diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md
index 1ec0b67f..363ed3ae 100644
--- a/.github/CONTRIBUTING.md
+++ b/.github/CONTRIBUTING.md
@@ -8,17 +8,19 @@ and feedback from users.
wish to contribute to GITM. Following these guidelines will ensure a positive
experience for all involved.
-## Outline
-
-- [Opening an Issue](#opening-an-issue)
- - [Bug Report](#bug-report)
- - [Feature Requests](#feature-requests)
-- [Pull Requests](#pull-requests)
- - [Committing Changes](#committing-changes)
- - [Commit Styling](#commit-styling)
-- [Code Formatting](#code-formatting)
- - [Automatic/Validating Code Formatting](#automaticvalidating-code-formatting)
- - [Style Guidelines \& `.fprettify.rc`](#style-guidelines--fprettifyrc)
+- [Contributing Guidelines](#contributing-guidelines)
+ - [Opening an Issue](#opening-an-issue)
+ - [Bug Report](#bug-report)
+ - [Feature Requests](#feature-requests)
+ - [Pull Requests](#pull-requests)
+ - [Committing Changes](#committing-changes)
+ - [Commit Styling](#commit-styling)
+ - [Testing GITM](#testing-gitm)
+ - [Code Formatting](#code-formatting)
+ - [Automatic/Validating Code Formatting](#automaticvalidating-code-formatting)
+ - [Style Guidelines \& `.fprettify.rc`](#style-guidelines--fprettifyrc)
+
+---
## Opening an Issue
@@ -30,15 +32,15 @@ are creating and then modify the contents of the template to describe your issue
### Bug Report
-If you notice a problkem with GITM and are unsure of how to fix it yourself, please
+If you notice a problem with GITM and are unsure of how to fix it yourself, please
create a bug report detailing the problem. The template has several optional sections,
so read through them all before adding information to the wrong section.
- **Do not open an issue for problems installing GITM on a specific system.** Since
there is no way to predict all possible systems which GITM will be used on, details on
specific systems cannot be provided. Try the steps in the [README](../README.md) first,
-then reach out to #TODO if you need mroe help.
-- Please include enough information to allow a maintainer to reproduce your bug
+then reach out to the development team if you need more help.
+- Please include enough information to allow a maintainer to reproduce your bug,
only seeing the information in the bug report. Forgetting to attach input files or
only saying "the code did not run on system X", for example, will result in a delay.
- Check if another issue is open (or closed) with the same problem. Duplicate issues
@@ -78,7 +80,7 @@ are working on a feature and notice an unrelated bug or typo, create a new branc
`develop`, fix it, and submit the pull request separately. There is no harm in
submitting many small pull requests!
- **Document your changes**. If you are introducing a new feature, please include
-a description of it and its uses in both the documentation (`docs/` folder) and
+a description of it and its uses in both the documentation (`srcDoc/` folder) and
in comments within the code.
- **Include new tests**. If you are adding a new feature, please add a sample `UAM.in`
file with this option enabled in the `srcTests/auto_test/` folder. We do not want future updates
@@ -134,6 +136,19 @@ FEAT: Hydrostatic density implementation.
Implemented hydrostatic density. (feature)
```
+## Testing GITM
+
+GITM has a number of tests that are maintained and run automatically on every
+release & pull-request. To run these yourself, run the script `run_all_tests.sh`
+from within `srcTests/auto_test`. New tests can be added by simply creating
+another UAM.in file, and will be run automatically if the file matches the
+pattern `UAM.in.*.test`.
+
+It is best practice to create tests as bugs are fixed. For example, if running
+GITM in a certain configuration causes a crash, it is recommended to create a
+test with this configuration which will help ensure the bug does not sneak back
+in with future development.
+
## Code Formatting
GITM now uses a custom implementation of the
diff --git a/.github/workflows/Format-Doc-Test.yml b/.github/workflows/Format-and-Test.yml
similarity index 78%
rename from .github/workflows/Format-Doc-Test.yml
rename to .github/workflows/Format-and-Test.yml
index d0ea04b9..0a5e5b5e 100644
--- a/.github/workflows/Format-Doc-Test.yml
+++ b/.github/workflows/Format-and-Test.yml
@@ -48,34 +48,13 @@ jobs:
cd GITM
python srcPython/format_GITM.py -l -s -v ${ALL_CHANGED_FILES}
- Documentation:
- runs-on: ubuntu-latest
- name: Build Documentation
- needs: [Format]
- steps:
- - name: Clone GITM repository
- uses: actions/checkout@v4
- - name: Compile LaTeX document
- uses: xu-cheng/latex-action@v3
- with:
- root_file: manual.tex
- working_directory: srcDoc
- - name: Rename GITM Manual
- run: mv srcDoc/manual.pdf GITM_manual.pdf
- - name: Upload PDF file
- uses: actions/upload-artifact@v4
- with:
- name: PDF
- path: GITM_manual.pdf
- retention-days: 31
-
Tests:
runs-on: ${{ matrix.os }}
strategy:
matrix:
os: [ubuntu-latest, macos-latest]
name: Run Automatic Tests
- needs: [Format, Documentation]
+ needs: [Format]
steps:
- name: Linux install gfortran & openmpi
if: runner.os == 'Linux'
@@ -85,6 +64,7 @@ jobs:
run: |
brew update
brew install gcc open-mpi
+ ln -s $(brew --prefix)/bin/gfortran-15 $(brew --prefix)/bin/gfortran
- name: Clone GITM repository
uses: actions/checkout@v4
- name: Run tests on MacOS (no output checking, only one test)
diff --git a/.github/workflows/build-docs.yml b/.github/workflows/build-docs.yml
deleted file mode 100644
index 4cb9ef5b..00000000
--- a/.github/workflows/build-docs.yml
+++ /dev/null
@@ -1,29 +0,0 @@
-name: Build Documentation
-
-on:
- schedule:
- # 0 minute, 0 hour, 1st day, every month, any day of week
- - cron: '0 0 1 * *'
- push:
- branches:
- main
-
-jobs:
- build_documentation:
- runs-on: ubuntu-latest
- steps:
- - name: Clone GITM repository
- uses: actions/checkout@v4
- - name: Compile LaTeX document
- uses: xu-cheng/latex-action@v3
- with:
- root_file: manual.tex
- working_directory: srcDoc
- - name: Rename GITM Manual
- run: mv srcDoc/manual.pdf GITM_manual.pdf
- - name: Upload PDF file
- uses: actions/upload-artifact@v4
- with:
- name: PDF
- path: GITM_manual.pdf
- retention-days: 31
diff --git a/.gitignore b/.gitignore
index 3941664d..a77757fe 100644
--- a/.gitignore
+++ b/.gitignore
@@ -61,4 +61,5 @@ ext/
share/component_share
util/component_util
-src/.version
\ No newline at end of file
+src/.version
+gitstatus.txt
\ No newline at end of file
diff --git a/.readthedocs.yaml b/.readthedocs.yaml
new file mode 100644
index 00000000..1e4ab3eb
--- /dev/null
+++ b/.readthedocs.yaml
@@ -0,0 +1,15 @@
+version: 2
+
+# Set the version of Python and other tools you might need
+build:
+ os: ubuntu-24.04
+ tools:
+ python: "3.12"
+
+mkdocs:
+ configuration: mkdocs.yml
+
+# Optionally declare the Python requirements required to build your docs
+python:
+ install:
+ - requirements: srcDoc/requirements.txt
diff --git a/Makefile b/Makefile
index 82f4124b..029597bc 100644
--- a/Makefile
+++ b/Makefile
@@ -37,9 +37,7 @@ NOMPI:
@cd ${NOMPIDIR}; make LIB
VERSION:
- printf 'character(25), parameter :: GitmVersion = "%s.%s"\n' \
- "$$(git log -1 --date=format:'%Y%m%d' --pretty='format:%ad')" \
- "$$(git status --porcelain | grep -v '^??' | wc -l | cut -f1 -d' ')" > src/.version
+ ./share/Scripts/Makeversion.sh
@echo
GITM:
@@ -87,6 +85,7 @@ clean:
if [ -d util ]; then cd util; make --no-print-directory cleanall; fi;
if [ -d srcSAMI ]; then cd srcSAMI; make --no-print-directory clean; fi;
if [ -d $(EIEDIR) ]; then cd $(EIEDIR); make --no-print-directory cleanall; fi;
+ if [ -f src/.version ]; then rm src/.version; fi
distclean:
diff --git a/README.md b/README.md
index 018a1588..21d02535 100644
--- a/README.md
+++ b/README.md
@@ -5,9 +5,9 @@ This is the home of the Global Ionosphere/Thermosphere Model (GITM).
GITM has been developed in fortran-90. It has been tested with gfortran
on Linux and MacOS as well as ifort on NASA's Pleiades computer.
-The latest version of the documentation can be accessed at:
+For the complete documentation, see [GITM's Read the Docs Page](https://gitm.readthedocs.io).
-[](https://github.com/GITMCode/GITM/actions/workflows/build-docs.yml)
+---
GITM's default branch recently changed names. To access the latest features, please update your local refs.
@@ -29,38 +29,38 @@ git remote prune origin
-## Dependencies
-
-1. GITM needs MPI to work.
-
## Quick Start
+> GITM needs MPI to work properly. This can be installed with your system's package manager, or loaded as a `module` on an HPC system.
+> See [the installation guide](https://gitm.readthedocs.io/en/latest/quick_start/#requirements) for more information.
+
1\. Clone the repository and cd into the repo folder
```shell
-git clone --recursive https://github.com/GITMCode/GITM
+git clone git@github.com:GITMCode/GITM.git
```
+Substitute the URL with the `https` link from the "Code" button above if you do not have SSH keys set up.
+
2\. Go into the repo directory
```shell
cd GITM
```
-3\. Configure the Fortran compiler (version 10)
+3\. Configure the Fortran compiler and download external electrodynamics library
+(gfortran versions 10+)
```shell
./Config.pl -install -earth -compiler=gfortran10
```
The biggest issue with the above command is that it assumes that you
-have the gfortran (version 10) compiler and things like mpif90 work
+have the gfortran (version 10+) compiler and things like mpif90 work
ok. If you don't have gfortran and mpif90, then you need to get these
things for your computer. If you have version 9 or before for gfortran,
you can do:
-3b\. Configure the Fortran compiler (version 9 or below)
-
```shell
./Config.pl -install -earth -compiler=gfortran
```
@@ -69,17 +69,15 @@ In theory, Mars, Venus, Titan, and LV-426 should work. These are in
various states of completion, so I wouldn't count on them being
perfect.
-If running on Pleiades (as of March 3, 2022), you need to have these
+If running on Pleiades, you need to have these
in your start-up script (.cshrc, .bashrc, etc):
```
-module load comp-intel/2016.2.181
-module load mpi-hpe/mpt
+module load comp-intel
+module load mpi-hpe
```
-And you can use 3c below to configure the code.
-
-3c\. Configure for Pleiades
+And you can use the below line below to configure the code:
```shell
./Config.pl -install -earth -compiler=ifort
@@ -127,7 +125,7 @@ lon. See below for how to set the resolution.
> see available options.
> The legacy postprocessors are still available, but are not built by default. To build
-> PostProcess.exe, run `make POST` and the csh script can be found at `src/pGITM`.
+> PostProcess.exe, run `make POST`. The csh script can be found at `src/pGITM`.
9\. Go into the output directory:
@@ -200,7 +198,9 @@ team. For example:
NCAR. The IGRF code that comes with it is also not developed at UM.
2. Many electrodynamics models (Weimer, Newell's Ovation Prime,
-Mitchell's Ovation SME, others in the util/EMPIRICAL/srcIE directory).
+Mitchell's Ovation SME, others in the
+[GITMCode/Electrodynamics](https://github.com/GITMCode/Electrodynamics)
+repository).
3. MSIS and IRI, which are in util/EMPIRICAL/srcUA. MSIS is used as a
lower BC at Earth and was developed at NRL. IRI is used to initialize
@@ -228,3 +228,7 @@ processors, you can change the parameters in `src/ModSize.f90` and adjust the
number of cells in each block to compensate. For example, you have 8
processors, so you can adjust `src/ModSize.f90` to have 18 cells in lat and
lon, then ask for 2 (lat) x 4 (lon) blocks to get 5 deg x 5 deg resolution.
+
+See the
+[grid page](https://gitm.readthedocs.io/en/latest/grid/#horizontal-resolution)
+in the documentation for more details and some examples.
diff --git a/mkdocs.yml b/mkdocs.yml
new file mode 100644
index 00000000..3636d51f
--- /dev/null
+++ b/mkdocs.yml
@@ -0,0 +1,90 @@
+site_name: GITM
+site_url: https://gitm.readthedocs.io
+site_description: >-
+ Official documentation for the Global Ionosphere Thermosphere Model (GITM)
+repo_name: GITMCode/GITM
+repo_url: https://github.com/GITMCode/GITM
+
+theme:
+ # name: readthedocs
+ # name: mkdocs
+ name: material
+ icon:
+ logo: material/earth
+ repo: material/github
+
+ features:
+ - navigation.tabs
+ - navigation.tabs.sticky
+ - navigation.footer
+ - toc.integrate
+ - content.code.annotate
+ - content.code.copy
+
+ palette:
+ # Palette toggle for automatic mode
+ - media: "(prefers-color-scheme)"
+ toggle:
+ icon: material/brightness-auto
+ name: Switch to light mode
+
+ # Palette toggle for light mode
+ - media: "(prefers-color-scheme: light)"
+ scheme: default
+ toggle:
+ icon: material/brightness-7
+ name: Switch to dark mode
+
+ # Palette toggle for dark mode
+ - media: "(prefers-color-scheme: dark)"
+ scheme: slate
+ toggle:
+ icon: material/brightness-4
+ name: Switch to system preference
+
+plugins:
+ - search # allow for search after being built
+ - mermaid2: # cool diagrams
+ javascript: js/mermaid.min.js # local path to mermaid javascript file
+
+markdown_extensions:
+ - pymdownx.extra #footnotes, abbreviations, tables, definitions, etc.
+ - pymdownx.fancylists # lists continuing after breaking for indentation
+ - pymdownx.saneheaders #allows for "#text" to not be parsed as a header
+ - pymdownx.tasklist
+ - markdown_katex # math
+ - admonition # note, warning, etc. blocks
+ - markdown_del_ins # strike-through & insert
+ - markdown_captions # figure captions.
+ - pymdownx.superfences:
+ # make exceptions to highlighting of code:
+ custom_fences:
+ - name: mermaid
+ class: mermaid
+ format: !!python/name:mermaid2.fence_mermaid
+
+docs_dir: srcDoc
+
+nav:
+ - Home: index.md
+ - Getting Started: install.md
+ - Inputs:
+ - Common Inputs: common_inputs.md
+ - All Inputs: set_inputs.md
+ - Outputs:
+ - Postprocessing: postprocessing.md
+ - Available Outputs: outputs.md
+ - Plotting Outputs: plotters.md
+ - Internals:
+ - Overview: internals/overview.md
+ - Grid: internals/grid.md
+ - Earth Chemistry: internals/chemistry.md
+ - Electrodynamics: internals/electrodynamics.md
+ - Development:
+ - Site Information: devstuff/devhome.md
+ - Contributing: https://github.com/GITMCode/GITM/blob/main/.github/CONTRIBUTING.md
+ - GITM Developers: https://github.com/GITMCode/GITM/graphs/contributors
+ - Markdown Reference: devstuff/markdown_ref.md
+ - GITM Outline: devstuff/outline.md
+ - Other Useful Links: devstuff/somelinks.md
+ - Getting Help: FAQ/faq.md
diff --git a/share/Scripts/Makeversion.sh b/share/Scripts/Makeversion.sh
new file mode 100755
index 00000000..8fde3ecd
--- /dev/null
+++ b/share/Scripts/Makeversion.sh
@@ -0,0 +1,76 @@
+#!/bin/bash
+
+# This file writes some 'version' info about GITM to a file
+# The file is located in src/.version and is compiled into GITM.
+# This info is then written out to run_information.txt.
+
+## Function we call if .git folder exists, and $(git status) has changed from last time
+writegitversion(){
+ # This is the float-type version placed in output files
+ # Format is (date of last commit).(# of files changed from HEAD)
+ printf 'character(25), parameter :: GitmVersion = & \n "%s.%s"\n' \
+ "$(git log -1 --date=format:'%Y%m%d' --pretty='format:%ad')" \
+ "$(git status --porcelain | grep -v '^??' | wc -l | cut -f1 -d' ')" > src/.version
+
+
+ # The "GitmVersionFull" variable has info about the last commit hash in addition to above
+ printf '\ncharacter(50), parameter :: GitmVersionFull = "%s_%s.%s"\n\n' \
+ "$(git rev-parse --abbrev-ref HEAD)" \
+ "$(git log -1 --date=format:'%Y%m%d' --pretty='format:%h-%ad')" \
+ "$(git status --porcelain | grep -v '^??' | wc -l | cut -f1 -d' ')" >> src/.version
+
+ # Same as above, but for Electrodynamics
+ printf '\ncharacter(50), parameter :: ElectrodynamicsVersionFull = "%s_%s.%s"\n\n' \
+ "$(git -C ext/Electrodynamics rev-parse --abbrev-ref HEAD)" \
+ "$(git -C ext/Electrodynamics log -1 --date=format:'%Y%m%d' --pretty='format:%h-%ad')" \
+ "$(git -C ext/Electrodynamics status --porcelain | grep -v '^??' | wc -l | cut -f1 -d' ')" \
+ >> src/.version
+
+
+ # Here, for completeness, all of the changes files are listed.
+ printf 'character(*), parameter :: DifferentFilesGitm = &\n"' >> src/.version
+
+ files=$(git status --porcelain | awk '{print $NF}')
+ for file in $files; do
+ echo "$file,&" >> src/.version
+ done
+ echo '"'>> src/.version
+
+ printf 'character(*), parameter :: DifferentFilesElectrodyunamics = &\n"' >> src/.version
+
+ files=$(git -C ext/Electrodynamics status --porcelain | awk '{print $NF}')
+ for file in $files; do
+ echo "$file,&" >> src/.version
+ done
+ echo '"'>> src/.version
+}
+
+################
+## MAIN ##
+################
+
+if [ -d .git ]; then # Check if .git/ directory exists
+
+ # check to see if git status has changed, saves time compiling if not
+ nFilesDiff=$(git status --porcelain | wc -l)
+ if [ -f gitstatus.txt ]; then
+ nFilesPrev=$(wc -l < gitstatus.txt)
+ else # Our first time here...
+ nFilesPrev=0
+ fi
+
+ if [ $nFilesDiff == $nFilesPrev ] && [ -f src/.version ]; then
+ echo "Version has not changed since last compile: $(head -n 2 src/.version | tail -n 1)"
+ exit 0
+ else
+ writegitversion
+ git status --porcelain > gitstatus.txt
+ echo "Writing GITM version to file: $(head -n 2 src/.version | tail -n 1)"
+
+ fi
+
+else # if .git/ does not exist, this is probably a release
+ cp version.def src/.version
+ echo "Wrote version file for GITM: $(head -n 2 src/.version | tail -n 1)"
+fi
+
diff --git a/src/ModGITM.f90 b/src/ModGITM.f90
index b7640d6b..6cd4c015 100644
--- a/src/ModGITM.f90
+++ b/src/ModGITM.f90
@@ -289,6 +289,7 @@ subroutine clean_mod_gitm
deallocate(dAltDLon_CB)
deallocate(dAltDLat_CB)
deallocate(Rho)
+ deallocate(ColumnIntegralRho)
deallocate(Temperature)
deallocate(Pressure)
deallocate(NDensity)
diff --git a/src/inputs_to_tex.pl b/src/inputs_to_tex.pl
index 72c24f42..a6f70e4a 100755
--- a/src/inputs_to_tex.pl
+++ b/src/inputs_to_tex.pl
@@ -46,4 +46,4 @@
close(INFILE);
close(OUTFILE);
-exit(1);
+exit(0);
diff --git a/src/set_inputs.f90 b/src/set_inputs.f90
index abcebbbf..6a28e618 100644
--- a/src/set_inputs.f90
+++ b/src/set_inputs.f90
@@ -781,21 +781,6 @@ subroutine set_inputs
IsDone = .true.
endif
- ! case ("#OVATIONSME")
- ! call read_in_logical(UseOvationSMEWave, iError)
- ! call read_in_logical(UseOvationSMEIon, iError)
- ! if (iError /= 0) then
- ! write(*, *) 'Incorrect format for #OVATIONSME'
- ! write(*, *) 'This is for using Betsy Michells aurora (OvationSME).'
- ! write(*, *) 'These are all False by default:'
- ! write(*, *) ''
- ! write(*, *) '#OVATIONSME'
- ! write(*, *) 'UseOvationSMEMono (logical)'
- ! write(*, *) 'UseOvationSMEWave (logical)'
- ! write(*, *) 'UseOvationSMEIon (logical)'
- ! IsDone = .true.
- ! endif
-
case ("#USECUSP")
call read_in_logical(UseCusp, iError)
call read_in_real(CuspAveE, iError)
@@ -1060,7 +1045,7 @@ subroutine set_inputs
IsDone = .true.
endif
- case ("#MODIFIYPLANET")
+ case ("#MODIFYPLANET")
call read_in_real(RotationPeriodInput, iError)
call read_in_real(DaysPerYearInput, iError)
call read_in_real(PlanetTiltInput, iError)
diff --git a/srcDoc/FAQ/faq.md b/srcDoc/FAQ/faq.md
new file mode 100644
index 00000000..c964874c
--- /dev/null
+++ b/srcDoc/FAQ/faq.md
@@ -0,0 +1,20 @@
+# Common Problems
+
+## The code won't compile!!
+
+Sorry about that. It is hard to test on every system type.
+
+There are some steps you can try before submitting a bug report or contacting the developers.
+
+1. First, try to un-install everything:
+```
+make distclean
+./Config.pl -uninstall
+```
+2. Then, check to see if any files are changed:
+```
+git status
+```
+3. If any of the Fortran or Make-files have changed, you may want to `git restore` the changes.
+4. Try to re-configure and then re-compile
+
diff --git a/srcDoc/chemistry_earth.pdf b/srcDoc/chemistry_earth.pdf
deleted file mode 100644
index c9e16479..00000000
Binary files a/srcDoc/chemistry_earth.pdf and /dev/null differ
diff --git a/srcDoc/chemistry_earth.tex b/srcDoc/chemistry_earth.tex
deleted file mode 100644
index 148fe260..00000000
--- a/srcDoc/chemistry_earth.tex
+++ /dev/null
@@ -1,524 +0,0 @@
-% Copyright (C) 2002 Regents of the University of Michigan, portions used with permission
-% For more information, see http://csem.engin.umich.edu/tools/swmf
-\documentclass[twoside,10pt]{book}
-\usepackage{times}
-\usepackage{graphicx}
-\usepackage{alltt}
-\usepackage{amsmath}
-\usepackage{epsfig}
-\usepackage{fancyhdr}
-\usepackage[square]{natbib}
-\usepackage{multicol}
-\usepackage{subfigure}
-\usepackage{fancyvrb}
-\usepackage{color}
-
-% use these lengths for a more uniform margin
-% this format is more pleasing for stapling
-\setlength{\oddsidemargin}{-.1 in}
-\setlength{\evensidemargin}{0.0 in}
-\setlength{\textwidth}{6.5 in}
-\setlength{\topmargin}{0 in}
-\setlength{\textheight}{8.5 in}
-
-\renewcommand{\deg}{^{\circ}}
-
-
-\title{GITM Chemical Scheme for Earth \\ \large Version 2.1}
-\author{A.J. Ridley}
-
-\begin{document}
-
-\pagestyle{fancy}
-\lhead[\fancyplain{}{\bfseries\thepage}]{\fancyplain{}{\bfseries\rightmark}}
-\rhead[\fancyplain{}{\bfseries\leftmark}]{\fancyplain{}{\bfseries\thepage}}
-\cfoot{}
-
-%\pagestyle{headings}
-
-\maketitle
-
-\tableofcontents
-
-\clearpage
-
-%Chapter 1
-\chapter{Introduction to GITM}
-\input{intro}
-\label{intro.ch}
-
-%Chapter 2
-\chapter{Chemistry}
-\label{chemistry.ch}
-
-\begin{equation}
-O_2 \rightarrow 2O
-\end{equation}
-EUV dissociation rate.
-
-\begin{equation}
-N_2 \rightarrow 2N
-\end{equation}
-EUV dissociation rate.
-
-\begin{equation}
-O + O + M \rightarrow O_2 + M, \hspace{0.5 in}
-R = 9.59 \times 10^{-46} e^{\frac{480}{T_n}}
-\end{equation}
-
-\begin{equation}
-N_2 \rightarrow N_2^+
-\end{equation}
-EUV Ionization Rate.
-
-\begin{equation}
-N_2 \rightarrow N_2^+
-\end{equation}
-Auroral Ionization Rate.
-
-\begin{equation}
-O_2 \rightarrow O_2^+
-\end{equation}
-EUV Ionization Rate.
-
-\begin{equation}
-O_2 \rightarrow O_2^+
-\end{equation}
-Auroral Ionization Rate.
-
-\begin{equation}
-O(^3P) \rightarrow O^+(^4S)
-\end{equation}
-EUV Ionization Rate.
-
-\begin{equation}
-O(^3P) \rightarrow O^+(^2D)
-\end{equation}
-EUV Ionization Rate.
-
-\begin{equation}
-O(^3P) \rightarrow O^+(^2P)
-\end{equation}
-EUV Ionization Rate.
-
-\begin{equation}
-\begin{split}
-O(^4S) \rightarrow & O^+(^4S) (40\%) \\
-O(^4S) \rightarrow & O^+(^2D) (40\%) \\
-O(^4S) \rightarrow & O^+(^2P) (20\%)
-\end{split}
-\end{equation}
-Auroral Ionization Rate.
-
-\begin{equation}
-\begin{split}
-O^+(^2D) + N_2 \rightarrow & N_2^+ + O + 1.33 eV \\
-R = & 8.0\times 10^{-16}
-\end{split}
-\end{equation}
-
-\begin{equation}
-\begin{split}
-O^+(^2P) + N_2 \rightarrow & N_2^+ + O + 3.02 eV \\
-R = & 4.8\times 10^{-16}
-\end{split}
-\end{equation}
-
-\begin{equation}
-\begin{split}
-N_2^+ + O_2 \rightarrow & O_2^+ + N_2 + 3.53 eV \\
-R = & 5.0\times 10^{-17} \times \bigg(\frac{T_n+T_i}{600}\bigg)^{-0.8}
-\end{split}
-\end{equation}
-
-\begin{equation}
-\begin{split}
-N_2^+ + O \rightarrow & NO^+ + N(^2D) + 0.7 eV \\
-R = & 1.4\times 10^{-16} \times \bigg(\frac{T_n+T_i}{600}\bigg)^{-0.44}
-\end{split}
-\end{equation}
-
-\begin{equation}
-\begin{split}
-N_2^+ + e^- \rightarrow & 2N(^2D) + 1.04 eV \\
-R = & 1.8\times 10^{-13} \times \bigg(\frac{T_e}{300}\bigg)^{-0.39}
-\end{split}
-\end{equation}
-
-\begin{equation}
-\begin{split}
-N_2^+ + O \rightarrow & O^+(^4S) + N_2 + 1.96 eV \\
-R = & 1.4\times 10^{-16} \times \bigg(\frac{T_n+T_i}{600}\bigg)^{-0.44}
-\end{split}
-\end{equation}
-I am not sure that this is correct, since it is the same as 2.8.
-
-\begin{equation}
-\begin{split}
-N_2^2 + NO \rightarrow & NO^+ + N_2 + 6.33 eV \\
-R = & 4.1 \times 10^{-16}
-\end{split}
-\end{equation}
-
-\begin{equation}
-\begin{split}
-O^+(^4S) + O_2 \rightarrow & O_2^+ + O + 1.55 eV \\
-R = & 2.82 \times 10^{-17} \\
- & - 7.740\times 10^{-18}(T_{O2}/300.0) \\
- & + 1.073\times 10^{-18}(T_{O2}/300.0)^2 \\
- & - 5.170\times 10^{-20}(T_{O2}/300.0)^3 \\
- & + 9.650\times 10^{-22}(T_{O2}/300.0)^4
-\end{split}
-\end{equation}
-
-\begin{equation}
-\begin{split}
-O^+(^2D) + O_2 \rightarrow & O_2^+ + 4.865 eV \\
-R = & 7.0 \times 10^{-16}
-\end{split}
-\end{equation}
-
-\begin{equation}
-\begin{split}
-N^+ + O_2 \rightarrow & O_2^+ + N(^4S) + 2.486 \\
-R = & 1.1 \times 10^{-16}
-\end{split}
-\end{equation}
-
-\begin{equation}
-\begin{split}
-N^+ + O_2 \rightarrow & O_2^+ + N(^4D) + 0.1 \\
-R = & 2.0 \times 10^{-16}
-\end{split}
-\end{equation}
-
-\begin{equation}
-\begin{split}
-O_2^+ + e^- \rightarrow & O(^1D) + O(^1D) + 3.06 eV (31\%) \\
-O_2^+ + e^- \rightarrow & O(^3P) + O(^1D) + 3.06 eV (42\%) \\
-O_2^+ + e^- \rightarrow & O(^3P) + O(^3P) + 3.06 eV (22\%) \\
-R = & 2.4\times 10^{-13} \bigg(\frac{T_e}{300}\bigg)^{-0.7}
-\end{split}
-\end{equation}
-
-\begin{equation}
-\begin{split}
-O_2^+ + N(^4S) \rightarrow & NO^+ + O + 4.25 eV \\
-R = & 1.5 \times 10^{-16}
-\end{split}
-\end{equation}
-
-\begin{equation}
-\begin{split}
-O_2^+ + NO \rightarrow & NO^+ + O_2 + 2.813 eV \\
-R = & 4.6 \times 10^{-16}
-\end{split}
-\end{equation}
-
-\begin{equation}
-\begin{split}
-O_2^+ + N_2 \rightarrow & NO^+ + NO + 0.9333 eV \\
-R = & 5.0 \times 10^{-22}
-\end{split}
-\end{equation}
-
-\begin{equation}
-\begin{split}
-O^+(^2D) + O \rightarrow & O^+(^4S) + O(^3P) + 3.31 eV \\
-O^+(^2D) + O \rightarrow & O^+(^4S) + O(^1D) + 1.35 eV \\
-R = & 1.0 \times 10^{-17}
-\end{split}
-\end{equation}
-
-\begin{equation}
-\begin{split}
-O^+(^2D) + e^- \rightarrow & O^+(^4S) + e^- + 3.31 eV \\
-R = & 7.8 \times 10^{-14}\bigg(\frac{T_e}{300}\bigg)^{-0.5}
-\end{split}
-\end{equation}
-
-\begin{equation}
-\begin{split}
-O^+(^2D) + N_2 \rightarrow & O^+(^4S) + N_2 + 3.31 eV \\
-R = & 8.0 \times 10^{-16}
-\end{split}
-\end{equation}
-
-\begin{equation}
-\begin{split}
-O^+(^2P) + O \rightarrow & O^+(^4S) + O + 5.0 eV \\
-R = & 5.2 \times 10^{-17}
-\end{split}
-\end{equation}
-
-\begin{equation}
-\begin{split}
-O^+(^2P) + e^- \rightarrow & O^+(^4S) + e^- + 5.0 eV \\
-R = & 4.0 \times 10^{-14}\bigg(\frac{T_e}{300}\bigg)^{-0.5}
-\end{split}
-\end{equation}
-
-\begin{equation}
-\begin{split}
-O^+(^2P) \rightarrow & O^+(^4S) + 247.0nm\\
-R = & 0.047
-\end{split}
-\end{equation}
-
-\begin{equation}
-\begin{split}
-N^+ O_2 \rightarrow & O^+(^4S) + NO + 2.31 eV\\
-R = & 3.0 \times 10^{-17}
-\end{split}
-\end{equation}
-
-\begin{equation}
-\begin{split}
-O^+(^4S) + N_2 \rightarrow & NO^+ + N(^4S) + 1.10 eV\\
-T_{eff} = & T_i + \frac{M_O}{M_O + M_{N_2}}\times\frac{M_{N_2} - M_b}{3k_b}V_i^2 \\
-M_b = &\frac{M_c}{M_{mc}} \\
-M_c = & \sum_n \frac{M_n\nu_{in}}{M_n + M_O} \\
-M_{mc} = & \sum_n \frac{ \nu_{in}}{M_n + M_O} \\
-R = & 1.533\times 10^{-18} - \\
- & 5.920\times 10^{-19} \bigg(\frac{T_{eff}}{300}\bigg) + \\
- & 8.600\times 10^{-20} \bigg(\frac{T_{eff}}{300}\bigg)^2 (T_{eff} < 1700) \\
-R = & 2.730\times 10^{-18} - \\
- & 1.155\times 10^{-18} \bigg(\frac{T_{eff}}{300}\bigg) + \\
- & 1.483\times 10^{-19} \bigg(\frac{T_{eff}}{300}\bigg)^2 (T_{eff} > 1700)
-\end{split}
-\end{equation}
-If $T_{eff} < 350$, then $T_{eff} = 350$.
-If $T_{eff} > 6000$, then $T_{eff} = 6000$.
-
-\begin{equation}
-\begin{split}
-O^+(^4S) + O_2 \rightarrow & O_2^+ + O + 1.55 eV\\
-R = & 2.820\times 10^{-17} - \\
- & 7.740\times 10^{-18} \bigg(\frac{T_{eff}}{300}\bigg) + \\
- & 1.073\times 10^{-18} \bigg(\frac{T_{eff}}{300}\bigg)^2 - \\
- & 5.170\times 10^{-20} \bigg(\frac{T_{eff}}{300}\bigg)^3 + \\
- & 9.650\times 10^{-22} \bigg(\frac{T_{eff}}{300}\bigg)^4\\
-T_{eff} = & T_i + \frac{M_O}{M_O + M_{O_2}}\times\frac{M_{O_2} - M_b}{3k_b}V_i^2
-\end{split}
-\end{equation}
-If $T_{eff} < 350$, then $T_{eff} = 350$.
-If $T_{eff} > 6000$, then $T_{eff} = 6000$.
-
-\begin{equation}
-\begin{split}
-O^+(^4S) + NO \rightarrow & NO^+ + O + 4.36 eV\\
-R = & 8.36\times 10^{-19} - \\
- & 2.02\times 10^{-19} \bigg(\frac{T_{eff}}{300}\bigg) + \\
- & 6.95\times 10^{-20} \bigg(\frac{T_{eff}}{300}\bigg)^2 (T_{eff} < 1500)\\
-R = & 5.33\times 10^{-19} - \\
- & 1.64\times 10^{-20} \bigg(\frac{T_{eff}}{300}\bigg) + \\
- & 4.72\times 10^{-20} \bigg(\frac{T_{eff}}{300}\bigg)^2 \\
- & 7.05\times 10^{-22} \bigg(\frac{T_{eff}}{300}\bigg)^3 (T_{eff} > 1500) \\
-T_{eff} = & T_i + \frac{M_O}{M_O + M_{NO}}\times\frac{M_{NO} - M_b}{3k_b}V_i^2
-\end{split}
-\end{equation}
-If $T_{eff} < 350$, then $T_{eff} = 350$.
-If $T_{eff} > 6000$, then $T_{eff} = 6000$.
-
-\begin{equation}
-\begin{split}
-O^+(^4S) + N(^2D) \rightarrow & N^+ + O + 1.45 eV\\
-R = & 1.3 \times 10^{-16}
-\end{split}
-\end{equation}
-
-\begin{equation}
-\begin{split}
-O^+(^2P) +e^- \rightarrow & O^+(^2D) + e^- + 1.69 eV\\
-R = & 1.3 \times 10^{-13} \bigg(\frac{T_e}{300}\bigg)^{-0.5} % te3m05
-\end{split}
-\end{equation}
-
-\begin{equation}
-\begin{split}
-O^+(^2P) \rightarrow & O^+(^2D) + 732nm\\
-R = & 0.171
-\end{split}
-\end{equation}
-
-\begin{equation}
-\begin{split}
-O^+(^2D) \rightarrow & O^+(^4S) + 372.6nm\\
-R = & 7.7\times 10^{-5}
-\end{split}
-\end{equation}
-
-\begin{equation}
-\begin{split}
-O^+(^2P) + N_2 \rightarrow & N^+ + NO + 0.70 eV\\
-R = & 1.0 \times 10^{-16}
-\end{split}
-\end{equation}
-
-\begin{equation}
-\begin{split}
-O^+_2 + N(^2D) \rightarrow & N^+ + O_2 \\
-R = & 2.5 \times 10^{-16}
-\end{split}
-\end{equation}
-
-\begin{equation}
-\begin{split}
-O^+(^2P) + N \rightarrow & N^+ + O + 2.7 eV \\
-R = & 1.0 \times 10^{-16}
-\end{split}
-\end{equation}
-
-\begin{equation}
-\begin{split}
-O^+(^2D) + N \rightarrow & N^+ + O + 1.0 eV \\
-R = & 7.5 \times 10^{-17}
-\end{split}
-\end{equation}
-
-\begin{equation}
-\begin{split}
-N^+ + O_2 \rightarrow & NO^+ + O(^1D) + 6.67 eV \\
-R = & 2.6 \times 10^{-16}
-\end{split}
-\end{equation}
-
-\begin{equation}
-\begin{split}
-N^+ + O \rightarrow & O^+(^4S) + N + 0.93 eV \\
-R = & 5.0 \times 10^{-19}
-\end{split}
-\end{equation}
-
-\begin{equation}
-\begin{split}
-NO^+ + e^- \rightarrow & O + N(^2D) + 0.38 eV \\
-R = & 4.0 \times 10^{-13} \bigg(\frac{T_e}{300}\bigg)^{-0.5} % te3m05
-\end{split}
-\end{equation}
-
-\begin{equation}
-\begin{split}
-N(^2D) + e^- \rightarrow & N(^4S) + e^- + 2.38 eV\\
-R = & 5.5 \times 10^{-16} \bigg(\frac{T_e}{300}\bigg)^{-0.5} % te3m05
-\end{split}
-\end{equation}
-
-\begin{equation}
-\begin{split}
-N(^2D) + O \rightarrow & N(^4S) + O(^3P) + 2.38 eV (90\%)\\
-N(^2D) + O \rightarrow & N(^4S) + O(^1D) + 0.42 eV (10\%)\\
-R = & 2.0 \times 10^{-18}
-\end{split}
-\end{equation}
-
-\begin{equation}
-\begin{split}
-N(^2D) \rightarrow & N(^4S) + 520nm \\
-R = & 1.06 \times 10^{-5}
-\end{split}
-\end{equation}
-
-\begin{equation}
-\begin{split}
-NO \rightarrow & N(^4S) + O \\
-R = & 4.5 \times 10^{-6} e^{(-1\times 10^{-8}([O_2]\times 10^{-6})^{0.38})}
-\end{split}
-\end{equation}
-
-\begin{equation}
-\begin{split}
-N(^4S) + O_2 \rightarrow & NO + O + 1.385 eV \\
-R = & 4.4 \times 10^{-18} e^{-\frac{3220}{T_n}}
-\end{split}
-\end{equation}
-
-\begin{equation}
-\begin{split}
-N(^4S) + NO \rightarrow & N_2 + O + 3.25 eV\\
-R = & 1.5 \times 10^{-18} \sqrt{T_n}
-\end{split}
-\end{equation}
-
-\begin{equation}
-\begin{split}
-N(^2P) \rightarrow & N(^2D) + 1040nm\\
-R = & 7.9 \times 10^{-2}
-\end{split}
-\end{equation}
-
-\begin{equation}
-\begin{split}
-N(^2D) + O_2 \rightarrow & NO + O(^3P) + 3.76 eV (90\%)\\
-N(^2D) + O_2 \rightarrow & NO + O(^1D) + 1.80 eV (10\%)\\
-R = & 6.2 \times 10^{-18} \frac{T_n}{300}
-\end{split}
-\end{equation}
-
-\begin{equation}
-\begin{split}
-N(^2D) + NO \rightarrow & N_2 + O + 5.63 eV\\
-R = & 7.0 \times 10^{-17}
-\end{split}
-\end{equation}
-
-\begin{equation}
-\begin{split}
-O(^1D) \rightarrow & O(^3P) + 630nm\\
-R = & 0.0071
-\end{split}
-\end{equation}
-
-\begin{equation}
-\begin{split}
-O(^1D) \rightarrow & O(^3P) + 636.4nm\\
-R = & 0.0022
-\end{split}
-\end{equation}
-I don't understand this...
-
-
-\begin{equation}
-\begin{split}
-O(^1D) + e^- \rightarrow & O(^3P) + e^- + 1.96 eV\\
-R = & 2.6 \times 10^{-17} T_e^(0.5)e^(-22740/T_e)
-\end{split}
-\end{equation}
-
-\begin{equation}
-\begin{split}
-O(^1D) + N_2 \rightarrow & O(^3P) + N_2 + 1.96 eV\\
-R = & 2.3 \times 10^{-17}
-\end{split}
-\end{equation}
-
-\begin{equation}
-\begin{split}
-O(^1D) + O_2 \rightarrow & O(^3P) + O_2 + 1.96 eV\\
-R = & 2.9 \times 10^{-17} e^{\frac{67.5}{T_n}}
-\end{split}
-\end{equation}
-
-\begin{equation}
-\begin{split}
-O(^1D) + O(^3P) \rightarrow & 2O(^3P) + 1.96 eV\\
-R = & 8.0 \times 10^{-18}
-\end{split}
-\end{equation}
-
-\begin{equation}
-\begin{split}
-NO \rightarrow & NO^+ + e^-\\
-R = & 5.88 \times 10^{-7}(1+0.2(F10.7-65)/100)e^F\cos(SZA)\\
-F = & (\frac{[O_2]}{1\times 10^{6}})^{0.8855}
-\end{split}
-\end{equation}
-
-
-%Bibliography
-\clearpage
-\addcontentsline{toc}{chapter}{Bibliography}
-\bibliographystyle{chicagoa}
-\bibliography{gitm}
-
-\end{document}
diff --git a/srcDoc/common_inputs.md b/srcDoc/common_inputs.md
new file mode 100644
index 00000000..5848f484
--- /dev/null
+++ b/srcDoc/common_inputs.md
@@ -0,0 +1,429 @@
+# Common Inputs {#indices.sec}
+
+This only touches on the most frequently changed input options. For a full
+reference of all available inputs, please see [All Inputs](set_inputs.md)
+
+## Time
+
+The start time and end time of a GITM simulation can be set using the following commands (as an example):
+
+```bash
+#TIMESTART
+2002 year
+12 month
+21 day
+00 hour
+00 minute
+00 second
+
+#TIMEEND
+2002 year
+12 month
+21 day
+00 hour
+05 minute
+00 second
+```
+
+Hopefully these are obvious what they are.
+
+## Setting the grid
+
+GITM can simulate the whole planet or a portion of the planet. Unless you know what you
+are doing, I would stick to modeling the whole planet. This can be done with the
+following command (as an example):
+
+```bash
+#GRID
+2 number of blocks in longitude
+2 number of blocks in latitude
+-90.0 minimum latitude to model
+90.0 maximum latitude to model
+0.0 longitude start to model (set to 0.0 for whole Earth)
+0.0 longitude end to model (set to 0.0 for whole Earth)
+```
+The first two numbers control the resolution. The higher these numbers, the finer the
+resolution, but the more processors you will need - you need one processor for each
+block that you asked for (2 x 2 = 4 blocks / processors). For example, if you wanted to
+run at 5 degrees by 5 degrees reolution, the following could be used:
+
+```bash
+#GRID
+8 number of blocks in longitude
+4 number of blocks in latitude
+-90.0 minimum latitude to model
+90.0 maximum latitude to model
+0.0 longitude start to model (set to 0.0 for whole Earth)
+0.0 longitude end to model (set to 0.0 for whole Earth)
+```
+and 32 processors would be needed.
+
+There is a lot more to learn here, so we have written a whole section on this. [See this grid description for more.](internals/grid.md).
+
+
+## Saving output files
+
+GITM outputs a wide variety of output files. [There is a whole section that describes them.](outputs.md)
+
+Output files are controlled with the `#SAVEPLOTS` command.
+
+The first line says how often to output restart files, which we will set aside for a
+bit. It is ok to leave this as 2 hours (7200 - these are all specified in seconds),
+unless you know what you are doing.
+
+The second line tells GITM how many types of output files you want.
+
+The following lines tell GITM what type of file output you want and how often you want
+them. The most common type of output is 3DALL, which includes all ion and neutral states
+(densities, temperatures, velocities).
+
+An example:
+```bash
+#SAVEPLOTS
+7200.0 dt for writing restart files
+1 how many output files do you want
+3DALL first output style
+900.0 dt for output (one every 15 min)
+```
+
+This will output restart files every 2 hours (this can be ignored) and 3DALL files every
+15 minutes. 2 hours is from 7200.0 seconds, and 15 minutes is from 900.0 seconds.
+
+Another example:
+```bash
+#SAVEPLOTS
+7200.0 dt for writing restart files
+3 how many output files do you want
+3DALL first output style
+900.0 dt for output (one every 15 min)
+2DGEL second output style
+300.0 dt for output (one every 15 min)
+3DTHM third output style
+900.0 dt for output (one every 15 min)
+```
+
+2DGEL files output things like the electric potential and auroral precipitation on the
+geographic grid at the top of the model. 3DTHM files are thermodynamic variables such
+as heating and cooling rates.
+
+!!!note
+ All of the auxiliary input (data) files can (and should) be kept in the same run directory
+ as the linked GITM executable and the `UAM.in` file. Otherwise, the path should be
+ specified in the UAM.in file relative to the run directory.
+
+## IMF and Solar Wind {#imf.sec}
+
+This file controls the high-latitude electric field and aurora when
+using models that depend on the solar wind and interplanetary magnetic
+field (IMF). It allows GITM to dynamically control these quantities. You
+can create either realistic IMF files or hypothetical ones.
+
+A script is provided to automatically download these files, and can be called
+using the `srcPython/omni_download_write_swmf.py` python file.
+
+Here is an example file:
+
+ This file was created by Aaron Ridley to do some wicked cool science thing.
+
+ The format is:
+ Year MM DD HH Mi SS mS Bx By Bz Vx Vy Vz N T
+
+ Year=year
+ MM = Month
+ DD = Day
+ HH = Hour
+ Mi = Minute
+ SS = Second
+ mS = Millisecond
+ Bx = IMF Bx GSM Component (nT)
+ By = IMF By GSM Component (nT)
+ Bz = IMF Bz GSM Component (nT)
+ Vx = Solar Wind Vx (km/s)
+ Vy = Solar Wind Vy (km/s)
+ Vz = Solar Wind Vz (km/s)
+ N = Solar Wind Density (/cm3)
+ T = Solar Wind Temperature (K)
+
+ #DELAY
+ 900.0
+
+ #START
+ 2000 3 20 2 53 0 0 0.0 0.0 2.0 -400.0 0.0 0.0 5.0 50000.0
+ 2000 3 20 2 54 0 0 0.0 0.0 2.0 -400.0 0.0 0.0 5.0 50000.0
+ 2000 3 20 2 55 0 0 0.0 0.0 2.0 -400.0 0.0 0.0 5.0 50000.0
+ 2000 3 20 2 56 0 0 0.0 0.0 2.0 -400.0 0.0 0.0 5.0 50000.0
+ 2000 3 20 2 57 0 0 0.0 0.0 2.0 -400.0 0.0 0.0 5.0 50000.0
+ 2000 3 20 2 58 0 0 0.0 0.0 2.0 -400.0 0.0 0.0 5.0 50000.0
+ 2000 3 20 2 59 0 0 0.0 0.0 2.0 -400.0 0.0 0.0 5.0 50000.0
+ 2000 3 20 3 0 0 0 0.0 0.0 -2.0 -400.0 0.0 0.0 5.0 50000.0
+ 2000 3 20 3 1 0 0 0.0 0.0 -2.0 -400.0 0.0 0.0 5.0 50000.0
+ 2000 3 20 3 2 0 0 0.0 0.0 -2.0 -400.0 0.0 0.0 5.0 50000.0
+ 2000 3 20 3 3 0 0 0.0 0.0 -2.0 -400.0 0.0 0.0 5.0 50000.0
+ 2000 3 20 3 4 0 0 0.0 0.0 -2.0 -400.0 0.0 0.0 5.0 50000.0
+
+This file is provided to GITM by setting the input:
+
+```bash
+#MHD_INDICES
+imf_file_name.dat
+```
+
+
+## SME Indices
+
+To use models such as FTA[^1] to drive the aurora, GITM must be provided with Auroral
+Electrojet (AE) indices. Normally this is from SuperMag (hence the name "SME":
+SuperMag auroral Electrojet), but any source may be used.
+
+[^1]: Wu, C., Ridley, A. J., DeJong, A. D., & Paxton, L. J. (2021). FTA: A Feature Tracking Empirical Model Of Auroral Precipitation. Space Weather, 19, e2020SW002629. .
+
+These files are normally of the format:
+
+ File created by python code using SuperMAGGetIndices
+
+ ============================================================
+
+ 2002 12 21 00 00 00 616.74 -354.47 262.26
+ 2002 12 21 00 01 00 623.75 -354.72 269.03
+ 2002 12 21 00 02 00 617.18 -349.28 267.90
+ 2002 12 21 00 03 00 633.56 -350.01 283.55
+ 2002 12 21 00 04 00 664.55 -357.88 306.68
+
+A python routine to download these files over a given date range can be found
+in `srcPython/supermag_download_ae.py`.
+
+The corresponding section in `UAM.in` is read as:
+```bash
+#SME_INDICES
+ae_file-name.dat ae file name
+none onset file
+T use AE for HP
+F don't automatically incorporate hemispheric asymmetries
+```
+
+The lines following the AE file-name are for the AL-onset file. This can be set to
+`none` if you do not have one or do not know what that means. The next line tells GITM
+whether to derive HP (Hemispheric Power) from AE or to use a NOAA HPI file (if one is
+required). Since production of hemispheric power was stopped by NOAA in 2013 (the world
+has moved on), it is best to use the HP derived from AE.
+
+Even if AE is not required, it is recommended to provide a SME file as input to
+derive HP, as it is often more representative of geomagnetic conditions than the NOAA
+HPI (maybe this is why they stopped producing it). The formula to calculate hemispheric
+power (HP) from AE is taken from (Wu et al., 2021)[^1] and is given as:
+
+```math
+\begin{align}
+HemisphericPower = 0.102 * AE + 8.953
+\end{align}
+```
+
+*[HP]: Hemispheric Power
+
+## Hemispheric Power {#hp.sec}
+
+The hemispheric power files describe the dynamic variation of the auroral power going
+into each hemisphere. Models such as FRE[^FRE] use the Hemispheric Power to determine
+which level of the model it should use. It is recommended to not use the NOAA provided
+HP files, but to use the AE derived HP, as described above. But, if you are a purist,
+the National Oceanic and Atmospheric Administration (NOAA) provides these hemispheric
+power files for public use online at .
+There are two types of formats used for hemispheric power files (due to a change in the
+NOAA output format in 2007). Both file formats can be used by GITM, and are shown in the
+examples below.
+
+[^FRE]: Fuller-Rowell, T. J., and D. S. Evans (1987), Height-integrated Pedersen
+ and Hall conductivity patterns inferred from the TIROS-NOAA satellite data,
+ J. Geophys. Res., 92(A7), 7606–7618,
+ doi:[10.1029/JA092iA07p07606](https://doi.org/10.1029/JA092iA07p07606).
+
+!!! tip
+ GITM can read a NOAA HPI file, however the recommended way to provide
+ hemispheric power is to have GITM derive HPI from the AE-index. Seriously.
+
+ See [SME Indices](#sme-indices) for more information.
+
+Example file 1 for data prior to 2007:
+
+ # Prepared by the U.S. Dept. of Commerce, NOAA, Space Environment Center.
+ # Please send comments and suggestions to sec@sec.noaa.gov
+ #
+ # Source: NOAA POES (Whatever is aloft)
+ # Units: gigawatts
+
+ # Format:
+
+ # The first line of data contains the four-digit year of the data.
+ # Each following line is formatted as in this example:
+
+ # NOAA-12(S) 10031 9.0 4 .914
+
+ # Please note that if the first line of data in the file has a
+ # day-of-year of 365 (or 366) and a HHMM of greater than 2300,
+ # that polar pass started at the end of the previous year and
+ # ended on day-of-year 001 of the current year.
+
+ # A7 NOAA POES Satellite number
+ # A3 (S) or (N) - hemisphere
+ # I3 Day of year
+ # I4 UT hour and minute
+ # F8.1 Estimated Hemispheric Power in gigawatts
+ # I3 Hemispheric Power Index (activity level)
+ # F8.3 Normalizing factor
+
+ 2000
+ NOAA-15(N) 10023 35.5 7 1.085
+ NOAA-14(S) 10044 25.3 7 .843
+ NOAA-15(S) 10114 29.0 7 .676
+ NOAA-14(N) 10135 108.7 10 1.682
+ NOAA-15(N) 10204 36.4 7 1.311
+ .
+ .
+ .
+
+Example file 2 for data in and after 2007:
+
+ :Data_list: power_2010.txt
+ :Created: Sun Jan 2 10:12:58 UTC 2011
+
+
+ # Prepared by the U.S. Dept. of Commerce, NOAA, Space Environment Center.
+ # Please send comments and suggestions to sec@sec.noaa.gov
+ #
+ # Source: NOAA POES (Whatever is aloft)
+ # Units: gigawatts
+
+ # Format:
+
+ # Each line is formatted as in this example:
+
+ # 2006-09-05 00:54:25 NOAA-16 (S) 7 29.67 0.82
+
+ # A19 Date and UT at the center of the polar pass as YYYY-MM-DD hh:mm:ss
+ # 1X (Space)
+ # A7 NOAA POES Satellite number
+ # 1X (Space)
+ # A3 (S) or (N) - hemisphere
+ # I3 Hemispheric Power Index (activity level)
+ # F7.2 Estimated Hemispheric Power in gigawatts
+ # F7.2 Normalizing factor
+
+ 2010-01-01 00:14:37 NOAA-17 (N) 1 1.45 1.16
+ 2010-01-01 00:44:33 NOAA-19 (N) 1 1.45 1.17
+ .
+ .
+ .
+
+The file type is automatically inferred. To provide an HPI file, use:
+
+```bash
+#NOAAHPI_INDICES
+hemi-power-file.txt
+```
+
+
+## Solar Irradiance {#solar_irradiance.sec}
+
+To provide GITM with realistic solar irradiance, the solar EUV must be
+specified. There are two pathways for doing this. The easiest is to simply specify the F10.7. GITM then runs some EUV empirical models of the irradiance (such as EUVAC), and uses these results to drive GITM. The F10.7 is provided with GITM, so you can just point GITM to this file and be done:
+```bash
+#NGDC_INDICES
+UA/DataIn/f107.txt
+```
+It should be noted that MSIS also needs F10.7, so really this command should be included in every UAM.in file.
+
+In addition, GITM can use the Flare Irradiance Spectrum Model specification of the EUV flux. Daily values of FISM can be used unless you are doing a flare study. These daily values are included with GITM and can be found in UA/DataIn/FISM. As an example, a yearly file can be used with the command (for example):
+```bash
+#EUV_DATA
+T Use FISM solar flux data
+UA/DataIn/FISM/fismflux_daily_2002.dat Filename for specific year
+```
+
+An example from the FISM model is shown below.
+
+ #START
+ 2009 3 20 0 0 0 0.00389548 0.00235693
+ 0.00127776 0.000907677 0.000652528 0.000372993 0.000250124 0.000194781
+ 0.000389686 0.000118650 0.00642058 0.00618358 0.000133490 7.67560e-05
+ 7.80045e-05 0.000145722 5.92577e-05 5.95070e-05 0.000102437 6.48526e-05
+ 8.94509e-05 0.000101928 5.94333e-05 5.36012e-05 1.51744e-05 1.10265e-05
+ 1.26937e-05 2.16591e-05 9.57055e-06 1.82608e-05 7.07992e-05 2.55451e-05
+ 1.12451e-05 6.89255e-05 3.03882e-05 2.33862e-05 2.98026e-05 4.44682e-05
+ 1.50847e-05 3.00909e-05 8.18379e-05 3.52176e-05 0.000416491 0.000269080
+ 0.000269080 0.000275734 6.60872e-05 4.46671e-05 0.000220697 0.000512933
+ 3.85239e-05 9.30928e-05 2.71239e-05 1.23011e-05 1.05722e-05 9.30876e-06
+ 7.08442e-07 3.54221e-07 1.77110e-07
+ 2009 3 20 0 1 0 0.00389548 0.00235693
+ 0.00127776 0.000907677 0.000652528 0.000372993 0.000250124 0.000194781
+ 0.000389686 0.000118650 0.00642058 0.00618358 0.000133490 7.67560e-05
+ 7.80045e-05 0.000145722 5.92577e-05 5.95070e-05 0.000102437 6.48526e-05
+ 8.94509e-05 0.000101928 5.94333e-05 5.36012e-05 1.51744e-05 1.10265e-05
+ 1.26937e-05 2.16591e-05 9.57055e-06 1.82608e-05 7.07992e-05 2.55451e-05
+ 1.12451e-05 6.89255e-05 3.03882e-05 2.33862e-05 2.98026e-05 4.44682e-05
+ 1.50847e-05 3.00909e-05 8.18379e-05 3.52176e-05 0.000416491 0.000269080
+ 0.000269080 0.000275734 6.60872e-05 4.46671e-05 0.000220697 0.000512933
+ 3.85239e-05 9.30928e-05 2.71239e-05 1.23011e-05 1.05722e-05 9.30876e-06
+ 7.08442e-07 3.54221e-07 1.77110e-07
+ .
+ .
+ .
+
+If you want to create your own files, there is a code in srcPython to download and produce the FISM files. You can use this python code to download daily values or flare values (although the flare files are huge compared to the yearly files).
+
+## Satellites {#sat_aux.sec}
+
+
+
+GITM can provide output data at a list of times and locations using the
+SATELLITE input option. Although this is designed to output data along
+a satellite orbit, any list of locations may be used. There is currently
+no routine to create a satellite input file, but the format is simple
+and may be easily constructed from a satellite ASCII data file using
+awk or Python. Here is a sample satellite input file:
+
+ year mm dd hh mm ss msec long lat alt
+ #START
+ 2002 4 16 23 34 25 0 299.16 -2.21 0.00
+ 2002 4 16 23 34 25 0 293.63 -1.21 0.00
+ 2002 4 16 23 34 25 0 291.28 -0.75 0.00
+ 2002 4 16 23 34 25 0 289.83 -0.45 0.00
+ 2002 4 16 23 34 25 0 288.79 -0.21 0.00
+ 2002 4 16 23 34 25 0 287.98 -0.01 0.00
+ 2002 4 16 23 34 25 0 287.32 0.16 0.00
+ 2002 4 16 23 34 25 0 286.76 0.31 0.00
+ 2002 4 16 23 34 25 0 286.26 0.46 0.00
+ 2002 4 16 23 34 25 0 285.81 0.60 0.00
+ 2002 4 16 23 34 25 0 285.39 0.74 0.00
+
+Note that the satellite output type is not specified in this sample file. This
+is because altitude entry doesn't matter at this time, GITM ignores the altitude
+and outputs altitudinal profiles of the atmospheric characteristics at each
+geographic location and universal time. Although millisecond accuracy is
+provided, GITM should not be output at a resolution smaller than 1 second. The
+temporal resolution in the satellite file does not need to match the output
+resolution.
+
+Because GITM by default outputs one file for every output time, if you use a satellite
+file, it produces a LOT of files.
+
+The types of outputs are specified in the `#SATELLITES` section of the UAM.in file. The
+number of satellites must be speficied along with the path to the locations, output type
+& cadence for each file. For example, if we want to output 3DALL files for one satellite
+every 2 minutes, we would use:
+
+ #SATELLITES
+ 1 nSats
+ satfile1.txt sat file name
+ 3DALL output type
+ 120.0 output cadence, in seconds
+
+Or for two satellites, every 1 minute:
+
+ #SATELLITES
+ 2 nSats
+ satfile1.txt sat file name
+ 3DALL output type
+ 60.0 output cadence, in seconds
+ satfile2.txt sat file name
+ 3DALL output type
+ 60.0 output cadence, in seconds
diff --git a/srcDoc/dev_team.md b/srcDoc/dev_team.md
deleted file mode 100644
index 91ee651d..00000000
--- a/srcDoc/dev_team.md
+++ /dev/null
@@ -1,42 +0,0 @@
-GITM Development Team
-=======================
-
-## Active Developers:
-
-Aaron Ridley (Source terms, Electrodynamics) - UM
-
-Jared Bell (Solvers) - NASA GSFC
-
-Brandon Ponder (Venus) - UM
-
-Dave Pawlowski (Mars, FISM) - EMU
-
-Garima Malhotra (Lower boundary) - NOAA/CU
-
-Xing Ming (Wave Perturbations, Localized Electrodynamics) - JPL
-
-Doga Ozturk (Localized Electrodynamics) - UAF
-
-Chen Wu (Lower boundary, Eclipse) - UM
-
-Angeline Burrell (python code and random things) - NRL
-
-Meghan Burleigh (Coupling to SWMF) - NRL
-
-Leonardo Regoli (Coupling to SWMF, Mars)
-
-## Past Developers:
-
-Jie Zhu (Ti + Te calculation) - Microsoft
-
-Xianjing Liu (Helium at Earth)
-
-Alexey Morozov (Coupling with DART)
-
-Darren De Zeeuw (Field-line integrator) - UM
-
-Yue Deng (Many aspects of the original code) - UTA
-
-Gabor Toth (Rusanov solvers) - UM
-
-Robert Oehmke (MPI / message passing) - NCAR?
\ No newline at end of file
diff --git a/srcDoc/devstuff/devhome.md b/srcDoc/devstuff/devhome.md
new file mode 100644
index 00000000..c8d6da18
--- /dev/null
+++ b/srcDoc/devstuff/devhome.md
@@ -0,0 +1,55 @@
+
+# Developers
+
+Here is some information which may be useful to developers.
+
+## Documentation Notes
+
+Some notes on the doc site:
+
+- See the [markdown style guide](markdown_ref.md) for info on what features are
+ available.
+- The documentation is organized according to a table of contents listed in
+ `GITM/mkdocs.yml`. So, to add new pages or organize things differently, look
+ there.
+- Within `mkdocs.yml`, paths are specified relative to `site_home` (cuttently
+ set to `srcDoc/`)
+- `index.md` is the "home page". The rest should be self-explanatory enough.
+
+Writing docs can be tricky. Formatting is sometimes not what you would expect.
+For example, we *need* four spaces to indent something, not just two. I tried
+changing this & couldn't!
+
+You can use Python to locally host the doc site which will auto-update when any
+files are changed. One command to configure, one to host. When first starting,
+either create a vitrual/conda environment for the docs, or don't, and from the
+root of the repo run: `pip install -r srcDoc/requirements.txt`. To actually host
+the docs, run (from `GITM/`):
+
+```bash
+mkdocs serve
+```
+
+And it should be auto-magic. open the link in your browser.
+
+## Versioning
+
+GITM now builds the code version into the executable automatically. This is sourced
+from `src/.version` within `src/ModGITMVersion.f90`.
+
+The version file is created when compiling, and checked every time the code is compiled.
+If the number of files that are different from HEAD changes, the version is updated.
+In practice this means that if the number of lines output from
+`git status --porcelain` changes, the version is updated.
+
+The version has information on the last commit date, the branch, the last commit hash,
+and the number of files changed since the last commit. This should provide enough
+information to track down any kinds of bugs or to ensure that results can be traced
+back to a certain state of the code.
+
+The file is created in the last step of compiling by the shell script
+`share/Scripts/Makeversion.sh`.
+
+If the `.git` folder does not exist (so the code was downloaded as a .zip from GitHub),
+the version info is taken from `version.def` at the root folder. This should be updated
+whenever the code is released.
diff --git a/srcDoc/devstuff/markdown_ref.md b/srcDoc/devstuff/markdown_ref.md
new file mode 100644
index 00000000..78b8ae1a
--- /dev/null
+++ b/srcDoc/devstuff/markdown_ref.md
@@ -0,0 +1,314 @@
+# Markdown Style Reference
+
+This document is not a markdown tutorial. It's merely a guide to the features
+available on this site. GITM's ReadTheDocs site is built using MkDocs and a
+number of plugins. This takes the (relatively) vanilla Markdown of MkDocs and
+extends its functionality.
+
+To develop locally, one can simply install the Python requirements in
+`srcDoc/requirements.txt` and then spin up a MkDocs server, previewing the
+documentation live! It's very useful.
+
+```bash
+pip install -r srcDoc/requirements.txt
+mkdocs serve
+```
+
+---
+
+Table of contents can be inserted with
+
+```markdown
+[TOC]
+```
+
+For example (ensuring there are newlines before & after):
+
+[TOC]
+
+## General Syntax
+
+Markdown can put *italics* and **bold** in really easily by surrounding the text
+with one and two asterisks \*, respectively (i.e. `*italics*` and `**bold**`).
+There are \*escape\* characters available too; use a backslash before an
+asterisk to have it shown `\*`. For **bold** and **italics**, use three
+***asterisks***.
+
+For a new paragraph, use two line breaks. otherwise it is the same paragraph.
+
+> we can note that something should be indented with `>` at the beginning of a
+> line.
+
+To mark something for ~~deletion~~, use two tilde `~~`, and to mark for
+++insertion++, use two pluses `++`.
+
+Headers work as one would expect; use a single # for header one, and more #'s
+for each sub-level. Horizontal lines can be made with ---, surrounded by
+newlines before & after.
+
+---
+
+### Lists
+
+Lists can be:
+
+1. Ordered
+1. Like this one
+5. Which is numbered automatically.
+ - automatic numbering is nice for ordered lists. Edits can be made without
+ the need to go back and change every single entry.
+ - we can nest lists, and switch between ordered/unordered.
+
+ ```python
+ print("hello world!")
+ ```
+
+6. The list should be smart enough to resume counting after we take a break to
+ do something, as long as it is indented
+
+### Code
+
+Code can be shown either inline: `print("hello world")`, or in a block:
+
+````md
+```python
+print("hello world")
+```
+````
+
+Code blocks' syntax (highlighting) can be set after the three backticks. The
+above block uses python syntax.
+
+Additionally, one can **include** the three backticks in a code block by
+surrounding it with a different number of backticks. As a ridiculous example:
+
+`````md
+````
+```python
+print("hello world!")
+```
+````
+`````
+
+### Links
+
+Links are specified with `[link text](the_link)`. The first option is the text
+to display, the second is the actual link. For example, [here is the link to the
+GITM repository](https:github.com/GITMCode/GITM.git). It is ok to have
+linebreaks within the link text.
+
+## More Complex Syntax
+
+### Comments, Abbreviations
+
+Comments use HTML syntax: ``
+
+Define an abbreviation with: `*[TEXT]: Definition`. Hover over HTML to see its
+definition.
+
+
+*[HTML]: Hypertext Markup Language
+
+That abbreviation will stick around across the entire page, as it is HTML.
+
+### Footnotes
+
+We can add a footnote, such as[^1]. Footnotes have a label, specified with
+`[^2]`, and that label can be anything we want, for example [^longerfootnote].
+
+[^1]: This is footnote content.
+
+Footnotes are automatically numbered. One can place the footnote definition
+anywhere in the document[^bottom]. The footnotes do not need to be defined in
+order as long as their labels are unique (i.e. we can put anything we want for a
+label, as long as it is unique, `[^aHJpxms]`, for example)[^notbottom].
+
+[^notbottom]: This footnote is defined out of order to when it is first
+ referenced. It affects the numbers given to other footnotes.
+
+[^longerfootnote]:
+
+ The links back to the text are handled automatically. Hover over the above
+ text if you do not see an arrow.
+
+ Multi-line comments are the same as body text - they need two newlines. To
+ continue writing the footnote, text must be indented with 4 spaces or a tab.
+
+ These descriptions can be placed anywhere within the document.
+
+Footnotes are great for citations!
+
+### References {gohere}
+
+We can add references to any header level. Links are automatically created, but
+we can make out own by adding `{#refname}` to the header. If we do not add
+anything, the name for `## a subheader section` would be `#a-subheader-section.`
+
+Then later we can point to it like any other hyperlink. For example,
+`[this link will go to the above subsection](#a-subheader-section)`.
+Or, a real one:
+[this link points to the More Complex Syntax](#more-complex-syntax) sub-header.
+
+## Admonitions
+
+Admonitions are these fancy boxes. See [here](https://squidfunk.github.io/mkdocs-material/reference/admonitions/#customization) for more information
+
+!!! tip
+ Our theme (material) supports some non-standard admonitions
+
+!!! warning
+ Here's a warning. new lines need two breaks.
+
+ Here's how to put multiple lines in an admonition
+
+!!! danger
+ This is for something very serious
+
+!!! bug "custom label"
+ notes can be given custom labels!
+
+ This uses the `bug` callout
+
+!!! OnlyTheFirstWordFromTheLabel is shown
+ Stick to using `!!!note "multi word label"` when possible.
+
+## Math
+
+Math can be done inline, differing from LaTex in that we need to use $\` and \`$
+to surround the math. For example, $`\pi \approx \frac{22}{7}`$ is an equation
+*inline*. For equation blocks we need to surround it with backticks, like so:
+
+
+````
+```math
+% comments can be placed in math mode
+\begin{align}
+ E=mc^2
+\end{align}
+```
+````
+
+Which produces:
+
+```math
+% comments can be placed in math mode
+\begin{align}
+ E=mc^2
+\end{align}
+```
+
+For numbered equations, use `\begin{align}` and `\end{align}` surrounding the
+equation. These are consistently numbered throughout the document.
+
+```math
+\pi \approx \frac{22}{7} = \mathbf{3.14}28...
+```
+
+```math
+\begin{align}
+ p(v_i=1|\mathbf{h}) & = \sigma\left(\sum_j w_{ij}h_j + b_i\right) \\
+ p(h_j=1|\mathbf{v}) & = \sigma\left(\sum_i w_{ij}v_i + c_j\right)
+\end{align}
+```
+
+## Images
+
+### Figures
+
+Insert images with ``. The caption will
+appear below the image, for example:
+
+
+
+This figure was made with the code:
+
+```md
+
+```
+
+Alternatively, you may not wish to write out the path inline if it may change
+later. Having all the paths to figures in one place will make moving things
+around later much easier. Figures can be made with a *reference*, then specify the
+path later, using:
+
+```md
+Some terrific, fantastic documentation.
+
+![Description of something cool.][ref1]
+
+More splendid documentation.
+
+[ref1]: /path/to/image
+```
+
+To forgo a caption entirely (they aren't even that useful), just do not include
+it in the ``. For example:
+
+
+
+See? No caption! It is possibly to define a new style for figures, and to
+uniquely number them, but it is probably not worth doing.
+
+### Flowcharts
+
+I'm including this because it's cool, but may not be too useful. We can utilize
+something called [Mermaid](https://mermaid.js.org/) to make flowcharts with
+relatively simple syntax. Some helpful links to get started would be this
+[beginner's guide](https://mermaid.js.org/intro/getting-started.html) and the
+[live editor](https://mermaid.live/), which allows for live development of a
+mermaid chart.
+
+Charts are put in automatically.
+
+```mermaid
+graph TD
+ A[Input] --> B[Think]
+ B --> C[Outcome One]
+ B --> D[Outcome Two]
+```
+
+The above example uses:
+
+````md
+
+```mermaid
+graph TD
+ A[Input] --> B[Think]
+ B --> C[Outcome One]
+ B --> D[Outcome Two]
+```
+````
+
+Labels can be added to the arrows. The following code has a simple example:
+
+````md
+``` mermaid
+graph LR
+ A[Start] --> B{Error?};
+ B -->|Yes| C[Hmm...];
+ C --> D[Debug];
+ D --> B;
+ B ---->|No| E[Yay!];
+```
+````
+
+
+``` mermaid
+graph LR
+ A[Start] --> B{Error?};
+ B -->|Yes| C[Hmm...];
+ C --> D[Debug];
+ D --> B;
+ B ---->|No| E[Yay!];
+```
+
+!!! note
+ The chart's direction is set with `TD` (top-down) and `LR` (left-right).
+
+ > More complex charts are available. Check the Mermaid documentation for
+ examples!
+
+---
+
+[^bottom]: This footnote is defined at the bottom of the document. Probably not
+ the best for making edits!
diff --git a/srcDoc/devstuff/outline.md b/srcDoc/devstuff/outline.md
new file mode 100644
index 00000000..b5901548
--- /dev/null
+++ b/srcDoc/devstuff/outline.md
@@ -0,0 +1,597 @@
+`main program` in **main.f90**
+
+- `init_mpi` in file **init_mpi.f90**
+
+ - `MPI_INIT`
+
+ - `MPI_COMM_RANK`
+
+ - `MPI_COMM_SIZE`
+
+- `start_timing` in file **timing.f90**
+
+- `delete_stop` in file **stop_file.f90**
+
+ - `report` in file library.f90
+
+- `init_planet` in file **ModEarth.f90**
+
+ - `time_int_to_real` in file time_routines.f90
+
+- `set_defaults` in file **ModInputs.f90**
+
+ - `set_strings` in file ModInputs.f90
+
+ - `time_int_to_real` in file time_routines.f90
+
+ - `set_planet_defaults` in file Earth.f90
+
+- `read_inputs` in file **read_inputs.f90**
+
+ - `report` in file library.f90
+
+ - `stop_gitm` in file library.f90
+
+ - `stop_gitm` in file library.f90
+
+ - `stop_gitm` in file library.f90
+
+ - `MPI_Bcast`
+
+ - `stop_gitm` in file library.f90
+
+ - `MPI_Bcast`
+
+ - `stop_gitm` in file library.f90
+
+- `set_inputs` in file **set_inputs.f90**
+
+ - `report` in file library.f90
+
+ - `read_in_int` in file set_inputs.f90
+
+ - `time_int_to_real` in file time_routines.f90
+
+ - `time_real_to_int` in file time_routines.f90
+
+ - `fix_vernal_time` in file set_inputs.f90
+
+ - `read_in_int` in file set_inputs.f90
+
+ - `time_int_to_real` in file time_routines.f90
+
+ - `read_in_time` in file set_inputs.f90
+
+ - `read_in_int` in file set_inputs.f90
+
+ - `read_in_real` in file set_inputs.f90
+
+ - `read_in_logical` in file set_inputs.f90
+
+ - `read_in_real` in file set_inputs.f90
+
+ - `read_in_real` in file set_inputs.f90
+
+ - `time_real_to_int` in file time_routines.f90
+
+ - `read_in_real` in file set_inputs.f90
+
+ - `read_in_real` in file set_inputs.f90
+
+ - `IO_set_f107_single`
+
+ - `IO_set_f107a_single`
+
+ - `read_in_logical` in file set_inputs.f90
+
+ - `read_in_logical` in file set_inputs.f90
+
+ - `read_in_real` in file set_inputs.f90
+
+ - `read_in_real` in file set_inputs.f90
+
+ - `read_in_real` in file set_inputs.f90
+
+ - `read_in_real` in file set_inputs.f90
+
+ - `read_in_real` in file set_inputs.f90
+
+ - `read_in_logical` in file set_inputs.f90
+
+ - `read_in_logical` in file set_inputs.f90
+
+ - `read_in_logical` in file set_inputs.f90
+
+ - `read_in_logical` in file set_inputs.f90
+
+ - `read_in_logical` in file set_inputs.f90
+
+ - `read_in_logical` in file set_inputs.f90
+
+ - `read_in_real` in file set_inputs.f90
+
+ - `IO_set_hpi_single`
+
+ - `read_in_real` in file set_inputs.f90
+
+ - `IO_set_kp_single`
+
+ - `read_in_real` in file set_inputs.f90
+
+ - `read_in_real` in file set_inputs.f90
+
+ - `read_in_real` in file set_inputs.f90
+
+ - `read_in_real` in file set_inputs.f90
+
+ - `read_in_real` in file set_inputs.f90
+
+ - `IO_set_imf_by_single`
+
+ - `IO_set_imf_bz_single`
+
+ - `IO_set_sw_v_single`
+
+ - `read_in_string` in file set_inputs.f90
+
+ - `IO_set_inputs`
+
+ - `read_MHDIMF_Indices`
+
+ - `read_in_logical` in file set_inputs.f90
+
+ - `read_in_logical` in file set_inputs.f90
+
+ - `read_in_logical` in file set_inputs.f90
+
+ - `read_in_logical` in file set_inputs.f90
+
+ - `read_in_logical` in file set_inputs.f90
+
+ - `read_in_logical` in file set_inputs.f90
+
+ - `read_in_string` in file set_inputs.f90
+
+ - `read_in_string` in file set_inputs.f90
+
+ - `read_in_string` in file set_inputs.f90
+
+ - `read_in_real` in file set_inputs.f90
+
+ - `read_in_int` in file set_inputs.f90
+
+ - `read_in_int` in file set_inputs.f90
+
+ - `read_in_real` in file set_inputs.f90
+
+ - `read_in_logical` in file set_inputs.f90
+
+ - `read_in_logical` in file set_inputs.f90
+
+ - `read_in_logical` in file set_inputs.f90
+
+ - `read_in_logical` in file set_inputs.f90
+
+ - `read_in_logical` in file set_inputs.f90
+
+ - `read_in_logical` in file set_inputs.f90
+
+ - `read_in_logical` in file set_inputs.f90
+
+ - `read_in_logical` in file set_inputs.f90
+
+ - `read_in_logical` in file set_inputs.f90
+
+ - `read_in_real` in file set_inputs.f90
+
+ - `read_in_real` in file set_inputs.f90
+
+ - `read_in_logical` in file set_inputs.f90
+
+ - `read_in_logical` in file set_inputs.f90
+
+ - `read_in_real` in file set_inputs.f90
+
+ - `read_in_logical` in file set_inputs.f90
+
+ - `read_in_logical` in file set_inputs.f90
+
+ - `read_in_logical` in file set_inputs.f90
+
+ - `read_in_logical` in file set_inputs.f90
+
+ - `read_in_real` in file set_inputs.f90
+
+ - `read_in_real` in file set_inputs.f90
+
+ - `read_in_real` in file set_inputs.f90
+
+ - `read_in_logical` in file set_inputs.f90
+
+ - `read_in_logical` in file set_inputs.f90
+
+ - `read_in_logical` in file set_inputs.f90
+
+ - `read_in_logical` in file set_inputs.f90
+
+ - `read_in_logical` in file set_inputs.f90
+
+ - `read_in_logical` in file set_inputs.f90
+
+ - `read_in_logical` in file set_inputs.f90
+
+ - `read_in_real` in file set_inputs.f90
+
+ - `read_in_int` in file set_inputs.f90
+
+ - `read_in_real` in file set_inputs.f90
+
+ - `read_in_logical` in file set_inputs.f90
+
+ - `read_in_logical` in file set_inputs.f90
+
+ - `read_in_logical` in file set_inputs.f90
+
+ - `read_in_logical` in file set_inputs.f90
+
+ - `read_in_logical` in file set_inputs.f90
+
+ - `read_in_logical` in file set_inputs.f90
+
+ - `read_in_logical` in file set_inputs.f90
+
+ - `read_in_logical` in file set_inputs.f90
+
+ - `read_in_string` in file set_inputs.f90
+
+ - `read_in_string` in file set_inputs.f90
+
+ - `read_in_real` in file set_inputs.f90
+
+ - `read_in_real` in file set_inputs.f90
+
+ - `read_in_real` in file set_inputs.f90
+
+ - `read_in_real` in file set_inputs.f90
+
+ - `read_in_real` in file set_inputs.f90
+
+ - `read_in_logical` in file set_inputs.f90
+
+ - `read_in_real` in file set_inputs.f90
+
+ - `read_in_real` in file set_inputs.f90
+
+ - `read_in_logical` in file set_inputs.f90
+
+ - `read_in_int` in file set_inputs.f90
+
+ - `read_in_int` in file set_inputs.f90
+
+ - `read_in_real` in file set_inputs.f90
+
+ - `read_in_real` in file set_inputs.f90
+
+ - `read_in_real` in file set_inputs.f90
+
+ - `read_in_real` in file set_inputs.f90
+
+ - `read_in_real` in file set_inputs.f90
+
+ - `read_in_real` in file set_inputs.f90
+
+ - `read_in_real` in file set_inputs.f90
+
+ - `read_in_logical` in file set_inputs.f90
+
+ - `read_in_logical` in file set_inputs.f90
+
+ - `read_in_time` in file set_inputs.f90
+
+ - `read_in_time` in file set_inputs.f90
+
+ - `read_in_real` in file set_inputs.f90
+
+ - `read_in_logical` in file set_inputs.f90
+
+ - `read_in_real` in file set_inputs.f90
+
+ - `read_in_int` in file set_inputs.f90
+
+ - `read_in_string` in file set_inputs.f90
+
+ - `read_in_real` in file set_inputs.f90
+
+ - `read_in_int` in file set_inputs.f90
+
+ - `read_in_string` in file set_inputs.f90
+
+ - `read_in_real` in file set_inputs.f90
+
+ - `read_satellites` in file satellites.f90
+
+ - `read_in_real` in file set_inputs.f90
+
+ - `read_in_real` in file set_inputs.f90
+
+ - `read_in_real` in file set_inputs.f90
+
+ - `read_in_logical` in file set_inputs.f90
+
+ - `read_in_string` in file set_inputs.f90
+
+ - `read_in_string` in file set_inputs.f90
+
+ - `read_in_real` in file set_inputs.f90
+
+ - `read_in_logical` in file set_inputs.f90
+
+ - `read_in_string` in file set_inputs.f90
+
+ - `Set_Euv` in file calc_euv.f90
+
+ - `read_in_logical` in file set_inputs.f90
+
+ - `read_in_real` in file set_inputs.f90
+
+ - `read_in_string` in file set_inputs.f90
+
+ - `IO_set_inputs`
+
+ - `read_NGDC_Indices`
+
+ - `read_in_string` in file set_inputs.f90
+
+ - `read_in_string` in file set_inputs.f90
+
+ - `IO_set_inputs`
+
+ - `read_SWPC_Indices`
+
+ - `read_in_string` in file set_inputs.f90
+
+ - `IO_set_inputs`
+
+ - `read_NOAAHPI_Indices`
+
+ - `stop_gitm` in file library.f90
+
+ - `time_int_to_real` in file time_routines.f90
+
+- `initialize_gitm` in file **initialize.f90**
+
+ - `init_radcooling` in file ModEarth.f90
+
+ - `start_timing` in file timing.f90
+
+ - `report` in file library.f90
+
+ - `time_real_to_int` in file time_routines.f90
+
+ - `fix_vernal_time` in file set_inputs.f90
+
+ - `get_f107`
+
+ - `get_f107a`
+
+ - `init_grid` in file init_grid.f90
+
+ - `read_inputs` in file read_inputs.f90
+
+ - `set_inputs` in file set_inputs.f90
+
+ - `read_restart` in file restart.f90
+
+ - `init_msis` in file init_msis.Earth.f90
+
+ - `set_RrTempInd` in file ModRates.Earth.f90
+
+ - `init_euv` in file calc_euv.f90
+
+ - `init_altitude` in file init_altitude.f90
+
+ - `UAM_gradient`
+
+ - `init_heating_efficiency` in file Earth.f90
+
+ - `init_magheat` in file ModEarth.f90
+
+ - `init_isochem` in file Mars.f90
+
+ - `init_aerosol` in file ModEarth.f90
+
+ - `init_isochem` in file Mars.f90
+
+ - `init_msis` in file init_msis.Earth.f90
+
+ - `get_temperature` in file init_altitude.f90
+
+ - `init_iri` in file init_iri.Earth.f90
+
+ - `read_waccm_tides` in file tides.f90
+
+ - `update_waccm_tides` in file tides.f90
+
+ - `read_tides` in file tides.f90
+
+ - `update_tides` in file tides.f90
+
+ - `init_b0` in file init_b0.f90
+
+ - `init_energy_deposition` in file init_energy_deposition.f90
+
+ - `report` in file library.f90
+
+ - `SUBSOLR`
+
+ - `exchange_messages_sphere` in file exchange_messages_sphere.f90
+
+ - `calc_pressure` in file calc_pressure.f90
+
+ - `UA_calc_electrodynamics` in file calc_electrodynamics.f90
+
+ - `calc_eddy_diffusion_coefficient` in file Earth.f90
+
+ - `calc_rates` in file calc_rates.Earth.f90
+
+ - `calc_viscosity` in file calc_rates.Earth.f90
+
+ - `calc_rates` in file calc_rates.Earth.f90
+
+ - `end_timing` in file timing.f90
+
+ - `calc_vtec` in file calc_tec.f90
+
+ - `calc_single_vtec` in file calc_tec.f90
+
+- `write_output` in file **write_output.f90**
+
+ - `output` in file output_common.f90
+
+ - `move_satellites` in file satellites.f90
+
+ - `write_restart` in file restart.f90
+
+ - `logfile` in file logfile.f90
+
+- `report` in file **library.f90**
+
+- Loop Start
+
+ - `calc_pressure` in file **calc_pressure.f90**
+
+ - `report` in file library.f90
+
+ - `calc_timestep_vertical` in file **calc_timestep.f90**
+
+ - `report` in file library.f90
+
+ - `MPI_AllREDUCE`
+
+ - `stop_gitm` in file library.f90
+
+ - `calc_timestep_horizontal` in file **calc_timestep.f90**
+
+ - `report` in file library.f90
+
+ - `MPI_AllREDUCE`
+
+ - `advance` in file **advance.f90**
+
+ - `report` in file library.f90
+
+ - `start_timing` in file timing.f90
+
+ - `update_tides` in file tides.f90
+
+ - `update_waccm_tides` in file tides.f90
+
+ - `advance_vertical_all` in file advance.f90
+
+ - `add_sources` in file add_sources.f90
+
+ - `advance_horizontal_all` in file advance.f90
+
+ - `time_real_to_int` in file time_routines.f90
+
+ - `get_f107`
+
+ - `stop_gitm` in file library.f90
+
+ - `get_f107a`
+
+ - `stop_gitm` in file library.f90
+
+ - `init_msis` in file init_msis.Earth.f90
+
+ - `init_iri` in file init_iri.Earth.f90
+
+ - `init_b0` in file init_b0.f90
+
+ - `end_timing` in file timing.f90
+
+ - `report` in file library.f90
+
+ - `start_timing` in file timing.f90
+
+ - `calc_rates` in file calc_rates.Earth.f90
+
+ - `calc_viscosity` in file calc_rates.Earth.f90
+
+ - `advance_vertical` in file advance_vertical.f90
+
+ - `end_timing` in file timing.f90
+
+ - `report` in file library.f90
+
+ - `start_timing` in file timing.f90
+
+ - `exchange_messages_sphere` in file
+ exchange_messages_sphere.f90
+
+ - `calc_rates` in file calc_rates.Earth.f90
+
+ - `calc_physics` in file calc_physics.f90
+
+ - `advance_horizontal` in file advance_horizontal.f90
+
+ - `calc_physics` in file calc_physics.f90
+
+ - `calc_rates` in file calc_rates.Earth.f90
+
+ - `advance_horizontal` in file advance_horizontal.f90
+
+ - `exchange_messages_sphere` in file
+ exchange_messages_sphere.f90
+
+ - `end_timing` in file timing.f90
+
+ - `check_stop` in file **stop_file.f90**
+
+ - `report` in file library.f90
+
+ - `start_timing` in file timing.f90
+
+ - `MPI_AllREDUCE`
+
+ - `check_start` in file stop_file.f90
+
+ - `end_timing` in file timing.f90
+
+ - `write_output` in file **write_output.f90**
+
+ - `output` in file output_common.f90
+
+ - `move_satellites` in file satellites.f90
+
+ - `write_restart` in file restart.f90
+
+ - `logfile` in file logfile.f90
+
+- Loop End
+
+- `finalize_gitm` in file **finalize.f90**
+
+ - `UA_calc_electrodynamics` in file calc_electrodynamics.f90
+
+ - `output` in file output_common.f90
+
+ - `write_restart` in file restart.f90
+
+ - `end_timing` in file timing.f90
+
+ - `report_timing` in file timing.f90
+
+ - `UAM_XFER_destroy` in file ModSphereInterface.f90
+
+ - `UAM_write_error` in file ModSphereInterface.f90
+
+ - `stop_gitm` in file library.f90
+
+ - `MPI_FINALIZE`
+
+- `stop_gitm` in file **library.f90**
+
+ - `CON_stop` in file main.f90
+
+ - `MPI_abort`
diff --git a/srcDoc/devstuff/somelinks.md b/srcDoc/devstuff/somelinks.md
new file mode 100644
index 00000000..176f9b12
--- /dev/null
+++ b/srcDoc/devstuff/somelinks.md
@@ -0,0 +1,16 @@
+# Useful Reference Links
+
+Here are links to some tutorials and other things that may be useful to students
+or people new to GITM.
+
+## Aether Student Page
+
+Contains:
+
+- Editor information
+- Package manager basics
+- Unix commands (how to use a terminal)
+- A git walkthrough
+
+[Link to the Aether Student Page](https://github.com/AetherModel/Aether/blob/main/doc/student.md)
+
diff --git a/srcDoc/grid.tex b/srcDoc/grid.tex
deleted file mode 100644
index 7e6f0563..00000000
--- a/srcDoc/grid.tex
+++ /dev/null
@@ -1,109 +0,0 @@
-\section{Setting the Grid}
-\label{grid.sec}
-
-Setting the grid resolution in GITM is not very complicated, but it
-does involve some thought. There are a few variables that control
-this. In {\tt ModSize.f90}, the following variables are defined:
-
-\begin{verbatim}
-integer, parameter :: nLons = 9
-integer, parameter :: nLats = 9
-integer, parameter :: nAlts = 50
-
-integer, parameter :: nBlocksMax = 4
-\end{verbatim}
-
-The first three variables (nLons, nLats and nAlts) define the size of a single block. In the example above, there are 9 cells in latitude, 9 cells in longitude and 50 cells in altitude. The latitude and longitude resolution in GITM is defined by the cell numbers specified here and the block numbers discussed in the following section. The size of the altitude cells are measured in scale heights instead of kilometers, as certain regions require higher resolutions than others based on the dominating chemical and dynamical processes. Each altitude cell contains $\frac{1}{3}$ of a scale height, starting at 80 km and typically reaching up to 500 km. Increasing the number of altitude blocks will increase the altitude range, but if this value is increased too much the model becomes unstable. This altitude limit makes it problematic to model the equatorial region during storms, where increased vertical plasma transport requires the model consider altitudes of 2000 km and higher.
-
-The final variable (nBlocksMax) defines the maximum number of blocks you can have on a single processor. Most people run with one single block per processor, as this is faster. So setting this to ``1'' is usually preferred, and is necessary when running with the Dynamo option on. This is a necessity because the Dynamo routine does not correctly transfer the geomagnetically oriented data into the geographic coordinates used in the ghost cells. Hopefully this will be updated in future versions, as allowing multiple blocks per node can, in theory, save memory.
-
-Don't forget, if you change any of these parameters you will need to recompile the code (run the Makefile again) so that a new executable using the newly defined variables can be produced.
-
-\subsection{Running 3D Over the Whole Globe}
-
-Once the number of cells is defined, then the number of blocks in latitude and longitude need to be defined. This is done in the {\tt UAM.in} file, as shown in section~\ref{uam.sec}. For example, the initial settings have 8 blocks in latitude and 8 in longitude:
-
-\begin{verbatim}
-#GRID
-8 lons
-8 lats
--90.0 minimum latitude to model
-90.0 maximum latitude to model
-0.0 minimum longitude to model
-0.0 maximum longitude to model
-\end{verbatim}
-
-The number of cells in the simulation domain will then be 72 in longitude, 72 in latitude, and 50 in altitude. Given that there are 360$\deg$ in longitude and $180\deg$ in latitude, the resolution would be $360\deg/72 = 5.0\deg$ and $180\deg/72 = 2.5\deg$ in latitude. If one block were put on each processor, 64 processors would be required.
-
-If one desired to run without the Dynamo turned on, the problem could also be run with multiple blocks per node. This grid fits quite nicely on either four- or eight-core processors. However, on 12-core processors this would not work very well at all. We have started to run simulations of $1\deg$ in latitude and $5\deg$ in longitude, which can fit nicely on a 12-core processor machine. For example, in {\tt ModSize.f90}:
-
-\begin{verbatim}
-integer, parameter :: nLons = 9
-integer, parameter :: nLats = 15
-\end{verbatim}
-
-and in {\tt UAM.in}:
-
-\begin{verbatim}
-#GRID
-8 lons
-12 lats
-\end{verbatim}
-
-This can then run on 96 cores, which is nicely divisible by 12. Essentially, an infinite combination of cells per block and number of blocks can be utilized. Typically, the number of blocks in latitude and longitude are even numbers.
-
-\subsection{Running 3D Over the Part of the Globe}
-
-GITM can be run over part of the globe - both in latitude and in
-longitude. It can be run over a single polar region (by setting
-either the minimum or maximum latitude to be greater (or less) than
-$\pm 90\deg$). If this is selected, message passing over the poles is
-implemented. If the pole is not selected, then boundary conditions
-have to be set in {\tt set\_horizontal\_bcs.f90}. By default, a
-continuous gradient boundary condition is used on the densities and
-temperatures, while a continuous value is used on the velocity. This
-is true in both latitude and longitude. In longitude, message passing
-is implemented all of the time, but the values are over-written by the
-boundary conditions if the maximum and minimum longitude are not equal
-to each other.
-
-The longitudinal resolution ($\Delta{\phi}$) is set by:
-\begin{equation}
-\Delta{\phi} = \frac{\phi_{end} - \phi_{start}}{nBlocksLon \times nCellsLon}
-\end{equation}
-while, the latitudinal resolution ($\Delta{\theta}$) is set by:
-\begin{equation}
-\Delta{\theta} = \frac{\theta_{end} - \theta_{start}}{nBlocksLat \times nCellsLat}
-\end{equation}
-
-\subsection{Running in 1D}
-
-GITM can run in 1D mode, in which the call to advance\_horizontal is
-not completed. This means that GITM runs exactly the same way, but
-ignoring all of the horizontal advection terms. You have to do two
-things to make GITM run in 1D. First, in {\tt ModSize.f90}:
-\begin{verbatim}
-integer, parameter :: nLons = 1
-integer, parameter :: nLats = 1
-integer, parameter :: nAlts = 50
-
-integer, parameter :: nBlocksMax = 1
-\end{verbatim}
-This tells the code that you only want one single latitude and
-longitude location. To specify the exact location, in {\tt UAM.in}:
-\begin{verbatim}
-#GRID
-1 lons
-1 lats
-41.75 minimum latitude to model
-41.75 maximum latitude to model
-275.0 minimum longitude to model
-275.0 maximum longitude to model
-\end{verbatim}
-This is pretty close to some place in Michigan. GITM will model this
-exact point for as long as you specify. One thing to keep in mind
-with running in 1D is that the Earth still rotates, so the spot will
-have a strong day to night variation in temperature. In 3D, the winds
-decrease some of the variability between day and night, but in 1D,
-this doesn't happen. So, the results are going to be perfect. But,
-1D is great for debugging.
diff --git a/srcDoc/index.md b/srcDoc/index.md
new file mode 100644
index 00000000..265c7f7f
--- /dev/null
+++ b/srcDoc/index.md
@@ -0,0 +1,104 @@
+# Introduction
+
+The Global Ionosphere Thermosphere Model (GITM) is a 3D model of the ionosphere and
+thermosphere that has been applied to Earth, Venus, Mars, Jupiter, and Saturn's moon
+Titan. The main repository for GITM is available on
+[GitHub](https://github.com/GITMCode/GITM). The first paper describing GITM is
+[here](https://www.sciencedirect.com/science/article/pii/S1364682606000071).
+
+## Quick Start
+
+If you have are confident downloading, compiling, and running codes, this is a good
+place to start. A more detailed explanation can be found on the
+[installation page](install.md).
+
+Dependencies: fortran (assuming gfortran), mpi (mpich doesn't seem to work), make, perl
+(we are old school!), and python 3+. The version should not matter as long as it is
+relatively recent.
+
+Download, configure, and run (`gfortran10` is for any gfortran version 10 or higher,
+for versions 9 and lower just use `-compiler=gfortran`):
+
+! note
+ The current documentation only applies to the develop branch of GITM.
+
+ After the seconds line below, run `git checkout develop`
+
+
+```bash
+git clone https://github.com/GITMCode/GITM.git
+cd GITM
+./Config.pl -install -compiler=gfortran10 -earth
+make
+make rundir
+cd run
+mpirun -np 4 ./GITM.exe
+./post_process.py
+```
+
+Then to produce a plot:
+```bash
+cd UA/data
+python3 ../../../srcPython/gitm_plot_simple.py -alt=250 -var=3 *bin
+```
+This should produce two png files showing the density across the globe at about 250 km
+altitude. This is a relatively simple plotter that will make cuts in altitude,
+latitude, and longitude. They are quite basic, but this should provide some framework
+for reading in GITM files and visualizing the results. More complex plotters exist,
+and dome of these are described in [this document](plotters.md).
+
+## A Bit More Explanation
+
+GITM is a fortran code that uses the message passing interface (MPI) to run on multiple
+processors, hence the need for a fortran compiler and MPI. If the code compiles
+correctly, then the biggest issue is setting up the run.
+
+GITM can create a run directory for you, so you don't have to worry about the executable
+and input files and everything being in the right place - it does it for you with the
+'make rundir' command. This will create a directory called 'run'. You can move this
+directory to where ever you want. Often the run directory is moved to a scratch disk
+and renamed. For example:
+
+```bash
+mv run /scratchdisk/mydirectory/run.gitm.event01
+ln -s /scratchdisk/mydirectory/run.gitm.event01 .
+```
+
+Then, within this directory, there is a file called 'UAM.in', which is what GITM reads
+to set all of its parameters.
+
+## Basic Inputs
+
+This is an extremely brief description of a few settings within `UAM.in` - to understand
+more, consult other pages in the documentation! Within this file, there are several
+things that need to be altered when running GITM:
+
+- Start time, given as year, month, day, hour, minute, second. Each on its own line.
+- End time, given as year, month, day, hour, minute, second.
+- The grid, given as start and end latitude, start and end longitude, and the number of
+ blocks (processors) to use in latitude and longitude. [See this grid description for
+ more](internals/grid.md).
+- Save plots, telling what type of plots to output (`3DALL` by default) and how often
+ (300s = 5 minutes). The restarts can be ignored unless you know you will need them.
+- MHD_Indices - This is the the path to a file which is used as inputs to the
+ high-latitude electrodynamics, specifying IMF and solar wind. There are instructions
+ in the UAM.in file on how to produce this with the correct format.
+- SME_Indices - this is the AE file that some auroral precipitation models need to
+ work. There are instructions in the UAM.in file on producing a file.
+- Dynamo - Settings for the low-latitude dynamo. If you are running with anything better
+ than 5 degrees by 5 degrees resolution, turn the dynamo on!
+
+Once these things are set, you should be able to run GITM for the event of your
+choosing.
+
+We provide a code in srcPython called gitm_makerun.py that will take the default UAM.in
+file, change the start/end times, download IMF and AE files, and flip switches that you
+may want.
+
+For more information on plotting, please see [the plotting description page](plotters.md).
+
+## The More Thorough Start
+
+Please see the [installation page](install.md) page for more info on how to
+download, configure, and install GITM.
+
diff --git a/srcDoc/install.md b/srcDoc/install.md
new file mode 100644
index 00000000..8c772dc7
--- /dev/null
+++ b/srcDoc/install.md
@@ -0,0 +1,216 @@
+# Installation
+
+If a fortran compiler & MPI are already installed on your system, you can skip down to
+[Getting the Code](#getting-the-code).
+
+If you are unsure whether or not things are installed & set up correctly, a good
+way to check is to print the version number with `gfortran --version` (change to
+`ifort` if using the Intel compiler). The MPI implementation can be checked
+with `mpirun --version`. If there is an error, something is not configured
+correctly.
+
+## Requirements
+
+At a minimum, you need:
+
+- a Fortran compiler (gfortran, ifort, ifx, etc.)
+- MPI (~~mpich~~, openmpi, mvapich, etc.)
+- GNU Make (`make`)
+- Python3 (most any version should work, but we have been testing with versions in the 3.10+ range)
+- Perl (for configuring the code). This comes installed on most machines.
+
+
+*[MPI]: Message Passing Interface
+
+On linux systems (including Windows Subsystem for Linux), gfortran is often used. This
+is the most robustly tested compiler for GITM. One problem with gfortran is that the
+gcc-10 and above version don't place well with MPI for some reason. A flag has to be
+specified to make them play nice, and therefore there are two different compiler options
+for gfortran when configuring (`-compiler=gfortran` for older versions and
+`-compiler=-gfortran10` for version 10+). There is a very good chance that you have 10+.
+
+There is no difference in the outputs between different compilers, however some
+compilers may produce slightly faster executables than others. For example,
+using ifort on [Pleiades](https://www.nas.nasa.gov/hecc/resources/pleiades.html)
+is faster than using gfortran (gcc) or aocc.
+
+As GITM can run on as many (or few) CPU cores as you wish, it is possible to run GITM on
+a laptop or a workstation. This is recommended for development, as the turnaround for
+test runs will be much faster. We develop GITM on 8+ core machines and can run the
+default test problem of 4 processors with no problems. Most modern computers are
+capable of this now.
+
+!!! warning "Using `conda` to install dependencies is not recommended"
+
+ In the past, people have had very strange errors when using Anaconda to get
+ dependencies installed. We highly recommend you use a system-wide package manager,
+ or install the dependencies manually, instead of using something language-specific.
+
+### Linux Install Dependencies
+
+On an Ubuntu-based linux distribution, the following commands will download GNU Make,
+the GCC Fortran compiler & Open-MPI:
+
+```bash
+sudo apt-get install gfortran libopenmpi-dev make
+```
+
+Similarly, Fedora-based distributions can use:
+
+```bash
+sudo yum install gcc-gfortran openmpi-devel
+```
+
+### MacOS Install Dependencies
+
+Installing gfortran on MacOS is most easily accomplished with a package manager like
+[Homebrew](https://brew.sh/) or [MacPorts](https://www.macports.org/). It is easiest to
+use a package manager, however it is also possible to install things manually. The
+following steps assume you are using a package manager.
+
+Homebrew users will need to run:
+
+```bash
+brew install gfortran open-mpi
+```
+
+And MacPorts users can run:
+
+```bash
+sudo port install gcc[??] open-mpi
+```
+> Make sure to specify a version number in place of `??` above! Use
+> `port search --name --glob 'gcc*'`, or `port search gfortran` to see
+> available Ports.
+
+
+### Recommended HPC Modules
+
+On some computer systems, there are multiple versions of compilers, MPI, and other
+things like python available. They deal with these things by making "modules". This
+means that in order to compile the code, modules need to be loaded. For example, on
+NASA's Pleiades computer, this line can be added to your shell startup script (.cshrc,
+.zshrc, or .bashrc):
+
+```bash
+module load comp-intel mpi-hpe
+```
+
+The modules that need to be loaded on different systems will differ. Feel free to
+contribute to this list of recommended modules if you have experience with GITM on other
+systems:
+
+- Pleiades
+ - `comp-intel`
+ - `mpi-hpe`
+- Derecho
+ - `intel`
+ - `cray-mpich`
+
+Consult the documentation for each system to see which modules are available and
+how to load them. The modules you use to compile GITM *may* also need to be
+loaded when running, so it may be wise to set these to your defaults, or at
+least take note of what was used so they can be loaded in the job script.
+
+## Getting the code
+
+GITM is hosted on GitHub. The `main` branch is stable and updated as important features
+are added (in the `develop` branch). The `main` branch is default and no additional
+steps are needed to use this version. Just clone the GITM repository, and all dependent
+libraries will be downloaded during configuration. The following command is assuming
+that you will be using GITM and not developing GITM.
+
+```
+git clone git@github.com:GITMCode/GITM.git
+cd GITM
+```
+
+!!! tip
+ Replace `git@github.com:GITMCode/GITM.git` with
+ `https://github.com/GITMCode/GITM.git` if you don't have Github ssh keys set up. If
+ you are going to be developing GITM, you may take the time to fork the repository
+ (including all of the branches!), and then substitute your forked repository
+ location in the git clone command. If you are NOT doing development, just use this
+ command.
+
+## Configuring & Compiling
+
+All of the following steps assume you have not changed out of the `GITM/` directory.
+Most will error if run from another location, but this will not break anything! Simply
+`cd` back to `GITM/` and try again. Installation needs to be done from within `GITM/`,
+then the code can be run from anywhere by moving the `run/` directory.
+
+This step configures the planet, compiler, and some paths GITM needs to
+work properly. To configure GITM for Earth using the `gfortran` compiler, run:
+
+```bash
+./Config.pl -install -earth -compiler=gfortran10
+```
+
+!!! warning
+
+ The above example assumes you are using gfortran
+ version 10+. If your gfortran version is <10 (you should upgrade your system!),
+ use `compiler=gfortran`
+
+The full list of available configuration options can be found by running
+`./Config.pl -h`. A useful flag while developing is `-debug` which will print a
+traceback if an error is encountered, as well as performing some additional
+validity checks when running.
+
+This should have downloaded all necessary external libraries and created some
+extra files necessary to compile. To compile, simply run:
+
+```bash
+make
+```
+
+!!! tip
+
+ Compilation can often take a while. This can be done in parallel using `make -j`,
+ which will use all available cores on your computer. To limit the number of cores,
+ for example, to 8 use `make -j8`
+
+If this runs without error, GITM is ready to be run! No changes are made to your system
+so if errors do occur, you can remove the `GITM/` directory and try again. If trying
+again does not work, you can always submit a
+[bug report](https://github.com/GITMCode/GITM/issues) on GitHub.
+
+## Running the Code
+
+This will have created the executable `src/GITM.exe`. This is not where we want
+to run it from, however. To create a directory where the GITM executable is run
+from and organize some input files, run the command:
+
+```bash
+make rundir
+```
+
+Now there should be a new directory in the GITM folder called `run/`. This
+folder can be moved, copied, renamed, etc. without issue. If a study requires multiple runs of GITM, it can be most time-effective to copy or move the folder that was just created to somewhere a lot of data can be stored. For example, one could now run:
+```bash
+mv run /path/to/scratch/storage/thisproject/run01
+ln -s /path/to/scratch/storage/thisproject/run01 .
+```
+The 'ln' command will just create a link to the run directory in the GITM directory, so you don't lose it. If you want to make yet another run directory (you can make as many as you want!), you could then do:
+```bash
+make rundir
+mv run /path/to/scratch/storage/thisproject/run02
+ln -s /path/to/scratch/storage/thisproject/run02 .
+```
+
+It is now time to do some runs! The folder we just created contains a `UAM.in`
+file which calls for 4 CPU cores and simulates 5 minutes in December of 2002.
+This all can, of course, be adjusted later. To start this run, we first need to
+`cd` into the run directory, then tell MPI to run `GITM.exe` on 4 cores.
+
+```bash
+cd run/
+mpirun -np 4 ./GITM.exe
+```
+
+Twiddle your thumbs for a moment... And if no errors are reported then congratulations! You have
+now run GITM!
+
+The next steps include exploring how to [postprocess](postprocessing.md) the
+outputs, and modifying the [input files](common_inputs.md).
diff --git a/srcDoc/internals/chemistry.md b/srcDoc/internals/chemistry.md
new file mode 100644
index 00000000..275fdb03
--- /dev/null
+++ b/srcDoc/internals/chemistry.md
@@ -0,0 +1,586 @@
+# Chemistry
+
+Chemical reactions in GITM for Earth
+
+---
+
+```math
+\begin{align}
+O_2 \rightarrow 2O
+\end{align}
+```
+
+EUV dissociation rate.
+
+```math
+\begin{align}
+N_2 \rightarrow 2N
+\end{align}
+```
+
+EUV dissociation rate.
+
+```math
+\begin{align}
+\begin{split}
+O + O + M \rightarrow O_2 + M \\
+R = 9.59 \times 10^{-46} \times e^{\frac{480}{T_n}}
+\end{split}
+\end{align}
+```
+
+```math
+\begin{align}
+N_2 \rightarrow N_2^+
+\end{align}
+```
+
+EUV Ionization Rate.
+
+```math
+\begin{align}
+N_2 \rightarrow N_2^+
+\end{align}
+```
+
+Auroral Ionization Rate.
+
+```math
+\begin{align}
+O_2 \rightarrow O_2^+
+\end{align}
+```
+
+EUV Ionization Rate.
+
+```math
+\begin{align}
+O_2 \rightarrow O_2^+
+\end{align}
+```
+
+Auroral Ionization Rate.
+
+```math
+\begin{align}
+O(^3P) \rightarrow O^+(^4S)
+\end{align}
+```
+
+EUV Ionization Rate.
+
+```math
+\begin{align}
+O(^3P) \rightarrow O^+(^2D)
+\end{align}
+```
+
+EUV Ionization Rate.
+
+```math
+\begin{align}
+O(^3P) \rightarrow O^+(^2P)
+\end{align}
+```
+
+EUV Ionization Rate.
+
+```math
+\begin{align}
+\begin{split}
+O(^4S) \rightarrow O^+(^4S) (40\%) \\
+O(^4S) \rightarrow O^+(^2D) (40\%) \\
+O(^4S) \rightarrow O^+(^2P) (20\%)
+\end{split}
+\end{align}
+```
+
+Auroral Ionization Rate.
+
+```math
+\begin{align}
+\begin{split}
+O^+(^2D) + N_2 \rightarrow N_2^+ + O + 1.33 eV \\
+R = 8.0\times 10^{-16}
+\end{split}
+\end{align}
+```
+
+```math
+\begin{align}
+\begin{split}
+O^+(^2P) + N_2 \rightarrow N_2^+ + O + 3.02 eV \\
+R = 4.8\times 10^{-16}
+\end{split}
+\end{align}
+```
+
+```math
+\begin{align}
+\begin{split}
+N_2^+ + O_2 \rightarrow O_2^+ + N_2 + 3.53 eV \\
+R = 5.0\times 10^{-17} \times \bigg(\frac{T_n+T_i}{600}\bigg)^{-0.8}
+\end{split}
+\end{align}
+```
+
+```math
+\begin{align}
+\begin{split}
+N_2^+ + O \rightarrow NO^+ + N(^2D) + 0.7 eV \\
+R = 1.4\times 10^{-16} \times \bigg(\frac{T_n+T_i}{600}\bigg)^{-0.44}
+\end{split}
+\end{align}
+```
+
+```math
+\begin{align}
+\begin{split}
+N_2^+ + e^- \rightarrow 2N(^2D) + 1.04 eV \\
+R = 1.8\times 10^{-13} \times \bigg(\frac{T_e}{300}\bigg)^{-0.39}
+\end{split}
+\end{align}
+```
+
+```math
+\begin{align}
+\begin{split}
+N_2^+ + O \rightarrow O^+(^4S) + N_2 + 1.96 eV \\
+R = 1.4\times 10^{-16} \times \bigg(\frac{T_n+T_i}{600}\bigg)^{-0.44}
+\end{split}
+\end{align}
+```
+
+I am not sure that this is correct, since it is the same as 2.8.
+
+```math
+\begin{align}
+\begin{split}
+N_2^2 + NO \rightarrow NO^+ + N_2 + 6.33 eV \\
+R = 4.1 \times 10^{-16}
+\end{split}
+\end{align}
+```
+
+```math
+\begin{align}
+O^+(^4S) + O_2 \rightarrow O_2^+ + O + 1.55 eV \\
+\begin{split}
+R = 2.82 \times 10^{-17} \\
+ & - 7.740\times 10^{-18}(T_{O2}/300.0) \\
+ & + 1.073\times 10^{-18}(T_{O2}/300.0)^2 \\
+ & - 5.170\times 10^{-20}(T_{O2}/300.0)^3 \\
+ & + 9.650\times 10^{-22}(T_{O2}/300.0)^4
+\end{split}
+\end{align}
+```
+
+```math
+\begin{align}
+\begin{split}
+O^+(^2D) + O_2 \rightarrow O_2^+ + 4.865 eV \\
+R = 7.0 \times 10^{-16}
+\end{split}
+\end{align}
+```
+
+```math
+\begin{align}
+\begin{split}
+N^+ + O_2 \rightarrow O_2^+ + N(^4S) + 2.486 \\
+R = 1.1 \times 10^{-16}
+\end{split}
+\end{align}
+```
+
+```math
+\begin{align}
+\begin{split}
+N^+ + O_2 \rightarrow O_2^+ + N(^4D) + 0.1 \\
+R = 2.0 \times 10^{-16}
+\end{split}
+\end{align}
+```
+
+```math
+\begin{align}
+\begin{split}
+O_2^+ + e^- \rightarrow O(^1D) + O(^1D) + 3.06 eV (31\%) \\
+O_2^+ + e^- \rightarrow O(^3P) + O(^1D) + 3.06 eV (42\%) \\
+O_2^+ + e^- \rightarrow O(^3P) + O(^3P) + 3.06 eV (22\%) \\
+R = 2.4\times 10^{-13} \bigg(\frac{T_e}{300}\bigg)^{-0.7}
+\end{split}
+\end{align}
+```
+
+```math
+\begin{align}
+\begin{split}
+O_2^+ + N(^4S) \rightarrow NO^+ + O + 4.25 eV \\
+R = 1.5 \times 10^{-16}
+\end{split}
+\end{align}
+```
+
+```math
+\begin{align}
+O_2^+ + NO \rightarrow NO^+ + O_2 + 2.813 eV \\
+R = 4.6 \times 10^{-16}
+\end{align}
+```
+
+```math
+\begin{align}
+\begin{split}
+O_2^+ + N_2 \rightarrow NO^+ + NO + 0.9333 eV \\
+R = 5.0 \times 10^{-22}
+\end{split}
+\end{align}
+```
+
+```math
+\begin{align}
+\begin{split}
+O^+(^2D) + O \rightarrow O^+(^4S) + O(^3P) + 3.31 eV \\
+O^+(^2D) + O \rightarrow O^+(^4S) + O(^1D) + 1.35 eV \\
+R = 1.0 \times 10^{-17}
+\end{split}
+\end{align}
+```
+
+```math
+\begin{align}
+\begin{split}
+O^+(^2D) + e^- \rightarrow O^+(^4S) + e^- + 3.31 eV \\
+R = 7.8 \times 10^{-14}\bigg(\frac{T_e}{300}\bigg)^{-0.5}
+\end{split}
+\end{align}
+```
+
+```math
+\begin{align}
+\begin{split}
+O^+(^2D) + N_2 \rightarrow O^+(^4S) + N_2 + 3.31 eV \\
+R = 8.0 \times 10^{-16}
+\end{split}
+\end{align}
+```
+
+```math
+\begin{align}
+\begin{split}
+O^+(^2P) + O \rightarrow O^+(^4S) + O + 5.0 eV \\
+R = 5.2 \times 10^{-17}
+\end{split}
+\end{align}
+```
+
+```math
+\begin{align}
+\begin{split}
+O^+(^2P) + e^- \rightarrow O^+(^4S) + e^- + 5.0 eV \\
+R = 4.0 \times 10^{-14}\bigg(\frac{T_e}{300}\bigg)^{-0.5}
+\end{split}
+\end{align}
+```
+
+```math
+\begin{align}
+\begin{split}
+O^+(^2P) \rightarrow O^+(^4S) + 247.0nm\\
+R = 0.047
+\end{split}
+\end{align}
+```
+
+```math
+\begin{align}
+\begin{split}
+N^+ O_2 \rightarrow O^+(^4S) + NO + 2.31 eV\\
+R = 3.0 \times 10^{-17}
+\end{split}
+\end{align}
+```
+
+---
+
+```math
+\begin{align}
+\begin{split}
+O^+(^4S) + N_2 \rightarrow NO^+ + N(^4S) + 1.10 eV \\
+T_{eff} = & T_i + \frac{M_O}{M_O + M_{N_2}}\times\frac{M_{N_2} - M_b}{3k_b}V_i^2 \\
+M_b = &\frac{M_c}{M_{mc}} \\
+M_c = & \sum_n \frac{M_n\nu_{in}}{M_n + M_O} \\
+M_{mc} = & \sum_n \frac{ \nu_{in}}{M_n + M_O} \\
+R = & 1.533\times 10^{-18} - \\
+ & 5.920\times 10^{-19} \bigg(\frac{T_{eff}}{300}\bigg) + \\
+ & 8.600\times 10^{-20} \bigg(\frac{T_{eff}}{300}\bigg)^2 \\
+ (T_{eff} < 1700) \\
+R = & 2.730\times 10^{-18} - \\
+ & 1.155\times 10^{-18} \bigg(\frac{T_{eff}}{300}\bigg) + \\
+ & 1.483\times 10^{-19} \bigg(\frac{T_{eff}}{300}\bigg)^2 \\
+ (T_{eff} > 1700)
+\end{split}
+\end{align}
+```
+
+If $`T_{eff} < 350`$, then $`T_{eff} = 350`$.
+
+If $`T_{eff} > 6000`$, then $`T_{eff} = 6000`$.
+
+---
+
+```math
+\begin{align}
+\begin{split}
+O^+(^4S) + O_2 \rightarrow O_2^+ + O + 1.55 eV\\
+R = & 2.820\times 10^{-17} - \\
+ & 7.740\times 10^{-18} \bigg(\frac{T_{eff}}{300}\bigg) + \\
+ & 1.073\times 10^{-18} \bigg(\frac{T_{eff}}{300}\bigg)^2 - \\
+ & 5.170\times 10^{-20} \bigg(\frac{T_{eff}}{300}\bigg)^3 + \\
+ & 9.650\times 10^{-22} \bigg(\frac{T_{eff}}{300}\bigg)^4\\
+T_{eff} = & T_i + \frac{M_O}{M_O + M_{O_2}}\times\frac{M_{O_2} - M_b}{3k_b}V_i^2
+\end{split}
+\end{align}
+```
+
+If $`T_{eff} < 350`$, then $`T_{eff} = 350`$.
+
+If $`T_{eff} > 6000`$, then $`T_{eff} = 6000`$.
+
+```math
+\begin{align}
+\begin{split}
+O^+(^4S) + NO \rightarrow NO^+ + O + 4.36 eV\\
+R = & 8.36\times 10^{-19} - \\
+ & 2.02\times 10^{-19} \bigg(\frac{T_{eff}}{300}\bigg) + \\
+ & 6.95\times 10^{-20} \bigg(\frac{T_{eff}}{300}\bigg)^2 (T_{eff} < 1500)\\
+R = & 5.33\times 10^{-19} - \\
+ & 1.64\times 10^{-20} \bigg(\frac{T_{eff}}{300}\bigg) + \\
+ & 4.72\times 10^{-20} \bigg(\frac{T_{eff}}{300}\bigg)^2 \\
+ & 7.05\times 10^{-22} \bigg(\frac{T_{eff}}{300}\bigg)^3 (T_{eff} > 1500) \\
+T_{eff} = & T_i + \frac{M_O}{M_O + M_{NO}}\times\frac{M_{NO} - M_b}{3k_b}V_i^2
+\end{split}
+\end{align}
+```
+
+If $`T_{eff} < 350`$, then $`T_{eff} = 350`$.
+
+If $`T_{eff} > 6000`$, then $`T_{eff} = 6000`$.
+
+```math
+\begin{align}
+\begin{split}
+O^+(^4S) + N(^2D) \rightarrow N^+ + O + 1.45 eV\\
+R = 1.3 \times 10^{-16}
+\end{split}
+\end{align}
+```
+
+```math
+\begin{align}
+\begin{split}
+O^+(^2P) +e^- \rightarrow O^+(^2D) + e^- + 1.69 eV\\
+R = 1.3 \times 10^{-13} \bigg(\frac{T_e}{300}\bigg)^{-0.5} % te3m05
+\end{split}
+\end{align}
+```
+
+```math
+\begin{align}
+\begin{split}
+O^+(^2P) \rightarrow O^+(^2D) + 732nm\\
+R = 0.171
+\end{split}
+\end{align}
+```
+
+```math
+\begin{align}
+\begin{split}
+O^+(^2D) \rightarrow O^+(^4S) + 372.6nm\\
+R = 7.7\times 10^{-5}
+\end{split}
+\end{align}
+```
+
+```math
+\begin{align}
+\begin{split}
+O^+(^2P) + N_2 \rightarrow N^+ + NO + 0.70 eV\\
+R = 1.0 \times 10^{-16}
+\end{split}
+\end{align}
+```
+
+```math
+\begin{align}
+\begin{split}
+O^+_2 + N(^2D) \rightarrow N^+ + O_2 \\
+R = 2.5 \times 10^{-16}
+\end{split}
+\end{align}
+```
+
+```math
+\begin{align}
+\begin{split}
+O^+(^2P) + N \rightarrow N^+ + O + 2.7 eV \\
+R = 1.0 \times 10^{-16}
+\end{split}
+\end{align}
+```
+
+```math
+\begin{align}
+\begin{split}
+O^+(^2D) + N \rightarrow N^+ + O + 1.0 eV \\
+R = 7.5 \times 10^{-17}
+\end{split}
+\end{align}
+```
+
+```math
+\begin{align}
+\begin{split}
+N^+ + O_2 \rightarrow NO^+ + O(^1D) + 6.67 eV \\
+R = 2.6 \times 10^{-16}
+\end{split}
+\end{align}
+```
+
+```math
+\begin{align}
+\begin{split}
+N^+ + O \rightarrow O^+(^4S) + N + 0.93 eV \\
+R = 5.0 \times 10^{-19}
+\end{split}
+\end{align}
+```
+
+```math
+\begin{align}
+\begin{split}
+NO^+ + e^- \rightarrow O + N(^2D) + 0.38 eV \\
+R = 4.0 \times 10^{-13} \bigg(\frac{T_e}{300}\bigg)^{-0.5} % te3m05
+\end{split}
+\end{align}
+```
+
+```math
+\begin{align}
+\begin{split}
+N(^2D) + e^- \rightarrow N(^4S) + e^- + 2.38 eV\\
+R = 5.5 \times 10^{-16} \bigg(\frac{T_e}{300}\bigg)^{-0.5} % te3m05
+\end{split}
+\end{align}
+```
+
+```math
+\begin{align}
+\begin{split}
+N(^2D) + O \rightarrow N(^4S) + O(^3P) + 2.38 eV (90\%)\\
+N(^2D) + O \rightarrow N(^4S) + O(^1D) + 0.42 eV (10\%)\\
+R = 2.0 \times 10^{-18}
+\end{split}
+\end{align}
+```
+
+```math
+\begin{align}
+\begin{split}
+N(^2D) \rightarrow N(^4S) + 520nm \\
+R = 1.06 \times 10^{-5}
+\end{split}
+\end{align}
+```
+
+```math
+\begin{align}
+\begin{split}
+NO \rightarrow N(^4S) + O \\
+R = 4.5 \times 10^{-6} e^{(-1\times 10^{-8}([O_2]\times 10^{-6})^{0.38})}
+\end{split}
+\end{align}
+```
+
+```math
+\begin{align}
+\begin{split}
+N(^4S) + O_2 \rightarrow NO + O + 1.385 eV \\
+R = 4.4 \times 10^{-18} e^{-\frac{3220}{T_n}}
+\end{split}
+\end{align}
+```
+
+```math
+\begin{align}
+\begin{split}
+N(^4S) + NO \rightarrow N_2 + O + 3.25 eV\\
+R = 1.5 \times 10^{-18} \sqrt{T_n}
+\end{split}
+\end{align}
+```
+
+```math
+\begin{align}
+\begin{split}
+N(^2P) \rightarrow N(^2D) + 1040nm\\
+R = 7.9 \times 10^{-2}
+\end{split}
+\end{align}
+```
+
+```math
+\begin{align}
+\begin{split}
+N(^2D) + O_2 \rightarrow NO + O(^3P) + 3.76 eV (90\%)\\
+N(^2D) + O_2 \rightarrow NO + O(^1D) + 1.80 eV (10\%)\\
+R = 6.2 \times 10^{-18} \frac{T_n}{300}
+\end{split}
+\end{align}
+```
+
+```math
+\begin{align}
+\begin{split}
+N(^2D) + NO \rightarrow N_2 + O + 5.63 eV\\
+R = 7.0 \times 10^{-17}
+\end{split}
+\end{align}
+```
+
+```math
+\begin{align}
+\begin{split}
+O(^1D) \rightarrow O(^3P) + 630nm\\
+R = 0.0071
+\end{split}
+\end{align}
+```
+
+```math
+\begin{align}
+\begin{split}
+O(^1D) \rightarrow O(^3P) + 636.4nm\\
+R = 0.0022
+\end{split}
+\end{align}
+```
+
+I don't understand this...
+
+```math
+\begin{align}
+\begin{split}
+O(^1D) + e^- \rightarrow O(^3P) + e^- + 1.96 eV\\
+R = 2.6 \times 10^{-17} T_e^(0.5)e^(-22740/T_e)
+\end{split}
+\end{align}
+```
+
+```math
+\begin{align}
+O(^1D) + N_2 \rightarrow O(^3P) +
+\end{align}
+```
\ No newline at end of file
diff --git a/srcDoc/internals/electrodynamics.md b/srcDoc/internals/electrodynamics.md
new file mode 100644
index 00000000..7e6c7898
--- /dev/null
+++ b/srcDoc/internals/electrodynamics.md
@@ -0,0 +1,194 @@
+# Electrodynamics
+
+GITM uses [an external library](https://github.com/gitmcode/electrodynamics.git)
+for high-latitude electrodynamics. This library is automatically cloned into
+`ext/Electrodynamics` when running `Config.pl`, though an update is not
+attempted.
+
+GITM has the ability to use external auroral and/or potential models. These are
+specified independently so one could, for instance, use AMIE (file-based) aurora
+and Weimer potentials.
+
+## Specifying Electrodynamics Drivers
+
+The Electrodynamics models are chosen in the `#ELECTRODYNAMICS` section of
+`UAM.in`. By default the values are set to:
+
+```
+#ELECTRODYNAMICS
+zero AuroralModel
+60.0 DtAurora
+zero PotentialModel
+60.0 DtPotential
+```
+
+This will cause warnings to be printed if running on Earth, as we often wish to
+provide high-latitude electrodynamics drivers when modeling the Earth. However,
+the run will complete.
+
+If, for example, one wishes to perform a scientific run using a commonsense
+configuration, the recommended settings are:
+
+```
+#ELECTRODYNAMICS
+fta AuroralModel
+60.0 DtAurora
+weimer05 PotentialModel
+60.0 DtPotential
+```
+
+This will use FTA[^1] and Weimer05[^2] for the auroral and potential models,
+respectively.
+
+[^1]: Wu, C., Ridley, A. J., DeJong, A. D., & Paxton, L. J. (2021). FTA: A Feature Tracking Empirical Model Of Auroral Precipitation. Space Weather, 19, e2020SW002629. .
+
+[^2]: Weimer, D. R. (2005), Improved ionospheric electrodynamic models and application to calculating Joule heating rates, J. Geophys. Res., 110, A05306, .
+
+
+The aurora and electric field model names are parsed in
+[`Electrodynamics/src/interpret_names.f90`](https://github.com/GITMCode/Electrodynamics/blob/main/src/interpret_names.f90).
+See this file for the most up-to-date list of available modules and the acceptable names.
+
+## Aurora
+
+The following Auroral models are available:
+
+- FTA
+- FRE
+- PEM
+- OVATION
+- AMIE
+
+From the auroral module, GITM expects to receive Average Energy and Energy Flux,
+for all of the selected auroral types. At the moment these all must be from the
+same module, so one cannot use FTA for diffuse electron precipitation and AMIE
+for monoenergetic electron precipitation.
+
+### Aurora Types
+
+Auroral types are specified in the `#AURORATYPES` section of `UAM.in`, and only
+electron diffuse aurora are included by default:
+
+```
+#AURORATYPES
+T UseDiffuseAurora (logical)
+F UseMonoAurora (logical)
+F UseWaveAurora (logical)
+F UseIonAurora (logical)
+```
+
+Some notes on the different auroral types:
+
+- `NormalizeAuroraToHP` is only recommended to be used in conjunction with FRE,
+- `#AURORATYPES` are not supported by all auroral models. Presently, only
+OVATION & MAGNIT (AMIE) can provide other than electron diffuse aurora.
+- `AllowAurWODiffuse` was added for stability with OVATION-Prime; it restricts
+mono/wave/ion aurora to only exist in locations which also contain electron
+diffuse aurora. This can be set in [`#AURORAMODS`](../set_inputs.md#auroramods)
+
+Internally, GITM represents Monoenergetic and Wave/broadband aurora with a
+gaussian centered at the average energy.
+
+### Aurora Mods
+
+The diffuse aurora can be represnted by
+either a Maxwellian or Kappa distribution using the `#AURORAMODS` section of
+`UAM.in`:
+
+```
+#AURORAMODS
+F NormalizeAuroraToHP (logical)
+1.0 AveEFactor (real)
+F IsKappaAurora (logical)
+1.0 AuroraKappa (real)
+F AllowAurWODiffuse (logical)
+50.0 MaxAveEAurora (real)
+```
+
+
+
+## Potentials
+
+The following electric field models can be used:
+
+- Weimer05
+- Millstone-Hill
+- Heppner Maynard
+- AMIE
+
+## Required Input Files
+
+Each electrodynamics module has different inputs. At initialization, a
+verification check will be performed where GITM ensures that all the required
+input data are present and that the data file covers the entire simulation time
+range. If an input file ends before the requested stop time for a run, errors
+will be raised.
+
+The check for valid data is located within
+[`Electrodynamics/src/indices_subroutines.f90`](https://github.com/GITMCode/Electrodynamics/blob/main/src/indices_subroutines.f90).
+Some required input file-types are listed below:
+
+
+| Model | IMF | AE | HP | Kp |
+| :--- | :---: | :---: | :---: | :---: |
+| Weimer | Yes | No | No | No |
+| FRE | Yes | No | Yes | No |
+| HepMay | Yes | No | No | Yes |
+| FTA | No | Yes | No | No |
+| PEM | No | No | Yes | No |
+| Ovation | Yes | No | No | Yes |
+
+HP can be derived from AE, and is not necessarily required to be in a standalone
+file. See [here](../common_inputs.md#sme-indices) for more details.
+
+## File-based Electrodynamics
+
+AMIE (Assimilative Mapping of Ionospheric Electrodynamics) is the name chosen
+for the type of files which can be interpreted by Electrodynamics. A number of
+[Python routines](https://github.com/GITMCode/Electrodynamics/tree/main/srcPython)
+can be found in Electrodynamics which may be useful when generating these inputs.
+
+AMIE files can be used, for instance, to input custom auroral patterns into
+GITM. Once could generate an AMIE file with nominal diffuse electron aurora and
+several intense monoenergetic beams at any number of locations.
+
+## Running Electrodynamics Only
+
+By using the [`#STATISTICALMODELSONLY`](../set_inputs.md#statisticalmodelsonly)
+option in `UAM.in`, it is possible to run any configuration of Electrodynamics
+models without GITM's physics, making the runs faster.
+
+By setting the desired output type to [`2DGEL`](../outputs.md#2dgel), and an
+appropriate Dt for `#STATISTICALMODELSONLY` and `#OUTPUT`, GITM will read in the
+necessary input files and output precipitation & potential patterns using the
+specified electrodynamics modules. An example of this is located in
+`srcTests/auto_test/UAM.in.04.ElectrodynamicsGeoCoords.test`.
+
+Additionally, one can output data on a magnetic grid instead of geographic,
+which is often desired when plotting outputs from the electrodynamics modules.
+To do this, one must manually control the magnetic field configuration through
+the use of `#APEX` and `#DIPOLE` in `UAM.in`.
+
+By setting `#APEX` to F, GITM will use a tilted, offset dipole for the magnetic
+field. The tilt and offset are normally set automatically, however with the use
+of the `#DIPOLE` option, it is possible to force zero offset and tilt,
+effectively aligning the geographic and magnetic poles. The output files will
+then be in magnetic coordinates, on a magnetic grid, rather than geographic.
+
+A complete example file for this can be found in
+`srcTests/auto_test/UAM.in.05.ElectrodynamicsMagCoords.test`, where the
+following sections are what differs this test from the previous:
+
+```
+#APEX
+F Apex is turned off (so a dipole is used)
+
+#DIPOLE
+0.0 Magnetic Pole rotation
+0.0 Magnetic pole tilt
+0.0 x Dipole Center
+0.0 y Dipole Center
+0.0 z Dipole Center
+
+```
+
diff --git a/srcDoc/internals/grid.md b/srcDoc/internals/grid.md
new file mode 100644
index 00000000..e00dad40
--- /dev/null
+++ b/srcDoc/internals/grid.md
@@ -0,0 +1,203 @@
+# Setting the Grid
+
+Setting the grid resolution in GITM is not very complicated, but it does involve
+some thought. There are a few variables that control this.
+
+In essence, GITM's resolution is dictated by the number of CPU cores it is run
+on. The number of cores must equal the product of the number of blocks in
+longitude and latitude, which are both set in `UAM.in`. The resolution in the
+longitudinal and latitudinal directions are, by default, 9 times the number of
+blocks in each direction.
+
+## Important Variables
+
+Each CPU core that GITM is run on is considered a **block**. Within each block,
+the grid is further divided into individual grid **cells**. The number of cells
+per block is set before compiling, and the number of blocks to model is decided
+at runtime. The number of blocks per core cannot change from 1. How many cores
+GITM is run on is specified in the `UAM.in` file, and the number of cells within
+each block is specified in `src/ModSize.f90`.
+
+### Blocks (UAM.in)
+
+When GITM is first creating its grid, the region of interest (usually the entire
+globe) if first divided into blocks. Each block is a region that is modeled on a
+single CPU core. This is the most common variable to adjust when trying to
+change the resolution.
+
+These values are set in the `UAM.in` file and read at runtime. So the same
+executable can be used for many different resolutions without needing to
+recompile!
+
+For example, the initial settings have 2 blocks in latitude and 2 in
+longitude:
+
+ #GRID
+ 2 lons
+ 2 lats
+ -90.0 minimum latitude to model
+ 90.0 maximum latitude to model
+ 0.0 longitude start to model (set to 0.0 for whole Earth)
+ 0.0 longitude end to model (set to 0.0 for whole Earth)
+
+The number of CPU cores required is the product of the number of blocks in
+longitude and latitude. Doubling the resolution in both latitude and longitude
+requires four times as many cores since
+$`(2*nLons) \times (2*nLats) = 4\times (nLons*nLats)`$.
+
+```math
+nCPUs = (nBlocksLon) \times (nBlocksLat)
+```
+
+
+### Cells
+
+In `ModSize.f90`, the following variables are defined:
+
+```fortran
+integer, parameter :: nLons = 9
+integer, parameter :: nLats = 9
+integer, parameter :: nAlts = 50
+
+integer, parameter :: nBlocksMax = 1
+```
+
+The first three variables (`nLons`, `nLats` and `nAlts`) define the size of each
+block. In the defaults shown above, there are 9 cells in latitude, 9 cells in
+longitude and 50 altitude cells on each block.
+
+The final variable (`nBlocksMax`) defines the maximum number of blocks you can
+have on a single processor. This is deprecated and will cause issues when set to
+something other than 1. It will be removed in a future release.
+
+!!! note
+ If you change any of these parameters, you have to recompile the code.
+
+
+## Horizontal Resolution
+
+The number of *total* grid cells in the examples above will then be
+$`(2\times9=)18`$ in both longitude & latitude, and 50 in altitude. Given that
+there are $`360^\circ`$ in longitude and $`180^\circ`$ in latitude, the
+resolution would be $`360^\circ/18 = 20.0^\circ`$ in longitude and
+$`180^\circ/18 =10^\circ`$ in latitude. These settings are useful for debugging
+and developing, but not for production runs.
+
+For production runs, the resolution typically desired is $`4^\circ`$ longitude
+by $`1^\circ`$ latitude. With the default values in `src/ModSize.f90`, this
+requires 200 processing cores and the following values in the `UAM.in` file:
+
+ #GRID
+ 10 lons
+ 20 lats
+ -90.0 minimum latitude to model
+ 90.0 maximum latitude to model
+ 0.0 longitude start to model (set to 0.0 for whole Earth)
+ 0.0 longitude end to model (set to 0.0 for whole Earth)
+
+The longitudinal resolution ($`\Delta{\phi}`$) is set by:
+
+```math
+\Delta{\phi} = \frac{\phi_{end} - \phi_{start}}{nBlocksLon \times nCellsLon}
+```
+
+While the latitudinal resolution ($`\Delta{\theta}`$) is set by:
+
+```math
+\Delta{\theta} = \frac{\theta_{end} - \theta_{start}}{nBlocksLat \times nCellsLat}
+```
+
+---
+
+Some settings are listed below. Machines like NASA's Pleiades have a certain number of cores (processors) per node, like Ivy has 20 cores/node. An ideal setup would minimize the
+unused cores on each node, while balancing runtime (increases with more cells
+per block) and the number of files created (increases with more cores (blocks)). What this practically means is that it is a good idea to have the total number of processors used being a multiple of the processors/node.
+
+| Resolution $`(^\circ Lon \times ^\circ Lat)`$ | Total Cores | nBlocks (nLons x nLats) | nCells (nLon x nLat) |
+| :--- | ---- | :-----: | :----: |
+| 4 x 1 | 200 | 10 x 20 | 9 x 9 |
+| 4 x 1 | 360 | 10 x 36 | 9 x 5 |
+| 4 x 1 | 120 | 6 x 20 | 15 x 9 |
+| 4 x 1 | 180 | 9 x 20 | 10 x 9 |
+| 4 x 1 | 10 | 2 x 5 | 45 x 36 |
+| 2 x 0.5 | 800 | 20 x 40 | 9 x 9 |
+
+Experimentation may be necessary to find the parameters which work best on the
+system GITM is run on. You can always increase nCells in order to run on fewer processors - GITM will just take longer to run, but should be fine. For example, the second to last line shows that GITM can run at production levels on 10 processors, which relatively high-end laptops have currently and many modern desktop machines have.
+
+## Running 3D Over Part of the Globe
+
+GITM can be run over part of the globe - both in latitude and in longitude. It
+can be run over a single polar region by setting either the minimum or maximum
+latitude to be greater (or less) than $`\pm 90^\circ`$). If this is selected,
+message passing over the poles is implemented. For example, this simulates the entire northern polar region at $`4^\circ`$ longitude and $`1^\circ`$ latitude resolution:
+ #GRID
+ 8 lons
+ 4 lats
+ 45.0 minimum latitude to model
+ 90.0 maximum latitude to model
+ 0.0 longitude start to model (set to 0.0 for whole Earth)
+ 0.0 longitude end to model (set to 0.0 for whole Earth)
+
+If only part of the globe is selected, then boundary conditions have to be set in `set_horizontal_bcs.f90`. By default, a
+continuous gradient boundary condition is used on the densities and
+temperatures, while a continuous value is used on the velocity. This is true in
+both latitude and longitude.
+
+Running in a small region does not capture the global-scale dynamics, since the EUV heating on the dayside would not be specified correctly in the regions that are not modeled. So, things like the global-scale neutral wind pattern will not be correct. This means that if the physics that you are desiring to simulate depends on things that are more global-scale, then it is not a good idea to run over an isolated region. But, if the physics is much more localized and the time-scales are significantly shorter than a day, this is a fine feature to use. Example of good and bad cases would include:
+
+- Good case: Exploring how an ionospheric travelling convection vortex interacts with the local thermosphere to drive strong vertical winds.
+-Bad case: Exploring how to meridional neutral winds drive field-aligned flows over Michigan.
+
+In order to mitigate the effects of this (but not completely eliminate the effects), we have implemented a feature that allows you to use global-scale simulation results as a horizontal boundary condition for a regional simulation. In addition, GITM initializes the states with the global-scale simulation, so that you don't have to run the regional-scale simulation for a long period to get rid of the initial condition. In order to do this, you need to do the following:
+
+- Run one simulation over the whole globe using some nominal resolution, outputting 3DALL files at a time-scale that is appropriate for capturing the global-scale dynamics (say every 15 minutes if there is nothing of geophysical interest occuring). Remember that it is always a good idea to run 24 hours before an event in order to get rid of the initial condition!
+- Post process the 3DALL files.
+- Move the UA/data directory into some place like UA/GlobalScaleOutputs.
+- Make a new UA/data directory.
+- Modify the UAM.in file so that the grid captures the region of interest, and the start/end times align with the time of interest. Also, set the number of blocks so that you have the resolution you desire.
+- Add the following line into the UAM.in file:
+ #GITMBCS
+ T
+ UA/GlobalScaleOutputs
+
+Then, when you run GITM, it will simulate only the region of interest.
+
+## Altitudes
+
+As defined in `src/ModEarth.f90`, the altitude spacing in GITM is 0.3
+scale heights. In the UAM.in file, the starting altitude is typically set to 100 km. Given that in ModSize.f90, the number of altitudes is 50 (by default), GITM simulates 15 scale heights, typically reaching up to ~500-700 km.
+Increasing the number of altitudes in ModSize.f90 will increase the altitude range, but
+if this value is increased too much the model may become unstable and/or inaccurate. It is also possible to reduce the starting altitude below 100 km, but decreasing it below the mesopause is not a great idea, since the physics of the mesopause (i.e., CO2 cooling) is not included in the current version of GITM. Therefore, moving the lower boundary below about 95 km is not recommended.
+
+## Running in 1D
+
+GITM can run in 1D mode, in which the call to advance_horizontal is not
+completed. This means that GITM runs exactly the same way, but ignoring
+all of the horizontal advection terms. You have to do two things to make
+GITM run in 1D. First, in `ModSize.f90`:
+
+ integer, parameter :: nLons = 1
+ integer, parameter :: nLats = 1
+ integer, parameter :: nAlts = 50
+
+ integer, parameter :: nBlocksMax = 1
+
+This tells the code that you only want one single latitude and longitude
+location. To specify the exact location, in `UAM.in`:
+
+ #GRID
+ 1 lons
+ 1 lats
+ 41.75 minimum latitude to model
+ 41.75 maximum latitude to model
+ 275.0 minimum longitude to model
+ 275.0 maximum longitude to model
+
+This is some place in Michigan. GITM will model this
+exact point for as long as you specify. One thing to keep in mind with
+running in 1D is that the Earth still rotates, so the spot will have a
+strong day to night variation in temperature and will not capture any horizontal dynamics at all, such as the horizontal neutral winds (which are primarily driven by pressure gradients). In 3D, the winds decrease
+some of the variability between day and night, but in 1D, this doesn't
+happen. So, the results are not going to be (even close to) perfect. But 1D is great for
+debugging, since it is incredibly fast and many days can be run within a few minutes.
diff --git a/srcDoc/internals/overview.md b/srcDoc/internals/overview.md
new file mode 100644
index 00000000..86857e02
--- /dev/null
+++ b/srcDoc/internals/overview.md
@@ -0,0 +1,66 @@
+# Overview
+
+The Global Ionosphere Thermosphere Model (GITM) is a 3D model of the
+upper atmosphere. It runs for Earth, Mars and Titan. A version is being
+worked on for Jupiter. GITM solves for the coupled continuity, momentum
+and energy equations of the neutrals and ions. For the ions, the time
+rate of change of the velocity is ignored, so the steady-state ion flow
+velocity is solved for. The ion temperature is a mixture of the electron
+and neutral temperature.
+
+The neutrals are solved for using the Navier Stokes Equations. The
+continuity equation is solved for for each major species. One of the
+problems with GITM that needs to be rectified is that there are no real
+tracer species, so a species is either solved for completely or is not
+at all. These species can still be included in the chemistry
+calculation. There is only one horizontal velocity that is computed,
+while there are vertical velocities for each of the major species. A
+bulk vertical velocity is calculated as a mass weighted average. The
+temperature is a bulk temperature.
+
+## Source Terms
+
+Chemistry is the only real source term for the continuity equation.
+Typically, diffusion is added in the continuity equation to allow for
+eddy diffusion, but this is not the case in GITM. What happens is that
+the vertical velocities are solved for, then a friction term is applied
+to that the velocities stay very close together in the eddy diffusion
+part of the code. This way, the velocities can't differ too much from
+each other. Diffusion is not needed, then.
+
+For the horizontal momentum equation, there are the following sources:
+(1) ion drag; (2) viscosity; and (3) gravity wave acceleration. For the
+vertical velocity, the source terms are ion drag and friction between
+the different neutral species.
+
+For the neutral temperature, the following source terms are included:
+(1) radiative cooling; (2) EUV heating; (3) auroral heating; (4) Joule
+heating; (5) conduction; and (6) chemical heating. The biggest pain for
+the temperature equation is the use of a normalized temperature. This
+means that the `temperature` variable in GITM does not contain the
+actual temperature, it contains the temperature multiplies by
+Boltzmann's Constant divided by the mean mass. This turns out to be a
+factor that is very similar to the specific heat, or roughly or order
+1000. In order to get the actual temperature, the variable has to be
+multiplied by `temp_unit`.
+
+## Ghost Cells
+
+GITM is a parallel code. It uses a 2D domain decomposition, with the
+altitude domain being the only thing that is not broken up. Blocks of
+latitude and longitude are used. These blocks are then distributed among
+different processors. In order to communicate between the processors,
+ghostcells are used. These are cells that essentially overlap with the
+neighboring block. MPI (message passing interface) is then used to move
+information from one block to another, filling in the ghostcells. The
+code then loops from 1-N, where the flux is calculated at the boundaries
+from the 0-1 boundary to the N-N+1 boundary. A second order scheme is
+used to calculate the fluxes, along with a flux limiter. Therefore, two
+ghost cells are needed.
+
+In the vertical direction, ghost cells are also used to set boundary
+conditions. The values in these cells are used to calculate the fluxes,
+just as described above. Different types of boundary conditions
+(constant values, constant fluxes, constant gradients, floating, zero
+fluxes, etc) can be set by carefully choosing the right values in the
+ghost cells.
diff --git a/srcDoc/js/mermaid.min.js b/srcDoc/js/mermaid.min.js
new file mode 100644
index 00000000..5243aba4
--- /dev/null
+++ b/srcDoc/js/mermaid.min.js
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e=0;e{this[n]==="calculated"&&(this[n]=void 0)}),typeof e!="object"){this.updateColors();return}let r=Object.keys(e);r.forEach(n=>{this[n]=e[n]}),this.updateColors(),r.forEach(n=>{this[n]=e[n]})}},oh=o(t=>{let e=new QC;return e.calculate(t),e},"getThemeVariables")});var ZC,N$,M$=N(()=>{"use strict";Ys();Ay();o0();ZC=class{static{o(this,"Theme")}constructor(){this.background="#f4f4f4",this.primaryColor="#cde498",this.secondaryColor="#cdffb2",this.background="white",this.mainBkg="#cde498",this.secondBkg="#cdffb2",this.lineColor="green",this.border1="#13540c",this.border2="#6eaa49",this.arrowheadColor="green",this.fontFamily='"trebuchet ms", verdana, arial, sans-serif',this.fontSize="16px",this.tertiaryColor=Dt("#cde498",10),this.primaryBorderColor=Ti(this.primaryColor,this.darkMode),this.secondaryBorderColor=Ti(this.secondaryColor,this.darkMode),this.tertiaryBorderColor=Ti(this.tertiaryColor,this.darkMode),this.primaryTextColor=wt(this.primaryColor),this.secondaryTextColor=wt(this.secondaryColor),this.tertiaryTextColor=wt(this.primaryColor),this.lineColor=wt(this.background),this.textColor=wt(this.background),this.THEME_COLOR_LIMIT=12,this.nodeBkg="calculated",this.nodeBorder="calculated",this.clusterBkg="calculated",this.clusterBorder="calculated",this.defaultLinkColor="calculated",this.titleColor="#333",this.edgeLabelBackground="#e8e8e8",this.actorBorder="calculated",this.actorBkg="calculated",this.actorTextColor="black",this.actorLineColor="calculated",this.signalColor="#333",this.signalTextColor="#333",this.labelBoxBkgColor="calculated",this.labelBoxBorderColor="#326932",this.labelTextColor="calculated",this.loopTextColor="calculated",this.noteBorderColor="calculated",this.noteBkgColor="#fff5ad",this.noteTextColor="calculated",this.activationBorderColor="#666",this.activationBkgColor="#f4f4f4",this.sequenceNumberColor="white",this.sectionBkgColor="#6eaa49",this.altSectionBkgColor="white",this.sectionBkgColor2="#6eaa49",this.excludeBkgColor="#eeeeee",this.taskBorderColor="calculated",this.taskBkgColor="#487e3a",this.taskTextLightColor="white",this.taskTextColor="calculated",this.taskTextDarkColor="black",this.taskTextOutsideColor="calculated",this.taskTextClickableColor="#003163",this.activeTaskBorderColor="calculated",this.activeTaskBkgColor="calculated",this.gridColor="lightgrey",this.doneTaskBkgColor="lightgrey",this.doneTaskBorderColor="grey",this.critBorderColor="#ff8888",this.critBkgColor="red",this.todayLineColor="red",this.personBorder=this.primaryBorderColor,this.personBkg=this.mainBkg,this.archEdgeColor="calculated",this.archEdgeArrowColor="calculated",this.archEdgeWidth="3",this.archGroupBorderColor=this.primaryBorderColor,this.archGroupBorderWidth="2px",this.labelColor="black",this.errorBkgColor="#552222",this.errorTextColor="#552222"}updateColors(){this.actorBorder=Ot(this.mainBkg,20),this.actorBkg=this.mainBkg,this.labelBoxBkgColor=this.actorBkg,this.labelTextColor=this.actorTextColor,this.loopTextColor=this.actorTextColor,this.noteBorderColor=this.border2,this.noteTextColor=this.actorTextColor,this.actorLineColor=this.actorBorder,this.cScale0=this.cScale0||this.primaryColor,this.cScale1=this.cScale1||this.secondaryColor,this.cScale2=this.cScale2||this.tertiaryColor,this.cScale3=this.cScale3||Me(this.primaryColor,{h:30}),this.cScale4=this.cScale4||Me(this.primaryColor,{h:60}),this.cScale5=this.cScale5||Me(this.primaryColor,{h:90}),this.cScale6=this.cScale6||Me(this.primaryColor,{h:120}),this.cScale7=this.cScale7||Me(this.primaryColor,{h:150}),this.cScale8=this.cScale8||Me(this.primaryColor,{h:210}),this.cScale9=this.cScale9||Me(this.primaryColor,{h:270}),this.cScale10=this.cScale10||Me(this.primaryColor,{h:300}),this.cScale11=this.cScale11||Me(this.primaryColor,{h:330}),this.cScalePeer1=this.cScalePeer1||Ot(this.secondaryColor,45),this.cScalePeer2=this.cScalePeer2||Ot(this.tertiaryColor,40);for(let e=0;e{this[n]=e[n]}),this.updateColors(),r.forEach(n=>{this[n]=e[n]})}},N$=o(t=>{let e=new ZC;return e.calculate(t),e},"getThemeVariables")});var JC,I$,O$=N(()=>{"use strict";Ys();o0();Ay();JC=class{static{o(this,"Theme")}constructor(){this.primaryColor="#eee",this.contrast="#707070",this.secondaryColor=Dt(this.contrast,55),this.background="#ffffff",this.tertiaryColor=Me(this.primaryColor,{h:-160}),this.primaryBorderColor=Ti(this.primaryColor,this.darkMode),this.secondaryBorderColor=Ti(this.secondaryColor,this.darkMode),this.tertiaryBorderColor=Ti(this.tertiaryColor,this.darkMode),this.primaryTextColor=wt(this.primaryColor),this.secondaryTextColor=wt(this.secondaryColor),this.tertiaryTextColor=wt(this.tertiaryColor),this.lineColor=wt(this.background),this.textColor=wt(this.background),this.mainBkg="#eee",this.secondBkg="calculated",this.lineColor="#666",this.border1="#999",this.border2="calculated",this.note="#ffa",this.text="#333",this.critical="#d42",this.done="#bbb",this.arrowheadColor="#333333",this.fontFamily='"trebuchet ms", verdana, arial, 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e=0;e{this[n]=e[n]}),this.updateColors(),r.forEach(n=>{this[n]=e[n]})}},I$=o(t=>{let e=new JC;return e.calculate(t),e},"getThemeVariables")});var To,q4=N(()=>{"use strict";D$();R$();_y();M$();O$();To={base:{getThemeVariables:_$},dark:{getThemeVariables:L$},default:{getThemeVariables:oh},forest:{getThemeVariables:N$},neutral:{getThemeVariables:I$}}});var ql,P$=N(()=>{"use strict";ql={flowchart:{useMaxWidth:!0,titleTopMargin:25,subGraphTitleMargin:{top:0,bottom:0},diagramPadding:8,htmlLabels:!0,nodeSpacing:50,rankSpacing:50,curve:"basis",padding:15,defaultRenderer:"dagre-wrapper",wrappingWidth:200},sequence:{useMaxWidth:!0,hideUnusedParticipants:!1,activationWidth:10,diagramMarginX:50,diagramMarginY:10,actorMargin:50,width:150,height:65,boxMargin:10,boxTextMargin:5,noteMargin:10,messageMargin:35,messageAlign:"center",mirrorActors:!0,forceMenus:!1,bottomMarginAdj:1,rightAngles:!1,showSequenceNumbers:!1,actorFontSize:14,actorFontFamily:'"Open Sans", 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character "'+r[0]+'"'+(" ("+r.charCodeAt(0)+")"),e)),s={type:"textord",mode:"text",loc:Xs.range(e),text:r};else return null;if(this.consume(),a)for(var d=0;d{e instanceof Element&&e.tagName==="A"&&e.hasAttribute("target")&&e.setAttribute(t,e.getAttribute("target")??"")}),ch.addHook("afterSanitizeAttributes",e=>{e instanceof Element&&e.tagName==="A"&&e.hasAttribute(t)&&(e.setAttribute("target",e.getAttribute(t)??""),e.removeAttribute(t),e.getAttribute("target")==="_blank"&&e.setAttribute("rel","noopener"))})}var nd,Y4e,X4e,BG,OG,Tr,K4e,Q4e,Z4e,J4e,FG,e3e,fr,t3e,r3e,ec,J7,n3e,i3e,PG,eA,pi,id,mh,Ze,gr=N(()=>{"use strict";u7();nd=/ /gi,Y4e=o(t=>t?FG(t).replace(/\\n/g,"#br#").split("#br#"):[""],"getRows"),X4e=(()=>{let t=!1;return()=>{t||(j4e(),t=!0)}})();o(j4e,"setupDompurifyHooks");BG=o(t=>(X4e(),ch.sanitize(t)),"removeScript"),OG=o((t,e)=>{if(e.flowchart?.htmlLabels!==!1){let r=e.securityLevel;r==="antiscript"||r==="strict"?t=BG(t):r!=="loose"&&(t=FG(t),t=t.replace(//g,">"),t=t.replace(/=/g,"="),t=J4e(t))}return t},"sanitizeMore"),Tr=o((t,e)=>t&&(e.dompurifyConfig?t=ch.sanitize(OG(t,e),e.dompurifyConfig).toString():t=ch.sanitize(OG(t,e),{FORBID_TAGS:["style"]}).toString(),t),"sanitizeText"),K4e=o((t,e)=>typeof t=="string"?Tr(t,e):t.flat().map(r=>Tr(r,e)),"sanitizeTextOrArray"),Q4e=o(t=>nd.test(t),"hasBreaks"),Z4e=o(t=>t.split(nd),"splitBreaks"),J4e=o(t=>t.replace(/#br#/g," "),"placeholderToBreak"),FG=o(t=>t.replace(nd,"#br#"),"breakToPlaceholder"),e3e=o(t=>{let e="";return t&&(e=window.location.protocol+"//"+window.location.host+window.location.pathname+window.location.search,e=e.replaceAll(/\(/g,"\\("),e=e.replaceAll(/\)/g,"\\)")),e},"getUrl"),fr=o(t=>!(t===!1||["false","null","0"].includes(String(t).trim().toLowerCase())),"evaluate"),t3e=o(function(...t){let e=t.filter(r=>!isNaN(r));return Math.max(...e)},"getMax"),r3e=o(function(...t){let e=t.filter(r=>!isNaN(r));return Math.min(...e)},"getMin"),ec=o(function(t){let e=t.split(/(,)/),r=[];for(let n=0;n0&&n+1Math.max(0,t.split(e).length-1),"countOccurrence"),n3e=o((t,e)=>{let r=J7(t,"~"),n=J7(e,"~");return r===1&&n===1},"shouldCombineSets"),i3e=o(t=>{let e=J7(t,"~"),r=!1;if(e<=1)return t;e%2!==0&&t.startsWith("~")&&(t=t.substring(1),r=!0);let n=[...t],i=n.indexOf("~"),a=n.lastIndexOf("~");for(;i!==-1&&a!==-1&&i!==a;)n[i]="<",n[a]=">",i=n.indexOf("~"),a=n.lastIndexOf("~");return r&&n.unshift("~"),n.join("")},"processSet"),PG=o(()=>window.MathMLElement!==void 0,"isMathMLSupported"),eA=/\$\$(.*)\$\$/g,pi=o(t=>(t.match(eA)?.length??0)>0,"hasKatex"),id=o(async(t,e)=>{t=await mh(t,e);let r=document.createElement("div");r.innerHTML=t,r.id="katex-temp",r.style.visibility="hidden",r.style.position="absolute",r.style.top="0",document.querySelector("body")?.insertAdjacentElement("beforeend",r);let i={width:r.clientWidth,height:r.clientHeight};return r.remove(),i},"calculateMathMLDimensions"),mh=o(async(t,e)=>{if(!pi(t))return t;if(!(PG()||e.legacyMathML||e.forceLegacyMathML))return t.replace(eA,"MathML is unsupported in this environment.");let{default:r}=await Promise.resolve().then(()=>(IG(),MG)),n=e.forceLegacyMathML||!PG()&&e.legacyMathML?"htmlAndMathml":"mathml";return t.split(nd).map(i=>pi(i)?`
+`}tablecell(e){let r=this.parser.parseInline(e.tokens),n=e.header?"th":"td";return(e.align?`<${n} align="${e.align}">`:`<${n}>`)+r+`${n}>
+`}strong({tokens:e}){return`${this.parser.parseInline(e)}`}em({tokens:e}){return`${this.parser.parseInline(e)}`}codespan({text:e}){return`${pc(e,!0)}`}br(e){return" "}del({tokens:e}){return`${this.parser.parseInline(e)}`}link({href:e,title:r,tokens:n}){let i=this.parser.parseInline(n),a=Fj(e);if(a===null)return i;e=a;let s='"+i+"",s}image({href:e,title:r,text:n}){let i=Fj(e);if(i===null)return pc(n);e=i;let a=`",a}text(e){return"tokens"in e&&e.tokens?this.parser.parseInline(e.tokens):"escaped"in e&&e.escaped?e.text:pc(e.text)}},p2=class{static{o(this,"_TextRenderer")}strong({text:e}){return e}em({text:e}){return e}codespan({text:e}){return e}del({text:e}){return e}html({text:e}){return e}text({text:e}){return e}link({text:e}){return""+e}image({text:e}){return""+e}br(){return""}},_l=class t{static{o(this,"_Parser")}options;renderer;textRenderer;constructor(e){this.options=e||Id,this.options.renderer=this.options.renderer||new fm,this.renderer=this.options.renderer,this.renderer.options=this.options,this.renderer.parser=this,this.textRenderer=new p2}static parse(e,r){return new t(r).parse(e)}static parseInline(e,r){return new t(r).parseInline(e)}parse(e,r=!0){let n="";for(let i=0;i{let l=a[s].flat(1/0);n=n.concat(this.walkTokens(l,r))}):a.tokens&&(n=n.concat(this.walkTokens(a.tokens,r)))}}return n}use(...e){let r=this.defaults.extensions||{renderers:{},childTokens:{}};return e.forEach(n=>{let i={...n};if(i.async=this.defaults.async||i.async||!1,n.extensions&&(n.extensions.forEach(a=>{if(!a.name)throw new Error("extension name required");if("renderer"in a){let s=r.renderers[a.name];s?r.renderers[a.name]=function(...l){let u=a.renderer.apply(this,l);return u===!1&&(u=s.apply(this,l)),u}:r.renderers[a.name]=a.renderer}if("tokenizer"in a){if(!a.level||a.level!=="block"&&a.level!=="inline")throw new Error("extension level must be 'block' or 'inline'");let s=r[a.level];s?s.unshift(a.tokenizer):r[a.level]=[a.tokenizer],a.start&&(a.level==="block"?r.startBlock?r.startBlock.push(a.start):r.startBlock=[a.start]:a.level==="inline"&&(r.startInline?r.startInline.push(a.start):r.startInline=[a.start]))}"childTokens"in a&&a.childTokens&&(r.childTokens[a.name]=a.childTokens)}),i.extensions=r),n.renderer){let a=this.defaults.renderer||new fm(this.defaults);for(let s in n.renderer){if(!(s in a))throw new Error(`renderer '${s}' does not exist`);if(["options","parser"].includes(s))continue;let l=s,u=n.renderer[l],h=a[l];a[l]=(...f)=>{let d=u.apply(a,f);return d===!1&&(d=h.apply(a,f)),d||""}}i.renderer=a}if(n.tokenizer){let a=this.defaults.tokenizer||new hm(this.defaults);for(let s in n.tokenizer){if(!(s in a))throw new Error(`tokenizer '${s}' does not exist`);if(["options","rules","lexer"].includes(s))continue;let l=s,u=n.tokenizer[l],h=a[l];a[l]=(...f)=>{let d=u.apply(a,f);return d===!1&&(d=h.apply(a,f)),d}}i.tokenizer=a}if(n.hooks){let a=this.defaults.hooks||new um;for(let s in n.hooks){if(!(s in a))throw new Error(`hook '${s}' does not exist`);if(["options","block"].includes(s))continue;let l=s,u=n.hooks[l],h=a[l];um.passThroughHooks.has(s)?a[l]=f=>{if(this.defaults.async)return Promise.resolve(u.call(a,f)).then(p=>h.call(a,p));let d=u.call(a,f);return h.call(a,d)}:a[l]=(...f)=>{let d=u.apply(a,f);return d===!1&&(d=h.apply(a,f)),d}}i.hooks=a}if(n.walkTokens){let a=this.defaults.walkTokens,s=n.walkTokens;i.walkTokens=function(l){let u=[];return u.push(s.call(this,l)),a&&(u=u.concat(a.call(this,l))),u}}this.defaults={...this.defaults,...i}}),this}setOptions(e){return this.defaults={...this.defaults,...e},this}lexer(e,r){return Al.lex(e,r??this.defaults)}parser(e,r){return _l.parse(e,r??this.defaults)}parseMarkdown(e){return o((n,i)=>{let a={...i},s={...this.defaults,...a},l=this.onError(!!s.silent,!!s.async);if(this.defaults.async===!0&&a.async===!1)return l(new Error("marked(): The async option was set to true by an extension. Remove async: false from the parse options object to return a Promise."));if(typeof n>"u"||n===null)return l(new Error("marked(): input parameter is undefined or null"));if(typeof n!="string")return l(new Error("marked(): input parameter is of type "+Object.prototype.toString.call(n)+", string expected"));s.hooks&&(s.hooks.options=s,s.hooks.block=e);let u=s.hooks?s.hooks.provideLexer():e?Al.lex:Al.lexInline,h=s.hooks?s.hooks.provideParser():e?_l.parse:_l.parseInline;if(s.async)return Promise.resolve(s.hooks?s.hooks.preprocess(n):n).then(f=>u(f,s)).then(f=>s.hooks?s.hooks.processAllTokens(f):f).then(f=>s.walkTokens?Promise.all(this.walkTokens(f,s.walkTokens)).then(()=>f):f).then(f=>h(f,s)).then(f=>s.hooks?s.hooks.postprocess(f):f).catch(l);try{s.hooks&&(n=s.hooks.preprocess(n));let f=u(n,s);s.hooks&&(f=s.hooks.processAllTokens(f)),s.walkTokens&&this.walkTokens(f,s.walkTokens);let d=h(f,s);return s.hooks&&(d=s.hooks.postprocess(d)),d}catch(f){return l(f)}},"parse")}onError(e,r){return n=>{if(n.message+=`
+Please report this to https://github.com/markedjs/marked.`,e){let i="