[MMTK] Re: Conjugate gradient minimization in 2.2b6

Konrad Hinsen hinsen@cnrs-orleans.fr
Mon, 20 Aug 2001 14:50:07 +0200

> This prints indeed 'l' (you meant the letter 'l', not the number '1',
> right?).

Right. 'l' for "long".

> before things are handed over to the C-function. I got an array with
> zeros, except for the elements 0,22,26,48, where there is '1', so at the
> same list positions as where you had the fixed atoms out of the
> NetCDFFile.

Sounds fine.

> Could it be that there is something wrong with some functions in my
> version of NumPy, and the minimization uses these functions? I could try

No, no NumPy functions are used in minimization except for the
creation of some temporary arrays. Your problem looks exactly like the
one in 2.0, where the array of "fixed" flags was accessed as an array
of bytes (which indeed it was in MMTK 1). Are you sure you are not
using an old 2.0 or 2.1 installation instead of the new one?

     from MMTK.Trajectory import TrajectorySet

that should raise an exception in any version before 2.2.

Konrad Hinsen                            | E-Mail: hinsen@cnrs-orleans.fr
Centre de Biophysique Moleculaire (CNRS) | Tel.: +33-
Rue Charles Sadron                       | Fax:  +33-
45071 Orleans Cedex 2                    | Deutsch/Esperanto/English/
France                                   | Nederlands/Francais