Commit 9d0b2277 authored by Mohamed, Fawzi Roberto (fawzi)'s avatar Mohamed, Fawzi Roberto (fawzi)
Browse files

normalization: logging, configuration_raw_gid, space group

parent b2463c20
......@@ -6,6 +6,42 @@
"kindStr": "type_abstract_document_content",
"name": "accessory_info",
"superNames": []
}, {
"contains": [
"calculation_context",
"section_stats"
],
"description": "Contains information relating to an archive.",
"kindStr": "type_context",
"name": "archive_context",
"superNames": []
}, {
"description": "unique identifier of an archive.",
"dtypeStr": "C",
"name": "archive_gid",
"superNames": [
"archive_context"
]
}, {
"description": "Atomic number Z of the a.",
"dtypeStr": "i",
"name": "atom_atom_number",
"shape": [
"number_of_sites"
],
"superNames": [
"section_system"
]
}, {
"description": "concentration of the atom species in a variable composition, by default it should be considered an array of ones. Summing these should give the number_of_sites",
"dtypeStr": "f",
"name": "atom_concentrations",
"shape": [
"number_of_atoms"
],
"superNames": [
"section_system"
]
}, {
"description": "Forces acting on the atoms, calculated as minus gradient of energy_free, **without** constraints. The derivatives with respect to displacements of nuclei are evaluated in Cartesian coordinates. The (electronic) energy_free contains the change in (fractional) occupation of the electronic eigenstates, which are accounted for in the derivatives, yielding a truly energy-conserved quantity. These forces may contain unitary transformations (center-of-mass translations and rigid rotations for non-periodic systems) that are normally filtered separately (see atom_forces_free for the filtered counterpart). Forces due to constraints such as fixed atoms, distances, angles, dihedrals, etc. are also considered separately (see atom_forces_free for the filtered counterpart).",
"dtypeStr": "f",
......@@ -454,6 +490,22 @@
"superNames": [
"section_method"
]
}, {
"contains": [
"section_run",
"section_stats"
],
"description": "Contains information relating to a calculation.",
"kindStr": "type_context",
"name": "calculation_context",
"superNames": []
}, {
"description": "unique identifier of a calculation.",
"dtypeStr": "C",
"name": "calculation_gid",
"superNames": [
"calculation_context"
]
}, {
"derived": true,
"description": "String that represents the method used to calculate the energy_current. If the method is perturbative, this string does not describe the starting point method, the latter being referenced to by section_method_to_method_refs. For self-consistent field (SCF) ab initio calculations, for example, this is composed by concatenating XC_method_current and basis_set. See [calculation_method_current wiki page](https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-meta-info/wikis/metainfo/calculation-method-current) for the details.",
......@@ -550,6 +602,14 @@
"superNames": [
"configuration_core"
]
}, {
"description": "checksum of the configuration_core, i.e. the geometry of the system. The values are not normalized in any way so equivalent configurations might have different values",
"dtypeStr": "C",
"name": "configuration_raw_gid",
"shape": [],
"superNames": [
"section_system"
]
}, {
"description": "A quantity that is preserved during the time propagation (for example, kinetic+potential energy during NVE).",
"kindStr": "type_abstract_document_content",
......@@ -2114,6 +2174,17 @@
"superNames": [
"scf_info"
]
}, {
"description": "number of sites in a variable composition representation. By default (no variable composition) it is the same as number_of_atoms.",
"dtypeStr": "i",
"kindStr": "type_dimension",
"name": "number_of_sites",
"shape": [
"number_of_atoms"
],
"superNames": [
"section_system"
]
}, {
"description": "Gives the number of energy values for the species-projected density of states (DOS) defined in section_species_projected_dos.",
"dtypeStr": "i",
......@@ -2315,6 +2386,76 @@
"superNames": [
"section_frame_sequence"
]
}, {
"description": "Id (name+version) of the processor that generated or added information to the current calculation.",
"dtypeStr": "C",
"name": "processor_id",
"superNames": [
"section_processor_info"
]
}, {
"description": "Level of the logging, a lower number has more priority. The levels are the same as log4j: FATAL -> 100, ERROR -> 200, WARN -> 300, INFO -> 400, DEBUG -> 500, TRACE -> 600",
"dtypeStr": "i",
"name": "processor_log_event_level",
"superNames": [
"section_processor_log_event"
]
}, {
"description": "The log message",
"dtypeStr": "C",
"name": "processor_log_event_message",
"superNames": [
"section_processor_log_event"
]
}, {
"description": "The processor id of the processor creating this log",
"dtypeStr": "C",
"name": "processor_log_processor_id",
"superNames": [
"section_processor_log"
]
}, {
"description": "Start of the log (in ansi notation YYYY-MM-TT...)",
"dtypeStr": "C",
"name": "processor_log_start",
"superNames": [
"section_processor_log"
]
}, {
"description": "number of contexts evaluated with this processor in the current current calculation.",
"dtypeStr": "i",
"name": "processor_number_of_evaluated_contexts",
"superNames": [
"section_processor_info"
]
}, {
"description": "number of contexts in the current current calculation that had failure for this processor.",
"dtypeStr": "i",
"name": "processor_number_of_failed_contexts",
"superNames": [
"section_processor_info"
]
}, {
"description": "number of contexts skipped by this processor in the current current calculation.",
"dtypeStr": "i",
"name": "processor_number_of_skipped_contexts",
"superNames": [
"section_processor_info"
]
}, {
"description": "number of contexts in the current calculation that where successfully handled by this processor.",
"dtypeStr": "i",
"name": "processor_number_of_successful_contexts",
"superNames": [
"section_processor_info"
]
}, {
"description": "detailed version information on the processor that generated or added information to the current calculation.",
"dtypeStr": "D",
"name": "processor_version_details",
"superNames": [
"section_processor_info"
]
}, {
"description": "The type of basis set used by the program to represent wave functions.\n\nValid values are:\n\n * Numeric AOs\n * Gaussians\n * (L)APW+lo\n * FLAPW (full-potential linearized augmented planewave)\n * Plane waves\n * Real-space grid\n * Local-orbital minimum-basis",
"dtypeStr": "C",
......@@ -2645,6 +2786,24 @@
"superNames": [
"section_run"
]
}, {
"description": "Section with information about a processor that generated or added information to the current calculation.",
"kindStr": "type_section",
"name": "section_processor_info",
"repeats": true,
"superNames": []
}, {
"description": "A log event",
"kindStr": "type_section",
"name": "section_processor_log_event",
"superNames": [
"section_processor_log"
]
}, {
"description": "log of a processor",
"kindStr": "type_section",
"name": "section_processor_log",
"superNames": []
}, {
"description": "Every section_run represents a single call of a program. What exactly is contained in a run depends on the run type (see for example section_method and section_single_configuration_calculation) and the program (see [program_info ](program_info)).",
"kindStr": "type_section",
......@@ -2674,6 +2833,18 @@
"superNames": [
"section_run"
]
}, {
"derived": true,
"description": "Section describing ome of the elements of the group",
"kindStr": "type_section",
"name": "section_spacegroup_3D_operation",
"shape": [
3,
3
],
"superNames": [
"section_system"
]
}, {
"description": "Section collecting the information on a species-projected density of states (DOS) evaluation.",
"kindStr": "type_section",
......@@ -2988,6 +3159,33 @@
"superNames": [
"section_run"
]
}, {
"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.",
"dtypeStr": "C",
"name": "spacegroup_3D_choice",
"shape": [],
"superNames": [
"section_system"
]
}, {
"derived": true,
"description": "Specifies the Hall symbol of the 3D space group, that defines the symmetry group of the simulated physical system (see section_system).",
"dtypeStr": "C",
"name": "spacegroup_3D_hall",
"shape": [],
"superNames": [
"section_system"
]
}, {
"derived": true,
"description": "Specifies the International Union of Crystallography (IUC) symbol of the 3D space group, that defines the symmetry group of the simulated physical system (see section_system).",
"dtypeStr": "C",
"name": "spacegroup_3D_international",
"shape": [],
"superNames": [
"section_system"
]
}, {
"derived": true,
"description": "Specifies the International Union of Crystallography (IUC) number of the 3D space group, that defines the symmetry group of the simulated physical system (see section_system).",
......@@ -2997,6 +3195,108 @@
"superNames": [
"section_system"
]
}, {
"derived": true,
"description": "Origin shift $t$ from standardized to input origin in reduced units: if $x_s$ are reduced standard coordinates, and $x$ the original coordinates, then $x_s = Hmat * x + t \\mod 1$ where $Hmat$ is spacegroup_3D_trasformation_matrix",
"dtypeStr": "f",
"name": "spacegroup_3D_origin_shift",
"shape": [
3
],
"superNames": [
"section_system"
]
}, {
"derived": true,
"description": "Point group symbol",
"dtypeStr": "C",
"name": "spacegroup_3D_pointgroup",
"shape": [],
"superNames": [
"section_system"
]
}, {
"derived": true,
"description": "rotations defining (together with spacegroup_3D_translation) the space group operations",
"dtypeStr": "f",
"name": "spacegroup_3D_rotation",
"shape": [
3,
3
],
"superNames": [
"section_spacegroup_3D_operation"
]
}, {
"derived": true,
"description": "Standardized lattice vectors of the conventional cell choose as described in https://atztogo.github.io/spglib/definition.html#def-standardized-unit-cell",
"dtypeStr": "f",
"name": "spacegroup_3D_std_lattice",
"shape": [
3,
3
],
"superNames": [
"section_system"
],
"units": "m"
}, {
"derived": true,
"description": "Standardized atom positions in reduced units",
"dtypeStr": "i",
"name": "spacegroup_3D_std_positions",
"shape": [
"number_of_atoms",
3
],
"superNames": [
"section_system"
]
}, {
"derived": true,
"description": "species types (atom number, like atom_species)",
"dtypeStr": "i",
"name": "spacegroup_3D_std_types",
"shape": [
"number_of_atoms"
],
"superNames": [
"section_system"
]
}, {
"derived": true,
"description": "translations defining together with spacegroup_3D_rotation the space group operations in reduced units",
"dtypeStr": "f",
"name": "spacegroup_3D_translation",
"shape": [
3
],
"superNames": [
"section_spacegroup_3D_operation"
]
}, {
"derived": true,
"description": "Transformation matrix $Tmat$ from input lattice lattice_vectors to standardized lattice spacegroup_3D_std_lattice: $L^{original} = L^{standardized} * Tmat$",
"dtypeStr": "f",
"name": "spacegroup_3D_trasformation_matrix",
"shape": [
3,
3
],
"superNames": [
"section_system"
]
}, {
"derived": true,
"description": "Wyckoff symbol of the atoms",
"dtypeStr": "i",
"name": "spacegroup_3D_wyckoff",
"shape": [
"number_of_atoms"
],
"superNames": [
"section_system"
]
}, {
"derived": true,
"description": "Contains the set of discrete energy values with respect to the top of the valence band for the species-projected density of states (DOS). It is derived from the species_projected_dos_energies species field.",
......
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