6. Tags in Paramater file
The parameter file uses tags to configure CryDisGen: indication tags (Region, Loop, Tetrahedron, Helix) specify the atom region or dislocation type, counter tags (nTetrahedron, nLoop, nHelix) define the number of dislocation objects, and parameter tags (e.g., -x, -bv) set detailed properties.
6.1. Indication tags
Note
Indication tags in CryDisGen’s parameter file supply the information of the input atomic region or define dislocation objects being configured. There are Four indication tags in current version: Region, Loop, Tetrahedron and Helix. These tags specify either the input atom region (e.g., the crystal lattice) or the type of dislocation object to be introduced (e.g., a loop or tetrahedron), providing the structural context for subsequent counter and parameter tags. Each tag initiates a block of settings that CryDisGen uses to construct the corresponding atomic-scale feature.
Region:
It has no trailing parameter on the same line and indicates the following block of parameter tags defines the input atomic region. This section provides some additional parameters for the atomic region. In the parameter file, only one Region tag and its associated block is required. If multiple Region tags are included, code will exit with an error. If multiple blocks are present, the last one will override any previous ones, ensuring a single, final definition of the crystal region.
Loop:
It has no trailing parameters on the same line and indicates the following block of parameter tags defines a dislocation loop. In the parameter file, each dislocation loop instance corresponds to an independent Loop tag with its associated block of parameter tags. Multiple dislocation loops can be included in a single parameter file, and there is no limitation to their number.
Tetrahedron:
It has no trailing parameter on the same line and indicates the following block of parameter tags defines a stacking fault tetrahedron. In the parameter file, Tetrahedron can be abbreviated as Tetra. Each stacking fault tetrahedron corresponds to an independent Tetrahedron tag with its associated block of parameter tags. Multiple stacking fault tetrahedrons can be included in a single parameter file, and there is no limitation to their number.
Helix:
It has no trailing parameter on the same line and indicates the following block of parameter tags defines a dislocation helix. In the parameter file, each dislocation helix corresponds to an indipendent Helix tag with its associated block of parameter tags. Multiple dislocation helices can be included in a single parameter file, and there is no limitation to their numer.
6.2. Counter tags
Note
Counter tags in CryDisGen’s parameter file specify the number of dislocation objects to be generated using a following integer. There are Three counter tags: nLoop, nTetrahedron and nHelix. These tags are only required when the associated the dislocation instances are configured, and can be put anywhere in the parameter file. The integer value following each counter tag must match the number of indication tags; otherwies, code will exit with an error.
nLoop N:
The counter tag nLoop specifies the number N of dislocation loop sections to be defined in CryDisGen’s parameter file. The value N is a positive integer (e.g., 1, 2, etc.) indicating how many Loop sections follow in the file.
nTetrhedron N:
The counter tag nTetrahedron specifies the number N of stacking fault tetrahedron sections to be defined in CryDisGen’s parameter file. The value N is a positive integer (e.g., 1, 2, etc.) that indicates how many Tetrahedron sections follow in the file. It can be abbreviated as nTetra N.
nHelix N:
The counter tag nHelix specifies the number N of stacking fault tetrahedron sections to be defined in CryDisGen’s parameter file. The value N is a positive integer (e.g., 1, 2, etc.) that indicates how many Tetrahedron sections follow.
6.3. Parameter tags
Note
Parameter tags in CryDisGen’s parameter file define the detailed configuration settings for the crystal region or dislocation objects specified by indication tags (Region, Loop, Tetrahedron, Helix). Prefixed with a hyphen (e.g., -x, -bv, -tc), these tags follow their associated indication tag and provide specific values—such as coordinates, vectors, or scalars—that CryDisGen uses to construct the atomic-scale structure. Each parameter tag is tailored to its section’s context, ensuring precise customization of the simulation model.
Region:
1#those started with '#' are comment lines
2#crystal region
3Region
4-x 1 -1 0 # lattice orientation in x-direction
5-y 1 1 -2 # lattice orientation in y-direction
6-z 1 1 1 # lattice orientation in z-direction
7-lat 3.615 # lattice constant
8-pbc 1 1 1 # boundary condition flag: '1': pbc, '0': non-pbc
Loop:
1#dislocation loop
2nLoop 1 # number of dislocation loop
3Loop # label of a dislocation section
4-bv 1 1 1 # orientation of Burgers vector
5-bs 1/3 # scalar coefficient of Burgers vector, e.g., 1/2 in: 1/2<110>
6-dnorm 1 1 1 # normal direction of plane with dislocation loop
7-dc 0.2 0 0 # center of dislocation loop
8-dr 25 # radius of dislocaiton loopS
9-lx 1 -1 0 # local x axis on slip plane
10-ly 1 1 -2 # local y axis on slip plane
11-ndisl 4 # segments of a discretized dislocation loop
Tetrahedron:
1#stacking fault tetrahedrion
2nTetrahedron 1 # number of stacking fault tetrahedron
3Tetrahedron # label of tetrahedron
4-tc 0. 0. 0. # center of the bottom face of tetrahedron
5-tr 40 # radius of the circumscribe circle of the bottom face
6-tnorm -1 -1 -1 # outward nomral direction bottom face of tetrahedron
7-lxt 1 -1 0 # local x axis on the bottom face
8-lyt -1 -1 2 # local y axis on the bottom face
Helix:
1#dislocation helix
2nHelix 1 # number dislocation helix
3Helix # lable of dislocation helix
4-bvh 1 1 1 # orientation of Burgers vector of helix
5-bsh 1/2 # scalar coefficient of Burgers vector helix
6-f mesh0.dat # mesh of helical surface
Tip
The lines of tags in the parameter file can be arranged in any order. To enhancethe readability, it is recommended to group parameter tags defining the same dislocation instance or atomic region together into a block, placing them after the corresponding indication and counter tags, as illustrated in the examples above.