ObcParameters.cpp

/* Portions copyright (c) 2006-2009 Stanford University and Simbios.
 * Contributors: Pande Group
 *
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#include <math.h>
#include <sstream>

#include "ObcParameters.h"
#include "../SimTKUtilities/SimTKOpenMMCommon.h"
#include "../SimTKUtilities/SimTKOpenMMLog.h"
#include "../SimTKUtilities/SimTKOpenMMUtilities.h"

// #define UseGromacsMalloc 1

#ifdef UseGromacsMalloc
extern "C" {
#include "smalloc.h" 
}
#endif

const std::string ObcParameters::ParameterFileName = std::string( "params.agb" );

/**---------------------------------------------------------------------------------------

   ObcParameters:

		Calculates for each atom

			(1) the van der Waal radii
         (2) volume
         (3) fixed terms in Obc equation gPol
         (4) list of atoms that should be excluded in calculating
				 force -- nonbonded atoms (1-2, and 1-3 atoms)

	Implementation:

		Slightly different sequence of calls when running on CPU vs GPU.
		Difference arise because the CPU-side data arrays for the Brook
		streams are allocated by the BrookStreamWrapper objects. These
		arrays are then used by ObcParameters when initializing the
		the values (vdwRadii, volume, ...) to be used in the calculation.

		Cpu:
			 ObcParameters* obcParameters = new ObcParameters( numberOfAtoms, log );
          obcParameters->initializeParameters( top );

		Gpu:

			obcParameters   = new ObcParameters( gpu->natoms, log );
			
			// set arrays for cpu using stream data field; 
			// initializeParameters() only allocates space for arrays if they are not set (==NULL)
			// also set flag so that ObcParameters destructor does not free arrays 
			
			obcParameters->setVdwRadii(  getBrookStreamWrapperAtIndex( GpuObc::obcVdwRadii  )->getData() );
			obcParameters->setVolume(    getBrookStreamWrapperAtIndex( GpuObc::obcVolume    )->getData() );
			obcParameters->setGPolFixed( getBrookStreamWrapperAtIndex( GpuObc::obcGpolFixed )->getData() );
			obcParameters->setBornRadii( getBrookStreamWrapperAtIndex( GpuObc::obcBornRadii )->getData() );
			
			obcParameters->setFreeArrays( false );
			
			obcParameters->initializeParameters( top );
 

   Issues:

		Tinker's atom radii are used. 
      The logic for mapping the Gromacs atom names to Tinker type may be incomplete;
      only tested for generic proteins
		see mapGmxAtomNameToTinkerAtomNumber()

   --------------------------------------------------------------------------------------- */


/**---------------------------------------------------------------------------------------

   ObcParameters constructor (Simbios) 

   @param numberOfAtoms       number of atoms
   @param obcType             OBC type (Eq. 7 or 8 in paper)

   --------------------------------------------------------------------------------------- */

ObcParameters::ObcParameters( int numberOfAtoms, ObcParameters::ObcType obcType ) : ImplicitSolventParameters( numberOfAtoms ), cutoff(false), periodic(false) {

   // ---------------------------------------------------------------------------------------

   // static const char* methodName = "\nObcParameters::ObcParameters";
   
   // ---------------------------------------------------------------------------------------

   _obcType                      = obcType;
   _dielectricOffset             = 0.009f;
   _ownScaledRadiusFactors       = 0;
   _scaledRadiusFactors          = NULL;

   setObcTypeParameters( obcType );

}

/**---------------------------------------------------------------------------------------

   ObcParameters destructor (Simbios) 

   --------------------------------------------------------------------------------------- */

ObcParameters::~ObcParameters( ){

   // ---------------------------------------------------------------------------------------

   // static const char* methodName = "\nObcParameters::~ObcParameters";
   
   // ---------------------------------------------------------------------------------------

   // in GPU runs, arrays may be 'owned' by BrookStreamWrapper -- hence they should not
   // be freed here, i.e., _freeArrays should be 'false'   

#ifdef UseGromacsMalloc

/*
   if( _freeArrays ){

      if( _vdwRadii != NULL ){
         save_free( "_vdwRadii", __FILE__, __LINE__, _vdwRadii );
      }
   
   } */

#else

   if( _ownScaledRadiusFactors ){
      delete[] _scaledRadiusFactors;
   }
/*
   if( getFreeArrays() ){

   } */

#endif

}

/**---------------------------------------------------------------------------------------

   Get OBC type

   @return OBC type

   --------------------------------------------------------------------------------------- */

ObcParameters::ObcType ObcParameters::getObcType( void ) const {

   // ---------------------------------------------------------------------------------------

   // static const char* methodName = "\nObcParameters::getObcType:";

   // ---------------------------------------------------------------------------------------

   return _obcType;
}

/**---------------------------------------------------------------------------------------

   Set OBC type specific parameters

   @param obcType OBC type (ObcTypeI or ObcTypeII -- Eq. 7 or 8)

   @return SimTKOpenMMCommon::DefaultReturn

   --------------------------------------------------------------------------------------- */

int ObcParameters::setObcTypeParameters( ObcParameters::ObcType obcType ){

   // ---------------------------------------------------------------------------------------

   // static const char* methodName = "\nObcParameters::setObcTypeParameters:";

   // ---------------------------------------------------------------------------------------

   if( obcType == ObcTypeI ){
      _alphaObc   = 0.8f;
      _betaObc    = 0.0f;
      _gammaObc   = 2.91f;
   } else {
      _alphaObc   = 1.0f;
      _betaObc    = 0.8f;
      _gammaObc   = 4.85f;
   }
   _obcType = obcType;

   return SimTKOpenMMCommon::DefaultReturn;
}

/**---------------------------------------------------------------------------------------

   Get dielectricOffset

   @return _dielectricOffset

   --------------------------------------------------------------------------------------- */

RealOpenMM ObcParameters::getDielectricOffset( void ) const {

   // ---------------------------------------------------------------------------------------

   // static const char* methodName = "\nObcParameters::getDielectricOffset:";

   // ---------------------------------------------------------------------------------------

   return _dielectricOffset;
}

/**---------------------------------------------------------------------------------------

   Get alpha OBC (Eqs. 6 & 7) in Proteins paper

   @return alphaObc

   --------------------------------------------------------------------------------------- */

RealOpenMM ObcParameters::getAlphaObc( void ) const {

   // ---------------------------------------------------------------------------------------

   // static const char* methodName = "\nObcParameters::getAlphaObc:";

   // ---------------------------------------------------------------------------------------

   return _alphaObc;
}

/**---------------------------------------------------------------------------------------

   Get beta OBC (Eqs. 6 & 7) in Proteins paper

   @return betaObc

   --------------------------------------------------------------------------------------- */

RealOpenMM ObcParameters::getBetaObc( void ) const {

   // ---------------------------------------------------------------------------------------

   // static const char* methodName = "\nObcParameters::getBetaObc:";

   // ---------------------------------------------------------------------------------------

   return _betaObc;
}

/**---------------------------------------------------------------------------------------

   Get gamma OBC (Eqs. 6 & 7) in Proteins paper

   @return gammaObc

   --------------------------------------------------------------------------------------- */

RealOpenMM ObcParameters::getGammaObc( void ) const {

   // ---------------------------------------------------------------------------------------

   // static const char* methodName = "\nObcParameters::getGammaObc:";

   // ---------------------------------------------------------------------------------------

   return _gammaObc;
}

/**---------------------------------------------------------------------------------------

   Get AtomicRadii array

   @return array of atomic radii

   --------------------------------------------------------------------------------------- */

RealOpenMM* ObcParameters::getAtomicRadii( void ) const {

   // ---------------------------------------------------------------------------------------

   // static const char* methodName = "\nImplicitSolventParameters::getAtomicRadii:";

   // ---------------------------------------------------------------------------------------

   RealOpenMM* atomicRadii = ImplicitSolventParameters::getAtomicRadii();

   // if dielectric offset applied, then unapply

   return atomicRadii;
}

/**---------------------------------------------------------------------------------------

   Set AtomicRadii array

   @param atomicRadii array of atomic radii

   @return SimTKOpenMMCommon::DefaultReturn

   --------------------------------------------------------------------------------------- */

int ObcParameters::setAtomicRadii( RealOpenMM* atomicRadii ){

   // ---------------------------------------------------------------------------------------

   // static const char* methodName = "\nObcParameters::setAtomicRadii:";

   // ---------------------------------------------------------------------------------------

   return ImplicitSolventParameters::setAtomicRadii( atomicRadii );
}

/**---------------------------------------------------------------------------------------

   Set AtomicRadii array

   @param atomicRadii vector of atomic radii

   @return SimTKOpenMMCommon::DefaultReturn

   --------------------------------------------------------------------------------------- */

int ObcParameters::setAtomicRadii( const RealOpenMMVector& atomicRadii ){

   // ---------------------------------------------------------------------------------------

   static const char* methodName = "\nObcParameters::setAtomicRadii:";

   // ---------------------------------------------------------------------------------------

   return ImplicitSolventParameters::setAtomicRadii( atomicRadii );
}

/**---------------------------------------------------------------------------------------

   Return OBC scale factors
   If not previously set, allocate space

   @return array 

   --------------------------------------------------------------------------------------- */

const RealOpenMM* ObcParameters::getScaledRadiusFactors( void ) const {

   // ---------------------------------------------------------------------------------------

   // static const char* methodName = "\nCpuObc::getScaledRadiusFactors";

   // ---------------------------------------------------------------------------------------

   if( _scaledRadiusFactors == NULL ){
      ObcParameters* localThis = const_cast<ObcParameters* const>(this);
      localThis->_scaledRadiusFactors    = new RealOpenMM[getNumberOfAtoms()];
      localThis->_ownScaledRadiusFactors = true;
      memset( _scaledRadiusFactors, 0, sizeof( RealOpenMM )*getNumberOfAtoms() );
   }   
   return _scaledRadiusFactors;
}

/**---------------------------------------------------------------------------------------

   Set flag indicating whether scale factors array should be deleted

   @param ownScaledRadiusFactors flag indicating whether scale factors 
                                 array should be deleted

   @return SimTKOpenMMCommon::DefaultReturn

   --------------------------------------------------------------------------------------- */

int ObcParameters::setOwnScaleFactors( int ownScaledRadiusFactors ){

   // ---------------------------------------------------------------------------------------

   // static const char* methodName = "\nCpuObc::setOwnScaleFactors";

   // ---------------------------------------------------------------------------------------

   _ownScaledRadiusFactors = ownScaledRadiusFactors;

   return SimTKOpenMMCommon::DefaultReturn;
}

/**---------------------------------------------------------------------------------------

   Set OBC scale factors

   @param scaledRadiusFactors  scaledRadiusFactors

   @return SimTKOpenMMCommon::DefaultReturn always

   --------------------------------------------------------------------------------------- */

int ObcParameters::setScaledRadiusFactors( RealOpenMM* scaledRadiusFactors ){

   // ---------------------------------------------------------------------------------------

   // static const char* methodName = "\nCpuObc::setScaledRadiusFactors";

   // ---------------------------------------------------------------------------------------

   if( _ownScaledRadiusFactors && _scaledRadiusFactors != scaledRadiusFactors ){
      delete[] _scaledRadiusFactors;
      _ownScaledRadiusFactors = false;
   }

   _scaledRadiusFactors = scaledRadiusFactors;

   return SimTKOpenMMCommon::DefaultReturn;

}

/**---------------------------------------------------------------------------------------

   Set OBC scale factors

   @param scaledRadiusFactors  scaledRadiusFactors

   @return SimTKOpenMMCommon::DefaultReturn always

   --------------------------------------------------------------------------------------- */

int ObcParameters::setScaledRadiusFactors( const RealOpenMMVector& scaledRadiusFactors ){

   // ---------------------------------------------------------------------------------------

   // static const char* methodName = "\nCpuObc::setScaledRadiusFactors";

   // ---------------------------------------------------------------------------------------

   if( _ownScaledRadiusFactors && _scaledRadiusFactors != NULL ){
      delete[] _scaledRadiusFactors;
   }
   _ownScaledRadiusFactors = true;
   _scaledRadiusFactors    = new RealOpenMM[getNumberOfAtoms()];
   for( int ii = 0; ii < (int) scaledRadiusFactors.size(); ii++ ){
      _scaledRadiusFactors[ii] = scaledRadiusFactors[ii];
   }

   return SimTKOpenMMCommon::DefaultReturn;
}

/**---------------------------------------------------------------------------------------

   Map Gmx atom name to Tinker atom number (Simbios)

   @param atomName            atom name (CA, HA, ...); upper and lower case should both work
   @param log                 if set, then print error messages to log file

   @return Tinker atom number if atom name is valid; else return -1

   --------------------------------------------------------------------------------------- */

int ObcParameters::mapGmxAtomNameToTinkerAtomNumber( const char* atomName, FILE* log ) const {

   // ---------------------------------------------------------------------------------------

   static int mapCreated = 0;
   static int atomNameMap[26];
        
   // ---------------------------------------------------------------------------------------

   // set up atomNameMap array on first call to this method

   // atomNameMap[ii] = Tinker atom number
   // where ii = (the ASCII index - 65) of the first character in the
   // input atom name; name may be lower case

   if( !mapCreated ){

      mapCreated = 1;

      for( int ii = 0; ii < 26; ii++ ){
         atomNameMap[ii] = -1;
      }

      // H
      atomNameMap[7]  = 1;

      // C
      atomNameMap[2]  = 6;

      // N
      atomNameMap[13] = 7;

      // O
      atomNameMap[14] = 8;

      // S
      atomNameMap[18] = 16;
   }

   // map first letter in atom name to Tinker atom number

   int firstAsciiValue = ((int) atomName[0]) - 65;

   // check for lower case

   if( firstAsciiValue > 25 ){
      firstAsciiValue -= 32;
   }

   // validate

   if( firstAsciiValue < 0 || firstAsciiValue > 25 ){ 
      if( log != NULL ){
         (void) fprintf( log, "Atom name=<%s> unrecognized.", atomName );
      }
      (void) fprintf( stderr, "Atom name=<%s> unrecognized.", atomName );
      return -1;
   }
   return atomNameMap[firstAsciiValue];
}

/**---------------------------------------------------------------------------------------
      
   Get string w/ state
   
   @param title               title (optional)
      
   @return string
      
   --------------------------------------------------------------------------------------- */

std::string ObcParameters::getStateString( const char* title ) const {

   // ---------------------------------------------------------------------------------------

   // static const char* methodName = "\nObcParameters::getStateString";

   // ---------------------------------------------------------------------------------------

   std::stringstream message;
   message << ImplicitSolventParameters::getStateString( title );

   std::string tab           = getStringTab();

   if( getObcType() == ObcTypeI ){
      message << tab << "OBC type:    Type I";
   } else {
      message << tab << "OBC type:    Type II";
   }
   message << tab << "Alpha:                " << getAlphaObc();
   message << tab << "Beta:                 " << getBetaObc();
   message << tab << "Gamma:                " << getGammaObc();

   return message.str();


}

/**---------------------------------------------------------------------------------------

     Set the force to use a cutoff.

     @param distance            the cutoff distance

     @return ReferenceForce::DefaultReturn

     --------------------------------------------------------------------------------------- */

int ObcParameters::setUseCutoff( RealOpenMM distance ) {

    cutoff = true;
    cutoffDistance = distance;
    return SimTKOpenMMCommon::DefaultReturn;
}

/**---------------------------------------------------------------------------------------

     Get whether to use a cutoff.

     --------------------------------------------------------------------------------------- */

bool ObcParameters::getUseCutoff() {
    return cutoff;
}

/**---------------------------------------------------------------------------------------

     Get the cutoff distance.

     --------------------------------------------------------------------------------------- */

RealOpenMM ObcParameters::getCutoffDistance() {
    return cutoffDistance;
}

/**---------------------------------------------------------------------------------------

     Set the force to use periodic boundary conditions.  This requires that a cutoff has
     also been set, and the smallest side of the periodic box is at least twice the cutoff
     distance.

     @param boxSize             the X, Y, and Z widths of the periodic box

     @return ReferenceForce::DefaultReturn

     --------------------------------------------------------------------------------------- */

int ObcParameters::setPeriodic( RealOpenMM* boxSize ) {

    assert(cutoff);
    assert(boxSize[0] >= 2.0*cutoffDistance);
    assert(boxSize[1] >= 2.0*cutoffDistance);
    assert(boxSize[2] >= 2.0*cutoffDistance);
    periodic = true;
    periodicBoxSize[0] = boxSize[0];
    periodicBoxSize[1] = boxSize[1];
    periodicBoxSize[2] = boxSize[2];
    return SimTKOpenMMCommon::DefaultReturn;
}

/**---------------------------------------------------------------------------------------

     Get whether to use periodic boundary conditions.

     --------------------------------------------------------------------------------------- */

bool ObcParameters::getPeriodic() {
    return periodic;
}

/**---------------------------------------------------------------------------------------

     Get the periodic box dimension

     --------------------------------------------------------------------------------------- */

const RealOpenMM* ObcParameters::getPeriodicBox() {
    return periodicBoxSize;
}