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[lammps-users] atom deposition_segmentation fault (core dumped)
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[lammps-users] atom deposition_segmentation fault (core dumped)


From: "Gaoyang" <582660199@...1204...>
Date: Wed, 28 Jun 2017 18:07:47 +0800

Hi Axel
Thanks for your reply!
I lengthened the releaxing time and the total energy tends to stbale.
But when it began to execte the commend "velocity", it shows errors as below:

I cannot understand what's wrong with it, and I hope to get your help.
Thanks again!

Best wishes!
Yang

------------------ 原始邮件 ------------------
发件人: "Axel Kohlmeyer";<akohlmey@...24...>;
发送时间: 2017年6月23日(星期五) 中午12:25
收件人: "Gaoyang"<582660199@...1204...>;
抄送: "lammps-users"<lammps-users@lists.sourceforge.net>;
主题: Re: [lammps-users] atom deposition_segmentation fault (core dumped)



On Fri, Jun 23, 2017 at 12:15 AM, Gaoyang <582660199@...1204...> wrote:
Hello everyone!
I want to simulation the process of Ag atoms depositing onto ZnO substrate.
I used the commands of "fix deposit" or "velocity" to control Ag atom to deposit. But in the atoms depostion, "segmentation fault (core dumped)" appears in output screen, and the program stoped. I used to change the timestep and depositing velocity, but it cannot sovle the problem.

This is my log file.


​[...]​

​your log file shows several *extremely* short simulation segments (only 10s of MD steps) until you start depositing.
you should rather start with equilibrating your "host" system. it looks like your system picks up a lot of kinetic energy in just a few time steps. that hints that your system is far from equilibrium and possibly your initial geometry not entirely correct. have you visualized it? has you discussed your simulation setup with somebody local?

after your system is equilibrated, does it conserve total energy (and kinetic energy) well enough when running without a thermostat?

i would not recommend starting deposition of atoms before you have a well working and equilibrated substrate.

axel.

 
--
Dr. Axel Kohlmeyer  
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.