|From:||Rodrigo Queiroz de Albuqurque <rqalbuquerque@...24...>|
|Date:||Thu, 02 Nov 2017 03:41:51 -0700 (PDT)|
On Nov 1, 2017, at 9:45 PM, Axel Kohlmeyer <akohlmey@...24...> wrote:On Wed, Nov 1, 2017 at 1:42 PM, Ray Shan <rshan@...1795...>wrote:This occurred because you can’t use two separate EAM potential files for this purpose.i don't think so. the documentation for pair style eam says, that LAMMPS *does* do the mixing, so only i i and j j parameters need to be provided.the important missing piece of information (as usual) is the LAMMPS version in use. between september 2016 and june 2017, there has been a bug in pair style eam, that would cancel all mixed interactions.so that is one possible explanation. another possible source of error could be the data file, which is not provided.axel.
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.htmlThen your pair_coeff command would be: "pair_coeff * * <file> Au Ag"Best regards,RayOn 11/1/17, 10:24 AM, "Rodrigo Queiroz de Albuqurque" <rqalbuquerque@...24...> wrote:Dear LAMMPS communityI 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 metalboundary f f fread_data coordinates
pair_style eampair_coeff 1 1 Ag_u3.eampair_coeff 2 2 Au_u3.eamrun_style verlet
thermo_style custom step temp press pe ke etotalmin_style sdminimize 1.0e-8 1.0e-6 10000 10000dump 2 all xyz 100000 trajectories.xyzdump_modify 2 element Silver Goldtimestep 0.00001velocity all create 2 158379 mom yes rot yes dist gaussian
fix 1 all nvt temp 2 2 0.001
thermo 1000run 10000000unfix 1undump 2- - - - - - -
Thanks in avanceRodrigo- -Dr. Rodrigo Q. Albuquerque, BSc MSc PhD FHEASenior Lecturer in Physical ChemistryLiverpool John Moores UniversityAddress:Byrom Street, James Parsons Building (R. 2.03b)L3 3AF Liverpool, UK
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