Adding first example to svMultiPhysics User Guide - #111

@justran-csuf The CFD User Guide content should be placed under simvascular.github.io/documentation/multi_physics/user-guide with the other user guide content

cardiac_electrophysiology/	hemodynamics/			nonlinear_solid_dynamics/
fluid_solid_interaction/	material_models/		readme.md

I think now that we are only supporting one solver, it makes sense to document how to run simulations with all the different physics one may want to use: CFD, EP, mechanics, etc. All of these will now be done with svMultiPhysics. Some of this content is already in the "SimCardio" section, so we should break that up and move the content to the relevant sections (for example there is quite a nice description there on how to run an EP simulation which needs to be updated). See the google slide I sent a while back with a possible outline. We could have a header on running simulations with svMultiPhycis, and in the main menu then list all the different physics options in an easy to find manner.

@ktbolt Got it, I will move it to that folder. Should this content be in its own folder? Maybe simvascular.github.io/documentation/multi_physics/user-guide/cfd? I see now that the User Guide is currently part of the multi_physics.html file but commented out. That page is getting pretty crowded already with everything that is there. Did you want me to take a look and organize that page? I think it would be good to split that page into separate pages. The 'Theory' section can probably be a separate page since most users will likely not be looking at the governing equations.

@justran-csuf It should be in its own folder. We will rearrange content later on.

@justran-csuf I don't see your content. Do you see it in a local browser ?

@justran-csuf I don't see the User Guide section in the documentation, seems like that is commented out, so you wll need to uncomment it and add your section.

@ktbolt I added my CFD User Guide content to the main multi_physics.html. I also created a "svmp_user_guide_staging.hrml" file if you want to view the content separately.

@justran-csuf You need to sync your fork with https://github.com/SimVascular/simvascular.github.io main branch.

@justran-csuf Wait, I am not seeing the new menu organization using my local web browser. Do you see it ?

@ktbolt I am not sure how to check the new menu organization. I only have been changing files in the "documentation" folder and created my own .html file for staging. I created my fork a while ago when we deleted the branches off the main repository. How often should I be syncing my fork? I have just been focused on getting the content finished.

@justran-csuf You should update your fork after you see a PR here.

Don't you use a local web server to see the changes that you've made ?

@ryanspilker Can you see the new menu organization using caddy ? I do see it if I load the index.html file in Chrome.

@ktbolt The problem appears to be that Justin’s feature branch is behind the repository’s main branch. PR #111 was created before PRs #110 and #109 were merged. Merging current main into the PR branch should complete without conflicts and bring the new menu together with Justin’s CFD examples.

@justran-csuf First make sure git status reports no uncommitted changes. Then, in your local clone, run:

git remote -v
git fetch upstream
git switch main
git merge --ff-only upstream/main
git push origin main
git switch 100-creating-cfd-user-guide
git merge main
git push origin 100-creating-cfd-user-guide

If git remote -v does not list https://github.com/SimVascular/simvascular.github.io.git as upstream, add it before running git fetch upstream:

git remote add upstream https://github.com/SimVascular/simvascular.github.io.git

Afterward, preview the repository from its root, and open documentation/multi_physics.html. That page tests the shared menu and your CFD content together. Once it works there, the temporary staging HTML file can be removed.

@ryanspilker My fork is synced but the web page still does not appear like the new organization when I use caddy. It looks fine when I load the index.html using Chrome so I guess I will use that.

Thanks @ryanspilker for the instructions. I think I did everything correctly... When I use the Live Server extension in Visual Studio on the "index.html", I can see the new table of contents. Then when I navigate to the svMultiPhysics page, I see my new content as well.

@ktbolt I have been using the Live Server extension in Visual Studio, but I was using it directly onto my staging file so I could view my content. I never tried using it on the index.html before now.