[CPMD-list] Simulation of Chemical reaction

[Julen Larrucea]

Hi
> 1. How can I set up this model? I am considering a 2D periodic
> structure.  Then, to simulate such a reaction, how many layers of iron
> atoms and how many organic atoms are needed?

   I think you can build an iron surface (with 3, 4, 5... layers of Fe
depending on the the accuracy needed) and then put the organic
molecule(s) placed close enough to the surface (around 2 angstroms (?)
).

  First of all you will probably run a geometry optimization so that
you will start your simulation from 0 K and then you can find the
temperature you are searching by running many CP simulations of some
picoseconds (at least a couple of them each one) by using for example:
  TEMPCONTROL IONS
    50.0  20.0
  after checking that the simulation didn't happen for some
picoseconds, stop the simulation (touch EXIT) and increase the
temperature by using annealing
  ANNEALING
    1.001
  until the fictitious ionic temperature reaches a couple of degrees
warmer, then stop and run again at "constant" (tempcontrol)
temperature for some time, annealing again... and so on.

  .> 2. For molecules, how to set up the initial positions of them?
  you can get an idea of the distance between molecule and surface by
for example running a constraint dynamics at temperature where the
reaction happens for sure.

   hope this helps
         Greetings,
                          Julen





On 8/22/07, Hua Bao <hbao at purdue.edu> wrote:
> Dear CPMD-user,
>
> I am trying to simulate a chemical reaction between iron surface and a
> liquid organic chemical. Our goal is to know at what condition
> (temperature pressure) will this reaction happen. I am completely new to
> this area. Therefore I want you ask some basic question about this
> simulation,
>
> 1. How can I set up this model? I am considering a 2D periodic
> structure.  Then, to simulate such a reaction, how many layers of iron
> atoms and how many organic atoms are needed?
>
> 2. For molecules, how to set up the initial positions of them?
>
> Thanks,
> Hua Bao
>
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>


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Julen Larrucea
Kimika Fakultatea
Euskal Herriko Unibertsitatea P.K.1072
20080 Donostia; Euskal Herria (Basque Country)
Voice : +34-943-015341
Fax   : +34-943-015270
http://www.sc.ehu.es/chemistry/theory
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