5. Parameter file

The paramater file is the central input of CryDisGen.

It is a structured ASCII text file designed to supply configuration details for CryDisGen. It uses a line-based format with different tags which may be followed by values or stand alone, and includes comments for clarity. The file is divided into sections that describe the crystal region and the defects to be introduced. Below is an inferred breakdown of its structure and key characteristics:

 1#lines starting with '#' are comments
 2#crystal region definition
 3Region
 4-x      1 -1  0      # lattice orientation along x-axis
 5-y      1  1  0      # lattice orientation along y-axis
 6-z      0  0  1      # lattice orientation along z-axis
 7-lat    3.615        # lattice constant
 8-pbc    1  1  1      # boundary condition flags along x/y/z-axes: '1' for periodic, '0'for non-periodic
 9-nu     0.33         # Poisson's ratio. **This option is supported only in Version 2.0 and later.**
10                     # When this tag is specified, the displacement field used to construct dislocation
11                     # includes both plastic and elastic contributions. When omitted, only the plastic
12                     # contribution is applied.
13
14#stacking fault tetrahedron
15nTetrahedron  1      # number of stacking fault tetrahedra
16Tetrahedron          # label for tetrahedron section
17-tc     0. 0. 0.     # center of the bottom face of the tetrahedron
18-tr     40           # radius of the circumscribed circle of the bottom face
19-tnorm -1 -1 -1      # outward normal direction at the tetrahedron's bottom face
20-lxt    1 -1  0      # local x-axis at the bottom face
21-lyt   -1 -1  2      # local y-axis at the bottom face
22
23#dislocation loop
24nLoop   1            # number of dislocation loops
25Loop                 # label for dislocaiton loop section
26-bv     1  1  1      # orientation of Burgers vector
27-bs     1/3          # scalar coefficient of Burgers vector, e.g., 1/2 in 1/2<110>
28-dnorm  1  1  1      # normal direction of dislocation plane
29-dc     0. 0  0      # center of dislocation loop
30-dr     25           # radius of dislocaiton loop
31-lx     1 -1  0      # local x-axis on dislocation plane
32-ly     1  1 -2      # local y-axis on dislocation plane
33-ndisl  4            # number of segments/vertices in a discretized dislocation loop
34
35#dislocation helix
36nHelix  1            # number of dislocation helices
37Helix                # label for dislocation helix section
38-bvh    1  1  1      # orientation of the Burgers vector for the helix
39-bsh    1/2          # scalar coefficient of Burgers vector, e.g., 1/2 in 1/2<110>
40-f      mesh.dat     # mesh data file of the helical surface

5.1. General Format

Comments: Lines beginning with # are comments, ignored by the program but used to annotate the file for user reading it (e.g., #crystal region).

Tags: Each non-comment line starts with a tag (e.g., Region, -x, nTetrahedron), often followed by numerical or symbolic values.

Whitespace: Tags and values are separated by spaces or tabs, with consistent spacing for readability.

Sections: Some tags (e.g., Region, Tetrahedron, Loop) act as section headers or labels, grouping related parameters.

5.2. Sections

Crystal Region

  • Purpose: Defines the lattice properties and boundary conditions of the crystal.

  • Tag:

    • Region (marks the start of this section).

Stacking Fault Tetrahedron

  • Purpose: Configures stacking fault tetrahedrons (SFTs).

  • Tags:

    • nTetrahedron: Specifies the number of tetrahedrons to generate (e.g., 1).

    • Tetrahedron: Labels the start of a tetrahedron definition

Dislocation Loop

  • Purpose: Defines dislocation loops.

  • Tags:

    • nLoop: Specifies the number of dislocation loops (e.g., 1).

    • Loop: Labels the start of a dislocation loop definition.

Dislocation Helix

  • Purpose: Defines dislocation helix.

  • Tags:

    • nHelix: Specifies the number of dislocation helix (e.g., 1).

    • Helix: Labels the start of a dislocation helix definition.

5.3. Key Characteristics

Hierarchical Structure: The file is organized into sections (Region, Tetrahedron, Loop), each with specific parameters, allowing modular defect definitions.

Vector-Based Inputs: Many parameters use three-component vectors (e.g., -x, -bv, -dnorm) to define orientations and positions in 3D space.

Flexibility: Supports multiple defects (e.g., nTetrahedron, nLoop) with customizable attributes, making it adaptable to various simulation needs.

Units: Assumed to align with MD conventions (e.g., angstroms for lengths), though not explicitly stated in the file.

Readability: Comments and consistent formatting enhance user understanding and editing.

5.4. Purpose and Usage

This file serves as the parameter_file input for CryDisGen (as described in the Usage section), complementing the crystal_file by defining defects to insert into the crystal structure. It enables users to specify complex dislocation configurations, leveraging CryDisGen’s ability to generate realistic atomic-scale models.