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Re: [lammps-users] Minimising monolayer graphene with vacancy defects
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Re: [lammps-users] Minimising monolayer graphene with vacancy defects


From: Axel Kohlmeyer <akohlmey@...24...>
Date: Fri, 27 Apr 2018 22:01:08 -0400

On Fri, Apr 27, 2018 at 9:16 PM, Mockele Nkrumah <mgmike20@...24...> wrote:
> In other words, how may I be sure that a graphene sheet with certain atoms
> missing is properly minimized if I am getting practically the same sheet
> size irrespective of how many atoms I'm deleting?

most likely you need to change your simulation setup and/or protocol.
it is a well known property of minimizers to not guarantee finding the
global minimum, but getting trapped in local minima, especially with
shallow potential hypersurfaces.

>  More deleted atoms means more buckling in the sheet which theoretically corresponds to a decrease in the sheet's length and width.

but how can you be certain, that this is not an activated process
and/or only observed as an average at temperatures different from 0K
(which is what a minimization corresponds to)?

it looks a lot like you are looking at your simulations from the
macroscopic perspective and disregard how things may be different on
the atomic length scale and typical time scales.

axel.

>
> Regards,
> Michael
>
> On Wed, Apr 25, 2018 at 1:35 PM, Mockele Nkrumah <mgmike20@...24...> wrote:
>>
>> Dear all,
>>
>> For the past couple of days, I have been running MD simulations to
>> calculate the Young's modulus of graphene at various percentage vacancy
>> defects.
>>
>> Prior to the deformation stage, I ran NVT followed by NPT.  Although the
>> fluctuation in the x and y dimension (z was fixed) was within an acceptable
>> range, all the structures were minimising to the same lengths.
>>
>> This surely is wrong since previous studies have indicated that increasing
>> the percentage defects should induce more ripples in the sheet, thereby
>> lowering the size of the x and y dimension[1].
>>
>> Yesterday, I thought that maybe I had to resort to the minimize command
>> prior to using NPT but this still was of no use; I have tried the
>> minimisation with and without the fix box/relax command and also varied the
>> dmax parameter.  Now, I have actually run out of options, at least given my
>> current understanding of the software.
>>
>> The pertinent commands are:
>>
>> velocity all create 300 10248676 dist gaussian
>> run 0
>> velocity all scale 300
>>
>> fix 1 all box/relax x 0.0 y 0.0 couple none vmax 0.01 nreset 100
>>
>> min_style cg
>> min_modify dmax 2.0 line quadratic
>> minimize 0 0 1000 100000
>>
>> fix 1 all nve/limit 0.1
>> fix 2 all langevin ${init_temp} 300 0.0006 123457
>>
>> fix 1 all npt temp ${init_temp} 300 0.1 tchain 6 x ${p_x} 0.0 1.0 y ${p_y}
>> 0.0 1.0 couple none pchain 6 drag 1.0 nreset 1
>> fix 2 all momentum 1 linear 1 1 1 rescale
>>
>> The tested timesteps were 0.5 fs and 1 fs, which produced similar results
>> i.e. 201.4 Å and 198.6 Å for the x- and y-dimension, respectively.  The
>> systems which were modelled had approximately 15000 atoms and the AIREBO
>> force-field was used.
>>
>>
>> Regards,
>> Michael
>
>
>
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-- 
Dr. Axel Kohlmeyer  akohlmey@...24...  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.