5.7. [config] section¶
This section specifies alloy coordination, etc. An example is shown as follows:
[config] unitcell = [[8.1135997772, 0.0000000000, 0.0000000000], [0.0000000000, 8.1135997772, 0.0000000000], [0.0000000000, 0.0000000000, 8.1135997772]] supercell = [1,1,1] [[config.base_structure]] type = "O" coords = [ [0.237399980, 0.237399980, 0.237399980], [0.762599945, 0.762599945, 0.762599945], ... [0.262599975, 0.262599975, 0.762599945], ] [[config.defect_structure]] coords = [ [0.000000000, 0.000000000, 0.000000000], [0.749999940, 0.249999985, 0.499999970], ... [0.124999993, 0.624999940, 0.124999993], ] [[config.defect_structure.groups]] name = 'Al' # species = ['Al'] # default # coords = [[[0,0,0]]] # default num = 16 [[config.defect_structure.groups]] name = 'Mg' # species = ['Mg'] # default # coords = [[[0,0,0]]] # default num = 8
5.7.1. Input Format¶
Keywords and their values are specified by a keyword and its value in the form keyword = value
.
Comments can also be entered by adding # (Subsequent characters are ignored).
5.7.2. Key words¶
Specify lattice
unitcell
Format : list
Description : Lattice vector \(\bf{a}, \bf{b}, \bf{c}\) by the list format [ \(\bf{a}, \bf{b}, \bf{c}\) ] .
supercell
Format : list
Description : The size of super lattice by the list format[ \(\bf{a}, \bf{b}, \bf{c}\) ].
[[config.base_structure]] section
type
andcoords
specify the atomic species that do not move in Monte Carlo calculation and their coordinates.If there are multiple atomic species, specify multiple [[config.base_structure]] sections.
type
Format : str
Description : Atomic specie.
coords
Format : list of lists or str
Description : Coordinates. Specify a list of N elements (number of atoms) arranged in 3 elements representing 3D coordinates, or a string of coordinates arranged in N rows and 3 columns.
[[config.defect_structure]] section
This sections specifies the lattice coordinates (coords) and atoms (or atom groups) (groups) that can reside on those lattice sites. Monte Carlo sampling is performed on the lattice specified in this section. In Ver. 1.0, conversion tools from POSCAR and cif will be available.
coords
Format : list of lists or str
Description : The coordinates of the lattice sites where atoms reside. A list of N elements (number of atoms) arranged in 3 elements representing 3D coordinates, or a string of coordinates arranged in N rows and 3 columns.
[[config.defect_structure.groups]] section
The atom group information to be updated by Monte Carlo.
name
Format : str
Description : The name of atomic group.
species
Format : list
Description : The atomic species belonging to the atom group. The default value is a list containing only one specified by
name
. A vacancy can be represented by an empty list[]
.
coords
Format : list of lists of lists or str
Description : The coordinates of each atom in the atom group in each direction of local orientation. N (number of atoms) three-element lists, each of which is a list of three elements representing three-dimensional coordinates, is specified as a three-fold list, arranged by orientation. For example, if there are two atoms in the atom group and there are three different orientations, x,y,z, then
coords
can be specified as:coords = [ [ # dir-1 [0.0, 0.0, 0.0], [0.5, 0.0, 0.0] ], [ # dir-2 [0.0, 0.0, 0.0], [0.0, 0.5, 0.0] ], [ # dir-3 [0.0, 0.0, 0.0], [0.0, 0.0, 0.5] ], ]
The default value is
[[0.0, 0.0, 0.0]]
, so this keyword can be omitted if there is only one atom in the atom group.relaxation
Format : list of lists or str
Description : Whether to optimize structure (coordinates) or not for each atom and dimension. A list of N elements (number of atoms) with 3 booleans (“true” or “false”), or a string of “true” or “false” arranged in N rows and 3 columns. Default is
["true", "true", "true"]
for all the atoms.magnetization
Format : list
Description : Magnetization (the difference between the number of up and down electrons) for each atom. Default is 0.0 for all the atoms.
num
Format : int
Description : The number of atom groups of the type specified in this section.