VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Mon Jun 14 2021 - 10:59:40 CDT

Atom style sphere does not support molecular data.

On Mon, Jun 14, 2021 at 11:57 AM MD Simulation <mdsimulationgroup_at_gmail.com>
wrote:

> No worries!
>
> In my question, I can write the first part of the sphere style, so the
> Atom information, but using "topo writelammpsdata test.data sphere", this
> does not write the Molecule information. Is that something I'll need to do
> after the function call?
>
> Thanks!
>
> On Mon, Jun 14, 2021 at 11:55 AM Axel Kohlmeyer <akohlmey_at_gmail.com>
> wrote:
>
>> apologies. I am responding to too many mailing list e-mails today and
>> lost track of the folder...
>>
>> On Mon, Jun 14, 2021 at 11:54 AM MD Simulation <
>> mdsimulationgroup_at_gmail.com> wrote:
>>
>>> Hey Axel,
>>>
>>> Thanks for the reply. Also, I did ask the question on the VMD mailing
>>> list 😁
>>>
>>> Cheers,
>>> Stacey
>>>
>>> On Mon, Jun 14, 2021, 11:52 AM Axel Kohlmeyer <akohlmey_at_gmail.com>
>>> wrote:
>>>
>>>> a) topotools is a *VMD* plugin, so you should ask your question on the
>>>> VMD mailing list, not a LAMMPS list
>>>> b) yes, topotools supports output to atom style sphere. It uses the
>>>> radius and (per-type) mass properties and converts them to diameter and
>>>> density
>>>>
>>>> On Mon, Jun 14, 2021 at 11:42 AM MD Simulation <
>>>> mdsimulationgroup_at_gmail.com> wrote:
>>>>
>>>>> Hello,
>>>>>
>>>>> Is there a setting for topotools to write the molecule information for
>>>>> the lammps style sphere?
>>>>>
>>>>> I would like an output file similar to the one here:
>>>>> https://urldefense.com/v3/__https://github.com/lammps/lammps/blob/master/examples/ASPHERE/box/data.box__;!!DZ3fjg!vdl1odsAJIeTLKrmCODo_PCmIlHtU-zaapqbZ9PUAr1ahrEYQOtuqP3cAznacMWlEw$
>>>>> <https://urldefense.com/v3/__https://github.com/lammps/lammps/blob/master/examples/ASPHERE/box/data.box__;!!DZ3fjg!uqDyRuC7edvJ4euZvBS1wg-O7Ix-hjaeX_LBQbG7M_s_Qx8kSlq6SvXEeVeYuAUjdA$>
>>>>>
>>>>> Thanks for the help,
>>>>> Stacey
>>>>>
>>>>
>>>>
>>>> --
>>>> Dr. Axel Kohlmeyer akohlmey_at_gmail.com https://urldefense.com/v3/__http://goo.gl/1wk0__;!!DZ3fjg!vdl1odsAJIeTLKrmCODo_PCmIlHtU-zaapqbZ9PUAr1ahrEYQOtuqP3cAzlzbYNAFw$
>>>> College of Science & Technology, Temple University, Philadelphia PA, USA
>>>> International Centre for Theoretical Physics, Trieste. Italy.
>>>>
>>>
>>
>> --
>> Dr. Axel Kohlmeyer akohlmey_at_gmail.com https://urldefense.com/v3/__http://goo.gl/1wk0__;!!DZ3fjg!vdl1odsAJIeTLKrmCODo_PCmIlHtU-zaapqbZ9PUAr1ahrEYQOtuqP3cAzlzbYNAFw$
>> College of Science & Technology, Temple University, Philadelphia PA, USA
>> International Centre for Theoretical Physics, Trieste. Italy.
>>
> 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  https://urldefense.com/v3/__http://goo.gl/1wk0__;!!DZ3fjg!vdl1odsAJIeTLKrmCODo_PCmIlHtU-zaapqbZ9PUAr1ahrEYQOtuqP3cAzlzbYNAFw$ 
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.