Re: [ESPResSo-users] Espressomd-users Digest, Vol 87, Issue 8

[Sebastian Bindgen]

Dear Joost and Pierre,

Rudolf has worked out a bond breakage feature that I use in my simulations. The bond breakage also works with the collision detection and deleted possible virtual sites etc. At the current state the tabulated and harmonic potential is "breakable.". Maybe you want to use that. It should be easy to add other breakable bonds. I think the limitation is that angle potentials are not breakable.

You can use the version of Rudolf: https://github.com/RudolfWeeber/espresso.git branch: breakable_bonds

or my version (the tabulated ia had a refactor in the meantime and the collision detection is also merged in this version): https://github.com/bindgens1/espresso.git branch: colldett_bb

Best,

Sebastian

On Wed, Jan 31, 2018 at 6:00 PM, <address@hidden> wrote:

Send Espressomd-users mailing list submissions to
        address@hidden

To subscribe or unsubscribe via the World Wide Web, visit
        https://lists.nongnu.org/mailman/listinfo/espressomd-users
or, via email, send a message with subject or body 'help' to
        espressomd-users-request@nongnu.org

You can reach the person managing the list at
        address@hiddenorg

When replying, please edit your Subject line so it is more specific
than "Re: Contents of Espressomd-users digest..."


Today's Topics:

   1. About import of cStringIO (Pierre de Buyl)
   2. Re: About import of cStringIO (Pierre de Buyl)
   3. Collision Bonds (Joost de Graaf)


----------------------------------------------------------------------

Message: 1
Date: Tue, 30 Jan 2018 21:20:21 +0100
From: Pierre de Buyl <address@hidden>
To: address@hidden
Subject: [ESPResSo-users] About import of cStringIO
Message-ID: <address@hidden>
Content-Type: text/plain; charset=us-ascii

Hi all,

in

src/python/espressomd/MDA_ESP/__init__.py

there is an import to cStringIO that is a Python 2 only feature. The
funcionality of cStringIO.StringIO is provided by io.StringIO in Python 3 but
six http://six.readthedocs.io/#module-six.moves allows to replace it by

from six.moves import cStringIO

and six is apparently an implied dependency anyway as it is required by MDAnalysis

https://github.com/MDAnalysis/mdanalysis/blob/develop/package/setup.py

If you think that it is useful, I attach a patch that I used on my computer. To
apply the patch, one can use "git apply".

Regards,

Pierre

--
-----------------------------------------------------------
Pierre de Buyl
KU Leuven - Institute for Theoretical Physics
T +32 16 3 27355
W http://pdebuyl.be/
-----------------------------------------------------------



------------------------------

Message: 2
Date: Wed, 31 Jan 2018 09:47:52 +0100
From: Pierre de Buyl <address@hidden>
To: address@hidden
Subject: Re: [ESPResSo-users] About import of cStringIO
Message-ID: <address@hidden>
Content-Type: text/plain; charset="us-ascii"

Of course, I forgot the attachement.

On Tue, Jan 30, 2018 at 09:20:21PM +0100, Pierre de Buyl wrote:
> Hi all,
>
> in
>
> src/python/espressomd/MDA_ESP/__init__.py
>
> there is an import to cStringIO that is a Python 2 only feature. The
> funcionality of cStringIO.StringIO is provided by io.StringIO in Python 3 but
> six http://six.readthedocs.io/#module-six.moves allows to replace it by
>
> from six.moves import cStringIO
>
> and six is apparently an implied dependency anyway as it is required by MDAnalysis
>
> https://github.com/MDAnalysis/mdanalysis/blob/develop/package/setup.py
>
> If you think that it is useful, I attach a patch that I used on my computer. To
> apply the patch, one can use "git apply".
>
> Regards,
>
> Pierre
-------------- next part --------------
A non-text attachment was scrubbed...
Name: 0001-Use-six-for-2-3-compatible-use-of-cStringIO.patch
Type: text/x-diff
Size: 743 bytes
Desc: not available
URL: <http://lists.nongnu.org/archive/html/espressomd-users/attachments/20180131/6c5b1ae5/attachment.patch>

------------------------------

Message: 3
Date: Wed, 31 Jan 2018 12:15:32 +0100
From: Joost de Graaf <address@hidden>
To: ESPResSo Users <address@hidden>
Subject: [ESPResSo-users] Collision Bonds
Message-ID:
        <CAGwzpnoq4YeUOpF_+AExeFbgybxZPyU=tW8Cap=YW=Om+address@hidden>
Content-Type: text/plain; charset="utf-8"

Dear Developers,

I have a question concerning the use of the collision-based bonds. I want
to set up a system where particles have a tendency to aggregate,
potentially using the dynamic bonding, but are also subjected to strains
which cause these bonds to break at some later time, when the particle
centers are sufficiently far apart.

Going through the mailing list only revealed a single question under "Bond
Breaking in Polymer Networks - United Atom Force Fields" but at the time
(2012) this kind of simulation was not possible in ESPResSo, and Axel
suggested periodically returning to the (then) Tcl level to break bonds by
hand.

Looking through the documentation, it is not clear whether any of what I
would like to do is possible now. Both "bind_centers" and
"bind_at_point_of_collision" harmonic bonds do not appear breakable, with
the latter having an additional complexity due to the virtual sites that
are created.

There is a small comment on tabulated bonds breaking outside of their
interaction range, but I think this is not what I am looking for, and more
a warning to ensure that particles stay inside the range.

So in summary, what I want to do is:

If particles are say 1 in diameter, there would be a pure repulsion up to 1
and a small, but deep attractive well between 1 and 1.05 separation. When
the particles are within this well, centered at say 1.025 separation, I
want to prevent them from rolling over each other using the
"bind_at_point_of_collision" method, but I want the bond to break again
when I pull the particles more than 1.05 apart and the particles to be able
to bind somewhere else.

I hope you can help.

Best Wishes,

Joost
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.nongnu.org/archive/html/espressomd-users/attachments/20180131/517fd386/attachment.html>

------------------------------

Subject: Digest Footer

_______________________________________________
Espressomd-users mailing list
address@hidden
https://lists.nongnu.org/mailman/listinfo/espressomd-users


------------------------------

End of Espressomd-users Digest, Vol 87, Issue 8
***********************************************