BALL  1.4.1
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Protected Member Functions | Protected Attributes | Friends
BALL::ForceField Class Reference

#include <BALL/MOLMEC/COMMON/forceField.h>

Inheritance diagram for BALL::ForceField:
BALL::AmberFF BALL::CharmmFF BALL::MMFF94

List of all members.

Public Types

Type Definitions
typedef std::vector< std::pair
< Atom *, Atom * > > 
PairVector

Public Member Functions

Constructors and Destructors
 ForceField ()
 ForceField (System &system)
 ForceField (System &system, const Options &options)
 ForceField (const ForceField &force_field)
virtual ~ForceField ()
virtual void clear ()
Assignments
ForceFieldoperator= (const ForceField &force_field)
Debugging and Diagnostics
bool isValid () const
Setup methods
bool setup (System &system)
bool setup (System &system, const Options &options)
virtual bool specificSetup () throw (Exception::TooManyErrors)
void setMaximumNumberOfErrors (Size nr)
Size getMaximumNumberOfErrors () const
HashSet< const Atom * > & getUnassignedAtoms ()
 Get the atoms, for which the force field setup failed.
Accessors
void setName (const String &name)
String getName () const
Size getNumberOfAtoms () const
Size getNumberOfMovableAtoms () const
BALL_INLINE const AtomVectorgetAtoms () const
BALL_INLINE SystemgetSystem ()
BALL_INLINE const SystemgetSystem () const
BALL_INLINE bool getUseSelection () const
BALL_INLINE void disableSelection ()
BALL_INLINE void enableSelection ()
BALL_INLINE bool isSelectionEnabled () const
ForceFieldParametersgetParameters ()
Size countComponents () const
const TimeStampgetUpdateTime () const
const TimeStampgetSetupTime () const
void insertComponent (ForceFieldComponent *force_field_component)
void removeComponent (const ForceFieldComponent *force_field_component)
void removeComponent (const String &name)
ForceFieldComponentgetComponent (const Size index) const
ForceFieldComponentgetComponent (const String &name) const
double getEnergy () const
double updateEnergy ()
void updateForces ()
double getRMSGradient () const
virtual Size getUpdateFrequency () const
virtual void update () throw (Exception::TooManyErrors)
virtual String getResults () const
std::ostream & error () throw (Exception::TooManyErrors)

Public Attributes

Public Attributes
Options options
PeriodicBoundary periodic_boundary

Protected Member Functions

void collectAtoms_ (const System &system)
void sortSelectedAtomVector_ ()
virtual void performRequiredUpdates_ ()

Protected Attributes

Systemsystem_
AtomVector atoms_
ForceFieldParameters parameters_
bool valid_
String name_
double energy_
vector< ForceFieldComponent * > components_
Size number_of_movable_atoms_
bool use_selection_
bool selection_enabled_
TimeStamp update_time_stamp_
TimeStamp setup_time_stamp_
HashSet< const Atom * > unassigned_atoms_
Size max_number_of_errors_
Size number_of_errors_

Friends

class ForceFieldComponent

Detailed Description

Force field class. This class is used to represent a general force field. Each force field by itself is composed by several different force field components which are represented by ForceFieldComponent objects.

Each ForceField object provides a list of components which may be manipulated by the user to generate the force field he needs.
ForceField only represents a baseclass to the specific force field implementations (e.g. AMBER ) and implements the common interface and the neccessary mechanisms to administer the force field components.
A typical force field contains a small number of components (e.g. bond stretch, bend, torsion and non-bonding interactions). A specialized forcefield has to implement each of these components (by deriving them from ForceFieldComponent and must be derived from ForceField. Basically only the default constructor for the new forcefield has to be modified to create an instance of each of the components and register them by calling insertComponent . But in order to implement the setup methods of the force field components efficiently, jobs like assigning atom types, reading parameter files and the such should be provided for all force field components by the corrseponding ForceField object. This should be implemented in the force field-specific specificSetup method.
For an efficient and easy to use implementation of a forcefield parameter file, please refer to ForceFieldParameters and its related objects.
Each force field provides as well energy and its derivatives, the force on each atom. A calculation of the energy is done by calling updateEnergy . This method iterates over the list of force field components and invokes the updateEnergy method of each of these components. The total energy may then be retrieved by calling getEnergy .
Analogously, a force calculation is performed by invoking updateForces . getForces returns a pointer to an array containing the forces for each atom.

Definition at line 85 of file forceField.h.


Member Typedef Documentation

typedef std::vector<std::pair<Atom*, Atom*> > BALL::ForceField::PairVector

Atom pair vector. This type is used to represent "pair lists". In fact, it is a vector of pairs of atom pointers.

Definition at line 99 of file forceField.h.


Constructor & Destructor Documentation

Default constructor. A default-constructed force field is not valid! It becomes valid after a successful call to setup.

Constructor. The successful setup of the force field can be verified by the isValid method.

BALL::ForceField::ForceField ( System system,
const Options options 
)

Constructor. The successful setup of the force field can be verified by the isValid method.

BALL::ForceField::ForceField ( const ForceField force_field)

Copy constructor

virtual BALL::ForceField::~ForceField ( ) [virtual]

Destructor.


Member Function Documentation

virtual void BALL::ForceField::clear ( ) [virtual]

Clear method.

Reimplemented in BALL::CharmmFF, BALL::AmberFF, and BALL::MMFF94.

void BALL::ForceField::collectAtoms_ ( const System system) [protected]

Returns the number of components registered by the force field.

Set the status of the selection mechanism

Set the status of the selection mechanism

Returns a reference to the atom vector

Return a pointer to the specified force field component. If the specified index does not exist, 0 is returned. The given index should be smaller than the value returned by countComponents. The first component in the list has the index zero.

Return a pointer to the specified force field component. If a component with the specified name does not exist, 0 is returned.

Return the sum of energies of all registered force field components. No calculation will be performed. This method simply returns the last value for the total energy calculated by updateEnergy.

Returns:
double - energy in kJ/mol

Get the number of atoms, for which the setup of the forcefield can fail, until the setup() methods aborts and return false.

Returns the force field name

Returns the number of atoms stored in the force field

Returns the number of non-fixed atoms stored in the force field. If the option SELECTION_FIXED is set to true or SELECTION_MOVABLE is set to true the atom array is split. The first section (indices 0 to getNumberOfMovableAtoms ) contains the atoms that are to be moved, the rest of the array contains the fixed atoms.

Returns a pointer to the parameter file

virtual String BALL::ForceField::getResults ( ) const [inline, virtual]

Get the current results in String form (Generic function to be overloaded in derived classes.)

Reimplemented in BALL::CharmmFF, BALL::MMFF94, and BALL::AmberFF.

Definition at line 347 of file forceField.h.

Calculates the RMS of the current gradient

Return the point of time of the last call to setup. ForceField contains a time stamp which is used to determine whether the selection or even the topology of the system has changed. Every time update is called, the update_time_stamp_ is updated. Similarly, all setup methods update the setup_time_stamp_

Returns a pointer to the system

Returns a const pointer to the system

Get the atoms, for which the force field setup failed.

virtual Size BALL::ForceField::getUpdateFrequency ( ) const [virtual]

Return the update frequency for pair lists etc. This method is used by minimizers or the MD simulation to determine the number of iterations between two calls to update .

Reimplemented in BALL::MMFF94, and BALL::AmberFF.

Return the point of time of the last call to update. ForceField contains a time stamp which is used to determine whether the selection or even the topology of the system has changed. Every time update is called, the update_time_stamp_ is updated. Similarly, all setup methods update the setup_time_stamp_

Return the status of the selection mechanism

void BALL::ForceField::insertComponent ( ForceFieldComponent force_field_component)

Insert a new component into the force field's component list. Responsability for the destruction of the component is passed on to the ForceField instance.

Return the status of the selection mechanism

Check the force field's validity. A force field is valid if it is bound to a system and setup was successful.

ForceField& BALL::ForceField::operator= ( const ForceField force_field)

Assignment operator

virtual void BALL::ForceField::performRequiredUpdates_ ( ) [protected, virtual]

Check whether the force field needs to be updated and perform the necessary steps

void BALL::ForceField::removeComponent ( const ForceFieldComponent force_field_component)

Remove a component from the force field's component list. The ForceFieldComponent will be destructed and removed from the component list.

void BALL::ForceField::removeComponent ( const String name)

Remove a component from the force field's component list.

Set the number of atoms, for which the setup of the forcefield can fail, until the setup() methods aborts and return false. By default, there is no limit set.

void BALL::ForceField::setName ( const String name)

Sets the force field name.

Sets up the force field and its components.

bool BALL::ForceField::setup ( System system,
const Options options 
)

Sets up the force field and its components.

Force field specific setup. This method is called by setup.

Reimplemented in BALL::CharmmFF, BALL::AmberFF, and BALL::MMFF94.

virtual void BALL::ForceField::update ( ) throw (Exception::TooManyErrors) [virtual]

Update internal data structures. The force field may use this method to update internal data structures (e.g. pair lists) periodically. The MD simulation class as well as the minimizer classes use getUpdateFrequency to determine the number of iterations between two calls to update.

The default implementation calls ForceFieldComponent::update for each component in the force field.

Calculate the sum of energies of all force field components and returns its value.

Calculate the forces caused by each component and updates the current forces.


Friends And Related Function Documentation

friend class ForceFieldComponent [friend]

Definition at line 89 of file forceField.h.


Member Data Documentation

Definition at line 392 of file forceField.h.

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Definition at line 438 of file forceField.h.

Definition at line 404 of file forceField.h.

Definition at line 440 of file forceField.h.

Definition at line 416 of file forceField.h.

Force field options

Definition at line 360 of file forceField.h.

Definition at line 396 of file forceField.h.

Periodic boundary

Definition at line 364 of file forceField.h.

Definition at line 424 of file forceField.h.

Definition at line 432 of file forceField.h.

Definition at line 388 of file forceField.h.

Definition at line 435 of file forceField.h.

Definition at line 428 of file forceField.h.

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Definition at line 400 of file forceField.h.

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