VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Wed Nov 01 2017 - 21:03:27 CDT

On Wed, Nov 1, 2017 at 7:59 PM, Vaidyanathan Sethuraman <vsethura_at_umn.edu>
wrote:

> Hi Axel/VMD Users
>
> Please find the script and datafiles that I use for testing
>
> testinp.data - datafile containing atom and bond info
> afterguess.data - datafile generated by topotools
> VMD_commands.png - A snapshot of the VMD commands used.
>
> VMD Version - 1.9.3 - Tested in both Windows 10 and Mac OS/X
>
> In testinp.data, the atom type of atom id 2 is also 2, whereas after
> using topo writelammpsdata, the atom type of atomid 2 is 12.
>
> I hope I have given all the required information. Please let me know if I
> am missing something or doing something stupid which is obvious.
>

​no, everything is fine. the issue is, that in order to determine numerical
atom types that match LAMMPS' requirements (start at 1, consecutive), those
need to be sorted​ and compiled into a unique list. since those atom types
cannot be assumed to be numerical (LAMMPS is the exception, not the rule),
the list is sorted alphabetically, which puts '2' between '1' and '19'. so
the trick is to override the atom type with something that sorts both
numerically and alphabetically in the same way, e.g. by prepending zeroes.
like in this script:

​package require topotools

topo readlammpsdata testinp.data full

# prepend type name for single digit types with a zero, so they sort
properly
foreach s [list 1 2 3 4 5 6 7 8 9] {
    set sel [atomselect top "type $s"]
    $sel set type "0$s"
    $sel delete
}

topo guessangles
topo guessdihedrals
topo writelammpsdata topology-added.data full
​
axel.

>
> Thanks
>
> Best Regards
>
> Vaidyanathan M S
>
> Postdoctoral Fellow
> Kevin Dorfman's Group
> Department of Chemical Engineering and Materials Science
> University of Minnesota Twin Cities
>
> On Wed, Nov 1, 2017 at 5:38 PM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:
>
>>
>>
>> On Wed, Nov 1, 2017 at 5:34 PM, Vaidyanathan Sethuraman <vsethura_at_umn.edu
>> > wrote:
>>
>>> Hi VMD/LAMMPS users
>>>
>>> I am trying to use topotools in VMD. Problem I am trying to resolve is
>>> as follows. Please let me know if there is an easier way as well. I have a
>>> LAMMPS datafile with atom IDs and bond list with bond data. I need the
>>> angle and dihedral list.
>>>
>>> So I use
>>> topo readlammpsdata filename full
>>> topo guessangles
>>> topo guessdihedrals
>>> topo writelammpsdata newfilename full
>>>
>>> This works perfectly except that when the number of atomtypes is greater
>>> than 10, it automatically renumbers the atomtypes . How can I stop that ?
>>> In a nutshell can I keep the atomtypes not to change while rewriting LAMMPS
>>> datafile.
>>>
>>
>> which version of topotools is this with?
>> can you post a minimal example file where this happens?​
>>
>> ​axel.​
>>
>>
>>
>>
>>> I tried going through mailing list. It would be great if you could point
>>> out had it been discussed and I missed it .
>>>
>>> PS: I sent the same email yesterday , but did not see the email in the
>>> mailing list. Please excuse if this is a replicate.
>>>
>>> Thanks in advance
>>>
>>> Vaidyanathan M S
>>>
>>
>>
>>
>> --
>> 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.
>>
>
> 

-- 
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.