Commit 454b256e authored by Mohamed, Fawzi Roberto (fawzi)'s avatar Mohamed, Fawzi Roberto (fawzi)
Browse files

common: improving method to method and calculation to calculation references

remove starting_point_method_ref and starting _point_calculation_ref and
replace them with section_method_to_method_refs and
section_calculation_to_calculation_refs that allow external references
and annotated references (not only starting point, but also qm_1 mm_1 and
similar for QM/MM methods...
parent 1e244119
......@@ -338,7 +338,7 @@
]
}, {
"derived": true,
"description": "String that represents the method used to calculate the energy_current. If the method is perturbative, this string does not describe the starting_point_method_ref. For normal ab-initio calculation, for example, this is composed of XC_method and basis_set and a unique sha, see [calculation\\_method\\_current wiki page](https://gitlab.mpcdf.mpg.de/nomad-lab/public-wiki/wikis/metainfo/calculation-method-current) for the details",
"description": "String that represents the method used to calculate the energy_current. If the method is perturbative, this string does not describe the starting point method which should be referenced through section_method_to_method_refs. For normal ab-initio calculation, for example, this is composed of XC_method and basis_set and a unique sha, see [calculation\\_method\\_current wiki page](https://gitlab.mpcdf.mpg.de/nomad-lab/public-wiki/wikis/metainfo/calculation-method-current) for the details",
"dtypeStr": "C",
"name": "calculation_method_current",
"repeats": false,
......@@ -357,7 +357,7 @@
]
}, {
"derived": true,
"description": "String that uniquely represents the method used to calculate energy_total, this consists of calculation_method_current plus '@' and calculation_method of the starting_point_method_ref for perturbative methods.",
"description": "String that uniquely represents the method used to calculate energy_total, this consists of calculation_method_current plus '@' and calculation_method of the method_to_method_ref with method_to_method_kind = starting\\_point for perturbative methods.",
"dtypeStr": "C",
"name": "calculation_method",
"repeats": false,
......@@ -365,6 +365,36 @@
"superNames": [
"section_method"
]
}, {
"description": "Url used to reference externally stored calculation as defined in the [calculation\\_to\\_calculation\\_external\\_url wiki page](https://gitlab.mpcdf.mpg.de/nomad-lab/public-wiki/wikis/metainfo/calculation-to-calculation-external-url)",
"dtypeStr": "C",
"name": "calculation_to_calculation_external_url",
"repeats": false,
"shape": [],
"superNames": [
"section_calculation_to_calculation_refs"
]
}, {
"description": "String defining the kind of relatioship that there is between this and the referenced calculation. Valid values are described in the [calculation\\_to\\_calculation\\_kind wiki page](https://gitlab.mpcdf.mpg.de/nomad-lab/public-wiki/wikis/metainfo/calculation-to-calculation-kind)",
"dtypeStr": "C",
"name": "calculation_to_calculation_kind",
"repeats": false,
"shape": [],
"superNames": [
"section_calculation_to_calculation_refs"
]
}, {
"description": "Reference to another calculation. If both this and calculation_to_calculation_external_url are given this is assumed to be a local copy of the url. The kind of relationship is specified by calculation_to_calculation_kind.",
"dtypeStr": "r",
"name": "calculation_to_calculation_ref",
"referencedSections": [
"section_single_configuration_calculation"
],
"repeats": false,
"shape": [],
"superNames": [
"section_calculation_to_calculation_refs"
]
}, {
"description": "Properties actually defining the current configuration",
"kindStr": "type_abstract_document_content",
......@@ -590,7 +620,7 @@
],
"units": "J"
}, {
"description": "energy calculated with calculation_method_current. energy_current is equal to energy_total for non perturbation methods, and to the correction (energy_total - starting_point_calculation_ref.energy_total) for preturbation methods. [energy\\_current wiki page](https://gitlab.mpcdf.mpg.de/nomad-lab/public-wiki/wikis/metainfo/energy-current)",
"description": "energy calculated with calculation_method_current. energy_current is equal to energy_total for non perturbation methods, and to the correction (energy_total - energy_total of the calculation_to_calculation_ref with calculation_to_calculation_kind = starting\\_point) for preturbation methods. [energy\\_current wiki page](https://gitlab.mpcdf.mpg.de/nomad-lab/public-wiki/wikis/metainfo/energy-current)",
"dtypeStr": "f",
"name": "energy_current",
"repeats": false,
......@@ -1428,6 +1458,31 @@
"superNames": [
"section_method_atom_kind"
]
}, {
"description": "Url used to reference externally stored methods as defined in the [method\\_to\\_method\\_external\\_url wiki page](https://gitlab.mpcdf.mpg.de/nomad-lab/public-wiki/wikis/metainfo/method-to-method-external-url)",
"dtypeStr": "C",
"name": "method_to_method_external_url",
"repeats": false,
"shape": [],
"superNames": [
"section_method_to_method_refs"
]
}, {
"description": "String describing the relationship between the referenced method and this one. Valid values are described in the [method\\_to\\_method\\_kind page](https://gitlab.mpcdf.mpg.de/nomad-lab/public-wiki/wikis/metainfo/method-to-method-kind).",
"dtypeStr": "C",
"name": "method_to_method_kind",
"shape": [],
"superNames": [
"section_method_to_method_refs"
]
}, {
"description": "Reference to a local method. If both this and method_to_method_external_url are given this is expected to contain a local copy of that value. The kind of relationship between this method and the referenced one is described by method_to_method_kind.",
"dtypeStr": "r",
"name": "method_to_method_ref",
"shape": [],
"superNames": [
"section_method_to_method_refs"
]
}, {
"description": "Reference to the topology and force fields to be used",
"dtypeStr": "r",
......@@ -1973,6 +2028,13 @@
"superNames": [
"section_single_configuration_calculation"
]
}, {
"description": "Section that describes relationships between single configuration calculations.",
"kindStr": "type_section",
"name": "section_calculation_to_calculation_refs",
"superNames": [
"section_single_configuration_calculation"
]
}, {
"description": "describes a constraint between arbitrary atoms",
"kindStr": "type_section",
......@@ -2047,6 +2109,14 @@
"superNames": [
"section_method"
]
}, {
"description": "Describes connections between methods (for example the starting point of a perturbation, or the QM and MM methods in a QM/MM method",
"kindStr": "type_section",
"name": "section_method_to_method_refs",
"shape": [],
"superNames": [
"section_method"
]
}, {
"description": "section_method contains the various parameters that define the theory used and the approximations done (convergence, thresholds,...) to perform a single configuration calculation. It does *not* contain the settings for dynamics, goemetry optimization,...",
"kindStr": "type_section",
......@@ -2390,30 +2460,6 @@
"superNames": [
"section_single_configuration_calculation"
]
}, {
"description": "Reference to the starting point (unperturbed) calculation, onto which the perturbative methods are constructed.",
"dtypeStr": "r",
"name": "starting_point_calculation_ref",
"referencedSections": [
"section_single_configuration_calculation"
],
"repeats": false,
"shape": [],
"superNames": [
"section_single_configuration_calculation"
]
}, {
"description": "Reference to the method of the starting point (unperturbed) calculation, onto which the perturbative methods are constructed.",
"dtypeStr": "r",
"name": "starting_point_method_ref",
"referencedSections": [
"section_method"
],
"repeats": false,
"shape": [],
"superNames": [
"section_method"
]
}, {
"description": "Method used to compute the stress tensor stored in stress_tensor_value. This is an *alternative* to the stress tensor defined in stress_tensor_method. The value of the latter is stored in stress_tensor and (if needed) it is the one used for dynamics, minimization,...",
"dtypeStr": "C",
......@@ -2782,7 +2828,7 @@
]
}, {
"derived": true,
"description": "Exchange correlation (XC) method used for energy_XC consisting of XC_method_current plus '@' and the XC_method of the starting_point_method_ref for perturbative methods.",
"description": "Exchange correlation (XC) method used for energy_XC consisting of XC_method_current plus '@' and the XC_method of the method_to_method_ref with method_to_method_kind = starting\\_point_method for perturbative methods.",
"dtypeStr": "C",
"name": "XC_method",
"repeats": false,
......
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