[Paraview] time series not working with xyz or lammps-dump reader && presenting millions of atoms by "spheres"

Tue Jul 10 03:52:08 EDT 2012

one thing to look out for : make sure depth peeling is turned off if you make use of the point sprite opacity features. The shader used by the depth peeling conflicts with the shader used in the point sprite.

JB

From: paraview-bounces at paraview.org [mailto:paraview-bounces at paraview.org] On Behalf Of LUO Jian
Sent: 10 July 2012 06:47
To: paraview at paraview.org
Subject: Re: [Paraview] time series not working with xyz or lammps-dump reader && presenting millions of atoms by "spheres"

Thanks very much, Christian.

1. The point sprite plugin is really cool. It allows efficient atomic presentation with control of the color, radius and opacity of individual atoms. I tried this on win7 64 system with precompiled 3.14 paraview.  It only works for the object loaded by xyz file reader not lammps dump file reader. And when I tune the atom radius and opacity back and forth from "constant value" to "c_1 (atomic scalar)", some warning shows up
"Warning: In ..\..\..\..\src\VTK\Rendering\vtkShaderProgram2.cxx, line 382
vtkShaderProgram2 (00000000135CBAB0): another program was used (id=5), our id is1."
And when I continue to tune atom radius and opacity, numerous such warnings show up and pavraview will not respond to my tuning, although I can still rotation or pan the object.

2. I registered CFDEM, but I somehow cannot download the attachment other than the two pdf files. So can you send them to me through email? Thanks a lot!

Jian

On Fri, Jul 6, 2012 at 6:31 AM, <paraview-request at paraview.org<mailto:paraview-request at paraview.org>> wrote:
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Today's Topics:

   1. Re: [EXTERNAL] ParaView looking for MPI when it shouldn't.
      (Scott, W Alan)
   2. How to save cull frontface (Chris)
   3. Re: time series not working with xyz or lammps-dump reader &&
      presenting millions of atoms by "spheres" (Christian Richter)

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Message: 1
Date: Thu, 5 Jul 2012 23:26:13 +0000
From: "Scott, W Alan" <wascott at sandia.gov<mailto:wascott at sandia.gov>>
Subject: Re: [Paraview] [EXTERNAL] ParaView looking for MPI when it
        shouldn't.
To: "andrew.amaclean at gmail.com<mailto:andrew.amaclean at gmail.com>" <andrew.amaclean at gmail.com<mailto:andrew.amaclean at gmail.com>>
Cc: "paraview at paraview.org<mailto:paraview at paraview.org>" <paraview at paraview.org<mailto:paraview at paraview.org>>
Message-ID:
        <9047EE0D4D3C8E43B93980DA10A073807C143B6A at EXMB04.srn.sandia.gov<mailto:9047EE0D4D3C8E43B93980DA10A073807C143B6A at EXMB04.srn.sandia.gov>>
Content-Type: text/plain; charset="us-ascii"

Correct.  I should have written up a bug before, but will do so now.

Alan

From: Andrew Maclean [mailto:andrew.amaclean at gmail.com<mailto:andrew.amaclean at gmail.com>]
Sent: Thursday, July 05, 2012 5:24 PM
To: Scott, W Alan
Cc: paraview at paraview.org<mailto:paraview at paraview.org>
Subject: Re: [EXTERNAL] [Paraview] ParaView looking for MPI when it shouldn't.

Thanks, Scott,

Yes, that does the trick. I guess this is not being seen on the dashboard because those machines all have MPI running.
So there is a need to look at the CMakeLists.txt files for examples and testing to make sure that if MPI is excluded then those examples/tests need to be excluded.

Thanks
Andrew
On Fri, Jul 6, 2012 at 9:11 AM, Scott, W Alan <wascott at sandia.gov<mailto:wascott at sandia.gov><mailto:wascott at sandia.gov<mailto:wascott at sandia.gov>>> wrote:
I had the same issue.  If I remember correctly, I "think" the solution was to turn off BUILD_EXAMPLES and BUILD_TESTING.

Alan

From: paraview-bounces at paraview.org<mailto:paraview-bounces at paraview.org><mailto:paraview-bounces at paraview.org<mailto:paraview-bounces at paraview.org>> [mailto:paraview-bounces at paraview.org<mailto:paraview-bounces at paraview.org><mailto:paraview-bounces at paraview.org<mailto:paraview-bounces at paraview.org>>] On Behalf Of Andrew Maclean
Sent: Thursday, July 05, 2012 5:08 PM
To: paraview at paraview.org<mailto:paraview at paraview.org><mailto:paraview at paraview.org<mailto:paraview at paraview.org>>
Subject: [EXTERNAL] [Paraview] ParaView looking for MPI when it shouldn't.

Hi All,
I am building ParaView from the Git repository and for some reason it is looking for MPI even though I have PARAVIEW_USE_MPI turned off.
I can't see any other setting that is forcing MPI to be turned on.

Is there something I am missing or is there an error in the configuration files?

My output is:
...
- Filter ZLIB is ON
-- Could NOT find MPI_C (missing:  MPI_C_LIBRARIES MPI_C_INCLUDE_PATH)
-- Could NOT find MPI_CXX (missing:  MPI_CXX_LIBRARIES MPI_CXX_INCLUDE_PATH)
CMake Error at VTK/Parallel/MPI/CMakeLists.txt:35 (message):
  MPIEXEC was empty.

-- Configuring incomplete, errors occurred!
make: *** [cmake_check_build_system] Error 1

Regards

--
___________________________________________
Andrew J. P. Maclean

___________________________________________

--
___________________________________________
Andrew J. P. Maclean

___________________________________________
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Message: 2
Date: Fri, 6 Jul 2012 08:10:41 +0200
From: Chris <chris.schweighofer at gmx.net<mailto:chris.schweighofer at gmx.net>>
Subject: [Paraview] How to save cull frontface
To: paraview at paraview.org<mailto:paraview at paraview.org>
Message-ID: <8DA92389-245C-4AE3-9C2F-0C9F1FCC87A0 at gmx.net<mailto:8DA92389-245C-4AE3-9C2F-0C9F1FCC87A0 at gmx.net>>
Content-Type: text/plain; charset=us-ascii

Hello people,

I try to save the animation cull frontface. It is available in the Display pannel. I tried to save it now in several formats. But it was not working.
Does someone know how I can save the animation?

Thx,
Chris

------------------------------

Message: 3
Date: Fri, 06 Jul 2012 12:23:32 +0200
From: Christian Richter <christian.richter at ovgu.de<mailto:christian.richter at ovgu.de>>
Subject: Re: [Paraview] time series not working with xyz or
        lammps-dump reader && presenting millions of atoms by "spheres"
To: paraview at paraview.org<mailto:paraview at paraview.org>
Message-ID: <4FF6BCA4.5080504 at ovgu.de<mailto:4FF6BCA4.5080504 at ovgu.de>>
Content-Type: text/plain; charset="iso-8859-1"; Format="flowed"

Hi Jian,

for 1.) have a look at my liggghts text- and binary reader at
http://web678.public1.linz.at/Drupal/?q=node/681 (you have to register
to see the attached files) as a starting point for your own implemention.
for 2.) you can use the PointSprite Plugin, I've written a HowTo here:
http://web678.public1.linz.at/Drupal/?q=system/files/howto_paraview.pdf

greez,
Christian

Am 05.07.2012 22:57, schrieb LUO Jian:
> Hello,
>
> I am new to this extremely powerful visualization tool and I use the
> 3.14 version of paraview binary on windows 7 . Both binary and
> compiled one on linux.
> I could not get the following 2 things to work for me.
>
> 1. The xyz and lammps-dump reader comes along with the binary, but I
> do not see them in the compiled one, why?
>     Then with the binary, I try to load up multi-block xyz or
> lammps-dump files, I can only get the first frame. I check
> "Information" tab on the left, the "Index" and "Value" of Time is
> blank. So there is something wrong. Both the xyz and lammps-dump files
> are produced by lammps and can be recognized by other visualization
> software. So I think I need to do something about the readers. So can
> someone tell me how to get this done?
>    Eventually, I want to be able to add whatever readers in paraview
> by myself so that I can stop converting hundreds of gigabytes of data
> from one format to another.  First, I want to find the xyz and
> lammps-dump readers within the source code and try to understand and
> tweak them. Then I can follow the more comprehensive manual to do more
> things. I just could not find them in the source folder, can someone
> point them to me?
>
> 2. For publication purpose, I want to render the points as spheres
> without "masking points". I tried the "sphere" option in "glyph"
> filter. It worked pretty well when the number of "spheres" were
> limited to 5000. But when I tried to represent a million atoms with
> spheres, paraview won't be responding for a long time and I have to
> kill the process. So I wondering if there is a way that I can present
> millions of atoms with "sphere" in paraview more efficiently ?
>
> Thanks for your attention
>
> Best,
> Jian
>
>
>
>
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Dipl.-Ing. Christian Richter
Lehrstuhl f?r Materialflusstechnik
Institut f?r Logistik und Materialflusstechnik (ILM)
Fakult?t f?r Maschinenbau (FMB)

Otto-von-Guericke-Universit?t Magdeburg
Universit?tsplatz 2
D-39106 Magdeburg
Geb?ude 10, Raum 213

University Magdeburg "Otto-von-Guericke"
Department of Material Handling
Institute of Logistics and Material Handling Systems (ILM)
Faculty for Mechanical Engineering (FMB)

E-Mail: christian.richter at ovgu.de<mailto:christian.richter at ovgu.de>
Tel.: +49 (0)391/67-*12690 NEU*
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