diff --git a/gui/tests/artifacts.js b/gui/tests/artifacts.js
index 83df419015bfab8f955c850772f3932f871127c6..a1fc76d9073d9af9d30d7a54e1d3a7d8b51716c3 100644
--- a/gui/tests/artifacts.js
+++ b/gui/tests/artifacts.js
@@ -13320,7 +13320,7 @@ window.nomadArtifacts = {
"m_parent_index": 0,
"m_parent_sub_section": "sub_sections",
"name": "species",
- "sub_section": "/packages/21/section_definitions/0",
+ "sub_section": "/packages/20/section_definitions/0",
"repeats": true
},
{
@@ -16919,7 +16919,7 @@ window.nomadArtifacts = {
"description": "Specific heat capacity values at constant volume.",
"type": {
"type_kind": "quantity_reference",
- "type_data": "/packages/19/section_definitions/15/quantities/5"
+ "type_data": "/packages/18/section_definitions/15/quantities/5"
},
"shape": []
},
@@ -16931,7 +16931,7 @@ window.nomadArtifacts = {
"description": "The temperatures at which heat capacities are calculated.",
"type": {
"type_kind": "quantity_reference",
- "type_data": "/packages/19/section_definitions/15/quantities/1"
+ "type_data": "/packages/18/section_definitions/15/quantities/1"
}
}
]
@@ -16951,7 +16951,7 @@ window.nomadArtifacts = {
"description": "The Helmholtz free energies per atom at constant volume.",
"type": {
"type_kind": "quantity_reference",
- "type_data": "/packages/19/section_definitions/15/quantities/7"
+ "type_data": "/packages/18/section_definitions/15/quantities/7"
},
"shape": []
},
@@ -16963,7 +16963,7 @@ window.nomadArtifacts = {
"description": "The temperatures at which Helmholtz free energies are calculated.",
"type": {
"type_kind": "quantity_reference",
- "type_data": "/packages/19/section_definitions/15/quantities/1"
+ "type_data": "/packages/18/section_definitions/15/quantities/1"
}
}
]
@@ -17050,7 +17050,7 @@ window.nomadArtifacts = {
"name": "volumes",
"type": {
"type_kind": "quantity_reference",
- "type_data": "/packages/19/section_definitions/7/quantities/1"
+ "type_data": "/packages/18/section_definitions/7/quantities/1"
}
},
{
@@ -17060,7 +17060,7 @@ window.nomadArtifacts = {
"name": "energies_raw",
"type": {
"type_kind": "quantity_reference",
- "type_data": "/packages/19/section_definitions/7/quantities/2"
+ "type_data": "/packages/18/section_definitions/7/quantities/2"
}
},
{
@@ -17070,7 +17070,7 @@ window.nomadArtifacts = {
"name": "energies_fit",
"type": {
"type_kind": "quantity_reference",
- "type_data": "/packages/19/section_definitions/6/quantities/1"
+ "type_data": "/packages/18/section_definitions/6/quantities/1"
}
}
]
@@ -17207,7 +17207,7 @@ window.nomadArtifacts = {
"description": "List of energy_total values gathered from the single configuration\ncalculations that are a part of the optimization trajectory.",
"type": {
"type_kind": "quantity_reference",
- "type_data": "/packages/19/section_definitions/9/quantities/10"
+ "type_data": "/packages/18/section_definitions/9/quantities/10"
}
},
{
@@ -59804,7 +59804,7 @@ window.nomadArtifacts = {
"name": "nomad_data_schema",
"type": {
"type_kind": "reference",
- "type_data": "/packages/22/section_definitions/3"
+ "type_data": "/packages/21/section_definitions/3"
}
}
],
@@ -61636,7 +61636,7 @@ window.nomadArtifacts = {
},
"name": "optimade",
"description": "Metadata used for the optimade API.",
- "sub_section": "/packages/21/section_definitions/1"
+ "sub_section": "/packages/20/section_definitions/1"
},
{
"m_def": "nomad.metainfo.metainfo.SubSection",
@@ -61748,7 +61748,7 @@ window.nomadArtifacts = {
"categories": [
"/packages/17/category_definitions/0"
],
- "sub_section": "/packages/19/section_definitions/34",
+ "sub_section": "/packages/18/section_definitions/34",
"repeats": true
},
{
@@ -61756,7 +61756,7 @@ window.nomadArtifacts = {
"m_parent_index": 4,
"m_parent_sub_section": "sub_sections",
"name": "workflow2",
- "sub_section": "/packages/20/section_definitions/3"
+ "sub_section": "/packages/19/section_definitions/3"
},
{
"m_def": "nomad.metainfo.metainfo.SubSection",
@@ -61801,7 +61801,7 @@ window.nomadArtifacts = {
"m_parent_index": 8,
"m_parent_sub_section": "sub_sections",
"name": "definitions",
- "sub_section": "/packages/22/section_definitions/4"
+ "sub_section": "/packages/21/section_definitions/4"
}
]
}
@@ -63390,214 +63390,181 @@ window.nomadArtifacts = {
"m_def": "nomad.metainfo.metainfo.Package",
"m_parent_index": 18,
"m_parent_sub_section": "packages",
- "name": "nomad.datamodel.metainfo.simulation.workflow",
+ "name": "nomad.datamodel.metainfo.workflow",
"section_definitions": [
{
"m_def": "nomad.metainfo.metainfo.Section",
"m_parent_index": 0,
"m_parent_sub_section": "section_definitions",
- "name": "SimulationWorkflowMethod",
- "base_sections": [
- "/packages/15/section_definitions/0"
- ]
- },
- {
- "m_def": "nomad.metainfo.metainfo.Section",
- "m_parent_index": 1,
- "m_parent_sub_section": "section_definitions",
- "name": "SimulationWorkflowResults",
- "base_sections": [
- "/packages/15/section_definitions/0"
- ],
+ "name": "Interface",
+ "description": "Section containing results of an interface (stacking fault, gamma surface, etc.) workflow.",
"quantities": [
{
"m_def": "nomad.metainfo.metainfo.Quantity",
"m_parent_index": 0,
"m_parent_sub_section": "quantities",
- "name": "calculation_result_ref",
- "description": "Reference to calculation result. In the case of serial workflows, this corresponds\nto the final step in the simulation. For the parallel case, it refers to the original system.",
- "categories": [
- "/packages/17/category_definitions/0"
- ],
+ "name": "energy_extrinsic_stacking_fault",
+ "description": "Value of the relaxed extrinsic stacking fault energy per unit area.",
"type": {
- "type_kind": "reference",
- "type_data": "/packages/2/section_definitions/36"
+ "type_kind": "numpy",
+ "type_data": "float64"
},
- "shape": []
- }
- ]
- },
- {
- "m_def": "nomad.metainfo.metainfo.Section",
- "m_parent_index": 2,
- "m_parent_sub_section": "section_definitions",
- "name": "SimulationWorkflow",
- "base_sections": [
- "/packages/20/section_definitions/3"
- ],
- "sub_sections": [
- {
- "m_def": "nomad.metainfo.metainfo.SubSection",
- "m_parent_index": 0,
- "m_parent_sub_section": "sub_sections",
- "name": "method",
- "sub_section": "/packages/18/section_definitions/0"
+ "shape": [],
+ "unit": "joule / meter ** 2"
},
- {
- "m_def": "nomad.metainfo.metainfo.SubSection",
- "m_parent_index": 1,
- "m_parent_sub_section": "sub_sections",
- "name": "results",
- "sub_section": "/packages/18/section_definitions/1"
- }
- ]
- },
- {
- "m_def": "nomad.metainfo.metainfo.Section",
- "m_parent_index": 3,
- "m_parent_sub_section": "section_definitions",
- "name": "Decomposition",
- "description": "Section containing information about the system to which an unstable compound will decompose to.",
- "quantities": [
{
"m_def": "nomad.metainfo.metainfo.Quantity",
- "m_parent_index": 0,
+ "m_parent_index": 1,
"m_parent_sub_section": "quantities",
- "name": "fraction",
- "description": "Amount of the resulting system.",
+ "name": "energy_intrinsic_stacking_fault",
+ "description": "Value of the relaxed intrinsic stacking fault energy per unit area.",
"type": {
"type_kind": "numpy",
"type_data": "float64"
},
- "shape": []
+ "shape": [],
+ "unit": "joule / meter ** 2"
},
{
"m_def": "nomad.metainfo.metainfo.Quantity",
- "m_parent_index": 1,
+ "m_parent_index": 2,
"m_parent_sub_section": "quantities",
- "name": "system_ref",
- "description": "Reference to the resulting system.",
+ "name": "dimensionality",
+ "description": "Dimensionality of the property, i.e. 1 for stacking fault energy and 2 for gamma\nsurface.",
"type": {
- "type_kind": "reference",
- "type_data": "/packages/1/section_definitions/6"
+ "type_kind": "numpy",
+ "type_data": "int32"
},
"shape": []
},
{
"m_def": "nomad.metainfo.metainfo.Quantity",
- "m_parent_index": 2,
+ "m_parent_index": 3,
"m_parent_sub_section": "quantities",
- "name": "formula",
- "description": "Chemical formula of the resulting system.",
+ "name": "shift_direction",
+ "description": "shift direction of the two crystal parts to calculate the fault energy.",
"type": {
"type_kind": "python",
"type_data": "str"
},
- "shape": []
- }
- ]
- },
- {
- "m_def": "nomad.metainfo.metainfo.Section",
- "m_parent_index": 4,
- "m_parent_sub_section": "section_definitions",
- "name": "Stability",
- "description": "Section containing information regarding the stability of the system.",
- "quantities": [
+ "shape": [
+ "dimensionality"
+ ]
+ },
{
"m_def": "nomad.metainfo.metainfo.Quantity",
- "m_parent_index": 0,
+ "m_parent_index": 4,
"m_parent_sub_section": "quantities",
- "name": "n_references",
- "description": "Number of reference systems.",
+ "name": "n_displacements",
+ "description": "Number of displacements in the shift to calculate the fault energy.",
"type": {
- "type_kind": "python",
- "type_data": "int"
+ "type_kind": "numpy",
+ "type_data": "int32"
},
"shape": []
},
{
"m_def": "nomad.metainfo.metainfo.Quantity",
- "m_parent_index": 1,
+ "m_parent_index": 5,
"m_parent_sub_section": "quantities",
- "name": "systems_ref",
- "description": "References to the reference systems.",
+ "name": "displacement_fraction",
+ "description": "Relative displacements of the two crystal parts along the direction indicated by\nshift_direction.",
"type": {
- "type_kind": "reference",
- "type_data": "/packages/1/section_definitions/6"
+ "type_kind": "numpy",
+ "type_data": "float64"
},
"shape": [
- "n_references"
+ "dimensionality",
+ "n_displacements"
]
},
{
"m_def": "nomad.metainfo.metainfo.Quantity",
- "m_parent_index": 2,
+ "m_parent_index": 6,
"m_parent_sub_section": "quantities",
- "name": "formation_energy",
- "description": "Calculated value of the formation energy of the compound.",
+ "name": "energy_fault_plane",
+ "description": "Value of the relaxed excess energy per unit area for each displacement.",
"type": {
"type_kind": "numpy",
"type_data": "float64"
},
- "shape": [],
- "unit": "joule"
+ "shape": [
+ "n_displacements"
+ ],
+ "unit": "joule / meter ** 2"
},
{
"m_def": "nomad.metainfo.metainfo.Quantity",
- "m_parent_index": 3,
+ "m_parent_index": 7,
"m_parent_sub_section": "quantities",
- "name": "delta_formation_energy",
- "description": "Energy with respect to the convex hull.",
+ "name": "gamma_surface",
+ "description": "Value of the gamma surface, i.e. the excess energy per unit area calculated for\neach displacement.",
"type": {
"type_kind": "numpy",
"type_data": "float64"
},
- "shape": [],
- "unit": "joule"
+ "shape": [
+ "n_displacements",
+ "n_displacements"
+ ],
+ "unit": "joule / meter ** 2"
},
{
"m_def": "nomad.metainfo.metainfo.Quantity",
- "m_parent_index": 4,
+ "m_parent_index": 8,
"m_parent_sub_section": "quantities",
- "name": "is_stable",
- "description": "Indicates if a compound is stable.",
+ "name": "slip_fraction",
+ "description": "Relative displacement between two crystal parts where the energy is maximum.",
"type": {
- "type_kind": "python",
- "type_data": "bool"
+ "type_kind": "numpy",
+ "type_data": "float64"
},
"shape": []
- }
- ],
- "sub_sections": [
+ },
{
- "m_def": "nomad.metainfo.metainfo.SubSection",
- "m_parent_index": 0,
- "m_parent_sub_section": "sub_sections",
- "name": "decomposition",
- "sub_section": "/packages/18/section_definitions/3",
- "repeats": true
+ "m_def": "nomad.metainfo.metainfo.Quantity",
+ "m_parent_index": 9,
+ "m_parent_sub_section": "quantities",
+ "name": "energy_unstable_stacking_fault",
+ "description": "Value of the relaxed unstable stacking fault energy per unit area.",
+ "type": {
+ "type_kind": "numpy",
+ "type_data": "float64"
+ },
+ "shape": [],
+ "unit": "joule / meter ** 2"
+ },
+ {
+ "m_def": "nomad.metainfo.metainfo.Quantity",
+ "m_parent_index": 10,
+ "m_parent_sub_section": "quantities",
+ "name": "energy_unstable_twinning_fault",
+ "description": "Value of the relaxed unstable twinning energy per unit area.",
+ "type": {
+ "type_kind": "numpy",
+ "type_data": "float64"
+ },
+ "shape": [],
+ "unit": "joule / meter ** 2"
}
]
},
{
"m_def": "nomad.metainfo.metainfo.Section",
- "m_parent_index": 5,
+ "m_parent_index": 1,
"m_parent_sub_section": "section_definitions",
- "name": "ThermodynamicsResults",
- "base_sections": [
- "/packages/18/section_definitions/1"
- ],
+ "name": "Raman",
+ "description": "Section containing results of a Raman workflow.",
"quantities": [
{
"m_def": "nomad.metainfo.metainfo.Quantity",
"m_parent_index": 0,
"m_parent_sub_section": "quantities",
- "name": "n_values",
- "description": "Number of thermodynamics property evaluations.",
+ "name": "n_modes",
+ "description": "Number of evaluated vibrational modes.",
"type": {
- "type_kind": "python",
- "type_data": "int"
+ "type_kind": "numpy",
+ "type_data": "int32"
},
"shape": []
},
@@ -63605,44 +63572,88 @@ window.nomadArtifacts = {
"m_def": "nomad.metainfo.metainfo.Quantity",
"m_parent_index": 1,
"m_parent_sub_section": "quantities",
- "name": "temperature",
- "description": "Specifies the temperatures at which properties such as the Helmholtz free energy\nare calculated.",
+ "name": "n_atoms",
+ "description": "Number of atoms in the simulation cell.",
"type": {
"type_kind": "numpy",
- "type_data": "float64"
+ "type_data": "int32"
},
- "shape": [
- "n_values"
- ],
- "unit": "kelvin"
+ "shape": []
},
{
"m_def": "nomad.metainfo.metainfo.Quantity",
"m_parent_index": 2,
"m_parent_sub_section": "quantities",
- "name": "pressure",
- "description": "Array containing the values of the pressure (one third of the trace of the stress\ntensor) corresponding to each property evaluation.",
+ "name": "frequencies",
+ "description": "Calculated value of the Raman frequencies.",
"type": {
"type_kind": "numpy",
"type_data": "float64"
},
"shape": [
- "n_values"
+ "n_modes"
],
- "unit": "pascal"
+ "unit": "1 / meter"
+ }
+ ]
+ },
+ {
+ "m_def": "nomad.metainfo.metainfo.Section",
+ "m_parent_index": 2,
+ "m_parent_sub_section": "section_definitions",
+ "name": "MagneticOrdering",
+ "description": "Section containing results of a magnetic ordering workflow.",
+ "quantities": [
+ {
+ "m_def": "nomad.metainfo.metainfo.Quantity",
+ "m_parent_index": 0,
+ "m_parent_sub_section": "quantities",
+ "name": "n_structures",
+ "description": "Number of magnetic structures evaluated.",
+ "type": {
+ "type_kind": "numpy",
+ "type_data": "int32"
+ },
+ "shape": []
+ },
+ {
+ "m_def": "nomad.metainfo.metainfo.Quantity",
+ "m_parent_index": 1,
+ "m_parent_sub_section": "quantities",
+ "name": "n_atoms",
+ "description": "Number of atoms in the simulation cell.",
+ "type": {
+ "type_kind": "numpy",
+ "type_data": "int32"
+ },
+ "shape": []
+ },
+ {
+ "m_def": "nomad.metainfo.metainfo.Quantity",
+ "m_parent_index": 2,
+ "m_parent_sub_section": "quantities",
+ "name": "labels",
+ "description": "Labels corresponding to each magnetic structure.",
+ "type": {
+ "type_kind": "python",
+ "type_data": "str"
+ },
+ "shape": [
+ "n_structures"
+ ]
},
{
"m_def": "nomad.metainfo.metainfo.Quantity",
"m_parent_index": 3,
"m_parent_sub_section": "quantities",
- "name": "helmholtz_free_energy",
- "description": "Helmholtz free energy per unit cell at constant volume.",
+ "name": "energies",
+ "description": "Calculated value of the energies corresponding to each magnetic structure.",
"type": {
"type_kind": "numpy",
"type_data": "float64"
},
"shape": [
- "n_values"
+ "n_structures"
],
"unit": "joule"
},
@@ -63650,216 +63661,231 @@ window.nomadArtifacts = {
"m_def": "nomad.metainfo.metainfo.Quantity",
"m_parent_index": 4,
"m_parent_sub_section": "quantities",
- "name": "heat_capacity_c_p",
- "description": "Heat capacity per cell unit at constant pressure.",
+ "name": "magnetic_moments",
+ "description": "Resulting atomic magnetic moments corresponding to each magnetic structure.",
"type": {
"type_kind": "numpy",
"type_data": "float64"
},
"shape": [
- "n_values"
+ "n_structures",
+ "n_atoms"
],
- "unit": "joule / kelvin"
+ "unit": "bohr_magneton"
},
{
"m_def": "nomad.metainfo.metainfo.Quantity",
"m_parent_index": 5,
"m_parent_sub_section": "quantities",
- "name": "heat_capacity_c_v",
- "description": "Heat capacity per cell unit at constant volume.",
+ "name": "magnetic_deformations",
+ "description": "Average atomic displacements after relaxation with respect to the non-magnetic\ncase for each magnetic structure.",
"type": {
"type_kind": "numpy",
"type_data": "float64"
},
"shape": [
- "n_values"
+ "n_structures"
],
- "unit": "joule / kelvin"
- },
+ "unit": "meter"
+ }
+ ]
+ },
+ {
+ "m_def": "nomad.metainfo.metainfo.Section",
+ "m_parent_index": 3,
+ "m_parent_sub_section": "section_definitions",
+ "name": "Adsorption",
+ "description": "Section containing results of a surface adsorption workflow.",
+ "quantities": [
{
"m_def": "nomad.metainfo.metainfo.Quantity",
- "m_parent_index": 6,
+ "m_parent_index": 0,
"m_parent_sub_section": "quantities",
- "name": "heat_capacity_c_v_specific",
- "description": "Specific heat capacity at constant volume.",
+ "name": "n_sites",
+ "description": "Number of sites for which the adsorption energy is evaluated.",
"type": {
"type_kind": "numpy",
- "type_data": "float64"
+ "type_data": "int32"
},
- "shape": [
- "n_values"
- ],
- "unit": "joule / kelvin / kilogram",
- "cached": true,
- "virtual": true
+ "shape": []
},
{
"m_def": "nomad.metainfo.metainfo.Quantity",
- "m_parent_index": 7,
+ "m_parent_index": 1,
"m_parent_sub_section": "quantities",
- "name": "vibrational_free_energy_at_constant_volume",
- "description": "Holds the vibrational free energy per cell unit at constant volume.",
+ "name": "slab_miller_index",
+ "description": "Miller index of the slab.",
"type": {
"type_kind": "numpy",
- "type_data": "float64"
+ "type_data": "int32"
},
"shape": [
- "n_values"
- ],
- "unit": "joule"
+ 3
+ ]
},
{
"m_def": "nomad.metainfo.metainfo.Quantity",
- "m_parent_index": 8,
+ "m_parent_index": 2,
"m_parent_sub_section": "quantities",
- "name": "vibrational_free_energy_at_constant_volume_specific",
- "description": "Stores the specific vibrational free energy at constant volume.",
+ "name": "slab",
+ "description": "Chemical formula of the slab.",
"type": {
- "type_kind": "numpy",
- "type_data": "float64"
+ "type_kind": "python",
+ "type_data": "str"
},
- "shape": [
- "n_values"
- ],
- "unit": "joule / kilogram",
- "cached": true,
- "virtual": true
+ "shape": []
},
{
"m_def": "nomad.metainfo.metainfo.Quantity",
- "m_parent_index": 9,
+ "m_parent_index": 3,
"m_parent_sub_section": "quantities",
- "name": "vibrational_free_energy",
- "description": "Calculated value of the vibrational free energy, F_vib.",
+ "name": "adsorbate",
+ "description": "Chemical formula of the adsorbate molecule.",
+ "type": {
+ "type_kind": "python",
+ "type_data": "str"
+ },
+ "shape": []
+ },
+ {
+ "m_def": "nomad.metainfo.metainfo.Quantity",
+ "m_parent_index": 4,
+ "m_parent_sub_section": "quantities",
+ "name": "adsorption_sites",
+ "description": "Coordinates of the adsorption sites corresponding to a minimum energy.",
"type": {
"type_kind": "numpy",
"type_data": "float64"
},
"shape": [
- "n_values"
- ],
- "unit": "joule"
+ "n_sites"
+ ]
},
{
"m_def": "nomad.metainfo.metainfo.Quantity",
- "m_parent_index": 10,
+ "m_parent_index": 5,
"m_parent_sub_section": "quantities",
- "name": "vibrational_internal_energy",
- "description": "Calculated value of the vibrational internal energy, U_vib.",
+ "name": "adsorption_energies",
+ "description": "Calculated value of the adsorption energy corresponding to each site.",
"type": {
"type_kind": "numpy",
"type_data": "float64"
},
"shape": [
- "n_values"
+ "n_sites"
],
"unit": "joule"
+ }
+ ]
+ },
+ {
+ "m_def": "nomad.metainfo.metainfo.Section",
+ "m_parent_index": 4,
+ "m_parent_sub_section": "section_definitions",
+ "name": "ConvexHull",
+ "description": "Section containing results of a convex hull workflow.",
+ "quantities": [
+ {
+ "m_def": "nomad.metainfo.metainfo.Quantity",
+ "m_parent_index": 0,
+ "m_parent_sub_section": "quantities",
+ "name": "n_elements",
+ "description": "Number of elements for which the thermal stability is evaluated. This represents\nthe dimensionality of the convex hull.",
+ "type": {
+ "type_kind": "numpy",
+ "type_data": "int32"
+ },
+ "shape": []
},
{
"m_def": "nomad.metainfo.metainfo.Quantity",
- "m_parent_index": 11,
+ "m_parent_index": 1,
"m_parent_sub_section": "quantities",
- "name": "vibrational_entropy",
- "description": "Calculated value of the vibrational entropy, S.",
+ "name": "n_points",
+ "description": "Number of points for which the energies are evaluated.",
"type": {
"type_kind": "numpy",
- "type_data": "float64"
+ "type_data": "int32"
},
- "shape": [
- "n_values"
- ],
- "unit": "joule / kelvin"
+ "shape": []
},
{
"m_def": "nomad.metainfo.metainfo.Quantity",
- "m_parent_index": 12,
+ "m_parent_index": 2,
"m_parent_sub_section": "quantities",
- "name": "gibbs_free_energy",
- "description": "Calculated value of the Gibbs free energy, G.",
+ "name": "compositions",
+ "description": "Normalized composition of the elements corresponding to each point for which the\nenergies are evaluated.",
"type": {
"type_kind": "numpy",
"type_data": "float64"
},
"shape": [
- "n_values"
- ],
- "unit": "joule"
+ "n_points",
+ "n_elements"
+ ]
},
{
"m_def": "nomad.metainfo.metainfo.Quantity",
- "m_parent_index": 13,
+ "m_parent_index": 3,
"m_parent_sub_section": "quantities",
- "name": "entropy",
- "description": "Calculated value of the entropy.",
+ "name": "references",
+ "description": "Specifies the reference structure for each element.",
"type": {
- "type_kind": "numpy",
- "type_data": "float64"
+ "type_kind": "python",
+ "type_data": "str"
},
"shape": [
- "n_values"
- ],
- "unit": "joule / kelvin"
+ "n_elements"
+ ]
},
{
"m_def": "nomad.metainfo.metainfo.Quantity",
- "m_parent_index": 14,
+ "m_parent_index": 4,
"m_parent_sub_section": "quantities",
- "name": "enthalpy",
- "description": "Calculated value of enthalpy.",
+ "name": "energy_of_formation",
+ "description": "Values of the heat of formation corresponding to each point.",
"type": {
"type_kind": "numpy",
"type_data": "float64"
},
"shape": [
- "n_values"
+ "n_points"
],
"unit": "joule"
},
{
"m_def": "nomad.metainfo.metainfo.Quantity",
- "m_parent_index": 15,
+ "m_parent_index": 5,
"m_parent_sub_section": "quantities",
- "name": "internal_energy",
- "description": "Calculated value of the internal energy, U.",
+ "name": "energy_hulll",
+ "description": "Values of the energy above the convex hull corresponding to each point.",
"type": {
"type_kind": "numpy",
"type_data": "float64"
},
"shape": [
- "n_values"
+ "n_points"
],
"unit": "joule"
}
- ],
- "sub_sections": [
- {
- "m_def": "nomad.metainfo.metainfo.SubSection",
- "m_parent_index": 0,
- "m_parent_sub_section": "sub_sections",
- "name": "stability",
- "sub_section": "/packages/18/section_definitions/4",
- "repeats": false
- }
]
},
{
"m_def": "nomad.metainfo.metainfo.Section",
- "m_parent_index": 6,
+ "m_parent_index": 5,
"m_parent_sub_section": "section_definitions",
- "name": "SinglePointResults",
- "base_sections": [
- "/packages/18/section_definitions/1"
- ],
+ "name": "NudgedElasticBand",
+ "description": "Section containing results of a nudged-elastic band workflow.",
"quantities": [
{
"m_def": "nomad.metainfo.metainfo.Quantity",
"m_parent_index": 0,
"m_parent_sub_section": "quantities",
- "name": "n_scf_steps",
- "description": "Number of self-consistent steps in the calculation.",
+ "name": "method",
+ "description": "Specifies the method used in calculating the minumum energy path. Can be one of\nstandard, improved_tangeant, full_spring_force, spline_interpolation, string.",
"type": {
"type_kind": "python",
- "type_data": "int"
+ "type_data": "str"
},
"shape": []
},
@@ -63867,21 +63893,20 @@ window.nomadArtifacts = {
"m_def": "nomad.metainfo.metainfo.Quantity",
"m_parent_index": 1,
"m_parent_sub_section": "quantities",
- "name": "final_scf_energy_difference",
- "description": "The difference in the energy between the last two scf steps.",
+ "name": "climbing_image",
+ "description": "Indicates if climbing image is used.",
"type": {
- "type_kind": "numpy",
- "type_data": "float64"
+ "type_kind": "python",
+ "type_data": "bool"
},
- "shape": [],
- "unit": "joule"
+ "shape": []
},
{
"m_def": "nomad.metainfo.metainfo.Quantity",
"m_parent_index": 2,
"m_parent_sub_section": "quantities",
- "name": "is_converged",
- "description": "Indicates if the convergence criteria were fullfilled.",
+ "name": "solid_state",
+ "description": "Indicates if solid state nudged-elastic band calculation is performed.",
"type": {
"type_kind": "python",
"type_data": "bool"
@@ -63892,11 +63917,11 @@ window.nomadArtifacts = {
"m_def": "nomad.metainfo.metainfo.Quantity",
"m_parent_index": 3,
"m_parent_sub_section": "quantities",
- "name": "n_data",
- "description": "",
+ "name": "optimizer",
+ "description": "Specifies the method used in energy minimization.",
"type": {
- "type_kind": "numpy",
- "type_data": "int32"
+ "type_kind": "python",
+ "type_data": "str"
},
"shape": []
},
@@ -63904,3339 +63929,20 @@ window.nomadArtifacts = {
"m_def": "nomad.metainfo.metainfo.Quantity",
"m_parent_index": 4,
"m_parent_sub_section": "quantities",
- "name": "dos",
- "description": "Reference to the electronic density of states data.",
+ "name": "n_images",
+ "description": "Number of images used in the calculation.",
"type": {
- "type_kind": "reference",
- "type_data": "/packages/2/section_definitions/17"
+ "type_kind": "numpy",
+ "type_data": "int32"
},
- "shape": [
- "n_data"
- ]
+ "shape": []
},
{
"m_def": "nomad.metainfo.metainfo.Quantity",
"m_parent_index": 5,
"m_parent_sub_section": "quantities",
- "name": "band_structure",
- "description": "Reference to the electronic band structure data.",
- "type": {
- "type_kind": "reference",
- "type_data": "/packages/2/section_definitions/14"
- },
- "shape": [
- "n_data"
- ]
- },
- {
- "m_def": "nomad.metainfo.metainfo.Quantity",
- "m_parent_index": 6,
- "m_parent_sub_section": "quantities",
- "name": "eigenvalues",
- "description": "Reference to the eigenvalues.",
- "type": {
- "type_kind": "reference",
- "type_data": "/packages/2/section_definitions/13"
- },
- "shape": [
- "n_data"
- ]
- },
- {
- "m_def": "nomad.metainfo.metainfo.Quantity",
- "m_parent_index": 7,
- "m_parent_sub_section": "quantities",
- "name": "potential",
- "description": "Reference to the potential data.",
- "type": {
- "type_kind": "reference",
- "type_data": "/packages/2/section_definitions/26"
- },
- "shape": [
- "n_data"
- ]
- },
- {
- "m_def": "nomad.metainfo.metainfo.Quantity",
- "m_parent_index": 8,
- "m_parent_sub_section": "quantities",
- "name": "density_charge",
- "description": "Reference to the charge density data.",
- "type": {
- "type_kind": "reference",
- "type_data": "/packages/2/section_definitions/27"
- },
- "shape": [
- "n_data"
- ]
- },
- {
- "m_def": "nomad.metainfo.metainfo.Quantity",
- "m_parent_index": 9,
- "m_parent_sub_section": "quantities",
- "name": "spectra",
- "description": "Reference to the spectral data.",
- "type": {
- "type_kind": "reference",
- "type_data": "/packages/2/section_definitions/28"
- },
- "shape": [
- "n_data"
- ]
- }
- ]
- },
- {
- "m_def": "nomad.metainfo.metainfo.Section",
- "m_parent_index": 7,
- "m_parent_sub_section": "section_definitions",
- "name": "SinglePointMethod",
- "base_sections": [
- "/packages/18/section_definitions/0"
- ],
- "quantities": [
- {
- "m_def": "nomad.metainfo.metainfo.Quantity",
- "m_parent_index": 0,
- "m_parent_sub_section": "quantities",
- "name": "method",
- "description": "Calculation method used.",
- "type": {
- "type_kind": "python",
- "type_data": "str"
- },
- "shape": []
- }
- ]
- },
- {
- "m_def": "nomad.metainfo.metainfo.Section",
- "m_parent_index": 8,
- "m_parent_sub_section": "section_definitions",
- "name": "SinglePoint",
- "base_sections": [
- "/packages/18/section_definitions/2"
- ],
- "sub_sections": [
- {
- "m_def": "nomad.metainfo.metainfo.SubSection",
- "m_parent_index": 0,
- "m_parent_sub_section": "sub_sections",
- "name": "method",
- "sub_section": "/packages/18/section_definitions/7"
- },
- {
- "m_def": "nomad.metainfo.metainfo.SubSection",
- "m_parent_index": 1,
- "m_parent_sub_section": "sub_sections",
- "name": "results",
- "sub_section": "/packages/18/section_definitions/6"
- }
- ]
- },
- {
- "m_def": "nomad.metainfo.metainfo.Section",
- "m_parent_index": 9,
- "m_parent_sub_section": "section_definitions",
- "name": "ParallelSimulation",
- "base_sections": [
- "/packages/18/section_definitions/2"
- ]
- },
- {
- "m_def": "nomad.metainfo.metainfo.Section",
- "m_parent_index": 10,
- "m_parent_sub_section": "section_definitions",
- "name": "SerialSimulation",
- "base_sections": [
- "/packages/18/section_definitions/2"
- ]
- },
- {
- "m_def": "nomad.metainfo.metainfo.Section",
- "m_parent_index": 11,
- "m_parent_sub_section": "section_definitions",
- "name": "GeometryOptimizationMethod",
- "base_sections": [
- "/packages/18/section_definitions/0"
- ],
- "quantities": [
- {
- "m_def": "nomad.metainfo.metainfo.Quantity",
- "m_parent_index": 0,
- "m_parent_sub_section": "quantities",
- "name": "type",
- "description": "The type of geometry optimization, which denotes what is being optimized.\n\nAllowed values are:\n\n| Type | Description |\n\n| ---------------------- | ----------------------------------------- |\n\n| `\"static\"` | no optimization |\n\n| `\"atomic\"` | the atomic coordinates alone are updated |\n\n| `\"cell_volume\"` | `\"atomic\"` + cell lattice paramters are updated isotropically |\n\n| `\"cell_shape\"` | `\"cell_volume\"` but without the isotropic constraint: all cell parameters are updated |",
- "type": {
- "type_kind": "Enum",
- "type_data": [
- "static",
- "atomic",
- "cell_shape",
- "cell_volume"
- ]
- },
- "shape": []
- },
- {
- "m_def": "nomad.metainfo.metainfo.Quantity",
- "m_parent_index": 1,
- "m_parent_sub_section": "quantities",
- "name": "method",
- "description": "The method used for geometry optimization. Some known possible values are:\n`\"steepest_descent\"`, `\"conjugant_gradient\"`, `\"low_memory_broyden_fletcher_goldfarb_shanno\"`.",
- "type": {
- "type_kind": "python",
- "type_data": "str"
- },
- "shape": []
- },
- {
- "m_def": "nomad.metainfo.metainfo.Quantity",
- "m_parent_index": 2,
- "m_parent_sub_section": "quantities",
- "name": "convergence_tolerance_energy_difference",
- "description": "The input energy difference tolerance criterion.",
- "type": {
- "type_kind": "numpy",
- "type_data": "float64"
- },
- "shape": [],
- "unit": "joule"
- },
- {
- "m_def": "nomad.metainfo.metainfo.Quantity",
- "m_parent_index": 3,
- "m_parent_sub_section": "quantities",
- "name": "convergence_tolerance_force_maximum",
- "description": "The input maximum net force tolerance criterion.",
- "type": {
- "type_kind": "numpy",
- "type_data": "float64"
- },
- "shape": [],
- "unit": "newton"
- },
- {
- "m_def": "nomad.metainfo.metainfo.Quantity",
- "m_parent_index": 4,
- "m_parent_sub_section": "quantities",
- "name": "convergence_tolerance_stress_maximum",
- "description": "The input maximum stress tolerance criterion.",
- "type": {
- "type_kind": "numpy",
- "type_data": "float64"
- },
- "shape": [],
- "unit": "pascal"
- },
- {
- "m_def": "nomad.metainfo.metainfo.Quantity",
- "m_parent_index": 5,
- "m_parent_sub_section": "quantities",
- "name": "convergence_tolerance_displacement_maximum",
- "description": "The input maximum displacement tolerance criterion.",
- "type": {
- "type_kind": "numpy",
- "type_data": "float64"
- },
- "shape": [],
- "unit": "meter"
- },
- {
- "m_def": "nomad.metainfo.metainfo.Quantity",
- "m_parent_index": 6,
- "m_parent_sub_section": "quantities",
- "name": "optimization_steps_maximum",
- "description": "Maximum number of optimization steps.",
- "type": {
- "type_kind": "python",
- "type_data": "int"
- },
- "shape": []
- }
- ]
- },
- {
- "m_def": "nomad.metainfo.metainfo.Section",
- "m_parent_index": 12,
- "m_parent_sub_section": "section_definitions",
- "name": "GeometryOptimizationResults",
- "base_sections": [
- "/packages/18/section_definitions/1"
- ],
- "quantities": [
- {
- "m_def": "nomad.metainfo.metainfo.Quantity",
- "m_parent_index": 0,
- "m_parent_sub_section": "quantities",
- "name": "optimization_steps",
- "description": "Number of saved optimization steps.",
- "type": {
- "type_kind": "python",
- "type_data": "int"
- },
- "shape": []
- },
- {
- "m_def": "nomad.metainfo.metainfo.Quantity",
- "m_parent_index": 1,
- "m_parent_sub_section": "quantities",
- "name": "energies",
- "description": "List of energy_total values gathered from the single configuration\ncalculations that are a part of the optimization trajectory.",
- "type": {
- "type_kind": "numpy",
- "type_data": "float64"
- },
- "shape": [
- "optimization_steps"
- ],
- "unit": "joule"
- },
- {
- "m_def": "nomad.metainfo.metainfo.Quantity",
- "m_parent_index": 2,
- "m_parent_sub_section": "quantities",
- "name": "steps",
- "description": "The step index corresponding to each saved configuration.",
- "type": {
- "type_kind": "numpy",
- "type_data": "int32"
- },
- "shape": [
- "optimization_steps"
- ]
- },
- {
- "m_def": "nomad.metainfo.metainfo.Quantity",
- "m_parent_index": 3,
- "m_parent_sub_section": "quantities",
- "name": "final_energy_difference",
- "description": "The difference in the energy_total between the last two steps during\noptimization.",
- "type": {
- "type_kind": "numpy",
- "type_data": "float64"
- },
- "shape": [],
- "unit": "joule"
- },
- {
- "m_def": "nomad.metainfo.metainfo.Quantity",
- "m_parent_index": 4,
- "m_parent_sub_section": "quantities",
- "name": "final_force_maximum",
- "description": "The maximum net force in the last optimization step.",
- "type": {
- "type_kind": "numpy",
- "type_data": "float64"
- },
- "shape": [],
- "unit": "newton"
- },
- {
- "m_def": "nomad.metainfo.metainfo.Quantity",
- "m_parent_index": 5,
- "m_parent_sub_section": "quantities",
- "name": "final_displacement_maximum",
- "description": "The maximum displacement in the last optimization step with respect to previous.",
- "type": {
- "type_kind": "numpy",
- "type_data": "float64"
- },
- "shape": [],
- "unit": "meter"
- },
- {
- "m_def": "nomad.metainfo.metainfo.Quantity",
- "m_parent_index": 6,
- "m_parent_sub_section": "quantities",
- "name": "is_converged_geometry",
- "description": "Indicates if the geometry convergence criteria were fulfilled.",
- "type": {
- "type_kind": "python",
- "type_data": "bool"
- },
- "shape": []
- }
- ]
- },
- {
- "m_def": "nomad.metainfo.metainfo.Section",
- "m_parent_index": 13,
- "m_parent_sub_section": "section_definitions",
- "name": "GeometryOptimization",
- "base_sections": [
- "/packages/18/section_definitions/10"
- ],
- "sub_sections": [
- {
- "m_def": "nomad.metainfo.metainfo.SubSection",
- "m_parent_index": 0,
- "m_parent_sub_section": "sub_sections",
- "name": "method",
- "sub_section": "/packages/18/section_definitions/11"
- },
- {
- "m_def": "nomad.metainfo.metainfo.SubSection",
- "m_parent_index": 1,
- "m_parent_sub_section": "sub_sections",
- "name": "results",
- "sub_section": "/packages/18/section_definitions/12"
- }
- ]
- },
- {
- "m_def": "nomad.metainfo.metainfo.Section",
- "m_parent_index": 14,
- "m_parent_sub_section": "section_definitions",
- "name": "ThermostatParameters",
- "description": "Section containing the parameters pertaining to the thermostat for a molecular dynamics run.",
- "quantities": [
- {
- "m_def": "nomad.metainfo.metainfo.Quantity",
- "m_parent_index": 0,
- "m_parent_sub_section": "quantities",
- "name": "thermostat_type",
- "description": "The name of the thermostat used for temperature control. If skipped or an empty string is used, it\nmeans no thermostat was applied.\n\nAllowed values are:\n\n| Thermostat Name | Description |\n\n| ---------------------- | ----------------------------------------- |\n\n| `\"\"` | No thermostat |\n\n| `\"andersen\"` | H.C. Andersen, [J. Chem. Phys.\n**72**, 2384 (1980)](https://doi.org/10.1063/1.439486) |\n\n| `\"berendsen\"` | H. J. C. Berendsen, J. P. M. Postma,\nW. F. van Gunsteren, A. DiNola, and J. R. Haak, [J. Chem. Phys.\n**81**, 3684 (1984)](https://doi.org/10.1063/1.448118) |\n\n| `\"brownian\"` | Brownian Dynamics |\n\n| `\"langevin_goga\"` | N. Goga, A. J. Rzepiela, A. H. de Vries,\nS. J. Marrink, and H. J. C. Berendsen, [J. Chem. Theory Comput. **8**, 3637 (2012)]\n(https://doi.org/10.1021/ct3000876) |\n\n| `\"langevin_schneider\"` | T. Schneider and E. Stoll,\n[Phys. Rev. B **17**, 1302](https://doi.org/10.1103/PhysRevB.17.1302) |\n\n| `\"nose_hoover\"` | S. Nos\u00e9, [Mol. Phys. **52**, 255 (1984)]\n(https://doi.org/10.1080/00268978400101201); W.G. Hoover, [Phys. Rev. A\n**31**, 1695 (1985) |\n\n| `\"velocity_rescaling\"` | G. Bussi, D. Donadio, and M. Parrinello,\n[J. Chem. Phys. **126**, 014101 (2007)](https://doi.org/10.1063/1.2408420) |\n\n| `\"velocity_rescaling_langevin\"` | G. Bussi and M. Parrinello,\n[Phys. Rev. E **75**, 056707 (2007)](https://doi.org/10.1103/PhysRevE.75.056707) |",
- "type": {
- "type_kind": "Enum",
- "type_data": [
- "andersen",
- "berendsen",
- "brownian",
- "langevin_goga",
- "langevin_schneider",
- "nose_hoover",
- "velocity_rescaling",
- "velocity_rescaling_langevin"
- ]
- },
- "shape": []
- },
- {
- "m_def": "nomad.metainfo.metainfo.Quantity",
- "m_parent_index": 1,
- "m_parent_sub_section": "quantities",
- "name": "reference_temperature",
- "description": "The target temperature for the simulation.",
- "type": {
- "type_kind": "numpy",
- "type_data": "float64"
- },
- "shape": [],
- "unit": "kelvin"
- },
- {
- "m_def": "nomad.metainfo.metainfo.Quantity",
- "m_parent_index": 2,
- "m_parent_sub_section": "quantities",
- "name": "coupling_constant",
- "description": "The time constant for temperature coupling. Need to describe what this means for the various\nthermostat options...",
- "type": {
- "type_kind": "numpy",
- "type_data": "float64"
- },
- "shape": [],
- "unit": "second"
- },
- {
- "m_def": "nomad.metainfo.metainfo.Quantity",
- "m_parent_index": 3,
- "m_parent_sub_section": "quantities",
- "name": "effective_mass",
- "description": "The effective or fictitious mass of the temperature resevoir.",
- "type": {
- "type_kind": "numpy",
- "type_data": "float64"
- },
- "shape": [],
- "unit": "kilogram"
- }
- ]
- },
- {
- "m_def": "nomad.metainfo.metainfo.Section",
- "m_parent_index": 15,
- "m_parent_sub_section": "section_definitions",
- "name": "BarostatParameters",
- "description": "Section containing the parameters pertaining to the barostat for a molecular dynamics run.",
- "quantities": [
- {
- "m_def": "nomad.metainfo.metainfo.Quantity",
- "m_parent_index": 0,
- "m_parent_sub_section": "quantities",
- "name": "barostat_type",
- "description": "The name of the barostat used for temperature control. If skipped or an empty string is used, it\nmeans no barostat was applied.\n\nAllowed values are:\n\n| Barostat Name | Description |\n\n| ---------------------- | ----------------------------------------- |\n\n| `\"\"` | No thermostat |\n\n| `\"berendsen\"` | H. J. C. Berendsen, J. P. M. Postma,\nW. F. van Gunsteren, A. DiNola, and J. R. Haak, [J. Chem. Phys.\n**81**, 3684 (1984)](https://doi.org/10.1063/1.448118) |\n\n| `\"martyna_tuckerman_tobias_klein\"` | G.J. Martyna, M.E. Tuckerman, D.J. Tobias, and M.L. Klein,\n[Mol. Phys. **87**, 1117 (1996)](https://doi.org/10.1080/00268979600100761);\nM.E. Tuckerman, J. Alejandre, R. L\u00f3pez-Rend\u00f3n, A.L. Jochim, and G.J. Martyna,\n[J. Phys. A. **59**, 5629 (2006)](https://doi.org/10.1088/0305-4470/39/19/S18)|\n\n| `\"nose_hoover\"` | S. Nos\u00e9, [Mol. Phys. **52**, 255 (1984)]\n(https://doi.org/10.1080/00268978400101201); W.G. Hoover, [Phys. Rev. A\n**31**, 1695 (1985) |\n\n| `\"parrinello_rahman\"` | M. Parrinello and A. Rahman,\n[J. Appl. Phys. **52**, 7182 (1981)](https://doi.org/10.1063/1.328693);\nS. Nos\u00e9 and M.L. Klein, [Mol. Phys. **50**, 1055 (1983) |\n\n| `\"stochastic_cell_rescaling\"` | M. Bernetti and G. Bussi,\n[J. Chem. Phys. **153**, 114107 (2020)](https://doi.org/10.1063/1.2408420) |",
- "type": {
- "type_kind": "Enum",
- "type_data": [
- "berendsen",
- "martyna_tuckerman_tobias_klein",
- "nose_hoover",
- "parrinello_rahman",
- "stochastic_cell_rescaling"
- ]
- },
- "shape": []
- },
- {
- "m_def": "nomad.metainfo.metainfo.Quantity",
- "m_parent_index": 1,
- "m_parent_sub_section": "quantities",
- "name": "coupling_type",
- "description": "Describes the symmetry of pressure coupling. Specifics can be inferred from the `coupling constant`\n\n| Type | Description |\n\n| ---------------------- | ----------------------------------------- |\n\n| `isotropic` | Identical coupling in all directions. |\n\n| `semi_isotropic` | Identical coupling in 2 directions. |\n\n| `anisotropic` | General case. |",
- "type": {
- "type_kind": "Enum",
- "type_data": [
- "isotropic",
- "semi_isotropic",
- "anisotropic"
- ]
- },
- "shape": []
- },
- {
- "m_def": "nomad.metainfo.metainfo.Quantity",
- "m_parent_index": 2,
- "m_parent_sub_section": "quantities",
- "name": "reference_pressure",
- "description": "The target pressure for the simulation, stored in a 3x3 matrix, indicating the values for individual directions\nalong the diagonal, and coupling between directions on the off-diagonal.",
- "type": {
- "type_kind": "numpy",
- "type_data": "float64"
- },
- "shape": [
- 3,
- 3
- ],
- "unit": "pascal"
- },
- {
- "m_def": "nomad.metainfo.metainfo.Quantity",
- "m_parent_index": 3,
- "m_parent_sub_section": "quantities",
- "name": "coupling_constant",
- "description": "The time constants for pressure coupling, stored in a 3x3 matrix, indicating the values for individual directions\nalong the diagonal, and coupling between directions on the off-diagonal. 0 values along the off-diagonal\nindicate no-coupling between these directions.",
- "type": {
- "type_kind": "numpy",
- "type_data": "float64"
- },
- "shape": [
- 3,
- 3
- ],
- "unit": "second"
- },
- {
- "m_def": "nomad.metainfo.metainfo.Quantity",
- "m_parent_index": 4,
- "m_parent_sub_section": "quantities",
- "name": "compressibility",
- "description": "An estimate of the system's compressibility, used for box rescaling, stored in a 3x3 matrix indicating the values for individual directions\nalong the diagonal, and coupling between directions on the off-diagonal. If None, it may indicate that these values\nare incorporated into the coupling_constant, or simply that the software used uses a fixed value that is not available in\nthe input/output files.",
- "type": {
- "type_kind": "numpy",
- "type_data": "float64"
- },
- "shape": [
- 3,
- 3
- ],
- "unit": "1 / pascal"
- }
- ]
- },
- {
- "m_def": "nomad.metainfo.metainfo.Section",
- "m_parent_index": 16,
- "m_parent_sub_section": "section_definitions",
- "name": "MolecularDynamicsMethod",
- "base_sections": [
- "/packages/18/section_definitions/0"
- ],
- "quantities": [
- {
- "m_def": "nomad.metainfo.metainfo.Quantity",
- "m_parent_index": 0,
- "m_parent_sub_section": "quantities",
- "name": "thermodynamic_ensemble",
- "description": "The type of thermodynamic ensemble that was simulated.\n\nAllowed values are:\n\n| Thermodynamic Ensemble | Description |\n\n| ---------------------- | ----------------------------------------- |\n\n| `\"NVE\"` | Constant number of particles, volume, and energy |\n\n| `\"NVT\"` | Constant number of particles, volume, and temperature |\n\n| `\"NPT\"` | Constant number of particles, pressure, and temperature |\n\n| `\"NPH\"` | Constant number of particles, pressure, and enthalpy |",
- "type": {
- "type_kind": "Enum",
- "type_data": [
- "NVE",
- "NVT",
- "NPT",
- "NPH"
- ]
- },
- "shape": []
- },
- {
- "m_def": "nomad.metainfo.metainfo.Quantity",
- "m_parent_index": 1,
- "m_parent_sub_section": "quantities",
- "name": "integrator_type",
- "description": "Name of the integrator.\n\nAllowed values are:\n\n| Integrator Name | Description |\n\n| ---------------------- | ----------------------------------------- |\n\n| `\"langevin_goga\"` | N. Goga, A. J. Rzepiela, A. H. de Vries,\nS. J. Marrink, and H. J. C. Berendsen, [J. Chem. Theory Comput. **8**, 3637 (2012)]\n(https://doi.org/10.1021/ct3000876) |\n\n| `\"langevin_schneider\"` | T. Schneider and E. Stoll,\n[Phys. Rev. B **17**, 1302](https://doi.org/10.1103/PhysRevB.17.1302) |\n\n| `\"leap_frog\"` | R.W. Hockney, S.P. Goel, and J. Eastwood,\n[J. Comp. Phys. **14**, 148 (1974)](https://doi.org/10.1016/0021-9991(74)90010-2) |\n\n| `\"velocity_verlet\"` | W.C. Swope, H.C. Andersen, P.H. Berens, and K.R. Wilson,\n[J. Chem. Phys. **76**, 637 (1982)](https://doi.org/10.1063/1.442716) |\n\n| `\"rRESPA_multitimescale\"` | M. Tuckerman, B. J. Berne, and G. J. Martyna\n[J. Chem. Phys. **97**, 1990 (1992)](https://doi.org/10.1063/1.463137) |",
- "type": {
- "type_kind": "Enum",
- "type_data": [
- "brownian",
- "conjugant_gradient",
- "langevin_goga",
- "langevin_schneider",
- "leap_frog",
- "rRESPA_multitimescale",
- "velocity_verlet"
- ]
- },
- "shape": []
- },
- {
- "m_def": "nomad.metainfo.metainfo.Quantity",
- "m_parent_index": 2,
- "m_parent_sub_section": "quantities",
- "name": "integration_timestep",
- "description": "The timestep at which the numerical integration is performed.",
- "type": {
- "type_kind": "numpy",
- "type_data": "float64"
- },
- "shape": [],
- "unit": "second"
- },
- {
- "m_def": "nomad.metainfo.metainfo.Quantity",
- "m_parent_index": 3,
- "m_parent_sub_section": "quantities",
- "name": "n_steps",
- "description": "Number of timesteps performed.",
- "type": {
- "type_kind": "python",
- "type_data": "int"
- },
- "shape": []
- },
- {
- "m_def": "nomad.metainfo.metainfo.Quantity",
- "m_parent_index": 4,
- "m_parent_sub_section": "quantities",
- "name": "coordinate_save_frequency",
- "description": "The number of timesteps between saving the coordinates.",
- "type": {
- "type_kind": "python",
- "type_data": "int"
- },
- "shape": []
- },
- {
- "m_def": "nomad.metainfo.metainfo.Quantity",
- "m_parent_index": 5,
- "m_parent_sub_section": "quantities",
- "name": "velocity_save_frequency",
- "description": "The number of timesteps between saving the velocities.",
- "type": {
- "type_kind": "python",
- "type_data": "int"
- },
- "shape": []
- },
- {
- "m_def": "nomad.metainfo.metainfo.Quantity",
- "m_parent_index": 6,
- "m_parent_sub_section": "quantities",
- "name": "force_save_frequency",
- "description": "The number of timesteps between saving the forces.",
- "type": {
- "type_kind": "python",
- "type_data": "int"
- },
- "shape": []
- },
- {
- "m_def": "nomad.metainfo.metainfo.Quantity",
- "m_parent_index": 7,
- "m_parent_sub_section": "quantities",
- "name": "thermodynamics_save_frequency",
- "description": "The number of timesteps between saving the thermodynamic quantities.",
- "type": {
- "type_kind": "python",
- "type_data": "int"
- },
- "shape": []
- }
- ],
- "sub_sections": [
- {
- "m_def": "nomad.metainfo.metainfo.SubSection",
- "m_parent_index": 0,
- "m_parent_sub_section": "sub_sections",
- "name": "thermostat_parameters",
- "sub_section": "/packages/18/section_definitions/14",
- "repeats": false
- },
- {
- "m_def": "nomad.metainfo.metainfo.SubSection",
- "m_parent_index": 1,
- "m_parent_sub_section": "sub_sections",
- "name": "barostat_parameters",
- "sub_section": "/packages/18/section_definitions/15",
- "repeats": false
- }
- ]
- },
- {
- "m_def": "nomad.metainfo.metainfo.Section",
- "m_parent_index": 17,
- "m_parent_sub_section": "section_definitions",
- "name": "EnsemblePropertyValues",
- "description": "Generic section containing information regarding the values of an ensemble property.",
- "quantities": [
- {
- "m_def": "nomad.metainfo.metainfo.Quantity",
- "m_parent_index": 0,
- "m_parent_sub_section": "quantities",
- "name": "label",
- "description": "Describes the atoms or molecule types involved in determining the property.",
- "type": {
- "type_kind": "python",
- "type_data": "str"
- },
- "shape": []
- },
- {
- "m_def": "nomad.metainfo.metainfo.Quantity",
- "m_parent_index": 1,
- "m_parent_sub_section": "quantities",
- "name": "n_bins",
- "description": "Number of bins.",
- "type": {
- "type_kind": "python",
- "type_data": "int"
- },
- "shape": []
- },
- {
- "m_def": "nomad.metainfo.metainfo.Quantity",
- "m_parent_index": 2,
- "m_parent_sub_section": "quantities",
- "name": "frame_start",
- "description": "Trajectory frame number where the ensemble averaging starts.",
- "type": {
- "type_kind": "python",
- "type_data": "int"
- },
- "shape": []
- },
- {
- "m_def": "nomad.metainfo.metainfo.Quantity",
- "m_parent_index": 3,
- "m_parent_sub_section": "quantities",
- "name": "frame_end",
- "description": "Trajectory frame number where the ensemble averaging ends.",
- "type": {
- "type_kind": "python",
- "type_data": "int"
- },
- "shape": []
- }
- ]
- },
- {
- "m_def": "nomad.metainfo.metainfo.Section",
- "m_parent_index": 18,
- "m_parent_sub_section": "section_definitions",
- "name": "RadialDistributionFunctionValues",
- "description": "Section containing information regarding the values of radial distribution functions (rdfs).",
- "base_sections": [
- "/packages/18/section_definitions/17"
- ],
- "quantities": [
- {
- "m_def": "nomad.metainfo.metainfo.Quantity",
- "m_parent_index": 0,
- "m_parent_sub_section": "quantities",
- "name": "bins",
- "description": "Distances along which the rdf was calculated.",
- "type": {
- "type_kind": "numpy",
- "type_data": "float64"
- },
- "shape": [
- "n_bins"
- ],
- "unit": "meter"
- },
- {
- "m_def": "nomad.metainfo.metainfo.Quantity",
- "m_parent_index": 1,
- "m_parent_sub_section": "quantities",
- "name": "value",
- "description": "Values of the property.",
- "type": {
- "type_kind": "numpy",
- "type_data": "float64"
- },
- "shape": [
- "n_bins"
- ]
- }
- ]
- },
- {
- "m_def": "nomad.metainfo.metainfo.Section",
- "m_parent_index": 19,
- "m_parent_sub_section": "section_definitions",
- "name": "EnsembleProperty",
- "description": "Generic section containing information about a calculation of any static observable from a trajectory (i.e., from an ensemble average).",
- "base_sections": [
- "/packages/15/section_definitions/0"
- ],
- "quantities": [
- {
- "m_def": "nomad.metainfo.metainfo.Quantity",
- "m_parent_index": 0,
- "m_parent_sub_section": "quantities",
- "name": "type",
- "description": "Describes if the observable is calculated at the molecular or atomic level.",
- "type": {
- "type_kind": "Enum",
- "type_data": [
- "molecular",
- "atomic"
- ]
- },
- "shape": []
- },
- {
- "m_def": "nomad.metainfo.metainfo.Quantity",
- "m_parent_index": 1,
- "m_parent_sub_section": "quantities",
- "name": "n_smooth",
- "description": "Number of bins over which the running average was computed for\nthe observable `values'.",
- "type": {
- "type_kind": "python",
- "type_data": "int"
- },
- "shape": []
- },
- {
- "m_def": "nomad.metainfo.metainfo.Quantity",
- "m_parent_index": 2,
- "m_parent_sub_section": "quantities",
- "name": "error_type",
- "description": "Describes the type of error reported for this observable.",
- "type": {
- "type_kind": "python",
- "type_data": "str"
- },
- "shape": []
- },
- {
- "m_def": "nomad.metainfo.metainfo.Quantity",
- "m_parent_index": 3,
- "m_parent_sub_section": "quantities",
- "name": "n_variables",
- "description": "Number of variables along which the property is determined.",
- "type": {
- "type_kind": "python",
- "type_data": "int"
- },
- "shape": []
- },
- {
- "m_def": "nomad.metainfo.metainfo.Quantity",
- "m_parent_index": 4,
- "m_parent_sub_section": "quantities",
- "name": "variables_name",
- "description": "Name/description of the independent variables along which the observable is defined.",
- "type": {
- "type_kind": "python",
- "type_data": "str"
- },
- "shape": [
- "n_variables"
- ]
- }
- ]
- },
- {
- "m_def": "nomad.metainfo.metainfo.Section",
- "m_parent_index": 20,
- "m_parent_sub_section": "section_definitions",
- "name": "RadialDistributionFunction",
- "description": "Section containing information about the calculation of radial distribution functions (rdfs).",
- "base_sections": [
- "/packages/18/section_definitions/19"
- ],
- "sub_sections": [
- {
- "m_def": "nomad.metainfo.metainfo.SubSection",
- "m_parent_index": 0,
- "m_parent_sub_section": "sub_sections",
- "name": "radial_distribution_function_values",
- "sub_section": "/packages/18/section_definitions/18",
- "repeats": true
- }
- ]
- },
- {
- "m_def": "nomad.metainfo.metainfo.Section",
- "m_parent_index": 21,
- "m_parent_sub_section": "section_definitions",
- "name": "TrajectoryProperty",
- "description": "Generic section containing information about a calculation of any observable defined and stored at each individual frame of a trajectory.",
- "base_sections": [
- "/packages/15/section_definitions/0"
- ],
- "quantities": [
- {
- "m_def": "nomad.metainfo.metainfo.Quantity",
- "m_parent_index": 0,
- "m_parent_sub_section": "quantities",
- "name": "type",
- "description": "Describes if the observable is calculated at the molecular or atomic level.",
- "type": {
- "type_kind": "Enum",
- "type_data": [
- "molecular",
- "atomic"
- ]
- },
- "shape": []
- },
- {
- "m_def": "nomad.metainfo.metainfo.Quantity",
- "m_parent_index": 1,
- "m_parent_sub_section": "quantities",
- "name": "error_type",
- "description": "Describes the type of error reported for this observable.",
- "type": {
- "type_kind": "python",
- "type_data": "str"
- },
- "shape": []
- },
- {
- "m_def": "nomad.metainfo.metainfo.Quantity",
- "m_parent_index": 2,
- "m_parent_sub_section": "quantities",
- "name": "label",
- "description": "Describes the atoms or molecule types involved in determining the property.",
- "type": {
- "type_kind": "python",
- "type_data": "str"
- },
- "shape": []
- },
- {
- "m_def": "nomad.metainfo.metainfo.Quantity",
- "m_parent_index": 3,
- "m_parent_sub_section": "quantities",
- "name": "n_frames",
- "description": "Number of frames for which the observable is stored.",
- "type": {
- "type_kind": "python",
- "type_data": "int"
- },
- "shape": []
- },
- {
- "m_def": "nomad.metainfo.metainfo.Quantity",
- "m_parent_index": 4,
- "m_parent_sub_section": "quantities",
- "name": "frames",
- "description": "Frames for which the observable is stored.",
- "type": {
- "type_kind": "numpy",
- "type_data": "int32"
- },
- "shape": [
- "n_frames"
- ]
- },
- {
- "m_def": "nomad.metainfo.metainfo.Quantity",
- "m_parent_index": 5,
- "m_parent_sub_section": "quantities",
- "name": "times",
- "description": "Times for which the observable is stored.",
- "type": {
- "type_kind": "numpy",
- "type_data": "float64"
- },
- "shape": [
- "n_frames"
- ],
- "unit": "second"
- },
- {
- "m_def": "nomad.metainfo.metainfo.Quantity",
- "m_parent_index": 6,
- "m_parent_sub_section": "quantities",
- "name": "value",
- "description": "Values of the property.",
- "type": {
- "type_kind": "numpy",
- "type_data": "float64"
- },
- "shape": [
- "n_frames"
- ]
- },
- {
- "m_def": "nomad.metainfo.metainfo.Quantity",
- "m_parent_index": 7,
- "m_parent_sub_section": "quantities",
- "name": "errors",
- "description": "Error associated with the determination of the property.",
- "type": {
- "type_kind": "numpy",
- "type_data": "float64"
- },
- "shape": [
- "*"
- ]
- }
- ]
- },
- {
- "m_def": "nomad.metainfo.metainfo.Section",
- "m_parent_index": 22,
- "m_parent_sub_section": "section_definitions",
- "name": "RadiusOfGyration",
- "description": "Section containing information about the calculation of radius of gyration (Rg).",
- "base_sections": [
- "/packages/18/section_definitions/21"
- ],
- "quantities": [
- {
- "m_def": "nomad.metainfo.metainfo.Quantity",
- "m_parent_index": 0,
- "m_parent_sub_section": "quantities",
- "name": "atomsgroup_ref",
- "description": "References to the atoms_group section containing the molecule for which Rg was calculated.",
- "type": {
- "type_kind": "reference",
- "type_data": "/packages/1/section_definitions/0"
- },
- "shape": [
- 1
- ]
- },
- {
- "m_def": "nomad.metainfo.metainfo.Quantity",
- "m_parent_index": 1,
- "m_parent_sub_section": "quantities",
- "name": "value",
- "description": "Values of the property.",
- "type": {
- "type_kind": "numpy",
- "type_data": "float64"
- },
- "shape": [
- "n_frames"
- ],
- "unit": "meter"
- }
- ]
- },
- {
- "m_def": "nomad.metainfo.metainfo.Section",
- "m_parent_index": 23,
- "m_parent_sub_section": "section_definitions",
- "name": "DiffusionConstantValues",
- "description": "Section containing information regarding the diffusion constants.",
- "quantities": [
- {
- "m_def": "nomad.metainfo.metainfo.Quantity",
- "m_parent_index": 0,
- "m_parent_sub_section": "quantities",
- "name": "value",
- "description": "Values of the diffusion constants.",
- "type": {
- "type_kind": "numpy",
- "type_data": "float64"
- },
- "shape": [],
- "unit": "meter ** 2 / second"
- },
- {
- "m_def": "nomad.metainfo.metainfo.Quantity",
- "m_parent_index": 1,
- "m_parent_sub_section": "quantities",
- "name": "error_type",
- "description": "Describes the type of error reported for this observable.",
- "type": {
- "type_kind": "python",
- "type_data": "str"
- },
- "shape": []
- },
- {
- "m_def": "nomad.metainfo.metainfo.Quantity",
- "m_parent_index": 2,
- "m_parent_sub_section": "quantities",
- "name": "errors",
- "description": "Error associated with the determination of the diffusion constant.",
- "type": {
- "type_kind": "numpy",
- "type_data": "float64"
- },
- "shape": [
- "*"
- ]
- }
- ]
- },
- {
- "m_def": "nomad.metainfo.metainfo.Section",
- "m_parent_index": 24,
- "m_parent_sub_section": "section_definitions",
- "name": "CorrelationFunctionValues",
- "description": "Generic section containing information regarding the values of a correlation function.",
- "quantities": [
- {
- "m_def": "nomad.metainfo.metainfo.Quantity",
- "m_parent_index": 0,
- "m_parent_sub_section": "quantities",
- "name": "label",
- "description": "Describes the atoms or molecule types involved in determining the property.",
- "type": {
- "type_kind": "python",
- "type_data": "str"
- },
- "shape": []
- },
- {
- "m_def": "nomad.metainfo.metainfo.Quantity",
- "m_parent_index": 1,
- "m_parent_sub_section": "quantities",
- "name": "n_times",
- "description": "Number of times windows for the calculation of the correlation function.",
- "type": {
- "type_kind": "python",
- "type_data": "int"
- },
- "shape": []
- }
- ]
- },
- {
- "m_def": "nomad.metainfo.metainfo.Section",
- "m_parent_index": 25,
- "m_parent_sub_section": "section_definitions",
- "name": "MeanSquaredDisplacementValues",
- "description": "Section containing information regarding the values of a mean squared displacements (msds).",
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- "type_data": "float64"
- },
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- },
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- "unit": "meter ** 2"
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- }
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- ],
- "quantities": [
- {
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- "m_parent_index": 0,
- "m_parent_sub_section": "quantities",
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- "atomic"
- ]
- },
- "shape": []
- },
- {
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- "name": "direction",
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- "y",
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- "xy",
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- "name": "error_type",
- "description": "Describes the type of error reported for this correlation function.",
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- }
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- },
- {
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- "description": "Section containing information about a calculation of any mean squared displacements (msds).",
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- "repeats": true
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- "m_def": "nomad.metainfo.metainfo.SubSection",
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- }
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- },
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- "sub_sections": [
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- },
- {
- "m_def": "nomad.metainfo.metainfo.Section",
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- "quantities": [
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- "type_data": "str"
- },
- "shape": []
- },
- {
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- "name": "mesh_density",
- "description": "Density of the k-mesh for sampling.",
- "type": {
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- "type_data": "float64"
- },
- "shape": [],
- "unit": "1 / meter ** 3"
- },
- {
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- "type": {
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- "type_data": "bool"
- },
- "shape": []
- },
- {
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- "m_parent_sub_section": "quantities",
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- "type": {
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- }
- ]
- },
- {
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- "quantities": [
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- "m_def": "nomad.metainfo.metainfo.Quantity",
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- "name": "n_imaginary_frequencies",
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- },
- "shape": []
- },
- {
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- "name": "n_bands",
- "description": "Number of phonon bands.",
- "type": {
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- "type_data": "int32"
- },
- "shape": []
- },
- {
- "m_def": "nomad.metainfo.metainfo.Quantity",
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- "description": "Number of q points for which phonon properties are evaluated.",
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- },
- "shape": []
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- {
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- "shape": [
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- 3
- ]
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- "unit": "meter / second"
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- {
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- "shape": []
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- ],
- "unit": "meter"
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- {
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- "name": "value",
- "description": "Values of the energy(units:J)/d2E(units:Pa)/cross-validation (depending on the\nvalue of strain_diagram_type)",
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- "type_data": "int"
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- "description": "Maximum strain applied to crystal.",
- "type": {
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- ]
- },
- {
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- ],
- "quantities": [
- {
- "m_def": "nomad.metainfo.metainfo.Quantity",
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- "description": "Number of deformed structures used to calculate the elastic constants. This is\ndetermined by the symmetry of the crystal.",
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- "type_data": "int32"
- },
- "shape": []
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- {
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- "description": "deformation types",
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- "type_data": "str_"
- },
- "shape": [
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- 6
- ]
- },
- {
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- "m_parent_sub_section": "quantities",
- "name": "n_strains",
- "description": "number of equally spaced strains applied to each deformed structure, which are\ngenerated between the maximum negative strain and the maximum positive one.",
- "type": {
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- "type_data": "int32"
- },
- "shape": []
- },
- {
- "m_def": "nomad.metainfo.metainfo.Quantity",
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- "m_parent_sub_section": "quantities",
- "name": "is_mechanically_stable",
- "description": "Indicates if structure is mechanically stable from the calculated values of the\nelastic constants.",
- "type": {
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- "type_data": "bool"
- },
- "shape": []
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- {
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- "m_parent_sub_section": "quantities",
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- },
- "shape": [
- 6,
- 6
- ]
- },
- {
- "m_def": "nomad.metainfo.metainfo.Quantity",
- "m_parent_index": 5,
- "m_parent_sub_section": "quantities",
- "name": "elastic_constants_matrix_second_order",
- "description": "2nd order elastic constant (stiffness) matrix in pascals",
- "type": {
- "type_kind": "numpy",
- "type_data": "float64"
- },
- "shape": [
- 6,
- 6
- ],
- "unit": "pascal"
- },
- {
- "m_def": "nomad.metainfo.metainfo.Quantity",
- "m_parent_index": 6,
- "m_parent_sub_section": "quantities",
- "name": "elastic_constants_matrix_third_order",
- "description": "3rd order elastic constant (stiffness) matrix in pascals",
- "type": {
- "type_kind": "numpy",
- "type_data": "float64"
- },
- "shape": [
- 6,
- 6,
- 6
- ],
- "unit": "pascal"
- },
- {
- "m_def": "nomad.metainfo.metainfo.Quantity",
- "m_parent_index": 7,
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- "description": "Calculated value of the pressure derivative of the bulk modulus.",
- "type": {
- "type_kind": "numpy",
- "type_data": "float64"
- },
- "shape": []
- },
- {
- "m_def": "nomad.metainfo.metainfo.Quantity",
- "m_parent_index": 4,
- "m_parent_sub_section": "quantities",
- "name": "equilibrium_volume",
- "description": "Calculated value of the equilibrium volume by fitting the volume-energy data.",
- "type": {
- "type_kind": "numpy",
- "type_data": "float64"
- },
- "shape": [],
- "unit": "meter ** 3"
- },
- {
- "m_def": "nomad.metainfo.metainfo.Quantity",
- "m_parent_index": 5,
- "m_parent_sub_section": "quantities",
- "name": "equilibrium_energy",
- "description": "Calculated value of the equilibrium energy by fitting the volume-energy data.",
- "type": {
- "type_kind": "numpy",
- "type_data": "float64"
- },
- "shape": [],
- "unit": "joule"
- },
- {
- "m_def": "nomad.metainfo.metainfo.Quantity",
- "m_parent_index": 6,
- "m_parent_sub_section": "quantities",
- "name": "rms_error",
- "description": "Root-mean squared value of the error in the fitting.",
- "type": {
- "type_kind": "numpy",
- "type_data": "float64"
- },
- "shape": []
- }
- ]
- },
- {
- "m_def": "nomad.metainfo.metainfo.Section",
- "m_parent_index": 50,
- "m_parent_sub_section": "section_definitions",
- "name": "EquationOfStateResults",
- "base_sections": [
- "/packages/18/section_definitions/1"
- ],
- "quantities": [
- {
- "m_def": "nomad.metainfo.metainfo.Quantity",
- "m_parent_index": 0,
- "m_parent_sub_section": "quantities",
- "name": "n_points",
- "description": "Number of volume-energy pairs in data.",
- "type": {
- "type_kind": "numpy",
- "type_data": "int32"
- },
- "shape": []
- },
- {
- "m_def": "nomad.metainfo.metainfo.Quantity",
- "m_parent_index": 1,
- "m_parent_sub_section": "quantities",
- "name": "volumes",
- "description": "Array of volumes per atom for which the energies are evaluated.",
- "type": {
- "type_kind": "numpy",
- "type_data": "float64"
- },
- "shape": [
- "n_points"
- ],
- "unit": "meter ** 3"
- },
- {
- "m_def": "nomad.metainfo.metainfo.Quantity",
- "m_parent_index": 2,
- "m_parent_sub_section": "quantities",
- "name": "energies",
- "description": "Array of energies corresponding to each volume.",
- "type": {
- "type_kind": "numpy",
- "type_data": "float64"
- },
- "shape": [
- "n_points"
- ],
- "unit": "joule"
- }
- ],
- "sub_sections": [
- {
- "m_def": "nomad.metainfo.metainfo.SubSection",
- "m_parent_index": 0,
- "m_parent_sub_section": "sub_sections",
- "name": "eos_fit",
- "sub_section": "/packages/18/section_definitions/49",
- "repeats": true
- }
- ]
- },
- {
- "m_def": "nomad.metainfo.metainfo.Section",
- "m_parent_index": 51,
- "m_parent_sub_section": "section_definitions",
- "name": "EquationOfState",
- "base_sections": [
- "/packages/18/section_definitions/9"
- ],
- "sub_sections": [
- {
- "m_def": "nomad.metainfo.metainfo.SubSection",
- "m_parent_index": 0,
- "m_parent_sub_section": "sub_sections",
- "name": "method",
- "sub_section": "/packages/18/section_definitions/48"
- },
- {
- "m_def": "nomad.metainfo.metainfo.SubSection",
- "m_parent_index": 1,
- "m_parent_sub_section": "sub_sections",
- "name": "results",
- "sub_section": "/packages/18/section_definitions/50"
- }
- ]
- }
- ]
- },
- {
- "m_def": "nomad.metainfo.metainfo.Package",
- "m_parent_index": 19,
- "m_parent_sub_section": "packages",
- "name": "nomad.datamodel.metainfo.workflow",
- "section_definitions": [
- {
- "m_def": "nomad.metainfo.metainfo.Section",
- "m_parent_index": 0,
- "m_parent_sub_section": "section_definitions",
- "name": "Interface",
- "description": "Section containing results of an interface (stacking fault, gamma surface, etc.) workflow.",
- "quantities": [
- {
- "m_def": "nomad.metainfo.metainfo.Quantity",
- "m_parent_index": 0,
- "m_parent_sub_section": "quantities",
- "name": "energy_extrinsic_stacking_fault",
- "description": "Value of the relaxed extrinsic stacking fault energy per unit area.",
- "type": {
- "type_kind": "numpy",
- "type_data": "float64"
- },
- "shape": [],
- "unit": "joule / meter ** 2"
- },
- {
- "m_def": "nomad.metainfo.metainfo.Quantity",
- "m_parent_index": 1,
- "m_parent_sub_section": "quantities",
- "name": "energy_intrinsic_stacking_fault",
- "description": "Value of the relaxed intrinsic stacking fault energy per unit area.",
- "type": {
- "type_kind": "numpy",
- "type_data": "float64"
- },
- "shape": [],
- "unit": "joule / meter ** 2"
- },
- {
- "m_def": "nomad.metainfo.metainfo.Quantity",
- "m_parent_index": 2,
- "m_parent_sub_section": "quantities",
- "name": "dimensionality",
- "description": "Dimensionality of the property, i.e. 1 for stacking fault energy and 2 for gamma\nsurface.",
- "type": {
- "type_kind": "numpy",
- "type_data": "int32"
- },
- "shape": []
- },
- {
- "m_def": "nomad.metainfo.metainfo.Quantity",
- "m_parent_index": 3,
- "m_parent_sub_section": "quantities",
- "name": "shift_direction",
- "description": "shift direction of the two crystal parts to calculate the fault energy.",
- "type": {
- "type_kind": "python",
- "type_data": "str"
- },
- "shape": [
- "dimensionality"
- ]
- },
- {
- "m_def": "nomad.metainfo.metainfo.Quantity",
- "m_parent_index": 4,
- "m_parent_sub_section": "quantities",
- "name": "n_displacements",
- "description": "Number of displacements in the shift to calculate the fault energy.",
- "type": {
- "type_kind": "numpy",
- "type_data": "int32"
- },
- "shape": []
- },
- {
- "m_def": "nomad.metainfo.metainfo.Quantity",
- "m_parent_index": 5,
- "m_parent_sub_section": "quantities",
- "name": "displacement_fraction",
- "description": "Relative displacements of the two crystal parts along the direction indicated by\nshift_direction.",
- "type": {
- "type_kind": "numpy",
- "type_data": "float64"
- },
- "shape": [
- "dimensionality",
- "n_displacements"
- ]
- },
- {
- "m_def": "nomad.metainfo.metainfo.Quantity",
- "m_parent_index": 6,
- "m_parent_sub_section": "quantities",
- "name": "energy_fault_plane",
- "description": "Value of the relaxed excess energy per unit area for each displacement.",
- "type": {
- "type_kind": "numpy",
- "type_data": "float64"
- },
- "shape": [
- "n_displacements"
- ],
- "unit": "joule / meter ** 2"
- },
- {
- "m_def": "nomad.metainfo.metainfo.Quantity",
- "m_parent_index": 7,
- "m_parent_sub_section": "quantities",
- "name": "gamma_surface",
- "description": "Value of the gamma surface, i.e. the excess energy per unit area calculated for\neach displacement.",
- "type": {
- "type_kind": "numpy",
- "type_data": "float64"
- },
- "shape": [
- "n_displacements",
- "n_displacements"
- ],
- "unit": "joule / meter ** 2"
- },
- {
- "m_def": "nomad.metainfo.metainfo.Quantity",
- "m_parent_index": 8,
- "m_parent_sub_section": "quantities",
- "name": "slip_fraction",
- "description": "Relative displacement between two crystal parts where the energy is maximum.",
- "type": {
- "type_kind": "numpy",
- "type_data": "float64"
- },
- "shape": []
- },
- {
- "m_def": "nomad.metainfo.metainfo.Quantity",
- "m_parent_index": 9,
- "m_parent_sub_section": "quantities",
- "name": "energy_unstable_stacking_fault",
- "description": "Value of the relaxed unstable stacking fault energy per unit area.",
- "type": {
- "type_kind": "numpy",
- "type_data": "float64"
- },
- "shape": [],
- "unit": "joule / meter ** 2"
- },
- {
- "m_def": "nomad.metainfo.metainfo.Quantity",
- "m_parent_index": 10,
- "m_parent_sub_section": "quantities",
- "name": "energy_unstable_twinning_fault",
- "description": "Value of the relaxed unstable twinning energy per unit area.",
- "type": {
- "type_kind": "numpy",
- "type_data": "float64"
- },
- "shape": [],
- "unit": "joule / meter ** 2"
- }
- ]
- },
- {
- "m_def": "nomad.metainfo.metainfo.Section",
- "m_parent_index": 1,
- "m_parent_sub_section": "section_definitions",
- "name": "Raman",
- "description": "Section containing results of a Raman workflow.",
- "quantities": [
- {
- "m_def": "nomad.metainfo.metainfo.Quantity",
- "m_parent_index": 0,
- "m_parent_sub_section": "quantities",
- "name": "n_modes",
- "description": "Number of evaluated vibrational modes.",
- "type": {
- "type_kind": "numpy",
- "type_data": "int32"
- },
- "shape": []
- },
- {
- "m_def": "nomad.metainfo.metainfo.Quantity",
- "m_parent_index": 1,
- "m_parent_sub_section": "quantities",
- "name": "n_atoms",
- "description": "Number of atoms in the simulation cell.",
- "type": {
- "type_kind": "numpy",
- "type_data": "int32"
- },
- "shape": []
- },
- {
- "m_def": "nomad.metainfo.metainfo.Quantity",
- "m_parent_index": 2,
- "m_parent_sub_section": "quantities",
- "name": "frequencies",
- "description": "Calculated value of the Raman frequencies.",
- "type": {
- "type_kind": "numpy",
- "type_data": "float64"
- },
- "shape": [
- "n_modes"
- ],
- "unit": "1 / meter"
- }
- ]
- },
- {
- "m_def": "nomad.metainfo.metainfo.Section",
- "m_parent_index": 2,
- "m_parent_sub_section": "section_definitions",
- "name": "MagneticOrdering",
- "description": "Section containing results of a magnetic ordering workflow.",
- "quantities": [
- {
- "m_def": "nomad.metainfo.metainfo.Quantity",
- "m_parent_index": 0,
- "m_parent_sub_section": "quantities",
- "name": "n_structures",
- "description": "Number of magnetic structures evaluated.",
- "type": {
- "type_kind": "numpy",
- "type_data": "int32"
- },
- "shape": []
- },
- {
- "m_def": "nomad.metainfo.metainfo.Quantity",
- "m_parent_index": 1,
- "m_parent_sub_section": "quantities",
- "name": "n_atoms",
- "description": "Number of atoms in the simulation cell.",
- "type": {
- "type_kind": "numpy",
- "type_data": "int32"
- },
- "shape": []
- },
- {
- "m_def": "nomad.metainfo.metainfo.Quantity",
- "m_parent_index": 2,
- "m_parent_sub_section": "quantities",
- "name": "labels",
- "description": "Labels corresponding to each magnetic structure.",
- "type": {
- "type_kind": "python",
- "type_data": "str"
- },
- "shape": [
- "n_structures"
- ]
- },
- {
- "m_def": "nomad.metainfo.metainfo.Quantity",
- "m_parent_index": 3,
- "m_parent_sub_section": "quantities",
- "name": "energies",
- "description": "Calculated value of the energies corresponding to each magnetic structure.",
- "type": {
- "type_kind": "numpy",
- "type_data": "float64"
- },
- "shape": [
- "n_structures"
- ],
- "unit": "joule"
- },
- {
- "m_def": "nomad.metainfo.metainfo.Quantity",
- "m_parent_index": 4,
- "m_parent_sub_section": "quantities",
- "name": "magnetic_moments",
- "description": "Resulting atomic magnetic moments corresponding to each magnetic structure.",
- "type": {
- "type_kind": "numpy",
- "type_data": "float64"
- },
- "shape": [
- "n_structures",
- "n_atoms"
- ],
- "unit": "bohr_magneton"
- },
- {
- "m_def": "nomad.metainfo.metainfo.Quantity",
- "m_parent_index": 5,
- "m_parent_sub_section": "quantities",
- "name": "magnetic_deformations",
- "description": "Average atomic displacements after relaxation with respect to the non-magnetic\ncase for each magnetic structure.",
- "type": {
- "type_kind": "numpy",
- "type_data": "float64"
- },
- "shape": [
- "n_structures"
- ],
- "unit": "meter"
- }
- ]
- },
- {
- "m_def": "nomad.metainfo.metainfo.Section",
- "m_parent_index": 3,
- "m_parent_sub_section": "section_definitions",
- "name": "Adsorption",
- "description": "Section containing results of a surface adsorption workflow.",
- "quantities": [
- {
- "m_def": "nomad.metainfo.metainfo.Quantity",
- "m_parent_index": 0,
- "m_parent_sub_section": "quantities",
- "name": "n_sites",
- "description": "Number of sites for which the adsorption energy is evaluated.",
- "type": {
- "type_kind": "numpy",
- "type_data": "int32"
- },
- "shape": []
- },
- {
- "m_def": "nomad.metainfo.metainfo.Quantity",
- "m_parent_index": 1,
- "m_parent_sub_section": "quantities",
- "name": "slab_miller_index",
- "description": "Miller index of the slab.",
- "type": {
- "type_kind": "numpy",
- "type_data": "int32"
- },
- "shape": [
- 3
- ]
- },
- {
- "m_def": "nomad.metainfo.metainfo.Quantity",
- "m_parent_index": 2,
- "m_parent_sub_section": "quantities",
- "name": "slab",
- "description": "Chemical formula of the slab.",
- "type": {
- "type_kind": "python",
- "type_data": "str"
- },
- "shape": []
- },
- {
- "m_def": "nomad.metainfo.metainfo.Quantity",
- "m_parent_index": 3,
- "m_parent_sub_section": "quantities",
- "name": "adsorbate",
- "description": "Chemical formula of the adsorbate molecule.",
- "type": {
- "type_kind": "python",
- "type_data": "str"
- },
- "shape": []
- },
- {
- "m_def": "nomad.metainfo.metainfo.Quantity",
- "m_parent_index": 4,
- "m_parent_sub_section": "quantities",
- "name": "adsorption_sites",
- "description": "Coordinates of the adsorption sites corresponding to a minimum energy.",
- "type": {
- "type_kind": "numpy",
- "type_data": "float64"
- },
- "shape": [
- "n_sites"
- ]
- },
- {
- "m_def": "nomad.metainfo.metainfo.Quantity",
- "m_parent_index": 5,
- "m_parent_sub_section": "quantities",
- "name": "adsorption_energies",
- "description": "Calculated value of the adsorption energy corresponding to each site.",
- "type": {
- "type_kind": "numpy",
- "type_data": "float64"
- },
- "shape": [
- "n_sites"
- ],
- "unit": "joule"
- }
- ]
- },
- {
- "m_def": "nomad.metainfo.metainfo.Section",
- "m_parent_index": 4,
- "m_parent_sub_section": "section_definitions",
- "name": "ConvexHull",
- "description": "Section containing results of a convex hull workflow.",
- "quantities": [
- {
- "m_def": "nomad.metainfo.metainfo.Quantity",
- "m_parent_index": 0,
- "m_parent_sub_section": "quantities",
- "name": "n_elements",
- "description": "Number of elements for which the thermal stability is evaluated. This represents\nthe dimensionality of the convex hull.",
- "type": {
- "type_kind": "numpy",
- "type_data": "int32"
- },
- "shape": []
- },
- {
- "m_def": "nomad.metainfo.metainfo.Quantity",
- "m_parent_index": 1,
- "m_parent_sub_section": "quantities",
- "name": "n_points",
- "description": "Number of points for which the energies are evaluated.",
- "type": {
- "type_kind": "numpy",
- "type_data": "int32"
- },
- "shape": []
- },
- {
- "m_def": "nomad.metainfo.metainfo.Quantity",
- "m_parent_index": 2,
- "m_parent_sub_section": "quantities",
- "name": "compositions",
- "description": "Normalized composition of the elements corresponding to each point for which the\nenergies are evaluated.",
- "type": {
- "type_kind": "numpy",
- "type_data": "float64"
- },
- "shape": [
- "n_points",
- "n_elements"
- ]
- },
- {
- "m_def": "nomad.metainfo.metainfo.Quantity",
- "m_parent_index": 3,
- "m_parent_sub_section": "quantities",
- "name": "references",
- "description": "Specifies the reference structure for each element.",
- "type": {
- "type_kind": "python",
- "type_data": "str"
- },
- "shape": [
- "n_elements"
- ]
- },
- {
- "m_def": "nomad.metainfo.metainfo.Quantity",
- "m_parent_index": 4,
- "m_parent_sub_section": "quantities",
- "name": "energy_of_formation",
- "description": "Values of the heat of formation corresponding to each point.",
- "type": {
- "type_kind": "numpy",
- "type_data": "float64"
- },
- "shape": [
- "n_points"
- ],
- "unit": "joule"
- },
- {
- "m_def": "nomad.metainfo.metainfo.Quantity",
- "m_parent_index": 5,
- "m_parent_sub_section": "quantities",
- "name": "energy_hulll",
- "description": "Values of the energy above the convex hull corresponding to each point.",
- "type": {
- "type_kind": "numpy",
- "type_data": "float64"
- },
- "shape": [
- "n_points"
- ],
- "unit": "joule"
- }
- ]
- },
- {
- "m_def": "nomad.metainfo.metainfo.Section",
- "m_parent_index": 5,
- "m_parent_sub_section": "section_definitions",
- "name": "NudgedElasticBand",
- "description": "Section containing results of a nudged-elastic band workflow.",
- "quantities": [
- {
- "m_def": "nomad.metainfo.metainfo.Quantity",
- "m_parent_index": 0,
- "m_parent_sub_section": "quantities",
- "name": "method",
- "description": "Specifies the method used in calculating the minumum energy path. Can be one of\nstandard, improved_tangeant, full_spring_force, spline_interpolation, string.",
- "type": {
- "type_kind": "python",
- "type_data": "str"
- },
- "shape": []
- },
- {
- "m_def": "nomad.metainfo.metainfo.Quantity",
- "m_parent_index": 1,
- "m_parent_sub_section": "quantities",
- "name": "climbing_image",
- "description": "Indicates if climbing image is used.",
- "type": {
- "type_kind": "python",
- "type_data": "bool"
- },
- "shape": []
- },
- {
- "m_def": "nomad.metainfo.metainfo.Quantity",
- "m_parent_index": 2,
- "m_parent_sub_section": "quantities",
- "name": "solid_state",
- "description": "Indicates if solid state nudged-elastic band calculation is performed.",
- "type": {
- "type_kind": "python",
- "type_data": "bool"
- },
- "shape": []
- },
- {
- "m_def": "nomad.metainfo.metainfo.Quantity",
- "m_parent_index": 3,
- "m_parent_sub_section": "quantities",
- "name": "optimizer",
- "description": "Specifies the method used in energy minimization.",
- "type": {
- "type_kind": "python",
- "type_data": "str"
- },
- "shape": []
- },
- {
- "m_def": "nomad.metainfo.metainfo.Quantity",
- "m_parent_index": 4,
- "m_parent_sub_section": "quantities",
- "name": "n_images",
- "description": "Number of images used in the calculation.",
- "type": {
- "type_kind": "numpy",
- "type_data": "int32"
- },
- "shape": []
- },
- {
- "m_def": "nomad.metainfo.metainfo.Quantity",
- "m_parent_index": 5,
- "m_parent_sub_section": "quantities",
- "name": "spring_constants",
- "description": "Spring constants for each spring.",
+ "name": "spring_constants",
+ "description": "Spring constants for each spring.",
"type": {
"type_kind": "numpy",
"type_data": "float64"
@@ -67429,7 +64135,7 @@ window.nomadArtifacts = {
"m_parent_index": 0,
"m_parent_sub_section": "sub_sections",
"name": "eos_fit",
- "sub_section": "/packages/19/section_definitions/6",
+ "sub_section": "/packages/18/section_definitions/6",
"repeats": true
}
]
@@ -68475,7 +65181,7 @@ window.nomadArtifacts = {
"m_parent_index": 0,
"m_parent_sub_section": "sub_sections",
"name": "strain_diagrams",
- "sub_section": "/packages/19/section_definitions/11",
+ "sub_section": "/packages/18/section_definitions/11",
"repeats": true
}
]
@@ -68603,7 +65309,7 @@ window.nomadArtifacts = {
"m_parent_index": 0,
"m_parent_sub_section": "sub_sections",
"name": "decomposition",
- "sub_section": "/packages/19/section_definitions/13",
+ "sub_section": "/packages/18/section_definitions/13",
"repeats": true
}
]
@@ -68848,7 +65554,7 @@ window.nomadArtifacts = {
"m_parent_index": 0,
"m_parent_sub_section": "sub_sections",
"name": "stability",
- "sub_section": "/packages/19/section_definitions/14",
+ "sub_section": "/packages/18/section_definitions/14",
"repeats": false
}
]
@@ -69112,7 +65818,7 @@ window.nomadArtifacts = {
"m_parent_index": 0,
"m_parent_sub_section": "sub_sections",
"name": "thermostat_parameters",
- "sub_section": "/packages/19/section_definitions/16",
+ "sub_section": "/packages/18/section_definitions/16",
"repeats": false
},
{
@@ -69120,7 +65826,7 @@ window.nomadArtifacts = {
"m_parent_index": 1,
"m_parent_sub_section": "sub_sections",
"name": "barostat_parameters",
- "sub_section": "/packages/19/section_definitions/17",
+ "sub_section": "/packages/18/section_definitions/17",
"repeats": false
}
]
@@ -69137,7 +65843,7 @@ window.nomadArtifacts = {
"m_parent_index": 0,
"m_parent_sub_section": "sub_sections",
"name": "radial_distribution_functions",
- "sub_section": "/packages/19/section_definitions/25",
+ "sub_section": "/packages/18/section_definitions/25",
"repeats": true
},
{
@@ -69145,7 +65851,7 @@ window.nomadArtifacts = {
"m_parent_index": 1,
"m_parent_sub_section": "sub_sections",
"name": "mean_squared_displacements",
- "sub_section": "/packages/19/section_definitions/30",
+ "sub_section": "/packages/18/section_definitions/30",
"repeats": true
}
]
@@ -69222,7 +65928,7 @@ window.nomadArtifacts = {
"m_parent_index": 0,
"m_parent_sub_section": "sub_sections",
"name": "integration_parameters",
- "sub_section": "/packages/19/section_definitions/18",
+ "sub_section": "/packages/18/section_definitions/18",
"repeats": false
},
{
@@ -69230,7 +65936,7 @@ window.nomadArtifacts = {
"m_parent_index": 1,
"m_parent_sub_section": "sub_sections",
"name": "results",
- "sub_section": "/packages/19/section_definitions/19",
+ "sub_section": "/packages/18/section_definitions/19",
"repeats": false
}
]
@@ -69433,7 +66139,7 @@ window.nomadArtifacts = {
"name": "RadialDistributionFunctionValues",
"description": "Section containing information regarding the values of radial distribution functions (rdfs).",
"base_sections": [
- "/packages/19/section_definitions/22"
+ "/packages/18/section_definitions/22"
],
"quantities": [
{
@@ -69474,7 +66180,7 @@ window.nomadArtifacts = {
"name": "RadialDistributionFunction",
"description": "Section containing information about the calculation of radial distribution functions (rdfs).",
"base_sections": [
- "/packages/19/section_definitions/23"
+ "/packages/18/section_definitions/23"
],
"sub_sections": [
{
@@ -69482,7 +66188,7 @@ window.nomadArtifacts = {
"m_parent_index": 0,
"m_parent_sub_section": "sub_sections",
"name": "radial_distribution_function_values",
- "sub_section": "/packages/19/section_definitions/24",
+ "sub_section": "/packages/18/section_definitions/24",
"repeats": true
}
]
@@ -69657,7 +66363,7 @@ window.nomadArtifacts = {
"name": "MeanSquaredDisplacementValues",
"description": "Section containing information regarding the values of a mean squared displacements (msds).",
"base_sections": [
- "/packages/19/section_definitions/26"
+ "/packages/18/section_definitions/26"
],
"quantities": [
{
@@ -69711,7 +66417,7 @@ window.nomadArtifacts = {
"m_parent_index": 0,
"m_parent_sub_section": "sub_sections",
"name": "diffusion_constant",
- "sub_section": "/packages/19/section_definitions/28",
+ "sub_section": "/packages/18/section_definitions/28",
"repeats": false
}
]
@@ -69723,7 +66429,7 @@ window.nomadArtifacts = {
"name": "MeanSquaredDisplacement",
"description": "Section containing information about a calculation of any mean squared displacements (msds).",
"base_sections": [
- "/packages/19/section_definitions/27"
+ "/packages/18/section_definitions/27"
],
"sub_sections": [
{
@@ -69731,7 +66437,7 @@ window.nomadArtifacts = {
"m_parent_index": 0,
"m_parent_sub_section": "sub_sections",
"name": "mean_squared_displacement_values",
- "sub_section": "/packages/19/section_definitions/29",
+ "sub_section": "/packages/18/section_definitions/29",
"repeats": true
}
]
@@ -69922,7 +66628,7 @@ window.nomadArtifacts = {
"description": "Reference to the input workflow.",
"type": {
"type_kind": "reference",
- "type_data": "/packages/19/section_definitions/34"
+ "type_data": "/packages/18/section_definitions/34"
},
"shape": []
},
@@ -69934,7 +66640,7 @@ window.nomadArtifacts = {
"description": "Reference to the output workflow.",
"type": {
"type_kind": "reference",
- "type_data": "/packages/19/section_definitions/34"
+ "type_data": "/packages/18/section_definitions/34"
},
"shape": []
},
@@ -70114,7 +66820,7 @@ window.nomadArtifacts = {
],
"type": {
"type_kind": "reference",
- "type_data": "/packages/19/section_definitions/34"
+ "type_data": "/packages/18/section_definitions/34"
},
"shape": [
"n_references"
@@ -70127,7 +66833,7 @@ window.nomadArtifacts = {
"m_parent_index": 0,
"m_parent_sub_section": "sub_sections",
"name": "task",
- "sub_section": "/packages/19/section_definitions/33",
+ "sub_section": "/packages/18/section_definitions/33",
"repeats": true
},
{
@@ -70138,7 +66844,7 @@ window.nomadArtifacts = {
"categories": [
"/packages/17/category_definitions/0"
],
- "sub_section": "/packages/19/section_definitions/32",
+ "sub_section": "/packages/18/section_definitions/32",
"repeats": false
},
{
@@ -70149,7 +66855,7 @@ window.nomadArtifacts = {
"categories": [
"/packages/17/category_definitions/0"
],
- "sub_section": "/packages/19/section_definitions/31",
+ "sub_section": "/packages/18/section_definitions/31",
"repeats": false
},
{
@@ -70160,7 +66866,7 @@ window.nomadArtifacts = {
"categories": [
"/packages/17/category_definitions/0"
],
- "sub_section": "/packages/19/section_definitions/9",
+ "sub_section": "/packages/18/section_definitions/9",
"repeats": false
},
{
@@ -70171,7 +66877,7 @@ window.nomadArtifacts = {
"categories": [
"/packages/17/category_definitions/0"
],
- "sub_section": "/packages/19/section_definitions/10",
+ "sub_section": "/packages/18/section_definitions/10",
"repeats": false
},
{
@@ -70179,7 +66885,7 @@ window.nomadArtifacts = {
"m_parent_index": 5,
"m_parent_sub_section": "sub_sections",
"name": "elastic",
- "sub_section": "/packages/19/section_definitions/12",
+ "sub_section": "/packages/18/section_definitions/12",
"repeats": false
},
{
@@ -70187,7 +66893,7 @@ window.nomadArtifacts = {
"m_parent_index": 6,
"m_parent_sub_section": "sub_sections",
"name": "molecular_dynamics",
- "sub_section": "/packages/19/section_definitions/20",
+ "sub_section": "/packages/18/section_definitions/20",
"repeats": false
},
{
@@ -70195,7 +66901,7 @@ window.nomadArtifacts = {
"m_parent_index": 7,
"m_parent_sub_section": "sub_sections",
"name": "debye_model",
- "sub_section": "/packages/19/section_definitions/8",
+ "sub_section": "/packages/18/section_definitions/8",
"repeats": false
},
{
@@ -70203,7 +66909,7 @@ window.nomadArtifacts = {
"m_parent_index": 8,
"m_parent_sub_section": "sub_sections",
"name": "equation_of_state",
- "sub_section": "/packages/19/section_definitions/7",
+ "sub_section": "/packages/18/section_definitions/7",
"repeats": false
},
{
@@ -70211,7 +66917,7 @@ window.nomadArtifacts = {
"m_parent_index": 9,
"m_parent_sub_section": "sub_sections",
"name": "nudged_elastic_band",
- "sub_section": "/packages/19/section_definitions/5",
+ "sub_section": "/packages/18/section_definitions/5",
"repeats": false
},
{
@@ -70219,7 +66925,7 @@ window.nomadArtifacts = {
"m_parent_index": 10,
"m_parent_sub_section": "sub_sections",
"name": "convex_hull",
- "sub_section": "/packages/19/section_definitions/4",
+ "sub_section": "/packages/18/section_definitions/4",
"repeats": false
},
{
@@ -70227,7 +66933,7 @@ window.nomadArtifacts = {
"m_parent_index": 11,
"m_parent_sub_section": "sub_sections",
"name": "adsorption",
- "sub_section": "/packages/19/section_definitions/3",
+ "sub_section": "/packages/18/section_definitions/3",
"repeats": false
},
{
@@ -70235,7 +66941,7 @@ window.nomadArtifacts = {
"m_parent_index": 12,
"m_parent_sub_section": "sub_sections",
"name": "magnetic_ordering",
- "sub_section": "/packages/19/section_definitions/2",
+ "sub_section": "/packages/18/section_definitions/2",
"repeats": false
},
{
@@ -70243,7 +66949,7 @@ window.nomadArtifacts = {
"m_parent_index": 13,
"m_parent_sub_section": "sub_sections",
"name": "raman",
- "sub_section": "/packages/19/section_definitions/1",
+ "sub_section": "/packages/18/section_definitions/1",
"repeats": false
},
{
@@ -70251,7 +66957,7 @@ window.nomadArtifacts = {
"m_parent_index": 14,
"m_parent_sub_section": "sub_sections",
"name": "interface",
- "sub_section": "/packages/19/section_definitions/0",
+ "sub_section": "/packages/18/section_definitions/0",
"repeats": false
},
{
@@ -70259,7 +66965,7 @@ window.nomadArtifacts = {
"m_parent_index": 15,
"m_parent_sub_section": "sub_sections",
"name": "thermodynamics",
- "sub_section": "/packages/19/section_definitions/15",
+ "sub_section": "/packages/18/section_definitions/15",
"repeats": false
}
]
@@ -70268,7 +66974,7 @@ window.nomadArtifacts = {
},
{
"m_def": "nomad.metainfo.metainfo.Package",
- "m_parent_index": 20,
+ "m_parent_index": 19,
"m_parent_sub_section": "packages",
"name": "nomad.datamodel.metainfo.workflow2",
"section_definitions": [
@@ -70360,7 +67066,7 @@ window.nomadArtifacts = {
"m_parent_sub_section": "sub_sections",
"name": "inputs",
"description": "All the links to sections that represent the inputs for this task.",
- "sub_section": "/packages/20/section_definitions/0",
+ "sub_section": "/packages/19/section_definitions/0",
"repeats": true
},
{
@@ -70369,7 +67075,7 @@ window.nomadArtifacts = {
"m_parent_sub_section": "sub_sections",
"name": "outputs",
"description": "All the links to sections that represent the outputs for this task.",
- "sub_section": "/packages/20/section_definitions/0",
+ "sub_section": "/packages/19/section_definitions/0",
"repeats": true
}
]
@@ -70381,7 +67087,7 @@ window.nomadArtifacts = {
"name": "TaskReference",
"description": "A proxy section that can be used to compose a workflow of tasks that are contained in a different entry or workflow.",
"base_sections": [
- "/packages/20/section_definitions/1"
+ "/packages/19/section_definitions/1"
],
"quantities": [
{
@@ -70399,7 +67105,7 @@ window.nomadArtifacts = {
"description": "A reference to the task that this section is a proxy for.",
"type": {
"type_kind": "reference",
- "type_data": "/packages/20/section_definitions/1"
+ "type_data": "/packages/19/section_definitions/1"
}
}
]
@@ -70414,7 +67120,7 @@ window.nomadArtifacts = {
"/packages/15/category_definitions/5"
],
"base_sections": [
- "/packages/20/section_definitions/1",
+ "/packages/19/section_definitions/1",
"/packages/15/section_definitions/1"
],
"sub_sections": [
@@ -70424,7 +67130,7 @@ window.nomadArtifacts = {
"m_parent_sub_section": "sub_sections",
"name": "tasks",
"description": "The tasks of this workflow as a repeating sub section. Use TaskReference if tasks cannot be contained.",
- "sub_section": "/packages/20/section_definitions/1",
+ "sub_section": "/packages/19/section_definitions/1",
"repeats": true
}
]
@@ -70433,7 +67139,7 @@ window.nomadArtifacts = {
},
{
"m_def": "nomad.metainfo.metainfo.Package",
- "m_parent_index": 21,
+ "m_parent_index": 20,
"m_parent_sub_section": "packages",
"name": "nomad.datamodel.optimade",
"section_definitions": [
@@ -71139,7 +67845,7 @@ window.nomadArtifacts = {
"m_parent_index": 0,
"m_parent_sub_section": "sub_sections",
"name": "species",
- "sub_section": "/packages/21/section_definitions/0",
+ "sub_section": "/packages/20/section_definitions/0",
"repeats": true
}
]
@@ -71148,7 +67854,7 @@ window.nomadArtifacts = {
},
{
"m_def": "nomad.metainfo.metainfo.Package",
- "m_parent_index": 22,
+ "m_parent_index": 21,
"m_parent_sub_section": "packages",
"name": "nomad.metainfo.metainfo",
"section_definitions": [
@@ -71214,7 +67920,7 @@ window.nomadArtifacts = {
"description": "All metainfo definitions can be put into one or more `categories`.\nCategories allow to organize the definitions themselves. It is different from\nsections, which organize the data (e.g. quantity values) and not the definitions\nof data (e.g. quantities definitions). See :ref:`metainfo-categories` for more\ndetails.",
"type": {
"type_kind": "reference",
- "type_data": "/packages/22/section_definitions/5"
+ "type_data": "/packages/21/section_definitions/5"
},
"shape": [
"0..*"
@@ -71291,7 +67997,7 @@ window.nomadArtifacts = {
"m_parent_sub_section": "sub_sections",
"name": "attributes",
"description": "The attributes that can further qualify property values.",
- "sub_section": "/packages/22/section_definitions/1",
+ "sub_section": "/packages/21/section_definitions/1",
"repeats": true
}
]
@@ -71303,7 +68009,7 @@ window.nomadArtifacts = {
"name": "Attribute",
"description": "Attributes can be used to qualify all properties (subsections and quantities) with simple scalar values.",
"base_sections": [
- "/packages/22/section_definitions/0"
+ "/packages/21/section_definitions/0"
],
"constraints": [
"is_primitive"
@@ -71343,7 +68049,7 @@ window.nomadArtifacts = {
"name": "Property",
"description": "A common base-class for section properties: subsections and quantities.",
"base_sections": [
- "/packages/22/section_definitions/0"
+ "/packages/21/section_definitions/0"
]
},
{
@@ -71353,7 +68059,7 @@ window.nomadArtifacts = {
"name": "Section",
"description": "Instances of the class :class:`Section` are created by writing Python classes that extend :class:`MSection` like this:\n\n.. code-block:: python\n\n class SectionName(BaseSection):\n ''' Section description '''\n m_def = Section(**section_attributes)\n\n quantity_name = Quantity(**quantity_attributes)\n sub_section_name = SubSection(**sub_section_attributes)\n\nWe call such classes *section classes*. They are not the *section definition*, but just\nrepresentation of it in Python syntax. The *section definition* (in instance of :class:`Section`)\nwill be created for each of these classes and stored in the ``m_def`` property. See\n:ref:`metainfo-reflection` for more details.\n\nMost of the attributes for a :class:`Section` instance will be set automatically from\nthe section class:",
"base_sections": [
- "/packages/22/section_definitions/0"
+ "/packages/21/section_definitions/0"
],
"constraints": [
"resolved_base_sections",
@@ -71367,7 +68073,7 @@ window.nomadArtifacts = {
"name": "base_sections",
"type": {
"type_kind": "reference",
- "type_data": "/packages/22/section_definitions/3"
+ "type_data": "/packages/21/section_definitions/3"
},
"shape": [
"0..*"
@@ -71381,7 +68087,7 @@ window.nomadArtifacts = {
"name": "extending_sections",
"type": {
"type_kind": "reference",
- "type_data": "/packages/22/section_definitions/3"
+ "type_data": "/packages/21/section_definitions/3"
},
"shape": [
"0..*"
@@ -71406,7 +68112,7 @@ window.nomadArtifacts = {
"name": "inheriting_sections",
"type": {
"type_kind": "reference",
- "type_data": "/packages/22/section_definitions/3"
+ "type_data": "/packages/21/section_definitions/3"
},
"shape": [
"0..*"
@@ -71583,7 +68289,7 @@ window.nomadArtifacts = {
"m_parent_index": 0,
"m_parent_sub_section": "sub_sections",
"name": "quantities",
- "sub_section": "/packages/22/section_definitions/6",
+ "sub_section": "/packages/21/section_definitions/6",
"repeats": true
},
{
@@ -71591,7 +68297,7 @@ window.nomadArtifacts = {
"m_parent_index": 1,
"m_parent_sub_section": "sub_sections",
"name": "sub_sections",
- "sub_section": "/packages/22/section_definitions/7",
+ "sub_section": "/packages/21/section_definitions/7",
"repeats": true
},
{
@@ -71605,7 +68311,7 @@ window.nomadArtifacts = {
"inner_sections",
"sections"
],
- "sub_section": "/packages/22/section_definitions/3",
+ "sub_section": "/packages/21/section_definitions/3",
"repeats": true
}
]
@@ -71617,7 +68323,7 @@ window.nomadArtifacts = {
"name": "Package",
"description": "Packages organize metainfo definitions alongside Python modules Each Python module with metainfo Definition (explicitly or implicitly) has a member\n``m_package`` with an instance of this class. Definitions (categories, sections) in\nPython modules are automatically added to the module's :class:`Package`.\nPackages are not nested and rather have the fully qualified Python module name as\nname.\n\nThis allows to inspect all definitions in a Python module and automatically puts\nmodule name and docstring as :class:`Package` name and description.\n\nBesides the regular :class:`Definition` attributes, packages can have the following\nattributes:",
"base_sections": [
- "/packages/22/section_definitions/0"
+ "/packages/21/section_definitions/0"
],
"quantities": [
{
@@ -71656,7 +68362,7 @@ window.nomadArtifacts = {
"section_defs",
"sections"
],
- "sub_section": "/packages/22/section_definitions/3",
+ "sub_section": "/packages/21/section_definitions/3",
"repeats": true
},
{
@@ -71668,7 +68374,7 @@ window.nomadArtifacts = {
"aliases": [
"category_defs"
],
- "sub_section": "/packages/22/section_definitions/5",
+ "sub_section": "/packages/21/section_definitions/5",
"repeats": true
}
]
@@ -71680,7 +68386,7 @@ window.nomadArtifacts = {
"name": "Category",
"description": "Categories allow to organize metainfo definitions (not metainfo data like sections do) Each definition, including categories themselves, can belong to a set of categories.\nCategories therefore form a hierarchy of concepts that definitions can belong to, i.e.\nthey form a `is a` relationship.",
"base_sections": [
- "/packages/22/section_definitions/0"
+ "/packages/21/section_definitions/0"
]
},
{
@@ -71690,7 +68396,7 @@ window.nomadArtifacts = {
"name": "Quantity",
"description": "To define quantities, instantiate :class:`Quantity` as a class attribute values in a `section classes`. The name of a quantity is automatically taken from its `section class`\nattribute. You can provide all other attributes to the constructor with keyword arguments\n\nSee :ref:`metainfo-sections` to learn about `section classes`.\nIn Python terms, ``Quantity`` is a descriptor. Descriptors define how to get and\nset attributes in a Python object. This allows us to use sections like regular\nPython objects and quantity like regular Python attributes.\n\nEach quantity must define a basic data type and a shape. The values of a quantity must\nfulfil the given type. The default shape is a single value. Quantities can also have\nphysical units. Units are applied to all values.",
"base_sections": [
- "/packages/22/section_definitions/2"
+ "/packages/21/section_definitions/2"
],
"constraints": [
"dimensions",
@@ -71842,7 +68548,7 @@ window.nomadArtifacts = {
"name": "SubSection",
"description": "Like quantities, subsections are defined in a `section class` as attributes of this class. Unlike quantities, each subsection definition becomes a property of\nthe corresponding `section definition` (parent). A subsection definition references\nanother `section definition` as the subsection (child). As a consequence, parent\n`section instances` can contain child `section instances` as subsections.\n\nContrary to the old NOMAD metainfo, we distinguish between subsection the section\nand subsection the property. This allows to use on child `section definition` as\nsubsection of many parent `section definitions`.",
"base_sections": [
- "/packages/22/section_definitions/2"
+ "/packages/21/section_definitions/2"
],
"constraints": [
"has_sub_section"
@@ -71861,7 +68567,7 @@ window.nomadArtifacts = {
],
"type": {
"type_kind": "reference",
- "type_data": "/packages/22/section_definitions/3"
+ "type_data": "/packages/21/section_definitions/3"
}
},
{
@@ -71915,7 +68621,7 @@ window.nomadArtifacts = {
"m_parent_sub_section": "sub_sections",
"name": "packages",
"description": "Packages in this environment.",
- "sub_section": "/packages/22/section_definitions/4",
+ "sub_section": "/packages/21/section_definitions/4",
"repeats": true
}
]
@@ -71924,21 +68630,7 @@ window.nomadArtifacts = {
}
]
},
- "parserMetadata": {
- "VASP": {
- "codeCategory": "Atomistic code",
- "codeLabel": "VASP",
- "codeLabelStyle": "All in capitals",
- "codeName": "vasp",
- "codeUrl": "https://www.vasp.at/",
- "parserDirName": "dependencies/electronic/electronicparsers/vasp/",
- "parserGitUrl": "https://github.com/nomad-coe/electronic-parsers.git",
- "parserSpecific": "",
- "preamble": "",
- "status": "production",
- "tableOfFiles": "|Input Filename| Description|\n|--- | --- |\n|`vasprun.xml` | **Mainfile** in plain-text (structured) XML format |\n|`OUTCAR` | plain-text (semi-structured) file, VAPS's detailed output. Read by NOMAD only as fallback to parse `outcar` data |\n"
- }
- },
+ "parserMetadata": {},
"toolkitMetadata": {
"tutorials": [
{
diff --git a/nomad/parsing/elabftw/elabftw.py b/nomad/parsing/elabftw/elabftw.py
index f8b649c42c3634b140b7f1ec4c34053c6446d1b9..7097461c5b1e2410c0ca94b45b4af7b61bff4d8e 100644
--- a/nomad/parsing/elabftw/elabftw.py
+++ b/nomad/parsing/elabftw/elabftw.py
@@ -20,16 +20,81 @@ from typing import Union, Iterable
import json
import re
+import numpy as np
+
from nomad.datamodel import EntryArchive, EntryData
from nomad.datamodel.data import ElnIntegrationCategory
from nomad.metainfo import Package, Quantity, JSON, MSection, Datetime, SubSection, Section
from nomad import utils
-from nomad.metainfo.util import camel_case_to_snake_case
+from nomad.metainfo.util import camel_case_to_snake_case, MEnum
from nomad.parsing.parser import MatchingParser
m_package = Package(name='elabftw')
+class ExtrafieldBase(MSection):
+ m_def = Section(label_quantity='name')
+ name = Quantity(type=str, a_eln=dict(component='StringEditQuantity'))
+ description = Quantity(type=str, a_eln=dict(component='StringEditQuantity'))
+
+
+class ExtrafieldURL(ExtrafieldBase):
+ url = Quantity(type=str, a_eln=dict(component='URLEditQuantity'))
+
+
+class ExtrafieldDate(ExtrafieldBase):
+ date = Quantity(type=Datetime, a_eln=dict(component='DateTimeEditQuantity'))
+
+
+class ExtrafieldText(ExtrafieldBase):
+ text = Quantity(type=str, a_eln=dict(component='StringEditQuantity'))
+
+
+class ExtrafieldRadio(ExtrafieldBase):
+
+ # def __init__(self, options):
+ # super()
+ # self.options = options
+ radio = Quantity(
+ type=MEnum([]),
+ shape=[],
+ description='extra field of type radio',
+ a_eln=dict(component='RadioEnumEditQuantity'))
+
+
+class ExtrafieldNumber(ExtrafieldBase):
+ number = Quantity(
+ type=np.dtype(np.float64),
+ shape=[],
+ description='extra field of type number',
+ a_eln=dict(component='NumberEditQuantity'))
+
+
+class ExtrafieldCheckbox(ExtrafieldBase):
+ checkbox = Quantity(
+ type=bool,
+ shape=[],
+ description='extra field of type checkbox',
+ a_eln=dict(component='BoolEditQuantity'))
+
+
+class ExtrafieldSelect(ExtrafieldBase):
+ select = Quantity(
+ type=MEnum([]),
+ description='extra field of type select',
+ a_eln=dict(component='AutocompleteEditQuantity'))
+
+
+class ELabFTWExtralinks(MSection):
+ url_fields = SubSection(sub_section=ExtrafieldURL, repeats=True)
+ date_fields = SubSection(sub_section=ExtrafieldDate, repeats=True)
+ text_fields = SubSection(sub_section=ExtrafieldText, repeats=True)
+ radio_fields = SubSection(sub_section=ExtrafieldRadio, repeats=True)
+ number_fields = SubSection(sub_section=ExtrafieldNumber, repeats=True)
+ checkbox_fields = SubSection(sub_section=ExtrafieldCheckbox, repeats=True)
+ select_fields = SubSection(sub_section=ExtrafieldSelect, repeats=True)
+
+
def _remove_at_sign_from_keys(obj):
for k, v in list(obj.items()):
if k.startswith('@'):
@@ -127,6 +192,7 @@ class ELabFTWExperimentData(MSection):
items_links = SubSection(sub_section=ELabFTWItemLink, repeats=True)
experiments_links = SubSection(sub_section=ELabFTWExperimentLink, repeats=True)
steps = SubSection(sub_section=ELabFTWSteps, repeats=True)
+ formatted_extra_fields = SubSection(sub_section=ELabFTWExtralinks)
class ELabFTWComment(MSection):
@@ -146,7 +212,7 @@ class ELabFTWBaseSection(MSection):
'''
General information on the exported files/experiment of the .eln file
'''
- m_def = Section(label_quantity='type')
+ m_def = Section(label_quantity='name')
id = Quantity(type=str, description='id of the current data-type')
type = Quantity(type=str, description='type of the data')
@@ -226,6 +292,15 @@ _element_type_section_mapping = {
'Dataset': ElabFTWDataset
}
+_extra_fields_mapping = {
+ 'url': ExtrafieldURL,
+ 'date': ExtrafieldDate,
+ 'text': ExtrafieldText,
+ 'radio': ExtrafieldRadio,
+ 'number': ExtrafieldNumber,
+ 'checkbox': ExtrafieldCheckbox,
+ 'select': ExtrafieldSelect,
+}
class ELabFTWParser(MatchingParser):
creates_children = True
@@ -284,8 +359,8 @@ class ELabFTWParser(MatchingParser):
try:
exp_external_id = raw_experiment['url'].split('&id=')[1]
exp_archive.metadata.external_id = exp_external_id
- except Exception:
- logger.error('Could not set the the external_id from the experiment url')
+ except Exception as e:
+ logger.error('Could not set the the external_id from the experiment url', exc_info=e)
author_full_name = ' '.join([raw_experiment['author']['given_name'], raw_experiment['author']['family_name']])
elabftw_experiment.post_process(full_name=author_full_name)
@@ -315,11 +390,31 @@ class ELabFTWParser(MatchingParser):
raise ELabFTWParserError(f'Couldn\'t find export-elabftw.json file.')
experiment_data = ELabFTWExperimentData()
+ experiment_data.formatted_extra_fields = ELabFTWExtralinks()
try:
experiment_data.m_update_from_dict(export_data[0])
experiment_data.extra_fields = export_data[0]['metadata']['extra_fields']
except IndexError:
logger.warning(f'Couldn\'t read and parse the data from export-elabftw.json file')
+
+ for element_name, element_content in experiment_data.extra_fields.items():
+ try:
+ element_type = element_content['type']
+ nomad_element = _extra_fields_mapping[element_type]()
+ except KeyError as e:
+ logger.error('element type in extra fields is not recognized.', exc_info=e)
+ continue
+ if options := element_content.get('options', None):
+ setattr(getattr(nomad_element.m_def.section_cls, element_type), 'type', MEnum(options))
+ nomad_element = nomad_element.m_def.section_cls()
+
+ nomad_element.name = element_name
+ nomad_element.description = element_content['description']
+ nomad_element_quantity = nomad_element.m_def.all_properties[element_type]
+ nomad_element.m_set(nomad_element_quantity, element_content['value'])
+
+ experiment_data.formatted_extra_fields[f"{element_type}_fields"].append(nomad_element)
+
elabftw_experiment.experiment_data = experiment_data
for file_id in raw_experiment['has_part']: