#include <BALL/MOLMEC/MDSIMULATION/molecularDynamics.h>
List of all members.
Detailed Description
Molecular Dynamics base class. This class is the base class for classical molecular dynamics simulations. Actual MD classes are derived from this class and then implement the actual simulation classes for the different ensembles or methods.
Constructor & Destructor Documentation
| BALL::MolecularDynamics::MolecularDynamics |
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| BALL::MolecularDynamics::MolecularDynamics |
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ForceField & |
force_field |
) |
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Constructor. It expects the forcefield
| virtual BALL::MolecularDynamics::~MolecularDynamics |
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[virtual] |
Member Function Documentation
| void BALL::MolecularDynamics::enableEnergyAbortCondition |
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bool |
state |
) |
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Specify if the MDSimulation aborts if the Energy is greater than abort_energy_
| bool BALL::MolecularDynamics::energyAbortConditionEnabled |
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const |
Query if the MDSimulation aborts if the Energy is greater than abort_energy_.
| Size BALL::MolecularDynamics::getEnergyOutputFrequency |
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const |
Get the energy output frequency
| float BALL::MolecularDynamics::getEnergyToAbort |
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const |
Query the energy to abort the simulation. The default value is 10^8.
| ForceField* BALL::MolecularDynamics::getForceField |
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const |
Get the force field the MD simulation is bound to
| double BALL::MolecularDynamics::getKineticEnergy |
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const |
Get the current kinetic energy of the system
| Size BALL::MolecularDynamics::getMaximalNumberOfIterations |
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const |
Get the maximal number of iterations of the MD simulation
| double BALL::MolecularDynamics::getMaximalSimulationTime |
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const |
Get the maximal simulation time of the MD simulation
| Size BALL::MolecularDynamics::getNumberOfIterations |
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const |
Get the current iteration of the MD simulation
| double BALL::MolecularDynamics::getPotentialEnergy |
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const |
Get the current potential energy of the system
| Size BALL::MolecularDynamics::getSnapShotFrequency |
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const |
Get the snapshot frequency
| double BALL::MolecularDynamics::getTemperature |
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const |
Get the current temperature of the system
| double BALL::MolecularDynamics::getTime |
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const |
Get the current time of the MD simulation
| double BALL::MolecularDynamics::getTimeStep |
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const |
Get the current time step
| double BALL::MolecularDynamics::getTotalEnergy |
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const |
Get the current total energy of the system
| bool BALL::MolecularDynamics::isValid |
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const |
Has the molecular dynamics class been successfully set up?
Assign a molecular dynamics objects.
| void BALL::MolecularDynamics::setCurrentTime |
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double |
time |
) |
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Set the current time of the MD run in picoseconds
| void BALL::MolecularDynamics::setEnergyOutputFrequency |
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Size |
number |
) |
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Set the energy output frequency. The current energies during the simulation will be printed every number steps.
| void BALL::MolecularDynamics::setEnergyToAbort |
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float |
value |
) |
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Specify the energy to abort the simulation. The default value is 10^8.
| void BALL::MolecularDynamics::setMaximalNumberOfIterations |
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Size |
number |
) |
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Set the maximal number of iterations that will be carried out. If the number of the start iteration is 0 (which is the default), this method sets the total number of simulated iterations.
| void BALL::MolecularDynamics::setMaximalSimulationTime |
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double |
time |
) |
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Set the maximal simulation time in ps that will be carried out. If the start time is zero(which is the default), then this method sets the total simulation time.
| void BALL::MolecularDynamics::setNumberOfIteration |
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Size |
number |
) |
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Set the number of the current iteration
| void BALL::MolecularDynamics::setReferenceTemperature |
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double |
temperature |
) |
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Set the reference temperature for the system. In isothermal ensembles, this is the simulation temperature set set by the thermostat.
| void BALL::MolecularDynamics::setSnapShotFrequency |
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Size |
number |
) |
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Set the snapshot frequency
| virtual void BALL::MolecularDynamics::setTimeStep |
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double |
step |
) |
[virtual] |
| bool BALL::MolecularDynamics::simulate |
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bool |
restart = false |
) |
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Start the molecular dynamics simulation. This method calls simulateIterations with the maximum number of iterations.
- See also:
- setMaximumNumberOfIterations
- Returns:
- false if an error occured, e.g. the energy was too high
| virtual bool BALL::MolecularDynamics::simulateIterations |
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Size |
number, |
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bool |
restart = false | |
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) |
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Start the molecular dynamics simulation and carry out the given number of iterations. This is the proper simulation method, which is implemented in the derived classes only. The implementation provided by MolecularDynamics is simply empty.
- Returns:
- false if an error occured, e.g. the energy was too high
Reimplemented in BALL::CanonicalMD, and BALL::MicroCanonicalMD.
| bool BALL::MolecularDynamics::simulateTime |
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double |
simulation_time, |
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bool |
restart = false | |
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Simulate a given time interval. This method determines the number of steps necessary to simulate a given time interval and executes a simulation for that interval by calling simulateIterations .
- Returns:
- false if an error occured, e.g. the energy was too high
| virtual bool BALL::MolecularDynamics::specificSetup |
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[virtual] |
| void BALL::MolecularDynamics::updateInstantaneousTemperature |
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[protected] |
Member Data Documentation
The options for this class
