AdunMolecularMechanicsForceField.h

/*
   Project: Adun

   Copyright (C) 2007 Michael Johnston & Jordi Villˆ--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 ADUN_MMFORCEFIELD
#define ADUN_MMFORCEFIELD

#include <stdio.h>
#include <stdlib.h>
#include <unistd.h>
#include <stdbool.h>
#include "Base/AdVector.h"
#include "Base/AdMatrix.h"
#include "Base/AdLinkedList.h"
#include "Base/AdForceFieldFunctions.h"
#include "AdunKernel/AdunForceField.h"
#include "AdunKernel/AdunNonbondedTerm.h"
#include "AdunKernel/AdunPureNonbondedTerm.h"
#include "AdunKernel/AdMatrixModification.h"

//Define strings for energy units
extern NSString* KCalPerMol;
extern NSString* KJPerMol;
extern NSString* SimUnit;

extern NSDictionary* conversionConstants;


@protocol AdForceFieldPotentials
- (NSArray*) potentials;
- (NSArray*) corePotentials;
- (double) valueForPotential: (NSString*) potential;
- (NSArray*) arrayOfValuesForPotentials: (NSArray*) array notFoundMarker: (id) anObject;
- (NSDictionary*) dictionaryOfValuesForPotentials: (NSArray*) array; 
- (NSArray*) arrayOfCorePotentialValues;
- (NSDictionary*) dictionaryOfCorePotentialValues; 
@end

@protocol AdForceFieldTermQueries
- (NSArray*) availableTerms;
- (NSArray*) coreTerms;
- (NSArray*) potentialsForTerm: (NSString*) aTerm;
- (NSArray*) potentialsForTerms: (NSArray*) array;
- (NSString*) termForPotential: (NSString*) aPotential;

@end

@interface AdMolecularMechanicsForceField:  AdForceField <AdMatrixModification>
{
        int no_of_atoms;
        int updateInterval;
        BOOL initialised;
        BOOL harmonicBond;
        BOOL harmonicAngle;
        BOOL fourierTorsion;
        BOOL improperTorsion;
        BOOL nonbonded;
        double bnd_pot;
        double ang_pot;
        double tor_pot;
        double itor_pot;
        double vdw_pot;
        double est_pot;
        double total_energy;
        double cutoff;
        double *reciprocalMasses;
        AdMatrix *bonds;
        AdMatrix *angles;
        AdMatrix *torsions;
        AdMatrix *improperTorsions;
        AdMatrix* forceMatrix;
        AdMatrix* accelerationMatrix;
        NSLock *forcesLock;
        NSLock *accelerationsLock;
        AdListHandler* nonbondedHandler;
        NSMutableDictionary* customTerms;
        NSMutableArray* customTermNames;
        NSMutableArray* availableTerms; 
        NSArray* coreTerms;             
        NSArray* corePotentials;        
        NSMutableDictionary* termPotentialMap;  
        NSMutableDictionary* state;     
        id system;
        id nonbondedTerm;  
        id bondedInteractions;
        id nonbondedInteractionTypes;
        NSString* vdwInteractionType;   //Identifies which vdw interaction is used.
        

        AdMatrix* forceSaveMatrix;
        AdMatrix* forceSaveTempMatrix;
        AdMatrix* energySaveMatrix;
        bool saveForces;
        bool saveEnergies;
        int saveAmount;
        NSMutableArray* saveTerms;
        int saveStep;
        
}
- (id) initWithDictionary: (NSDictionary*) dictionary;  
+ (id) forceFieldForSystem: (AdSystem*) system;
- (id) init;
- (id) initWithSystem: (id) system;
- (id) initWithSystem: (id) system nonbondedTerm: (AdNonbondedTerm*) anObject;
- (id) initWithSystem: (id) system 
        nonbondedTerm: (AdNonbondedTerm*) anObject
        customTerms: (NSDictionary*) aDict;
- (AdDataMatrix*) evaluateFiniteDifferenceForcesForTerm: (NSString*) aTerm;
- (void) evaluateFiniteDifferenceForces;
- (void) setSystem: (id) anObject;
- (void) setNonbondedTerm: (AdNonbondedTerm*) anObject;
- (AdNonbondedTerm*) nonbondedTerm;
- (NSString*) vdwInteractionType;

@end

@interface AdMolecularMechanicsForceField (PotentialMethods) <AdForceFieldPotentials>
@end

@interface AdMolecularMechanicsForceField (TermQueries) <AdForceFieldTermQueries>
@end

@interface AdMolecularMechanicsForceField (TermState) <AdForceFieldTermState>
@end

@interface AdMolecularMechanicsForceField (CustomTerms) <AdForceFieldExtension>
@end

@interface AdMolecularMechanicsForceField (DeprecatedMethods)
- (NSArray*) allTerms;
- (NSArray*) allEnergies;

- (NSArray*) arrayOfEnergiesForTerms: (NSArray*) terms notFoundMarker: (id) anObject;
- (NSArray*) arrayOfCoreTermEnergies;
- (NSDictionary*) dictionaryOfCoreTermEnergies;



@end


@interface AdMolecularMechanicsForceField (PrivateInternals)
- (void) _systemCleanUp;
- (void) _updateAccelerations;
- (void) _initialisationForSystem;
- (void) _createReciprocalMassArray;
- (void) _handleSystemContentsChange: (NSNotification*) aNotification;
- (AdMatrix*) _internalDataStorageForGroups: (AdDataMatrix*) groups parameters: (AdDataMatrix*) parameters;
@end


@interface AdMolecularMechanicsForceField (CrashInformation)
- (void) logForceSaveMatrix: (NSString*) fileName;
- (void) _clearForceSaveMatrix;
- (void) _saveForcesForStep:(int) step forForce: (int) i;
- (bool) savesForces;
- (void) setOptions: (NSDictionary*) opt;


@end



#endif