nathalie at cbu.uib.no
Fri Jun 17 10:10:16 CEST 2005
thanks for your quick response.
> On Jun 16, 2005, at 16:52, Nathalie Reuter wrote:
>> I used to calculate vector fields (of normal modes vibrations) and it
>> worked really fine with MMTK-2.4.1.
>> I upgraded to 2.5.7 and got the following error message:
> I thought I had fixed that in 2.5.7, but I will check again.
>> Has something been changed in the Modes object?
> Yes, a lot. The normal mode module has been replaced by a subpackage
> containing separate modules for energetic, vibrational, and Brownian
> normal modes. The error message you get is due to that restructuring,
> as some internal attribute names have changed. When modes created with
> older versions are loaded into 2.5, they need to be adapted, and
> apparently that doesn't yet work as well as I thought it did.
> If your mode calculation is not expensive, just redo it with 2.5.
Ok, now I did the modes calc. with 2.5 and I got a different error message:
File "vector_field.py", line 24, in ?
field = AtomicVectorField(universe, 0.3, modes)
line 256, in __init__
AtomicField.__init__(self, system, grid_size, values)
line 43, in __init__
line 80, in _setField
array[indices] = v
AttributeError: Vector instance has no attribute '__float__'
> Otherwise, be patient for a while, I won't be able to look into this
> before next week.
That is absolutely ok for me. My main objective was simply to upgrade to
v2.5. It is just by chance that I chose a modes file calc. with v2.4 to
test my 25. installation ;o).
> If you have an example file that you can send me, that speeds thing up.
> BTW, note that mode files generated with 2.5 cannot be read with 2.4.
Good to know.
> I may or may not fix that in the future, it certainly does not have a
> high priority. In any case, only vibrational modes could be made
> backwards compatible.
That is fine for me, I don't need to use files from one version to the
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