AdunSmoothedGBTerm.h

/*
 Project: AdunKernel
 
 Copyright (C) 2008 Michael Johnston & Jordi Villà--Freixa
 
 Author: Michael Johnston
 
 This application is free software; you can redistribute it and/or
 modify it under the terms of the GNU General Public
 License as published by the Free Software Foundation; either
 version 2 of the License, or (at your option) any later version.
 
 This application is distributed in the hope that it will be useful,
 but WITHOUT ANY WARRANTY; without even the implied warranty of
 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
 Library General Public License for more details.
 
 You should have received a copy of the GNU General Public
 License along with this library; if not, write to the Free
 Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111 USA.
 */
#ifndef ADSMOOTHED_GBTERM
#define ADSMOOTHED_GBTERM

#include "Base/AdMatrix.h"
#include "Base/AdVector.h"
#include "Base/AdLinkedList.h"
#include "Base/AdGeneralizedBornFunctions.h"
#include "Base/AdVolumeFunctions.h"
#include "Base/AdQuadratureFunctions.h"
#include "AdunKernel/AdunMoleculeCavity.h"
#include "AdunKernel/AdunGrid.h"
#include "AdunKernel/AdForceFieldTerm.h"
#include "AdunKernel/AdunDefinitions.h"
#include "AdunKernel/AdunNonbondedTerm.h"
#include "AdunKernel/AdunSystem.h"
#include "AdunKernel/AdunDataMatrix.h"
#include "AdunKernel/AdunNonbondedTerm.h"
#include "AdunKernel/AdunMemoryManager.h"
#include "AdunKernel/AdunListHandler.h"
#include "AdunKernel/AdunCellListHandler.h"
#include "AdunKernel/AdunCuboidBox.h"
#include "AdunKernel/AdunThreadManager.h"

@interface AdSmoothedGBTerm: NSObject
- (id) initWithSystem: (id) aSystem 
        nonbondedTerm: (id) aTerm 
      smoothingLength: (double) length 
  solventPermittivity: (double) epsilonSol
   tensionCoefficient: (double) gamma
       updateInterval: (unsigned int) interval;
@end

@interface AdSmoothedGBTermSerial: NSObject
{
        BOOL autoUpdateBornRadii;       
        int numberOfAtoms;              
        double coefficentOne;           
        double coefficentTwo;           
        double smoothingLength;         
        double integrationStartPoint;   
        double solventPermittivity;
        double solutePermittivity;
        double tensionCoefficient;
        double cutBuffer;               
        double meshSize;                
        double cutoff;
        id nonbondedTerm;               
        id system;                      
        AdMemoryManager* memoryManager;
        
        //Energy and force variables
        double totalSelfESTPotential;   
        double totalPairESTPotential;   
        double totalNonpolarPotential;  
        double totalSasa;               
        AdMatrix* forces;               
        
        //Born Radius
        int radialEnd;                  
        double* charges;                
        double* pbRadii;                
        double* bornRadii;              
        double* atomSasas;              
        AdMatrix* selfEnergy;           
        
        //Born Radius Derivatives
        //Do not access outside of relevant methods
        AdMatrix* selfGradients;        
        
        //SoluteGrid
        //The grid cutoff point is the distance from each atom at which there are 
        //no more grid points and hence no more atoms - there is no need to integrate beyond this point
        int** neighbourTable;           
        IntArrayStruct numberNeighbours;        
        AdMatrix* gridCutMatrix;        
        AdGrid* soluteGrid;             
        AdCuboidBox* cavity;            
        uint_fast8_t *overlapBuffer;    
        int (*getIndex)(id,SEL,Vector3D*);
        SEL gridSelector;
        NSZone* lookupZone;
        
        //Integration Points
        int numberRadialPoints;
        int numberAngularPoints;
        AdMatrix* radialInfo;   //The radial distances of each integration ''shell'' and the integration weight
        AdMatrix* angularInfo;  //The angles of the points in each shell and their integration weights
        Vector3D** integrationPoints;   
        
        //Precomputed Constants
        float integrationFactorOne;     
        float integrationFactorTwo;     
        float tau;                      
        float piFactor;                 
}
- (id) initWithDictionary: (NSDictionary*) dict;
- (id) initWithSystem: (id) system 
        nonbondedTerm: (id) term 
        smoothingLength: (double) length 
        solventPermittivity: (double) epsilonSol
        tensionCoefficient: (double) gamma
        updateInterval: (unsigned int) interval;
- (void) calculateBornRadii;
- (void) setAutoUpdateBornRadii: (BOOL) value;
- (BOOL) autoUpdateBornRadii;
- (double) screeningEnergy;
- (double) selfEnergy;
- (AdDataMatrix*) selfEnergyData;
- (double) nonPolarEnergy;
- (void) setSolventPermittivity: (double) value;
- (void) setSolutePermittivity: (double) value;
- (double) solutePermittivity;
- (double) solventPermittivity;

@end
 
@interface AdSmoothedGBTermSerial (AdForceFieldTermMethods) <AdForceFieldTerm>
@end 
 
/*
 * Categories
 */ 
 
@interface AdSmoothedGBTermSerial (IntegrationMethods)
- (void) _initIntegrationVariables;
- (void) _cleanUpIntegrationVariables;
@end

@interface AdSmoothedGBTermSerial (LookupTableMethods)
- (BOOL) _createLookupTable;
- (void) _createGrid;
- (void) _initLookupTableVariables;
- (void) updateLookupTable;
- (void) _cleanUpLookupTableVariables;
- (void) _freeNeighbourTable;
@end

@interface AdSmoothedGBTermSerial (BornRadiusMethods)
- (void) _initBornRadiiVariables;
- (void) _cleanUpBornRadiiVariables;
- (void) _calculateBornRadiusAndCFATermsForAtom: (int) atomIndex;
- (void) _calculateBornRadiiAndCFATermsForAtomsInRange: (NSRange) range;
- (void) _calculateBornRadiiAndCFATerms;
@end

@interface AdSmoothedGBTermSerial (BornNonPolarMethods)
- (double) _calculateSASAForAtom: (int) atomIndex;
- (void) _calculateSASAForAtomsInRange: (NSRange) range;
- (void) _calculateSASA;
@end 
 
@interface AdSmoothedGBTermSerial (BornRadiusDerivative)
 - (BOOL) _calculateDerivativesOfBornRadiusOfAtom:(int) mainAtom 
                contributingAtoms: (NSMutableIndexSet*) indexSet
                radiusGradients: (AdMatrix*) radiusGradients;
- (AdMatrix*) _calculateSelfEnergyDerivative; 
@end
 
//Contains optimised atomic radii from Nina et al.
extern NSDictionary* generalizedBornRadiiDict; 

@interface AdSmoothedGBTermThreaded: AdSmoothedGBTermSerial
{
        //Thread variables
        ListElement** listPositions;
        AdThreadManager* threadManager;
        NSLock* threadLock;
        NSMutableIndexSet* atomQueue;
        NSMutableArray* threadForces;   
        NSMutableArray* threadRanges;   
        NSMutableArray* energyInvocations;
        NSMutableArray* pairForceInvocations;
        NSMutableArray* selfForceInvocations;
        NSMutableArray* sasaInvocations;
        NSMutableArray* bornRadiiInvocations;
        double* threadPairEnergies;     
        double* threadSelfEnergies;     
        double* radiusCoefficients;     
        double** perThreadCoefficients; 
}
- (void) _threadedEnergyEvaluation: (unsigned int) threadNumber;
- (void) _threadedPairForceEvaluation: (unsigned int) threadNumber;
- (void) _threadedSelfForceEvaluation: (unsigned int) threadNumber;
- (void) _threadedBornRadiiCalculation: (unsigned int) threadNumber;
- (void) _threadedSASACalculation: (unsigned int) threadNumber;
@end
 
#endif