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Re: [lammps-users] Request to add question to the forum (can not get high enough sp3 atoms while preparing amorphous carbon)
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Re: [lammps-users] Request to add question to the forum (can not get high enough sp3 atoms while preparing amorphous carbon)

From: Axel Kohlmeyer <akohlmey@...24...>
Date: Sat, 16 Sep 2017 10:09:40 -0400

On Thu, Sep 14, 2017 at 6:34 PM, Shahriar Mufid <shahriar238@...36.....24...> wrote:


My research is related to the molecular dynamics simulation of amorphous carbon (a-C). Recently I had to prepare amorphous carbon containing different amount of sp2/sp3 atoms. So I tried the method described in this paper ( where they followed the method of preparing a-C from their previous paper published in 2013 ( I followed the same procedure using airebo potential, but unfortunately I could not get such high percentage of sp3 atoms in the prepared a-C. For instance, when I used density of 2.8g/cc (20A*20A*20A box, 1122 atoms), I got less than 20% sp3 atoms while the paper reported 64.58% sp3. 

I have included my input file below. Would you kindly have a look and let me know what I did wrong?

please note that ​it is not the responsibility of this forum to review and correct your work.​ people here have their own research to worry about.
if you have questions about the procedure in the paper you are referencing, you need to either contact the authors of the paper, but beforehand i strongly recommend, you discuss with your adviser/supervisor.


Your help is highly appreciated. Thank you very much for your consideration.

My input file:

# Lammps version: LAMMPS (9 Dec 2014)

​please note that the AIREBO implementation in LAMMPS and LAMMPS in general have seen multiple important bugfixes​ since 2014. it is strongly recommended in case of problems, to test whether they persist with the latest version of LAMMPS


# ----------------------------
units metal
dimension 3
boundary p p p
atom_style charge
# --------------------------------------
region box block 0 20 0 20 0 20 units box
create_box 1 box
create_atoms 1 random 1122 964723 box
mass 1 12.0107
group all region box
set type 1 charge 0
# -----------------------------------
pair_style airebo 3 1 1 
pair_coeff * * CH.airebo C
# -----------------------------------
minimize 1.0e-8 1.0e-8 1000000 1000000
reset_timestep 0
timestep 0.00025

fix 1 all langevin 300 300 0.025 9536418
fix 2 all nve

thermo_style custom step temp press vol enthalpy ke pe etotal lx ly lz density atoms
thermo_modify lost warn
thermo 1000
run 20000

unfix 1
fix 1 all langevin 300 8000 0.025 7268134
run 40000

unfix 1
fix 1 all langevin 8000 8000 0.025 541397
run 8000

unfix 1
fix 1 all langevin 8000 300 0.025 9536418
run 8000

unfix 1
fix 1 all langevin 300 300 0.025 9536418
dump 2 all custom 10000 dlc_final.dump id type q x y z vx vy vz
compute 1 all coord/atom 1.75
dump 4 all custom 10000 coordination.dump c_1
run 20000

Best regards,
Shahriar Mufid Rahman,,
Texas Tech University,
Lubbock, TX, 79415.

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Dr. Axel Kohlmeyer  akohlmey@...12...24...
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.