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Re: [lammps-users] Atoms overlapping - Au-Ag alloy
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Re: [lammps-users] Atoms overlapping - Au-Ag alloy


From: Ray Shan <rshan@...1795...>
Date: Wed, 1 Nov 2017 17:42:42 +0000

This occurred because you can’t use two separate EAM potential files for this purpose.  Your type 1 and type 2 atoms effectively have no interaction parameters defined.  You need to use an EAM potential file with both Au and Ag parameterized, such as this one: https://www.ctcms.nist.gov/potentials/Zhou04.html

Then your pair_coeff command would be: "pair_coeff  * * <file> Au Ag"

Best regards,
Ray

On 11/1/17, 10:24 AM, "Rodrigo Queiroz de Albuqurque" <rqalbuquerque@...24...> wrote:

Dear LAMMPS community

I am senior lecturer at Liverpool John Moores University (UK) and would be glad if you could help me with a LAMMPS issue. 

I am trying to run a NVT simulation of a Silver-Gold alloy (86000 atoms, 20% of Au) using the respective EAM potentials (universal 3, distributed in the potentials directory of lammps). I know that when we use two different metals combined in an alloy, the EAM parameters for the alloy are automatically generated by standard mixing rules (the best approach would be to have the alloy-EAM potential already parametrized for the Ag-Au alloy, but I don’t find it). The problem is that, although I begin with a nanoalloy well centered on a cubic box (18 nm of side) and which shows a clear first RDF peak of Au-Ag at 2.9 Angstroms, after I start the simulation even at low temperature, atoms begin to strongly overlap, until they get as close as 0.1 Angstroms (revealed by the RDF analysis as well as by visual inspection using VMD of the trajectories file). Also, my simulation finishes normally without any errors. Would it be necessary to use SHAKE to prevent atoms from coming so close during the simulation? Or perhaps the repulsive part of the EAM potential only works for pure Ag or pure Au nanoparticles? Adopting the same procedure to simulate Au-Pt alloys by combining two different individual EAM potential files works fine… 

I am running the calculation on a MacPro (24 logical cores) using mpirun with 24 logical cores and my input is shown below:

- - - - - - -
units metal 

boundary f f f 
read_data coordinates 
pair_style eam
pair_coeff 1 1 Ag_u3.eam
pair_coeff 2 2 Au_u3.eam

run_style verlet
thermo_style custom step temp press pe ke etotal 

 min_style sd
 minimize 1.0e-8 1.0e-6 10000 10000

 dump 2 all xyz 100000 trajectories.xyz
 dump_modify 2 element Silver Gold

timestep 0.00001

velocity all create 2 158379 mom yes rot yes dist gaussian 
  
   fix 1 all nvt temp 2 2 0.001
    thermo 1000
      run 10000000
   unfix 1

 undump 2
- - - - - - -

Thanks in avance
Rodrigo

- -
Dr. Rodrigo Q. Albuquerque, BSc MSc PhD FHEA
Senior Lecturer in Physical Chemistry
Liverpool John Moores University

Tel: +44 (0) 151 904-6287
Web: www.labsuprachem.com

Address: 
Byrom Street, James Parsons Building (R. 2.03b)
L3 3AF Liverpool, UK