Re: [vmtk-users] Beginner question
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Re: [vmtk-users] Beginner question
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From: Vincent Ip <drv...@gm...> - 2013-04-12 17:56:54
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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 <drv...@gm...> 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 <luc...@gm...> 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 <luc...@gm...> 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 <drv...@gm...> 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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