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How to Create a Polycrystal Containing Grain Boundaries

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We introduce how to install Atomsk into Matlantis and create polycrystals with grain boundaries.

Atomsk* is a free and open-source command-line tool specialized in creating and editing crystal and molecular structure data for atomic-level simulations in computational materials chemistry.

*Atomsk: https://atomsk.univ-lille.fr/

 

Table of Contents

 

 

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Installation

  1. Download the program (tar.gz file). Please obtain the Linux amd64 (64-bit) version from the following site. We have confirmed that the beta-0.13.1 version works.
    Download site: https://atomsk.univ-lille.fr/dl.php

  2. Move the tar.gz file to the location where you want to install Atomsk in the Matlantis environment. In this example, we'll explain how to install it in /home/jovyan/tools.

  3. Extract the file and rename the directory to "atomsk".

    When running in a notebook: *Note: "!" is not needed if running in a terminal.

    !tar xvzf ~/tools/atomsk_b0.13.1_Linux-amd64.tar.gz
    !mv ~/tools/atomsk_b0.13.1_Linux-amd64 ~/tools/atomsk
  4. The installation is successful if you can run the atomsk command as shown below.
    %%bash
    $HOME/tools/atomsk/atomsk

    example output : 
    ___________________________________________________
    | ___________ |
    | o---o A T O M S K |
    | o---o| Version Beta 0.13.1 |
    | | |o (C) 2010 Pierre Hirel |
    | o---o https://atomsk.univ-lille.fr |
    |___________________________________________________|
    *** Working out of office hours? You should sleep sometimes. :-)
    >>> Atomsk is a free, Open Source software.
    To learn more, enter 'license'.
    >>> Atomsk command-line interpreter:
    ..> Type "help" for a summary of commands.

    @atomsk:20240621_atomsk> \o/ Program terminated successfully!
    Total time: 0.001 s.; CPU time: 0.000 s.

    As an intput file, the small version of HEA structure is used.

 

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Creating polycrystal

We introduce how to create grain boundaries in the high-entropy alloy CoCrFeMnNi.

The following tutorial was referenced:

  1. First, prepare the seed crystal. This can be generated in Atomsk as follows. You can also create structures using ASE. Here is how:

    %%bash
    ## create Ni(fcc)
    $HOME/tools/atomsk/atomsk --create fcc 3.52 Ni Ni.xsf
    ## build supercell 3x3x3
    $HOME/tools/atomsk/atomsk Ni.xsf -duplicate 3 3 3 Ni333.xsf
    # randomly substitute 20% Ni atoms with Cr
    $HOME/tools/atomsk/atomsk Ni333.xsf -select random 20% Ni -substitute Ni Cr NiCr.xsf
    # randomly substitute 20% Ni atoms with Co
    $HOME/tools/atomsk/atomsk NiCr.xsf -select random 20% Ni -substitute Ni Co NiCrCo.xsf
    # randomly substitute 20% Ni atoms with Fe
    $HOME/tools/atomsk/atomsk NiCrCo.xsf -select random 20% Ni -substitute Ni Fe NiCrCoFe.xsf
    # randomly substitute 20% Ni atoms with Mn
    $HOME/tools/atomsk/atomsk NiCrCoFe.xsf -select random 20% Ni -substitute Ni Mn CoCrFeMnNi.xsf
      

  2. Next, create a parameter file (in text format) specifying details such as the size of the cell box you wish to create. For example, to create a polycrystal with four grains within a 180×180×180 Å cell box, we created the following polycrystal_large.txt file.


    box 180 180 180 # the size of cell
    random 4 # the number of polycrystal


  3.  Finally, use Atomsk in --polycrystal mode with the configuration file created in step 2 (in this case, polycrystal_large.txt) to create the polycrystal polycrystal_large.cfg. The polycrystal_param.txt file generated at the same time can be used to reproduce the same polycrystal.


    %%bash
    $HOME/tools/atomsk/atomsk --polycrystal CoCrFeMnNi.xsf polycrystal_large.txt polycrystal_large.cfg -wrap

    When visualized in Ovito, it can be seen as follows.

    (Upper: original elemental color, Lower: result of pattern matching (FCC: green))

    atomsk_orign.pngatomsk_pattern.png

 

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Tips: Using ASE for Creating Structures

You can also create seed crystal using ASE. For example, you can create a unit cell as follows:

 

1. Create the fcc structure for Al

from ase.build import bulk
atoms = bulk(crystalstructure="fcc", name="Al", a=3.584, cubic=True)

2. Define a function to randomly replace elements

import numpy as np

def random_replace(atoms, elements, replacement_rate=0.75):
    # Copy the Atoms object
    atoms_c = atoms.copy()

    # Calculate the number of atoms to randomly select for replacement
    total_atoms = len(atoms_c)
    num_replacements_per_element = int(total_atoms * replacement_rate / len(elements))

    for e in elements:
        # Select random indices
        rand_indices = np.random.choice(total_atoms, num_replacements_per_element, replace=False)
        # Replace elements
        atoms_c.numbers[rand_indices] = e

    return atoms_c

3. Specify the elements to be replaced and randomly replace the elements

elements = [24, 26, 27, 28] # Cr, Fe, Co, Ni
atoms_HEA = random_replace(atoms*(3, 3, 3), elements)

4. Visualize and check the results

from pfcc_extras import view_ngl
view_ngl(atoms_HEA)

Proceed to Creating polytical step2

 

 

 

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