7. Tools

These are the subdirectories in ./tools, where several useful tools are released alongside CryDisGen.

Items

Description

Bcc

Create single crystal BCC sample as inpu of CryDisGen

Fcc

Create single crystal FCC sample as inpu of CryDisGen

Helical_surface

Generate a mesh of helical surface used for dislocaiton hexlix

ModelClip

Cut a cylinder out of a crystal block

para_file_loop_array

Generate parameter file for an array of dislocation loops

para_file_nested_loop

Generate parameter file for an array of nested dislocation loops

para_file_tetrahedron_array

Generate parameter file for an array of stacking fault tetrahedrons

Several codes are published with CryDisGen to supply some extra functions

7.1. Create BCC region

The ./tools/Bcc directory provides a tool for generating body-centered cubic (BCC) crystal structures, which can be used as input for CryDisGen or LAMMPS. The BCC structure is defined by specifying the simulation region size, lattice orientations, and element type, as demonstrated in the screenshot below:

_images/tool1.png

7.2. Create FCC region

Similary, the ./tools/Fcc directory provides a tool for generating face-centered cubic (FCC) crystal structures, which can be used as input for CryDisGen or LAMMPS. The FCC structure is defined using the same parameters—simulation region size, lattice orientations, and element type—as demonstrated in the screenshot below:

_images/tool2.png

7.3. Helical surface

In the ./tools/Helical_surface directory, a tool provided to generate a mesh of a helical surface, whic is necessary for creating a dislocation helix. The command-line input parameters include the global coordinate system of the atomic region, local coordinate system defining the helix’s orientation, as well as the rotation angle, pitch and radius of the helix, as shown in the screenshot below:

_images/tool3.png

7.4. Clip a crystal region

In the ./tools/ModelClip directory, a tool provided to carve a cylinder out of a cubic crystal region. The input parameters include the file name of the crystal region, the axis orientation of the cylinder, and the position of cylinder axis in the other two dimensions.

_images/tool4.png

7.5. Parameter file for loop array

In the ./tools/para_file_loop_array diectory, a shell scrip is provided to generate the Parameter file used by CryDisGen. This file enables the creating of an array of full dislocation loops in a BCC crysatl region as demonstrated in examples <Examp_array_loop>.

_images/tool5.png

To make the script executable, run the following command in a Terminal first:

1chmod +x gen_para_file.sh

7.6. Parameter file for nested loops

In the ./tools/para_file_nested_loop diectory, a shell scrip is provided to generate the Parameter file used by CryDisGen. This file enables the creating of a group of nested full dislocation loops in a BCC crysatl region as demonstrated in examples <Examp_loop_nested>.

_images/tool6.png

To make the script executable, run the following command in a Terminal first:

1chmod +x gen_para_file.sh

7.7. Parameter file for tetrahedron array

In the ./tools/para_file_tetrahedron_array diectory, a shell scrip is provided to generate the Parameter file used by CryDisGen. This file enables the creating of an arra of stacking fault tetrahedrons in a FCC crysatl region, as demonstrated in examples <Examp_array_sft>.

_images/tool7.png

To make the script executable, run the following command in a Terminal first:

1chmod +x gen_para_file.sh