velph.toml-crystal structure sections

The [unitcell], [primitive_cell], and [symmetry] sections describe the crystal structure and its symmetry. They are written by velph init from the input cell file.

Note

These sections are generated automatically and are normally not edited by hand. They are the reference structure for the whole project, and the reproducibility of a calculation depends on them staying unchanged. This page explains how to read them; edit them only if you understand the consequences.

[unitcell] and [primitive_cell]

Both sections use the same layout: a lattice table followed by one [[...points]] entry per atom.

[unitcell]
lattice = [
  [     6.000000000000000,     0.000000000000000,     0.000000000000000 ], # a
  [     0.000000000000000,     6.000000000000000,     0.000000000000000 ], # b
  [     0.000000000000000,     0.000000000000000,     6.000000000000000 ], # c
]
[[unitcell.points]]  # 1
symbol = "Na"
coordinates = [  0.000000000000000,  0.000000000000000,  0.000000000000000 ]
mass = 22.989769
[[unitcell.points]]  # 2
symbol = "Cl"
coordinates = [  0.500000000000000,  0.500000000000000,  0.500000000000000 ]
mass = 35.453000

• lattice : the three lattice vectors a, b, c as rows, in Angstrom.

• [[unitcell.points]] / [[primitive_cell.points]] : a TOML array of tables, one per atom, in the order the atoms are stored. The trailing # 1, # 2, … comments are the 1-based atom indices, written for readability only.

Each point entry accepts the following keys:

Key	Type	Meaning
symbol	str	Chemical element symbol.
coordinates	list[float] (3)	Fractional coordinates in the cell.
mass	float	Atomic mass in AMU. See the note below.
magnetic_moment	float or list[float] (optional)	Collinear (scalar) or non-collinear (3-vector) magnetic moment.

Note

mass is written explicitly so that velph.toml is self-describing: the masses do not depend on the default atomic-mass table and can be edited (e.g. for isotopes). These values may differ from the masses used internally by VASP (POMASS). magnetic_moment is written only when the structure carries magnetic moments (e.g. set through the --magmom option of velph init).

The [primitive_cell] section is written with the same layout as [unitcell]. When the primitive cell differs from the unit cell, the transformation between them is recorded as primitive_matrix in the [symmetry] section.

[symmetry]

This section records the symmetry of the unit cell as found by spglib.

[symmetry]
spacegroup_type = "Fm-3m"
tolerance = 1e-05
primitive_matrix = [
  [  0.000000000000000,  0.500000000000000,  0.500000000000000 ],
  [  0.500000000000000,  0.000000000000000,  0.500000000000000 ],
  [  0.500000000000000,  0.500000000000000,  0.000000000000000 ],
]

Key	Type	Meaning
spacegroup_type	str	International space-group symbol (non-magnetic structures).
uni_number	int	Magnetic space-group “uni number” (written instead of spacegroup_type for magnetic structures).
tolerance	float	Symmetry-search tolerance in Angstrom, set by the --tolerance option of velph init.
primitive_matrix	list[list[float]] (3x3)	Transformation from the unit cell to the primitive cell. Written only when the primitive cell is smaller than the unit cell.

For a non-magnetic structure, spacegroup_type holds the international symbol (e.g. "P1", "Fm-3m"). For a magnetic structure, uni_number is written instead. The primitive_matrix appears only when the unit cell and primitive cell have different numbers of atoms.