27th Nov, 2016

University of Limerick

Question

Asked 25th Nov, 2016

I am using Morse potential to address the interactions between the pair of atoms. The cutoff usually I see in papers is very small (~5 angstrom). The typical potential from used in simulations is

E = De.((1-exp(-a(r-r0)))**2 - 1.0)

The problem that I am facing is that when I am using a cutoff less than r0 (equilibrium distance) I am getting the correct structure parameters and there is no issue. If I increase the cutoff more than r0 I am not getting correct results. If anyone used this Morse potential before please help me .

**Get help with your research**

Join ResearchGate to ask questions, get input, and advance your work.

What you mean by structure parameters??RDF? Whats the system you are working on??how did you measure the structure parameters? Fix the cut-off to 12 Angstroms.

I am using GULP program to calculate the bulk modulus, elastic constants and equilibrium lattice constant. The material is SnTe it is a solid thermoelectric material. I am using different cutoff for different pair of atoms for example, 5 angs fro Sn-Sn interactions and 4 angs for Sn-Te interactions and so on. The Morse potential form is shown below

E = De.((1-exp(-a(r-r0)))**2 - 1.0)

We are fitting the potential parameters for this SnTe material using DFT data. During fitting I am getting r0 > rcut for Sn-Sn pair. This potential is able to reproduce the all above mentioned experimental values with <2% error. But my doubt is that is it correct using r0>rcut?

How to work with SiC particles in Al matrix using LAMMPS? All pair coeffs are not set, why I’m getting this error?

Question

2 answers

- Asked 26th Aug, 2020

- Jaswanth Bommidi

# ------------ Variables definition -----------------------------------------

variable a equal 4.04527 # Al lattice parameter - FCC

variable b equal 4.3484 # SiC lattice parameter - diamond cubic material

variable c equal $a+$b

variable d equal 10*$c

variable e equal $a*10

variable f equal $b*10

#-------------- Crystal Structure definition ------------------------------

region whole block 0 $d 0 $d 0 $d units box

create_box 3 whole

lattice fcc $a orient x 1 0 0 orient y 0 1 0 orient z 0 0 1 spacing 1 1 1 origin 0 0 0

region box block 0 $e 0 $e 0 $e units box

create_atoms 1 region box

lattice diamond $b orient x 1 0 0 orient y 0 1 0 orient z 0 0 1 spacing 1 1 1

region box2 block $e $d $e $d $e $d units box

create_atoms 2 region box2

set type 2 type/fraction 3 0.5 34567

#------------ Defining the interaction between potentials ----------------

pair_style hybrid/overlay eam/fs tersoff

pair_style eam/fs

pair_coeff * * Al_mm.eam.fs Al NULL NULL

pair_style tersoff

pair_coeff * * SiC.tersoff NULL Si C

#------------ Relaxing the structure -------------------------------------------------------

minimize 1e-25 1e-25 10000 10000

# ---------------- Error after running the program ----------------------

ERROR: All pair coeffs are not set (../pair.cpp:236)

Last command: minimize 1e-25 1e-25 10000 10000

All pair coeffs are not set ---- why I am getting this error???

LAMMPS tutorial on fracture of graphene

Discussion

2 replies

- Asked 2nd Sep, 2022

- Nuwan Dewapriya

This GitHub repository (https://github.com/nuwan-d/fracture_of_grahene) contains a MATLAB script to generate the LAMMPS input files for the molecular dynamics simulation shown below. Additional MATLAB scripts are available to post-process the simulation outputs.
This tutorial can be helpful to graduate students who are relatively new to MD simulations.
Good luck!

Article

- Jan 1984

Analysis of freeway traffic flow data reveals a discontinuity in the equilibrium relationship between speed and density, supporting the dual-mode or two-regime theories of traffic flow. This work was done during the development of an appropriate equilibrium speed-density relationship for a dynamic macroscopic freeway simulation model, FREFLO. This...

Article

- Feb 1996

Porous materials hysteretic moisture characteristics : influence on water content distributions in buildings walls. Comparison of two simulation models. Two models for determining the temperature and moisture distributions within a wall are presented. The first one is a direct application of the classical Philip and de Vries model. The second one,...

Article

- Apr 2000

Inbreeding depression may induce rapid extinction due to positive feedbacks between inbreeding depression and reduction of
population size, which is often referred to as extinction vortex by inbreeding depression. The present analysis has demonstrated
that the extinction vortex is likely to happen with realistic parameter values of genomic mutation...

Get high-quality answers from experts.