...
 
Commits (24)
......@@ -49,3 +49,5 @@ TAGS
lib/
env/
*.egg-info
{
"type": "nomad_meta_info_1_0",
"description": "file collecting all the meta info files for the ems nomad (i.e. with all method specific parts)",
"dependencies": [
{ "relativePath": "general.experimental.nomadmetainfo.json" },
{ "parser": "skeletonparser", "path": "skeleton.nomadmetainfo.json" },
{ "parser": "mpesparser", "path": "mpes.nomadmetainfo.json" }
],
"metaInfos": [ ]
}
{
"type": "nomad_meta_info_1_0",
"description": "meta info used by the BAND parser, all names are expected to start with x_band_",
"dependencies": [ {
"relativePath": "common.nomadmetainfo.json"
}, {
"relativePath": "meta_types.nomadmetainfo.json"
}],
"metaInfos": [ ]
}
......@@ -1240,5 +1240,13 @@
"superNames": [
"section_excited_states"
]
},
{
"description": "Most systems in a run are only minor variations of each other. Systems marked representative where chosen to be representative for all systems in the run.",
"name": "is_representative",
"dtypeStr": "b",
"superNames": [
"section_system"
]
}]
}
......@@ -52,9 +52,9 @@
"superNames": [
"x_elastic_section_fitting_parameters" ]
}, {
"description": "polinomial order used to fit the Energy vs. volume curve and to calculate the elastic constants",
"description": "polynomial order used to fit the Energy vs. volume curve and to calculate the elastic constants",
"dtypeStr": "i",
"name": "x_elastic_fitting_parameters_polinomial_order",
"name": "x_elastic_fitting_parameters_polynomial_order",
"shape": ["x_elastic_number_of_deformations"],
"superNames": [
"x_elastic_section_fitting_parameters" ]
......@@ -83,9 +83,9 @@
"superNames": [
"x_elastic_section_strain_diagrams" ]
}, {
"description": "Order of the polinomial fit",
"description": "Order of the polynomial fit",
"dtypeStr": "i",
"name": "x_elastic_strain_diagram_polinomial_fit_order",
"name": "x_elastic_strain_diagram_polynomial_fit_order",
"shape": [],
"superNames": [
"x_elastic_section_strain_diagrams" ]
......
{
"type":"nomad_meta_info_1_0",
"description":"General definitions for experiment data, not specific to any experimental method or parser.",
"dependencies":[
{ "relativePath":"general.experimental.nomadmetainfo.json" }
],
"metaInfos":[
{
"description":"This section contains information about the stored data.",
"kindStr":"type_section",
"name":"section_data",
"superNames":[
"section_experiment"
]
},
{
"description":"The name of the repository, where the data is stored.",
"dtypeStr":"C",
"name":"data_repository_name",
"superNames":["section_data"]
},
{
"description":"An URL to the repository, where the data is stored.",
"dtypeStr":"C",
"name":"data_repository_url",
"superNames":["section_data"]
},
{
"description":"An URL to an image file that contains a preview.",
"dtypeStr":"C",
"name":"data_preview_url",
"superNames":["section_data"]
}
]
}
\ No newline at end of file
{
"type":"nomad_meta_info_1_0",
"description":"General definitions for experiment data, not specific to any experimental method or parser.",
"dependencies":[
{ "relativePath":"general.experimental.nomadmetainfo.json" }
],
"metaInfos":[
{
"description": "This section contains information about the applied experimental method.",
"kindStr":"type_section",
"name":"section_method",
"superNames":["section_experiment"]
},
{
"description": "Full name of the experimental method in use",
"name": "experiment_method_name",
"dtypeStr": "C",
"superNames":[ "section_method" ]
},
{
"description": "Abbreviated name (i.e. acronym) of the experimental method",
"name": "experiment_method_abbreviation",
"dtypeStr": "C",
"superNames":[ "section_method" ]
},
{
"description": "Name or model of the equipment (e.g. in full or an acronym).",
"name": "equipment_description",
"dtypeStr": "C",
"superNames":[ "section_method" ]
},
{
"description":"The probing method used",
"dtypeStr":"C",
"superNames":["section_method"],
"name":"probing_method",
"values": [
"laser pulses",
"electric pulsing",
"x-rays",
"electrons"
]
}
]
}
\ No newline at end of file
{
"type":"nomad_meta_info_1_0",
"description":"General definitions for experiment data, not specific to any experimental method or parser.",
"dependencies":[
{ "relativePath":"general.nomadmetainfo.json" },
{ "relativePath":"general.experimental.method.nomadmetainfo.json" },
{ "relativePath":"general.experimental.sample.nomadmetainfo.json" },
{ "relativePath":"general.experimental.data.nomadmetainfo.json" }
],
"metaInfos":[
{
"description":"The root section for all (meta)data that belongs to a single experiment.",
"kindStr":"type_section",
"name":"section_experiment",
"superNames":[]
},
{
"description": "A descriptive summary of the content of the experiment.",
"name": "experiment_summary",
"dtypeStr": "C",
"superNames": ["section_experiment"]
},
{
"description":"Name of the city and country the experiment took place, format 'Country, City'",
"dtypeStr":"C",
"name":"experiment_location",
"superNames":[
"section_experiment"
]
},
{
"description": "Name of the institution hosting the experimental facility (e.g. in full or an acronym).",
"name": "experiment_facility_institution",
"dtypeStr": "C",
"superNames": ["section_experiment"]
},
{
"description": "Name of the experimental facility (e.g. in full or an acronym).",
"name": "experiment_facility_name",
"dtypeStr": "C",
"superNames": ["section_experiment"]
},
{
"description":"The datetime of the beginning of the experiment in seconds since epoch.",
"dtypeStr":"i64",
"name":"experiment_time",
"superNames":[
"section_experiment"
],
"units":"s"
},
{
"description":"The datetime of the experiment end in seconds since epoch.",
"dtypeStr":"i64",
"name":"experiment_end_time",
"superNames":[
"section_experiment"
],
"units":"s"
},
{
"description":"This section contains information about the stored data.",
"kindStr":"type_section",
"name":"section_data",
"superNames":[
"section_experiment"
]
},
{
"description":"The name of the repository, where the data is stored.",
"dtypeStr":"C",
"name":"data_repository_name",
"superNames":["section_data"]
},
{
"description":"An URL to the repository, where the data is stored.",
"dtypeStr":"C",
"name":"data_repository_url",
"superNames":["section_data"]
},
{
"description":"An URL to an image file that contains a preview.",
"dtypeStr":"C",
"name":"data_preview_url",
"superNames":["section_data"]
}
]
}
\ No newline at end of file
{
"type":"nomad_meta_info_1_0",
"description":"General definitions for experiment data, not specific to any experimental method or parser.",
"dependencies":[
{ "relativePath":"general.experimental.nomadmetainfo.json" }
],
"metaInfos":[
{
"description":"The section for all sample related (meta)data that was used in the experiment.",
"kindStr":"type_section",
"name":"section_sample",
"superNames":[
"section_experiment"
]
},
{
"description": "Description of the sample used in the experiment.",
"name": "sample_description",
"dtypeStr": "C",
"shape": [],
"superNames": ["section_sample"],
"units": ""
},
{
"description": "Identification number or signatures of the sample used.",
"name": "sample_id",
"dtypeStr": "C",
"shape": [],
"superNames": ["section_method"],
"units": ""
},
{
"description":"The physical state of the sample.",
"dtypeStr":"C",
"name":"sample_state",
"superNames":["section_sample"],
"values":{
"gas":"Gas",
"liquid":"Liquid",
"solution":"Solution"
}
},
{
"description":"The chemical formula that describes the sample",
"dtypeStr":"C",
"superNames":["section_sample"],
"name":"sample_chemical_formula"
},
{
"description":"The chemical name that describes the sample",
"dtypeStr":"C",
"superNames":["section_sample"],
"name":"sample_chemical_name"
},
{
"description":"The chemical name that describes the sample",
"dtypeStr":"C",
"superNames":["section_sample"],
"name":"sample_atom_labels",
"shape": ["n"]
},
{
"description": "Number of distinct chemical elements in the sample.",
"name": "number_of_elements",
"dtypeStr": "i",
"kindStr": "type_dimension",
"shape": [],
"superNames": ["section_sample"]
},
{
"description": "Space group of the sample compound (if crystalline).",
"name": "sample_space_group",
"dtypeStr": "i",
"shape": [],
"superNames": ["section_sample"],
"units": ""
},
{
"description":"The temperature of the sample during the experiment in K.",
"dtypeStr":"f",
"superNames":["section_sample"],
"name":"sample_temperature",
"units": "K"
},
{
"description":"The sample microstructure",
"dtypeStr":"C",
"superNames":["section_sample"],
"name":"sample_microstructure",
"values": [
"thin films",
"nanoscale objects",
"bulk sample, single-crystalline",
"bulk sample, polycrystalline"
]
},
{
"description":"The constituents",
"dtypeStr":"C",
"superNames":["section_sample"],
"name":"sample_constituents",
"values": [
"multi phase",
"single phase"
]
}
]
}
\ No newline at end of file
{
"type":"nomad_meta_info_1_0",
"description":"General definitions, not specific to any domain, field, or parser",
"dependencies":[],
"metaInfos":[
{
"description":"General information about this entry that is independent from its domain, field, or used parser",
"kindStr":"type_section",
"name":"section_entry_info",
"superNames":[]
},
{
"description":"Upload datetime, given as total number of seconds is the elapsed since the unix epoch (1 January 1970)",
"dtypeStr":"i64",
"name":"entry_upload_time",
"superNames":[
"section_entry_info"
]
},
{
"description":"Name of the uploader, given as lastname, firstname.",
"dtypeStr":"C",
"name":"entry_uploader_name",
"superNames":[
"section_entry_info"
]
},
{
"description":"The id of the uploader.",
"dtypeStr":"C",
"name":"entry_uploader_id",
"superNames":[
"section_entry_info"
]
},
{
"description":"Nomad upload id",
"dtypeStr":"C",
"name":"upload_id",
"superNames":[
"section_entry_info"
]
},
{
"description":"Nomad calc id.",
"dtypeStr":"C",
"name":"calc_id",
"superNames":[
"section_entry_info"
]
},
{
"description":"Calculation hash based on raw file contents.",
"dtypeStr":"C",
"name":"calc_hash",
"superNames":[
"section_entry_info"
]
},
{
"description":"Path to the main file within the upload.",
"dtypeStr":"C",
"name":"mainfile",
"superNames":[
"section_entry_info"
]
},
{
"description":"Name of the parser used to extract this information.",
"dtypeStr":"C",
"name":"parser_name",
"superNames":[
"section_entry_info"
]
},
{
"description":"Filepaths of files that belong to this entry, i.e. files in the same directory. Filepaths are relative to the upload.",
"dtypeStr":"C",
"name":"filepaths",
"shape":[
"number_of_files"
],
"superNames":[
"section_entry_info"
]
},
{
"description":"Number of files that belong to this entry.",
"dtypeStr":"i",
"kindStr":"type_dimension",
"name":"number_of_files",
"superNames":[
"section_entry_info"
]
},
{
"description":"Information about the used archive processing steps and their execution.",
"kindStr":"type_section",
"name":"section_archive_processing_info",
"repeats":true,
"superNames":[
"section_entry_info"
]
},
{
"description":"Name of the applied archive processing program.",
"dtypeStr":"C",
"name":"archive_processor_name",
"superNames":[
"section_archive_processing_info"
]
},
{
"description":"The main error during execution of the archive processing program that failed the program.",
"dtypeStr":"C",
"name":"archive_processor_error",
"superNames":[
"section_archive_processing_info"
]
},
{
"description":"Number of warnings during execution of the archive processing program.",
"dtypeStr":"i",
"kindStr":"type_dimension",
"name":"number_of_archive_processor_warnings",
"superNames":[
"section_archive_processing_info"
]
},
{
"description":"Warnings during execution of the archive processing program.",
"dtypeStr":"C",
"name":"archive_processor_warnings",
"shape":[
"number_of_archive_processor_warnings"
],
"superNames":[
"section_archive_processing_info"
]
},
{
"description":"Status returned by archive processing program.",
"dtypeStr":"C",
"name":"archive_processor_status",
"superNames":[
"section_archive_processing_info"
],
"values":{
"Failure":"The program failed.",
"Success":"The program was successful.",
"WithWarnings":"The program had serious warnings."
}
}
]
}
\ No newline at end of file
{
"type": "nomad_meta_info_1_0",
"description": "Public meta info, not specific to any code",
"dependencies": [ {
"relativePath": "repository.nomadmetainfo.json"
},{
"relativePath": "general.nomadmetainfo.json"
}],
"metaInfos": [ {
"description": "Information that *in theory* should not affect the results of the calculations (e.g., timing).",
"kindStr": "type_abstract_document_content",
......@@ -684,25 +689,6 @@
"superNames": [
"section_restricted_uri"
]
}, {
"description": "The list of files that are subject to restriction. The files are given with their relative paths to the main_file of parsing.",
"dtypeStr": "C",
"name": "restricted_uri_files",
"repeats": true,
"shape": [
"number_of_restricted_uri_files"
],
"superNames": [
"section_restricted_uri"
]
}, {
"description": "repository pid of this calculation",
"dtypeStr": "C",
"name": "calculation_pid",
"shape": [],
"superNames": [
"section_calculation_info"
]
}, {
"description": "URL used to reference an externally stored calculation. The kind of relationship between the present and the referenced section_single_configuration_calculation is specified by calculation_to_calculation_kind.",
"dtypeStr": "C",
......@@ -751,24 +737,6 @@
"superNames": [
"section_calculation_to_folder_refs"
]
}, {
"description": "Upload date of the calculation, given as total number of milliseconds is the elapsed since the unix epoch (1 January 1970)",
"dtypeStr": "i64",
"name": "calculation_upload_date",
"repeats": true,
"shape": [],
"superNames": [
"section_calculation_info"
]
}, {
"description": "Name of the uploader of this calculation, given as lastamen, firstname",
"dtypeStr": "C",
"name": "calculation_uploader_name",
"repeats": true,
"shape": [],
"superNames": [
"section_calculation_info"
]
}, {
"derived": true,
"description": "String that specifies the centering, origin and basis vector settings of the 3D space group that defines the symmetry group of the simulated physical system (see section_system). Values are as defined by spglib.",
......@@ -2112,14 +2080,6 @@
"superNames": [
"section_system"
]
}, {
"description": "nomad uri identifying the main file corresponding to this calculation",
"dtypeStr": "C",
"name": "main_file_uri",
"shape": [],
"superNames": [
"section_calculation_info"
]
}, {
"description": "An array of the dimension of number_of_atoms where each atom (identified by the index in the array) is assigned to an atom-centered basis set, for this section_single_configuration_calculation. The actual definition of the atom-centered basis set is in the section_basis_set_atom_centered that is referred to by this metadata.",
"dtypeStr": "r",
......@@ -2583,9 +2543,6 @@
"dtypeStr": "i",
"kindStr": "type_dimension",
"name": "number_of_sites",
"shape": [
"number_of_atoms"
],
"superNames": [
"section_system"
]
......@@ -2663,36 +2620,6 @@
"superNames": [
"accessory_info"
]
}, {
"description": "Status returned by the first parser that thranslated the main_file_uri",
"dtypeStr": "C",
"name": "parse_status",
"shape": [],
"superNames": [
"section_calculation_info"
],
"values": {
"ParseFailure": "The parser failed to parse this main file",
"ParseSkipped": "The parser skipped this main file",
"ParseSuccess": "Parsing was successfull (does not mean that the file is valid or meaningful, simply that the parser could process it)",
"ParseWithWarnings": "The Parser had serious warnings"
}
}, {
"description": "id of the parser used to extract this information",
"dtypeStr": "C",
"name": "parser_id",
"shape": [],
"superNames": [
"section_calculation_info"
]
}, {
"description": "name of the parser used to extract this information",
"dtypeStr": "C",
"name": "parser_name",
"shape": [],
"superNames": [
"section_calculation_info"
]
}, {
"description": "This field is used for debugging messages of the parsing program associated with a run, see section_run.",
"dtypeStr": "C",
......@@ -3125,11 +3052,6 @@
"kindStr": "type_section",
"name": "section_restricted_uri",
"superNames": []
}, {
"description": "Information on this calculation (main file)",
"kindStr": "type_section",
"name": "section_calculation_info",
"superNames": []
}, {
"description": "Section that describes the relationship between different section_single_configuration_calculation sections.\n\nFor instance, one calculation is a perturbation performed using a self-consistent field (SCF) calculation as starting point, or a simulated system is partitioned in regions with different but connected Hamiltonians (e.g., QM/MM, or a region treated via Kohn-Sham DFT embedded into a region treated via orbital-free DFT).\n\nThe kind of relationship between the calculation defined in this section and the referenced one is described by calculation_to_calculation_kind. The referenced section_single_configuration_calculation is identified via calculation_to_calculation_ref (typically used for a section_single_configuration_calculation in the same section_run) or calculation_to_calculation_external_url.",
"kindStr": "type_section",
......@@ -3295,6 +3217,13 @@
"kindStr": "type_section",
"name": "section_run",
"superNames": []
}, {
"description": "An optional calculation id, if one is found in the code input/output files.",
"name": "raw_id",
"dtypeStr": "C",
"superNames": [
"section_run"
]
}, {
"description": "Section containing the settings describing a (potential-energy surface) sampling method.\n\nResults and monitored quantities of such sampling are collected in a sequence of frames, section_frame_sequence.",
"kindStr": "type_section",
......@@ -3669,24 +3598,6 @@
"superNames": [
"settings_smearing"
]
}, {
"description": "Identifier used in the source of this calculation. This is an uri like string, with a prefix identifying the source. For example `aflow:<aflow_uid>, `oqmd:<>`, `materials-project:<>`...",
"dtypeStr": "C",
"name": "source_id",
"repeats": true,
"shape": [],
"superNames": [
"section_calculation_info"
]
}, {
"description": "Link to a webpage describing the object, material,... within the project that calculated this of this calculation. For example a link to aflow lib calculation, oqmd or material project material",
"dtypeStr": "C",
"name": "source_link",
"repeats": true,
"shape": [],
"superNames": [
"section_calculation_info"
]
}, {
"derived": true,
"description": "Specifies the International Union of Crystallography (IUC) number of the 3D space group of this system.",
......@@ -4751,5 +4662,30 @@
"superNames": [
"section_single_configuration_calculation"
]
}]
}, {
"description": "The chemical composition as full formula of the system, based on atom species.",
"dtypeStr": "C",
"name": "chemical_composition",
"shape": [],
"superNames": [
"section_system"
]
}, {
"description": "The chemical composition as reduced formula of the system, based on atom species.",
"dtypeStr": "C",
"name": "chemical_composition_reduced",
"shape": [],
"superNames": [
"section_system"
]
}, {
"description": "The chemical composition as reduced bulk formula of the system, based on atom species.",
"dtypeStr": "C",
"name": "chemical_composition_bulk_reduced",
"shape": [],
"superNames": [
"section_system"
]
}
]
}
......@@ -120,7 +120,6 @@
"description": "Gid of a raw data archives that contains this calculation",
"dtypeStr": "C",
"name": "repository_archive_gid",
"repeats": true,
"superNames": [
"section_repository_info"
]
......@@ -132,6 +131,13 @@
"superNames": [
"section_repository_parserdata"
]
}, {
"description": "Number of atomic elements used in this calculation",
"dtypeStr": "i",
"name": "repository_atomic_elements_count",
"superNames": [
"section_repository_parserdata"
]
}, {
"description": "String identifying the type of basis set used in this calculation",
"dtypeStr": "C",
......@@ -253,6 +259,13 @@
"superNames": [
"section_repository_parserdata"
]
}, {
"description": "space group of the geometry of this calculation as international short symbol",
"dtypeStr": "i",
"name": "repository_spacegroup_symbol",
"superNames": [
"section_repository_parserdata"
]
}, {
"description": "String identifying the type of system of this calculation",
"dtypeStr": "C",
......@@ -278,6 +291,7 @@
"description": "Information about the authors of data uploaded to NOMAD repository",
"kindStr": "type_section",
"name": "section_author_info",
"repeats": true,
"superNames": [
"section_repository_userdata"
]
......@@ -285,18 +299,19 @@
"description": "Section describing a citation",
"kindStr": "type_section",
"name": "section_citation",
"repeats": true,
"superNames": [
"section_repository_userdata"
]
}, {
"description": "Information on a raw data archive that contain open access data of this upload",
"description": "Information on a raw data archive that contains data of this upload",
"kindStr": "type_section",
"name": "section_raw_data",
"superNames": [
"section_repository_info"
]
}, {
"description": "Base path of the raw data in the upload, these directories are *not* created in the archive",
"description": "Base path of the raw data in the upload",
"dtypeStr": "C",
"name": "raw_data_base_path",
"superNames": [
......@@ -328,6 +343,7 @@
}, {
"description": "NOMAD repository dataset tagging info",
"kindStr": "type_section",
"repeats": true,
"name": "section_repository_dataset",
"superNames": [
"section_repository_userdata"
......@@ -340,6 +356,7 @@
}, {
"description": "Information about the person with whom this calculation is shared with",
"kindStr": "type_section",
"repeats": true,
"name": "section_shared_with",
"superNames": [
"section_repository_userdata"
......@@ -403,14 +420,14 @@
}, {
"description": "Date/time when the data was uploaded to NOMAD repository (offset from *Unix epoch* (00:00:00 UTC on 1 January 1970) in seconds)",
"dtypeStr": "f",
"name": "upload_date",
"name": "repository_upload_date",
"superNames": [
"section_repository_info"
]
}, {
"description": "Unique ID of the upload 'block' (upload could have been split into many archives)",
"dtypeStr": "i",
"name": "upload_id",
"name": "repository_upload_id",
"superNames": [
"section_repository_info"
]
......
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{
"type":"nomad_meta_info_1_0",
"description":"meta info used by the Vasp parser, all names are expected to start with x_vasp_",
"dependencies":[
{
"relativePath":"common.nomadmetainfo.json"
},
{
"relativePath":"meta_types.nomadmetainfo.json"
}
],
"metaInfos":[
{
"name":"x_vasp_incarUnknown_param",
"description":"Unknown incar parameters. By 'unknown' we refer to incar parameters in the OLD (predated Sept.2019) 'vasp.nomadmetainfo.json' that are **not** listed in the current (Oct.2019) VaspWiki",
"kindStr":"type_abstract_document_content",
"superNames":[
"section_method"
]
},
{
"description":"Maximum cutoff (normally specified only in POTCAR). Value prinded out after evaluating the input.",
"dtypeStr":"f",
"name":"x_vasp_incarOut_ENMAX",
"shape":[
],
"superNames":[
"x_vasp_incarOut_param"
]
},
{
"description":"Maximum cutoff (normally specified only in POTCAR). Value prinded out after evaluating the input.",
"dtypeStr":"f",
"name":"x_vasp_incar_ENMAX",
"shape":[
],
"superNames":[
"x_vasp_incar_param"
]
},
{
"name":"x_vasp_incarOut_LCOMPAT",
"description":"In vasp.4.2 the augmentation charges are forced to be zero at the boundary of the augmentation sphere, therefore results are slightly different from vasp.3.2 (usually differences are smaller than 0.01 meV). The old behavior can be restored by setting LCOMPAT = .TRUE. in the INCAR file.",
"dtypeStr":"b",
"shape":[
],
"superNames":[
"x_vasp_incarOut_param"
]
}
]
}
# Copyright 2016-2018 Fawzi Mohamed, Lauri Himanen, Danio Brambila, Ankit Kariryaa, Henning Glawe
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
from setuptools import setup, find_packages
def main():
setup(
name='nomadmetainfo',
version='0.1',
description='NOMAD meta info.',
license='APACHE 2.0',
package_dir={'': 'meta_info'},
packages=find_packages('meta_info'),
package_data={
'nomad_meta_info': ['*.json']
}
)
if __name__ == '__main__':
main()