#include <BALL/MOLMEC/COMMON/forceField.h>
List of all members.
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
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 |
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Default constructor. A default-constructed force field is not valid! It becomes valid after a successful call to setup.
| BALL::ForceField::ForceField |
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System & |
system |
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Constructor. The successful setup of the force field can be verified by the isValid method.
| BALL::ForceField::ForceField |
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System & |
system, |
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const Options & |
options | |
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Constructor. The successful setup of the force field can be verified by the isValid method.
| BALL::ForceField::ForceField |
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const ForceField & |
force_field |
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| virtual BALL::ForceField::~ForceField |
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[virtual] |
Member Function Documentation
| virtual void BALL::ForceField::clear |
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| void BALL::ForceField::collectAtoms_ |
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const System & |
system |
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| Size BALL::ForceField::countComponents |
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const |
Returns the number of components registered by the force field.
| BALL_INLINE void BALL::ForceField::disableSelection |
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Set the status of the selection mechanism
| BALL_INLINE void BALL::ForceField::enableSelection |
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Set the status of the selection mechanism
| BALL_INLINE const AtomVector& BALL::ForceField::getAtoms |
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Returns a reference to the atom vector
Return a pointer to the specified force field component. If a component with the specified name does not exist, 0 is returned.
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 |
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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::getMaximumNumberOfErrors |
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Get the number of atoms, for which the setup of the forcefield can fail, until the setup() methods aborts and return false.
| String BALL::ForceField::getName |
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const |
Returns the force field name
| Size BALL::ForceField::getNumberOfAtoms |
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const |
Returns the number of atoms stored in the force field
| Size BALL::ForceField::getNumberOfMovableAtoms |
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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 |
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const [inline, virtual] |
| double BALL::ForceField::getRMSGradient |
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const |
Calculates the RMS of the current gradient
| const TimeStamp& BALL::ForceField::getSetupTime |
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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_
| BALL_INLINE const System* BALL::ForceField::getSystem |
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Returns a const pointer to the system
| BALL_INLINE System* BALL::ForceField::getSystem |
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Returns a pointer to the system
| HashSet<const Atom*>& BALL::ForceField::getUnassignedAtoms |
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Get the atoms, for which the force field setup failed.
| virtual Size BALL::ForceField::getUpdateFrequency |
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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 |
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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_
| BALL_INLINE bool BALL::ForceField::getUseSelection |
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Return the status of the selection mechanism
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.
| BALL_INLINE bool BALL::ForceField::isSelectionEnabled |
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Return the status of the selection mechanism
| bool BALL::ForceField::isValid |
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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 |
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const String & |
name |
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Remove a component from the force field's component list.
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 |
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Size |
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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 |
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const String & |
name |
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Sets the force field name.
Sets up the force field and its components.
Sets up the force field and its components.
| void BALL::ForceField::sortSelectedAtomVector_ |
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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.
| double BALL::ForceField::updateEnergy |
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Calculate the sum of energies of all force field components and returns its value.
| void BALL::ForceField::updateForces |
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Calculate the forces caused by each component and updates the current forces.
Friends And Related Function Documentation
Member Data Documentation
