CascadeSim

End to end scripts for LAMMPS simulating cascade and OVITO extracting defect.

Features

• You can finish a series of cascade simulation jobs almost by one key. Only a few paremeters are required to be concerned.
• You will know SIA directions or defect cluster informations.

Prerequisites

• Lammps compiled with voronoi package.
• Python 3.6 or newer.
• Python libraries:
  • ovito 2.9
  • numpy
  • matplotlib

It is recommanded to install python and the libraries in a conda enviroment, which is the only way the author has tested.

conda create -n CascadeSim python=3 numpy matplotlib conda-forge::ovito=2.9

If your device is not able to access the Internet directly, ask your system administrator to establish a ssh tunel for temperary download. Ancient saying: as long as your personal PC can access your server, there is always a way to make your server access the Internet.

Installation

Simply download scripts. git clone https://github.com/permissionx/CascadeSim.git

🚀Usage

1. Assign input arguments in lammps in file in and run the LAMMPS.

#-----------------------------------------------------
#-------------------------INTPUT----------------------
#-----------------------------------------------------

# -loop variables
variable        env_temp index 500 300 #enviroment temperature
label           loop_env_temp

variable        E_PKA index 10 20 30  # unit: keV
label           loop_E_PKA
# --angle loop
variable        d_x index 0 1  #direction
variable        d_y index 0 3
variable        d_z index -1 5
variable        angle index 1 2
label           loop_angle

variable        random loop 10
label           loop_random

# -stop critical
variable        halt_dt equal -0.0000005*${env_temp}+0.00125
###This relationship should be determined by futher calculations.

# -box variable
variable        box_r equal 35 # the number of atoms > 25 times the energy of the projectile in eV (eg: 500 000 atoms for 20 keV)
variable        fix_th equal 2   # fix thickness
variable        bath_th equal 3   # bath thickness
variable        center equal 10

variable        lattice_constant equal 3.14

#------------------------------------------------------------
#-------------------------END-OF-INTPUT----------------------
#------------------------------------------------------------

Example above will calculate 2(temps)*3(energies)*2(angles)*10(random seeds) = 120 cases.

2. After finish the LAMMPS calculation. lammps trajetory files will writen in the dump folder. And a file folder_name.csv will be generated to store the names of all the calculated cases. To extract Step into cascade_scripts. Modify input paras in extract_defect.py.

3. Execuate defect extraction by typing python extract_defect.py in the shell. Results of the defects during and after cascade will be stored in [cluster_dump_folder]

Known issues

• Cannot extract defect for too many cases (may over 500) at once. Splitting the execuation into mutiple times by modifying extract_defect.py can solve this problem temporarily.

Things to do

• Update the OVITO interfact to 3.x.
• Add basic data statistics, such as defect nums VS sizes.

Acknowledgements

Any bug reports and feature requests are highly welcome.