banner MD simulation of crack propagation in brittle crystals

118094 - Introduction to Computational Physics - Fall 2012/13
Liron Ben-Bashat Bergman
Overview Theory Setup Results Manual
 

 

Manual

The project uses LAMMPS to run MD simulations. LAMMPS is a classical MD free and open source C++ code which supports MPI (message passing library).  It is mainly designed for parallel computers. Using LAMMPS it is possible to model ensembles of particles (from few to millions) in various states and a variety of force fields and boundary conditions. LAMMPS integrates Newton's equations of motion for groups of particles and follows the system's behavior over time.

LAMMPS can be downloaded from http://lammps.sandia.gov/.

It is also available on the TAMNUN. (For more information contact Technion computer center:

http://tcc.technion.ac.il/index.php?page_name=usg_mis_consulting&cat=T_software).

Instructions:
In your TAMNUN account create a folder and extract into it the following files: lammps

Explanation of each file:

1.       Si_110_1-10_1225x245x10_s50.imdconf.lammps - Initial atom positions with initial 5%   strain implemented.
2.       in.crack - Input file.
3.       Si.sw – modified stillinger weber potential parameters.
4.       Lammps_suzi – Executable script for tamnun users. Edit the following line in the script:  <PBS_O_WORKDIR=...> by changing the address to your current folder.

Editing the input file:

PDF format of input file with explanations: Input.pdf


Strain:
At step 4 in the input file change the scale value (default - scale 1)    and see how the crack velocity and propagation path changes (the initial strain is 5% = 1. Changing the scale from 1 to 1.01 would result in 6% strain).

Temperature:

Default temperature is currently close to zero kelvin. To change the initial temperature of the system modify the 0.0001 value in the following line:
velocity all create 0.0001 4928459 dist gaussian

Timestep:
Number of timesteps at each experimental stage (2-5) can be determined by changing the number of run cycles.

Running:

For submitting a job in the TAMNUN using the job script, type the qsub command in the terminal:

qsub <executable filename>


To check running status type:

qstat | grep <username> 


Visualisation and Analysis


The program output file is named log.lammps. Copy the file to a different environment from the TAMNUN (TAMNUN does not support some of the required programms and new versions of python).

The simulation writes out the mean temperature, kinetic and potential energy of the system at each time step.

In order to plot one of the system properties mentioned above versus timestep download the following file: log.py

Open an ipython shell ( by typing in terminal: ipython -pylab) and import the file (For installing ipython on linux type in terminal: sudo apt-get install ipython).

line 1 : import log as ll
line 2: a,b,c=ll.read_prop_vs_step("log.lammps", "KinEng")


 
The KinEng may be replaced by PotEng, Fnorm or Temp.

To plot the property vs. time:


line 3: plot(b,c)


Visualization using atomeye:

Download the following file: A3 and type in the terminal: ./A3 <filename.cfg>

In order to jump between timesteps press Insert/Delete.

Viewing bonds: press b.

 Unperspective mode - tab

Kinetic energy values: Alt 1 (use ctrl pageUp/pageDown to view atoms from certain Ek threshold).
 
Potential energy values: Alt 0 (use ctrl pageup/pageDown to view atoms from certain Ep threshold).

1-9 keyboards control the sensitivity of the change (1- gentle, 9- rough change).

Further instructions on how to use atomeye: http://li.mit.edu/Archive/Graphics/A/ .



In order t
o convert a series of jpg files to an avi movie that can be displayed by, for example, Quicktime Player with no addone, use:

in the atomeye window press y and enter (atomeye will convert all the .cfg files to .jpg's)

then install mencoder:

s
udo apt_get install mencoder

after installation ended type:

mencoder "mf://*.jpg" –o movie.avi –ovc lavc –lavcopts vcodec=mjpeg