CpuImplicitSolvent.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
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 * 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
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#include "../SimTKUtilities/SimTKOpenMMCommon.h"
#include "../SimTKUtilities/SimTKOpenMMLog.h"
#include "../SimTKUtilities/SimTKOpenMMUtilities.h"
#include "CpuImplicitSolvent.h"

#include <cstdio>

using namespace OpenMM;
using namespace std;

//#define UseGromacsMalloc 1

// Replacement new/delete w/ Gromac's smalloc() and sfree()

// static data member created by call to cpuSetImplicitSolventParameters() 
// stores parameter settings, ...
// used to calculate GBSA forces/energy

CpuImplicitSolvent* CpuImplicitSolvent::_cpuImplicitSolvent                     = NULL;

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

   CpuImplicitSolvent constructor

   @param implicitSolventParameters      implicitSolventParameters object
   
   --------------------------------------------------------------------------------------- */

CpuImplicitSolvent::CpuImplicitSolvent( ImplicitSolventParameters* implicitSolventParameters ){

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

   // static const char* methodName = "\nCpuImplicitSolvent::CpuImplicitSolvent(2)";

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

   _initializeDataMembers( );
   _implicitSolventParameters = implicitSolventParameters;

}

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

   CpuImplicitSolvent destructor

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

CpuImplicitSolvent::~CpuImplicitSolvent( ){

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

   // static const char* methodName = "\nCpuImplicitSolvent::~CpuImplicitSolvent";

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

   delete _implicitSolventParameters;
}

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

   Initialize data members

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

void CpuImplicitSolvent::_initializeDataMembers( void ){

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

   // static const char* methodName = "\nCpuImplicitSolvent::_initializeDataMembers";

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

   _includeAceApproximation             = 0;

   _forceConversionFactor               = (RealOpenMM) 1.0;
   _energyConversionFactor              = (RealOpenMM) 1.0;

   _forceCallIndex                      = 0;

   _implicitSolventEnergy               = (RealOpenMM) 0.0;
}

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

   Return number of atoms

   @return number of atoms

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

int CpuImplicitSolvent::getNumberOfAtoms( void ) const {

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

   // static const char* methodName = "\nCpuImplicitSolvent::getNumberOfAtoms";

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

   return _implicitSolventParameters->getNumberOfAtoms();

}

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

   Return energy 

   @return energy

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

RealOpenMM CpuImplicitSolvent::getEnergy( void ) const {

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

   // static const char* methodName = "\nCpuImplicitSolvent::getEnergy";

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

   return _implicitSolventEnergy;

}

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

   Delete static _cpuImplicitSolvent object if set

   @return SimTKOpenMMCommon::DefaultReturn if _cpuImplicitSolvent was set; 
           otherwise return SimTKOpenMMCommon::ErrorReturn

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

int CpuImplicitSolvent::deleteCpuImplicitSolvent( void ){

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

   // static const char* methodName = "\nCpuImplicitSolvent::deleteCpuImplicitSolvent";

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

   if( _cpuImplicitSolvent != NULL ){
      delete _cpuImplicitSolvent;
      _cpuImplicitSolvent = NULL;
      return SimTKOpenMMCommon::DefaultReturn;
   } else {
      return SimTKOpenMMCommon::ErrorReturn;
   }
}

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

   Set static member _cpuImplicitSolvent

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

void CpuImplicitSolvent::setCpuImplicitSolvent( CpuImplicitSolvent* cpuImplicitSolvent ){

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

   // static const char* methodName = "\nCpuImplicitSolvent::setCpuImplicitSolvent";

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

   _cpuImplicitSolvent = cpuImplicitSolvent;
}

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

   Get static member cpuImplicitSolvent

   @return static member cpuImplicitSolvent

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

CpuImplicitSolvent* CpuImplicitSolvent::getCpuImplicitSolvent( void ){

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

   // static const char* methodName = "\nCpuImplicitSolvent::getCpuImplicitSolvent";

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

   return _cpuImplicitSolvent;

}
/**---------------------------------------------------------------------------------------

   Set energy 

   @param energy

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

void CpuImplicitSolvent::setEnergy( RealOpenMM energy ){

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

   // static const char* methodName = "\nCpuImplicitSolvent::setEnergy";

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

   _implicitSolventEnergy = energy;
}

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

   Return ImplicitSolventParameters

   @return ImplicitSolventParameters

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

ImplicitSolventParameters* CpuImplicitSolvent::getImplicitSolventParameters( void ) const {

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

   // static const char* methodName = "\nCpuImplicitSolvent::getImplicitSolventParameters";

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

   return _implicitSolventParameters;

}

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

   Set ImplicitSolventParameters

   @param ImplicitSolventParameters

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

void CpuImplicitSolvent::setImplicitSolventParameters( ImplicitSolventParameters* implicitSolventParameters ){

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

   // static const char* methodName = "\nCpuImplicitSolvent::setImplicitSolventParameters";

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

   _implicitSolventParameters = implicitSolventParameters;
}

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

   Return flag signalling whether AceApproximation for nonpolar term is to be included

   @return flag

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

int CpuImplicitSolvent::includeAceApproximation( void ) const {

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

   // static const char* methodName = "\nCpuImplicitSolvent::includeAceApproximation";

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

   return _includeAceApproximation;

}

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

   Set flag indicating whether AceApproximation is to be included

   @param includeAceApproximation new includeAceApproximation value

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

void CpuImplicitSolvent::setIncludeAceApproximation( int includeAceApproximation ){

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

   // static const char* methodName = "\nCpuImplicitSolvent::setImplicitSolventParameters";

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

   _includeAceApproximation = includeAceApproximation;
}

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

   Return ForceConversionFactor for units

   @return ForceConversionFactor

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

RealOpenMM CpuImplicitSolvent::getForceConversionFactor( void ) const {

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

   // static const char* methodName = "\nCpuImplicitSolvent::getForceConversionFactor";

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

   return _forceConversionFactor;

}

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

   Set ForceConversionFactor

   @param ForceConversionFactor (units conversion)

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

void CpuImplicitSolvent::setForceConversionFactor( RealOpenMM forceConversionFactor ){

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

   // static const char* methodName = "\nCpuImplicitSolvent::setForceConversionFactor";

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

   _forceConversionFactor = forceConversionFactor;
}

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

   Return EnergyConversionFactor for units

   @return EnergyConversionFactor

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

RealOpenMM CpuImplicitSolvent::getEnergyConversionFactor( void ) const {

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

   // static const char* methodName = "\nCpuImplicitSolvent::getEnergyConversionFactor";

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

   return _energyConversionFactor;

}

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

   Set EnergyConversionFactor

   @param EnergyConversionFactor (units conversion)

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

void CpuImplicitSolvent::setEnergyConversionFactor( RealOpenMM energyConversionFactor ){

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

   // static const char* methodName = "\nCpuImplicitSolvent::setEnergyConversionFactor";

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

   _energyConversionFactor = energyConversionFactor;
}

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

   Return ForceCallIndex -- number of times forces have been calculated

   @return ForceCallIndex

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

int CpuImplicitSolvent::getForceCallIndex( void ) const {

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

   // static const char* methodName = "\nCpuImplicitSolvent::getForceCallIndex";

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

   return _forceCallIndex;

}

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

   Increment ForceCallIndex

   @return incremented forceCallIndex

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

int CpuImplicitSolvent::incrementForceCallIndex( void ){

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

   // static const char* methodName = "\nCpuImplicitSolvent::incrementForceCallIndex";

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

   _forceCallIndex++;

   return _forceCallIndex;

}

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

   Return bornForce, a work array of size _implicitSolventParameters->getNumberOfAtoms()*sizeof( RealOpenMM )
   On first call, memory for array is allocated if not set

   @return array

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

vector<RealOpenMM>& CpuImplicitSolvent::getBornForce( void ){

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

   // static const char* methodName = "\nCpuImplicitSolvent::getImplicitSolventBornForce";

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

   if( _bornForce.size() == 0 ){
      _bornForce.resize(_implicitSolventParameters->getNumberOfAtoms());
   }
   return _bornForce;

}

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

   Return Born radii: size = _implicitSolventParameters->getNumberOfAtoms()
   On first call, memory for array is allocated if it is not set

   @return array

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

vector<RealOpenMM>& CpuImplicitSolvent::getBornRadii( void ){

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

   // static const char* methodName = "\nCpuImplicitSolvent::getBornRadii";

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

   if( _bornRadii.size() == 0 ){
      _bornRadii.resize(_implicitSolventParameters->getNumberOfAtoms(), 0.0);
   }
   return _bornRadii;
}

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

   Return Born radii: size = _implicitSolventParameters->getNumberOfAtoms()

   @return array

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

const vector<RealOpenMM>& CpuImplicitSolvent::getBornRadiiConst( void ) const {

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

   // static const char* methodName = "\nCpuImplicitSolvent::getBornRadii";

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

   return _bornRadii;
}

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

   Return Born radii temp work array of size=_implicitSolventParameters->getNumberOfAtoms()
   On first call, memory for array is allocated if not set

   @return array

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

vector<RealOpenMM>& CpuImplicitSolvent::getBornRadiiTemp( void ){

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

   // static const char* methodName = "\nCpuImplicitSolvent::getImplicitSolventBornRadiiTemp";

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

   if( _tempBornRadii.size() == 0 ){
      _tempBornRadii.resize(_implicitSolventParameters->getNumberOfAtoms(), 0.0);
   }
   return _tempBornRadii;
}

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

   Compute Born radii

   @param atomCoordinates     atomic coordinates
   @param bornRadii           output array of Born radii
   @param obcChain            output array of Obc chain derivatives

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

void CpuImplicitSolvent::computeBornRadii( vector<RealVec>& atomCoordinates, vector<RealOpenMM>& bornRadii ){

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

   static const char* methodName = "\nCpuImplicitSolvent::computeBornRadii";

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

   std::stringstream message;
   message << methodName;
   message << " Error: calling from base class.";
   SimTKOpenMMLog::printError( message );
}

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

   Get Born energy and forces

   @param atomCoordinates     atomic coordinates
   @param partialCharges      partial charges
   @param forces              forces (output)
   @param updateBornRadii     if set, then Born radii are updated for current configuration; 
                              otherwise radii correspond to configuration from previous iteration

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

void CpuImplicitSolvent::computeImplicitSolventForces( vector<RealVec>& atomCoordinates,
                                                      const RealOpenMM* partialCharges,
                                                      vector<RealVec>& forces, int updateBornRadii ){

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

   static const char* methodName = "\nCpuImplicitSolvent::computeImplicitSolventForces";

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

   int callId = incrementForceCallIndex();

   // check parameters have been initialized

   ImplicitSolventParameters* implicitSolventParameters =  getImplicitSolventParameters();
   if( !implicitSolventParameters ){
      std::stringstream message;
      message << methodName;
      message << " implicitSolventParameters has not been initialized!";
      SimTKOpenMMLog::printError( message );
   }

   // check to see if Born radii have been previously calculated
   // if not, then calculate;
   // logic here assumes that the radii are intitialized to zero 
   // and then once computed, always greater than zero.

   // after first iteration Born radii are updated in force calculation (computeBornEnergyForces())
   // unless updateBornRadii is set

   vector<RealOpenMM>& bornRadii = getBornRadii();
   if( updateBornRadii || bornRadii[0] < (RealOpenMM) 0.0001 || callId == 1 ){
      computeBornRadii( atomCoordinates, bornRadii );
   }

   // compute forces

   computeBornEnergyForces( getBornRadii(), atomCoordinates, partialCharges, forces );
}

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

   Get Born energy and forces based on J. Phys. Chem. A V101 No 16, p. 3005 (Simbios)

   @param bornRadii           Born radii -- optional; if NULL, then ImplicitSolventParameters 
                              entry is used
   @param atomCoordinates     atomic coordinates
   @param partialCharges      partial charges
   @param forces              forces

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

void CpuImplicitSolvent::computeBornEnergyForces( vector<RealOpenMM>& bornRadii,
                                                 vector<RealVec>& atomCoordinates,
                                                 const RealOpenMM* partialCharges,
                                                 vector<RealVec>& forces ){

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

   static const char* methodName = "\nCpuImplicitSolvent::computeBornEnergyForces";

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

   std::stringstream message;
   message << methodName;
   message << " Error: calling from base class.";
   SimTKOpenMMLog::printError( message );
}

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

   Get nonpolar solvation force constribution via ACE approximation

   @param implicitSolventParameters parameters
   @param vdwRadii                  Vdw radii
   @param bornRadii                 Born radii
   @param energy                    energy (output): value is incremented from input value 
   @param forces                    forces: values are incremented from input values

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

void CpuImplicitSolvent::computeAceNonPolarForce( const ImplicitSolventParameters* implicitSolventParameters,
                                                 const vector<RealOpenMM>& bornRadii, RealOpenMM* energy,
                                                 vector<RealOpenMM>& forces ) const {

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

   // static const char* methodName = "\nCpuImplicitSolvent::computeAceNonPolarForce";

   static const RealOpenMM minusSix = -6.0;

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

   // compute the nonpolar solvation via ACE approximation

   const RealOpenMM probeRadius          = implicitSolventParameters->getProbeRadius();
   const RealOpenMM surfaceAreaFactor    = implicitSolventParameters->getPi4Asolv();

   const RealOpenMM* atomicRadii         = implicitSolventParameters->getAtomicRadii();
   int numberOfAtoms                     = implicitSolventParameters->getNumberOfAtoms();

   // 1 + 1 + pow + 3 + 1 + 2 FLOP

   // the original ACE equation is based on Eq.2 of

   // M. Schaefer, C. Bartels and M. Karplus, "Solution Conformations
   // and Thermodynamics of Structured Peptides: Molecular Dynamics
   // Simulation with an Implicit Solvation Model", J. Mol. Biol.,
   // 284, 835-848 (1998)  (ACE Method)

   // The original equation includes the factor (atomicRadii[atomI]/bornRadii[atomI]) to the first power,
   // whereas here the ratio is raised to the sixth power: (atomicRadii[atomI]/bornRadii[atomI])**6

   // This modification was made by Jay Ponder who observed it gave better correlations w/
   // observed values. He did not think it was important enough to write up, so there is
   // no paper to cite.

   for( int atomI = 0; atomI < numberOfAtoms; atomI++ ){
      if( bornRadii[atomI] > 0.0 ){
         RealOpenMM r            = atomicRadii[atomI] + probeRadius;
         RealOpenMM ratio6       = POW( atomicRadii[atomI]/bornRadii[atomI], (RealOpenMM) 6.0 );
         RealOpenMM saTerm       = surfaceAreaFactor*r*r*ratio6;
         *energy                += saTerm;
         forces[atomI]          += minusSix*saTerm/bornRadii[atomI]; 
      }
   }
}

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

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

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

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

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

   std::stringstream message;
   if( title ){
      message << title;
   }

   message << "\nImplicitSolvent info:";
   message << "\nForce conversion=" << getForceConversionFactor() << " Energy conversion=" << getEnergyConversionFactor();
   message << "\nInclude ACE approximation=";
   if( includeAceApproximation() ){
      message << "Y";
   } else {
      message << "N";
   }

   // get parameters

   message << getImplicitSolventParameters()->getStateString( NULL );

   return message.str();
}