[MMTK] symeig change to eigh

ra.biehl ra.biehl at fz-juelich.de
Wed Mar 28 16:05:44 UTC 2012

Dear Konrad

I was trying to reduce a bit the memory usage of the normal mode calculation of a large system.
I found by this in NormalModes/Core.py the function
symeig from an external source

This project or better the source is not available anymore, but the wrapper for the underlying lapack functions has moved to scipy and is included as scipy.linalg.eig
Changing the small pieces attached at the end allow the usage of scipy.linalg.eigh instead of symeig in NormalModes/Core.py

Testing with AmberFF  and insulin.pdb in mode='all' the Normal mode calculation is a bit faster
(232 s instead of 291s ) but unfortunately the memory usage is not changed.

Viele Grüsse
and best wishes


#####line 20-30
eigh = None
if array_package == "NumPy":
        from scipy.linalg import eigh
    except ImportError:

####line 260-265
        if eigh is not None:
            ev, modes = eigh(self.array, overwrite_a=True)
            self.array = N.transpose(modes)


Dr. Ralf Biehl
Jülich Centre for Neutron Science (JCNS-1) &
Institute for Complex Systems (ICS-1)
Forschungszentrum Jülich
52425 Jülich

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