Documentation of the EMI model
This is a summary of email communication with other contributors regarding the documentation of EMI. Any further help or comments are welcome.
cc: @fatemeh @wissambouymedj @joshuasteyer @axel.loewe
Local instance of LaTeX
You can find the source code in the opencarp git repository (the one you install the opencarp from), in the location docs/manual/
.
Depending on the operating system that there are different ways to install the texlive package (which contains the necessary files). The simplest approach is to install it from the software repositories (e.g. on Debian GNU/Linux distribution via the command sudo apt install texlive-full
). There might be similar commands on other operating systems, but I'm not familiar with it. Otherwise there is always the option to download the software from the internet and install it manually (as is described here: https://tug.org/texlive/ ).
I have now also included a Dockerfile
that contains the instructions on how to install the required dependencies within the container. Then I have put the recipe to build and start the container to the docs/manual/makefile
so you can setup a working latex environment with the following commands from the root of openCARP repo:
cd docs/manual/
make docker # WARNING: 5GB in size, use only if you don't want or have texlive installed in your system
LATEX_FLAGS=-pvc make emi.pdf
Then you can edit emi-doc.tex
, this automatically updates the document emi.pdf
. Check the command line from time to time, for compilation errors, that might appear in red (but which won't break the compilation automatically).
It would be very useful, if you could look more into the documentation I was writing on EMI. I would like to have it as understandable as possible for someone with a basic mathematical knowledge.
The aim is to have a complete definition of the EMI model and the FEM solution of it similar to the one described in the opencarp-manual-June23.pdf for monodomain model.
If something in the current emi-doc.tex documentation is not completely clear please point it out, or just make a note in the document. I am using a \note{}
latex macro, e.g.
\note{this is not clear}
in the document, to write this kind of notes (which are shown red in the draft and can be easily removed from the final document).
The variable definitions are kept in the notations.tex
file. So they are defined in one place are shorhand version of latex notations and can be easily redefined, if a naming collision may appear. Please have a look which variables are already defined and in case you need any additional definitions, just place it in the notations.tex
file. (The variables without parameters are defined as \+{}{}
, with one parameter \1{}{}
etc., the #1
is then the parameter within the definitions).
The main text is then in emi-doc.tex
and follows the latex syntax. You can edit it or 1) localy or 2) on overleaf.com. I will here describe the two ways, if you decide for one and not the other, just read one of the options.