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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,12 @@ | ||
| { | ||
| "hash": "80e294a73e06e47b40b43cfdbb332c36", | ||
| "result": { | ||
| "engine": "jupyter", | ||
| "markdown": "---\ntitle: All Options\n---\n\n\n\nFor all KIMMDY options see [here](https://graeter-group.github.io/kimmdy/guide/references/input.html#all-options).\n\n\n\n\n## Homolysis\n\n```yaml\nreactions:\n homolysis: ...\n```\n\n### edis\n\nDissociation energies data file\n\n\n**Type**: Path\n\n\n**Default**: edissoc.dat\n\n\n### itp\n\nAdditional itp file with bonded parameters\n\n\n**Type**: Path\n\n\n**Default**: ffbonded.itp\n\n\n### kmc\n\nKMC algorithm for this reaction.\n\n\n**Type**: str\n\n\n**Options**: ['rfkmc', 'frm', 'extrande', 'extrande_mod']\n\n\n**Default**: rfkmc\n\n\n### check_bound\n\nCheck the topology for bonds between plumed atom pairs\n\n\n**Type**: bool\n\n\n**Default**: False\n\n\n### arrhenius_equation\n\nFor setting values in the arrhenius equation\n\n\n\n\n## Dummy Reaction\n\n```yaml\nreactions:\n dummyreaction: ...\n```\n\n### example\n\nThis is an example of an option for a reaction.\n\n\n**Type**: float\n\n\n**Default**: 0.0\n\n\n### example2\n\nThis is another example of an option for a reaction.\n\n\n**Type**: str\n\n\n**Default**: hello\n\n\n### kmc\n\nKMC algorithm for this reaction.\n\n\n**Type**: str\n\n\n**Options**: ['rfkmc', 'frm', 'extrande', 'extrande_mod']\n\n\n**Default**: extrande_mod\n\n\n\n\n## Naive HAT\n\n```yaml\nreactions:\n hat_naive: ...\n```\n\n### frequency_factor\n\nFrequency factor\n\n\n**Type**: float\n\n\n**Default**: 1\n\n\n### h_cutoff\n\nCutoff for H atom\n\n\n**Type**: float\n\n\n**Default**: 4\n\n\n### polling_rate\n\nPolling rate\n\n\n**Type**: float\n\n\n**Default**: 1\n\n\n### kmc\n\nKMC algorithm for this reaction.\n\n\n**Type**: str\n\n\n**Options**: ['rfkmc', 'frm', 'extrande', 'extrande_mod']\n\n\n**Default**: extrande_mod\n\n\n\n\n", | ||
| "supporting": [ | ||
| "config_files" | ||
| ], | ||
| "filters": [], | ||
| "includes": {} | ||
| } | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,68 @@ | ||
| ## All Options | ||
|
|
||
| For all KIMMDY options see [here](https://graeter-group.github.io/kimmdy/guide/references/input.html#all-options). | ||
|
|
||
| ```{python} | ||
| #| echo: false | ||
| from kimmdy.schema import get_combined_scheme, flatten_scheme, generate_markdown_table, convert_schema_to_dict | ||
| from pathlib import Path | ||
| import json | ||
| def cat_options(reaction: str): | ||
| path = Path(f"./src/{reaction}/kimmdy-yaml-schema.json") | ||
| with path.open("r") as f: | ||
| schema = json.load(f) | ||
| scheme = convert_schema_to_dict(schema) | ||
| flat_scheme = flatten_scheme(scheme) | ||
| for item in flat_scheme: | ||
| print(f"### {item['key']}\n") | ||
| print(f"{item['desc']}\n\n") | ||
| if item['type'] != "": | ||
| print(f"**Type**: {item['type']}\n\n") | ||
| if item['enum'] != "": | ||
| print(f"**Options**: {item['enum']}\n\n") | ||
| if item['default'] != "": | ||
| print(f"**Default**: {item['default']}\n\n") | ||
| ``` | ||
|
|
||
| ## Homolysis | ||
|
|
||
| ```yaml | ||
| reactions: | ||
| homolysis: ... | ||
| ``` | ||
| ```{python} | ||
| #| echo: false | ||
| #| output: asis | ||
| cat_options("homolysis") | ||
| ``` | ||
|
|
||
| ## Dummy Reaction | ||
|
|
||
| ```yaml | ||
| reactions: | ||
| dummyreaction: ... | ||
| ``` | ||
| ```{python} | ||
| #| output: asis | ||
| #| echo: false | ||
| cat_options("dummyreaction") | ||
| ``` | ||
|
|
||
| ## Naive HAT | ||
|
|
||
| ```yaml | ||
| reactions: | ||
| hat_naive: ... | ||
| ``` | ||
| ```{python} | ||
| #| output: asis | ||
| #| echo: false | ||
| cat_options("hat_naive") | ||
| ``` | ||
|
|
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