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Re: [lammps-users] MD simulation for 3d polydisperse system
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Re: [lammps-users] MD simulation for 3d polydisperse system

From: Axel Kohlmeyer <akohlmey@...24...>
Date: Wed, 16 Aug 2017 15:09:31 -0400

On Wed, Aug 16, 2017 at 12:01 PM, Notan Tah <tahnotan@...24...> wrote:


How i will do a Molecular dynamics simulation of 3d polydisperse (with 11% polydispercity) system using LJ potential in lammps. Mainly my question is how i will assign the different diameter in lammps as my system is polydisperse.
My main question how i assign the pair_coeff for different paricles. Because here all particle has different diameter.

​for each atom with a different sigma, you need to reserve an atom type.
correspondingly you need to assign a pair_coeff​ statement to each pair of atom types.
the latter can be mostly automated, if you can apply a mixing rule for the mixed interactions.
example. for three atom types, it may be sufficient to specify:

pair_coeff 1 1 1.0 1.0
pair_coeff 2 2 1.0 1.5
pair_coeff 3 3 1.0 2.0

...and then LAMMPS will compute the remaining pairs:

1 2, 1 3, 2 3 from mixing. for details on that, please see the documentation for pair_modify


ere is my script how i modify it:

dimension 3
boundary p p p
restart 3000000 restart.3dAMLJ_60
units lj    #all quantities are expressed in terms of Lennard Jones parameters

atom_style atomic

neighbor 0.3 bin
neigh_modify delay 4

lattice fcc 0.82
region box block 0 13 0 13 0 13
#create_box 2 box
create_atoms 1 box #initial position

#mass 1 1.0

pair_style lj/cut 2.5

pair_coeff  x y \epsilon \sigma cut_off   #(/ Here All particles has different sigma)

compute new liq temp
print "Seed: ${seed}"
velocity liq create 0.0080 ${seed} temp new

fix 1 liq nvt temp 0.0080 0.0080 0.1

timestep 0.005 #delta T
thermo 10000 #output
thermo_modify temp new

run 199904

reset_timestep 0
thermo 100000 #output
thermo_modify temp new

variable f1 file tmp.txt

variable s equal next(f1)

dump 3 liq custom 1 dump.liq x y z type
dump_modify 3 every v_s sort id

run 199904



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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.