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Re: [lammps-users] Therm/cond - molecules
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Re: [lammps-users] Therm/cond - molecules


From: Steve Plimpton <sjplimp@...24...>
Date: Tue, 15 May 2018 08:09:19 -0600

The hard part will be how to compute and assign KE to an entire molecule.
If the molecule is not entirely on one proc that will require coordination
between procs.  In principle a molecule could span several procs.  Also,
compute the COM to figure out which rNEMD bin the molecule is "in"
will be non-trivial.  There might be no good alternative to doing MPI_Allreduce
operations and using something like compute com/chunk.

Steve

On Mon, May 14, 2018 at 4:09 PM, Romain Perriot <rperriot@...824...> wrote:
Thanks for the reply Axel. 
Indeed, I didn't see any mention of molecule's KE exchange in the documentation, and rNEMD is presented in the literature as very efficient (especially compared to the "direct" thermostated method).

Anyway, I'll look at the other methods, and maybe also the fix itself to see if it can be easily modified.

Best,
Romain


On Fri, May 11, 2018 at 4:30 PM, Axel Kohlmeyer <akohlmey@...24...> wrote:


On Thu, May 10, 2018 at 12:54 PM, Romain Perriot <rperriot@...2126...4...> wrote:

Hi,

 

Is it possible for the fix therm/cond command to exchange KE between moelcules rather than atoms?


​if it is not mentioned in the documentation (and i assume you are asking because you looked at it and didn't see anything), then it is not available.
LAMMPS comes without a GUI but it is WYSITMIWYG (i.e. any supported feature is documented).

you may have to consider using an alternate approach to determine thermal conductivity.

axel.

 

I’m trying to measure the thermal conductivity of a molecular crystal via rNEMD.

 

Thanks,

Romain


---------------------------------------------------------------------------------- 

Romain Perriot

Theoretical Division T-1

Los Alamos National Laboratory

Los Alamos, NM 87544




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--
Dr. Axel Kohlmeyer  akohlmey@...33....24...  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.



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Romain Perriot, PhD               
University of South Florida, Department of Physics
4202 East Fowler Avenue, Tampa, Fl 33620-5700   USA
phone: (813) 974-2314                           
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