SoftMatterDynamics

Included in QATK.Dynamics

SoftMatterDynamics(configuration, trajectory_filename=None, steps=None, log_interval=None, method=None, profiles=None, hook_functions=None, write_velocities=True, write_forces=False, write_stress=False, trajectory_interval=None, trajectory_object_id=None)

Function for performing a molecular dynamics simulation using the soft matter framework.

Parameters:

  • configuration (MoleculeConfiguration | BulkConfiguration) – The initial configuration for the simulation.

  • trajectory_filename (str | None) – The filename of the file to be used for storing the trajectory, or None if no trajectory should be written.
    Default: None.

  • steps (int) – The number of time-steps to take in the simulation.
    Default: 10000.

  • log_interval (int) – The interval at which information, such as time, energy, temperature, etc. is written to the log output.
    Default: 1000.

  • method (BaseMDmethod) – The molecular dynamics method used for the simulation.
    Default: NVEDynamics.

  • profiles (SimulationQuantityProfile based | list) – The profiles to use for the simulation.
    Default: None.

  • hook_functions (SoftMatterDynamicsHook based | list) – The hook functions to use for the simulation.
    Default: None.

  • write_velocities (bool) – Write the velocities to the trajectory file every trajectory_interval steps.
    Default: True.

  • write_forces (bool) – Write the forces to the trajectory file every trajectory_interval steps.
    Default: False.

  • write_stress – Write the stress to the trajectory file every trajectory_interval steps.
    Default: False.

  • trajectory_interval (int) – Spacing in number of steps between images written to the trajectory..
    Default: The same value as log_interval.

  • trajectory_object_id (str | None) – The object id of the trajectory written to trajectory_filename. If a value of None is given, then an object id will be chosen automatically.
    Default: None.

Returns:

The trajectory from the simulation.

Return type:

MDTrajectory

Notes

The SoftMatterDynamics() function performs a molecular dynamics simulation on a given structure using the soft matter dynamics framework. This function is a companion to the MolecularDynamics() function that performs molecular dynamics using general dynamics framework. Both functions take similar arguments and both return an MDTrajectory. One difference is in the profiles and hook_functions arguments. These take profiles and hook functions that are designed for use with the soft matter dynamics framework. These are different from those used in the MolecularDynamics() function. Some molecular dynamics methods are only supported in one framework or the other. See the documentation on the SoftMatterDynamicsSimulation to see a table of which frameworks support which molecular dynamics method.

The molecular dynamics performed by this function is implemented in the SoftMatterDynamicsSimulation class. It is recommended to use the class directly to perform simulations.