diff --git a/docs/Custom_atomic_data/Custom_atomic_data.ipynb b/docs/Custom_atomic_data/Custom_atomic_data.ipynb new file mode 100644 index 00000000..7007f678 --- /dev/null +++ b/docs/Custom_atomic_data/Custom_atomic_data.ipynb @@ -0,0 +1,101 @@ +{ + "cells": [ + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## Using Your Own Atomic Data\n", + " To run a simulation, STARDIS requires an atomic data file that has information on the properties of atoms and molecules needed by STARDIS. While [\"kurucz_cd23_chianti_H_He.h5\"](https://dev.azure.com/tardis-sn/TARDIS/_apis/git/repositories/tardis-refdata/items?path=atom_data/kurucz_cd23_chianti_H_He.h5&resolveLfs=true) is the default atomic data used by STARDIS, you can create and use other atomic data files by using [CARSUS](https://tardis-sn.github.io/carsus/). For more information on using CARSUS you can access the [CARSUS documentation](https://tardis-sn.github.io/carsus/index.html)." + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "### Relevant CARSUS Data to Collect\n", + "While CARSUS accumulates all sorts of data when compiling the atomic data files, not everything it can include is necessary or relevant for running STARDIS. Here is a list of what data/readers you should make sure to include when running CARSUS:\n", + "- [atomic weights & ionization energy from NIST](https://tardis-sn.github.io/carsus/io/nist.html)\n", + "- [Robert Kurucz’s Atomic Linelist (GFALL)](https://tardis-sn.github.io/carsus/io/gfall.html)\n", + "- [atomic and molecular transitions from VALD](https://tardis-sn.github.io/carsus/io/vald.html)\n", + "- [Molecular formation from Barklem & Collet 2016](https://tardis-sn.github.io/carsus/io/barklem2016.html)\n" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "Use CARSUS and follow their documentation to get a data file:\n", + "\n", + "[https://tardis-sn.github.io/carsus/](https://tardis-sn.github.io/carsus/)" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "To use new atomic data file in a simulation, add/edit the line in your yaml file `atom_data: `. This path can be *either* the relative or absolute path. Your atomic data file should have the file extension '.h5'." + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "The file 'kurucz_cd23_chianti_H_He.h5' referenced below is the default atomic_data used by STARDIS.\n", + "``` yaml\n", + "stardis_config_version: 1.0\n", + "atom_data: kurucz_cd23_chianti_H_He.h5 # <----- put the relative or absolute path here\n", + "model:\n", + "...\n", + "```" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "### Using VALD linelists\n", + "\n", + "Possibly one of the most important reasons you would want to use a custom atomic data file would be to take advantage of a tailored VALD linelist. You can refer to [VALD's documentation](https://www.astro.uu.se/valdwiki) for information on these lists if you are unfamiliar. To create a detailed and accurate stellar spectrum, we highly recommend looking into using a VALD linelist bundled into your atomic data." + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "If you have included a VALD linelist in your atom_data file, then you **must** make the following change to your Yaml file for the linelist to be used:\n", + "``` yaml\n", + "...\n", + "line:\n", + " disable: False\n", + " broadening: [radiation, linear_stark, quadratic_stark, van_der_waals]\n", + " vald_linelist: #<-----\n", + " use_linelist: True #<----- will default to false, so must set to True\n", + " shortlist: #<----- VALD can output lists in 'long' form or 'short' form; set accordingly\n", + "no_of_thetas: 20\n", + "...\n", + "```" + ] + } + ], + "metadata": { + "kernelspec": { + "display_name": "stardis", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.12.4" + } + }, + "nbformat": 4, + "nbformat_minor": 2 +} diff --git a/docs/index.rst b/docs/index.rst index e0741768..41cce916 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -10,6 +10,7 @@ This is the documentation for STARDIS. Quickstart Downloading and Installation Physics of STARDIS + Custom Atomic Data Possible STARDIS Outputs Custom Star Model Using STARDIS in Parallel