ObcParameters.cpp

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

#include "openmm/OpenMMException.h"
#include "ObcParameters.h"
#include "SimTKOpenMMCommon.h"

using std::vector;
using namespace OpenMM;

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

    ObcParameters constructor 

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

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

ObcParameters::ObcParameters( int numberOfAtoms, ObcParameters::ObcType obcType ) :
                               _numberOfAtoms(numberOfAtoms),
                               _solventDielectric( 78.3 ),
                               _soluteDielectric( 1.0 ),
                               _electricConstant(-0.5*ONE_4PI_EPS0),
                               _probeRadius(0.14),
                               _pi4Asolv( 28.3919551),
                               _dielectricOffset( 0.009 ),
                               _obcType( obcType ),
                               _cutoff(false),
                               _periodic(false) {

    _atomicRadii.resize( numberOfAtoms );
    _scaledRadiusFactors.resize( numberOfAtoms );
    setObcTypeParameters( obcType );

}

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

    ObcParameters destructor 

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

ObcParameters::~ObcParameters( ){
}

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

   Get number of atoms

   @return number of atoms

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

int ObcParameters::getNumberOfAtoms( void ) const {
    return _numberOfAtoms;
}

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

    Get OBC type

    @return OBC type

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

ObcParameters::ObcType ObcParameters::getObcType( void ) const {
    return _obcType;
}

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

    Set OBC type specific parameters

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

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

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

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

    Get dielectricOffset

    @return _dielectricOffset

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

RealOpenMM ObcParameters::getDielectricOffset( void ) const {
    return _dielectricOffset;
}

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

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

    @return alphaObc

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

RealOpenMM ObcParameters::getAlphaObc( void ) const {
    return _alphaObc;
}

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

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

    @return betaObc

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

RealOpenMM ObcParameters::getBetaObc( void ) const {
    return _betaObc;
}

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

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

    @return gammaObc

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

RealOpenMM ObcParameters::getGammaObc( void ) const {
    return _gammaObc;
}

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

   Get solvent dielectric

   @return solvent dielectric

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

RealOpenMM ObcParameters::getSolventDielectric( void ) const {
    return _solventDielectric;
}

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

   Set solvent dielectric

   @param solventDielectric solvent dielectric

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

void ObcParameters::setSolventDielectric( RealOpenMM solventDielectric ){
    _solventDielectric = solventDielectric;
}
/**---------------------------------------------------------------------------------------

   Get solute dielectric

   @return soluteDielectric

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

RealOpenMM ObcParameters::getSoluteDielectric( void ) const {
    return _soluteDielectric;
}

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

   Set solute dielectric

   @param soluteDielectric solute dielectric

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

void ObcParameters::setSoluteDielectric( RealOpenMM soluteDielectric ){
    _soluteDielectric = soluteDielectric;
}

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

   Get electric constant 

   @return electricConstant

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

RealOpenMM ObcParameters::getElectricConstant( void ) const {
    return _electricConstant;
}

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

   Get probe radius 

   @return probeRadius

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

RealOpenMM ObcParameters::getProbeRadius( void ) const {
    return _probeRadius;
}

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

   Set probe radius  

   @param probeRadius   probe radius

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

void ObcParameters::setProbeRadius( RealOpenMM probeRadius ){
    _probeRadius = probeRadius;
}

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

   Get pi*4*Asolv:  used in ACE approximation for nonpolar term  
         ((RealOpenMM) M_PI)*4.0f*0.0049*1000.0; (Still) 
         ((RealOpenMM) M_PI)*4.0f*0.0054*1000.0; (OBC) 

   @return pi4Asolv

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

RealOpenMM ObcParameters::getPi4Asolv( void ) const {
    return _pi4Asolv;
}

void ObcParameters::setPi4Asolv(RealOpenMM pi4Asolv) {
    _pi4Asolv = pi4Asolv;
}

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

    Get AtomicRadii array

    @return array of atomic radii

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

const RealOpenMMVector& ObcParameters::getAtomicRadii( void ) const {
    return _atomicRadii;
}

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

    Set AtomicRadii array

    @param atomicRadii vector of atomic radii

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

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

    if( atomicRadii.size() == _atomicRadii.size() ){
        for( unsigned int ii = 0; ii < atomicRadii.size(); ii++ ){
            _atomicRadii[ii] = atomicRadii[ii];
        }   
    } else {
        std::stringstream msg;
        msg << "ObcParameters: input size for atomic radii does not agree w/ current size: input=";
        msg << atomicRadii.size();
        msg << " current size=" << _atomicRadii.size();
        throw OpenMM::OpenMMException(msg.str());
    }   

}

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

    Return OBC scale factors

    @return array 

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

const RealOpenMMVector& ObcParameters::getScaledRadiusFactors( void ) const {
    return _scaledRadiusFactors;
}

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

    Set OBC scale factors

    @param scaledRadiusFactors  scaledRadiusFactors

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

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

    if( scaledRadiusFactors.size() == _scaledRadiusFactors.size() ){
        for( unsigned int ii = 0; ii < scaledRadiusFactors.size(); ii++ ){
            _scaledRadiusFactors[ii] = scaledRadiusFactors[ii];
        }   
    } else {
        std::stringstream msg;
        msg << "ObcParameters: input size for scaled radius factors does not agree w/ current size: input=";
        msg << scaledRadiusFactors.size();
        msg << " current size=" << _scaledRadiusFactors.size();
        throw OpenMM::OpenMMException(msg.str());
    }   

}

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

      Set the force to use a cutoff.

      @param distance            the cutoff distance

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

void ObcParameters::setUseCutoff( RealOpenMM distance ) {

     _cutoff         = true;
     _cutoffDistance = distance;
}

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

      Get whether to use a cutoff.

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

bool ObcParameters::getUseCutoff() const {
     return _cutoff;
}

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

      Get the cutoff distance.

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

RealOpenMM ObcParameters::getCutoffDistance() const {
     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 vectors    the vectors defining the periodic box

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

void ObcParameters::setPeriodic(OpenMM::RealVec* vectors) {

    assert(_cutoff);

    assert(boxSize[0][0] >= 2.0*_cutoffDistance);
    assert(boxSize[1][1] >= 2.0*_cutoffDistance);
    assert(boxSize[2][2] >= 2.0*_cutoffDistance);

    _periodic           = true;
    _periodicBoxVectors[0] = vectors[0];
    _periodicBoxVectors[1] = vectors[1];
    _periodicBoxVectors[2] = vectors[2];
}

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

      Get whether to use periodic boundary conditions.

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

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

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

      Get the periodic box dimension

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

const OpenMM::RealVec* ObcParameters::getPeriodicBox() {
     return _periodicBoxVectors;
}