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Redefine species.mass as a list of floats #344

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Dec 17, 2020
Merged

Redefine species.mass as a list of floats #344

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df797e8
Redefining 'species'.'mass' as a list of float.
merkys Dec 17, 2020
e4d795b
Update optimade.rst
merkys Dec 17, 2020
4b6a144
Update optimade.rst
merkys Dec 17, 2020
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11 changes: 6 additions & 5 deletions optimade.rst
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Expand Up @@ -2119,7 +2119,7 @@ species
- :property:`concentration`: list of float (REQUIRED)
- :property:`attached`: list of strings (OPTIONAL)
- :property:`nattached`: list of integers (OPTIONAL)
- :property:`mass`: float (OPTIONAL)
- :property:`mass`: list of floats (OPTIONAL)
- :property:`original_name`: string (OPTIONAL).

- **Requirements/Conventions**:
Expand Down Expand Up @@ -2153,7 +2153,8 @@ species
The implementation MUST include either both or none of the :field:`attached` and :field:`nattached` keys, and if they are provided, they MUST be of the same length.
Furthermore, if they are provided, the `structure_features`_ property MUST include the string :val:`site_attachments`.

- **mass**: OPTIONAL. If present MUST be a float expressed in a.m.u.
- **mass**: OPTIONAL. If present MUST be a list of floats, with the same length as :property:`chemical_symbols`, providing element masses expressed in a.m.u.
Elements denoting vacancies MUST have masses equal to 0.
- **original\_name**: OPTIONAL. Can be any valid Unicode string, and SHOULD contain (if specified) the name of the species that is used internally in the source database.

Note: With regards to "source database", we refer to the immediate source being queried via the OPTIMADE API implementation.
Expand All @@ -2168,9 +2169,9 @@ species

- :val:`[ {"name": "Ti", "chemical_symbols": ["Ti"], "concentration": [1.0]} ]`: any site with this species is occupied by a Ti atom.
- :val:`[ {"name": "Ti", "chemical_symbols": ["Ti", "vacancy"], "concentration": [0.9, 0.1]} ]`: any site with this species is occupied by a Ti atom with 90 % probability, and has a vacancy with 10 % probability.
- :val:`[ {"name": "BaCa", "chemical_symbols": ["vacancy", "Ba", "Ca"], "concentration": [0.05, 0.45, 0.5], "mass": 88.5} ]`: any site with this species is occupied by a Ba atom with 45 % probability, a Ca atom with 50 % probability, and by a vacancy with 5 % probability. The mass of this site is (on average) 88.5 a.m.u.
- :val:`[ {"name": "C12", "chemical_symbols": ["C"], "concentration": [1.0], "mass": 12.0} ]`: any site with this species is occupied by a carbon isotope with mass 12.
- :val:`[ {"name": "C13", "chemical_symbols": ["C"], "concentration": [1.0], "mass": 13.0} ]`: any site with this species is occupied by a carbon isotope with mass 13.
- :val:`[ {"name": "BaCa", "chemical_symbols": ["vacancy", "Ba", "Ca"], "concentration": [0.05, 0.45, 0.5], "mass": [0.0, 137.327, 40.078]} ]`: any site with this species is occupied by a Ba atom with 45 % probability, a Ca atom with 50 % probability, and by a vacancy with 5 % probability.
- :val:`[ {"name": "C12", "chemical_symbols": ["C"], "concentration": [1.0], "mass": [12.0]} ]`: any site with this species is occupied by a carbon isotope with mass 12.
- :val:`[ {"name": "C13", "chemical_symbols": ["C"], "concentration": [1.0], "mass": [13.0]} ]`: any site with this species is occupied by a carbon isotope with mass 13.
- :val:`[ {"name": "CH3", "chemical_symbols": ["C"], "concentration": [1.0], "attached": ["H"], "nattached": [3]} ]`: any site with this species is occupied by a methyl group, -CH3, which is represented without specifying precise positions of the hydrogen atoms.

assemblies
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