Commit 4e4a6f3a authored by Adam Fekete's avatar Adam Fekete Committed by Mohamed, Fawzi Roberto (fawzi)

typo, restructuring, new section_group

parent aa7261ee
......@@ -523,36 +523,6 @@
],
"units": "J"
},
{
"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": "interaction_atoms",
"shape": [
"number_of_interactions",
"number_of_atoms_per_interaction"
],
"superNames": [
"section_interaction"
]
},
{
"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": "interaction_kind",
"shape": [],
"superNames": [
"section_interaction"
]
},
{
"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": "interaction_parameters",
"shape": [],
"superNames": [
"section_interaction"
]
},
{
"description": "Reference to an atom-centered basis set defined in section_basis_set_atom_centered and to the atom kind as defined in section_method_atom_kind.",
"dtypeStr": "r",
......@@ -590,115 +560,6 @@
"section_method_basis_set"
]
},
{
"description": "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",
"shape": [
"number_of_molecule_constraints",
"number_of_atoms_per_molecule_constraint"
],
"superNames": [
"section_molecule_constraint"
]
},
{
"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": "molecule_constraint_kind",
"shape": [],
"superNames": [
"section_molecule_constraint"
]
},
{
"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": "molecule_constraint_parameters",
"shape": [],
"superNames": [
"section_molecule_constraint"
]
},
{
"description": "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": "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_interaction"
]
},
{
"description": "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_interaction"
]
},
{
"description": "Name of the molecule.",
"dtypeStr": "C",
"name": "molecule_type_name",
"shape": [],
"superNames": [
"section_molecule_type"
]
},
{
"description": "Number of atoms in this molecule.",
"dtypeStr": "i",
"kindStr": "type_dimension",
"name": "number_of_atoms_in_molecule",
"shape": [],
"superNames": [
"section_molecule_type"
]
},
{
"description": "Number of atoms involved in this interaction.",
"dtypeStr": "i",
"kindStr": "type_dimension",
"name": "number_of_atoms_per_interaction",
"shape": [],
"superNames": [
"section_interaction"
]
},
{
"description": "Number of atoms, in this molecule, involved in this constraint.",
"dtypeStr": "i",
"kindStr": "type_dimension",
"name": "number_of_atoms_per_molecule_constraint",
"shape": [],
"superNames": [
"section_molecule_constraint"
]
},
{
"description": "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": "String describing the use of the basis set, i.e, if it used for expanding a wavefunction or an electron density. Allowed values are listed in the [basis\\_set\\_kind wiki page](https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-meta-info/wikis/metainfo/basis-set-kind).",
"dtypeStr": "i",
......@@ -731,36 +592,6 @@
"section_excited_states"
]
},
{
"description": "Number of interactions of this type.",
"dtypeStr": "i",
"kindStr": "type_dimension",
"name": "number_of_interactions",
"shape": [],
"superNames": [
"section_interaction"
]
},
{
"description": "Number of constraints of this type.",
"dtypeStr": "i",
"kindStr": "type_dimension",
"name": "number_of_molecule_constraints",
"shape": [],
"superNames": [
"section_molecule_constraint"
]
},
{
"description": "Number of bonded interactions of this type.",
"dtypeStr": "i",
"kindStr": "type_dimension",
"name": "number_of_molecule_interactions",
"shape": [],
"superNames": [
"section_molecule_interaction"
]
},
{
"description": "number of soap coefficients",
"dtypeStr": "i",
......@@ -836,24 +667,6 @@
"section_method"
]
},
{
"description": "Section describing a constraint between atoms within a molecule.",
"kindStr": "type_section",
"name": "section_molecule_constraint",
"superNames": [
"section_molecule_type",
"settings_constraint"
]
},
{
"description": "Section describing a bonded interaction between atoms within a molecule.",
"kindStr": "type_section",
"name": "section_molecule_interaction",
"superNames": [
"section_molecule_type",
"settings_interaction"
]
},
{
"description": "Messages outputted by the program formatting the data in the current response",
"kindStr": "type_section",
......@@ -878,14 +691,6 @@
"section_system"
]
},
{
"description": "Parameters of an atom within a molecule.",
"kindStr": "type_abstract_document_content",
"name": "settings_atom_in_molecule",
"superNames": [
"section_molecule_type"
]
},
{
"description": "Some parameters that describe a constraint",
"kindStr": "type_abstract_document_content",
......@@ -1139,7 +944,6 @@
"section_excited_states"
]
},
//============================== deprecated ==================================
{
"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",
......@@ -1281,25 +1085,148 @@
"units": "C"
},
{
"description": "(deprecated) Reference to the topology and force fields to be used.",
"dtypeStr": "r",
"name": "method_to_topology_ref",
"referencedSections": [
"section_topology"
"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",
"shape": [
"number_of_molecule_constraints",
"number_of_atoms_per_molecule_constraint"
],
"superNames": [
"section_molecule_constraint"
]
},
{
"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_method"
"section_molecule_constraint"
]
},
//============================== unchanged ==================================
{
"description": "Section containing the definition of topology (connectivity among atoms in force fileds), force field, and constraints of a system.",
{
"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) 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) 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_interaction"
]
},
{
"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_interaction"
]
},
{
"description": "(deprecated) Name of the molecule.",
"dtypeStr": "C",
"name": "molecule_type_name",
"shape": [],
"superNames": [
"section_molecule_type"
]
},
{
"description": "(deprecated) Number of atoms in this molecule.",
"dtypeStr": "i",
"kindStr": "type_dimension",
"name": "number_of_atoms_in_molecule",
"shape": [],
"superNames": [
"section_molecule_type"
]
},
{
"description": "(deprecated) Number of atoms, in this molecule, involved in this constraint.",
"dtypeStr": "i",
"kindStr": "type_dimension",
"name": "number_of_atoms_per_molecule_constraint",
"shape": [],
"superNames": [
"section_molecule_constraint"
]
},
{
"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) Number of constraints of this type.",
"dtypeStr": "i",
"kindStr": "type_dimension",
"name": "number_of_molecule_constraints",
"shape": [],
"superNames": [
"section_molecule_constraint"
]
},
{
"description": "(deprecated) Number of bonded interactions of this type.",
"dtypeStr": "i",
"kindStr": "type_dimension",
"name": "number_of_molecule_interactions",
"shape": [],
"superNames": [
"section_molecule_interaction"
]
},
{
"description": "(deprecated) Section describing a constraint between atoms within a molecule.",
"kindStr": "type_section",
"name": "section_topology",
"name": "section_molecule_constraint",
"superNames": [
"section_run"
"section_molecule_type",
"settings_constraint"
]
},
{
"description": "(deprecated) Section describing a bonded interaction between atoms within a molecule.",
"kindStr": "type_section",
"name": "section_molecule_interaction",
"superNames": [
"section_molecule_type",
"settings_interaction"
]
},
{
"description": "(deprecated) Parameters of an atom within a molecule.",
"kindStr": "type_abstract_document_content",
"name": "settings_atom_in_molecule",
"superNames": [
"section_molecule_type"
]
},
{
......@@ -1312,10 +1239,20 @@
"section_topology"
]
},
//============================== new ==================================
{
"description": "Reference to the topology used for this system, constraints and force fields.",
"description": "Reference to the topology and force fields to be used.",
"dtypeStr": "r",
"name": "method_to_topology_ref",
"referencedSections": [
"section_topology"
],
"shape": [],
"superNames": [
"section_method"
]
},
{
"description": "Reference to the topology used for this system.",
"dtypeStr": "r",
"name": "single_configuration_calculation_to_topology_ref",
"referencedSections": [
......@@ -1328,9 +1265,9 @@
]
},
{
"description": "Section describing a constraint between arbitrary atoms.",
"description": "Section containing the definition of topology (connectivity among atoms) of a system.",
"kindStr": "type_section",
"name": "section_constraints",
"name": "section_topology",
"superNames": [
"section_run"
]
......@@ -1338,20 +1275,28 @@
{
"description": "Section describing an atom in the system.",
"kindStr": "type_section",
"name": "section_atoms",
"name": "section_atom",
"superNames": [
"section_topology"
]
},
{
"description": "Charge of the atom type.",
"dtypeStr": "f",
"name": "atom_charge",
"description": "Name (label) of the atom type.",
"dtypeStr": "C",
"name": "atom_name",
"shape": [],
"superNames": [
"section_atoms"
],
"units": "C"
"section_atom"
]
},
{
"description": "Atomic number Z of the atom.",
"dtypeStr": "i",
"name": "atom_number",
"shape": [],
"superNames": [
"section_atom"
]
},
{
"description": "Mass of the atom type.",
......@@ -1359,38 +1304,84 @@
"name": "atom_mass",
"shape": [],
"superNames": [
"section_atoms"
"section_atom"
],
"units": "kg"
},
{
"description": "Name (label) of the atom type.",
"dtypeStr": "C",
"name": "atom_name",
"description": "Charge of the atom type.",
"dtypeStr": "f",
"name": "atom_charge",
"shape": [],
"superNames": [
"section_atoms"
"section_atom"
],
"units": "C"
},
{
"description": "Section describing a group (pairs, angles, molecules, etc.) between arbitrary atoms.",
"kindStr": "type_section",
"name": "section_group",
"superNames": [
"section_topology"
]
},
{
"description": "Atomic number Z of the atom.",
"dtypeStr": "i",
"name": "atom_number",
"description": "Short and unique name for this group type. Valid names are described in the [group\\_kind wiki page](https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-meta-info/wikis/metainfo/group-kind).",
"dtypeStr": "C",
"name": "group_kind",
"shape": [],
"superNames": [
"section_atoms"
"section_group"
]
},
{
"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 group. The fist atom has index 1, the last number_of_topology_atoms.",
"dtypeStr": "i",
"name": "constraint_atoms",
"name": "group_atoms",
"shape": [
"number_of_constraints",
"number_of_atoms_per_constraint"
"number_of_groups",
"number_of_atoms_per_group"
],
"superNames": [
"section_constraint"
"section_group"
]
},
{
"description": "Number of groups of this type.",
"dtypeStr": "i",
"kindStr": "type_dimension",
"name": "number_of_groups",
"shape": [],
"superNames": [
"section_group"
]
},
{
"description": "Number of atoms involved in this group.",
"dtypeStr": "i",
"kindStr": "type_dimension",
"name": "number_of_atoms_per_group",
"shape": [],
"superNames": [
"section_group"
]
},
{
"description": "Section describing a constraint between arbitrary atoms.",
"kindStr": "type_section",
"name": "section_constraints",
"superNames": [
"section_run"
]
},
{
"description": "Section describing a constraint between arbitrary atoms.",
"kindStr": "type_section",
"name": "section_constraint",
"superNames": [
"section_constraints",
"settings_constraint"
]
},
{
......@@ -1411,6 +1402,31 @@
"section_constraint"
]
},
{
"description": "Reference to the topological group of atoms which is used to define contraint on it.",
"dtypeStr": "r",
"name": "constraint_to_topology_group_ref",
"referencedSections": [
"section_group"
],
"repeats": false,
"shape": [],
"superNames": [
"section_constraint"
]
},
{
"description": "List of the indexes involved in this constraint. The fist atom has index 1, the last number_of_topology_atoms.",
"dtypeStr": "i",
"name": "constraint_atoms",
"shape": [
"number_of_constraints",
"number_of_atoms_per_constraint"
],
"superNames": [
"section_constraint"
]
},
{
"description": "Number of constraints of this type.",
"dtypeStr": "i",
......@@ -1432,19 +1448,16 @@
]
},
{
"description": "Reference to the topological group of atoms.",
"dtypeStr": "r",
"name": "constraint_to_topology_group_ref",
"referencedSections": [
"section_groups"
],
"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_constraint"
"section_topology"
]
},
//============================== modified ==================================
{
"description": "Section containing the description of a bonded interaction between arbitrary atoms.",
"kindStr": "type_section",
......@@ -1455,16 +1468,67 @@
]
},
{
"description": "Section describing a constraint between arbitrary atoms.",
"kindStr": "type_section",
"name": "section_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).",
"dtypeStr": "C",
"name": "interaction_kind",
"shape": [],
"superNames": [
"section_constraints",
"settings_constraint"
"section_interaction"
]
},
{
"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": "interaction_parameters",
"shape": [],
"superNames": [
"section_interaction"
]
},
{
"description": "Reference to the topological group of atoms which is used to define contraint on it.",
"dtypeStr": "r",
"name": "interaction_to_topology_group_ref",
"referencedSections": [
"section_topology"
],
"repeats": false,
"shape": [],
"superNames": [
"section_interaction"
]
},
{
"description": "List of the indexes involved in this interaction. The fist atom has index 1, the last atom index number_of_topology_atoms.",