[ase-users] ASE + LAMMPS

[Marcin Dulak]

On 02/22/13 15:04, Adam Cadien wrote:
> I forgot to mention the version installed from the default 
> Ubuntu-12.10 repos was broken in the same way.
>
> From svnversion.py it looks like my version of ASE is "exportado"... I 
> think I will look for a different repo.  Thanks for the help Marcin.
that sounds like tarball used for packaging on Ubuntu 12.10 was 
generated from an exported Spanish svn.
We should use svn checkout not export for creating release tarballs ase 
described at https://wiki.fysik.dtu.dk/ase/development/newrelease.html
Otherwise the svnversion is not written.

>
> Anyone working on the LAMMPS interface please contact me, I'd be happy 
> to help with the debugging or porting the LAMMPS interface over to the 
> lammps.py wrapper which would cut down on disk IO and speed things up 
> a bit.
please note that we are in a process of restructuring ASE interfaces:
https://wiki.fysik.dtu.dk/ase/development/proposals/proposals.html
The work is happening in the 
https://trac.fysik.dtu.dk/projects/ase/browser/branches/aep1 branch.
You are welcome to join the effort for lammps there.

Best regards,

Marcin


>
> -AdamC
>
>
>
>
> On Fri, Feb 22, 2013 at 3:18 AM, Marcin Dulak 
> <Marcin.Dulak at fysik.dtu.dk <mailto:Marcin.Dulak at fysik.dtu.dk>> wrote:
>
>     Hi,
>
>
>     On 02/21/13 20:16, Adam Cadien wrote:
>>     I've got ASE running on one machine running Ubuntu 12.04, tested
>>     on many examples with a couple of different calculators and
>>     everything works. I grabbed the repo from here:
>>
>>     http://download.opensuse.org/repositories/home:/dtufys/xUbuntu_12.04/
>>
>>     On another machine I'm running Ubuntu 12.10 and I took the repo
>>     from here:
>>
>>     http://download.opensuse.org/repositories/home:/dtufys/xUbuntu_12.10/
>>
>>     However whenever I try to run example that requires the LAMMPS
>>     calculator I get an error (relevant part of the traceback):
>>
>>     File
>>     "/usr/lib/python2.7/dist-packages/ase/calculators/lammps.py",
>>     line 253, in run
>>         self.write_lammps_in(lammps_in=fd, lammps_trj=lammps_trj,
>>     lammps_data=lammps_data)
>>       File
>>     "/usr/lib/python2.7/dist-packages/ase/calculators/lammps.py",
>>     line 313, in write_lammps_in
>>         ('variable data_file string "%s"\n' % lammps_data))
>     I would recommend to try the trunk first.
>     Hopefully someone who who is familiar with lammps will be able to
>     help here.
>     I think there are no lammps tests in ASE, so there is little
>     chance that the interface is working.
>     Olga provided some details how lammps could be tested (with ase
>     command line)
>     https://listserv.fysik.dtu.dk/pipermail/ase-users/2012-April/001369.html
>     but we need someone with lammps installed who will test and commit
>     the tests.
>
>>
>>     So I poked around ase/dist-packages/ase/calculators/lammps.py and
>>     it seems the version for 12.10 is considerably different from the
>>     12.04 version.  Sadly I don't have the time to fix this myself,
>>     so I figured I'd ping you guys.
>     could it be due to the fact that python-ase is available also as a
>     part of 12.10 distribution?
>     Still i think Ask released the last 3.6.0.2515 release so there
>     should be no differences.
>
>>
>>     I'm running python2.7, I've set the LAMMPS_COMMAND properly and
>>     LAMMPS on both machines works properly and have been
>>     tested thoroughly.  I'm convinced the problem is with the ASE
>>     library, but let me know if you would like any more info about my
>>     system setup.
>>
>>     Finally, since the ase.__version__  variable is not set how do
>>     you keep track of which version of the ASE library is installed?
>     $ cat /usr/lib/python2.7/dist-packages/ase/svnversion.py
>     svnversion = "2515"
>     python -c "from ase.version import version; print version"
>     3.6.0.2515
>
>     Best regards,
>
>     Marcin
>
>>
>>     -AdamC
>>
>>
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>
>
>     -- 
>     ***********************************
>       
>     Marcin Dulak
>     Technical University of Denmark
>     Department of Physics
>     Building 307, Room 229
>     DK-2800 Kongens Lyngby
>     Denmark
>     Tel.:(+45) 4525 3157  <tel:%28%2B45%29%204525%203157>
>     Fax.:(+45) 4593 2399  <tel:%28%2B45%29%204593%202399>
>     email:Marcin.Dulak at fysik.dtu.dk  <mailto:Marcin.Dulak at fysik.dtu.dk>
>
>     ***********************************
>
>


-- 
***********************************
  
Marcin Dulak
Technical University of Denmark
Department of Physics
Building 307, Room 229
DK-2800 Kongens Lyngby
Denmark
Tel.: (+45) 4525 3157
Fax.: (+45) 4593 2399
email: Marcin.Dulak at fysik.dtu.dk

***********************************

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