mirror of https://github.com/phonopy/phonopy.git
40 lines
2.3 KiB
Markdown
40 lines
2.3 KiB
Markdown
# Crystal symmetry
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## Tolerance used in crystal symmetry search
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Phonon calculation is based on the assumption that atoms have their own
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equilibrium positions where forces on these atoms are zero. In addition, there
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is a unit cell that contains these atoms and the unit cell are repeated in the
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direct space, i.e., it forms a lattice. The lattice vectors (or basis vectors)
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and points of atoms in this unit cell give the information of the crystal
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structure.
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The crystal structure may have a specific symmetry. The categorization of the
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crystal symmetrized is achieved by the group theory about symmetry operations,
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and there are the 230 different space group types. In phonopy, the crystal
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symmetry is automatically analyzed from the input unit cell structure file that
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doesn't contain the symmetry information. Symmetries are searched by attempting
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possible symmetry operations to the crystal structure and checking if the
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crystal structure after the symmetry operation is overlapping to the original
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crystal structures. In this analysis, a tolerance of distance is used to
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tolerate small deviation of overlapping. This tolerance is the user's choice.
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The default value is `1e-5`.
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Often we know the space group type of our crystal. Therefore it is recommended
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to check whether the space group type of the input unit cell is the correct one
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or not with very tight value such as `--tolerance=1e-8` ({ref}`tolerance_tag`).
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If an input unit cell structure is naively distorted for which the distortion is
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about the same order of the chosen tolerance, inconsistency in symmetry handling
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may occur and it can result in a crash of the calculation or induce a strange
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calculation result. This can be checked by changing the tolerance value
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variously and watching the obtained space group type. If an input unit cell
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structure is distorted, different space group types are found with respect to
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the different tolerance values.
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The detailed space group information is obtained by {ref}`symmetry_option`
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option. As a result of using this option and the chosen tolerance value,
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`BPOSCAR` file is obtained. This is a standardized conventional unit cell (see
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https://spglib.github.io/spglib/definition.html#conventions-of-standardized-unit-cell),
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and its distortion against the crystal symmetry is very small. It is recommended
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to used this structure as the starting point of phonopy calculation.
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