README.md

Welcome to the Github repository of the radtrancode project. This project is the development area for the Radtrans and Nemesis codes for radiative transfer calculations and retrievals, originally written in Oxford University.

If you want to use radtrancode/nemesis you have one of three options:

1. You can check out the repository and compile it yourself on your system (details are below).
2. You can pull a pre-compiled 'image' of the code from Docker Hub at https://hub.docker.com/r/patrickirwinoxford/docker_nemesis and run it with Docker.
3. You can make your own Docker image of the code and use this with Docker.

So what is the advantage of Docker? As some of you will have discovered, getting Nemesis to compile and run can be a challenge. It can be done reasonabally painlessly if you use Linux as we do here in Oxford for our main number-crunching, but it has proven increasingly difficult to get it to compile on other operating systems, such as MacOS, for example. Docker runs the code in a virtual machine 'container' in such a way that system differences no longer matter.

If you want to use Nemesis with Docker, you will first need to install the Docker Desktop from (www.docker.com). You can then either download the current precompiled release 'image' from the Docker Hub (see above), or you can make your own inage from your local copy of the code (make sure you are in the radtrancode directory) using:

docker-compose build

You will also need to add aliases to your shell setup file, which can be found at https://github.com/shubhamvkulkarni/Docker_aliases_for_NEMESIS.git. Depending on whether you use .cshrc, .bashrc or .zsh, you need to download the appropriate add_nemesis_docker_aliases file AND the list of executables, nemesis_executables.txt, into your home directory and run the shell script there. This will add aliases to your shell setup file so that when you run Nemesis, or any other of the radtrancode executables, the system will automatically run the Docker build. All input/output files are passed seamlessly into and out of the Docker 'container'. I am infinitely grateful to my recently graduated D.Phil. student, Shubham Kulkarni, for setting up the Docker route, and to Anna Conly (NSMU) for also developing the Docker implementation.

If you want to compile radtrancode/nemesis yourself (and thus be able to edit the code and recompile as you wish), please do the following steps:

---

On your system go to the directory where you want to put the radtrancode git repository, i.e.,

cd somewhere safe, for example

cd ~/repositories

then type

git clone https://github.com/nemesiscode/radtrancode.git

You should now have the current git repository in your safe directory.

Now on your system type the command:

git config --global --list

If you don’t see something like:

user.name=Firstname Lastname						{obviously your name here}
user.email=firstname.lastname@...             {obviously your email address here}

then you should add them before checking anything in or out. To do this type:

git config --global user.name “Firstname Lastname" 
git config --global user.email “firstname.lastname@...  “ 

Also, if you want to change the default git editor from “vi” or “vim” type something like: git config --global core.editor “pico"

Finally, if you want the system to give you colour-coded git status messages (which do look quite pretty) type:

git config --global color.ui "auto"

To update your copy with the latest version on github the command is:

git pull origin

(updates the default branch master)

To check in your updates to github you type

git push origin <branchname>

To compile the code, please look at the instrunctions in AACOMPILE.txt. Remember to check the ISYS variable for your specific compilation (check AACOMPILE.txt). It is also helpful to add the following to your BASHRC/CSHRC file:

export RADREPO=/PATH-TO/radtrancode/

...as this will prevent you having to update the dataarchive.f code every time to point to your raddata directory.