Add svFSIplus documentation

[ktbolt]

Use Case

It would be helpful to users to have documentation describing how to use svFSIplus.

Problem

There is no svFSIplus documentation.

Solution

Write svFSIplus documentation.

Alternatives considered

Don't write svFSIplus documentation.

Additional context

No response

Code of Conduct

• I agree to follow this project's Code of Conduct and Contributing Guidelines

[ktbolt]

I am going to start on this.

@alisonmarsden Should I remove the svFSI documentation?

[alisonmarsden]

Yes ok to remove old documentation as soon as new docs are available. Eventually we should also remove svSolver docs as well.

…

--------------------------------------------------------------- Alison Marsden, PhD (she / her) Douglass M. and Nola Leishman Professor of Cardiovascular Disease Professor of Pediatrics and Bioengineering, and by courtesy of Mechanical Engineering Institute for Computational and Mathematical Engineering Stanford University https://cbcl.stanford.edu/ www.simvascular.org<http://www.simvascular.org> Co-Director CHIP T32 Program https://med.stanford.edu/cvi/education/chip-t32.html#appl From: Dave Parker ***@***.***> Date: Saturday, May 11, 2024 at 2:11 PM To: SimVascular/simvascular.github.io ***@***.***> Cc: Alison Lesley Marsden ***@***.***>, Mention ***@***.***> Subject: Re: [SimVascular/simvascular.github.io] Add svFSIplus documentation (Issue #19) I am going to start on this. @alisonmarsden<https://github.com/alisonmarsden> Should I remove the svFSI documentation? — Reply to this email directly, view it on GitHub<#19 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ADJGJZ23BRPVGLHY7DJLL2TZB2CORAVCNFSM6AAAAABGTW6NVSVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCMBWGAZTEMJTGU>. You are receiving this because you were mentioned.Message ID: ***@***.***>

[ktbolt]

I've taken the svFSI docs and reorganized them for svFSIplus, not sure of the final format yet.

[ktbolt]

I am also experimenting with documenting the solver input XML file by showing the XML element name, type and a link (blue) to the parameter definition.

[ktbolt]

I've added more solver input XML file documentation: mesh, equation, linear solver and boundary condition parameters

I am currently documenting parameters in two sections

1. XML format

2. Description

clicking on the blue XML format moves the page to that parameter's description.

I thought this would help show the XML structure better because it can have nested sections.

But maybe having the XML format and description together would be better.

[ktbolt]

I've changed the parameter format to have the XML format and description together

This is super tedious to write but I think it works better.

[ktbolt]

I've mostly finished the XML parameter documentation, still a bunch of parameters that are not documented, no definitions in the svFSI svFSI_master.inp file.

[ktbolt]

I'm now writing a Running svFSI section to explain element types and node ordering, VTK mesh files, BC data files formats, etc.

[ktbolt]

I've added most of the FSI Tool documentation, still need to add some of the parameter descriptions though.

[ktbolt]

I've added a Tutorial for setting up a fluids simulation.

[ktbolt]

I've added a rough User Guide section taking material from the svFSI documentation

This section is going to require a lot more work.

[ktbolt]

I've now added a Data File Format section documenting the formats of

• Text files used for boundary conditions and domain IDs
• VTK files for mesh, initial conditions and boundary conditions

[ktbolt]

I'm now adding a bit of Developer Guide documentation.

[ktbolt]

I've added a Code Organization section documenting the organization of the files and such.

[ktbolt]

I've added an Implementation Details section which covers some useful details of the well, implementation

In the Flow of Control section I outline the calling sequence and such of the program

and

[ktbolt]

I've added Linear Algebra Interface

and VTK Interface implementation sections

[ktbolt]

@MatteoSalvador @aabrown100-git @mrp089 @menon-karthik @dcodoni @zasexton @kharold23 @elenasmartinez @lpapamanolis @msbazzi I've finished all that I can do for the documentation.

I now need people to

• check for errors
• suggest any rewrite/reorganization
• add docs for xml parameters that I couldn't explain, especially for electrophysiology
• write a theory section
• rewrite the User Guide sections; these were take from the svFSI docs

Clone the https://github.com/ktbolt/simvascular.github.io/tree/Add-svFSIplus-documentation_19 branch and have a look.

I use caddy to view the web pages

• install
• cd to simvascular.github.io
• run caddy file-server --listen localhost:2015