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Re: [lammps-users] Implementation of a numerical Hessian via a new fix
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Re: [lammps-users] Implementation of a numerical Hessian via a new fix


From: Axel Kohlmeyer <akohlmey@...24...>
Date: Sat, 2 Dec 2017 15:56:53 -0500



On Sat, Dec 2, 2017 at 1:43 PM, Johannes P. Dürholt via lammps-users <lammps-users@lists.sourceforge.net> wrote:
Dear users,

I want to implement the computation of a finite difference based Hessian in LAMMPS. My Idea is to write a new fix. The fix should use the methods initial_integrate and final_integrate. In the initial_integrate method the an atoms coordinate is displaced, and in the final_integrate method the actual finite differencing should be done. By storing the current atom and coordinate (x,y or z) as private variables of the fix class, it is always known which is the next atom to process.

Since this is the first time I write an extension to LAMMPS I want to ask two questions:
  • Does this approach make sense, or is there a more clever/easier way of doing this?
  • How do I have to setup the actual Hessian matrix  (2d array) so that I can access it after the computation of the Hessian? The ideal case would be to extract it directly with the extract_fix method of the python interface.
​if you are already planning to do the processing from the python interface, why not do the bulk of the steps in python and only ​run LAMMPS in between with "run 0" to compute the forces?

axel.


 
Best

Johannes Dürholt
-- 
Johannes P. Dürholt
Computational Materials Chemistry Group
Chair of Inorganic Chemistry II, NC 02/32
Ruhr-Universität Bochum
Universitätsstr. 150
D-44780 Bochum
Germany

Tel.: +49-234-32-24372
E-mail: johannes.duerholt@...4545...5...

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--
Dr. Axel Kohlmeyer  akohlmey@...12...24...  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.