...
 
Commits (14)
......@@ -49,3 +49,5 @@ TAGS
lib/
env/
*.egg-info
{
"type": "nomad_meta_info_1_0",
"description": "file collecting all the meta info files (i.e. with all code specific parts)",
"dependencies": [ {
"relativePath": "general.experimental.nomadmetainfo.json"
}, {
"relativePath": "../skeletonparser/skeleton.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": [ ]
}
......@@ -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.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":"The general name of the experimental method used",
"dtypeStr":"C",
"name":"experiment_method_name",
"superNames":[
"section_method"
]
},
{
"description":"The general location of the experiment",
"dtypeStr":"C",
"name":"experiment_location",
"superNames":[
"section_experiment"
]
},
{
"description":"The datetime of the experiment in seconds since epoch.",
"dtypeStr":"i64",
"name":"experiment_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"]
},
{
"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":"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":"The temperature of the sample during the experiment in K.",
"dtypeStr":"f",
"superNames":["section_sample"],
"name":"sample_temperature",
"units": "K"
},
{
"description": "This section contains information about the applied experimental method.",
"kindStr":"type_section",
"name":"section_method",
"superNames":["section_experiment"]
},
{
"description":"The ...",
"dtypeStr":"C",
"superNames":["section_sample"],
"name":"sample_microstructure",
"values": [
"thin films",
"nanoscale objects",
"bulk sample, single-crystalline",
"bulk sample, polycrystalline"
]
},
{
"description":"The ...",
"dtypeStr":"C",
"superNames":["section_sample"],
"name":"sample_constituents",
"values": [
"multi phase",
"single phase"
]
},
{
"description":"The ...",
"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, 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",
......@@ -2663,36 +2623,6 @@
"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 +3055,6 @@
"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",
......@@ -3669,24 +3594,6 @@
"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 +4658,30 @@
"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"
]
......
# 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()