Commit 1e244119 authored by Mohamed, Fawzi Roberto (fawzi)'s avatar Mohamed, Fawzi Roberto (fawzi)
Browse files

common: normalize ref naming

try to use source_to_target_ref dropping the section part as name for
references as much as possible (i.e. unless some that wold not give
the intent well)
parent 0ef79e33
...@@ -55,12 +55,9 @@ ...@@ -55,12 +55,9 @@
], ],
"units": "N" "units": "N"
}, { }, {
"description": "Reference to the atom type of each atom in the molecule.", "description": "Name (label) of each atom in the molecule.",
"dtypeStr": "r", "dtypeStr": "f",
"name": "atom_in_molecule_atom_type_ref", "name": "atom_in_molecule_charge",
"referencedSections": [
"section_atom_type"
],
"shape": [ "shape": [
"number_of_atoms_in_molecule" "number_of_atoms_in_molecule"
], ],
...@@ -69,8 +66,8 @@ ...@@ -69,8 +66,8 @@
] ]
}, { }, {
"description": "Name (label) of each atom in the molecule.", "description": "Name (label) of each atom in the molecule.",
"dtypeStr": "f", "dtypeStr": "C",
"name": "atom_in_molecule_charge", "name": "atom_in_molecule_name",
"shape": [ "shape": [
"number_of_atoms_in_molecule" "number_of_atoms_in_molecule"
], ],
...@@ -78,9 +75,12 @@ ...@@ -78,9 +75,12 @@
"settings_atom_in_molecule" "settings_atom_in_molecule"
] ]
}, { }, {
"description": "Name (label) of each atom in the molecule.", "description": "Reference to the atom type of each atom in the molecule.",
"dtypeStr": "C", "dtypeStr": "r",
"name": "atom_in_molecule_name", "name": "atom_in_molecule_to_atom_type_ref",
"referencedSections": [
"section_atom_type"
],
"shape": [ "shape": [
"number_of_atoms_in_molecule" "number_of_atoms_in_molecule"
], ],
...@@ -1115,6 +1115,19 @@ ...@@ -1115,6 +1115,19 @@
"section_frame_sequence" "section_frame_sequence"
], ],
"units": "J" "units": "J"
}, {
"description": "Reference to local frames (which are just section_single_configuration_calculation), if not defined then frame_sequence_external_url *must* be defined, if both are defined this is expected to be a local copy of the reference.",
"dtypeStr": "r",
"name": "frame_sequence_local_frames_ref",
"referencedSections": [
"section_single_configuration_calculation"
],
"shape": [
"number_of_frames_in_sequence"
],
"superNames": [
"section_frame_sequence"
]
}, { }, {
"description": "Average potential energy and standard deviation of this frame sequence. This should be defined if number_of_frames_in_sequence is large.", "description": "Average potential energy and standard deviation of this frame sequence. This should be defined if number_of_frames_in_sequence is large.",
"dtypeStr": "f", "dtypeStr": "f",
...@@ -1159,17 +1172,6 @@ ...@@ -1159,17 +1172,6 @@
"section_frame_sequence" "section_frame_sequence"
], ],
"units": "Pa" "units": "Pa"
}, {
"description": "Reference to the sampling method section defining the parameters used in this frame sequence.",
"dtypeStr": "r",
"name": "frame_sequence_section_sampling_ref",
"referencedSections": [
"section_sampling_method"
],
"shape": [],
"superNames": [
"section_frame_sequence"
]
}, { }, {
"description": "Average temperature and standard deviation of this frame sequence. This should be defined if number_of_frames_in_sequence is large.", "description": "Average temperature and standard deviation of this frame sequence. This should be defined if number_of_frames_in_sequence is large.",
"dtypeStr": "f", "dtypeStr": "f",
...@@ -1203,6 +1205,17 @@ ...@@ -1203,6 +1205,17 @@
"section_frame_sequence" "section_frame_sequence"
], ],
"units": "s" "units": "s"
}, {
"description": "Reference to the sampling method section defining the parameters used in this frame sequence.",
"dtypeStr": "r",
"name": "frame_sequence_to_sampling_ref",
"referencedSections": [
"section_sampling_method"
],
"shape": [],
"superNames": [
"section_frame_sequence"
]
}, { }, {
"description": "Name of the user defined quantity.", "description": "Name of the user defined quantity.",
"dtypeStr": "C", "dtypeStr": "C",
...@@ -1268,19 +1281,6 @@ ...@@ -1268,19 +1281,6 @@
"superNames": [ "superNames": [
"section_interaction" "section_interaction"
] ]
}, {
"description": "Reference to local frames, if not defined then frame_sequence_external_url *must* be defined, if both are defined this is expected to be a local copy of the reference.",
"dtypeStr": "r",
"name": "local_frames_ref",
"referencedSections": [
"section_single_configuration_calculation"
],
"shape": [
"number_of_frames_in_sequence"
],
"superNames": [
"section_frame_sequence"
]
}, { }, {
"description": "Assignent, for each section_basis_set, of a basis set (as given in section_basis_set_atom_centered) to an atom.", "description": "Assignent, for each section_basis_set, of a basis set (as given in section_basis_set_atom_centered) to an atom.",
"dtypeStr": "r", "dtypeStr": "r",
...@@ -2320,22 +2320,22 @@ ...@@ -2320,22 +2320,22 @@
"section_single_configuration_calculation" "section_single_configuration_calculation"
] ]
}, { }, {
"description": "Reference to the method used for the calculation", "description": "Reference to the system (atomic configuration, cell, ...) that is calculated",
"dtypeStr": "r", "dtypeStr": "r",
"name": "single_configuration_calculation_method_ref", "name": "single_configuration_calculation_to_system_description_ref",
"referencedSections": [ "referencedSections": [
"section_method" "section_system_description"
], ],
"shape": [], "shape": [],
"superNames": [ "superNames": [
"section_single_configuration_calculation" "section_single_configuration_calculation"
] ]
}, { }, {
"description": "Reference to the system (atomic configuration, cell, ...) that is calculated", "description": "Reference to the method used for the calculation",
"dtypeStr": "r", "dtypeStr": "r",
"name": "single_configuration_calculation_system_description_ref", "name": "single_configuration_to_calculation_method_ref",
"referencedSections": [ "referencedSections": [
"section_system_description" "section_method"
], ],
"shape": [], "shape": [],
"superNames": [ "superNames": [
......
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