From: Pavan Miriyala (pavan.kumar9111_at_gmail.com)
Date: Wed Sep 03 2014 - 10:14:35 CDT

Dear Axel,
              Thanks a lot :)
I have taken data of all atoms forming angles in this form {1 0 5 } ( atoms
1,0,5 are forming angle).
but can measure command works with variables?

I'm getting an error:

>Main< (pavan) 91 % set angl { {1 0 5} }
 {1 0 5}
>Main< (pavan) 93 % measure angle $angl
 measure angle: must specify exactly three atoms in a list

where as
>Main< (pavan) 94 % measure angle {1 0 5}
120.00004577636719

why it can't read variables ?

Thanks & Regards,
Venkata Pavan Kumar. Miriyala
pavan.kumar9111_at_gmail.com,
contact number: +91-9032307746

On Wed, Sep 3, 2014 at 3:35 PM, Pavan Miriyala <pavan.kumar9111_at_gmail.com>
wrote:

> Thank you axel
>
> Thanks & Regards,
> Venkata Pavan Kumar. Miriyala
> pavan.kumar9111_at_gmail.com,
> contact number: +91-9032307746
>
>
>
> On Wed, Sep 3, 2014 at 1:37 PM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:
>
>> On Wed, Sep 3, 2014 at 9:08 AM, Pavan Miriyala
>> <pavan.kumar9111_at_gmail.com> wrote:
>> > Yes exactly, thank you :) , using restart file, rerunning it can give
>> > information. but using many body potential is it possible? Please give
>> me
>> > some references in literature or any examples.
>>
>> i already mentioned to you twice, what you need to do. you obviously
>> have locked in you mind a certain thing that you believe that you need
>> to do and a certain way how it would work. but it an very convinced
>> that you are looking at the problem from the wrong angle and thus are
>> desperately trying something that will lead nowhere. the issue is that
>> you refuse to see that your problem needs to be solved in multiple
>> steps. i am outlining them one more time.
>>
>> what you need to do is to determine all "topological angles" (in the
>> way i explained before), that is you need to identify all atom
>> triplets that you want to compute the angle of, i.e. those where two
>> bonds share an atom. since you also don't have the bonds, you need to
>> determine them as well (e.g. based on a distance guess). this is
>> extremely similar to what needs to be done for building a topology for
>> a "regular" force field. it doesn't matter that you are using a
>> manybody potential, you do not need to use that topology for your
>> simulation, only for analysis.
>>
>> and as explained before, that can be used with LAMMPS using "rerun"
>> and than can be used with VMD using measure or with a standalone
>> postprocessing program. only there is not one single command, one
>> single tool that will do it right away. you do have to write a
>> script/program that systematically does all the steps and then
>> collects the information you need (by looping over the topological
>> angle triples) and creating the histograms from it.
>>
>> this really isn't a complicated operation and people are doing similar
>> things all the time (a lot of the VMD script library and plugins
>> started like that).
>>
>> in the end, the problem you are facing is not really a problem of the
>> science of your task, but simply an issue that you need to have a
>> better strategy to solve a problem. common problems can be solved by
>> reusing a solution that somebody else provided, but anything beyond
>> that has to be solved by yourself and the best way to solve a complex
>> problem is to break it down into smaller more easily solvable
>> problems.
>> i have outlined such a strategy for you multiple times already. short
>> sitting down myself and writing such a script for you (you need to
>> contract me for that), that is all i can do.
>>
>> since you ask for literature. here is my favorite book on that topic.
>> http://www.nostarch.com/thinklikeaprogrammer
>>
>> axel.
>>
>> >
>> > Thanks & Regards,
>> > Venkata Pavan Kumar. Miriyala
>> > pavan.kumar9111_at_gmail.com,
>> > contact number: +91-9032307746
>> >
>> >
>> >
>> > On Wed, Sep 3, 2014 at 12:30 PM, Dudo <dudomail_at_gmail.com> wrote:
>> >>
>> >> well, you may want to determine what your typical angle is,
>> >> because although the energy minimum for a given potential could
>> >> be 120 deg but the equilibrium angle for the molecule may be different.
>> >> for this purpose you can calculate angular-radial distrubution map
>> >> and your actual bonding angles will be seen as a pattern of increased
>> >> occurence on the map.. for this you just need the double loop
>> >> as suggested earlier..
>> >>
>> >>
>> >> On Wed, Sep 3, 2014 at 8:21 AM, Pavan Miriyala <
>> pavan.kumar9111_at_gmail.com>
>> >> wrote:
>> >>>
>> >>> thank you karthik and axel,
>> >>> Axel, I think I have not communicated
>> the
>> >>> problem well, you are guiding me to find out angles when sheet has
>> ideal
>> >>> bonds and angles using programming or permutations. But in my case,
>> the
>> >>> ideal angle is 120, at the time step where crack propagation begins
>> angles
>> >>> will be in the range of 80-140. how I guess it mathematically or
>> programming
>> >>> ?
>> >>> I want to know exact thing happened in sheet.
>> >>> After trying few commands in the sense, not just trials :)
>> >>>
>> >>>
>> >>> Thanks & Regards,
>> >>> Venkata Pavan Kumar. Miriyala
>> >>> pavan.kumar9111_at_gmail.com,
>> >>> contact number: +91-9032307746
>> >>>
>> >>>
>> >>>
>> >>> On Tue, Sep 2, 2014 at 7:12 PM, Axel Kohlmeyer <akohlmey_at_gmail.com>
>> >>> wrote:
>> >>>>
>> >>>> On Tue, Sep 2, 2014 at 2:11 PM, Pavan Miriyala
>> >>>> <pavan.kumar9111_at_gmail.com> wrote:
>> >>>> > Dear Axel,
>> >>>> > just like topo getanglelist, can we measure all the
>> >>>> > angles
>> >>>> > in the molecule with out specifying three atoms using measure
>> command.
>> >>>> > Sorry, for disturbing you I have gone through the vmd user's guide
>> and
>> >>>> > tried
>> >>>> > few commands.
>> >>>>
>> >>>> you cannot learn these kind of things by just "trying a few commands"
>> >>>> and waiting for a perfect solution to drop down on you. programming
>> >>>> doesn't work like this and neither does research. you need to
>> >>>> think(!!!) about your problem and solve it in steps.
>> >>>>
>> >>>> what you are asking for is not rocket science and the process of
>> >>>> solving it yourself will also be highly educational and prepare you
>> >>>> for solving the next and more complicated problem.
>> >>>>
>> >>>> axel.
>> >>>>
>> >>>> >
>> >>>> >
>> >>>> > Thanks & Regards,
>> >>>> > Venkata Pavan Kumar. Miriyala
>> >>>> > pavan.kumar9111_at_gmail.com,
>> >>>> > contact number: +91-9032307746
>> >>>> >
>> >>>> >
>> >>>> >
>> >>>> > On Mon, Sep 1, 2014 at 6:49 PM, Axel Kohlmeyer <akohlmey_at_gmail.com
>> >
>> >>>> > wrote:
>> >>>> >>
>> >>>> >> On Mon, Sep 1, 2014 at 2:36 PM, Pavan Miriyala
>> >>>> >> <pavan.kumar9111_at_gmail.com> wrote:
>> >>>> >> > Dear all,
>> >>>> >> > How can we get bond angles and bond length
>> distribution
>> >>>> >> > using
>> >>>> >> > VMD
>> >>>> >> > through lammps xyz trajectories. Is there any processing
>> extension
>> >>>> >> > for
>> >>>> >> > getting distribution of bond angles and lengths all over the
>> sheet.
>> >>>> >>
>> >>>> >> i already answered your question on the LAMMPS mailing list.
>> >>>> >>
>> >>>> >> >
>> >>>> >> > Thanking you
>> >>>> >> >
>> >>>> >>
>> >>>> >>
>> >>>> >>
>> >>>> >> --
>> >>>> >> 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.
>> >>>
>> >>>
>> >>
>> >>
>> >>
>> >> --
>> >> ____________________
>> >> Ing. Dusan Racko, PhD
>> >> https://www.researchgate.net/profile/Dusan_Racko
>> >> Polymer Institute of the Slovak Academy of Sciences
>> >> Dubravska cesta 3
>> >> 845 41 Bratislava, Slovak Republic
>> >> tel: +421 2 3229 4321
>> >
>> >
>>
>>
>>
>> --
>> 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.
>>
>
>