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Re: [lammps-users] Melting Metallic Particles on Graphene
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Re: [lammps-users] Melting Metallic Particles on Graphene

From: Stefan Paquay <stefanpaquay@...24...>
Date: Mon, 14 Aug 2017 11:19:39 -0400

Please reply to the mailing list, not to me.

If you want to know how to do it, you should check the available literature. However, you started by saying you had a setup that worked but now produces inconsistent results. Maybe you want to figure out why that is instead? What you are describing now sounds like unstable dynamics, so either your initial setup is bad or your time step is too large.

On Fri, Aug 11, 2017 at 4:11 AM, Rosita Masoudi <rositamasoudi@...24...> wrote:
Dear Stefan

Thanks for your reply
it is not related to boundary conditions... with all kind of boundary conditions graphene explodes after some heating.
i have tested it with periodic boundary conditions before.

generally, i want to know if somebody wants to melt a metallic nanoparticle on graphene, what fixes shoud he use?

thanks for your help

On Sat, Aug 5, 2017 at 6:55 PM, Stefan Paquay <stefanpaquay@...24...> wrote:
In which sense can you not reproduce the same results? Do the pe-T plots look different? 

As for the lost atoms, assuming the dynamics are not unstable, it could be that if you heat both the graphene and metal, some atoms cross the z-boundary, which is "f", so you will lose them.
To prevent this you could either use fully periodic boundaries in z or put a wall underneath the sheet or something. 

On Aug 5, 2017 4:04 AM, "Rosita Masoudi" <rositamasoudi@...24...> wrote:
Dear All

I am trying to melt metallic nanoparticles on graphene and compare them with free (without graphene state).
The model is visualized here:
(the graphene is periodic and particles are about 5-7.7 nm)

I did this before (3 years ago) and results were reasonable.
( Attached Here: )
But recently i tried to produce the same results and i cant, even with the same input.

I Plot the Potential Energy - Temp. for determining melting points and the results are nearly the same. and the curves are very similar: both Free Particle (Without Graphene) and Graphene Supported Supported 
I uploaded the new curves here:

I test this for many inputs like different metals and even core-shells.
I think the problem is with my input
I attached it here:
and it is written bellow:

dimension 3
units metal
atom_style atomic
boundary p p f

mass 1 195.084
mass 2 12

pair_style hybrid eam airebo 3.0 lj/cut 6
pair_coeff 1 1 eam Pt_u3.eam
pair_coeff * * airebo CH.airebo NULL C
pair_coeff 1 2 lj/cut 0.1365 1.6 6

group graphene type 2
group particle type 1

velocity all create 298 8927079

neighbor 2 bin
neigh_modify every 20 delay 0 check no

compute 6 particle pe/atom
compute 7 particle reduce sum c_6
compute 8 particle temp
compute 10 all temp
compute 11 graphene temp

thermo_style custom step temp pe c_8 c_7 c_10 c_11

dump 1 all atom 250 dump-allheat1.atom
timestep 0.003
thermo 25

fix 1 all nvt temp 298 298 0.1
run 1000000

unfix 1
fix 2 particle nvt temp 298 2000 0.01
run 5000000

unfix 2
fix 3 particle nvt temp 2000 2000 0.1
run 1000000

for Free state it is simple and i plot the potential energy vs temp.
for the graphene supported state, I compute potential energy and temp of particle (compute 7 & 8) and plot them.
But i think i am making a mistake here.
because when i plot the total potential energy (including grahene atoms) vs temp i got the transition temp very different and i attached the picture here (it is the new blue curve):

Another Important Problem:
I used NVT for All particles just in relaxing in 298K temp.
During heating from 298, i can only heat the particle,
if i use NVT for all (in fix 2) the graphene will explode after some time and i will face LOST ATOMS error... 
i really dont know how to heat particle and graphene together

could you please tell me what is the proper way to heat a particle on graphene??
and the correct way of computing potential energy and ploting PE-T curve? 
(I tried different Cut offs different damping for NVT and everything... I know i am making a mistake in computing)

Sorry for taking your time and my awful English.
Thank you all


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