The modes follow similarly to the modes you find when using atomsk. The modes will be listed below alongside their syntax and other usage instructions. As a note, if a mode is being used then it has to come first.
Default duplicate is `1 1 1`. This is used to replicate the element along each dimensions. This cannot be used if the keyword dimensions is included. By default jagged edges along boundaries are filled if duplicate is greater than `1 1 1`.
There is no default dimensions as duplicate is the default option. This command assigns a box with user-assigned dimensions and fills it with the desired element. By default atoms fill in the jagged edges at the boundaries if the dimensions command is included.
This command will rerun the creation algorithm with multiple times starting with an esize of `esize` and decreasing it by half on every iteration in an effort to maximize the reduction of degrees of freedom in the system.
`dim` - the dimension they are to be stacked along, can be either `x`, `y`, or `z`. If the argument `none` is passed then the cells are just overlaid. Future options will include a delete overlap command.
If the shift command is passed to mode merge then each file after the first file in the merge command is displaced by the vector `[x, y, z]`. This is additive so if you are merging three files and this command is passed then the second file is shifted by `[x,y,z]` and the third file is shifted by `2*[x,y,z]`.
Example: `cacmb --merge z 2 Cu.mb Cu2.mb Cu3.mb Cumerged.mb shift 2 0 0` will shift the atomic and element positions in the `Cu2.mb` file by `[2,0,0]` and the positions in `Cu3.mb` by `[4,0,0]`.
**Wrap**
```
wrap
```
This will wrap atomic positions back inside the box. Effectively as if periodic boundary conditions are applied so that atoms which exit from one side of the simulation cell enter back in through the other.
Options are additional portions of code which have additional functionality. Options are performed in the order that they appear in the argument list and can be added to any mode. If wanting to use strictly options use `--convert` to specify input and output files.
This options adds an arbitrarily oriented dislocation into your model based on user inputs using the volterra displacement fields. The options are below
`loop_normal` - The box dimension which defines the normal to the loop plane. As of now this dimension must be a closed back direction, meaning that for fcc a box dimension has to be of the (111) family of planes. Either `x`, `y`, or `z`.
This option creates a circular planar vacancy cluster of radius `radius` normal to the `loop_normal` centered on position `x y z`. Upon relaxing or energy minimization this cluster should become a prismatic dislocation loop.
`select_type` - Either `atoms`, `elements`, or 'both'. `elements` selects elements based on whether the element center is within the group. `both` selects elements based on the element center and atoms based on their position.
`group_shape` - Specifies what shape the group takes and dictates which options must be passed. Each shape requires different arguments and these arguments are represented by the placeholder `shape_arguments`. The accepted group shapes and arguments are below:
This selects a group which are within a wedge shape. The options are given as follows:
`dim1` - The dimension containing the plane normal of the wedge base.
`dim2` - The thickness dimension. Wedge groups are currently required to span the entire cell thickness in one dimensions which is normal to the triangular face. This through thickness dimension is dim2.
This shape is similar to a wedge shape except instead of becoming atomically sharp, it finishes in a rounded tip with tip radius `tr`. Options are as follows.
`dim1` - The dimension containing the plane normal of the wedge base.
`dim2` - The thickness dimension. Wedge groups are currently required to span the entire cell thickness in one dimensions which is normal to the triangular face. This through thickness dimension is dim2.
This command remeshes the atoms/elements within the group to the new element size `esize`. Currently only accepts an `esize` of 2 which refines it to full atomistics. When remeshing to atomistics the group can contain any orientations of elements but when remeshing to different finite elements, the group must contain all atoms/elements with the same orientation. `lattice_parameter` is the lattice parameter for the elements within the group and `lattice_type` is the lattice type (integer) that these new elements will be assigned to.
This command attempts to reduce the degrees of freedom in the model by replacing them with graded elements. This code works by starting at elements with size `esize` and then checks all degrees of freedom to see which ones can be replaced by inserting the element. It then iterates over elements of `esize-2` to `esize=2` which is full atomic resolution.
This command selects `n` random atoms and `n` random elements within your group bounds. If using group type `atoms` or `elements` then only `n` random atoms or elements are selected. This random atoms/elements then form the new group.
This allows the user to specify the boundary conditions for the model being outputted. The format is a 3 character string with `p` indicating periodic and `s` indicating shrink-wrapped.
Specifying positions in cacmb can be done through a variety of ways. Examples of each format is shown below.
`val` - Where `val` is a number, then that value in Angstroms is used as the position. As an example, `11.1` would be read in as a position of 11.1 $\AA$.
`-inf` - This specifies the lower box boundary in the specific dimension. The vector `-inf -inf -inf` specifies the bottom corner of the simulation cell which also acts as the simulation cell origin. The vector `-inf 10 3` instead puts only the x position at the simulation cell origin.
`inf` - Similar to `-inf` but references the upper boundary of the box in that dimension
`inf-val` - Using a minus sign reduces the position from the **upper boundary** by `val`. `inf-10` would be at a distance of $10 \AA$ from the upper boundary in that dimension.
`inf+val` - This increases the position from the **lower boundary**. `inf+10` would be a position $10\AA$ from the lower boundary within the cell.
`inf*val` - This gives you a fractional position in the simulation cell. As an example `inf*0.5` gives you the center point of the simulation cell.
`rand` - Returns a random position that lies within the simulation cell.
`rande[facenum]` - Returns a random position in an interelement boundary which is offset of the element face `facenum`. Face numbers are based on the which vertices comprise the face. Vertex numbers are shown in the figure below for the primitive fcc unit cell which is what the fcc rhombohedral element is based from. The face numbers are:
