VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Wed Sep 03 2014 - 10:30:27 CDT

On Wed, Sep 3, 2014 at 5:23 PM, Pavan Miriyala
<pavan.kumar9111_at_gmail.com> wrote:
> No, even If I assign a variable with just integer, not a list. It is not
> reading it as a integer
>
>>Main< (pavan) 97 % set a 1
> 1
>>Main< (pavan) 98 % set b 0
> 0
>>Main< (pavan) 99 % set c 5
> 5
>>Main< (pavan) 100 % measure angle $a $b $c
> measure angle: must specify exactly three atoms in a list
>>Main< (pavan) 101 % measure angle { $a $b $c }
> expected integer but got "$a" measure angle: bad atom index

again, please look up the Tcl tutorial on how to create lists {}
creates a quoted string.
in the previous example you created a list which contained 1 element,
which was a list of 3 elements.

this is all *fundamental* Tcl stuff. it is all explained over there
and that tutorial is very good and accessible. it will be more than
worth your time to go over it and learn what you need properly. i
don't have time to be your personal Tcl tutor.
if you don't like writing Tcl, use LAMMPS with rerun as steve
suggested or write a script/program in whatever your favorite
scripting/programming language is. or find somebody that will do it
for you. in any case, as far as i am concerned, i have spend as much
time as i am willing to spend on this thing.

good luck,
    axel.

>>Main< (pavan) 102 %
>
> But this only works
>>Main< (pavan) 102 % measure angle {1 0 5}
> 120.00004577636719
>
>
> Thanks & Regards,
> Venkata Pavan Kumar. Miriyala
> pavan.kumar9111_at_gmail.com,
> contact number: +91-9032307746
>
>
>
> On Wed, Sep 3, 2014 at 8:47 PM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:
>>
>> 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.
>
> 

-- 
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.