Hi Vincent,
what I would do to try to understand what goes wrong is to try simplifying the
process: in the second pipe, set -boundarylayer 0, then just write out as msh
directly after scaling:
vmtksurfacereader -ifile
/Users/Vincent/Desktop/CFD/Temp/level_sets_sm_ct_ex_2.vtp --pipe
vmtkcenterlines -endpoints 1 -seedselector openprofiles --pipe
vmtkdistancetocenterlines -useradius 1 --pipe vmtkmeshgenerator
-elementsizemode edgelengtharray -edgelengtharray DistanceToCenterlines
-edgelengthfactor 0.3 -boundarylayer 0 -ofile
/Users/Vincent/Desktop/CFD/Temp/level_sets_sm_ct_ex_2.vtu --pipe
vmtkmeshscaling -scale 0.1 --pipe vmtkmeshwriter -entityidsarray CellEntityIds
-ofile /Users/Vincent/Desktop/CFD/Temp/level_sets_sm_ct_ex_2_q_scaled_t_l.msh
Let's see what this produces.
Luca
--
Luca Antiga, PhD
Cofounder and Principal Scientist, Orobix Srl
via L.A. Muratori 3, 24123 Bergamo, Italy
orobix: www.orobix.com
home: lantiga.github.com
twitter: twitter.com/lantiga
On Apr 12, 2013, at 7:56 PM, Vincent Ip wrote:
> And when I tried to open it with Fluent, it shows the following error
> messages:
>
> > Reading
> > "\psf\Home\Desktop\CFD\Temp\level_sets_sm_ct_ex_2_q_scaled_t_l.msh"...
> 563043 nodes.
> 94612 mixed wall faces, zone 3.
> 476 mixed wall faces, zone 4.
> 456 mixed wall faces, zone 5.
> 464 mixed wall faces, zone 6.
> Error: read: face 5234350, zone 7.
> Reading Faces: failed while reading section 13.
>
> Clearing partially read grid.
>
> Error: Read_Grid_Section: Aborted due to critical error.
> Error Object: #f
>
> Error: Error reading
> "\psf\Home\Desktop\CFD\Temp\level_sets_sm_ct_ex_2_q_scaled_t_l.msh".
> Error Object: #f
>
> Interrupting...
> Done.
>
> Vincent
>
> On Apr 12, 2013, at 10:01 AM, Vincent Ip <drvincen...@gmail.com> wrote:
>
>> Thanks Luca for your prompt response!
>>
>> Here are the command lines I used:
>>
>> vmtksurfacereader -ifile
>> /Users/Vincent/Desktop/CFD/Temp/level_sets_sm_ct.vtp --pipe vmtkcenterlines
>> -seedselector openprofiles --pipe vmtkflowextensions -adaptivelength 1
>> -extensionratio 20 -normalestimationratio 1 -interactive 0 -extensionmode
>> boundarynormal --pipe vmtksurfacewriter -ofile
>> /Users/Vincent/Desktop/CFD/Temp/level_sets_sm_ct_ex_2.vtp
>>
>> vmtksurfacereader -ifile
>> /Users/Vincent/Desktop/CFD/Temp/level_sets_sm_ct_ex_2.vtp --pipe
>> vmtkcenterlines -endpoints 1 -seedselector openprofiles --pipe
>> vmtkdistancetocenterlines -useradius 1 --pipe vmtkmeshgenerator
>> -elementsizemode edgelengtharray -edgelengtharray DistanceToCenterlines
>> -edgelengthfactor 0.3 -boundarylayer 1 -ofile
>> /Users/Vincent/Desktop/CFD/Temp/level_sets_sm_ct_ex_2.vtu
>>
>> vmtklineartoquadratic -ifile
>> /Users/Vincent/Desktop/CFD/Temp/level_sets_sm_ct_ex_2.vtu -ofile
>> /Users/Vincent/Desktop/CFD/Temp/level_sets_sm_ct_ex_2_q.vtu -rfile
>> /Users/Vincent/Desktop/CFD/Temp/level_sets_sm_ct_ex_2.vtp -entityidsarray
>> CellEntityIds
>>
>> vmtkmeshscaling -ifile
>> /Users/Vincent/Desktop/CFD/Temp/level_sets_sm_ct_ex_2_q.vtu -scale 0.1
>> -ofile /Users/Vincent/Desktop/CFD/Temp/level_sets_sm_ct_ex_2_q_scaled.vtu
>>
>> vmtkmeshboundaryinspector -ifile
>> /Users/Vincent/Desktop/CFD/Temp/level_sets_sm_ct_ex_2_q_scaled.vtu
>> -entityidsarray CellEntityIds
>>
>> vmtkmeshtetrahedralize -ifile
>> /Users/Vincent/Desktop/CFD/Temp/level_sets_sm_ct_ex_2_q_scaled.vtu -ofile
>> /Users/Vincent/Desktop/CFD/Temp/level_sets_sm_ct_ex_2_q_scaled_t.vtu
>>
>> vmtkmeshlinearize -ifile
>> /Users/Vincent/Desktop/CFD/Temp/level_sets_sm_ct_ex_2_q_scaled_t.vtu -ofile
>> /Users/Vincent/Desktop/CFD/Temp/level_sets_sm_ct_ex_2_q_scaled_t_l.vtu
>>
>> vmtkmeshwriter -ifile
>> /Users/Vincent/Desktop/CFD/Temp/level_sets_sm_ct_ex_2_q_scaled_t_l.vtu
>> -entityidsarray CellEntityIds -ofile
>> /Users/Vincent/Desktop/CFD/Temp/level_sets_sm_ct_ex_2_q_scaled_t_l.msh
>>
>> And I am currently using MacOS 10.8.3 and my laptop is a 2.7GHz quad-core
>> with 16GB ram. And I am using ANSYS 14.0.
>>
>> Please kindly advise on what steps should I follow for subsequent processing.
>> Many many thanks indeed.
>>
>> Vincent
>>
>> On Apr 12, 2013, at 3:56 AM, Luca Antiga <luca.ant...@gmail.com> wrote:
>>
>>> Hi Vincent,
>>> for the future please keep messages on the list. I'm not the only
>>> one that can solve your problem, by posting on the list you have
>>> better chances to get useful feedback in shorter times.
>>>
>>> Hey, relax! No need to be desperate. Things can be tricky at the
>>> beginning as there is a learning curve, but you'll be ok soon.
>>>
>>> I personally don't think the model is odd. The orientation of
>>> the flow extensions is debatable (vmtk tries to take a representative
>>> direction of the vessel upstream the end section, but it can generate
>>> non particularly representative extensions in the case there are
>>> high curvatures near the end section, as in your case). You can
>>> try with
>>> -extensionmode boundarynormal
>>> for extensions that have the direction of the normal to the boundary,
>>> and see what happens.
>>>
>>> In any case, I don't think the direction is odd enough to cause troubles,
>>> so let's see the mesh. Can you send me the exact command line you
>>> used to generate the mesh all the way to the generation of the msh
>>> file?
>>>
>>>
>>> Luca
>>>
>>>
>>> On Apr 12, 2013, at 8:45 AM, Vincent Ip wrote:
>>>
>>>> Thanks Luca,
>>>>
>>>> I almost cried when I saw your email. You have no idea how desperate I am
>>>> right now.
>>>> Alright, I've attached a picture of what did I mean the model is odd after
>>>> adding the flow extension.
>>>> Please kindly comment.
>>>> Many thanks!!!
>>>>
>>>> Vincent
>>>>
>>>> <PastedGraphic-1.tiff>
>>>> On Apr 11, 2013, at 11:36 PM, Luca Antiga <luca.ant...@gmail.com> wrote:
>>>>
>>>>> Hi Vincent,
>>>>> welcome to vmtk.
>>>>> In order to help you we need some more information about what's the
>>>>> actual issue you're coming across. Let's start with your first question:
>>>>> can you post a screenshot?
>>>>> Cheers
>>>>>
>>>>> Luca
>>>>>
>>>>> On 12/apr/2013, at 08:15, Vincent Ip <drvincen...@gmail.com> wrote:
>>>>>
>>>>>> I am a new beginner in learning how to reconstruct blood vessel from MR
>>>>>> angiogram source image for CFD analysis.
>>>>>>
>>>>>> I followed the VMTK tutorial step by step to reconstruct the middle
>>>>>> cerebral artery and then export it to mesh for FLUENT. But it just
>>>>>> doesn't work!
>>>>>>
>>>>>> I have a few questions that I don't understand and I really hope someone
>>>>>> could show me some guidances (I'm really desperate!!)
>>>>>> - After adding the flow extension, the mesh seems a bit odd and it
>>>>>> doesn't look like the one which is depicted as an example on the page of
>>>>>> 'generating a mesh'. Is it really necessary to make it or anything I
>>>>>> missed to do during the meshing
>>>>>> - And the *.msh file generated (for Fluent) is not readable by Fluent
>>>>>> - I tried the netgen way but I don't know how to use it
>>>>>>
>>>>>> I am not sure what did I do wrong but I would appreciate if anyone could
>>>>>> advise me on how to generate a proper CFD model from MRA.
>>>>>> Many thanks in advance.
>>>>>>
>>>>>> Vincent
>>>>>> ------------------------------------------------------------------------------
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>>>>
>>>
>>
>
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apps and a phenomenal toolset for data science. Developers can use
our toolset for easy data analysis & visualization. Get a free account!
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