CODEWITHSUNDEEP
linuxvisualization
Yotam
Yotam

Reputation: 10685

particle visualization in Linux

I have generated files of the scheme

x \t y \t z \t charge \t type \t id

and I want to display them the in a similar way to this picture: MD result of NaCl melting

I also need to have the ability to browse though the space of my simulation (rotate it and zoom in and out). I tried rasmol and pymol but they don't speak with my simple file format.

Is there any other tool to do this that I hadn't find? Edit: solution I have created a small program to chnge my data to the xyz format.

Upvotes: 2

Views: 518

Answers (3)

Open the way
Open the way

Reputation: 27339

Pymol can perfectly handle that kind of data. In your case you could just convert each point to a sphere doing soemthing like 

pseudoatom BEAD3, pos=[26.8600, 79.4690, 135.9360], b=-67.927313
cmd.show("spheres","BEAD3")

for me it works nicely.

Upvotes: 1

SiggyF
SiggyF

Reputation: 23165

You could make such a plot using the mayavi2 point3d function. Or any other vtk based software. Mayavi2 allows you to navigate through your 3D space and allow for stereo rendering (press "3"). 

import enthought.mayavi.mlab as mlab
from numpy.random import random
mlab.point3d(random(1000), random(1000), random(1000),range(1000))

point3d

Upvotes: 3

janneb
janneb

Reputation: 37208

Probably easier to change your program to output data in one of the common formats, such as

XYZ: http://openbabel.org/wiki/XYZ_%28format%29

GRO: http://manual.gromacs.org/current/online/gro.html

Alternatively, create a tiny program to convert your data into one of the common formats. That's a lot less work than creating a visualization program from scratch.

Upvotes: 3

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