BALL::MolecularDynamics Class Reference
[Molecular
Dynamics Simulation]
Molecular
Dynamics base class. More...
#include <molecularDynamics.h>
Classes |
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| struct | Option |
| Local classes for option names and
default option values for all MD(sub)classes. More... |
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Public Member Functions |
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Constructors and Destructors
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| MolecularDynamics () | |
| Default constructor. |
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| MolecularDynamics (ForceField &force_field) | |
| Constructor. |
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| MolecularDynamics (const MolecularDynamics &rhs) | |
| Copy constructor. |
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| virtual | ~MolecularDynamics () |
| Destructor. |
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Assignments
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| const MolecularDynamics & | operator= (const MolecularDynamics &rhs) |
| Assignment operator. |
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| void | set (const MolecularDynamics &rhs) |
| Assign a molecular dynamics
objects. |
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Debugging and Diagnostics
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| bool | isValid () const |
| Has the molecular dynamics class
been successfully set up? |
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Setup methods
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| virtual bool | setup (ForceField &force_field, SnapShotManager *snapshot_man) |
| Set up the molecular
dynamics. |
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| virtual bool | setup (ForceField &forcefield, SnapShotManager *snapshot_man, const Options &myoptions) |
| Set up the molecular
dynamics. |
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| virtual bool | specificSetup () |
| Specific setup; derived class can
use this method for additional preparations if
necessary. |
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Accessors
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| void | setNumberOfIteration (Size number) |
| Set the number of the current
iteration. |
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| void | setMaximalNumberOfIterations (Size number) |
| Set the maximal number of iterations
that will be carried out. |
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| void | setMaximalSimulationTime (double time) |
| Set the maximal simulation time in
ps that will be carried out. |
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| virtual void | setTimeStep (double step) |
| Set the time step in ps. |
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| void | setReferenceTemperature (double temperature) |
| Set the reference temperature for
the system. |
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| void | setCurrentTime (double time) |
| Set the current time of the MD run
in picoseconds. |
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| void | setEnergyOutputFrequency (Size number) |
| Set the energy output frequency.
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| void | setSnapShotFrequency (Size number) |
| Set the snapshot
frequency. |
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| Size | getEnergyOutputFrequency () const |
| Get the energy output
frequency. |
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| Size | getNumberOfIterations () const |
| Get the current iteration of the MD
simulation. |
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| Size | getMaximalNumberOfIterations () const |
| Get the maximal number of iterations
of the MD simulation. |
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| double | getMaximalSimulationTime () const |
| Get the maximal simulation time of
the MD simulation. |
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| double | getTimeStep () const |
| Get the current time
step. |
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| Size | getSnapShotFrequency () const |
| Get the snapshot
frequency. |
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| double | getTemperature () const |
| Get the current temperature of the
system. |
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| double | getTime () const |
| Get the current time of the MD
simulation. |
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| double | getTotalEnergy () const |
| Get the current total energy of the
system. |
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| double | getPotentialEnergy () const |
| Get the current potential energy of
the system. |
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| double | getKineticEnergy () const |
| Get the current kinetic energy of
the system. |
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| ForceField * | getForceField () const |
| Get the force field the MD
simulation is bound to. |
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| bool | simulate (bool restart=false) |
| Start the molecular dynamics
simulation. |
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| bool | simulateTime (double simulation_time, bool restart=false) |
| Simulate a given time interval.
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| virtual bool | simulateIterations (Size number, bool restart=false) |
| Start the molecular dynamics
simulation and carry out the given number of iterations.
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| void | enableEnergyAbortCondition (bool state) |
| Specify if the MDSimulation aborts
if the Energy is greater than abort_energy_. |
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| bool | energyAbortConditionEnabled () const |
| Query if the MDSimulation aborts if
the Energy is greater than abort_energy_. |
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| void | setEnergyToAbort (float value) |
| Specify the energy to abort the
simulation. |
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| float | getEnergyToAbort () const |
| Query the energy to abort the
simulation. |
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Public Attributes |
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Public Attributes
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| Options | options |
| The options for this
class. |
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Protected Member Functions |
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| void | updateInstantaneousTemperature () |
Protected Attributes |
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| bool | valid_ |
| ForceField * | force_field_ptr_ |
| System * | system_ptr_ |
| AtomVector | atom_vector_ |
| Size | number_of_iteration_ |
| Size | maximal_number_of_iterations_ |
| double | time_step_ |
| double | reference_temperature_ |
| double | current_temperature_ |
| double | kinetic_energy_ |
| double | total_energy_ |
| double | current_time_ |
| Size | energy_output_frequency_ |
| Size | snapshot_frequency_ |
| SnapShotManager * | snapshot_manager_ptr_ |
| bool | abort_by_energy_enabled_ |
| float | abort_energy_ |
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 | ( | ForceField & | force_field | ) |
Constructor.
It expects the forcefield
Member Function Documentation
| float BALL::MolecularDynamics::getEnergyToAbort | ( | ) | const |
Query the energy to abort the simulation.
The default value is 10^8.
| void BALL::MolecularDynamics::setEnergyOutputFrequency | ( | Size | number | ) |
Set the energy output frequency.
The current energies during the simulation will be printed every number steps.
| void BALL::MolecularDynamics::setEnergyToAbort | ( | float | value | ) |
Specify the energy to abort the simulation.
The default value is 10^8.
| void BALL::MolecularDynamics::setMaximalNumberOfIterations | ( | Size | number | ) |
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 | ( | double | time | ) |
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::setReferenceTemperature | ( | double | temperature | ) |
Set the reference temperature for the system.
In isothermal ensembles, this is the simulation temperature set set by the thermostat.
| virtual void BALL::MolecularDynamics::setTimeStep | ( | double | step | ) | [virtual] |
Set the time step in ps.
Note that this will change the maximum simulation time.
Reimplemented in BALL::CanonicalMD, and BALL::MicroCanonicalMD.
| bool BALL::MolecularDynamics::simulate | ( | bool | restart =
false |
) |
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 | ( | Size | number, | |
| bool | restart =
false |
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| ) | [virtual] |
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 | ( | double | simulation_time, | |
| 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
