latest--kimmdy-yaml-schema

shared
Type object
Schema URL https://catalog.lintel.tools/schemas/schemastore/kimmdy-config-file/_shared/latest--kimmdy-yaml-schema.json
Parent schema kimmdy-config-file
Type: object

Settings for HAT reaction plugin

Properties

arrhenius_equation object

For setting values in the arrhenius equation

2 nested properties
frequency_factor float required

Frequency factor

Default: 0.288
min=0
temperature float required

Temperature

Default: 300
min=0
h_cutoff float

Cutoff for H atom

Default: 3
cap boolean

If true, cap structures for prediction. Default False.

Default: false
model string

Model name, optional. If not defined, will choose based on grappa usage in KIMMDY.

Default: null
Values: "grappa" "classic"
ensemble_size integer

Number of models to use, defaults to all, optional

Default: null
prediction_scheme string

How to predict the reaction barrier. Current options: efficient, all_models and parallel. parallel combines the underlying models into one. efficient first predicts the barriers with one model, and if a barrier is sufficiently low, recalculates it with the complete ensemble. In the all_models scheme, all reactions are evaluated using all models one after the other. Default: parallel

Default: "parallel"
Values: "all_models" "efficient" "parallel"
polling_rate integer

Polling rate, defaults to 10

Default: 10
n_unique integer

Only consider the n frames per reaction with the smallest translation distances. Set to 0 to consider all, defaults to 100

Default: 100
trajectory_format string

Use either trr or xtc trajectory. Assumes no solvent atoms in xtc', defaults to xtc

Default: "xtc"
Values: "trr" "xtc"
radicals integer

Space-separated string of radical atom ids, can be empty, usually supplyed through kimmdy, optional

Default: null
change_coords string

How to change coordinates. H can be placed at the new position, or a (lambda)-dynamics simulation can be performed. For lambda-dynamics, set up the coordinate changer with slow_growth=True. Default: place

Default: "place"
Values: "place" "lambda"
kmc string

KMC algorithm for this reaction. Default: extrande_mod

Default: "extrande_mod"
Values: "rfkmc" "frm" "extrande" "extrande_mod"
keep_structures boolean

For each reaction a structure is generated. If true, those are kept on disk, otherwise they are only kept in case of a failure. Default: False

Default: false