[Paraview] File Format for Particles

Fri Nov 28 11:25:15 EST 2008

Legacy VTK files store data always in big endian so there is no 
compatibility problem. With XML you probably can specify.

Dominik

Shi Jin wrote:
> Thank you Bryn and Ivo.
> 
> I agree binary format is more efficient. But I am reluctant to do that because of the issue of portability. I may run the code on both Linux clusters and IBM machines. My earlier experience shows me that the binary files on the two system are not compatible, i.e., I cannot load the data generated on a IBM machine  on a Linux system. Does the little/big endian parameter  solve this problem in paraview? 
> Thanks.
> 
> Shi
> 
>  
> 
> 
> ----- Original Message ----
>> From: Bryn Lloyd <blloyd at vision.ee.ethz.ch>
>> To: Ivo Roghair <ivoroghair at gmail.com>
>> Cc: Shi Jin <jinzishuai at yahoo.com>; paraview at paraview.org
>> Sent: Friday, November 28, 2008 12:17:39 AM
>> Subject: Re: [Paraview] File Format for Particles
>>
>> Hi Shi,
>>
>> Yes, for large amounts of data you should use the binary (not ascii) formats. It 
>> is very simple to switch between ascii/binary. In the writer classes (e.g. 
>> vtkPolyDataWriter) you can usually call the function SetFileTypeToBinary() or 
>> SetFileTypeToASCII().
>>
>>
>> An unstructured grid can of course be used to visualize your data in paraview. 
>> Since you not have cells (tetrahedra, hexahedra, etc.) a vtkPolyData data 
>> structure and associated file type might be better, since it uses slightly less 
>> storage and if you add the points as "Verts" Paraview will automatically display 
>> them using glyphs (sphere,arrow,..)
>>
>> File formats are described here:
>> http://www.vtk.org/pdf/file-formats.pdf
>>
>>
>> --Bryn
>>
>>
>>
>>
>>
>> Ivo Roghair wrote:
>>> Hi Shi,
>>>
>>> Saving such amounts of data in ascii format is not going to be efficient. We 
>> just accepted this fact, otherwise we should go to binary formats.
>>> In our group we have discrete particle simulations, and we export vtk files 
>> (xml format -- an unstructured grid to be precise) that contains all the 
>> particle data. I have included an example of such a file below. You write the 
>> point positions of the particles first, followed by data concerning the movement 
>> of the particle, the diameter and other stuff like rotation, temperature, etc... 
>> I don't see what you mean by redundant data. When you load this file into 
>> Paraview choose the glyph option, choose 'sphere', set 'radius' to 1 (it is 
>> initially set to 0.5), scale mode to 'scalar' and scale factor to 1. You can 
>> then draw the particles. You can color them by velocity, temperature, rotation 
>> or whatever you included in the file, or you can choose to show arrows (another 
>> glyph) to display the particle movement.
>>> For the flow field, which is calculated on a structured grid, you can use 
>> another file format, e.g. rectilinear grid. In all cases the kitware/vtk file 
>> formats documentation is going to be useful.
>>> Regards,
>>> Ivo Roghair
>>>
>>> PhD student at Fundamentals of Chemical Reaction Engineering
>>> University of Twente, The Netherlands
>>>
>>> ------------------ BEGIN EXAMPLE FILE ---------------------
>>>
>>>  
>>>    
>>>      
>>>        
>> format="ascii">
>>>        0 0 0 1 1 1 0 0 1
>>>        
>>>      
>>>      
>>>        
>> format="ascii">
>>>        4 4 4 4 0 0 2 2 -2
>>>        
>>>    
>>>        0.1 0.5 1
>>>        
>>>    
>>>        273 300 350
>>>        
>>>      
>>>      
>>>        
>>>        
>>>        
>>>        
>>>        
>>>        
>>>      
>>>    
>>>  
>>>
>>> ---------- END EXAMPLE FILE --------------
>>>
>>> Shi Jin wrote:
>>>> Hi there,
>>>>
>>>> I am doing a simulation of fluid-particle interactions, in which I generate a 
>> lot of data for particles. I am looking for the efficient file format to store 
>> my particle information for visualization with paraview. For example, is there a 
>> file format that allows me to store all the particle information at a given time 
>> in a single ascii file, which looks like
>>>> #1-id 2-radius 3-rho_p 4-fixed 5-x 6-y 7-z 8-u 9-v 10-z 11-w1 12-w2 13-w3 
>> 14-alpha 15-theta 17-phi
>>>> 0 0.500000 1.200000 0 2.077176 2.678227 8.649375 0.000000 0.000000 0.000000 
>> 0.000000 0.000000 0.000000 0.000000 0.000000
>>>> 1 0.500000 0.800 0 2.728281 0.873571 6.806029 0.000000 0.000000 0.000000 
>> 0.000000 0.000000 0.000000 0.000000 0.000000
>>>> ...
>>>>
>>>> I guess for the purpuse of visualization, we need radius, rho_p(for color), 
>> x,y and z at least. The rotation information would be nice to have but is 
>> considered optional at this stage.
>>>> I am thinking to save different time results in different files to make the 
>> loading efficient in terms of memory since I have a lot of particles here. Then 
>> we can produce animation using time control. I guess we could use VTK formats 
>> but that has lots of redundant information.
>>>> I saw some very early discussion on a similar topic in the forum but didn't 
>> get the conclusive answer. I would appreciate some advice for the current 
>> version of paraview.
>>>> Thank you very much.
>>>>
>>>>  --
>>>> Shi Jin, PhD
>>>>
>>>>
>>>>
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>>
>> -- -------------------------------------------------
>> Bryn Lloyd
>> Computer Vision Laboratory
>> ETH Zürich, Sternwartstrasse 7
>> CH - 8092 Zürich, Switzerland
>> Tel: +41 44 63 27690
>> Fax: +41 44 63 21199
>> -------------------------------------------------
> 
> 
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-- 
Dominik Szczerba, PhD
Computational Physics Group
IT'IS Foundation
http://www.itis.ethz.ch