Post Processing

I am trying to covert a dump file to vtk format. No issue with the first two steps.

1. d = dump("dump.filename")
2. v = vtk(d)
3. v.manyGran()
When I execute the third step i get the below error message.

Traceback (most recent call last):
File "", line 1, in ?
File "/home/s02/s1061629/pizza-16Mar09/src/vtk.py", line 124, in manyGran
particleGran(file,atoms,names,len(self.data.snaps[0].atoms[0]))
File "/home/s02/s1061629/pizza-16Mar09/src/vtk.py", line 321, in particleGran
print >>f,atom[18]
IndexError: index out of bounds

Hi all,

I'm still learning LIGGGHTS, and am currently playing with dumping pair/gran/local snapshots. I was hoping that the granular pizza.py version would have a command to read and manipulate these in the same way as "normal" snapshots, but I can't find anything - am I missing something?

No doubt I can put something together from the dump and LAMMPS bdump (bond dump) commands, but thought I'd check first!

Cheers, Mark

Hi all,

I ran a simulation with different size of particles and got some output files. I converted them into .vtk files and successfully visualized the difference in particle size in Paraview. Now I'd like to plot a distribution function where I can visualize distribution of each radius of particles with respect to an axis, say x.

Is there anyway to do that in Paraview?

Thanks!

--Emre

Hey

For some reason the dump command doesn't seem to want to read in all snapshots from my dump file

It reads in 21 snapshots, and ignores the others. There are infact 12000 snapshots! So why is it missing them off and how can I resolve this. Its quite a large simulation (dump file 2Gb!!), so is it struggling with the large file size?

Thanks

Jay

Hello

I have a similar problem to a posting about 8 months ago. Basically pizza.py isn't recognising the command dump.

I am currently using python 2.7 and all relevant packages required have been installed (Tk, Numeric, Tcl etc). The version of pizza.py I am using is 24Nov10.

here is the output I have from running python, then pizza.py, then trying to use the d = dump() function:

[root@Jay src]# python
Python 2.7 (r27:82500, Sep 16 2010, 18:03:06)
[GCC 4.5.1 20100907 (Red Hat 4.5.1-3)] on linux2
Type "help", "copyright", "credits" or "license" for more information.

Hello.
I want to post process LIGGGHTS results with my python script.
So, I do convert from the dump to vtk by pizza.py and next want to read that vtk in my script in order to add some data to it. But I have a problem with reading. I do:

from vtk import *
rdr=vtkPolyDataReader()
rdr.SetFileName(fileIn)
rdr.Update()
grd=rdr.GetOutput()
pdata=grd.GetPointData()

Problem is pdata have only 2 arrays:

In [22]: pdata.GetNumberOfArrays()
Out[22]: 2
In [23]: pdata.GetArrayName(0)
Out[23]: 'v'
In [24]: pdata.GetArrayName(1)
Out[24]: 'atom_type'

So, no 'radius' and other arrays.

Hello,

When I'm processing the dump-files of the example "pour-dev" I get a file named tmp.vtk. After opening this one with Paraview, I am not able to see the particles falling and so on - I just see all the positions over time of all particles in one picture. Where is the problem?
Do I have to tell it to LAMMPS/LIGGGHTS that it should dump in a different way?

Thanks in advance!

Hi,

I run a simulation of a sphere packing problem, How should I visualize them by their actual size other than a lot of points without contact in paraview? Thanks!

Lenard

Hi,
I'm trying to export any field (not only "atom_type") from dump file in vtk using pizza tool.
I found in the forum the commad

v.manyGran()

But when I obtain:

File "", line 1, in ?
AttributeError: vtk instance has no attribute 'manyGran'

Any help?

Thanks

Andrea

Dear all,

I have already done some triaxial tests and simple shear tests, but I want to know the contact normal among the particles and then realise them in paraview to further generate the force-chain.

Is there someone who has done the force-chain stuff before? Could you tell me how to do this or give me some hints?

Thanks in advance!

Best,
Tong