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Re: [ESPResSo-users] Copy_particles and the right numeration
From: |
Axel Arnold |
Subject: |
Re: [ESPResSo-users] Copy_particles and the right numeration |
Date: |
Tue, 18 Feb 2014 23:53:47 +0100 |
User-agent: |
Mozilla/5.0 (Macintosh; Intel Mac OS X 10.9; rv:24.0) Gecko/20100101 Thunderbird/24.3.0 |
Hi Aleksei,
for technical reasons, I prefer copy_particles to use consecutive
identities. Because the particle ids that you give the routine might
very well not be consecutive, a simple "index + shift" would not work.
Now, if you add the parameter "-integer" to the lsort in copy_particles
(scripts/auxiliary.tcl), then the particles are at least in order of
increasing id. And in the special case you copy a single, consecutive
range, the given ids will be consecutive as well, so that would give the
behavior you desire.
For a general solution, I prefer to just return the mapping of the old
ids to the new ones, which is the solution I put into the git.
copy_particles then just returns a list of old-new pairs, which can be
converted to an array, so that you can find the new identities simply by
asking array(old id).
Best regards,
Axel
On 17.02.14 14:01, Aleksei Kabedev wrote:
Dear all,
I experience another problem with copy_particles procedure.
It seems to me, that if I copy a big structure with bonds between
internal particles, the second molecule's particles won't have numbers
"as originals + constant shift". Perhaps it happens when I copy set
of particles once, then add some new particles, bond them and finally
copy all the range once again. In all examples I experienced this
problem, there were branched structures, where I mixed numbers, but
they are not matches respectively anyway.
I need numbers, for example, if there are few branches from one point
and I have to know what are the id's of particles closest to the core
particle and what are the id's of next level, so that I could use
angle bonds after creating them. Here is a simple sample (sorry, it's
not really good). As you can see, particles with different types
should be at the same positions.
--
Kind regards,
Aleksei Kabedev
--
JP Dr. Axel Arnold
ICP, Universität Stuttgart
Allmandring 3
70569 Stuttgart, Germany
Email: address@hidden
Tel: +49 711 685 67609
auxiliary.tcl
Description: Tcl script