@@ -4,9 +4,9 @@ This python package helps you create orthogonal grain boundary supercells for at
# Overview
# Overview
There are two main scripts: [_csl_generator.py_](./csl_generator.py) and [_gb_generator.py_](./csl_generator.py) which you need to use in this order to produce the final grain boundary (GB) structure. These scripts are both modules (a collection of functions/classes) and can be executed
There are two main scripts: [_csl_generator.py_](./csl_generator.py) and [_gb_generator.py_](./csl_generator.py) which you need to use in this order to produce the final grain boundary (GB) structure. These scripts are both modules (a collection of functions/classes) and can be executed
from the command line.
from the command line.
In this README I will explain the steps to use the code in the Terminal and I have also attached two _jupyter notebooks_ ([Usage_of_GB_code.ipynb](./Usage_of_GB_code.ipynb), [Dichromatic_pattern_CSL.ipynb](./Dichromatic_pattern_CSL.ipynb)) in the Test directory which describe how the code can be accessed and used in the notebooks by various examples. These notebooks have extra functionality. The former is for the general usage of the code with some tips to locate GBs of interest, the latter depicts how CSL construction can be used for different purposes.
In this README I will explain the steps to use the code in the Terminal and I have also attached two _jupyter notebooks_ ([Usage_of_GB_code.ipynb](./Usage_of_GB_code.ipynb), [Dichromatic_pattern_CSL.ipynb](./Dichromatic_pattern_CSL.ipynb)) in the [Test](./Test) directory which describe how the code can be accessed and used in the notebooks by various examples. These notebooks have extra functionality. The former is for the general usage of the code with some tips to locate GBs of interest, the latter depicts how CSL construction can be used for different purposes.
You can use [this link](https://mybinder.org/v2/gh/oekosheri/GB_code/master) for an interactive Jupyter notebook environment provided by Binder. [](https://mybinder.org/v2/gh/oekosheri/GB_code/master)
You can use [this link](https://mybinder.org/v2/gh/oekosheri/GB_code/master) for an interactive Jupyter notebook environment provided by Binder. [](https://mybinder.org/v2/gh/oekosheri/GB_code/master)
To use it locally, you will need python3 and numpy1.14 for the main scripts and additionally matplotlib and pandas to use the auxilliary Jupyter notebooks.
To use it locally, you will need `python> 3.5.1` and `numpy > 1.14` for the main scripts and additionally matplotlib and pandas to use the auxilliary Jupyter notebooks.
# Installation guide
# Installation guide
For installation simply clone or download the code in your terminal and in the main directory of the package type:
For installation simply clone or download the code in your terminal and in the main directory of the package type:
@@ -173,10 +173,11 @@ I often do a three stage minimization at 0K followed by an MD annealing simulati
The 0K miminimization is composed of: A conjugate gradient minimization of the energy of atoms, the simulation box and then atoms again;
The 0K miminimization is composed of: A conjugate gradient minimization of the energy of atoms, the simulation box and then atoms again;
similar to a procedure explained [here](https://icme.hpc.msstate.edu/mediawiki/index.php/LAMMPS_Input_Deck_for_Grain_boundary_generation).
similar to a procedure explained [here](https://icme.hpc.msstate.edu/mediawiki/index.php/LAMMPS_Input_Deck_for_Grain_boundary_generation).
For the annealing simulations I use an _nvt_ ensemble followed by damped dynamics. Depending on the GB structure and your final purpose you can run annealing simulations for different time spans.
For the annealing simulations I use an _nvt_ ensemble followed by damped dynamics. Depending on the GB structure and your final purpose you can run annealing simulations for different time spans.
# Questions/Contribution
# Questions/Contributions
If you have any questions, raise an issue or contact [me](mailto:shahrzadhadian@gmail.com).
If you have any questions, raise an issue or contact [me](mailto:shahrzadhadian@gmail.com).
Feel free to use the code anyway you like, if you find it useful please cite the paper.
Feel free to use the code anyway you like, if you find it useful please cite the paper.
At the moment I am the main contributor of this code. If I decide to accept contributions I will anounce it here.
This project is currently under development and at the moment I am not accepting contributions from other users.
Should this change in the future I'll provide detailed information on how to contribute to the project.
