From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Wed Sep 03 2014 - 10:17:38 CDT

On Wed, Sep 3, 2014 at 5:14 PM, Pavan Miriyala
<pavan.kumar9111_at_gmail.com> wrote:
> 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 ?

this has nothing to do with variables. your variable contains a list,
but the command expects three individual numbers. that is different.
have another look or two into the Tcl tutorial on www.tcl.tk. these
are not VMD problems, but Tcl problems.

axel.

>
>
>
> 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.
>>
>>
>

-- 
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.