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Re: [lammps-users] [Non-DoD Source] Minimising monolayer graphene with vacancy defects (UNCLASSIFIED)
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Re: [lammps-users] [Non-DoD Source] Minimising monolayer graphene with vacancy defects (UNCLASSIFIED)

From: "Shumeyko, Christopher M CTR USARMY RDECOM ARL (US)" <christopher.m.shumeyko.ctr@...2733...>
Date: Wed, 25 Apr 2018 12:15:17 +0000



The paper you referenced has detailed documentation on the authors' simulation methodologies- I would suggest you re-read that more carefully as there are several discrepancies between your simulation and theirs. If results still differ once the methodologies are identical, then there is something to look into. 

Most notably, if you're trying to observe out-of-plane buckling/wrinkles, how will the graphene sheet accommodate them if you've fixed the z dimension?



-----Original Message-----
From: Mockele Nkrumah [mailto:mgmike20@...24...] 
Sent: Wednesday, April 25, 2018 7:36 AM
To: LAMMPS Users Mailing List <>
Subject: [Non-DoD Source] [lammps-users] Minimising monolayer graphene with vacancy defects

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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] < Caution- > .

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.