The configuration file uses the INI-format. In the configuration file you tell Nanocut
Each of them corresponds to a section in the file with additional options within. For example, in order to cut out a spherical diamond cluster with a radius of 10 Angstrom, the configuration file would look as follows:
[geometry]
# Diamond lattice vectors in Angstrom
lattice_vectors:
0.000 1.790 1.790
1.790 0.000 1.790
1.790 1.790 0.000
basis:
C 0.0 0.0 0.0
C 0.25 0.25 0.25
[periodicity]
period_type: 0D
[sphere:1]
radius: 10
Please note, that option values going over more than one line require that the continuation lines are indented by at least one whitespace character (like for the options lattice_vectors and basis above). Lines starting with hashmark (#) are treated as comments.
Below you find the detailed description of all the options. For complete examples see the chapter Examples.
The [geometry] section contains all information regarding the crystal structure. Following options should be specified:
Defines the three lattice vectors of the crystal structure in Cartesian coordinates in Angstrom units.
For example the diamond fcc lattice would look like:
lattice_vectors:
0.000 1.785 1.785
1.785 0.000 1.785
1.785 1.785 0.000
Chemical symbol of each basis atom followed by its coordinates. Coordinates are interpreted as fractional coordinates, unless specified differently in the option basis_coordsys.
Again taking the diamond unit cell as example, you would have to use:
basis:
C 0.00 0.00 0.00
C 0.25 0.25 0.25
Defines the coordinate system of the basis. Possible values are lattice (fractional coordinates) and cartesian (Cartesian coordinates in Angstrom) with lattice being default.
To indicate that coordinates in the basis section are Cartesian coordinates in Angstrom (instead of fractional coordinates), you would have to write:
basis_coordsys: cartesian
It shifts the coordinates of the basis atoms by the given amount. You can use it to create structures with a different origin as the one you would obtain based on the specified coordinates. It is specified in fractional coordinates, unless set differently in shift_vector_coordsys.
If you wanted the diamond lattice from the example above being centered around a tetrahedral interstitial site (instead of the atom in the origin), you could issue:
shift_vector: 0.25 0.25 0.25
Specifies the conventional Bravais cell as linear combination of the primitve lattice vectors (3x3 integers). If set, the axis specifications in the periodicity section and any Miller indices in the input file will interpreted with respect to the conventional Bravais cell.
The cubic Bravais cell of diamond would require the input:
bravais_cell:
-1 1 1
1 -1 1
1 1 -1
You can use the superlattice option in the periodicity section to find out the transformation matrix for the Bravais cell (see Periodicity).
Structures with periodicity in one or two dimensions require the [periodicity] section defining the type of periodicity and the axis or axes of the translations. Following options can be specified:
Defines the axis/axes alongside which the supercell is periodic for the 1D, 2D and 3D cases. You must specifiy one vector (3 elements) for 1D, two vectors (6 elements) for 2D and three vectors (9 elements) for 3D, respectively. Depending on the settings in the [geometry] section (Geometry), the numbers are interpreted as fractional coordinates of either the primitive lattice or the conventional Bravais lattice. The numbers must be integers. For 2D and 3D periodicity you can alternatively use the keywords miller_indices or superlattice to specify the periodicity.
A nanowire along the 001 direction can be specified as:
[periodicity]
period_type: 1D
axis: 0 0 1
A slab in the plane of the vectors 100 and 010 can be specified as:
[periodicity]
period_type: 2D
axis:
1 0 0
0 1 0
A possible 3D supercell definition could look like:
[periodicity]
period_type: 3D
axis:
-1 1 1
1 -1 1
1 1 -1
Integer scaling factors for the translational vectors. Nanocut creates per default the smallest possible unit cell along the specified periodicity axes, which can be repeated by using this option. It requires one (1D), two (2D) or three (3D) integer numbers. Default value is one for all axis (no enlargment of the cell).
In order to enlarge a 3D supercell by a factor of 2 along every direction, you would have to enter:
axis_repetition: 2 2 2
In the case of 2D periodicity, you can specify the Miller indices of the slab plane with this keyword (instead of specfying two axis vectors with the axis keyword). It needs 3 integer numbers. The program will create the shortes possible unit cell on the surface, which you can enlarge using the axis_repetition keyword if needed. Depending on the settings in the [geometry] section (Geometry), the numbers are interpreted with respect to the primitive lattice or the conventional Bravais lattice.
The following example shows the input for a 211 surface slab:
[periodicity]
miller_indices: 2 1 1
Allows to specify the Cartesian coordinates of a superlattice (instead of specifying the relative coordinates with the axis keyword). It needs 9 real numbers (components of the three superlattice vectors). Nanocut will try to build an integer linear combination of the lattice vectors of the primitive lattice (or the Bravais lattice, if specified) to create a superlattice similar to the specified one. The absolute sizes of the superlattice vectors are irrelevant, but their relative sizes and their angles must yield a lattice which is compatible with the original one. Nanocut will create the smallest possible 3D cell, which can be enlarged using the axis_repetition keyword if necessary.
For example, in order to search for a cubic supercell for a given lattice, you should specify:
[periodicity]
superlattice:
1.0 0.0 0.0
0.0 1.0 0.0
0.0 0.0 1.0
The configuration file can contain an arbitrary number of sections defining bodies. Each body section is opened by [BODY: NAME] where BODY defines the body’s type and NAME is an unique name to distinguish different bodies with equal types. The bodies are cut from the crystal in the order they appear in the configuration file. Depending on their flag, they are added to or removed from the result of the previous cut. Trivially, the first cut should be additive.
Below you find the individual specification for each body. All of them support the following options:
Shifts the defined body with the given vector.
To shift the origin of the cutting body by 1 Angstrom along the z-axis, you should specify:
shift_vector: 0.0 0.0 1.0
shift_vector_coordsys: cartesian
Specifies whether the atoms inside the given body should be added to or subtracted from the previous structure (default: true).
In order to subtract a given body from the previous results, specify:
additive: false
Specified as [sphere: NAME] with following options:
To cut a sphere with a radius of 10 Angstrom, enter:
[sphere: 1]
radius = 10
Specified as [cylinder: NAME]. It creates a body with circular base and top areas being orthogonal to the difference vector of their centers. The circumference of the circles at the top and the bottom are connected by the smallest lateral area possible. As the radius of the circles can be different, you can also create truncated cones.
Example for a truncated cone along the 111 Cartesian direction:
[cylinder: 1]
point1: 0 0 0
point2: 10 10 10
point2_coordsys: cartesian
radius1: 5
radius2: 9
Specified as [polyhedron: NAME] for a convex polyhedron defined by its delimiting planes. Planes can be defined by their Miller indices or by their normal vectors.
Example for an octahedron defined via the Miller indices of eight planes, each of them being displaced by 5 Angstrom from the origin:
[polyhedron: 1]
planes_miller:
1 1 1 5
-1 1 1 5
1 -1 1 5
-1 -1 1 5
1 1 -1 5
-1 1 -1 5
1 -1 -1 5
-1 -1 -1 5
The section [periodic_1D_cylinder: NAME] specifies a supercell of an infinitely long cylinder with a circular base area. The base area’s center is the origin and its normal vector is parallel to the axis specified in the [periodicity] section.
A cylindrical nanowire with a radius of 5 Angstrom can be defined as:
[periodic_1D_cylinder:1]
radius: 5
Using [periodic_1D_prism: NAME] one specifies an infinitely long prism with a convex polygon as base area. The prism is defined by its lateral planes. A plane can be defined using it’s Miller indices or it’s normal vector. The planes must be parallel to the periodicity axis specified in the [periodicity] section.
Example for a 001 wire with quadratic cross section:
[periodic_1D_prism:1]
planes_miller:
1 1 0 10.0
1 -1 0 10.0
-1 1 0 10.0
-1 -1 0 10.0
The [periodic_2D_plane:NAME] section specifies a slab delimited by two parallel planes and being periodic along the planes. The upper and lower limiting planes are equidistant from the origin. The direction of the limiting planes are automatically derived from the periodicity specified in the [periodicity] section.
Sample input for a slab with thickness of 20 Angstrom:
[periodic_2D_plane:slab]
thickness: 20
The [periodic_3D_supercell:NAME] section specifies a supercell built from the unit cell of the original crystal. It does not take any further options, everything is derived from the settings in the [periodicity] section:
[periodic_3D_supercell:mycell]