[MMTK] setConfiguration -> frames are not aligned

Ralf Biehl ra.biehl at fz-juelich.de
Thu Apr 16 17:04:10 UTC 2009

Hi Konrad

r_[something] is a shorthand in numpy for array(something) and produces 
and numpy array of shape (N,3) in
r_[[a.position() for a in universe.atomList()]]
In that way it guaranties that i have an array with the same dimension 
as the universe.configuration() (tested with shape()    )
As the output is an array, order of atoms should not matter
ParticleVector(universe,array )  should then create a particleVector for 
the universe.

I want to fit Small angle neutron scattering data with a standard 
fitting routine.
My goal was to modify the configuration  by some  small  vector (for 
each atom) like in the energy minimization.
The result should be a new configuration that describe my SANS data.
Therefore i need a particleVector of the universe that gives the 
direction for the configurational change.



Konrad Hinsen schrieb:
> On Apr 16, 2009, at 13:38, Ralf Biehl wrote:
>> Hi all
>> Following sequence produces an error as shown in the code below
>> __MMTK.__version__
>> '2.5.24'
>> org=universe.copyConfiguration()
>> new=ParticleVector(universe,r_[[a.position() for a in 
>> universe.atomList()]])
>> org+new
>> .....
> The second argument to ParticleVector must be an array of shape (N, 
> 3), where N is the number of atoms in the universe. I don't understand 
> the syntax r_[...] you are using, is that perhaps some IPython 
> abbreviation? Anyway, I suppose it does not create an array of the 
> required shape.
> Note also that the order of the atoms in the array is the one defined 
> by the attribute atom.index of each atom object. This is in general 
> NOT the same as the order of the atoms in universe.atomList(). Do you 
> have a specific reason for creating a ParticleVector by looping over 
> universe.atomList()? Perhaps your goal can be reached more easily.
> 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
> Web: http://dirac.cnrs-orleans.fr/~hinsen/
> ---------------------------------------------------------------------


Dr. Ralf Biehl
Institut für Festkörerforschung
Forschungszentrum Jülich
D-52425 Jülich

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