Chemical Formulas

pyEQL interprets the chemical formula of a substance to calculate its molecular weight and formal charge. The formula is also used as a key to search the database for parameters (e.g. diffusion coefficient) that are used in subsequent calculations.

How to Enter Valid Chemical Formulas

Generally speaking, type the chemical formula of your solute the “normal” way and pyEQL should be able to inerpret it. Internally, pyEQL uses the pymatgen.core.ion.Ion class to “translate” chemical formulas into a consistent format. Anything that the Ion class can understand will be processed into a valid formula by pyEQL.

Here are some examples:

Substance	You enter	pyEQL understands
Sodium Chloride	“NaCl”, “NaCl(aq)”, or “ClNa”	“NaCl(aq)”
Sodium Sulfate	“Na(SO4)2” or “NaS2O8”	“Na(SO4)2(aq)”
Sodium Ion	“Na+”, “Na+1”, “Na1+”, or “Na[+]”	“Na[+1]”
Magnesium Ion	“Mg+2”, “Mg++”, or “Mg[++]”	“Mg[+2]”
Methanol	“CH3OH”, “CH4O”	“‘CH3OH(aq)’”

Specifically, pyEQL uses Ion.from_formula(<formula>).reduced_formla (shown in the right hand column of the table) to identify solutes. Notice that for charged species, the charges are always placed inside square brackets (e.g., Na[+1]) and always include the charge number (even for monovalent ions). Uncharged species are always suffixed by (aq) to disambiguate them from solids.

Important

When writing multivalent ion formulas, it is strongly recommended that you put the charge number AFTER the + or - sign (e.g., type “Mg+2” NOT “Mg2+”). The latter formula is ambiguous - it could mean \(`Mg_2^+`\) or \(`Mg^{+2}`\)

Manually testing a formula

If you want to make sure pyEQL is understanding your formula correctly, you can manually test it via pymatgen as follows:

>>> from pymatgen.core.ion import Ion
>>> Ion.from_formula(<your_formula>).reduced_formula
...

Formulas you will see when using Solution

When using the Solution class,

• When creating a Solution, you can enter chemical formulas in any format you prefer, as long as pymatgen can understand it (see manual testing).

• The keys (solute formulas) in Solution.components are preserved in the same format the user enters them. So if you entered Na+ for sodium ion, it will stay that way.

• Arguments to Solution.get_property can be entered in any format you prefer. When pyEQL queries the database, it will automatically convert the formula to the canonical one from pymatgen

• Property data in the database is uniquely identified by the canonical ion formula (output of Ion.from_formula(<formula>).reduced_formla, e.g. “Na[+1]” for sodium ion).