The documentation has simulation results sections for various User Guides and Clinical Cases describing converting solver results and visualizing OSI. However, it fails to mention that to get OSI results you must set the convert results Start step to be non-zero.

I'm not sure if I should add this to the documentation or fix svpost, this kind of implicit behavior causes a lot of problems for the user.

A user has encountered several problems while trying to use GenBC on Windows OS. The following steps were needed to allow creating a GenBC executable

1. Install Mingw to compile GenBC fortran code
2. Add -pg flag when compiling
3. Create executable named GenBC not GenBC.exe

I will add these steps to the GenBC documentation.

Now that svFSI has its own dedicated pages, the existing SimCardio page can be restructured to better demonstrate the scope of the project. I would like to propose a change like this:

Here, Cardiac Geometric Modeling Tools describes Fanwei's machine-learning based cardiac modeling workflow. Multiphysics finite element solver will direct readers to svFSI page. Purkinje Network Plugin showcases the generation of Purkinje network using SimVascular plugin.

The current 3D segmentation documentation http://simvascular.github.io/docsQuickGuide.html#imagenavigator is out of date

1. The Colliding Fronts documentation describes a panel that does not look anything like the current panel. The way to access this panel is also not correct, Colliding Fronts is no longer accessed under the SV Data Manager Segmentations menu.

2. The SV MITKSegmentation tool it not even described.

I will figure out how to use these tools and then document them.

Vijay should be added to the developer team on the main SV website under "our team".

There is no documentation for the ROM 1D Simulation stenosis model.

@JonathanPham or @mrp089 Can you please add the documentation? If you send me the text and equations I can add it.

Documentation describing the SimVascular Python API needs to be added to the SimVascular web site.

This replaces the SimVascular GitHub Issue #519.

I've added a Python Interface entry under User Guides documentation and several sections to the Python Interface page.

The svOneDSolver documentation needs to be updated with the current documentation in https://github.com/SimVascular/svOneDSolver/tree/master/docs.

It is a royal pain to have two places for documentation. The documentation in https://github.com/SimVascular/svOneDSolver/tree/master/docs is really not that useful to users because you have to clone the repo, install sphinx and then build the documentation.

1D Simulations plugin has been renamed to the Reduced-Order Model Simulation plugin. This plugin now supports both 1D and 0D simulations.

We need to do a simple clean up of the documentation

1. Remove old content

2. Fix installation links

3. Fix menus

The tutorial videos on the SV youtube channel may be quite useful to the user community and the link should be featured more prominently in the documentation. The SV youtube channel is here: https://www.youtube.com/channel/UCT61XgTRqpfb39Hyio9IqGQ
These were created in the summer of 2020 and have already had quite a few views.

svFSI documentation on http://simvascular.github.io is currently split between two sections: SVFSI GUIDE and SIMCARDIO GUIDE. It might be better to merge all svFSI related contents to SVFSI GUIDE so that users can find everything in one place.

Documentation describing the SimVascular 1D Simulation Tool and 1D Solver needs to be added to the SimVascular web site.

The website should have a page with a summary of features and capabilities for both the front end and the solvers, grouped into categories.

The main page Team section needs to be updated.

When using the cap_with_ids returns error vmtk.Error: Vmtk.cap_with_ids() Error creating cap with ids. "cap" works fine, but does not return proper array name for later steps.

The last reference for the theory on the 0D Solver is blocked by the "Copyright © SimVascular Development Team - 2017" sign (see image below). Is there a way to fix this issue?

In the Simulation Guide - Example 3 section the following text is supposed to describe how to setup a deformable wall simulation in svSolver

Different from Example 2, the step also solves initial displacement, write the initial displacment to a vtp file “displacement.vtp” to review the solution, and finaly append it to restar.0.1 we just copied from restart.500.0 of Example 2.

Even without the spelling mistakes it is not at all clear what this means; append a vtp file to a restart file?

We can probably just remove this bit.

The link to the python interface is missing from the menu at the top of the documentation pages. It should be added as a link in the menu bar under user guides at the top of this page: http://simvascular.github.io/docsPythonInterface.html

When selecting the 1D SIMULATION GUIDE menu item from SV Documentation the 1D Simulation Guide page text does not display. The TOC does show up but not text.

I think it would be more efficient if the "documentation" button at the top of the main SV homepage took you directly to a documentation landing page. We could eliminate the documentation section of the main page and take users directly to the documentation sites. Right now it requires two clicks to get to documentation when it could be one.

The Colliding Fronts plugin has been rewritten with a new GUI (see SimVascular/SimVascular#706). I need to now update the SV web documentation.

The Colliding Fronts documentation is under the Modeling Guide / Segmentation / Segmenting an image with 3D segmentation section.

I also need to make sure all GUI widgets have Qt documentation that appears when the mouse hovers over the widget, most widgets are already documented.

Ethan Kung's group has developed a useful protocol for adaptive meshing.

Add a description of the protocol to the Meshing Adaptive section. Also add a reference to the paper.

We should list NSF SSI and NIH NLM to acknowledge funding sources supporting SimVascular.

The MathJax mathematical notation JavaScript library is not loading because of increased security measures on MacOS and Windows platforms.

The 3-D Segmentation section in http://simvascular.github.io/docsQuickGuide.html is wrong, seems to be describing an old implementation of colliding fronts.

The Segmenting an image with 3D segmentation section in http://simvascular.github.io/docsModelGuide.html#modeling3DSeg section seems OK except it references a different colliding fronts icon in the SV toolbar.

Note that there is no documentation for the SV MITKSegmentation tool.

It's currently difficult to quickly figure out what features / functionality SimVascular provides. I think the website needs a concise list of features with short descriptions or link to documentation. For example:

• FSI with ALE
• FSI with CMM
• electrophysiology simulations
• reduced order model generation
• boundary conditions with OD models
• etc.

I can't find anywhere on the main SimVascular website where it says we provide cross platform support. You have to go to the simtk.org downloads site to see that there are installers available for mac, windows, and linux. Since this is a major selling point of our project, we should highlight it more.

Exporting models to different formats differs in how face information is retained. The .stl and .ply formats don't retain face information, the .vtp format does.

There are two ONLINE TUTORIALS sections in the home web page, remove one.

I main page WORKSHOPS is out of date. I'll update it for the three 2021 Workshops.

The Modeling Guide blending documentation shows the following Modeling tool Blend panel

However, the Blend panel in the current SV GUI looks like

None of the parameters in the lower part of this panel are documented.

The mostly older documentation has numerous spelling mistakes, I found six in a single section in the Modeling Guide.

The newer documentation looks pretty good but the simcardio docs seem to have a few.

Spelling is easy to check and correct with aspell, will go though the docs and fix the spelling missteaks.

We are getting a Known security vulnerabilities detected alert from GitHub for

activesupport
rack
sprockets
ffi

We need to update the versions of these guys.

The discussion of theBCT file format in http://simvascular.github.io/docsFlowSolver.html#bctfile is missing the definition of nn

np nl
x1 y1 z1 nl nn
vx1  vy1  vz1  t1
 .    .    .    .
 .    .    .    .
 .    .    .    .
vxnl vynl vznl tnl

nn is the global node ID of an inlet node. I had to look in the svSolver source to figure this out!

This description could be made clearer by using subscripts (vxnl) and why not use descriptive names rather than two-characters: np -> NumFaceNodes.

ParaView is typically used to visualize SV simulation results. There are several short discussions about visualizing results in various sections of the documentation but I think it would be helpful to users to have a section dedicated to using ParaView, add more detailed information.

The Quick Guide Simulation section does not mention that you need to install svSolver to run a simulation.

The Simulation Guide section wrongly states

Notice: To get full functions from the Simulation tool, it uses three solvers: Presolver (svPre), Flowsolver (svSolver), Postsolver (svPost). Normally, SimVascular already includes the solvers and can find them automatically. Users don’t need to set up the solvers. However, in case SimVascular can’t find them while users are using the Simulation tool, refer to Solver Configuration.

There are not three solvers and they are not included in SV.

In the Simulation Guide/Configurating Solvers (Optional) section contradicts the above section and does hint that you may need to install svSolver.

SimVascular solvers(presolver, flowsolver, postsolver) are used as individual executable programs. They are called by SV Simulation tool to create data files, run simulation, and convert results to files in VTK formats. Normally those solvers are installed separately. However, SimVascular can automatically find those solvers. In case your SimVascular can’t find them, or you want to use different solvers, you need to explicitly tell SimVascular where to find or how to use them.

I will add a section (not optional) that states that svSolver needs to be installed and how to install it.

I got some Fortran code and a bit of text from Weiguang to add a new section to the GenBC tutorial for a pressure waveform boundary condition.

The GenBC tutorial did not work as described so I did some rewrite to correct it and make it a bit more more concise.

It was not clear how to use the code but I got it finally working with help from Weiguang. I will now add the steps to the tutorial needed to reproduce the correct solver.inp and .svpre files.

We need to add some information about the SimCardio project to the SV website.

I am a student at Clemson University and requested access to the Simvascular Supercomputing Gateway last week in order to run CFD's with Simvascular models. What is the normal timeline to expect for being approved?

Thanks,
Daniel Custer

The documentation for the 0D solver is outdated, due to the addition of the BloodVessel block, which replaced the following elements:

• Resistor
• RC
• RL
• RLC.

Need to update the 0D solver documentation to reflect this update in svZeroDSolver.

Ignoring the README here that states DO NOT edit the master branch files! and not followiing the existing documentation practices the initial SimCardio Guide documentation was incorrectly added to the master branch as html. That was later moved into .erb files but the documentation does not display correctly.

I will add the files to the source branch and see if I can get the documentation to display correctly.

@CZHU20 found that the links to the 1D input files in the ROM simulation guide are no longer working because we moved them to a different folder. There are two occasions of

The complete 1D Simulation input file is available

@ktbolt I tried to fix them myself but I didn't understand the edit/build instructions. Thank you!!

Add a link to the SimVascular Supercomputing Gateway web page.

The make a donation link under "contact us" is broken and can be removed.

In the Simulations Guide svPre Commands section there is a list of commands used in svPre. Some of these command names do not match the names used by svPre. For example

The documentation gives **read_restart_displacements** but it should be **read_displacements_restart**

The SV 1D Simulation Guide documentation is truly a work of art but it is still not perfect, missing an example download.