[MMTK] Conjugate gradient minimization in 2.2b6

[Konrad Hinsen]

> I am trying to do conjugate gradient minimization with fixed atoms, now
> with the beta version of MMTK, 2.2b6, and I encounter the same problems
> as I described in an earlier email.

I just checked it with my installation, and it works as it should.
Here's a script to check the trajectory:

   from Scientific.IO.NetCDF import NetCDFFile
   from Numeric import *

   t = NetCDFFile('gly_allCH3.nc')

   conf = t.variables['configuration'][:]
   natoms = conf.shape[1]

   for i in range(natoms):
       at = conf[:, i, :]
       equal_values = add.reduce(add.reduce(equal(at, at[0:1])))
       if equal_values == multiply.reduce(at.shape):
	   print i

   t.close()

It prints the indices of all atoms that don't move, not even using MMTK,
so I am not cheating ;-)  Here's what it prints for me:

   0
   22
   26
   48

What system are you running this on? What versions of Python/NumPy
do you use?

Konrad.
-- 
-------------------------------------------------------------------------------
Konrad Hinsen                            | E-Mail: hinsen@cnrs-orleans.fr
Centre de Biophysique Moleculaire (CNRS) | Tel.: +33-2.38.25.56.24
Rue Charles Sadron                       | Fax:  +33-2.38.63.15.17
45071 Orleans Cedex 2                    | Deutsch/Esperanto/English/
France                                   | Nederlands/Francais
-------------------------------------------------------------------------------