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/*
Project: Adun
Copyright (C) 2007 Michael Johnston & Jordi Villa-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.
*/
#import "AdunKernel/AdunMolecularMechanicsForceField.h"
#import "AdunKernel/AdunEnzymixForceField.h"
#import "AdunKernel/AdunCharmmForceField.h"
static NSArray* forceFields;
BOOL forceFieldDebug = NO;
@implementation AdMolecularMechanicsForceField
+ (void) initialize
{
static BOOL didInitialize = NO;
BOOL diagnoseBondedFunctions, diagnoseNonbondedFunctions, diagnoseForceFieldFunctions;
BOOL checkForceMagnitudes;
NSUserDefaults* userDefaults = [NSUserDefaults standardUserDefaults];
if(didInitialize)
return;
forceFields = [NSArray arrayWithObjects:
@"Enzymix",
@"Amber",
@"Charmm27",
nil];
[forceFields retain];
//Register base debug defaults - turned off
[userDefaults registerDefaults:
[NSDictionary dictionaryWithObjectsAndKeys:
NO, @"DiagnoseForceFieldFunctions",
NO, @"DiagoseBondedForceFieldFunctions",
NO, @"DiagnoseNonbondedForceFieldFunctions",
nil]];
//Now read the values of the above defaults.
//If the user didnt set their own values then the
//above values will be returned.
diagnoseForceFieldFunctions = [userDefaults boolForKey: @"DiagnoseForceFieldFunctions"];
//If this is turned on the bonded and nonbonded diagnosing is turned on by default.
if(diagnoseForceFieldFunctions)
{
diagnoseBondedFunctions = YES;
diagnoseNonbondedFunctions = YES;
}
else
{
diagnoseBondedFunctions = [userDefaults boolForKey:
@"DiagnoseBondedForceFieldFunctions"];
diagnoseNonbondedFunctions = [userDefaults boolForKey:
@"DiagnoseNonbondedForceFieldFunctions"];
}
//Turn on the relevant debugging by setting the value of the debug
//globals in AdForceFieldFunctions.h to 1
if(diagnoseBondedFunctions)
{
NSLog(@"Bonded force field term diagnostics turned on");
__HarmonicBondForceDebug__ = true;
__HarmonicBondEnergyDebug__ = true;
__HarmonicAngleEnergyDebug__ = true;
__HarmonicAngleForceDebug__ = true;
__FourierTorsionEnergyDebug__ = true;
__FourierTorsionForceDebug__ = true;
__HarmonicImproperTorsionEnergyDebug__ = true;
__HarmonicImproperTorsionForceDebug__ = true;
forceFieldDebug = YES;
AdHarmonicBondDebugInfo();
AdHarmonicAngleDebugInfo();
AdFourierTorsionDebugInfo();
AdHarmonicImproperTorsionDebugInfo();
fflush(stderr);
NSLog(@"Force debug lines contain the force magnitude as a final term\n");
}
if(diagnoseNonbondedFunctions)
{
NSLog(@"Nonbonded force field term diagnostics turned on");
__NonbondedEnergyDebug__ = true;
__NonbondedForceDebug__ = true;
__ShiftedNonbondedForceDebug__ = true;
__ShiftedNonbondedEnergyDebug__ = true;
__GRFNonbondedForceDebug__ = true;
__GRFNonbondedEnergyDebug__ = true;
forceFieldDebug = YES;
AdNonbondedDebugInfo();
fflush(stderr);
}
checkForceMagnitudes = [userDefaults boolForKey: @"CheckForceMagnitudes"];
if(checkForceMagnitudes)
{
NSLog(@"Force magnitude checking turned on.");
NSLog(@"All force mangitudes will be checked for inifities and Nan's");
__CheckForceMagnitude__ = true;
forceFieldDebug = YES;
}
didInitialize = YES;
}
+ (id) classForForceField: (NSString*) forceFieldName
{
if(![forceFields containsObject: forceFieldName])
{
NSWarnLog(@"Unknown force field %@", forceFieldName);
NSWarnLog(@"Defaulting to enzymix");
return [AdEnzymixForceField class];
}
else if([forceFieldName isEqual: @"Amber"])
return [AdMolecularMechanicsForceField class];
else if([forceFieldName isEqual: @"Enzymix"])
return [AdEnzymixForceField class];
else if([forceFieldName isEqual: @"Charmm27"])
return [AdCharmmForceField class];
return nil;
}
+ (id) forceFieldForSystem: (AdSystem*) system
{
Class forceFieldClass;
NSString* forceFieldName;
AdDataSource* dataSource;
dataSource = [system dataSource];
forceFieldName = [dataSource valueForMetadataKey: @"ForceField"];
if(forceFieldName == nil)
return nil;
forceFieldClass = [self classForForceField: forceFieldName];
if(forceFieldClass == nil)
return nil;
return [[[forceFieldClass alloc] initWithSystem: system] autorelease];
}
- (id) init
{
return [self initWithSystem: nil];
}
- (id) initWithSystem: (id) aSystem
{
return [self initWithSystem: aSystem nonbondedTerm: nil];
}
- (id) initWithSystem: (id) aSystem nonbondedTerm: (AdNonbondedTerm*) aTerm
{
return [self initWithSystem: aSystem
nonbondedTerm: aTerm
customTerms: nil];
}
- (id) initWithSystem: (id) system
nonbondedTerm: (AdNonbondedTerm*) anObject
customTerms: (NSDictionary*) aDict
{
if((self = [super init]))
{
//Get the vdw interaction type of the subclass
vdwInteractionType = [self vdwInteractionType];
[vdwInteractionType retain];
}
return self;
}
- (void) dealloc
{
AdMemoryManager* memoryManager = [AdMemoryManager appMemoryManager];
[[NSNotificationCenter defaultCenter]
removeObserver: self];
[system release];
[state release];
[availableTerms release];
[customTerms release];
[customTermNames release];
[nonbondedTerm release];
[vdwInteractionType release];
[memoryManager freeMatrix: bonds];
[memoryManager freeMatrix: angles];
[memoryManager freeMatrix: torsions];
[memoryManager freeMatrix: improperTorsions];
[memoryManager freeMatrix: forceMatrix];
[memoryManager freeMatrix: accelerationMatrix];
[memoryManager freeArray: reciprocalMasses];
[super dealloc];
}
//Force & Energy calculation methods.
//Here we just flush stderr if debugging is turned on.
- (void) evaluateForces
{
if(forceFieldDebug)
fflush(stderr);
}
- (void) evaluateForcesDueToElements: (NSIndexSet*) elementIndexes
{
if(forceFieldDebug)
fflush(stderr);
}
- (void) evaluateEnergies
{
if(forceFieldDebug)
fflush(stderr);
}
- (void) evaluateEnergiesUsingInteractionsInvolvingElements: (NSIndexSet*) elementIndexes
{
if(forceFieldDebug)
fflush(stderr);
}
- (AdMatrix*) evaluateFiniteDifferenceForcesForTerm: (NSString*) term
{
AdMatrix* coordinates = NULL;
//Deactivate all energy terms
//Activate the requested term only
//do finite difference
/*coordinates = [[self system] coordinates];
for(i=0; i<coordinates->no_rows; i++)
{
for(j=0;j<coordinates->no_columns; j++)
{
//Perturb-atom position
[system object: self willBeginWritingToMatrix:
}
}*/
return coordinates;
}
//custom term methods
- (void) addCustomTerm: (id) object withName: (NSString*) name
{
if([object conformsToProtocol: @protocol(AdForceFieldTerm)])
{
if([customTerms objectForKey: name] != nil)
{
[NSException raise: NSInvalidArgumentException
format: @"A custom term called %@ already exists."
" Remove it before adding a new term with the same name"];
}
//Custom terms is a dictionry (hash).
//This means the keys are not ordered which would lead to a problem
//for the allTerms/allEnergies methods - they would not return terms in
//the same order each time.
//In order to overcome this we have to keep an additional customTermName array.
[customTerms setObject: object forKey: name];
[customTermNames addObject: name];
[availableTerms addObject: name];
[[state valueForKey: @"CustomTerms"]
setObject: [NSNumber numberWithInt: 0]
forKey: name];
}
else
[NSException raise: NSInvalidArgumentException
format: @"Invalid class for custom force object. Must conform to AdForceFieldTerm"];
}
- (void) addCustomTerms: (NSDictionary*) aDict
{
NSEnumerator* keyEnum;
NSString* key;
keyEnum = [aDict keyEnumerator];
while((key = [keyEnum nextObject]))
[self addCustomTerm: [aDict objectForKey: key]
withName: key];
}
- (void) setCustomTerms: (NSDictionary*) aDict
{
NSEnumerator* keyEnum;
NSString* termName;
NSMutableArray* oldNames;
NSMutableDictionary* oldTerms;
//Remove all previous terms
oldTerms = [[customTerms mutableCopy] autorelease];
oldNames = [[customTermNames mutableCopy] autorelease];
[customTerms removeAllObjects];
[customTermNames removeAllObjects];
keyEnum = [aDict keyEnumerator];
while((termName = [keyEnum nextObject]))
{
NS_DURING
{
[self addCustomTerm: [aDict objectForKey: termName]
withName: termName];
}
NS_HANDLER
{
[customTerms removeAllObjects];
[customTermNames removeAllObjects];
//Restore the old terms
customTerms = [oldTerms retain];
customTermNames = [oldNames retain];
[localException raise];
}
NS_ENDHANDLER
}
}
- (void) removeCustomTermWithName: (NSString*) name
{
[customTerms removeObjectForKey: name];
[customTermNames removeObject: name];
[[state valueForKey: @"CustomTerms"]
removeObjectForKey: name];
[availableTerms removeObject: name];
}
//Activating/Deactivating Terms
- (NSArray*) activatedTerms
{
NSMutableArray* terms;
terms = [self availableTerms];
[terms removeObjectsInArray: [self deactivatedTerms]];
return terms;
}
- (NSArray*) deactivatedTerms
{
return [[[state valueForKey: @"InactiveTerms"] copy] autorelease];
}
- (void) deactivateTerm: (NSString*) termName
{
if([availableTerms containsObject: termName])
{
if(![[state valueForKey: @"InactiveTerms"] containsObject: termName])
{
if([termName isEqual: @"HarmonicBond"])
harmonicBond = NO;
if([termName isEqual: @"HarmonicAngle"])
harmonicAngle = NO;
if([termName isEqual: @"FourierTorsion"])
fourierTorsion = NO;
if([termName isEqual: @"HarmonicImproperTorsion"])
improperTorsion = NO;
if([termName isEqual: @"Nonbonded"])
nonbonded = NO;
[[state valueForKey: @"InactiveTerms"] addObject: termName];
}
}
}
- (void) deactivateTermsWithNames: (NSArray*) names
{
NSEnumerator* termEnum;
id term;
termEnum = [names objectEnumerator];
while((term = [termEnum nextObject]))
[self deactivateTerm: term];
}
- (void) activateTerm: (NSString*) termName
{
if([availableTerms containsObject: termName])
{
if([[state valueForKey: @"InactiveTerms"] containsObject: termName])
{
if([termName isEqual: @"HarmonicBond"])
harmonicBond = YES;
if([termName isEqual: @"HarmonicAngle"])
harmonicAngle = YES;
if([termName isEqual: @"FourierTorsion"])
fourierTorsion = YES;
if([termName isEqual: @"HarmonicImproperTorsion"])
improperTorsion = YES;
if([termName isEqual: @"Nonbonded"])
nonbonded = YES;
[[state valueForKey: @"InactiveTerms"] removeObject: termName];
}
}
}
- (void) activateTermsWithNames: (NSArray*) names
{
NSEnumerator* termEnum;
id term;
termEnum = [names objectEnumerator];
while((term = [termEnum nextObject]))
[self activateTerm: term];
}
- (void) clearForces
{
int i,j;
for(i=0; i<forceMatrix->no_rows; i++)
for(j=0; j<3; j++)
forceMatrix->matrix[i][j] = 0;
[self _updateAccelerations];
}
- (AdMatrix*) forces
{
return forceMatrix;
}
- (AdMatrix*) accelerations
{
return accelerationMatrix;
}
/********************
Accessors
********************/
- (double) totalEnergy
{
return total_energy;
}
- (id) availableTerms
{
return [[availableTerms copy] autorelease];
}
- (NSArray*) arrayOfEnergiesForTerms: (NSArray*) terms notFoundMarker: (id) anObject
{
int index, count = 0;
double value;
NSArray* potentials;
NSMutableArray* array = [NSMutableArray array];
NSMutableArray* notFound = [NSMutableArray array];
NSEnumerator* potentialsEnum, *notFoundEnum;
NSString* termName;
id object;
potentials = [[state valueForKey: @"TermPotentials"]
objectsForKeys: terms notFoundMarker: anObject];
potentialsEnum = [potentials objectEnumerator];
while((object = [potentialsEnum nextObject]))
{
if(object != anObject)
{
value = *(double*)[object pointerValue];
[array addObject: [NSNumber numberWithDouble: value]];
}
else
{
[array addObject: anObject];
[notFound addObject: [terms objectAtIndex: count]];
}
count++;
}
//Check if any of the terms not found above are custom terms.
notFoundEnum = [notFound objectEnumerator];
while((termName = [notFoundEnum nextObject]))
{
if([customTermNames containsObject: termName])
{
object = [customTerms objectForKey: termName];
if([object canEvaluateEnergy])
{
index = [terms indexOfObject: termName];
[array replaceObjectAtIndex: index
withObject: [NSNumber numberWithDouble: [object energy]]];
}
}
}
return array;
}
- (NSDictionary*) dictionaryOfEnergiesForTerms: (NSArray*) array
{
NSArray* energies;
energies = [self arrayOfEnergiesForTerms: array notFoundMarker: [NSNull null]];
return [NSDictionary dictionaryWithObjects: energies
forKeys: array];
}
//FIMXE: Their is an ambiguity in the meaning of 'term'.
//Its refering both to components AND energies.
//For example Nonbonded is listed as an availableTerm.
//but coreTerms returns both vdw and electrostatic contributions - nonbonded is not present
- (NSArray*) allTerms
{
NSMutableArray* array = [NSMutableArray array];
NSEnumerator* nameEnum;
NSString* termName;
id object;
[array addObjectsFromArray: [self coreTerms]];
nameEnum = [customTermNames objectEnumerator];
while((termName = [nameEnum nextObject]))
{
object = [customTerms objectForKey: termName];
if([object canEvaluateEnergy])
[array addObject: termName];
}
return [[array copy] autorelease];
}
- (NSArray*) allEnergies
{
NSMutableArray* array = [NSMutableArray array];
NSEnumerator* nameEnum;
NSString* termName;
id object;
[array addObjectsFromArray: [self arrayOfCoreTermEnergies]];
nameEnum = [customTermNames objectEnumerator];
while((termName = [nameEnum nextObject]))
{
object = [customTerms objectForKey: termName];
if([object canEvaluateEnergy])
[array addObject: [NSNumber numberWithDouble: [object energy]]];
}
return [[array copy] autorelease];
}
- (NSArray*) coreTerms
{
return [[coreTerms retain] autorelease];
}
- (NSArray*) arrayOfCoreTermEnergies
{
NSArray* array;
array = [NSArray arrayWithObjects:
[NSNumber numberWithDouble: bnd_pot],
[NSNumber numberWithDouble: ang_pot],
[NSNumber numberWithDouble: tor_pot],
[NSNumber numberWithDouble: itor_pot],
[NSNumber numberWithDouble: vdw_pot],
[NSNumber numberWithDouble: est_pot],
nil];
return array;
}
- (NSDictionary*) dictionaryOfCoreTermEnergies
{
NSArray* energies;
energies = [self arrayOfCoreTermEnergies];
return [NSDictionary dictionaryWithObjects: energies
forKeys: coreTerms];
}
- (id) system
{
return [[system retain] autorelease];
}
- (void) setSystem: (id) object
{
if(system != nil)
{
[system release];
[[NSNotificationCenter defaultCenter]
removeObserver:self name:nil object: system];
//clean up all variables relating to the last system
[self _systemCleanUp];
}
system = [object retain];
[self _initialisationForSystem];
if(nonbondedTerm != nil)
{
if(system != [nonbondedTerm system])
[nonbondedTerm setSystem: system];
[nonbondedTerm setExternalForceMatrix: forceMatrix];
}
[[NSNotificationCenter defaultCenter]
addObserver: self
selector: @selector(_handleSystemContentsChange:)
name: @"AdSystemContentsDidChangeNotification"
object: system];
}
- (void) setNonbondedTerm: (AdNonbondedTerm*) aTerm
{
[nonbondedTerm release];
nonbondedTerm = aTerm;
[nonbondedTerm retain];
if(system != nil)
{
if(system != [aTerm system] )
[aTerm setSystem: system];
[nonbondedTerm setExternalForceMatrix: forceMatrix];
}
[state setObject: NSStringFromClass([aTerm class])
forKey: @"NonbondedTerm"];
}
- (AdNonbondedTerm*) nonbondedTerm
{
return [[nonbondedTerm retain] autorelease];
}
- (NSString*) vdwInteractionType
{
return @"TypeOneVDWInteraction";
}
- (NSString*) description
{
int i;
NSMutableString* description;
NSDictionary* energies;
NSArray* array;
NSEnumerator* termEnum;
id term, object;
description = [NSMutableString string];
[description appendFormat: @"ForceField: %@\n", [state objectForKey: @"ForceField"]];
[description appendString: @"Available Terms for computation:\n"];
for(i=0; i<(int)[availableTerms count]; i++)
[description appendFormat: @"\t%@\n", [availableTerms objectAtIndex: i]];
[description appendString: @"NonbondedTerm:\n"];
if(nonbondedTerm == nil)
[description appendString: @"\tNone\n"];
else
[description appendFormat: @"\t%@", [nonbondedTerm description]];
[description appendString: @"CustomTerms:\n"];
if([customTerms count] == 0)
[description appendString: @"\tNone\n"];
else
{
termEnum = [customTerms objectEnumerator];
while((term = [termEnum nextObject]))
[description appendFormat: @"\t%@\n", [term description]];
}
array = [state valueForKey: @"InactiveTerms"];
if([array count] != 0)
{
[description appendString: @"InactiveTerms:\n"];
for(i=0; i<(int)[array count]; i++)
[description appendFormat: @"\t%@\n", [array objectAtIndex: i]];
}
if(system != nil)
{
[description appendFormat: @"System: %@\n", [system systemName]];
[self evaluateEnergies];
energies = [self dictionaryOfCoreTermEnergies];
termEnum = [energies keyEnumerator];
while((term = [termEnum nextObject]))
[description appendFormat: @"\t%25@: %10.5lf Sim Units\n",
term, [[energies objectForKey: term] doubleValue]];
termEnum = [customTerms keyEnumerator];
while((term = [termEnum nextObject]))
{
object = [customTerms objectForKey: term];
if([object canEvaluateEnergy])
[description appendFormat: @"\t%25@: %10.5lf Sim Units\n",
term, [object energy]];
}
}
return description;
}
@end
@implementation AdMolecularMechanicsForceField (PrivateInternals)
/*
* Resets variables and frees memory associated with the current system.
* FIXME: Does not handle custom terms properly
*/
- (void) _systemCleanUp
{
AdMemoryManager* memoryManager = [AdMemoryManager appMemoryManager];
[availableTerms removeAllObjects];
[[state valueForKey:@"InactiveTerms"] removeAllObjects];
[nonbondedTerm setSystem: nil];
[memoryManager freeMatrix: bonds];
[memoryManager freeMatrix: angles];
[memoryManager freeMatrix: torsions];
[memoryManager freeMatrix: improperTorsions];
[memoryManager freeMatrix: forceMatrix];
[memoryManager freeMatrix: accelerationMatrix];
[memoryManager freeArray: reciprocalMasses];
harmonicBond = harmonicAngle = fourierTorsion = improperTorsion = nonbonded = NO;
bnd_pot = ang_pot = tor_pot = vdw_pot = est_pot = itor_pot = total_energy = 0;
bonds = angles = torsions = improperTorsions = forceMatrix = accelerationMatrix = NULL;
reciprocalMasses = NULL;
}
- (void) _createReciprocalMassArray
{
int i;
NSArray* massArray;
AdMemoryManager* memoryManager = [AdMemoryManager appMemoryManager];
massArray = [system elementMasses];
reciprocalMasses = [memoryManager allocateArrayOfSize: [massArray count]*sizeof(double)];
for(i=0; i<(int)[massArray count]; i++)
reciprocalMasses[i] = 1/[[massArray objectAtIndex: i] doubleValue];
}
/*
* The information provided by AdSystem is in the form of AdDataMatrices.
* We need to convert this information into a more primitive and efficent
* form i.e. AdMatrix stuctures, for use with the C force field functions.
*/
- (AdMatrix*) _internalDataStorageForGroups: (AdDataMatrix*) groups parameters: (AdDataMatrix*) parameters
{
int numberRows, numberColumns;
AdMatrix* interaction;
numberRows = [groups numberOfRows];
numberColumns = [groups numberOfColumns] + [parameters numberOfColumns];
interaction = [[AdMemoryManager appMemoryManager]
allocateMatrixWithRows: numberRows
withColumns: numberColumns];
return interaction;
}
- (void) _initialisationForSystem
{
int i, j;
NSArray* interactionTypes;
AdDataMatrix *groups, *parameters;
NSDebugLLog(@"AdMolecularMechanicsForceField",
@"Beginning system initialisation");
no_of_atoms = [system numberOfElements];
//allocate a force and acceleration matrix
forceMatrix = [[AdMemoryManager appMemoryManager]
allocateMatrixWithRows: no_of_atoms
withColumns: 3];
accelerationMatrix = [[AdMemoryManager appMemoryManager]
allocateMatrixWithRows: no_of_atoms
withColumns: 3];
[self _createReciprocalMassArray];
/*
* Check what interaction types the system provides information for
* and which of these are core terms of this force field.
* For each one that is a core terms we convert the information
* provided into an internal representation which we will use with
* the primitive C force field functions.
*/
interactionTypes = [system availableInteractions];
if([interactionTypes containsObject: @"HarmonicBond"])
{
harmonicBond = YES;
groups = [system groupsForInteraction: @"HarmonicBond"];
parameters = [system parametersForInteraction: @"HarmonicBond"];
bonds = [self _internalDataStorageForGroups: groups
parameters: parameters];
for(i=0; i<bonds->no_rows; i++)
{
for(j=0; j<2; j++)
bonds->matrix[i][j] = [[groups elementAtRow: i column: j] doubleValue];
bonds->matrix[i][2] = [[parameters elementAtRow: i
ofColumnWithHeader: @"Constant"] doubleValue];
bonds->matrix[i][3] = [[parameters elementAtRow: i
ofColumnWithHeader: @"Separation"] doubleValue];
}
[availableTerms addObject: @"HarmonicBond"];
}
else
harmonicBond = NO;
if([interactionTypes containsObject: @"HarmonicAngle"])
{
harmonicAngle = YES;
groups = [system groupsForInteraction: @"HarmonicAngle"];
parameters = [system parametersForInteraction: @"HarmonicAngle"];
angles = [self _internalDataStorageForGroups: groups
parameters: parameters];
for(i=0; i<angles->no_rows; i++)
{
for(j=0; j<(int)[groups numberOfColumns]; j++)
angles->matrix[i][j] = [[groups elementAtRow: i column: j] doubleValue];
angles->matrix[i][3] = [[parameters elementAtRow: i
ofColumnWithHeader: @"Constant"] doubleValue];
angles->matrix[i][4] = [[parameters elementAtRow: i
ofColumnWithHeader: @"Angle"] doubleValue];
}
[availableTerms addObject: @"HarmonicAngle"];
}
else
harmonicAngle = NO;
if([interactionTypes containsObject: @"FourierTorsion"])
{
fourierTorsion = YES;
groups = [system groupsForInteraction: @"FourierTorsion"];
parameters = [system parametersForInteraction: @"FourierTorsion"];
torsions = [self _internalDataStorageForGroups: groups
parameters: parameters];
for(i=0; i<torsions->no_rows; i++)
{
for(j=0; j<(int)[groups numberOfColumns]; j++)
torsions->matrix[i][j] = [[groups elementAtRow: i column: j] doubleValue];
torsions->matrix[i][4] = [[parameters elementAtRow: i
ofColumnWithHeader: @"Constant"] doubleValue];
torsions->matrix[i][5] = [[parameters elementAtRow: i
ofColumnWithHeader: @"Periodicity"] doubleValue];
torsions->matrix[i][6] = [[parameters elementAtRow: i
ofColumnWithHeader: @"Phase"] doubleValue];
}
[availableTerms addObject: @"FourierTorsion"];
}
else
fourierTorsion = NO;
if([interactionTypes containsObject: @"HarmonicImproperTorsion"])
{
improperTorsion = YES;
groups = [system groupsForInteraction: @"HarmonicImproperTorsion"];
parameters = [system parametersForInteraction: @"HarmonicImproperTorsion"];
improperTorsions = [self _internalDataStorageForGroups: groups
parameters: parameters];
for(i=0; i<improperTorsions->no_rows; i++)
{
for(j=0; j<(int)[groups numberOfColumns]; j++)
improperTorsions->matrix[i][j] = [[groups elementAtRow: i column: j] doubleValue];
improperTorsions->matrix[i][4] = [[parameters elementAtRow: i
ofColumnWithHeader: @"Constant"] doubleValue];
improperTorsions->matrix[i][5] = [[parameters elementAtRow: i
ofColumnWithHeader: @"Angle"] doubleValue];
}
[availableTerms addObject: @"HarmonicImproperTorsion"];
}
else
improperTorsion = NO;
/*
* For VDW and Electrostatic interactions simply check
* if they exist. The actual calculation will be done by
* a nonbonded list handler object
*/
if([interactionTypes containsObject: @"CoulombElectrostatic"] &&
[interactionTypes containsObject: vdwInteractionType])
{
nonbonded = YES;
[availableTerms addObject: @"Nonbonded"];
}
else
nonbonded = NO;
}
/**
Called when we recieve an AdSystemContentsDidChangeNotification
due to the system reloading its data source.
We dont know what exactly changed so we have to reinitialise
everything.
*/
- (void) _handleSystemContentsChange: (NSNotification*) aNotification
{
NSEnumerator* inactiveTermsEnum;
NSMutableArray* inactiveTerms;
NSMutableArray* removedTerms = [NSMutableArray array];
NSString* termName;
AdMemoryManager* memoryManager = [AdMemoryManager appMemoryManager];
/*
* 1) Remove the system dependant terms from available terms.
* 2) Assume that custom terms (including nonbonded terms)
* will handle their own updating.
* 3) Free topology matrices
* 4) Reacquire the system topology matrices.
* 5) Update inactive terms
* 6) Update the custom terms & nonbonded term with new force matrix
*/
NSDebugLLog(@"AdMolecularMechanicsForceField", @"System is %@", [system systemName]);
NSDebugLLog(@"AdMolecularMechanicsForceField", @"Received an system contents change message");
NSDebugLLog(@"AdMolecularMechanicsForceField", @"Currently available terms %@", availableTerms);
[availableTerms removeAllObjects];
NSDebugLLog(@"AdMolecularMechanicsForceField", @"Freeing topology and force related matrices");
[memoryManager freeMatrix: bonds];
[memoryManager freeMatrix: angles];
[memoryManager freeMatrix: torsions];
[memoryManager freeMatrix: improperTorsions];
[memoryManager freeMatrix: forceMatrix];
[memoryManager freeMatrix: accelerationMatrix];
[memoryManager freeArray: reciprocalMasses];
harmonicBond = harmonicAngle = fourierTorsion = improperTorsion = nonbonded = NO;
bnd_pot = ang_pot = tor_pot = vdw_pot = est_pot = itor_pot = total_energy = 0;
bonds = angles = torsions = improperTorsions = forceMatrix = accelerationMatrix = NULL;
reciprocalMasses = NULL;
NSDebugLLog(@"AdMolecularMechanicsForceField", @"Reaquiring system information");
[self _initialisationForSystem];
NSDebugLLog(@"AdMolecularMechanicsForceField", @"Rebuilding available terms");
//Add custom terms back into available terms
[availableTerms addObjectsFromArray: [customTerms allKeys]];
NSDebugLLog(@"AdMolecularMechanicsForceField",
@"Available terms after reinitialising %@", availableTerms);
//Check if all inactive terms are still present
//If they are make sure they have the same state
inactiveTerms = [state objectForKey: @"InactiveTerms"];
NSDebugLLog(@"AdMolecularMechanicsForceField", @"Previous inactive terms %@", inactiveTerms);
NSDebugLLog(@"AdMolecularMechanicsForceField",
@"Updating inactive terms and resetting state where necessary");
inactiveTermsEnum = [inactiveTerms objectEnumerator];
while((termName = [inactiveTermsEnum nextObject]))
{
if(![availableTerms containsObject: termName])
[removedTerms addObject: termName];
else
{
if([termName isEqual: @"HarmonicBond"])
harmonicBond = NO;
if([termName isEqual: @"HarmonicAngle"])
harmonicAngle = NO;
if([termName isEqual: @"FourierTorsion"])
fourierTorsion = NO;
if([termName isEqual: @"HarmonicImproperTorsion"])
improperTorsion = NO;
if([termName isEqual: @"Nonbonded"])
nonbonded = NO;
}
}
[inactiveTerms removeObjectsInArray: removedTerms];
NSDebugLLog(@"AdMolecularMechanicsForceField",
@"Current inactive terms %@", inactiveTerms);
NSDebugLLog(@"AdMolecularMechanicsForceField"
, @"Updating nonbonded term with new force matrix");
[nonbondedTerm setExternalForceMatrix: forceMatrix];
NSDebugLLog(@"AdMolecularMechanicsForceField", @"Update complete");
}
- (void) _updateAccelerations
{
int i,j;
for(i=0; i<accelerationMatrix->no_rows; i++)
for(j=0; j<3; j++)
accelerationMatrix->matrix[i][j] = forceMatrix->matrix[i][j]*reciprocalMasses[i];
}
@end
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