visualization with vmd

[taher ghasimakbari]

Hi all,

Hope you doing well! I used to load hoomd config to vmd and visualize them graphically, but recently it produces the most bizarre graphical figures. I have the cubic box and vmd produces the random shape figure. I suspect the particles are not shifted into the box in the final configuration dump using the min_image convention. Have you dealt with this issue?

Cheers,

Taher

[Michael Howard]

The hoomd plugin in vmd 1.9.1 works just fine with hoomd 1.3 on OS X for me.

--Mike

[taher ghasimakbari]

Hi Micheal,

I reinstalled the vmd1.9.2 and I have the hoomd I got 2015. The simulation is in a cubic box, however I am getting the following image attached.

Cheers,
Taher 

[Joshua Anderson]

HOOMD correctly outputs particles wrapped in the box. VMD's hoomd plugin unwraps them when image data is available. If this behavior is not desired, do not save the image tags to the XML file.

------
Joshua A. Anderson, Ph.D.
Research Area Specialist, Chemical Engineering, University of Michigan
Phone: 734-647-8244
http://www-personal.umich.edu/~joaander/

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[taher ghasimakbari]

HI Joshua,

Thanks for the response. I tried what you mentioned. I am getting better results bot still the figure which is suppose to be a cubic box looks fussy! I have attached the result.

Cheers,

Taher

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[Joshua Anderson]

You will get better VMD support on the VMD users mailing list. I personally have only run VMD a few times in the last several years.

------
Joshua A. Anderson, Ph.D.
Research Area Specialist, Chemical Engineering, University of Michigan
Phone: 734-647-8244
http://www-personal.umich.edu/~joaander/

[Eric Jankowski]

Hi Taher,

I'd recommend digging in the VMD documentation;

http://www.ks.uiuc.edu/Research/vmd/current/ug/ 

and more specifically, the pbctools plugin:

http://www.ks.uiuc.edu/Research/vmd/plugins/pbctools/

if you want to control how things are visualized and how the periodic boundaries are handled.

Eric

[taher ghasimakbari]

Thanks Joshua.

[Åsmund Ervik]

Apropos this topic: I'm pretty sure there is a bug related to unwrapping somewhere in dump_dcd() when unwrap_rigid = True. I've been meaning to report it, but I've been super busy lately. Usually it works fine, but when you

* Run an initial simulation which resizes the box (no dump_dcd)
* Save an xml file at the end of that simulation
* Restart another simulation from this xml file
* In this second simulation, run dump_dcd(...,unwrap_rigid=True) [no resizing of box happens in this simulation]
* Open the the xml and dcd files in VMD
* Use pcbtools to wrap everything back into the unit cell

the unit cell VMD picks up is wrong. Since this only happens when one restarts a HOOMD simulation, I'm inclined to think it's a HOOMD bug. (Or it could be I'm doing something stupid.)

Let me know if you want a pair of scripts which reproduce this behavior.

Also, Joshua: what are you using, if not VMD?

[Joshua Anderson]

Do you include image information in the xml you save at the end of the simulation? If not, then I would expect this behavior. If a rigid body gets split across the box boundary, and there are no image tags in the xml file, hoomd thinks the rigid body is a box width wide when it reads in the xml file.

This behavior is not possible in hoomd v2.0. In the rewritten composite body framework, users specify composite bodies in a local reference frame, and the rigid body is initialized from the position/orientation of a central particle.

Regarding visualization tools, VMD cannot draw polygon or polyhedral shaped particles. We have a number of internal tools in glotzer group that do. Some are python based and allow users to write custom workflows - i.e. coloring individual particles with different colors in a custom color map based on the output of an analysis routine from another python module. That type of workflow simply is not possible in VMD.

http://arxiv.org/abs/1606.00687
http://dx.doi.org/10.1016/j.cpc.2016.02.024
http://dx.doi.org/10.1039/C5SM01351H

------
Joshua A. Anderson, Ph.D.
Research Area Specialist, Chemical Engineering, University of Michigan
Phone: 734-647-8244
http://www-personal.umich.edu/~joaander/

[taher ghasimakbari]

Thanks guys.