Carve geometry
Description
This function carves a specific shape from a parent system. The following geometries can be created:
-
Sphere: Defined by its center and radius.
-
Cuboid: Defined by its three side lengths.
The parent system is replicated as needed to fill the selected geometry. For example, if the parent system is a box of 7 nm and the cuboid to carve is a 10 nm cube, the parent system will be replicated once in each direction before carving the new geometry from the resulting supercell. Note that this process breaks the periodicity of the parent system, which is not automatically preserved by this function.
Additionally, surface termination retains only the molecules that have ALL atoms within the defined geometry. If even one atom is outside the shape, the atoms belonging to the same component will be excluded as well. This means the surface will not be perfectly flat, but will be terminated by complete molecules. This limitation is due to the current inability to remove atoms from the Gromacs potential.
By default, the system cell is set to be tangent to the specified shape, but this can be modified (e.g. add vacuum to the system) using the corresponding input. The center of the geometry can also be defined through a dedicated input field.
Latest version
Allowed number of parents: 1
| Parameter | Description | Value type | Value restrictions | Default value | Units |
|---|---|---|---|---|---|
Shape |
The geometric shape to carve out |
selector |
sphere, cuboid |
sphere |
N/A |
Sphere radius |
The radius of the sphere to carve out - relevant only when |
float |
>0 |
0.0 |
Angstrom |
Cuboid side lengths |
The side length of the cuboid (x,y,z) - relevant only when |
float |
>0 |
[0.0, 0.0, 0.0] |
Angstrom |
Cell definition |
Whether the cell shall be defined automatically (size of the carved shape) or manually |
selector |
automatic, manual |
automatic |
N/A |
Cell dimensions |
The three cell lengths (x, y,z) - relevant only if “Cell definition” is |
float |
>0 |
[0.0, 0.0, 0.0] |
Angstrom |
Shape center definition |
Whether the center of the carved shape shall be defined automatically (center of the cell) or manually |
selector |
automatic, manual |
automatic |
N/A |
Shape center |
The center of the carved shape - relevant only if “Cell definition” is |
float |
any float |
[0.0, 0.0, 0.0] |
Angstrom |