Config Files

Anatomy

Config files are used by presto to generate Trajectory objects with the desired parameters. They are structure-independent, so a single config file can be used for a whole set of trajectory initiated from different starting configurations. Config files are written in the YAML format, making them easily human-readable and editable.

The following code illustrates how a config file can be used to build a Trajectory object:

  > trajectory = presto.build("config.yaml", "save.chk")
  > print(trajectory)
  Trajectory(243 frames)

Here is an example of a simple config file (from tutorial 00):

  # presto config file

  timestep: 1
  stop_time: 250
  anchor: 1
  save_interval: 5
  checkpoint_interval: 25

  integrator:
      type: langevin
      viscosity: 0.0001

  calculator:
      type: xtb
      gfn : 2
      parallel: 8

  bath_scheduler:
      type: constant
      target_temp: 298

  potential:
      type: spherical_harmonic
      radius: 10

This config file:

defines a timestep (1 fs), a stop time (250 fs), how often to save (every 25 fs), and which frames to save (every 5th).
specifies that a spherical harmonic potential with a cutoff radius of 10 Å is to be applied, and that atom #1 is to be "anchored" to the center of the simulation.
dictates that a Langevin integrator is to be employed, and the temperature held at 298 K.
specifies that the GFN2 method in xtb is to be used to calculate forces.

A (hopefully complete) list of config file options is found below.

Required Information

timestep (int/float):

The time which elapses between frames, in fs. Values of 0.5 or 1.0 fs are typical -- at high temperatures or in the gas phase, smaller values might be needed. Above 1.0 fs, errors may begin to accumulate, resulting in energy creep.

stop_time (int/float):

How long to run the trajectory for, in fs. Should be a multiple of ``timestep``.

integrator (dict):

(placeholder description)

calculator (dict):

(placeholder description)

Optional Information

initialization (dict):

(placeholder description)

termination (dict):

(placeholder description)

high_atoms (atomlist):

(placeholder description)

active_atoms or inactive_atoms (atomlist):

(placeholder description)

save_interval (int):

(placeholder description)

checkpoint_interval (int):

(placeholder description)

anchor (int):

(placeholder description)

forwards (bool):

(placeholder description)

potential (dict):

(placeholder description)

bath_scheduler (dict):

(placeholder description)

constraints (dict):

(placeholder description)

monitor (dict):

(placeholder description)