• ## Outreach

From: Pavan Miriyala (pavan.kumar9111_at_gmail.com)
Date: Wed Sep 03 2014 - 10:23:12 CDT

No, even If I assign a variable with just integer, not a list. It is not

>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
>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.
> >>> >>>> >>
> >>> >>>> >>
> >>> >>>> >> >
> >>> >>>> >> > Thanking you
> >>> >>>> >> >
> >>> >>>> >>
> >>> >>>> >>
> >>> >>>> >>
> >>> >>>> >> --
> >>> >>>> >> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
> >>> >>>> >> College of Science & Technology, Temple University,
> >>> >>>> >> 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.
>