[MMTK] MMTK for plasmas?

Konrad Hinsen hinsen at cnrs-orleans.fr
Mon Feb 12 08:46:12 UTC 2007


On 10.02.2007, at 00:06, Mark Heslep wrote:

> 1. I'm interesting in doing some plasma simulations (fusion).    The
> MMTK emphasis is obviously molecular chem/bio but I was drawn to it
> because a) it appears to use Fast Multipole M. for N body and b) its
> open source python on the frontend.  Is MMTK a good candidate for  
> my area?

I can't say, not knowing enough about plasma simulations. The  
fundamental limitation of MMTK is the use of classical point  
particles. If you need either quantum particles or particles that are  
not point masses, then you are not likely to profit much from MMTK.  
Otherwise, you can very probably use MMTK, but you may have too add  
things (force field terms, integrators) yourself if your algorithmic  
needs are different from molecular simulations.

> 2. Installation/Examples.  Have MMTK 2.5.16, have it compile and
> installed on Fedora Core 6 after patching setup.py to find netcdf
> include headers and libs.  Now 'import MMTK' works, but most all of  
> the
> examples fail immediately with
>> IOError: Database entry Atoms/ar not found
> or similar from ../MMTK/Database.py line 51 in databasePath.
>
> The manual suggests no database manipulation is required for default
> operation but this suggests I need some Atom entries, in my local
> database path?

They should be there. If they aren't, then something went wrong  
during installation or configuration.

Please check the following (in Python):

	from MMTK.Database import path
	print path

This should print a list containing a single element that ends in
'site-packages/MMTK/Database'. In that directory, you should find a  
directory "Atoms" containing all the atom definitions, including "ar".

If "print path" yields anything else, then you have probably set the  
environment variable MMTKDATABASE to something wrong. Note that you  
do not need to set it at all if you use just the default database.

Konrad.
--
---------------------------------------------------------------------
Konrad Hinsen
Centre de Biophysique Moléculaire, CNRS Orléans
Synchrotron Soleil - Division Expériences
Saint Aubin - BP 48
91192 Gif sur Yvette Cedex, France
Tel. +33-1 69 35 97 15
E-Mail: hinsen at cnrs-orleans.fr
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--
---------------------------------------------------------------------
Konrad Hinsen
Centre de Biophysique Moléculaire, CNRS Orléans
Synchrotron Soleil - Division Expériences
Saint Aubin - BP 48
91192 Gif sur Yvette Cedex, France
Tel. +33-1 69 35 97 15
E-Mail: hinsen at cnrs-orleans.fr
---------------------------------------------------------------------



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