Commit 0f78e215 authored by Adam Fekete's avatar Adam Fekete Committed by Mohamed, Fawzi Roberto (fawzi)

rearranging the modifications

parent c464c884
......@@ -944,60 +944,6 @@
"section_excited_states"
]
},
{
"description": "(deprecated) A unique string idenfiying the force field defined in this section. Strategies to define it are discussed in the [topology\\_force\\_field\\_name](https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-meta-info/wikis/metainfo/topology-force-field-name).",
"dtypeStr": "C",
"name": "topology_force_field_name",
"shape": [],
"superNames": [
"section_topology"
]
},
{
"description": "(deprecated) Reference to the topology used for this system; if not given, the trivial topology should be assumed.",
"dtypeStr": "r",
"name": "topology_ref",
"referencedSections": [
"section_topology"
],
"repeats": false,
"shape": [],
"superNames": [
"section_system"
]
},
{
"description": "(deprecated) Section describing a type of molecule in the system.",
"kindStr": "type_section",
"name": "section_molecule_type",
"superNames": [
"section_topology"
]
},
{
"description": "(deprecated) Number of molecules in the system, as described by this topology.",
"dtypeStr": "i",
"kindStr": "type_dimension",
"name": "number_of_topology_molecules",
"shape": [],
"superNames": [
"section_topology"
]
},
{
"description": "(deprecated) Reference to the atom type of each atom in the molecule.",
"dtypeStr": "r",
"name": "atom_in_molecule_to_atom_type_ref",
"referencedSections": [
"section_atom_type"
],
"shape": [
"number_of_atoms_in_molecule"
],
"superNames": [
"settings_atom_in_molecule"
]
},
{
"description": "(deprecated) Section describing a type of atom in the system.",
"kindStr": "type_section",
......@@ -1007,17 +953,16 @@
]
},
{
"description": "Charge of the atom type.",
"dtypeStr": "f",
"name": "atom_type_charge",
"description": "(deprecated) Name (label) of the atom type.",
"dtypeStr": "C",
"name": "atom_type_name",
"shape": [],
"superNames": [
"section_atom_type"
],
"units": "C"
]
},
{
"description": "Mass of the atom type.",
"description": "(deprecated) Mass of the atom type.",
"dtypeStr": "f",
"name": "atom_type_mass",
"shape": [],
......@@ -1027,13 +972,14 @@
"units": "kg"
},
{
"description": "Name (label) of the atom type.",
"dtypeStr": "C",
"name": "atom_type_name",
"description": "(deprecated) Charge of the atom type.",
"dtypeStr": "f",
"name": "atom_type_charge",
"shape": [],
"superNames": [
"section_atom_type"
]
],
"units": "C"
},
{
"description": "(deprecated) Table mapping atom to molecules: the first column is the index of the molecule and the second column the index of the atom, signifying that the atom in the second column belongs to the molecule in the first column in the same row.",
......@@ -1047,20 +993,6 @@
"section_topology"
]
},
{
"description": "(deprecated) Mapping from molecules to molecule types.",
"dtypeStr": "r",
"name": "molecule_to_molecule_type_map",
"referencedSections": [
"section_molecule_type"
],
"shape": [
"number_of_topology_molecules"
],
"superNames": [
"section_topology"
]
},
{
"description": "(deprecated) Name (label) of each atom in the molecule.",
"dtypeStr": "C",
......@@ -1085,102 +1017,115 @@
"units": "C"
},
{
"description": "(deprecated) List of the indexes involved in this constraint. The fist atom has index 1, the last index is number_of_atoms_in_molecule.",
"dtypeStr": "i",
"name": "molecule_constraint_atoms",
"description": "(deprecated) Reference to the atom type of each atom in the molecule.",
"dtypeStr": "r",
"name": "atom_in_molecule_to_atom_type_ref",
"referencedSections": [
"section_atom_type"
],
"shape": [
"number_of_molecule_constraints",
"number_of_atoms_per_molecule_constraint"
"number_of_atoms_in_molecule"
],
"superNames": [
"section_molecule_constraint"
"settings_atom_in_molecule"
]
},
{
"description": "(deprecated) Short and unique name for this constraint type. Valid names are described in the [constraint\\_kind wiki page](https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-meta-info/wikis/metainfo/constraint-kind).",
"dtypeStr": "C",
"name": "molecule_constraint_kind",
"shape": [],
"description": "(deprecated) Parameters of an atom within a molecule.",
"kindStr": "type_abstract_document_content",
"name": "settings_atom_in_molecule",
"superNames": [
"section_molecule_constraint"
"section_molecule_type"
]
},
{
"description": "(deprecated) Explicit constraint parameters for this kind of constraint (depending on the constraint type some might be given implicitly through other means).",
"dtypeStr": "D",
"name": "molecule_constraint_parameters",
"description": "(deprecated) Section describing a type of molecule in the system.",
"kindStr": "type_section",
"name": "section_molecule_type",
"superNames": [
"section_topology"
]
},
{
"description": "(deprecated) Name of the molecule.",
"dtypeStr": "C",
"name": "molecule_type_name",
"shape": [],
"superNames": [
"section_molecule_constraint"
"section_molecule_type"
]
},
{
"description": "(deprecated) List of the indexes involved in this bonded interaction within a molecule. The first atom has index 1, the last index is number_of_atoms_in_.",
"dtypeStr": "i",
"name": "molecule_interaction_atoms",
"description": "(deprecated) Mapping from molecules to molecule types.",
"dtypeStr": "r",
"name": "molecule_to_molecule_type_map",
"referencedSections": [
"section_molecule_type"
],
"shape": [
"number_of_molecule_interactions",
"number_of_atoms_per_molecule_interaction"
"number_of_topology_molecules"
],
"superNames": [
"section_molecule_interaction"
"section_topology"
]
},
{
"description": "(deprecated) Short and unique name for this interaction type, used for bonded interactions for atoms in a molecule. Valid names are described in the [interaction\\_kind wiki page](https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-meta-info/wikis/metainfo/interaction-kind).",
"dtypeStr": "C",
"name": "molecule_interaction_kind",
"description": "(deprecated) Number of molecules in the system, as described by this topology.",
"dtypeStr": "i",
"kindStr": "type_dimension",
"name": "number_of_topology_molecules",
"shape": [],
"superNames": [
"section_molecule_interaction"
"section_topology"
]
},
{
"description": "(deprecated) Explicit interaction parameters for this kind of interaction (depending on the interaction type some might be given implicitly through other means), used for bonded interactions for atoms in a molecule.",
"dtypeStr": "D",
"name": "molecule_interaction_parameters",
"description": "(deprecated) Number of atoms in this molecule.",
"dtypeStr": "i",
"kindStr": "type_dimension",
"name": "number_of_atoms_in_molecule",
"shape": [],
"superNames": [
"section_molecule_interaction"
"section_molecule_type"
]
},
{
"description": "(deprecated) Name of the molecule.",
"dtypeStr": "C",
"name": "molecule_type_name",
"shape": [],
"description": "(deprecated) Section describing a constraint between atoms within a molecule.",
"kindStr": "type_section",
"name": "section_molecule_constraint",
"superNames": [
"section_molecule_type"
"section_molecule_type",
"settings_constraint"
]
},
{
"description": "(deprecated) Number of atoms in this molecule.",
"dtypeStr": "i",
"kindStr": "type_dimension",
"name": "number_of_atoms_in_molecule",
"description": "(deprecated) Short and unique name for this constraint type. Valid names are described in the [constraint\\_kind wiki page](https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-meta-info/wikis/metainfo/constraint-kind).",
"dtypeStr": "C",
"name": "molecule_constraint_kind",
"shape": [],
"superNames": [
"section_molecule_type"
"section_molecule_constraint"
]
},
{
"description": "(deprecated) Number of atoms, in this molecule, involved in this constraint.",
"dtypeStr": "i",
"kindStr": "type_dimension",
"name": "number_of_atoms_per_molecule_constraint",
"description": "(deprecated) Explicit constraint parameters for this kind of constraint (depending on the constraint type some might be given implicitly through other means).",
"dtypeStr": "D",
"name": "molecule_constraint_parameters",
"shape": [],
"superNames": [
"section_molecule_constraint"
]
},
{
"description": "(deprecated) Number of atoms, in this molecule, involved in this interaction.",
"description": "(deprecated) List of the indexes involved in this constraint. The fist atom has index 1, the last index is number_of_atoms_in_molecule.",
"dtypeStr": "i",
"kindStr": "type_dimension",
"name": "number_of_atoms_per_molecule_interaction",
"shape": [],
"name": "molecule_constraint_atoms",
"shape": [
"number_of_molecule_constraints",
"number_of_atoms_per_molecule_constraint"
],
"superNames": [
"section_molecule_interaction"
"section_molecule_constraint"
]
},
{
......@@ -1194,51 +1139,96 @@
]
},
{
"description": "(deprecated) Number of bonded interactions of this type.",
"description": "(deprecated) Number of atoms, in this molecule, involved in this constraint.",
"dtypeStr": "i",
"kindStr": "type_dimension",
"name": "number_of_molecule_interactions",
"name": "number_of_atoms_per_molecule_constraint",
"shape": [],
"superNames": [
"section_molecule_interaction"
"section_molecule_constraint"
]
},
{
"description": "(deprecated) Section describing a constraint between atoms within a molecule.",
"description": "(deprecated) Section describing a bonded interaction between atoms within a molecule.",
"kindStr": "type_section",
"name": "section_molecule_constraint",
"name": "section_molecule_interaction",
"superNames": [
"section_molecule_type",
"settings_constraint"
"settings_interaction"
]
},
{
"description": "(deprecated) Section describing a bonded interaction between atoms within a molecule.",
"kindStr": "type_section",
"name": "section_molecule_interaction",
"description": "(deprecated) Short and unique name for this interaction type, used for bonded interactions for atoms in a molecule. Valid names are described in the [interaction\\_kind wiki page](https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-meta-info/wikis/metainfo/interaction-kind).",
"dtypeStr": "C",
"name": "molecule_interaction_kind",
"shape": [],
"superNames": [
"section_molecule_type",
"settings_interaction"
"section_molecule_interaction"
]
},
{
"description": "(deprecated) Parameters of an atom within a molecule.",
"kindStr": "type_abstract_document_content",
"name": "settings_atom_in_molecule",
"description": "(deprecated) Explicit interaction parameters for this kind of interaction (depending on the interaction type some might be given implicitly through other means), used for bonded interactions for atoms in a molecule.",
"dtypeStr": "D",
"name": "molecule_interaction_parameters",
"shape": [],
"superNames": [
"section_molecule_type"
"section_molecule_interaction"
]
},
{
"description": "Number of atoms in the system described by this topology.",
"description": "(deprecated) List of the indexes involved in this bonded interaction within a molecule. The first atom has index 1, the last index is number_of_atoms_in_.",
"dtypeStr": "i",
"name": "molecule_interaction_atoms",
"shape": [
"number_of_molecule_interactions",
"number_of_atoms_per_molecule_interaction"
],
"superNames": [
"section_molecule_interaction"
]
},
{
"description": "(deprecated) Number of bonded interactions of this type.",
"dtypeStr": "i",
"kindStr": "type_dimension",
"name": "number_of_topology_atoms",
"name": "number_of_molecule_interactions",
"shape": [],
"superNames": [
"section_molecule_interaction"
]
},
{
"description": "(deprecated) Number of atoms, in this molecule, involved in this interaction.",
"dtypeStr": "i",
"kindStr": "type_dimension",
"name": "number_of_atoms_per_molecule_interaction",
"shape": [],
"superNames": [
"section_molecule_interaction"
]
},
{
"description": "(deprecated) A unique string idenfiying the force field defined in this section. Strategies to define it are discussed in the [topology\\_force\\_field\\_name](https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-meta-info/wikis/metainfo/topology-force-field-name).",
"dtypeStr": "C",
"name": "topology_force_field_name",
"shape": [],
"superNames": [
"section_topology"
]
},
{
"description": "Reference to the topology used for this system; if not given, the trivial topology should be assumed.",
"dtypeStr": "r",
"name": "topology_ref",
"referencedSections": [
"section_topology"
],
"repeats": false,
"shape": [],
"superNames": [
"section_system"
]
},
{
"description": "Reference to the topology and force fields to be used.",
"dtypeStr": "r",
......@@ -1272,6 +1262,16 @@
"section_run"
]
},
{
"description": "Number of atoms in the system described by this topology.",
"dtypeStr": "i",
"kindStr": "type_dimension",
"name": "number_of_topology_atoms",
"shape": [],
"superNames": [
"section_topology"
]
},
{
"description": "Section describing an atom in the system.",
"kindStr": "type_section",
......@@ -1368,166 +1368,166 @@
]
},
{
"description": "Section describing a constraint between arbitrary atoms.",
"kindStr": "type_section",
"name": "section_constraints",
"derived": true,
"description": "Species of the atom (normally the atomic number Z, 0 or negative for unidentifed species or particles that are not atoms.",
"dtypeStr": "i",
"name": "atom_species",
"repeats": true,
"shape": [],
"superNames": [
"section_run"
"section_topology"
]
},
{
"description": "Section describing a constraint between arbitrary atoms.",
"description": "Section containing the description of a bonded interaction between arbitrary atoms.",
"kindStr": "type_section",
"name": "section_constraint",
"name": "section_interaction",
"superNames": [
"section_constraints",
"settings_constraint"
"section_method",
"settings_interaction"
]
},
{
"description": "Short and unique name for this constraint type. Valid names are described in the [constraint\\_kind wiki page](https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-meta-info/wikis/metainfo/constraint-kind).",
"description": "Short and unique name for this interaction type. Valid names are described in the [interaction\\_kind wiki page](https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-meta-info/wikis/metainfo/interaction-kind).",
"dtypeStr": "C",
"name": "constraint_kind",
"name": "interaction_kind",
"shape": [],
"superNames": [
"section_constraint"
"section_interaction"
]
},
{
"description": "Explicit constraint parameters for this kind of constraint (depending on the constraint type, some might be given implicitly through other means).",
"description": "Explicit interaction parameters for this kind of interaction (depending on the interaction_kind some might be given implicitly through other means).",
"dtypeStr": "D",
"name": "constraint_parameters",
"name": "interaction_parameters",
"shape": [],
"superNames": [
"section_constraint"
"section_interaction"
]
},
{
"description": "Reference to the topological group of atoms which is used to define contraint on it.",
"dtypeStr": "r",
"name": "constraint_to_topology_group_ref",
"name": "interaction_to_topology_group_ref",
"referencedSections": [
"section_group"
"section_topology"
],
"repeats": false,
"shape": [],
"superNames": [
"section_constraint"
"section_interaction"
]
},
{
"description": "List of the indexes involved in this constraint. The fist atom has index 1, the last number_of_topology_atoms.",
"description": "List of the indexes involved in this interaction. The fist atom has index 1, the last atom index number_of_topology_atoms.",
"dtypeStr": "i",
"name": "constraint_atoms",
"name": "interaction_atoms",
"shape": [
"number_of_constraints",
"number_of_atoms_per_constraint"
"number_of_interactions",
"number_of_atoms_per_interaction"
],
"superNames": [
"section_constraint"
"section_interaction"
]
},
{
"description": "Number of constraints of this type.",
"description": "Number of interactions of this type.",
"dtypeStr": "i",
"kindStr": "type_dimension",
"name": "number_of_constraints",
"name": "number_of_interactions",
"shape": [],
"superNames": [
"section_constraint"
"section_interaction"
]
},
{
"description": "Number of atoms involved in this constraint.",
"description": "Number of atoms involved in this interaction.",
"dtypeStr": "i",
"kindStr": "type_dimension",
"name": "number_of_atoms_per_constraint",
"name": "number_of_atoms_per_interaction",
"shape": [],
"superNames": [
"section_constraint"
"section_interaction"
]
},
{
"derived": true,
"description": "Species of the atom (normally the atomic number Z, 0 or negative for unidentifed species or particles that are not atoms.",
"dtypeStr": "i",
"name": "atom_species",
"repeats": true,
"shape": [],
"description": "Section describing a constraint between arbitrary atoms.",
"kindStr": "type_section",
"name": "section_constraints",
"superNames": [
"section_topology"
"section_run"
]
},
{
"description": "Section containing the description of a bonded interaction between arbitrary atoms.",
"description": "Section describing a constraint between arbitrary atoms.",
"kindStr": "type_section",
"name": "section_interaction",
"name": "section_constraint",
"superNames": [
"section_method",
"settings_interaction"
"section_constraints",
"settings_constraint"
]
},
{
"description": "Short and unique name for this interaction type. Valid names are described in the [interaction\\_kind wiki page](https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-meta-info/wikis/metainfo/interaction-kind).",
"description": "Short and unique name for this constraint type. Valid names are described in the [constraint\\_kind wiki page](https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-meta-info/wikis/metainfo/constraint-kind).",
"dtypeStr": "C",
"name": "interaction_kind",
"name": "constraint_kind",
"shape": [],
"superNames": [
"section_interaction"
"section_constraint"
]
},
{
"description": "Explicit interaction parameters for this kind of interaction (depending on the interaction_kind some might be given implicitly through other means).",
"description": "Explicit constraint parameters for this kind of constraint (depending on the constraint type, some might be given implicitly through other means).",
"dtypeStr": "D",
"name": "interaction_parameters",
"name": "constraint_parameters",
"shape": [],
"superNames": [
"section_interaction"
"section_constraint"
]
},
{
"description": "Reference to the topological group of atoms which is used to define contraint on it.",
"dtypeStr": "r",
"name": "interaction_to_topology_group_ref",
"name": "constraint_to_topology_group_ref",
"referencedSections": [
"section_topology"
"section_group"
],
"repeats": false,
"shape": [],
"superNames": [
"section_interaction"
"section_constraint"
]
},
{
"description": "List of the indexes involved in this interaction. The fist atom has index 1, the last atom index number_of_topology_atoms.",
"description": "List of the indexes involved in this constraint. The fist atom has index 1, the last number_of_topology_atoms.",
"dtypeStr": "i",
"name": "interaction_atoms",
"name": "constraint_atoms",
"shape": [
"number_of_interactions",
"number_of_atoms_per_interaction"
"number_of_constraints",
"number_of_atoms_per_constraint"
],
"superNames": [
"section_interaction"
"section_constraint"
]
},
{
"description": "Number of interactions of this type.",
"description": "Number of constraints of this type.",
"dtypeStr": "i",
"kindStr": "type_dimension",
"name": "number_of_interactions",
"name": "number_of_constraints",
"shape": [],
"superNames": [
"section_interaction"
"section_constraint"
]
},
{
"description": "Number of atoms involved in this interaction.",
"description": "Number of atoms involved in this constraint.",
"dtypeStr": "i",
"kindStr": "type_dimension",
"name": "number_of_atoms_per_interaction",
"name": "number_of_atoms_per_constraint",
"shape": [],
"superNames": [
"section_interaction"
"section_constraint"
]
}
]
......
......@@ -4806,31 +4806,43 @@
]
},
{
"description": "(deprecated) Reference to the method used for the calculation in section_single_configuration_calculation.",
"description": "(deprecated) Reference from each frame (a frame is one section_single_configuration_calculation) in this section_frame_sequence to the corresponding section_single_configuration_calculation. Each section_frame_sequence binds a collection of section_single_configuration_calculation, because they all belong to, e.g., a molecular dynamics trajectory, or geometry optimization. The full information for each frame is stored in section_single_configuration_calculation and this metadata establishes the link for each frame.",
"dtypeStr": "r",
"name": "single_configuration_to_calculation_method_ref",
"name": "frame_sequence_local_frames_ref",
"referencedSections": [
"section_method"
"section_single_configuration_calculation"
],
"shape": [