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Add example of species with attached hydrogens
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rartino committed Jun 13, 2020
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Expand Up @@ -1947,6 +1947,7 @@ species
- :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": "-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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