Simulation Box

Name BoxCenter
Section Mesh::Simulation Box
Type float

This block defines the coordinate center of the simulation box

Name BoxCgalFile
Section Mesh::Simulation Box
Type string

Filename to be read in by the cgal library. It should describe a shape that is used for the simulation box

Name BoxShape
Section Mesh::Simulation Box
Type integer

This variable decides the shape of the simulation box. The default is minimum for finite systems and parallelepiped for periodic systems. Note that some incompatibilities apply:

• Spherical or minimum mesh is not allowed for periodic systems.
• Cylindrical mesh is not allowed for systems that are periodic in more than one dimension.
• box_image is only allowed in 2D.

• sphere:
  The simulation box will be a sphere of radius Radius. (In 2D, this is a circle.)
  
• cylinder:
  The simulation box will be a cylinder with radius Radius and height (in the x-direction) of 2 Xlength.
  
• minimum:
  The simulation box will be constructed by adding spheres created around each atom (or user-defined potential), of radius Radius.
  
• parallelepiped:
  The simulation box will be a parallelepiped whose dimensions are taken from the variable Lsize.
  
• box_image:
  The simulation box will be defined through an image, specified with BoxShapeImage. White (RGB = 255,255,255) means that the point is contained in the simulation box, while any other color means that the point is out. The image will be scaled to fit Lsize, while its resolution will define the default Spacing. The actual box may be slightly larger than Lsize to ensure one grid point = one pixel for default Spacing.
  
• box_cgal:
  The simulation box will be defined by a file read using the CGAL library. The file name needs to be specified with BoxCgalFile. Lsize needs to be large enough to contain the shape defined in the file.
  
• user_defined:
  The shape of the simulation box will be read from the variable BoxShapeUsDef.
  

Name BoxShapeImage
Section Mesh::Simulation Box
Type string

Name of the file that contains the image that defines the simulation box when BoxShape = box_image. No default. Will search in current directory and OCTOPUS-HOME/share/.

Name BoxShapeUsDef
Section Mesh::Simulation Box
Type string

Boolean expression that defines the interior of the simulation box. For example, BoxShapeUsDef = "(sqrt(x^2+y^2) <= 4) && z>-2 && z<2" defines a cylinder with axis parallel to the z-axis.

Name LatticeParameters
Section Mesh::Simulation Box
Type block

The lattice parameters (a, b, c). This variable is mandatory for periodic systems and is ignored otherwise. When PeriodicDimensions = 3, a second optional line can be used to define the angles between the lattice vectors. If the angles are not provided, then the variable LatticeVectors must be set. The number of parameters specified in the block must be at least equal to the number of periodic dimensions, but it is not mandatory to specify parameters for the non-periodic dimensions (in that case they are set to 1).

Name LatticeVectors
Section Mesh::Simulation Box
Type block
Default simple cubic

Primitive lattice vectors. Vectors are stored in rows. LatticeVectors are normalized and then used, if both LatticeParameters and LatticeVectors are defined, norm of LatticeVectors are used as multipliers of lattice parameters. Default:

%LatticeVectors
  1.0 | 0.0 | 0.0
  0.0 | 1.0 | 0.0
  0.0 | 0.0 | 1.0
%

Name Lsize
Section Mesh::Simulation Box
Type block

If BoxShape is parallelepiped, box_image, or user_defined, this is a block of the form:

%Lsize
  sizex | sizey | sizez | …
%

where the size* are half the lengths of the box in each direction.

The number of columns must match the dimensionality of the calculation. If you want a cube you can also set Lsize as a single variable.

Name Radius
Section Mesh::Simulation Box
Type float

Defines the radius for BoxShape = sphere, cylinder, or minimum. Must be a positive number.

Name SymmetryBreakDir
Section Mesh::Simulation Box
Type block

This variable specifies a direction in which the symmetry of the system will be broken. This is useful for generating k-point grids when an external perturbation is applied.

Name Xlength
Section Mesh::Simulation Box
Type float
Default Radius

If BoxShape is cylinder, the total length of the cylinder is twice Xlength. Note that when PeriodicDimensions = 1, then the length of the cylinder is determined from the lattice vectors.