Re: [ESPResSo-users] OIF_Implementation - Creating Template

[Iveta Jancigova]

Hi Markus,

I tried your script with the triangulation files you sent:
The problem seems to be the additional parameter *1* you put after the keyword 
*orientation*. When I remove it, everything seems to be working as it should.

*orientation* does not take any arguments (unlike the *repair*, which takes 
two: the name of the output file, where the properly oriented triangulation 
will be saved, and id of method to be used for proper orientation. As of now, 
only one method has been implemented, but we have another one on our todo list 
that would also work for concave objects.) The whole oif_mesh_analyze was 
originally meant as just our internal quick-fix utility procedure, but it seems 
that the time has come to make it more intuitive/user friendly. Sorry, for the 
inconvenience.

Best,
Iva      

> On 12 Mar 2015, at 13:51, Wink, Markus <address@hidden> wrote:
> 
> Hello Iva,
> 
> thanks for your reply. I am using the Espresso-3.3.0 distribution.
> 
> I doubled check for typos, but I cannot find any. Attached you will find the 
> scripts and node/triangle-files. 
> If I check for the wrong triangle-file, I get the output, that the facets are 
> wrongly oriented. 
> If I repair it and check again, I get the error Message "error s".
> 
> Do you see any mistake I did?
> 
> Greetings
> 
> Markus
> 
> 
> 
> -----Ursprüngliche Nachricht-----
> Von: address@hidden [mailto:address@hidden Im Auftrag von Iveta Jancigova
> Gesendet: Mittwoch, 11. März 2015 13:45
> An: address@hidden
> Betreff: Re: [ESPResSo-users] OIF_Implementation - Creating Template
> 
> Hello Markus,
> 
> Firstly, my apologies for the cryptic error message. In the newer version of 
> object-in-fluid implementation, these have been fixed.
> 
> But it seems that what happened is that you have used an incorrect keyword in 
> the oif_mesh_analyze procedure (perhaps a typo "orientatin 1" as I'm reading 
> in your message, instead of "orientation 1"). If the triangulation is 
> correct, oif_mesh_analyze does not produce any error messages.
> 
> Best,
> Iva
> 
> ps just a tip: You don't actually have to create a template to check a 
> triangulation. You can use oif_mesh_analyze directly after oif_init
> 
>> Predmet:     [ESPResSo-users] OIF_Implementation - Creating Template
>> Dátum:       Wed, 11 Mar 2015 09:31:11 +0000
>> Od:  Wink, Markus <address@hidden>
>> Pre:         'address@hidden' <address@hidden>
>> 
>> 
>> 
>> Hello everybody,
>> 
>> I have got a question concerning creating a template for using the 
>> oif-implementation.
>> 
>> After creating my mesh-nodes and triangulization, I wanted to check, 
>> whether I have done it correctly. For that I used the command
>> 
>> *oif_mesh_analyze nodes-file $fileNodes triangles-file $output 
>> orientation 1*
>> 
>> I noticed, that the facets of the triangles showed in the wrong 
>> direction. So I used
>> 
>> *oif_mesh_analyze nodes-file $fileNodes triangles-file $fileTriangles 
>> repair $output 1*
>> 
>> **
>> 
>> to achieve the right orientation of the facets. But: After checking, 
>> if the repaired facets are correct (using the command "orientatin 1" 
>> again on the new triangle-file), I get as an output "error s" (see 
>> output at the bottom of the message).
>> 
>> Does anybody knows where does error message comes from? Shall I be 
>> worried about it?
>> 
>> Thank you very much for your help.
>> 
>> Greetings
>> 
>> Markus
>> 
>> /_Output:_/
>> 
>> __
>> 
>> The following oif_template will be created:
>> 
>>        nodes-file:     sphere_nodes.dat
>> 
>>        triangles-file: sphere_triangles.dat
>> 
>> ks:             0.0
>> 
>>        kb:             0.0
>> 
>>        kal:            0.0
>> 
>>        kag:            0.0
>> 
>>        kv:             0.0
>> 
>> stretch:        1.0 1.0 1.0
>> 
>> Data extracted from the input files:
>> 
>>        nnodes:         234
>> 
>>        ntriangles:     464
>> 
>> The following oif_object will be created:
>> 
>>        template_id:    0
>> 
>>        mass:           1
>> 
>>        particle_type:  0
>> 
>>        mol:            0
>> 
>>        rotate:         0 0 0
>> 
>>        origin:         50 50 50
>> 
>> generating particles
>> 
>> error s
>> 
>> 
>> 
> 
> --------------------------------------------------------------------------
> Iveta Jancigova, PhD student
> Faculty of Management Science and Informatics University of Zilina, Slovakia 
> cell-in-fluid research group: http://cell-in-fluid.fri.uniza.sk
> 
> 
> 
> <sphere_nodes.dat><sphere_triangles.dat><sphere_triangles_repaired.dat><test.tcl>

--------------------------------------------------------------------------
Iveta Jancigova, PhD student
Faculty of Management Science and Informatics
University of Zilina, Slovakia
cell-in-fluid research group: http://cell-in-fluid.fri.uniza.sk