VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Tue Mar 10 2015 - 15:11:59 CDT

On Tue, Mar 10, 2015 at 1:12 PM, Albert Solernou <a.solernou_at_leeds.ac.uk> wrote:
> Hi John,
> what do you think about Pawel's approach? Is it feasible at all? To me that
> would be the preferred solution. In the meantime I am spending my time
> reading on VisIt.

you can try using the polyhedra representation and experiment with the
distance cutoff setting. it won't work for all kinds of geometries,
but might be sufficient for simple ones with fairly regular meshes.

another option to turn pure position data into surface objects could
be the Quicksurf representation.

axel.

>
> Best,
> Albert
>
>
>
> On 03/10/2015 12:44 PM, Axel Kohlmeyer wrote:
>>
>> On Tue, Mar 10, 2015 at 11:53 AM, Albert Solernou
>> <a.solernou_at_leeds.ac.uk> wrote:
>>>
>>> Hi John,
>>> thanks for the answer. Although it is not the ideal solution, and
>>> although I
>>> don't know tcl... I could give it a go. Could you point me to the right
>>> documentation?
>>
>> http://www.ks.uiuc.edu/Research/vmd/plugins/multimolanim/
>>
>>> In addition I have a few extra questions:
>>> - Will I be able to define/label different bodies or parts so that I can
>>> click on them, change colors, and show/hide?
>>
>> nope. VMD is not really a good tool for such things. you might be
>> better off to look into a tool like ParaView or VisIt, for example.
>>
>> http://www.paraview.org/
>>
>> https://wci.llnl.gov/simulation/computer-codes/visit
>>
>>> - In that case how will that integrate with the next timestep given that
>>> it
>>> is a "different" molecule?
>>
>> each timestep has to be a "molecule" (i.e. in "molecule" in VMD is the
>> term for dataset), the rest is handled by the plugin GUI, which
>> emulates the regular animation controls and instead shows/hides
>> individual molecules/datasets
>>
>>> - I have currently a Tkinter interface that I plan to port to, and I read
>>> that you support it. Could you point me to the right documentation site
>>> to
>>> do so? Do you have any suggestion?
>>
>> Tkinter is a significant challenge with VMD, since python runtimes are
>> so incredible non-portable and so large that they are no longer
>> bundled with VMD. so to have access to tkinter, you first will need to
>> compile a custom version of VMD that includes python.
>>
>> axel.
>>
>>> Cheers,
>>> Albert
>>>
>>>
>>> On 03/09/2015 06:00 PM, John Stone wrote:
>>>>
>>>> Hi,
>>>> At present, VMD doesn't provide for time-varying mesh data.
>>>> In the short term, you could overcome this limitation by loading
>>>> different trajectory timesteps into separate molecules. Once loaded
>>>> you can animate the mesh trajectory using the multimolanim plugin.
>>>> Let us know if you need help to get this working.
>>>>
>>>> Cheers,
>>>> John Stone
>>>> vmd_at_ks.uiuc.edu
>>>>
>>>> On Mon, Mar 09, 2015 at 03:11:26PM +0000, Albert Solernou wrote:
>>>>>
>>>>> Dear all,
>>>>> I am writing a new plugin that should enable VMD to work with Finite
>>>>> Element Trajectories. Currently, my plugin reads correctly the input
>>>>> file, through:
>>>>> plugin.open_file_read
>>>>> then loads and displays the surface triangles through:
>>>>> plugin.read_rawgraphics
>>>>> and finally releases my handler:
>>>>> plugin.close_file_read
>>>>>
>>>>> The next step should be to load the whole trajectory, and this is
>>>>> where I need some advice. I understand that this should be done
>>>>> through:
>>>>> plugin.read_next_timestep
>>>>> but, will it update the vertices of the triangles? How can I do so
>>>>> using molfile_timestep_t? Is there an easy workaround?
>>>>>
>>>>> Thanks in advance,
>>>>> Albert
>>>>>
>>>>> --
>>>>> ---------------------------------
>>>>> Dr Albert Solernou
>>>>> EPSRC Research Fellow,
>>>>> Department of Physics and Astronomy,
>>>>> University of Leeds
>>>
>>>
>>> --
>>> ---------------------------------
>>> Dr Albert Solernou
>>> EPSRC Research Fellow,
>>> Department of Physics and Astronomy,
>>> University of Leeds
>>>
>>
>>
>
> --
> ---------------------------------
> Dr Albert Solernou
> EPSRC Research Fellow,
> Department of Physics and Astronomy,
> University of Leeds
> 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.