturn
+      
+         --------------------------------------------------------------------------------------- */
+      
+      int calculateBondIxn( int* atomIndices, RealOpenMM** atomCoordinates,
+                            RealOpenMM* parameters, RealOpenMM** forces,
+                            RealOpenMM* energiesByBond, RealOpenMM* energiesByAtom ) const;
+      
+
+};
+
+// ---------------------------------------------------------------------------------------
+
+#endif // __ReferenceAngleBondIxn_H__

platforms/reference/src/ReferenceBondForce.cpp

+
+/* Portions copyright (c) 2006 Stanford University and Simbios.
+ * Contributors: Pande Group
+ *
+ * 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 <string.h>
+#include <sstream>
+
+#include "SimTKOpenMMCommon.h"
+#include "SimTKOpenMMLog.h"
+#include "SimTKOpenMMUtilities.h"
+#include "ReferenceBondForce.h"
+
+/**---------------------------------------------------------------------------------------
+
+   ReferenceBondForce constructor
+
+   --------------------------------------------------------------------------------------- */
+
+ReferenceBondForce::ReferenceBondForce( ){
+
+   // ---------------------------------------------------------------------------------------
+
+   // static const char* methodName = "\nReferenceBondForce::ReferenceBondForce";
+
+   // ---------------------------------------------------------------------------------------
+
+}
+
+/**---------------------------------------------------------------------------------------
+
+   ReferenceBondForce destructor
+
+   --------------------------------------------------------------------------------------- */
+
+ReferenceBondForce::~ReferenceBondForce( ){
+
+   // ---------------------------------------------------------------------------------------
+
+   // static const char* methodName = "\nReferenceBondForce::~ReferenceBondForce";
+
+   // ---------------------------------------------------------------------------------------
+
+}
+
+/**---------------------------------------------------------------------------------------
+
+   Calculate forces/energy for bonds
+
+   @param numberOfBonds    number of bonds
+   @param atomIndices      indices of atoms participating in bond ixn: atomIndices[bondIndex][indices]
+   @param atomCoordinates  atom coordinates: atomCoordinates[atomIndex][3]
+   @param parameters       parameters: parameters[bondIndex][*]; contents of array 
+                           depend on ixn
+   @param forces           force array (forces added to current values): forces[atomIndex][3]
+   @param energiesByBond   energies by bond: energiesByBond[bondIndex]
+   @param energiesByAtom   energies by atom: energiesByAtom[atomIndex]
+   @param totalEnergy      totalEnergy: sum over { energies[atomIndex] }
+   @param ReferenceBondIxn ixn to be calculated
+
+   @return  ReferenceForce::DefaultReturn
+
+   --------------------------------------------------------------------------------------- */
+
+int ReferenceBondForce::calculateForce( int numberOfBonds, int** atomIndices,
+                                        RealOpenMM** atomCoordinates,
+                                        RealOpenMM** parameters,
+                                        RealOpenMM** forces, 
+                                        RealOpenMM* energiesByBond, 
+                                        RealOpenMM* energiesByAtom, 
+                                        RealOpenMM *totalEnergy, 
+                                        ReferenceBondIxn& referenceBondIxn ){
+
+
+   // ---------------------------------------------------------------------------------------
+
+   static const char* methodName = "\nReferenceBondForce::calculateForce";
+
+   // ---------------------------------------------------------------------------------------
+
+   for( int ii = 0; ii < numberOfBonds; ii++ ){
+
+      // diagnostics
+
+      if( 0 ){
+         std::stringstream message;
+         message << methodName << " " << ii;
+         //message << " XAtm" << (unsigned int) atomIndices << " " << (unsigned int) atomIndices[0];
+         //message << " atm[" << atomIndices[ii][0] << " " << atomIndices[ii][1] << "]";
+         SimTKOpenMMLog::printMessage( message );
+      }
+
+      // calculate bond ixn
+
+      referenceBondIxn.calculateBondIxn( atomIndices[ii], atomCoordinates, parameters[ii], 
+                                         forces, (energiesByBond == NULL ? NULL : energiesByBond + ii), energiesByAtom ); 
+
+      if( energiesByBond != NULL ){
+         *totalEnergy += energiesByBond[ii];
+      }
+   }
+
+   return ReferenceForce::DefaultReturn;
+}
+

platforms/reference/src/ReferenceBondForce.h

+
+/* Portions copyright (c) 2006 Stanford University and Simbios.
+ * Contributors: Pande Group
+ *
+ * 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.
+ */
+
+#ifndef __ReferenceBondForce_H__
+#define __ReferenceBondForce_H__
+
+#include "ReferenceForce.h"
+#include "ReferenceBondIxn.h"
+
+// ---------------------------------------------------------------------------------------
+
+class ReferenceBondForce : public ReferenceForce {
+
+   private:
+
+   public:
+
+      /**---------------------------------------------------------------------------------------
+      
+         Constructor
+      
+         --------------------------------------------------------------------------------------- */
+
+       ReferenceBondForce( );
+
+      /**---------------------------------------------------------------------------------------
+      
+         Destructor
+      
+         --------------------------------------------------------------------------------------- */
+
+       ~ReferenceBondForce( );
+
+      /**---------------------------------------------------------------------------------------
+      
+         Calculate forces/energy for bonds
+      
+         @param numberOfBonds    number of bonds
+         @param atomIndices      indices of atoms participating in bond ixn: atomIndices[bondIndex][indices]
+         @param atomCoordinates  atom coordinates: atomCoordinates[atomIndex][3]
+         @param parameters       parameters: parameters[bondIndex][*]; contents of array 
+                                 depend on ixn
+         @param forces           force array (forces added to current values): forces[atomIndex][3]
+         @param energiesByBond   energies by bond: energiesByBond[bondIndex]
+         @param energiesByAtom   energies by atom: energiesByAtom[atomIndex]
+         @param totalEnergy      totalEnergy: sum over { energies[atomIndex] }
+         @param ReferenceBondIxn ixn to be calculated
+      
+         @return  ReferenceForce::DefaultReturn
+      
+         --------------------------------------------------------------------------------------- */
+      
+       int calculateForce( int numberOfBonds, int** atomIndices, 
+                           RealOpenMM** atomCoordinates,
+                           RealOpenMM** parameters, RealOpenMM** forces, 
+                           RealOpenMM* energiesByBond, RealOpenMM* energiesByAtom, 
+                           RealOpenMM* totalEnergy, ReferenceBondIxn& referenceBondIxn );
+
+};
+
+// ---------------------------------------------------------------------------------------
+
+#endif // __ReferenceBondForce_H__

platforms/reference/src/ReferenceBondIxn.cpp

+
+/* Portions copyright (c) 2006 Stanford University and Simbios.
+ * Contributors: Pande Group
+ *
+ * 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 <string.h>
+#include <sstream>
+
+#include "SimTKOpenMMCommon.h"
+#include "SimTKOpenMMLog.h"
+#include "SimTKOpenMMUtilities.h"
+#include "ReferenceForce.h"
+#include "ReferenceBondIxn.h"
+
+/**---------------------------------------------------------------------------------------
+
+   ReferenceBondIxn constructor
+
+   --------------------------------------------------------------------------------------- */
+
+ReferenceBondIxn::ReferenceBondIxn( ){
+
+   // ---------------------------------------------------------------------------------------
+
+   // static const char* methodName = "\nReferenceBondIxn::ReferenceBondIxn";
+
+   // ---------------------------------------------------------------------------------------
+
+}
+
+/**---------------------------------------------------------------------------------------
+
+   ReferenceBondIxn destructor
+
+   --------------------------------------------------------------------------------------- */
+
+ReferenceBondIxn::~ReferenceBondIxn( ){
+
+   // ---------------------------------------------------------------------------------------
+
+   // static const char* methodName = "\nReferenceBondIxn::~ReferenceBondIxn";
+
+   // ---------------------------------------------------------------------------------------
+
+}
+
+/**---------------------------------------------------------------------------------------
+
+   Update energy
+
+   @param  energy               energy value to update 
+   @param  energyByBond         ptr to energyByBond accumulator (may be null)
+   @param  numberOfAtomIndices  number of atoms in bond
+   @param  atomIndices          array of atom indices of size 'numberOfAtomIndices'
+   @param  energyByAtom         array of energies by atom (may be null)
+
+   @return ReferenceForce::DefaultReturn 
+
+   --------------------------------------------------------------------------------------- */
+
+int ReferenceBondIxn::updateEnergy( RealOpenMM energy, RealOpenMM* energyByBond,
+                                    int numberOfAtomIndices, int* atomIndices, RealOpenMM* energyByAtom ) const {
+
+   // ---------------------------------------------------------------------------------------
+
+   // static const std::string methodName = "\nReferenceBondIxn::updateEnergy";
+
+   // ---------------------------------------------------------------------------------------
+
+   if( energyByBond ){
+      *energyByBond += energy;
+   }
+   if( energyByAtom ){
+      for( int ii = 0; ii < numberOfAtomIndices; ii++ ){
+         energyByAtom[atomIndices[ii]] += energy;
+      }
+   }
+
+   return ReferenceForce::DefaultReturn;
+
+}
+
+/**---------------------------------------------------------------------------------------
+      
+   Calculate Bond Ixn -- virtual method -- does nothing
+      
+   @param atomIndices      bond indices
+   @param atomCoordinates  atom coordinates
+   @param parameters       parameters
+   @param forces           force array (forces added)
+   @param energyByBond     bond energy 
+   @param energy           atom energy
+      
+   --------------------------------------------------------------------------------------- */
+     
+   int ReferenceBondIxn::calculateBondIxn( int* atomIndices, RealOpenMM** atomCoordinates,
+                                           RealOpenMM* parameters, RealOpenMM** forces,
+                                           RealOpenMM* energyByBond, RealOpenMM* energyByAtom ) const {
+   // ---------------------------------------------------------------------------------------
+
+   // static const std::string methodName = "\nReferenceBondIxn::calculateBondIxn";
+
+   // ---------------------------------------------------------------------------------------
+
+   return ReferenceForce::DefaultReturn;
+
+}
+ 
+/**---------------------------------------------------------------------------------------
+
+   Get normed dot product between two vectors
+
+   Do computation in double?
+
+   @param  vector1				first vector
+   @param  vector2			   second vector
+   @param  hasREntry          if set, then vector1[ReferenceForce::RIndex] = norm of vector
+                              defaults to 0 (i.e., R unavailable)
+
+   @return dot product
+
+   --------------------------------------------------------------------------------------- */
+
+RealOpenMM ReferenceBondIxn::getNormedDotProduct( RealOpenMM* vector1, RealOpenMM* vector2,
+                                                  int hasREntry = 0 ) const {
+
+   // ---------------------------------------------------------------------------------------
+
+   // static const std::string methodName = "\nReferenceBondIxn::getNormedDotProduct";
+
+   static const RealOpenMM zero        = 0.0;
+   static const RealOpenMM one         = 1.0;
+
+   // ---------------------------------------------------------------------------------------
+
+   RealOpenMM dotProduct = DOT3( vector1, vector2 );
+   if( dotProduct != zero ){
+      if( hasREntry ){
+         dotProduct       /= ( vector1[ReferenceForce::RIndex]*vector2[ReferenceForce::RIndex] );
+      } else {
+         RealOpenMM norm1  = DOT3( vector1, vector1 );
+         RealOpenMM norm2  = DOT3( vector2, vector2 );
+         dotProduct       /= SQRT( norm1*norm2 );
+      }
+   }
+      
+   // clamp dot product to [-1,1]
+
+   if( dotProduct > one ){
+      dotProduct = one;
+   } else if( dotProduct < -one ){
+      dotProduct = -one;
+   }
+
+   return dotProduct;
+
+}
+
+/**---------------------------------------------------------------------------------------
+
+   Get angle between two vectors
+
+   @param  vector1				first vector
+   @param  vector2			   second vector
+   @param  outputDotProduct   output cosine of angle between two vectors (optional)
+   @param  hasREntry          if set, then vector1[ReferenceForce::RIndex] = norm of vector
+                              defaults to 0 -> R unavailable
+
+   @return cosine of angles in radians
+
+   --------------------------------------------------------------------------------------- */
+
+RealOpenMM ReferenceBondIxn::getAngleBetweenTwoVectors( RealOpenMM* vector1, RealOpenMM* vector2, 
+                                                        RealOpenMM* outputDotProduct = NULL,
+                                                        int hasREntry = 0 ) const {
+
+   // ---------------------------------------------------------------------------------------
+
+   // static const std::string methodName = "\nReferenceBondIxn::getAngle";
+
+   static const RealOpenMM zero        = 0.0;
+   static const RealOpenMM one         = 1.0;
+
+   // ---------------------------------------------------------------------------------------
+
+   // get dot product betweenn vectors and then angle
+
+   RealOpenMM dotProduct = getNormedDotProduct( vector1, vector2, hasREntry );
+
+   RealOpenMM angle;
+   if( dotProduct >= one ){
+      angle = zero;
+   } else if( dotProduct <= -one ){
+      angle = PI_M;
+   } else {
+      angle = ACOS(dotProduct);
+   }
+
+   if( outputDotProduct ){
+      *outputDotProduct = dotProduct;
+   }
+
+   return angle;
+
+}
+
+/**---------------------------------------------------------------------------------------
+
+   Get dihedral angle between three vectors
+
+   @param  vector1				first vector
+   @param  vector2			   second vector
+   @param  vector3			   third vector
+   @param  outputCrossProduct output cross product vectors
+   @param  cosineOfAngle      cosine of angle (output)
+   @param  signVector         vector to test sign (optional)
+   @param  signOfAngle        sign of angle (output) (optional)
+   @param  hasREntry          if set, then vector1[ReferenceForce::RIndex] = norm of vector
+                              defaults to 0
+
+   @return cosine of dihedral angle in radians
+
+   --------------------------------------------------------------------------------------- */
+
+RealOpenMM ReferenceBondIxn::getDihedralAngleBetweenThreeVectors( RealOpenMM*  vector1,
+                                                                  RealOpenMM*  vector2, 
+                                                                  RealOpenMM*  vector3, 
+                                                                  RealOpenMM** outputCrossProduct  = NULL, 
+                                                                  RealOpenMM*  cosineOfAngle       = NULL, 
+                                                                  RealOpenMM*  signVector          = NULL, 
+                                                                  RealOpenMM*  signOfAngle         = NULL, 
+                                                                   int          hasREntry = 0 ) const {
+
+   // ---------------------------------------------------------------------------------------
+
+   // static const std::string methodName = "\nReferenceBondIxn::getDihedralAngleBetweenThreeVectors";
+
+   static const RealOpenMM zero        = 0.0;
+   static const RealOpenMM one         = 1.0;
+
+   RealOpenMM   tempVectors[6]         = { zero, zero, zero, zero, zero, zero };
+
+   // ---------------------------------------------------------------------------------------
+
+   // get cross products between vectors and then angle between cross product vectors
+
+   RealOpenMM* crossProduct[2];
+   if( outputCrossProduct ){
+      crossProduct[0] = outputCrossProduct[0];
+      crossProduct[1] = outputCrossProduct[1];
+   } else {
+      crossProduct[0] = tempVectors;
+      crossProduct[1] = tempVectors + 3;
+   }
+   
+   SimTKOpenMMUtilities::crossProductVector3( vector1, vector2, crossProduct[0] );
+   SimTKOpenMMUtilities::crossProductVector3( vector2, vector3, crossProduct[1] );
+
+   RealOpenMM angle         = getAngleBetweenTwoVectors( crossProduct[0], crossProduct[1], cosineOfAngle, 0 );
+
+   // take care of sign of angle
+
+   if( signVector ){
+      RealOpenMM dotProduct = DOT3( signVector, crossProduct[1] );
+      RealOpenMM sign       = dotProduct < zero ? -one : one; 
+      if( signOfAngle ){
+         *signOfAngle = sign;
+      }
+      angle *= sign;
+   }
+
+   return angle;
+
+}

platforms/reference/src/ReferenceBondIxn.h

+
+/* Portions copyright (c) 2006 Stanford University and Simbios.
+ * Contributors: Pande Group
+ *
+ * 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.
+ */
+
+#ifndef __ReferenceBondIxn_H__
+#define __ReferenceBondIxn_H__
+
+// #include "ReferenceIxn.h"
+
+// ---------------------------------------------------------------------------------------
+
+class ReferenceBondIxn {
+
+   private:
+
+   public:
+
+      /**---------------------------------------------------------------------------------------
+      
+         Constructor
+      
+         --------------------------------------------------------------------------------------- */
+
+       ReferenceBondIxn( );
+
+      /**---------------------------------------------------------------------------------------
+      
+         Destructor
+      
+         --------------------------------------------------------------------------------------- */
+
+       ~ReferenceBondIxn( );
+
+      /**---------------------------------------------------------------------------------------
+      
+         Calculate Bond Ixn -- virtual method
+      
+         @param atomIndices      bond indices
+         @param atomCoordinates  atom coordinates
+         @param parameters       parameters
+         @param forces           force array (forces added)
+         @param energyByBond     bond energy 
+         @param energy           atom energy
+      
+         --------------------------------------------------------------------------------------- */
+      
+      virtual int calculateBondIxn( int* atomIndices, RealOpenMM** atomCoordinates,
+                                    RealOpenMM* parameters, RealOpenMM** forces,
+                                    RealOpenMM* energyByBond, RealOpenMM* energyByAtom ) const;
+
+      /**---------------------------------------------------------------------------------------
+      
+         Update energy
+      
+         @param  energy               energy value to update 
+         @param  energyByBond         ptr to energyByBond accumulator (may be null)
+         @param  numberOfAtomIndices  number of atoms in bond
+         @param  atomIndices          array of atom indices of size 'numberOfAtomIndices'
+         @param  energyByAtom         array of energies by atom (may be null)
+      
+         @return ReferenceForce::DefaultReturn 
+      
+         --------------------------------------------------------------------------------------- */
+      
+      int updateEnergy( RealOpenMM energy, RealOpenMM* energyByBond,
+                        int numberOfAtomIndices, int* atomIndices, RealOpenMM* energyByAtom ) const;
+      
+      
+      /**---------------------------------------------------------------------------------------
+      
+         Get normed dot product between two vectors
+      
+         @param  vector1            first vector
+         @param  vector2            second vector
+         @param  hasREntry          if set, then vector1[ReferenceForce::RIndex] = norm of vector;
+                                    defaults to 0
+      
+         @return dot product
+      
+         --------------------------------------------------------------------------------------- */
+      
+      RealOpenMM getNormedDotProduct( RealOpenMM* vector1, RealOpenMM* vector2, int hasREntry ) const;
+      
+      /**---------------------------------------------------------------------------------------
+      
+         Get angle between two vectors
+      
+         @param  vector1            first vector
+         @param  vector2            second vector
+         @param  outputDotProduct   cosine of angle between two vectors (optional)
+         @param  hasREntry          if set, then vector1[ReferenceForce::R2Index] = square norm of vector;
+                                    defaults to 0
+      
+         @return cosine of angles in radians
+      
+         --------------------------------------------------------------------------------------- */
+      
+      RealOpenMM getAngleBetweenTwoVectors( RealOpenMM* vector1, RealOpenMM* vector2, 
+                                            RealOpenMM* outputDotProduct, int hasREntry ) const;
+      
+      /**---------------------------------------------------------------------------------------
+      
+         Get dihedral angle between two vectors
+      
+         @param  vector1            first vector
+         @param  vector2            second vector
+         @param  vector3            third vector
+         @param  outputCrossProduct output cross product vectors
+         @param  cosineOfAngle      cosine of angle (output)
+         @param  signVector         vector to test sign (optional)
+         @param  signOfAngle        sign of angle (output) (optional)
+         @param  hasREntry          if set, then vector1[ReferenceForce::R2Index] = square norm of vector
+                                    defaults to 0
+      
+         @return cosine of angles in radians
+      
+         --------------------------------------------------------------------------------------- */
+      
+      RealOpenMM getDihedralAngleBetweenThreeVectors( RealOpenMM* vector1, RealOpenMM* vector2, 
+                                                      RealOpenMM* vector3, RealOpenMM** outputCrossProduct, 
+                                                      RealOpenMM* cosineOfAngle, RealOpenMM* signVector, 
+                                                      RealOpenMM* signOfAngle, int hasREntry ) const;
+      
+};
+
+// ---------------------------------------------------------------------------------------
+
+#endif // __ReferenceBondIxn_H__

platforms/reference/src/ReferenceConstraint.cpp

+
+/* Portions copyright (c) 2006 Stanford University and Simbios.
+ * Contributors: Pande Group
+ *
+ * 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 <string.h>
+#include <sstream>
+
+#include "SimTKOpenMMCommon.h"
+#include "SimTKOpenMMLog.h"
+#include "SimTKOpenMMUtilities.h"
+#include "ReferenceConstraint.h"
+#include "ReferenceDynamics.h"
+
+/**---------------------------------------------------------------------------------------
+
+   ReferenceConstraint constructor
+
+   --------------------------------------------------------------------------------------- */
+
+ReferenceConstraint::ReferenceConstraint( ){
+
+   // ---------------------------------------------------------------------------------------
+
+   //static const char* methodName = "\nReferenceConstraint::ReferenceConstraint";
+
+   // ---------------------------------------------------------------------------------------
+
+}
+
+/**---------------------------------------------------------------------------------------
+
+   ReferenceConstraint destructor
+
+   --------------------------------------------------------------------------------------- */
+
+ReferenceConstraint::~ReferenceConstraint( ){
+
+   // ---------------------------------------------------------------------------------------
+
+   // static const char* methodName = "\nReferenceConstraint::~ReferenceConstraint";
+
+   // ---------------------------------------------------------------------------------------
+
+}
+
+/**---------------------------------------------------------------------------------------
+
+   ReferenceShakeConstraint constructor
+
+   @param numberOfAtoms  number of atoms
+   @param deltaT         delta t for dynamics
+   @param tau            viscosity
+   @param temperature    temperature
+
+   --------------------------------------------------------------------------------------- */
+
+ReferenceShakeConstraint::ReferenceShakeConstraint( int atomIndex1, int atomIndex2, 
+                                                    RealOpenMM constraintDistance, 
+                                                    RealOpenMM inverseMass1,
+                                                    RealOpenMM inverseMass2 ) : ReferenceConstraint( ) {
+
+   // ---------------------------------------------------------------------------------------
+
+   static const char* methodName = "\nReferenceShakeConstraint::ReferenceShakeConstraint";
+
+   // ---------------------------------------------------------------------------------------
+
+   // insure heavy atom is in 0 slot
+
+   if( inverseMass1 > inverseMass2 ){
+      int temp         = atomIndex1;
+      atomIndex1       = atomIndex2;
+      atomIndex2       = temp;
+
+      RealOpenMM tempR = inverseMass1;
+      inverseMass1     = inverseMass2;
+      inverseMass2     = tempR;
+   }
+
+   _atomIndices[0]     = atomIndex1;
+   _atomIndices[1]     = atomIndex2;
+
+   _inverseMasses[0]   = inverseMass1;
+   _inverseMasses[1]   = inverseMass2;
+
+   _constraintDistance = constraintDistance;
+
+}
+
+/**---------------------------------------------------------------------------------------
+
+   ReferenceShakeConstraint destructor
+
+   --------------------------------------------------------------------------------------- */
+
+ReferenceShakeConstraint::~ReferenceShakeConstraint( ){
+
+   // ---------------------------------------------------------------------------------------
+
+   // static const char* methodName = "\nReferenceShakeConstraint::~ReferenceShakeConstraint";
+
+   // ---------------------------------------------------------------------------------------
+
+}
+
+/**---------------------------------------------------------------------------------------
+
+   Get constraint distance
+
+   @return constraintDistance
+
+   --------------------------------------------------------------------------------------- */
+
+RealOpenMM ReferenceShakeConstraint::getConstraintDistance( void ){
+
+   // ---------------------------------------------------------------------------------------
+
+   // static const char* methodName  = "\nReferenceShakeConstraint::getConstraintDistance";
+
+   // ---------------------------------------------------------------------------------------
+
+   return _constraintDistance;
+}
+
+/**---------------------------------------------------------------------------------------
+
+   Get inverse mass of heavy atom
+
+   @return inverse mass
+
+   --------------------------------------------------------------------------------------- */
+
+RealOpenMM ReferenceShakeConstraint::getHeavyAtomInverseMass( void ){
+
+   // ---------------------------------------------------------------------------------------
+
+   // static const char* methodName  = "\nReferenceShakeConstraint::getHeavyAtomInverseMass";
+
+   // ---------------------------------------------------------------------------------------
+
+   return _inverseMasses[0];
+}
+
+/**---------------------------------------------------------------------------------------
+
+   Get inverse mass of light atom
+
+   @return inverse mass
+
+   --------------------------------------------------------------------------------------- */
+
+RealOpenMM ReferenceShakeConstraint::getLightAtomInverseMass( void ){
+
+   // ---------------------------------------------------------------------------------------
+
+   // static const char* methodName  = "\nReferenceShakeConstraint::getLightAtomInverseMass";
+
+   // ---------------------------------------------------------------------------------------
+
+   return _inverseMasses[1];
+}
+
+/**---------------------------------------------------------------------------------------
+
+   Get index of heavy atom
+
+   @return index
+
+   --------------------------------------------------------------------------------------- */
+
+int ReferenceShakeConstraint::getHeavyAtomIndex( void ){
+
+   // ---------------------------------------------------------------------------------------
+
+   // static const char* methodName  = "\nReferenceShakeConstraint::getHeavyAtomIndex";
+
+   // ---------------------------------------------------------------------------------------
+
+   return _atomIndices[0];
+}
+
+/**---------------------------------------------------------------------------------------
+
+   Get index of light atom
+
+   @return index
+
+   --------------------------------------------------------------------------------------- */
+
+int ReferenceShakeConstraint::getLightAtomIndex( void ){
+
+   // ---------------------------------------------------------------------------------------
+
+   // static const char* methodName  = "\nReferenceShakeConstraint::getLightAtomIndex";
+
+   // ---------------------------------------------------------------------------------------
+
+   return _atomIndices[1];
+}
+
+
+/**---------------------------------------------------------------------------------------
+
+   Print state
+
+   @param message             message
+
+   @return ReferenceDynamics::DefaultReturn
+
+   --------------------------------------------------------------------------------------- */
+
+int ReferenceShakeConstraint::printState( std::stringstream& message ){
+
+   // ---------------------------------------------------------------------------------------
+
+   // static const char* methodName  = "\nReferenceShakeConstraint::printState";
+
+   // ---------------------------------------------------------------------------------------
+
+   // print state
+
+   message << " atoms[" << _atomIndices[0] << " " << _atomIndices[1] << "]";
+   message << " d=" << _constraintDistance;
+   message << " massI[" << _inverseMasses[0] << " " << _inverseMasses[1] << "]";
+
+   return ReferenceDynamics::DefaultReturn;
+
+}

platforms/reference/src/ReferenceConstraint.h

+
+/* Portions copyright (c) 2006 Stanford University and Simbios.
+ * Contributors: Pande Group
+ *
+ * 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.
+ */
+
+#ifndef __ReferenceConstraint_H__
+#define __ReferenceConstraint_H__
+
+// ---------------------------------------------------------------------------------------
+
+class ReferenceConstraint {
+
+   private:
+
+   public:
+
+      /**---------------------------------------------------------------------------------------
+      
+         Constructor
+
+         --------------------------------------------------------------------------------------- */
+
+       ReferenceConstraint( );
+
+      /**---------------------------------------------------------------------------------------
+      
+         Destructor
+      
+         --------------------------------------------------------------------------------------- */
+
+       ~ReferenceConstraint( );
+
+};
+
+class ReferenceShakeConstraint : public ReferenceConstraint {
+
+   private:
+
+      // force heavy atom into index 0
+
+      int _atomIndices[2];
+      RealOpenMM _inverseMasses[2];
+      RealOpenMM _constraintDistance;
+
+   public:
+
+      /**---------------------------------------------------------------------------------------
+      
+         Constructor
+
+         @param atomIndex1     atom index 1
+         @param atomIndex2     atom index 2
+         @param distance       distance constraint
+         @param inverseMass1   inverseMass of atom 1
+         @param inverseMass2   inverseMass of atom 2
+      
+         --------------------------------------------------------------------------------------- */
+
+       ReferenceShakeConstraint( int atomIndex1, int atomIndex2, RealOpenMM distance,
+                                 RealOpenMM inverseMass1, RealOpenMM inverseMass2 );
+
+      /**---------------------------------------------------------------------------------------
+      
+         Destructor
+      
+         --------------------------------------------------------------------------------------- */
+
+       ~ReferenceShakeConstraint( );
+
+      /**---------------------------------------------------------------------------------------
+      
+         Get constraint distance
+      
+         @return distance
+      
+         --------------------------------------------------------------------------------------- */
+      
+      RealOpenMM getConstraintDistance( void );
+
+      /**---------------------------------------------------------------------------------------
+      
+         Get inverse mass of heavy atom
+      
+         @return inverse mass
+      
+         --------------------------------------------------------------------------------------- */
+      
+      RealOpenMM getHeavyAtomInverseMass( void );
+      
+      /**---------------------------------------------------------------------------------------
+      
+         Get inverse mass of light atom
+      
+         @return inverse mass
+      
+         --------------------------------------------------------------------------------------- */
+      
+      RealOpenMM getLightAtomInverseMass( void );
+
+      /**---------------------------------------------------------------------------------------
+      
+         Get index of heavy atom
+      
+         @return index
+      
+         --------------------------------------------------------------------------------------- */
+      
+      int getHeavyAtomIndex( void );
+
+      /**---------------------------------------------------------------------------------------
+      
+         Get index of light atom
+      
+         @return index
+      
+         --------------------------------------------------------------------------------------- */
+      
+      int getLightAtomIndex( void );
+      
+      /**---------------------------------------------------------------------------------------
+      
+         Print state
+      
+         @param message             message
+      
+         @return ReferenceDynamics::DefaultReturn
+      
+         --------------------------------------------------------------------------------------- */
+      
+      int printState( std::stringstream& message );
+      
+};
+
+typedef std::vector<ReferenceShakeConstraint*> ShakeVector;
+typedef ShakeVector::iterator ShakeVectorI;
+typedef std::map<int, ShakeVector*> IntShakeMap;
+typedef IntShakeMap::iterator IntShakeMapI;
+
+// ---------------------------------------------------------------------------------------
+
+#endif // __ReferenceShakeConstraint_H__

platforms/reference/src/ReferenceDynamics.h

+
+/* Portions copyright (c) 2006 Stanford University and Simbios.
+ * Contributors: Pande Group
+ *
+ * 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.
+ */
+
+#ifndef __ReferenceDynamics_H__
+#define __ReferenceDynamics_H__
+
+#include "ReferenceShakeAlgorithm.h"
+
+// ---------------------------------------------------------------------------------------
+
+/**---------------------------------------------------------------------------------------
+
+Abstract class for dynamics
+
+Main method (virtual) is update()
+
+'Random' numbers are currently fixed to allow testing
+
+--------------------------------------------------------------------------------------- */
+
+class ReferenceDynamics {
+
+   public:
+
+      /**---------------------------------------------------------------------------------------
+      
+         Fixed static variables
+      
+         --------------------------------------------------------------------------------------- */
+
+       static const int DefaultReturn      = 0;
+       static const int ErrorReturn        = -1;
+
+   private:
+
+      int _numberOfAtoms;
+      int _timeStep;
+
+      RealOpenMM _deltaT;
+      RealOpenMM _temperature;
+      RealOpenMM _randomNumberSeed;
+
+      int _numberOf2DTempArrays;
+      RealOpenMM*** _twoDTempArrays;
+
+      int _numberOf1DTempArrays;
+      RealOpenMM** _oneDTempArrays;
+
+      int _ownReferenceShake;
+      ReferenceShakeAlgorithm* _referenceShake;
+
+      /**---------------------------------------------------------------------------------------
+      
+         Free memory associated w/ 2D arrays
+      
+         @return ReferenceDynamics::DefaultReturn
+      
+         --------------------------------------------------------------------------------------- */
+      
+      int _freeTwoDArrays( void );
+      
+      /**---------------------------------------------------------------------------------------
+      
+         Free memory associated w/ 1D arrays
+      
+         @return ReferenceDynamics::DefaultReturn
+      
+         --------------------------------------------------------------------------------------- */
+      
+      int _freeOneDArrays( void );
+      
+   protected:
+
+      /**---------------------------------------------------------------------------------------
+      
+         Allocate memory associated w/ 2D arrays
+      
+         @param dimension1        first dimension
+         @param dimension2        second dimension
+         @param numberOfArrays    number of arrays to allocate
+      
+         @return ReferenceDynamics::DefaultReturn
+      
+         --------------------------------------------------------------------------------------- */
+      
+      int allocate2DArrays( int dimension1, int dimension2, int numberOfArrays );
+      
+      /**---------------------------------------------------------------------------------------
+      
+         Get array at specified index
+      
+         @param index             array index
+      
+         @return array or NULL if index invalid or arrays not allocated
+      
+         --------------------------------------------------------------------------------------- */
+      
+      RealOpenMM** get2DArrayAtIndex( int index ) const;
+      
+      /**---------------------------------------------------------------------------------------
+      
+         Allocate memory associated w/ 1D arrays
+      
+         @param dimension1        dimension
+         @param numberOfArrays    number of arrays to allocate
+      
+         @return DefaultReturn
+      
+         --------------------------------------------------------------------------------------- */
+      
+      int allocate1DArrays( int dimension, int numberOfArrays );
+      
+      /**---------------------------------------------------------------------------------------
+      
+         Get array at specified index
+      
+         @param index             array index
+      
+         @return array or NULL if index invalid or arrays not allocated
+      
+         --------------------------------------------------------------------------------------- */
+      
+      RealOpenMM* get1DArrayAtIndex( int index ) const;
+      
+   public:
+
+      /**---------------------------------------------------------------------------------------
+      
+         Constructor
+      
+         @param numberOfAtoms  number of atoms
+         @param deltaT         delta t for dynamics
+         @param temperature    temperature
+
+         --------------------------------------------------------------------------------------- */
+
+       ReferenceDynamics( int numberOfAtoms, RealOpenMM _deltaT, RealOpenMM temperature );
+
+      /**---------------------------------------------------------------------------------------
+      
+         Destructor
+      
+         --------------------------------------------------------------------------------------- */
+
+       ~ReferenceDynamics( );
+
+      /**---------------------------------------------------------------------------------------
+      
+         Get number of atoms
+      
+         @return number of atoms
+      
+         --------------------------------------------------------------------------------------- */
+      
+      int getNumberOfAtoms( void ) const;
+      
+      /**---------------------------------------------------------------------------------------
+      
+         Get time step
+      
+         @return time step
+      
+         --------------------------------------------------------------------------------------- */
+      
+      int getTimeStep( void ) const;
+      
+      /**---------------------------------------------------------------------------------------
+      
+         Increment time step
+      
+         @return incremented time step
+      
+         --------------------------------------------------------------------------------------- */
+      
+      int incrementTimeStep( void );
+      
+      /**---------------------------------------------------------------------------------------
+      
+         Get delta t
+      
+         @return deltaT
+      
+         --------------------------------------------------------------------------------------- */
+      
+      RealOpenMM getDeltaT( void ) const;
+
+      /**---------------------------------------------------------------------------------------
+      
+         Get temperature
+      
+         @return temperature
+      
+         --------------------------------------------------------------------------------------- */
+    
+      RealOpenMM getTemperature( void ) const;
+    
+      /**---------------------------------------------------------------------------------------
+      
+         Remove total linear momentum
+      
+         @param numberOfAtoms      number of atoms
+         @param masses             masses
+         @param velocities         velocities
+      
+         @return ReferenceDynamics::DefaultReturn
+      
+         --------------------------------------------------------------------------------------- */
+      
+      int removeTotalLinearMomentum( int numberOfAtoms, RealOpenMM* masses, RealOpenMM** velocities ) const;
+      
+      /**---------------------------------------------------------------------------------------
+      
+         Print parameters
+      
+         @param message message
+
+         @return ReferenceDynamics::DefaultReturn
+      
+         --------------------------------------------------------------------------------------- */
+          
+      int printParameters( std::stringstream& message ) const;
+
+      /**---------------------------------------------------------------------------------------
+      
+         Update
+      
+         @param numberOfAtoms       number of atoms
+         @param atomCoordinates     atom coordinates
+         @param velocities          velocities
+         @param forces              forces
+         @param masses              atom masses
+      
+         @return ReferenceDynamics::DefaultReturn
+      
+         --------------------------------------------------------------------------------------- */
+      
+      virtual int update( int numberOfAtoms, RealOpenMM** atomCoordinates,
+                          RealOpenMM** velocities, RealOpenMM** forces, RealOpenMM* masses );
+      
+      /**---------------------------------------------------------------------------------------
+      
+         Get normally distributed random number
+      
+         @return random value
+      
+         --------------------------------------------------------------------------------------- */
+      
+      RealOpenMM getNormallyDistributedRandomNumber( void );
+      
+      /**---------------------------------------------------------------------------------------
+      
+         Get random number seed
+      
+         @return random number seed
+      
+         --------------------------------------------------------------------------------------- */
+      
+      RealOpenMM getRandomNumberSeed( void ) const;
+      
+      /**---------------------------------------------------------------------------------------
+      
+         Set random number seed
+      
+         @param seed    new seed value
+      
+         @return DefaultReturn
+      
+         --------------------------------------------------------------------------------------- */
+      
+      int setRandomNumberSeed( RealOpenMM seed );
+
+      /**---------------------------------------------------------------------------------------
+      
+         Get ReferenceShake
+      
+         @return referenceShake  object
+      
+         --------------------------------------------------------------------------------------- */
+      
+      ReferenceShakeAlgorithm* getReferenceShakeAlgorithm( void ) const;
+      
+      /**---------------------------------------------------------------------------------------
+      
+         Set ReferenceShake
+      
+         @param referenceShake  referenceShake object
+      
+         @return ReferenceDynamics::DefaultReturn
+      
+         --------------------------------------------------------------------------------------- */
+      
+      int setReferenceShakeAlgorithm( ReferenceShakeAlgorithm* referenceShake );
+      
+      /**---------------------------------------------------------------------------------------
+      
+         Write state
+      
+         @param numberOfAtoms       number of atoms
+         @param atomCoordinates     atom coordinates
+         @param velocities          velocities
+         @param forces              forces
+         @param masses              atom masses
+         @param state               0 if initial state; otherwise nonzero
+         @param baseFileName        base file name
+      
+         @return ReferenceDynamics::DefaultReturn
+      
+         --------------------------------------------------------------------------------------- */
+    
+      int writeState( int numberOfAtoms, RealOpenMM** atomCoordinates,
+                      RealOpenMM** velocities, RealOpenMM** forces, RealOpenMM* masses,
+                      int state, const std::string& baseFileName ) const;
+
+      /**---------------------------------------------------------------------------------------
+      
+         Write state
+      
+         @param stateFile       file to write to
+         @param scalarNameI     vector of scalar names for ints
+         @param scalarI         vector of scalar ints
+         @param scalarNameR     vector of scalar names for real
+         @param scalarR         vector of scalar reals
+         @param dimension1      size of first dimension for 1D & 2D real arrays
+         @param scalarNameR1    vector of names for 1D real arrays
+         @param scalarR1        vector of 1D real arrays
+         @param dimension2      size of second dimension for 2D real arrays
+         @param scalarNameR2    vector of names for 2D real arrays
+         @param scalarR2        vector of 2D real arrays
+      
+         @return ReferenceDynamics::DefaultReturn
+      
+         --------------------------------------------------------------------------------------- */
+      
+      int writeStateToFile( FILE* stateFile, StringVector& scalarNameI, IntVector& scalarI,
+                            StringVector& scalarNameR, RealOpenMMVector& scalarR,
+                            int dimension1, StringVector& scalarNameR1, RealOpenMMPtrVector& scalarR1,
+                            int dimension2, StringVector& scalarNameR2, RealOpenMMPtrPtrVector& scalarR2 ) const;
+      
+};
+
+// ---------------------------------------------------------------------------------------
+
+#endif // __ReferenceDynamics_H__

platforms/reference/src/ReferenceForce.cpp

+
+/* Portions copyright (c) 2006 Stanford University and Simbios.
+ * Contributors: Pande Group
+ *
+ * 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 <string.h>
+#include <sstream>
+
+#include "SimTKOpenMMCommon.h"
+#include "SimTKOpenMMLog.h"
+#include "SimTKOpenMMUtilities.h"
+#include "ReferenceForce.h"
+
+/**---------------------------------------------------------------------------------------
+
+   ReferenceForce constructor
+
+   --------------------------------------------------------------------------------------- */
+
+ReferenceForce::ReferenceForce( ){
+
+   // ---------------------------------------------------------------------------------------
+
+   // static const char* methodName = "\nReferenceForce::ReferenceForce";
+
+   // ---------------------------------------------------------------------------------------
+
+}
+
+/**---------------------------------------------------------------------------------------
+
+   ReferenceForce destructor
+
+   --------------------------------------------------------------------------------------- */
+
+ReferenceForce::~ReferenceForce( ){
+
+   // ---------------------------------------------------------------------------------------
+
+   // static const char* methodName = "\nReferenceForce::~ReferenceForce";
+
+   // ---------------------------------------------------------------------------------------
+
+}
+
+/**---------------------------------------------------------------------------------------
+
+   Get deltaR and distance and distance**2 between atomI and atomJ (static method)
+   deltaR: j - i
+
+   @param atomCoordinatesI    atom i coordinates
+   @param atomCoordinatesI    atom j coordinates
+   @param deltaR              deltaX, deltaY, deltaZ, R2, R upon return
+
+   @return ReferenceForce::DefaultReturn
+
+   --------------------------------------------------------------------------------------- */
+
+int ReferenceForce::getDeltaR( const RealOpenMM* atomCoordinatesI, const RealOpenMM* atomCoordinatesJ,
+                               RealOpenMM* deltaR ){
+
+   // ---------------------------------------------------------------------------------------
+
+   // static const std::string methodName = "\nReferenceForce::getDeltaR";
+
+   // ---------------------------------------------------------------------------------------
+
+   deltaR[XIndex]    = atomCoordinatesJ[0] - atomCoordinatesI[0];
+   deltaR[YIndex]    = atomCoordinatesJ[1] - atomCoordinatesI[1];
+   deltaR[ZIndex]    = atomCoordinatesJ[2] - atomCoordinatesI[2];
+
+   deltaR[R2Index]   = DOT3( deltaR, deltaR );
+   deltaR[RIndex]    = (RealOpenMM) SQRT( deltaR[R2Index] );
+
+   return ReferenceForce::DefaultReturn;
+}
+
+/**---------------------------------------------------------------------------------------
+
+   Get deltaR between atomI and atomJ (static method); deltaR: j - i
+
+   @param atomCoordinatesI    atom i coordinates
+   @param atomCoordinatesI    atom j coordinates
+   @param deltaR              deltaX, deltaY, deltaZ upon return
+
+   @return ReferenceForce::DefaultReturn
+
+   --------------------------------------------------------------------------------------- */
+
+int ReferenceForce::getDeltaROnly( const RealOpenMM* atomCoordinatesI,
+                                   const RealOpenMM* atomCoordinatesJ,
+                                   RealOpenMM* deltaR ){
+
+   // ---------------------------------------------------------------------------------------
+
+   // static const std::string methodName = "\nReferenceForce::getDeltaR";
+
+   // ---------------------------------------------------------------------------------------
+
+   deltaR[XIndex]    = atomCoordinatesJ[0] - atomCoordinatesI[0];
+   deltaR[YIndex]    = atomCoordinatesJ[1] - atomCoordinatesI[1];
+   deltaR[ZIndex]    = atomCoordinatesJ[2] - atomCoordinatesI[2];
+
+   return ReferenceForce::DefaultReturn;
+}
+
+/**---------------------------------------------------------------------------------------
+
+   Write coordinates, energies and forces (Simbios)
+
+   @param numberOfAtoms       number of atoms
+   @param atomsPerBond        atoms/bond
+   @param atomCoordinates     atomic coordinates
+   @param forces              forces
+   @param energies            energies (optional)
+   @param resultsFileName     output file name
+   @param lengthConversion    length conversion (optional defaults to 1)
+   @param energyConversion    energy conversion (optional defaults to 1)
+   @param forceConversion     force  conversion (optional defaults to 1)
+
+
+   @return ReferenceForce::DefaultReturn unless
+           file cannot be opened
+           in which case return ReferenceForce::ErrorReturn
+
+   --------------------------------------------------------------------------------------- */
+
+int ReferenceForce::writeForces( int numberOfAtoms, int atomsPerBond,
+                                 RealOpenMM** atomCoordinates, RealOpenMM** forces,
+                                 RealOpenMM* energies, const std::string& resultsFileName,
+                                 RealOpenMM lengthConversion  = 1.0,
+                                 RealOpenMM forceConversion   = 1.0,
+                                 RealOpenMM energyConversion  = 1.0 ){
+
+   // ---------------------------------------------------------------------------------------
+
+   static const char* methodName  = "\nReferenceForce::writeBornEnergyForces";
+   static const RealOpenMM zero   = 0.0;
+
+   // ---------------------------------------------------------------------------------------
+
+   // open file -- return if unsuccessful
+
+   FILE* resultsFile = NULL;
+#ifdef WIN32
+   fopen_s( &resultsFile, resultsFileName.c_str(), "w" );
+#else
+   resultsFile = fopen( resultsFileName.c_str(), "w" );
+#endif
+
+   // ---------------------------------------------------------------------------------------
+
+   // diagnostics
+
+   std::stringstream message;
+   message << methodName;
+   if( resultsFile != NULL ){
+      std::stringstream message;
+      message << methodName;
+      message << " Opened file=<" << resultsFileName << ">.";
+      SimTKOpenMMLog::printMessage( message );
+   } else {
+      std::stringstream message;
+      message << methodName;
+      message << "  could not open file=<" << resultsFileName << "> -- abort output.";
+      SimTKOpenMMLog::printMessage( message );
+      return ReferenceForce::ErrorReturn;
+   }
+
+   // total energy and normalize by number of atoms/bond
+
+   RealOpenMM totalEnergy = zero;
+   if( energies ){
+
+      for( int ii = 1; ii < numberOfAtoms; ii++ ){
+         totalEnergy += energies[ii];
+      }
+      if( atomsPerBond > 0 ){
+         totalEnergy /= (RealOpenMM) atomsPerBond;
+      }
+   }
+ 
+   // header
+
+   (void) fprintf( resultsFile, "# %d atoms E=%.7e  format: coords(3) forces(3) energies\n",
+                   numberOfAtoms, totalEnergy );
+
+   // output
+
+   if( forces != NULL && atomCoordinates != NULL ){
+
+      for( int ii = 0; ii < numberOfAtoms; ii++ ){
+            (void) fprintf( resultsFile, "%5d %15.7e %15.7e %15.7e  %15.7e %15.7e %15.7e", ii,
+                            lengthConversion*atomCoordinates[ii][0],
+                            lengthConversion*atomCoordinates[ii][1], 
+                            lengthConversion*atomCoordinates[ii][2],
+                            forceConversion*forces[ii][0],
+                            forceConversion*forces[ii][1],
+                            forceConversion*forces[ii][2] 
+                          );
+         if( energies != NULL ){
+            (void) fprintf( resultsFile, "  %15.7e", energyConversion*energies[ii] );
+         }
+         (void) fprintf( resultsFile, "\n" );
+      }
+   }
+   (void) fclose( resultsFile );
+
+   return ReferenceForce::DefaultReturn;
+
+}

platforms/reference/src/ReferenceForce.h

+
+/* Portions copyright (c) 2006 Stanford University and Simbios.
+ * Contributors: Pande Group
+ *
+ * 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.
+ */
+
+#ifndef __ReferenceForce_H__
+#define __ReferenceForce_H__
+
+// ---------------------------------------------------------------------------------------
+
+class ReferenceForce {
+
+   private:
+
+   public:
+
+      /**---------------------------------------------------------------------------------------
+      
+         Constructor
+      
+         --------------------------------------------------------------------------------------- */
+
+       ReferenceForce( );
+
+      /**---------------------------------------------------------------------------------------
+      
+         Destructor
+      
+         --------------------------------------------------------------------------------------- */
+
+       ~ReferenceForce( );
+
+      /**---------------------------------------------------------------------------------------
+      
+         Static variables
+      
+         --------------------------------------------------------------------------------------- */
+
+       static const int XIndex             = 0;
+       static const int YIndex             = 1;
+       static const int ZIndex             = 2;
+       static const int R2Index            = 3;
+       static const int RIndex             = 4;
+       static const int LastDeltaRIndex    = 5;
+
+       static const int DeltaRMaxIndex     = 5;
+
+       static const int DefaultReturn      = 0;
+       static const int ErrorReturn        = -1;
+   
+      /**---------------------------------------------------------------------------------------
+      
+         Get deltaR and distance and distance**2 between atomI and atomJ (static method)
+         deltaR: j - i
+      
+         @param atomCoordinatesI    atom i coordinates
+         @param atomCoordinatesI    atom j coordinates
+         @param deltaR              deltaX, deltaY, deltaZ, R2, R upon return
+      
+         @return ReferenceForce::DefaultReturn
+      
+         --------------------------------------------------------------------------------------- */
+      
+      static int getDeltaR( const RealOpenMM* atomCoordinatesI, const RealOpenMM* atomCoordinatesJ,
+                            RealOpenMM* deltaR );
+      
+      /**---------------------------------------------------------------------------------------
+      
+         Get deltaR between atomI and atomJ (static method): deltaR: j - i
+      
+         @param atomCoordinatesI    atom i coordinates
+         @param atomCoordinatesI    atom j coordinates
+         @param deltaR              deltaX, deltaY, deltaZ upon return
+      
+         @return ReferenceForce::DefaultReturn
+      
+         --------------------------------------------------------------------------------------- */
+      
+      static int getDeltaROnly( const RealOpenMM* atomCoordinatesI, const RealOpenMM* atomCoordinatesJ,
+                                RealOpenMM* deltaR );
+      
+      /**---------------------------------------------------------------------------------------
+      
+         Write coordinates, energies and forces (Simbios)
+      
+         @param numberOfAtoms       number of atoms
+         @param atomsPerBond        atoms/bond (used to normalize total energy)
+         @param atomCoordinates     atomic coordinates
+         @param forces              forces
+         @param energies            energies (optional)
+         @param resultsFileName     output file name
+         @param lengthConversion    length conversion (optional defaults to 1)
+         @param forceConversion     force  conversion (optional defaults to 1)
+         @param energyConversion    energy conversion (optional defaults to 1)
+      
+         @return ReferenceForce::DefaultReturn unless
+                 file cannot be opened
+                 in which case return ReferenceForce::ErrorReturn
+      
+         --------------------------------------------------------------------------------------- */
+      
+      static int writeForces( int numberOfAtoms, int atomsPerBond, RealOpenMM** atomCoordinates,
+                              RealOpenMM** forces, RealOpenMM* energies,
+                              const std::string& resultsFileName,
+                              RealOpenMM lengthConversion, RealOpenMM forceConversion,
+                              RealOpenMM energyConversion );
+      
+};
+
+// ---------------------------------------------------------------------------------------
+
+#endif // __ReferenceForce_H__

platforms/reference/src/ReferenceHarmonicBondIxn.cpp

+
+/* Portions copyright (c) 2006 Stanford University and Simbios.
+ * Contributors: Pande Group
+ *
+ * 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 <string.h>
+#include <sstream>
+
+#include "SimTKOpenMMCommon.h"
+#include "SimTKOpenMMLog.h"
+#include "SimTKOpenMMUtilities.h"
+#include "ReferenceHarmonicBondIxn.h"
+#include "ReferenceForce.h"
+
+/**---------------------------------------------------------------------------------------
+
+   ReferenceHarmonicBondIxn constructor
+
+   --------------------------------------------------------------------------------------- */
+
+ReferenceHarmonicBondIxn::ReferenceHarmonicBondIxn( ){
+
+   // ---------------------------------------------------------------------------------------
+
+   // static const char* methodName = "\nReferenceHarmonicBondIxn::ReferenceHarmonicBondIxn";
+
+   // ---------------------------------------------------------------------------------------
+
+}
+
+/**---------------------------------------------------------------------------------------
+
+   ReferenceHarmonicBondIxn destructor
+
+   --------------------------------------------------------------------------------------- */
+
+ReferenceHarmonicBondIxn::~ReferenceHarmonicBondIxn( ){
+
+   // ---------------------------------------------------------------------------------------
+
+   // static const char* methodName = "\nReferenceHarmonicBondIxn::~ReferenceHarmonicBondIxn";
+
+   // ---------------------------------------------------------------------------------------
+
+}
+
+/**---------------------------------------------------------------------------------------
+
+   Calculate Harmonic Bond Ixn
+
+   @param atomIndices      atom indices of atom participating in bond
+   @param atomCoordinates  atom coordinates
+   @param parameters       parameters: parameters[0] = ideal bond length
+                                       parameters[1] = bond k
+   @param forces           force array (forces added to input values)
+   @param energiesByBond   energies by bond: energiesByBond[bondIndex]
+   @param energiesByAtom   energies by atom: energiesByAtom[atomIndex]
+
+   @return ReferenceForce::DefaultReturn;
+
+   --------------------------------------------------------------------------------------- */
+
+int ReferenceHarmonicBondIxn::calculateBondIxn( int* atomIndices,
+                                                RealOpenMM** atomCoordinates,
+                                                RealOpenMM* parameters,
+                                                RealOpenMM** forces,
+                                                RealOpenMM* energiesByBond, 
+                                                RealOpenMM* energiesByAtom ) const {
+
+   // ---------------------------------------------------------------------------------------
+
+   // static const char* methodName = "\nReferenceHarmonicBondIxn::calculateBondIxn";
+
+   // ---------------------------------------------------------------------------------------
+
+   static const std::string methodName = "\nReferenceHarmonicBondIxn::calculateBondIxn";
+
+   static const int twoI               = 2;
+
+   static const RealOpenMM zero        = 0.0;
+   static const RealOpenMM two         = 2.0;
+   static const RealOpenMM half        = 0.5;
+
+   RealOpenMM deltaR[ReferenceForce::LastDeltaRIndex];
+
+   // ---------------------------------------------------------------------------------------
+
+   // get deltaR, R2, and R between 2 atoms
+
+   int atomAIndex = atomIndices[0];
+   int atomBIndex = atomIndices[1];
+   ReferenceForce::getDeltaR( atomCoordinates[atomAIndex], atomCoordinates[atomBIndex], deltaR );  
+
+   // deltaIdeal = r - r_0
+
+   RealOpenMM deltaIdeal      = deltaR[ReferenceForce::RIndex] - parameters[0];
+   RealOpenMM deltaIdeal2     = deltaIdeal*deltaIdeal;
+
+   RealOpenMM dEdR            = parameters[1]*deltaIdeal;
+
+   // chain rule
+
+   dEdR                       = deltaR[ReferenceForce::RIndex] > zero ? (dEdR/deltaR[ReferenceForce::RIndex]) : zero;
+
+   forces[atomAIndex][0]     += dEdR*deltaR[ReferenceForce::XIndex];
+   forces[atomAIndex][1]     += dEdR*deltaR[ReferenceForce::YIndex];
+   forces[atomAIndex][2]     += dEdR*deltaR[ReferenceForce::ZIndex];
+
+   forces[atomBIndex][0]     -= dEdR*deltaR[ReferenceForce::XIndex];
+   forces[atomBIndex][1]     -= dEdR*deltaR[ReferenceForce::YIndex];
+   forces[atomBIndex][2]     -= dEdR*deltaR[ReferenceForce::ZIndex];
+
+   RealOpenMM energy          = half*parameters[1]*deltaIdeal2;
+   updateEnergy( energy, energiesByBond, twoI, atomIndices, energiesByAtom );
+
+   return ReferenceForce::DefaultReturn;
+}

platforms/reference/src/ReferenceHarmonicBondIxn.h

+
+/* Portions copyright (c) 2006 Stanford University and Simbios.
+ * Contributors: Pande Group
+ *
+ * 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.
+ */
+
+#ifndef __ReferenceHarmonicBondIxn_H__
+#define __ReferenceHarmonicBondIxn_H__
+
+#include "ReferenceBondIxn.h"
+
+// ---------------------------------------------------------------------------------------
+
+class ReferenceHarmonicBondIxn : public ReferenceBondIxn {
+
+   private:
+
+   public:
+
+      /**---------------------------------------------------------------------------------------
+      
+         Constructor
+      
+         --------------------------------------------------------------------------------------- */
+
+       ReferenceHarmonicBondIxn( );
+
+      /**---------------------------------------------------------------------------------------
+      
+         Destructor
+      
+         --------------------------------------------------------------------------------------- */
+
+       ~ReferenceHarmonicBondIxn( );
+
+      /**---------------------------------------------------------------------------------------
+      
+         Calculate Harmonic Bond Ixn
+      
+         @param atomIndices      two bond indices
+         @param atomCoordinates  atom coordinates
+         @param parameters       parameters: parameters[0] = ideal bond length
+                                             parameters[1] = bond k
+         @param forces           force array (forces added)
+         @param energiesByBond   energies by bond: energiesByBond[bondIndex]
+         @param energiesByAtom   energies by atom: energiesByAtom[atomIndex]
+
+         --------------------------------------------------------------------------------------- */
+      
+      int calculateBondIxn( int* atomIndices, RealOpenMM** atomCoordinates,
+                            RealOpenMM* parameters, RealOpenMM** forces,
+                            RealOpenMM* energiesByBond, RealOpenMM* energiesByAtom ) const;
+      
+
+};
+
+// ---------------------------------------------------------------------------------------
+
+#endif // _ReferenceHarmonicBondIxn___

platforms/reference/src/ReferenceLJ14.cpp

+
+/* Portions copyright (c) 2006 Stanford University and Simbios.
+ * Contributors: Pande Group
+ *
+ * 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 <string.h>
+#include <sstream>
+
+#include "SimTKOpenMMCommon.h"
+#include "SimTKOpenMMLog.h"
+#include "SimTKOpenMMUtilities.h"
+#include "ReferenceLJ14.h"
+#include "ReferenceForce.h"
+
+/**---------------------------------------------------------------------------------------
+
+   ReferenceLJ14 constructor
+
+   --------------------------------------------------------------------------------------- */
+
+ReferenceLJ14::ReferenceLJ14( ){
+
+   // ---------------------------------------------------------------------------------------
+
+   // static const char* methodName = "\nReferenceLJ14::ReferenceLJ14";
+
+   // ---------------------------------------------------------------------------------------
+
+}
+
+/**---------------------------------------------------------------------------------------
+
+   ReferenceLJ14 destructor
+
+   --------------------------------------------------------------------------------------- */
+
+ReferenceLJ14::~ReferenceLJ14( ){
+
+   // ---------------------------------------------------------------------------------------
+
+   // static const char* methodName = "\nReferenceLJ14::~ReferenceLJ14";
+
+   // ---------------------------------------------------------------------------------------
+
+}
+
+/**---------------------------------------------------------------------------------------
+
+   Calculate parameters for LJ 1-4 ixn
+
+   @param c6               c6
+   @param c12              c12
+   @param q1               q1 charge atom 1
+   @param q2               q2 charge atom 2
+   @param epsfac           epsfac ????????????/
+   @param parameters       output parameters:
+										parameter[0]= c6*c6/c12
+										parameter[1]= (c12/c6)**1/6
+										parameter[2]= epsfactor*q1*q2
+
+   @return ReferenceForce::DefaultReturn
+
+   --------------------------------------------------------------------------------------- */
+
+int ReferenceLJ14::getDerivedParameters( RealOpenMM c6, RealOpenMM c12, RealOpenMM q1,
+                                         RealOpenMM q2, RealOpenMM epsfac,
+                                         RealOpenMM* parameters ) const {
+
+   // ---------------------------------------------------------------------------------------
+
+   // static const char* methodName = "\nReferenceLJ14::getDerivedParameters";
+
+   static const RealOpenMM zero       =  0.0;
+   static const RealOpenMM one        =  1.0;
+   static const RealOpenMM six        =  6.0;
+   static const RealOpenMM oneSixth   =  one/six;
+
+   // ---------------------------------------------------------------------------------------
+
+   if( c12 <= zero ){
+      parameters[0] = one;
+      parameters[1] = zero;
+   } else {
+      parameters[0] = (c6*c6)/c12;
+      parameters[1] = POW( (c12/c6), oneSixth );
+   }
+   parameters[2] = epsfac*q1*q2;
+
+   return ReferenceForce::DefaultReturn;
+}
+
+/**---------------------------------------------------------------------------------------
+
+   Calculate LJ 1-4 ixn
+
+   @param atomIndices      atom indices of 4 atoms in bond
+   @param atomCoordinates  atom coordinates
+   @param parameters       two parameters:
+										parameter[0]= c6*c6/c12
+										parameter[1]= (c12/c6)**1/6
+										parameter[2]= epsfac*q1*q2
+   @param forces           force array (forces added to current values)
+   @param energiesByBond   energies by bond: energiesByBond[bondIndex]
+   @param energiesByAtom   energies by atom: energiesByAtom[atomIndex]
+
+   @return ReferenceForce::DefaultReturn
+
+   --------------------------------------------------------------------------------------- */
+
+int ReferenceLJ14::calculateBondIxn( int* atomIndices, RealOpenMM** atomCoordinates,
+                                     RealOpenMM* parameters, RealOpenMM** forces,
+                                     RealOpenMM* energiesByBond,
+                                     RealOpenMM* energiesByAtom ) const {
+
+   // ---------------------------------------------------------------------------------------
+
+   // static const char* methodName = "\nReferenceLJ14::calculateBondIxn";
+
+   // ---------------------------------------------------------------------------------------
+
+   static const std::string methodName = "\nReferenceLJ14::calculateBondIxn";
+
+   // constants -- reduce Visual Studio warnings regarding conversions between float & double
+
+   static const RealOpenMM zero        =  0.0;
+   static const RealOpenMM one         =  1.0;
+   static const RealOpenMM two         =  2.0;
+   static const RealOpenMM three       =  3.0;
+   static const RealOpenMM six         =  6.0;
+   static const RealOpenMM twelve      = 12.0;
+   static const RealOpenMM oneM        = -1.0;
+
+   static const int threeI             = 3;
+
+   // number of parameters
+
+   static const int numberOfParameters = 3;
+
+   // debug flag
+
+   static const int debug              = 0;
+
+   static const int LastAtomIndex      = 2;
+
+   RealOpenMM deltaR[2][ReferenceForce::LastDeltaRIndex];
+
+   // ---------------------------------------------------------------------------------------
+
+   // get deltaR, R2, and R between 2 atoms
+
+   int atomAIndex = atomIndices[0];
+   int atomBIndex = atomIndices[1];
+   ReferenceForce::getDeltaR( atomCoordinates[atomBIndex], atomCoordinates[atomAIndex], deltaR[0] );  
+
+   RealOpenMM inverseR  = one/(deltaR[0][ReferenceForce::RIndex]);
+   RealOpenMM sig2      = inverseR*parameters[1];
+              sig2     *= sig2;
+   RealOpenMM sig6      = sig2*sig2*sig2;
+
+   RealOpenMM dEdR      = parameters[0]*( twelve*sig6 - six )*sig6;
+              dEdR     += parameters[2]*inverseR;
+              dEdR     *= inverseR*inverseR;
+
+   // accumulate forces
+
+   for( int ii = 0; ii < 3; ii++ ){
+      RealOpenMM force        = dEdR*deltaR[0][ii];
+      forces[atomAIndex][ii] += force;
+      forces[atomBIndex][ii] -= force;
+   }
+
+   RealOpenMM energy = 0.0;
+
+   // accumulate energies
+
+   //updateEnergy( energy, energiesByBond, LastAtomIndex, atomIndices, energiesByAtom );
+
+   // debug 
+
+   if( debug ){
+      static bool printHeader = false;
+      std::stringstream message;
+      message << methodName;
+      message << std::endl;
+      if( !printHeader  ){  
+         printHeader = true;
+         message << std::endl;
+         message << methodName.c_str() << " a0 k [c q p s] r1 r2  angle dt rp p[] dot cosine angle dEdR*r F[]" << std::endl;
+      }   
+
+      message << std::endl;
+      for( int ii = 0; ii < LastAtomIndex; ii++ ){
+         message << " Atm " << atomIndices[ii] << " [" << atomCoordinates[atomIndices[ii]][0] << " " << atomCoordinates[atomIndices[ii]][1] << "] ";
+      }
+      message << std::endl << " Delta:";
+      for( int ii = 0; ii < (LastAtomIndex - 1); ii++ ){
+         message << " [";
+         for( int jj = 0; jj < ReferenceForce::LastDeltaRIndex; jj++ ){
+            message << deltaR[ii][jj] << " ";
+         }
+         message << "]";
+      }
+      message << std::endl;
+
+      message << " p1="     << parameters[0];
+      message << " p2="     << parameters[1];
+      message << " p3="     << parameters[2];
+      message << std::endl << "  ";
+
+      message << " dEdR=" << dEdR;
+      message << " E=" << energy << " force factors: ";
+      message << "F=compute force; f=cumulative force";
+
+      message << std::endl << "  ";
+      for( int ii = 0; ii < LastAtomIndex; ii++ ){
+         message << " F" << (ii+1) << "[";
+         SimTKOpenMMUtilities::formatRealStringStream( message, deltaR[0], threeI, dEdR );
+         message << "]";
+      }   
+      message << std::endl << "  ";
+
+      for( int ii = 0; ii < LastAtomIndex; ii++ ){
+         message << " f" << (ii+1) << "[";
+         SimTKOpenMMUtilities::formatRealStringStream( message, forces[atomIndices[ii]], threeI );
+         message << "]";
+      }
+
+      SimTKOpenMMLog::printMessage( message );
+   }   
+
+   return ReferenceForce::DefaultReturn;
+}

platforms/reference/src/ReferenceLJ14.h

+
+/* Portions copyright (c) 2006 Stanford University and Simbios.
+ * Contributors: Pande Group
+ *
+ * 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.
+ */
+
+#ifndef __ReferenceLJ14_H__
+#define __ReferenceLJ14_H__
+
+#include "ReferenceBondIxn.h"
+
+// ---------------------------------------------------------------------------------------
+
+class ReferenceLJ14 : public ReferenceBondIxn {
+
+   private:
+
+   public:
+
+      /**---------------------------------------------------------------------------------------
+      
+         Constructor
+      
+         --------------------------------------------------------------------------------------- */
+
+       ReferenceLJ14( );
+
+      /**---------------------------------------------------------------------------------------
+      
+         Destructor
+      
+         --------------------------------------------------------------------------------------- */
+
+       ~ReferenceLJ14( );
+
+      /**---------------------------------------------------------------------------------------
+      
+         Calculate parameters for LJ 1-4 ixn
+      
+         @param c6               c6
+         @param c12              c12
+         @param q1               q1 charge atom 1
+         @param q2               q2 charge atom 2
+         @param epsfac           epsfac ????????????/
+         @param parameters       output parameters:
+                                    parameter[0]= c6*c6/c12
+                                    parameter[1]= (c12/c6)**1/6
+                                    parameter[2]= epsfactor*q1*q2
+      
+         @return ReferenceForce::DefaultReturn
+      
+         --------------------------------------------------------------------------------------- */
+      
+      int ReferenceLJ14::getDerivedParameters( RealOpenMM c6, RealOpenMM c12, RealOpenMM q1, 
+                                               RealOpenMM q2, RealOpenMM epsfac,
+                                               RealOpenMM* parameters ) const;
+      
+      /**---------------------------------------------------------------------------------------
+      
+         Calculate Ryckaert-Bellemans bond ixn
+      
+         @param atomIndices      atom indices of 4 atoms in bond
+         @param atomCoordinates  atom coordinates
+         @param parameters       six RB parameters
+         @param forces           force array (forces added to current values)
+         @param energiesByBond   energies by bond: energiesByBond[bondIndex]
+         @param energiesByAtom   energies by atom: energiesByAtom[atomIndex]
+      
+         @return ReferenceForce::DefaultReturn
+            
+         --------------------------------------------------------------------------------------- */
+      
+      int calculateBondIxn( int* atomIndices, RealOpenMM** atomCoordinates,
+                            RealOpenMM* parameters, RealOpenMM** forces,
+                            RealOpenMM* energiesByBond, RealOpenMM* energiesByAtom ) const;
+      
+
+};
+
+// ---------------------------------------------------------------------------------------
+
+#endif // __ReferenceLJ14_H__

platforms/reference/src/ReferenceLJCoulombIxn.cpp

+
+/* Portions copyright (c) 2006 Stanford University and Simbios.
+ * Contributors: Pande Group
+ *
+ * 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 <string.h>
+#include <sstream>
+
+#include "SimTKOpenMMCommon.h"
+#include "SimTKOpenMMLog.h"
+#include "SimTKOpenMMUtilities.h"
+#include "ReferenceLJCoulombIxn.h"
+#include "ReferenceForce.h"
+
+/**---------------------------------------------------------------------------------------
+
+   ReferenceLJCoulombIxn constructor
+
+   --------------------------------------------------------------------------------------- */
+
+ReferenceLJCoulombIxn::ReferenceLJCoulombIxn( ){
+
+   // ---------------------------------------------------------------------------------------
+
+   // static const char* methodName = "\nReferenceLJCoulombIxn::ReferenceLJCoulombIxn";
+
+   // ---------------------------------------------------------------------------------------
+
+}
+
+/**---------------------------------------------------------------------------------------
+
+   ReferenceLJCoulombIxn destructor
+
+   --------------------------------------------------------------------------------------- */
+
+ReferenceLJCoulombIxn::~ReferenceLJCoulombIxn( ){
+
+   // ---------------------------------------------------------------------------------------
+
+   // static const char* methodName = "\nReferenceLJCoulombIxn::~ReferenceLJCoulombIxn";
+
+   // ---------------------------------------------------------------------------------------
+
+}
+
+/**---------------------------------------------------------------------------------------
+
+   Calculate parameters for LJ Coulomb ixn
+
+   @param c6               c6
+   @param c12              c12
+   @param q1               q1 charge atom 1
+   @param epsfac           epsfacSqrt ????????????/
+   @param parameters       output parameters:
+										parameter[SigIndex]  = sqrt(c6*c6/c12)
+										parameter[EpsIndex]  = 0.5*( (c12/c6)**1/6 )
+										parameter[QIndex]    = epsfactorSqrt*q1
+
+   @return ReferenceForce::DefaultReturn
+
+   --------------------------------------------------------------------------------------- */
+
+int ReferenceLJCoulombIxn::getDerivedParameters( RealOpenMM c6, RealOpenMM c12, RealOpenMM q1,
+                                                 RealOpenMM epsfacSqrt,
+                                                 RealOpenMM* parameters ) const {
+
+   // ---------------------------------------------------------------------------------------
+
+   // static const char* methodName = "\nReferenceLJCoulombIxn::getDerivedParameters";
+
+   static const RealOpenMM zero          =  0.0;
+   static const RealOpenMM one           =  1.0;
+   static const RealOpenMM six           =  6.0;
+   static const RealOpenMM half          =  0.5;
+   static const RealOpenMM oneSixth      =  one/six;
+   static const RealOpenMM oneTweleth    =  half*oneSixth;
+
+   // ---------------------------------------------------------------------------------------
+
+   if( c12 <= 0.0 ){
+
+      parameters[EpsIndex] = zero;
+      parameters[SigIndex] = half;
+
+   } else {
+ 
+      parameters[EpsIndex]    = c6*SQRT( one/c12 );
+   
+      parameters[SigIndex]    = POW( (c12/c6), oneSixth );
+      parameters[SigIndex]   *= half;
+   }
+
+   parameters[QIndex]   = epsfacSqrt*q1;
+
+   return ReferenceForce::DefaultReturn;
+}
+
+/**---------------------------------------------------------------------------------------
+
+   Calculate LJ Coulomb pair ixn
+
+   @param numberOfAtoms    number of atoms
+   @param atomCoordinates  atom coordinates
+   @param atomParameters   atom parameters                             atomParameters[atomIndex][paramterIndex]
+   @param exclusions       atom exclusion indices                      exclusions[atomIndex][atomToExcludeIndex]
+                           exclusions[atomIndex][0] = number of exclusions
+                           exclusions[atomIndex][1-no.] = atom indices of atoms to excluded from
+                           interacting w/ atom atomIndex
+   @param fixedParameters  non atom parameters (not currently used)
+   @param forces           force array (forces added)
+   @param energyByAtom     atom energy
+   @param totalEnergy      total energy
+
+   @return ReferenceForce::DefaultReturn
+      
+   --------------------------------------------------------------------------------------- */
+    
+int ReferenceLJCoulombIxn::calculatePairIxn( int numberOfAtoms, RealOpenMM** atomCoordinates,
+                                             RealOpenMM** atomParameters, int** exclusions,
+                                             RealOpenMM* fixedParameters, RealOpenMM** forces,
+                                             RealOpenMM* energyByAtom, RealOpenMM* totalEnergy ) const {
+
+   // ---------------------------------------------------------------------------------------
+
+   // static const char* methodName = "\nReferenceLJCoulombIxn::calculatePairIxn";
+
+   // ---------------------------------------------------------------------------------------
+
+   static const std::string methodName = "\nReferenceLJCoulombIxn::calculatePairIxn";
+
+   // constants -- reduce Visual Studio warnings regarding conversions between float & double
+
+   static const RealOpenMM zero        =  0.0;
+   static const RealOpenMM one         =  1.0;
+   static const RealOpenMM two         =  2.0;
+   static const RealOpenMM three       =  3.0;
+   static const RealOpenMM six         =  6.0;
+   static const RealOpenMM twelve      = 12.0;
+   static const RealOpenMM oneM        = -1.0;
+
+   static const int threeI             = 3;
+
+   // debug flag
+
+   static const int debug              = -1;
+
+   static const int LastAtomIndex      = 2;
+
+   RealOpenMM deltaR[2][ReferenceForce::LastDeltaRIndex];
+
+   // ---------------------------------------------------------------------------------------
+
+   // allocate and initialize exclusion array
+
+   int* exclusionIndices = new int[numberOfAtoms];
+   for( int ii = 0; ii < numberOfAtoms; ii++ ){
+      exclusionIndices[ii] = -1;
+   }
+
+   for( int ii = 0; ii < numberOfAtoms; ii++ ){
+
+      // set exclusions
+
+      for( int jj = 1; jj <= exclusions[ii][0]; jj++ ){
+         exclusionIndices[exclusions[ii][jj]] = ii;
+      }
+     
+      // loop over atom pairs
+
+      for( int jj = ii+1; jj < numberOfAtoms; jj++ ){
+
+         if( exclusionIndices[jj] != ii ){
+
+            // get deltaR, R2, and R between 2 atoms
+
+            ReferenceForce::getDeltaR( atomCoordinates[jj], atomCoordinates[ii], deltaR[0] );  
+
+            RealOpenMM inverseR  = one/(deltaR[0][ReferenceForce::RIndex]);
+            RealOpenMM sig       = atomParameters[ii][SigIndex] +  atomParameters[jj][SigIndex];
+            RealOpenMM sig2      = inverseR*sig;
+                       sig2     *= sig2;
+            RealOpenMM sig6      = sig2*sig2*sig2;
+             
+            RealOpenMM eps       = atomParameters[ii][EpsIndex]*atomParameters[jj][EpsIndex];
+            RealOpenMM dEdR      = eps*( twelve*sig6 - six )*sig6;
+                       dEdR     += atomParameters[ii][QIndex]*atomParameters[jj][QIndex]*inverseR;
+                       dEdR     *= inverseR*inverseR;
+         
+            // accumulate forces
+         
+            for( int kk = 0; kk < 3; kk++ ){
+               RealOpenMM force  = dEdR*deltaR[0][kk];
+               forces[ii][kk]   += force;
+               forces[jj][kk]   -= force;
+            }
+         
+            RealOpenMM energy = 0.0;
+         
+            // accumulate energies
+         
+            *totalEnergy += energy;
+            if( energyByAtom ){
+               energyByAtom[ii] += energy;
+               energyByAtom[jj] += energy;
+            }
+         
+            // debug 
+         
+            if( debug == ii ){
+               static bool printHeader = false;
+               std::stringstream message;
+               message << methodName;
+               message << std::endl;
+               int pairArray[2] = { ii, jj };
+               if( !printHeader  ){  
+                  printHeader = true;
+                  message << std::endl;
+                  message << methodName.c_str() << " a0 k [c q p s] r1 r2  angle dt rp p[] dot cosine angle dEdR*r F[]" << std::endl;
+               }   
+         
+               message << std::endl;
+               for( int kk = 0; kk < 2; kk++ ){
+                  message << " Atm " << pairArray[kk] << " [" << atomCoordinates[pairArray[kk]][0] << " " << atomCoordinates[pairArray[kk]][1] << " " << atomCoordinates[pairArray[kk]][2] << "] ";
+               }
+               message << std::endl << " Delta:";
+               for( int kk = 0; kk < (LastAtomIndex - 1); kk++ ){
+                  message << " [";
+                  for( int jj = 0; jj < ReferenceForce::LastDeltaRIndex; jj++ ){
+                     message << deltaR[kk][jj] << " ";
+                  }
+                  message << "]";
+               }
+               message << std::endl;
+         
+               for( int kk = 0; kk < 2; kk++ ){
+                  message << " p" << pairArray[kk] << " [";
+                  message << atomParameters[pairArray[kk]][0] << " " << atomParameters[pairArray[kk]][1] << " " << atomParameters[pairArray[kk]][2];
+                  message << "]";
+               }
+              message << std::endl;
+         
+               message << " dEdR=" << dEdR;
+               message << " E=" << energy << " force factors: ";
+               message << "F=compute force; f=cumulative force";
+         
+               message << std::endl << "  ";
+               message << " f" << ii << "[";
+               SimTKOpenMMUtilities::formatRealStringStream( message, deltaR[0], threeI, dEdR );
+               message << "]";
+
+               for( int kk = 0; kk < 2; kk++ ){
+                  message << " F" <<  pairArray[kk] << " [";
+                  SimTKOpenMMUtilities::formatRealStringStream( message, forces[pairArray[kk]], threeI );
+                  message << "]";
+               }
+         
+               SimTKOpenMMLog::printMessage( message );
+            }
+         }
+      }
+   }
+
+   delete[] exclusionIndices;
+
+   return ReferenceForce::DefaultReturn;
+}

platforms/reference/src/ReferenceLJCoulombIxn.h

+
+/* Portions copyright (c) 2006 Stanford University and Simbios.
+ * Contributors: Pande Group
+ *
+ * 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.
+ */
+
+#ifndef __ReferenceLJCoulombIxn_H__
+#define __ReferenceLJCoulombIxn_H__
+
+#include "ReferencePairIxn.h"
+
+// ---------------------------------------------------------------------------------------
+
+class ReferenceLJCoulombIxn : public ReferencePairIxn {
+
+   private:
+
+      // parameter indices
+
+      static const int SigIndex = 0;
+      static const int EpsIndex = 1;
+      static const int   QIndex = 2;
+
+   public:
+
+      /**---------------------------------------------------------------------------------------
+      
+         Constructor
+      
+         --------------------------------------------------------------------------------------- */
+
+       ReferenceLJCoulombIxn( );
+
+      /**---------------------------------------------------------------------------------------
+      
+         Destructor
+      
+         --------------------------------------------------------------------------------------- */
+
+       ~ReferenceLJCoulombIxn( );
+
+      /**---------------------------------------------------------------------------------------
+      
+         Calculate parameters for LJ 1-4 ixn
+      
+         @param c6               c6
+         @param c12              c12
+         @param q1               q1 charge atom
+         @param epsfacSqrt       epsfacSqrt ????????????/
+         @param parameters       output parameters:
+                                    parameter[SigIndex]  = sqrt(c6*c6/c12)
+                                    parameter[EpsIndex]  = 0.5*( (c12/c6)**1/6 )
+                                    parameter[QIndex]    = epsfactorSqrt*q1
+      
+         @return ReferenceForce::DefaultReturn
+      
+         --------------------------------------------------------------------------------------- */
+      
+      int getDerivedParameters( RealOpenMM c6, RealOpenMM c12, RealOpenMM q1, 
+                                RealOpenMM epsfacSqrt,
+                                RealOpenMM* parameters ) const;
+      
+      /**---------------------------------------------------------------------------------------
+      
+         Calculate LJ Coulomb pair ixn
+      
+         @param numberOfAtoms    number of atoms
+         @param atomCoordinates  atom coordinates
+         @param atomParameters   atom parameters (charges, c6, c12, ...)     atomParameters[atomIndex][paramterIndex]
+         @param exclusions       atom exclusion indices                      exclusions[atomIndex][atomToExcludeIndex]
+                                 exclusions[atomIndex][0] = number of exclusions
+                                 exclusions[atomIndex][1-no.] = atom indices of atoms to excluded from
+                                 interacting w/ atom atomIndex
+         @param fixedParameters  non atom parameters (not currently used)
+         @param forces           force array (forces added)
+         @param energyByAtom     atom energy
+         @param totalEnergy      total energy
+      
+         @return ReferenceForce::DefaultReturn
+            
+         --------------------------------------------------------------------------------------- */
+          
+      int calculatePairIxn( int numberOfAtoms, RealOpenMM** atomCoordinates,
+                            RealOpenMM** atomParameters, int** exclusions,
+                            RealOpenMM* fixedParameters, RealOpenMM** forces,
+                            RealOpenMM* energyByAtom, RealOpenMM* totalEnergy ) const;
+      
+};
+
+// ---------------------------------------------------------------------------------------
+
+#endif // __ReferenceLJCoulombIxn_H__

platforms/reference/src/ReferencePairIxn.cpp

+
+/* Portions copyright (c) 2006 Stanford University and Simbios.
+ * Contributors: Pande Group
+ *
+ * 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 <string.h>
+#include <sstream>
+
+#include "SimTKOpenMMCommon.h"
+#include "SimTKOpenMMLog.h"
+#include "SimTKOpenMMUtilities.h"
+#include "ReferenceForce.h"
+#include "ReferencePairIxn.h"
+
+/**---------------------------------------------------------------------------------------
+
+   ReferencePairIxn constructor
+
+   --------------------------------------------------------------------------------------- */
+
+ReferencePairIxn::ReferencePairIxn( ){
+
+   // ---------------------------------------------------------------------------------------
+
+   // static const char* methodName = "\nReferencePairIxn::ReferencePairIxn";
+
+   // ---------------------------------------------------------------------------------------
+
+}
+
+/**---------------------------------------------------------------------------------------
+
+   ReferencePairIxn destructor
+
+   --------------------------------------------------------------------------------------- */
+
+ReferencePairIxn::~ReferencePairIxn( ){
+
+   // ---------------------------------------------------------------------------------------
+
+   // static const char* methodName = "\nReferencePairIxn::~ReferencePairIxn";
+
+   // ---------------------------------------------------------------------------------------
+
+}

platforms/reference/src/ReferencePairIxn.h

+
+/* Portions copyright (c) 2006 Stanford University and Simbios.
+ * Contributors: Pande Group
+ *
+ * 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.
+ */
+
+#ifndef __ReferencePairIxn_H__
+#define __ReferencePairIxn_H__
+
+// #include "ReferenceIxn.h"
+
+// ---------------------------------------------------------------------------------------
+
+class ReferencePairIxn {
+
+   private:
+
+   public:
+
+      /**---------------------------------------------------------------------------------------
+      
+         Constructor
+      
+         --------------------------------------------------------------------------------------- */
+
+       ReferencePairIxn( );
+
+      /**---------------------------------------------------------------------------------------
+      
+         Destructor
+      
+         --------------------------------------------------------------------------------------- */
+
+       ~ReferencePairIxn( );
+
+      /**---------------------------------------------------------------------------------------
+      
+         Calculate pair ixn
+      
+         @param numberOfAtoms    number of atoms
+         @param atomCoordinates  atom coordinates
+         @param atomParameters   atom parameters (charges, c6, c12, ...)     atomParameters[atomIndex][paramterIndex]
+         @param exclusions       atom exclusion indices                      exclusions[atomIndex][atomToExcludeIndex]
+         @param fixedParameters  non-atom parameters
+         @param forces           force array (forces added)
+         @param energyByAtom     atom energy
+         @param totalEnergy      total energy
+      
+         @return ReferenceForce::DefaultReturn
+            
+         --------------------------------------------------------------------------------------- */
+          
+      virtual int calculatePairIxn( int numberOfAtoms, RealOpenMM** atomCoordinates,
+                            RealOpenMM** atomParameters, int** exclusions,
+                            RealOpenMM* fixedParameters, RealOpenMM** forces,
+                            RealOpenMM* energyByAtom, RealOpenMM* totalEnergy ) const = 0;
+      
+};
+
+// ---------------------------------------------------------------------------------------
+
+#endif // __ReferencePairIxn_H__