mdsuite.database.scheme module¶

MDSuite: A Zincwarecode package.

License¶

This program and the accompanying materials are made available under the terms of the Eclipse Public License v2.0 which accompanies this distribution, and is available at https://www.eclipse.org/legal/epl-v20.html

SPDX-License-Identifier: EPL-2.0

Copyright Contributors to the Zincwarecode Project.

Contact Information¶

email: zincwarecode@gmail.com github: https://github.com/zincware web: https://zincwarecode.com/

Citation¶

If you use this module please cite us with:

Summary¶

class mdsuite.database.scheme.Computation(**kwargs)[source]¶

Bases: Base

Class for the computation table.

computation_attributes¶

property computation_parameter: dict¶

Get a dict of all used computation parameters.

Examples

The following example is taken from the RDF calculator {

“number_of_bins”: null, “number_of_configurations”: 100, “correlation_time”: 1, “atom_selection”: “slice(None, None, None)”, “data_range”: 1, “cutoff”: null, “start”: 0, “stop”: null, “species”: null, “molecules”: false, “version”: 1

}

computation_results¶

property data_dict: dict¶

returns: species_dict – A dictionary of the type

{

Li:

{: a: 1.2, uncert: 0.1, time: [1, 2, 3, ], msd: [0.1, 0.3, 0.7]

},

Cl:

{: a: 1.2, uncert: 0.1, time: [1, 2, 3, ], msd: [0.1, 0.3, 0.7]

},

} where the keys are defined by species (multiple species are joined by “_”) and the dimension argument of the computation_data

Return type:: dict

property data_range: int¶: Get the data_range stored in computation_attributes.

experiment¶

experiment_id¶

id¶

keys() → list[source]¶: Map the data_dict keys.

name¶

property subjects: list¶: Get the subjects stored in computation_attributes.

class mdsuite.database.scheme.ComputationAttribute(**kwargs)[source]¶

Bases: Base

Class for the meta data of a computation.

computation¶

computation_id¶

data¶

id¶

name¶

class mdsuite.database.scheme.ComputationResult(**kwargs)[source]¶

Bases: Base

raw computation data of a calculation.

computation¶

computation_id¶

data¶

id¶

species¶

class mdsuite.database.scheme.Experiment(**kwargs)[source]¶

Bases: Base

Class for the experiment table associated with the Project table.

active¶

computations¶

experiment_attributes¶

get_molecules() → dict[source]¶: Get the molecules information for the experiment.

get_species() → dict[source]¶: Get the species information for the experiment.

id¶

name¶

project¶

project_id¶

species¶

class mdsuite.database.scheme.ExperimentAttribute(**kwargs)[source]¶

Bases: Base

Class for the experiment data table.

This table is arbitrarily defined and therefore anything can be added to it.

id¶

Unique identifier of the row.

Type:: int

name¶

name of the property being recorded.

Type:: str

value¶

numeric value of the property.

Type:: float

str_value¶

String value of the property.

Type:: str

data¶

experiment¶

experiment_id¶

id¶

name¶

class mdsuite.database.scheme.ExperimentSpecies(**kwargs)[source]¶

Bases: Base

Table for storing species information.

This table is used to store species and molecule information that can be related to a specific experiment

computation_result¶

data¶

experiment¶

experiment_id¶

id¶

molecule¶

name¶

class mdsuite.database.scheme.Project(**kwargs)[source]¶

Bases: Base

Project table.

description¶

experiments¶

id¶

class mdsuite.database.scheme.SpeciesAssociation(**kwargs)[source]¶

Bases: Base

Connection between Computations and Experiment Species.

This table is required to be defined specifically, because we need add the count, e.g. Na - Na would otherwise only appear as Na.

computation_result¶

computation_results_id¶

count¶

experiment_species_id¶

property name¶: Get the name of the species.

species¶