Property Database¶

pyEQL is distributed with a database of solute properties and model parameters needed to perform its calculations. The database includes:

Molecular weight, charge, and other chemical informatics information for any species
Diffusion coefficients for 104 ions
Pitzer model activity correction coefficients for 157 salts
Pitzer model partial molar volume coefficients for 120 salts
Jones-Dole “B” coefficients for 83 ions
Hydrated and ionic radii for 23 ions
Dielectric constant model parameters for 18 ions
Partial molar volumes for 24 ions

pyEQL can automatically infer basic chemical informatics such as molecular weight and charge by passing a solute’s formula to pymatgen.core.ion.Ion (See chemical formulas). For other physicochemical properties, it relies on data compiled into the included database. A list of the data and species covered is available below

Format¶

The database is distributed as a .json file containing serialized Solute objects that define the schema for aggregated property data (see below). By default, each instance of Solution loads this file as a maggma JSONStore and queries data from it using the Store interface.

If desired, users can point a Solution instance to an alternate database by using the database keyword argument at creation. The argument should contain either 1) the path to an alternate .json file (as a str) or 2) a maggma.Store instance. The data in the file or Store must match the schema defined by Solute, with the field formula used as the key field (unique identifier).

s1 = Solution(database='/path/to/my_database.json')

or

from maggma.core import JSONStore

db_store = JSONStore('/path/to/my_database.json', key='formula')
s1 = Solution(database=db_store)

The `Solute` class¶

pyEQL.Solute is a dataclass that defines a schema for organizing solute property data. You can think of the schema as a structured dictionary: Solute defines the naming and organization of the keys. You can create a basic Solute from just the solute’s formula as follows:

>>> from pyEQL.solute import Solute
>>> Solute.from_formula('Ti+2')
Solute(formula='Ti[+2]', charge=2, molecular_weight='47.867 g/mol', elements=['Ti'], chemsys='Ti', pmg_ion=Ion: Ti1 +2, formula_html='Ti<sup>+2</sup>', formula_latex='Ti$^{+2}$', formula_hill='Ti', formula_pretty='Ti^+2', oxi_state_guesses=({'Ti': 2.0},), n_atoms=1, n_elements=1, size={'radius_ionic': None, 'radius_hydrated': None, 'radius_vdw': None, 'molar_volume': None}, thermo={'ΔG_hydration': None, 'ΔG_formation': None}, transport={'diffusion_coefficient': None}, model_parameters={'activity_pitzer': {'Beta0': None, 'Beta1': None, 'Beta2': None, 'Cphi': None, 'Max_C': None}, 'molar_volume_pitzer': {'Beta0': None, 'Beta1': None, 'Beta2': None, 'Cphi': None, 'V_o': None, 'Max_C': None}, 'viscosity_jones_dole': {'B': None}})

This method uses pymatgen to populate the Solute with basic chemical information like molecular weight. You can access top-level keys in the schema via attribute, e.g.

>>> s.molecular_weight
'47.867 g/mol'
>>> s.charge
2.0

Other properties that are present in the schema, but not set, are None. For example, here we have not specified a diffusion coefficient. If we inspect the transport attribute, we see

>>> s.transport
{'diffusion_coefficient': None}

You can convert a Solute into a regular dictionary using Solute.as_dict()

>>> s.as_dict()
{'formula': 'Ti[+2]', 'charge': 2, 'molecular_weight': '47.867 g/mol', 'elements': ['Ti'], 'chemsys': 'Ti', 'pmg_ion': Ion: Ti1 +2, 'formula_html': 'Ti<sup>+2</sup>', 'formula_latex': 'Ti$^{+2}$', 'formula_hill': 'Ti', 'formula_pretty': 'Ti^+2', 'oxi_state_guesses': ({'Ti': 2.0},), 'n_atoms': 1, 'n_elements': 1, 'size': {'radius_ionic': None, 'radius_hydrated': None, 'radius_vdw': None, 'molar_volume': None}, 'thermo': {'ΔG_hydration': None, 'ΔG_formation': None}, 'transport': {'diffusion_coefficient': None}, 'model_parameters': {'activity_pitzer': {'Beta0': None, 'Beta1': None, 'Beta2': None, 'Cphi': None, 'Max_C': None}, 'molar_volume_pitzer': {'Beta0': None, 'Beta1': None, 'Beta2': None, 'Cphi': None, 'V_o': None, 'Max_C': None}, 'viscosity_jones_dole': {'B': None}}}

Searching the database¶

Once you have a created a Solution, it will automatically search the database for needed parameters whenever it needs to perform a calculation. For example, if you call get_transport_number, pyEQL will search the property database for diffusion coefficient data to use in the calculation. No user action is needed.

If you want to search the database yourself, or to inspect the values that pyEQL uses for a particular parameter, you can do so via the get_property method. First, create a Solution

>>> from pyEQL import Solution
>>> s1 = pyEQL.Solution

Next, call get_property with a solute name and the name of the property you need. Valid property names are any key in the Solute schema. Nested keys can be separated by periods, e.g. “model_parameters.activity_pitzer”:

>>> s1.get_property('Mg+2', 'transport.diffusion_coefficient')
<Quantity(0.00705999997, 'centimeter ** 2 * liter * pascal * second / kilogram / meter ** 2')>

If the property exists, it will be returned as a pint Quantity object, which you can convert to specific units if needed, e.g.

>>> s1.get_property('Mg+2', 'transport.diffusion_coefficient').to('m**2/s')
<Quantity(7.05999997e-10, 'meter ** 2 / second')>

If the property does not exist in the database, None will be returned.

>>> s1.get_property('Mg+2', 'transport.randomproperty')
>>>

Although the database contains additional context about each and every property value, such as a citation, this information is not currently exposed via the Solution interface. Richer methods for exploring and adding to the database may be added in the future.

Species included¶

The database currently contains one or more physichochemical properties for each of the solutes listed below. More detailed information about which properties are available for which solutes may be added in the future.

 - Ac[+3]
 - Ag(CN)2[-1]
 - AgNO3(aq)
 - Ag[+1]
 - Ag[+2]
 - Ag[+3]
 - Al2(SO4)3(aq)
 - Al[+3]
 - AsO4[-3]
 - Au(CN)2[-1]
 - Au(CN)4[-1]
 - Au[+1]
 - Au[+2]
 - Au[+3]
 - B(H5C6)4[-1]
 - B(OH)3(aq)
 - B(OH)4[-1]
 - BF4[-1]
 - BO2[-1]
 - Ba(ClO4)2(aq)
 - Ba(NO3)2(aq)
 - BaBr2(aq)
 - BaC4O.3H2O(aq)
 - BaCl2(aq)
 - BaI2(aq)
 - Ba[+2]
 - BeSO4(aq)
 - Be[+2]
 - Bi[+3]
 - BrO3[-1]
 - Br[-0.33333333]
 - Br[-1]
 - C2N3[-1]
 - CH3COO[-1]
 - CNO[-1]
 - CN[-1]
 - CO3[-2]
 - CSN[-1]
 - CSeN[-1]
 - Ca(ClO4)2(aq)
 - Ca(NO3)2(aq)
 - CaBr2(aq)
 - CaCl2(aq)
 - CaI2(aq)
 - Ca[+2]
 - Cd(ClO4)2(aq)
 - Cd(NO2)2(aq)
 - Cd(NO3)2(aq)
 - CdSO4(aq)
 - Cd[+2]
 - CeCl3(aq)
 - Ce[+3]
 - Ce[+4]
 - ClO2[-1]
 - ClO3[-1]
 - ClO4[-1]
 - Cl[-1]
 - Co(CN)6[-3]
 - Co(H3N)6[-3]
 - Co(NO3)2(aq)
 - CoBr2(aq)
 - CoCl2(aq)
 - CoI2(aq)
 - Co[+2]
 - Co[+3]
 - Cr(NO3)3(aq)
 - CrCl3(aq)
 - CrO4[-2]
 - Cr[+2]
 - Cr[+3]
 - Cs2SO4(aq)
 - CsBr(aq)
 - CsCl(aq)
 - CsF(aq)
 - CsHC2O.1H2O(aq)
 - CsI(aq)
 - CsNO2(aq)
 - CsNO3(aq)
 - CsOH(aq)
 - Cs[+1]
 - Cu(NO3)2(aq)
 - CuCl2(aq)
 - CuSO4(aq)
 - Cu[+1]
 - Cu[+2]
 - Cu[+3]
 - Dy[+2]
 - Dy[+3]
 - Er[+2]
 - Er[+3]
 - Eu(NO3)3(aq)
 - EuCl3(aq)
 - Eu[+2]
 - Eu[+3]
 - F[-1]
 - Fe(CN)6[-3]
 - Fe(CN)6[-4]
 - FeCl2(aq)
 - FeCl3(aq)
 - Fe[+2]
 - Fe[+3]
 - Ga[+3]
 - GdCl3(aq)
 - Gd[+3]
 - Ge[+2]
 - H2CO3(aq)
 - H2O(aq)
 - H2SNO3[-1]
 - H2SO4(aq)
 - H3O[+1]
 - H4BrN(aq)
 - H4IN(aq)
 - H4N2O3(aq)
 - H4NCl(aq)
 - H4NClO4(aq)
 - H4N[+1]
 - H4SNO4(aq)
 - H5C6O7[-3]
 - H5N2[+1]
 - H8S(NO2)2(aq)
 - HBr(aq)
 - HCO2[-1]
 - HCO3[-1]
 - HCl(aq)
 - HClO4(aq)
 - HF2[-1]
 - HI(aq)
 - HNO3(aq)
 - HO2[-1]
 - HOsO5[-1]
 - HSO3[-1]
 - HSO4[-1]
 - HS[-1]
 - HSeO3[-1]
 - H[+1]
 - Hf[+4]
 - Hg[+2]
 - Ho[+2]
 - Ho[+3]
 - IO3[-1]
 - IO4[-1]
 - I[-1]
 - In[+1]
 - In[+2]
 - In[+3]
 - IrO4[-1]
 - Ir[+3]
 - K2CO3(aq)
 - K2PHO4(aq)
 - K2SO4(aq)
 - K3Fe(CN)6(aq)
 - K3PO4(aq)
 - K4Fe(CN)6(aq)
 - KBr(aq)
 - KBrO3(aq)
 - KCSN(aq)
 - KCl(aq)
 - KClO3(aq)
 - KClO4(aq)
 - KCrO4(aq)
 - KF(aq)
 - KHC2O.1H2O(aq)
 - KHCO3(aq)
 - KI(aq)
 - KNO2(aq)
 - KNO3(aq)
 - KOH(aq)
 - KPO3.1H2O(aq)
 - K[+1]
 - La(NO3)3(aq)
 - LaCl3(aq)
 - La[+3]
 - Li2SO4(aq)
 - LiBr(aq)
 - LiCl(aq)
 - LiClO4(aq)
 - LiHC2O.1H2O(aq)
 - LiI(aq)
 - LiNO2(aq)
 - LiNO3(aq)
 - LiOH(aq)
 - Li[+1]
 - Lu[+3]
 - Mg(ClO4)2(aq)
 - Mg(NO3)2(aq)
 - MgBr2(aq)
 - MgC4O.3H2O(aq)
 - MgCl2(aq)
 - MgI2(aq)
 - MgSO4(aq)
 - Mg[+2]
 - MnCl2(aq)
 - MnO4[-1]
 - MnSO4(aq)
 - Mn[+2]
 - Mn[+3]
 - MoO4[-2]
 - Mo[+3]
 - NO2[-1]
 - NO3[-1]
 - N[-0.33333333]
 - Na2CO3(aq)
 - Na2PHO4(aq)
 - Na2S2O3(aq)
 - Na2SO4(aq)
 - Na3PO4(aq)
 - NaBr(aq)
 - NaBrO3(aq)
 - NaCSN(aq)
 - NaCl(aq)
 - NaClO4(aq)
 - NaCrO4(aq)
 - NaF(aq)
 - NaHC2O.1H2O(aq)
 - NaHC3.2H2O(aq)
 - NaHCO2(aq)
 - NaHCO3(aq)
 - NaI(aq)
 - NaNO2(aq)
 - NaNO3(aq)
 - NaOH(aq)
 - NaPO3.1H2O(aq)
 - Na[+1]
 - Nb[+3]
 - Nd(NO3)3(aq)
 - NdCl3(aq)
 - Nd[+2]
 - Nd[+3]
 - Ni(NO3)2(aq)
 - NiCl2(aq)
 - NiSO4(aq)
 - Ni[+2]
 - Ni[+3]
 - Np[+3]
 - Np[+4]
 - OH[-1]
 - Os[+3]
 - P(HO2)2[-1]
 - P(OH)2[-1]
 - P2O7[-4]
 - P3O10[-5]
 - PF6[-1]
 - PH9(NO2)2(aq)
 - PHO4[-2]
 - PO3F[-2]
 - PO3[-1]
 - PO4[-3]
 - Pa[+3]
 - Pb(ClO4)2(aq)
 - Pb(NO3)2(aq)
 - Pb[+2]
 - Pd[+2]
 - Pm[+2]
 - Pm[+3]
 - Po[+2]
 - PrCl3(aq)
 - Pr[+2]
 - Pr[+3]
 - Pt[+2]
 - Pu[+2]
 - Pu[+4]
 - Ra[+2]
 - Rb2SO4(aq)
 - RbBr(aq)
 - RbCl(aq)
 - RbF(aq)
 - RbHC2O.1H2O(aq)
 - RbI(aq)
 - RbNO2(aq)
 - RbNO3(aq)
 - RbOH(aq)
 - Rb[+1]
 - ReO4[-1]
 - Re[+1]
 - Re[+3]
 - Re[-1]
 - Rh[+3]
 - Ru[+2]
 - Ru[+3]
 - S2O3[-2]
 - SO2[-1]
 - SO3[-1]
 - SO3[-2]
 - SO4[-1]
 - SO4[-2]
 - S[-2]
 - Sb(HO2)2[-1]
 - Sb(OH)6[-1]
 - ScCl3(aq)
 - Sc[+2]
 - Sc[+3]
 - SeO3[-1]
 - SeO4[-1]
 - SeO4[-2]
 - SiF6[-2]
 - SmCl3(aq)
 - Sm[+2]
 - Sm[+3]
 - Sn[+2]
 - Sn[+4]
 - Sr(ClO4)2(aq)
 - Sr(NO3)2(aq)
 - SrBr2(aq)
 - SrCl2(aq)
 - SrI2(aq)
 - Sr[+2]
 - Ta[+3]
 - Tb[+3]
 - TcO4[-1]
 - Tc[+2]
 - Tc[+3]
 - Th(NO3)4(aq)
 - Th[+4]
 - Ti[+2]
 - Ti[+3]
 - Tl(ClO4)3(aq)
 - Tl(NO2)3(aq)
 - Tl(NO3)3(aq)
 - TlH(C3O)2.4H2O(aq)
 - Tl[+1]
 - Tl[+3]
 - Tm[+2]
 - Tm[+3]
 - U(ClO)2(aq)
 - U(ClO5)2(aq)
 - U(NO4)2(aq)
 - UO2[+1]
 - UO2[+2]
 - USO6(aq)
 - U[+3]
 - U[+4]
 - VO2[+1]
 - V[+2]
 - V[+3]
 - WO4[-1]
 - WO4[-2]
 - W[+3]
 - YCl3(aq)
 - YNO3(aq)
 - Y[+3]
 - Yb[+2]
 - Yb[+3]
 - Zn(ClO4)2(aq)
 - Zn(NO3)2(aq)
 - ZnBr2(aq)
 - ZnCl2(aq)
 - ZnI2(aq)
 - ZnSO4(aq)
 - Zn[+2]
 - Zr[+4]

Property Database¶

Format¶

The Solute class¶

Searching the database¶

Species included¶

The `Solute` class¶