BALL::ForceField Class Reference
[General
Force Field Classes.]
Force field class.
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#include <forceField.h>
Public Types |
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Type Definitions
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| typedef std::vector< std::pair < Atom *, Atom * > > |
PairVector |
| Atom pair
vector. |
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Public Member Functions |
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Constructors and Destructors
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| ForceField () | |
| Default constructor. |
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| ForceField (System &system) | |
| Constructor. |
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| ForceField (System &system, const Options &options) | |
| Constructor. |
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| ForceField (const ForceField &force_field) | |
| Copy constructor. |
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| virtual | ~ForceField () |
| Destructor. |
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| virtual void | clear () |
| Clear method. |
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Assignments
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| ForceField & | operator= (const ForceField &force_field) |
| Assignment operator. |
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Debugging and Diagnostics
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| bool | isValid () const |
| Check the force field's validity.
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Setup methods
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| bool | setup (System &system) |
| Sets up the force field and its
components. |
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| bool | setup (System &system, const Options &options) |
| Sets up the force field and its
components. |
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| virtual bool | specificSetup () throw (Exception::TooManyErrors) |
| Force field specific setup. |
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| void | setMaximumNumberOfErrors (Size nr) |
| Set the number of atoms, for which
the setup of the forcefield can fail, until the setup()
methods aborts and return false. |
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| Size | getMaximumNumberOfErrors () const |
| Get the number of atoms, for which
the setup of the forcefield can fail, until the setup()
methods aborts and return false. |
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| HashSet< const Atom * > & | getUnassignedAtoms () |
| Get the atoms, for which the force
field setup failed. |
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Accessors
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| void | setName (const String &name) |
| Sets the force field
name. |
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| String | getName () const |
| Returns the force field
name. |
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| Size | getNumberOfAtoms () const |
| Returns the number of atoms stored
in the force field. |
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| Size | getNumberOfMovableAtoms () const |
| Returns the number of non-fixed
atoms stored in the force field. |
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| const AtomVector & | getAtoms () const |
| Returns a reference to the atom
vector. |
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| System * | getSystem () |
| Returns a pointer to the
system. |
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| const System * | getSystem () const |
| Returns a const pointer to the
system. |
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| bool | getUseSelection () const |
| Return the status of the selection
mechanism. |
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| void | disableSelection () |
| Set the status of the selection
mechanism. |
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| void | enableSelection () |
| Set the status of the selection
mechanism. |
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| bool | isSelectionEnabled () const |
| Return the status of the selection
mechanism. |
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| ForceFieldParameters & | getParameters () |
| Returns a pointer to the parameter
file. |
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| Size | countComponents () const |
| Returns the number of components
registered by the force field. |
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| const TimeStamp & | getUpdateTime () const |
| Return the point of time of the last
call to update. |
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| const TimeStamp & | getSetupTime () const |
| Return the point of time of the last
call to setup. |
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| void | insertComponent (ForceFieldComponent *force_field_component) |
| Insert a new component into the
force field's component list. |
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| void | removeComponent (const ForceFieldComponent *force_field_component) |
| Remove a component from the force
field's component list. |
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| void | removeComponent (const String &name) |
| Remove a component from the force
field's component list. |
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| ForceFieldComponent * | getComponent (const Size index) const |
| Return a pointer to the specified
force field component. |
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| ForceFieldComponent * | getComponent (const String &name) const |
| Return a pointer to the specified
force field component. |
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| double | getEnergy () const |
| Return the sum of energies of all
registered force field components. |
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| double | updateEnergy () |
| Calculate the sum of energies of all
force field components and returns its value. |
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| void | updateForces () |
| Calculate the forces caused by each
component and updates the current forces. |
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| double | getRMSGradient () const |
| Calculates the RMS of the current
gradient. |
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| virtual Size | getUpdateFrequency () const |
| Return the update frequency for pair
lists etc. |
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| virtual void | update () throw (Exception::TooManyErrors) |
| Update internal data structures.
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| virtual String | getResults () const |
| Get the current results in String form (Generic function
to be overloaded in derived classes. |
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| std::ostream & | error () throw (Exception::TooManyErrors) |
Public Attributes |
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Public Attributes
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| Options | options |
| Force field options. |
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| PeriodicBoundary | periodic_boundary |
| Periodic boundary. |
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Protected Member Functions |
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| void | collectAtoms_ (const System &system) |
| void | sortSelectedAtomVector_ () |
Protected Attributes |
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| System * | system_ |
| 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 |
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| 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.
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.
Constructor & Destructor Documentation
| BALL::ForceField::ForceField | ( | ) |
Default constructor.
A default-constructed force field is not valid! It becomes valid after a successful call to setup.
| BALL::ForceField::ForceField | ( | System & | system | ) |
Constructor.
The successful setup of the force field can be verified by the isValid method.
Constructor.
The successful setup of the force field can be verified by the isValid method.
Member Function Documentation
| ForceFieldComponent* BALL::ForceField::getComponent | ( | const String & | name | ) | const |
Return a pointer to the specified force field component.
If a component with the specified name does not exist, 0 is returned.
| ForceFieldComponent* BALL::ForceField::getComponent | ( | const Size | index | ) | const |
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.
| double BALL::ForceField::getEnergy | ( | ) | const |
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
| Size BALL::ForceField::getNumberOfMovableAtoms | ( | ) | const |
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.
| virtual String BALL::ForceField::getResults | ( | ) | const [virtual] |
Get the current results in String form (Generic function to be overloaded in derived classes.
)
Reimplemented in BALL::AmberFF, BALL::CharmmFF, and BALL::MMFF94.
| const TimeStamp& BALL::ForceField::getSetupTime | ( | ) | const |
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_
| 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::AmberFF, and BALL::MMFF94.
| const TimeStamp& BALL::ForceField::getUpdateTime | ( | ) | const |
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_
| 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.
| bool BALL::ForceField::isValid | ( | ) | const |
Check the force field's validity.
A force field is valid if it is bound to a system and setup was successful.
| 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::setMaximumNumberOfErrors | ( | Size | nr | ) |
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.
| virtual bool BALL::ForceField::specificSetup | ( | ) | throw (Exception::TooManyErrors)
[virtual] |
Force field specific setup.
This method is called by setup.
Reimplemented in BALL::AmberFF, BALL::CharmmFF, 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.
