Commit 80aafeac authored by Lauri Himanen's avatar Lauri Himanen

Renaming and restructuring of the symmetry information.

parent 0cd61d43
...@@ -2327,15 +2327,6 @@ ...@@ -2327,15 +2327,6 @@
"superNames": [ "superNames": [
"section_method" "section_method"
] ]
}, {
"description": "Gives the number of symmetry operations.",
"dtypeStr": "i",
"kindStr": "type_dimension",
"name": "number_of_symmetry_operations",
"shape": [],
"superNames": [
"section_system"
]
}, { }, {
"description": "Gives the number of temperature frames (frame_sequence_temperature) used in the section_frame_sequence. A sequence is a trajectory, which can have number_of_frames_in_sequence each representing one section_single_configuration_calculation section.", "description": "Gives the number of temperature frames (frame_sequence_temperature) used in the section_frame_sequence. A sequence is a trajectory, which can have number_of_frames_in_sequence each representing one section_single_configuration_calculation section.",
"dtypeStr": "i", "dtypeStr": "i",
...@@ -2663,31 +2654,6 @@ ...@@ -2663,31 +2654,6 @@
"superNames": [ "superNames": [
"section_system" "section_system"
] ]
}, {
"description": "The transformation matrix in reduced coordinates and real space for each symmetry operation. For periodic crystals, these can be expressed purely in integers, but for arbitrary point groups, this is not possible.",
"dtypeStr": "f",
"name": "reduced_symmetry_matrices",
"repeats": false,
"shape": [
"number_of_symmetry_operations",
3,
3
],
"superNames": [
"section_system"
]
}, {
"description": "The translation vector in reduced coordinates (without a factor of $2\\pi$ ) for each symmetry operation.",
"dtypeStr": "f",
"name": "reduced_symmetry_translations",
"repeats": false,
"shape": [
"number_of_symmetry_operations",
3
],
"superNames": [
"section_system"
]
}, { }, {
"description": "Describes the relativistic treatment used for the calculation of the final energy and related quantities. If skipped or empty, no relativistic treatment is applied.", "description": "Describes the relativistic treatment used for the calculation of the final energy and related quantities. If skipped or empty, no relativistic treatment is applied.",
"dtypeStr": "C", "dtypeStr": "C",
...@@ -3351,238 +3317,293 @@ ...@@ -3351,238 +3317,293 @@
"superNames": [ "superNames": [
"section_run" "section_run"
] ]
}, {
"description": "Section containing information about the symmetry properties of the system.",
"kindStr": "type_section",
"name": "section_symmetry",
"superNames": [
"section_system"
]
}, {
"description": "Section containing symmetry information that is specific to the primitive system. The primitive system is derived from the standardized system with a transformation that is specific to the centring. The transformation matrices can be found e.g. from here: https://atztogo.github.io/spglib/definition.html#transformation-to-the-primitive-cell",
"kindStr": "type_section",
"name": "section_primitive_system",
"superNames": [
"section_symmetry"
]
}, {
"description": "Section containing symmetry information that is specific to the standardized system. The standardized system is defined as given by spglib and the details can be found from https://arxiv.org/abs/1506.01455",
"kindStr": "type_section",
"name": "section_std_system",
"superNames": [
"section_symmetry"
]
}, {
"description": "Section containing symmetry information that is specific to the original system.",
"kindStr": "type_section",
"name": "section_original_system",
"superNames": [
"section_symmetry"
]
}, {
"derived": true,
"description": "Identifies the source of the symmetry information contained within this section. If equal to 'spg_normalized' the information comes from a normalization step.",
"dtypeStr": "C",
"name": "symmetry_method",
"shape": [],
"superNames": [
"section_symmetry"
]
}, { }, {
"derived": true, "derived": true,
"description": "Identifier for the Bravais lattice in Pearson notation. The first lowercase letter identifies the crystal family and can be one of the following: a (triclinic), b (monoclinic), o (orthorhombic), t (tetragonal), h (hexagonal) or c (cubic). The second uppercase letter identifies the centring and can be one of the following: P (primitive), S (face centred), I (body centred), R (rhombohedral centring) or F (all faces centred).", "description": "Identifier for the Bravais lattice in Pearson notation. The first lowercase letter identifies the crystal family and can be one of the following: a (triclinic), b (monoclinic), o (orthorhombic), t (tetragonal), h (hexagonal) or c (cubic). The second uppercase letter identifies the centring and can be one of the following: P (primitive), S (face centred), I (body centred), R (rhombohedral centring) or F (all faces centred).",
"dtypeStr": "C", "dtypeStr": "C",
"name": "space_group_3D_bravais_lattice", "name": "bravais_lattice",
"shape": [], "shape": [],
"superNames": [ "superNames": [
"section_system" "section_symmetry"
] ]
}, { }, {
"derived": true, "derived": true,
"description": "String that specifies the centering, origin and basis vector settings of the 3D space group that defines the symmetry group of the simulated physical system (see section_system). Values are as defined by spglib.", "description": "String that specifies the centering, origin and basis vector settings of the 3D space group that defines the symmetry group of the simulated physical system (see section_system). Values are as defined by spglib.",
"dtypeStr": "C", "dtypeStr": "C",
"name": "space_group_3D_choice", "name": "choice",
"shape": [], "shape": [],
"superNames": [ "superNames": [
"section_system" "section_symmetry"
] ]
}, { }, {
"derived": true, "derived": true,
"description": "Name of the crystal system. Can be one of the following: triclinic, monoclinic, orthorhombic, tetragonal, trigonal, hexagonal or cubic.", "description": "Name of the crystal system. Can be one of the following: triclinic, monoclinic, orthorhombic, tetragonal, trigonal, hexagonal or cubic.",
"dtypeStr": "C", "dtypeStr": "C",
"name": "space_group_3D_crystal_system", "name": "crystal_system",
"shape": [], "shape": [],
"superNames": [ "superNames": [
"section_system" "section_symmetry"
] ]
}, { }, {
"derived": true, "derived": true,
"description": "The Hall number for this system.", "description": "The Hall number for this system.",
"dtypeStr": "i", "dtypeStr": "i",
"name": "space_group_3D_hall_number", "name": "hall_number",
"shape": [], "shape": [],
"superNames": [ "superNames": [
"section_system" "section_symmetry"
] ]
}, { }, {
"derived": true, "derived": true,
"description": "The Hall symbol for this system.", "description": "The Hall symbol for this system.",
"dtypeStr": "C", "dtypeStr": "C",
"name": "space_group_3D_hall_symbol", "name": "hall_symbol",
"shape": [], "shape": [],
"superNames": [ "superNames": [
"section_system" "section_symmetry"
] ]
}, { }, {
"derived": true, "derived": true,
"description": "Specifies the International Union of Crystallography (IUC) short symbol of the 3D space group of this system", "description": "Specifies the International Union of Crystallography (IUC) short symbol of the 3D space group of this system",
"dtypeStr": "C", "dtypeStr": "C",
"name": "space_group_3D_international_short", "name": "international_short_symbol",
"shape": [], "shape": [],
"superNames": [ "superNames": [
"section_system" "section_symmetry"
] ]
}, { }, {
"derived": true, "derived": true,
"description": "Specifies the International Union of Crystallography (IUC) number of the 3D space group of this system.", "description": "Specifies the International Union of Crystallography (IUC) number of the 3D space group of this system.",
"dtypeStr": "i", "dtypeStr": "i",
"name": "space_group_3D_number", "name": "space_group_number",
"shape": [], "shape": [],
"superNames": [ "superNames": [
"section_system" "section_symmetry"
] ]
}, { }, {
"derived": true, "derived": true,
"description": "Vector $\\mathbf{p}$ from the origin of the standardized system to the origin of the original system. Together with the matrix $\\mathbf{P}$, found in space_group_3D_transformation_matrix, the transformation between the standardized coordinates $\\mathbf{x}_s$ and original coordinates $\\mathbf{x}$ is then given by $\\mathbf{x}_s = \\mathbf{P} \\mathbf{x} + \\mathbf{p}$.", "description": "Vector $\\mathbf{p}$ from the origin of the standardized system to the origin of the original system. Together with the matrix $\\mathbf{P}$, found in space_group_3D_transformation_matrix, the transformation between the standardized coordinates $\\mathbf{x}_s$ and original coordinates $\\mathbf{x}$ is then given by $\\mathbf{x}_s = \\mathbf{P} \\mathbf{x} + \\mathbf{p}$.",
"dtypeStr": "f", "dtypeStr": "f",
"name": "space_group_3D_origin_shift", "name": "origin_shift",
"shape": [ "shape": [
3 3
], ],
"superNames": [ "superNames": [
"section_system" "section_symmetry"
] ]
}, { }, {
"derived": true, "derived": true,
"description": "Gives a mapping table of atoms to symmetrically independent atoms in the original cell. This is used to find symmetrically equivalent atoms.", "description": "Gives a mapping table of atoms to symmetrically independent atoms in the original cell. This is used to find symmetrically equivalent atoms.",
"dtypeStr": "i", "dtypeStr": "i",
"name": "space_group_3D_original_equivalent_atoms", "name": "original_equivalent_atoms",
"shape": [ "shape": [
"number_of_atoms" "number_of_atoms"
], ],
"superNames": [ "superNames": [
"section_system" "section_original_system"
] ]
}, { }, {
"derived": true, "derived": true,
"description": "Wyckoff letters for atoms in the original cell.", "description": "Wyckoff letters for atoms in the original cell.",
"dtypeStr": "C", "dtypeStr": "C",
"name": "space_group_3D_original_wyckoff_letters", "name": "original_wyckoff_letters",
"shape": [ "shape": [
"number_of_atoms" "number_of_atoms"
], ],
"superNames": [ "superNames": [
"section_system" "section_original_system"
] ]
}, { }, {
"derived": true, "derived": true,
"description": "Symbol of the crystallographic point group in the Hermann-Mauguin notation.", "description": "Symbol of the crystallographic point group in the Hermann-Mauguin notation.",
"dtypeStr": "C", "dtypeStr": "C",
"name": "space_group_3D_point_group", "name": "point_group",
"shape": [], "shape": [],
"superNames": [ "superNames": [
"section_system" "section_symmetry"
]
}, {
"description": "Number of atoms in primitive system.",
"dtypeStr": "i",
"kindStr": "type_dimension",
"name": "number_of_atoms_primitive",
"shape": [],
"superNames": [
"section_primitive_system"
] ]
}, { }, {
"derived": true, "derived": true,
"description": "Atomic numbers in the primitive cell.", "description": "Atomic numbers in the primitive cell.",
"dtypeStr": "i", "dtypeStr": "i",
"name": "space_group_3D_primitive_atomic_numbers", "name": "primitive_atomic_numbers",
"shape": [ "shape": [
"primitive_number_of_atoms" "primitive_number_of_atoms"
], ],
"superNames": [ "superNames": [
"section_system" "section_primitive_system"
] ]
}, { }, {
"derived": true, "derived": true,
"description": "Gives a mapping table of atoms to symmetrically independent atoms in the primitive cell. This is used to find symmetrically equivalent atoms.", "description": "Gives a mapping table of atoms to symmetrically independent atoms in the primitive cell. This is used to find symmetrically equivalent atoms.",
"dtypeStr": "i", "dtypeStr": "i",
"name": "space_group_3D_primitive_equivalent_atoms", "name": "primitive_equivalent_atoms",
"shape": [ "shape": [
"primitive_number_of_atoms" "primitive_number_of_atoms"
], ],
"superNames": [ "superNames": [
"section_system" "section_primitive_system"
] ]
}, { }, {
"derived": true, "derived": true,
"description": "Primitive lattice vectors. The vectors are the rows of this matrix.", "description": "Primitive lattice vectors. The vectors are the rows of this matrix.",
"dtypeStr": "f", "dtypeStr": "f",
"name": "space_group_3D_primitive_lattice", "name": "primitive_lattice",
"shape": [ "shape": [
3, 3,
3 3
], ],
"superNames": [ "superNames": [
"section_system" "section_primitive_system"
], ],
"units": "m" "units": "m"
}, { }, {
"derived": true, "derived": true,
"description": "Atom positions in the primitive cell in reduced units.", "description": "Atom positions in the primitive cell in reduced units.",
"dtypeStr": "f", "dtypeStr": "f",
"name": "space_group_3D_primitive_positions", "name": "primitive_positions",
"shape": [ "shape": [
"primitive_number_of_atoms", "primitive_number_of_atoms",
3 3
], ],
"superNames": [ "superNames": [
"section_system" "section_primitive_system"
] ]
}, { }, {
"derived": true, "derived": true,
"description": "Wyckoff letters for atoms in the primitive cell.", "description": "Wyckoff letters for atoms in the primitive cell.",
"dtypeStr": "C", "dtypeStr": "C",
"name": "space_group_3D_primitive_wyckoff_letters", "name": "primitive_wyckoff_letters",
"shape": [ "shape": [
"primitive_number_of_atoms" "primitive_number_of_atoms"
], ],
"superNames": [ "superNames": [
"section_system" "section_primitive_system"
]
}, {
"description": "Number of atoms in standardized system.",
"dtypeStr": "i",
"kindStr": "type_dimension",
"name": "number_of_atoms_std",
"shape": [],
"superNames": [
"section_std_system"
] ]
}, { }, {
"derived": true, "derived": true,
"description": "Atomic numbers of the atoms in the standardized cell.", "description": "Atomic numbers of the atoms in the standardized cell.",
"dtypeStr": "i", "dtypeStr": "i",
"name": "space_group_3D_std_atomic_numbers", "name": "std_atomic_numbers",
"shape": [ "shape": [
"number_of_atoms" "number_of_atoms"
], ],
"superNames": [ "superNames": [
"section_system" "section_std_system"
] ]
}, { }, {
"derived": true, "derived": true,
"description": "Gives a mapping table of atoms to symmetrically independent atoms in the standardized cell. This is used to find symmetrically equivalent atoms.", "description": "Gives a mapping table of atoms to symmetrically independent atoms in the standardized cell. This is used to find symmetrically equivalent atoms.",
"dtypeStr": "i", "dtypeStr": "i",
"name": "space_group_3D_std_equivalent_atoms", "name": "std_equivalent_atoms",
"shape": [ "shape": [
"std_number_of_atoms" "std_number_of_atoms"
], ],
"superNames": [ "superNames": [
"section_system" "section_std_system"
] ]
}, { }, {
"derived": true, "derived": true,
"description": "Standardized lattice vectors of the conventional cell chosen as described in https://atztogo.github.io/spglib/definition.html#def-standardized-unit-cell. The vectors are the rows of this matrix.", "description": "Standardized lattice vectors of the conventional cell chosen as described in https://atztogo.github.io/spglib/definition.html#def-standardized-unit-cell. The vectors are the rows of this matrix.",
"dtypeStr": "f", "dtypeStr": "f",
"name": "space_group_3D_std_lattice", "name": "std_lattice",
"shape": [ "shape": [
3, 3,
3 3
], ],
"superNames": [ "superNames": [
"section_system" "section_std_system"
], ],
"units": "m" "units": "m"
}, { }, {
"derived": true, "derived": true,
"description": "Standardized atom positions in reduced units.", "description": "Standardized atom positions in reduced units.",
"dtypeStr": "f", "dtypeStr": "f",
"name": "space_group_3D_std_positions", "name": "std_positions",
"shape": [ "shape": [
"number_of_atoms", "number_of_atoms_std",
3 3
], ],
"superNames": [ "superNames": [
"section_system" "section_std_system"
] ]
}, { }, {
"derived": true, "derived": true,
"description": "Wyckoff letters for atoms in the standardized cell.", "description": "Wyckoff letters for atoms in the standardized cell.",
"dtypeStr": "C", "dtypeStr": "C",
"name": "space_group_3D_std_wyckoff_letters", "name": "std_wyckoff_letters",
"shape": [ "shape": [
"std_number_of_atoms" "std_number_of_atoms"
], ],
"superNames": [ "superNames": [
"section_system" "section_std_system"
] ]
}, { }, {
"derived": true, "derived": true,
"description": "Matrix $\\mathbf{P}$ that is used to transform the standardized coordinates to the original coordinates. Together with the vector $\\mathbf{p}$, found in space_group_3D_origin_shift, the transformation between the standardized coordinates $\\mathbf{x}_s$ and original coordinates $\\mathbf{x}$ is then given by $\\mathbf{x}_s = \\mathbf{P} \\mathbf{x} + \\mathbf{p}$.", "description": "Matrix $\\mathbf{P}$ that is used to transform the standardized coordinates to the original coordinates. Together with the vector $\\mathbf{p}$, found in space_group_3D_origin_shift, the transformation between the standardized coordinates $\\mathbf{x}_s$ and original coordinates $\\mathbf{x}$ is then given by $\\mathbf{x}_s = \\mathbf{P} \\mathbf{x} + \\mathbf{p}$.",
"dtypeStr": "f", "dtypeStr": "f",
"name": "space_group_3D_transformation_matrix", "name": "transformation_matrix",
"shape": [ "shape": [
3, 3,
3 3
], ],
"superNames": [ "superNames": [
"section_system" "section_symmetry"
] ]
}, { }, {
"derived": true, "derived": true,
......
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