[MMTK] Nose-Hoover chain thermostat

Yoonjung Huh yhuh at ualberta.ca
Thu Mar 15 16:22:46 UTC 2007

Yes, I had to modify MMTK/Dynamics.py as well as MMTK/Features.py.   
Thank you, Konrad!
I am defining new variables associated with chain thermostat in Src/ 
MMTK_dynamics.c, just as for NoseThermostat (e.g. PyArrayObject  
ct_coordinates instead of t_coordinates).  For now I would like to  
make the chain thermostat do just the same as NoseThermostat.  After  
I've done that, I hope to modify further (e.g. multiple thermostat  
variables) to have chain thermostat.

I can build and install MMTK with such modifications, but the  
trajectories look different for two thermostats.  I am checking again  
if I have done this "copying" of NoseThermostat correctly.

I am wondering though, if there are better ways to implement chain  
thermostat in MMTK...

Thank you very much!!


On 15-Mar-07, at 1:36 AM, Konrad Hinsen wrote:

> On 14.03.2007, at 22:04, Yoonjung Huh wrote:
>> I am wondering if anyone has included Nose-Hoover chain thermostat in
>> MMTK.  I have been trying to do that, first by creating a new
>> thermostat that does exactly the same as the existing
>> NoseThermostat.  I have been modifying MMTK/Environment.py and Src/
>> MMTK_dynamics.c to make a copy of NoseThermostat, but I am having
>> some troubles...  Any suggestions will be really appreciated!!
> Sorry, this is a bit too vague to comment on - what are your troubles?
> The only hint I can give from what you write is that you also need  
> to look at MMTK/Dynamics.py, just search for "thermostat". In fact,  
> you can consider MMTK_dynamics.c the C part of MMTK/Dynamics.py;  
> the two modules very much depend on each other.
> Konrad.
> --
> ---------------------------------------------------------------------
> Konrad Hinsen
> Centre de Biophysique Moléculaire, CNRS Orléans
> Synchrotron Soleil - Division Expériences
> Saint Aubin - BP 48
> 91192 Gif sur Yvette Cedex, France
> Tel. +33-1 69 35 97 15
> E-Mail: hinsen at cnrs-orleans.fr
> ---------------------------------------------------------------------

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