Documentation for ibamr

[Suresh Naidu]

Hi,

I am new to ibamr and just managed to compile and run the examples.

I am not able to compile the doxygen documentation as i have never used it.

Anyone has a pdf copy or latex copy of the documentation describing the examples,

how to set the input values, upload geometry, etc. Will really appreciate it.

Thks,

Suresh

[boy...@gmail.com]

Suresh --

Doxygen source code documentation is provided at ibamr.github.io:

http://ibamr.github.io/IBAMR/ibamr/html/

http://ibamr.github.io/IBAMR/ibtk/html/

http://ibamr.github.io/IBAMR/samrai/2.4.4/html/

Unfortunately, there is not a full manual at this time. There is also limited documentation for the examples. I will work to rationalize the examples --- some of them are really tests, not examples, whereas others really are examples.

The Doxygen-based source code documentation is not automatically generated. To build it, run doxygen in the doc subdirectory --- although you also will probably have to modify some of the settings in the Doxyfile that is provided. Please see this recent thread from ibamr-dev for more information:

https://groups.google.com/forum/#!topic/ibamr-dev/HVhUJi4ZmRA

Best,

-- Boyce

--
You received this message because you are subscribed to the Google Groups "IBAMR Users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to ibamr-users...@googlegroups.com.
To post to this group, send email to ibamr...@googlegroups.com.
For more options, visit https://groups.google.com/d/optout.

[Suresh Naidu]

HI Prof. Boyce,

Thank you for your quick response and comments regarding the documentation.

I am intending to use the ibamr code to simulate flapping wing kinematics (drosophilia) similar

to the video posted on youtube which i believe you performed. I have a few questions.

1. Which example shld i study or run so that i can learn how to simulate such a model?

2. Can i decouple the FSI? I just want to run a NS solution to benchmark dickinson Robofly first.

3. How do we add our own FSI method subroutine to the code? Source filenames may help.

4. I am unable to view the geometry, flow variables etc in VisIT. Not sure why?

5. Can i use Paraview instead of VisIT to view hd5 or silo files?

6. What is the difference between the folders IB, Navier-stokes and IBFE in the examples folder?

Thank you for your help.

suresh 

[Amneet Bhalla]

You might want to try examples/ConstraintIB/eel2d or eel3d. Follow the discussion 

https://groups.google.com/forum/#!topic/ibamr-dev/TcIYJ7G7XqI

for some additional details on the method to see its suitability for your case. 

--
You received this message because you are subscribed to the Google Groups "IBAMR Users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to ibamr-users...@googlegroups.com.
To post to this group, send email to ibamr...@googlegroups.com.
For more options, visit https://groups.google.com/d/optout.

--

--Amneet 

[Boyce Griffith]

> On Nov 13, 2014, at 11:08 PM, Suresh Naidu <suresh....@gmail.com> wrote:
>
> Thank you for your quick response and comments regarding the documentation.
> I am intending to use the ibamr code to simulate flapping wing kinematics (drosophilia) similar
> to the video posted on youtube which i believe you performed. I have a few questions.

Laura Miller and her group have used IBAMR to do these kinds of simulations in the past. I have helped out in getting these set up, but her group did most of the work and actually performed the simulations.

Amneet Bhalla (who also responded) has done some related work using some code that is also now part of IBAMR.

> 1. Which example shld i study or run so that i can learn how to simulate such a model?

One question is whether you want to do prescribed motion, prescribed kinematics, or fluid-solid interaction involving an elastic structure.

> 2. Can i decouple the FSI? I just want to run a NS solution to benchmark dickinson Robofly first.

This sounds like you want to do prescribed motion for the structure.

> 3. How do we add our own FSI method subroutine to the code? Source filenames may help.

What sort of methods do you want to add.

> 4. I am unable to view the geometry, flow variables etc in VisIT. Not sure why?

Me neither? :-)

What example(s) are you running, and what are you trying to visualize?

> 5. Can i use Paraview instead of VisIT to view hd5 or silo files?

I think so, but I have essentially no experience with Paraview. The main question is whether Paraview can read in SAMRAI viz files. I don't know the answer, but I will ask a contact at Kitware.

> 6. What is the difference between the folders IB, Navier-stokes and IBFE in the examples folder?

IB examples are for the "classical" IB method; IBFE is for a method that uses a finite element representation of the structure. The rest are tests/examples for specific subsolvers: Navier-Stokes; advection-diffusion; and pure advection.

-- Boyce