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CONFIG.md

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Config Files

Overview

Config files are the simplest way to interact with presto. Using config files allows for routine use of presto without having to interact with the underlying API, which is generally much safer and simpler.

presto config files are written in the YAML format and are generally 20-100 lines long. Since no coordinates are stored in the config file, each one can be reused for multiple trajectories with identical run parameters (e.g. duplicates).

A presto trajectory can be created from a config file through presto.config.build, as shown below:

import presto

trajectory1 = presto.build("config.yaml", "checkpoint1.chk", geometry="solvated_ts.xyz")
trajectory2 = presto.build("config.yaml", "checkpoint2.chk", geometry="solvated_ts.xyz")

Options

Here are a list of all the possible top-level config file options.

Required

type: What type of trajectory this file represents. Must be either reaction or equilibration.

timestep: The desired timestep, in femtoseconds (usually 0.5 or 1).

stop_time: The maximum run time, in femtoseconds.

integrator:

calculator:

Optional

Lists of atoms (for high_atoms, active_atoms, and inactive_atoms) can be specified as individual atom numbers or as ranges. Ranges are inclusive on both ends. For instance, high_atoms: 1-4, 7, 9 will be parsed into the list [1, 2, 3, 4, 7, 9].

high_atoms: Which atoms belong to the "high" ONIOM layer. Defaults to None.

active_atoms: Which atoms are active (all by default).

inactive_atoms: Which atoms are inactive. Will be overridden by active_atoms if both are present.

save_interval: Which frames to save. The default value of 1 saves every frame, while setting this to 10 will save every 10th frame.

checkpoint_interval: How frequently to save to the checkpoint file. The default value of 10 saves the trajectory to disk after every 10 frames.

buffer: How many frames to keep in Python memory.

anchor: If present, tells presto to apply a weak harmonic potential between the origin and the specified atom number, to keep a given molecule centered.

forwards: Whether to run a trajectory forwards in time (True, default) or backwards (False). You would only want to run a ReactionTrajectory backwards in time, usually from a transition state.

potential:

bath_scheduler (EquilibrationTrajectory only):

constraints:

checks:

  • **fadein

initialization (ReactionTrajectory only):

  • output_file

  • temperature

  • init_method

  • max_attempts

  • tolerance

termination_function (ReactionTrajectory only):

monitor: