[MMTK] Conjugate gradient minimization in 2.2b6

Konrad Hinsen hinsen@cnrs-orleans.fr
Fri, 17 Aug 2001 12:15:53 +0200


> 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.
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