diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 1518cb4..36b4af0 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -49,4 +49,4 @@ repos:
- id: check-json
- id: pretty-format-json
exclude_types: [jupyter]
- args: [--autofix]
+ args: [--autofix, --indent=4]
diff --git a/.zenodo.json b/.zenodo.json
index 390b32d..2e2d770 100644
--- a/.zenodo.json
+++ b/.zenodo.json
@@ -1,25 +1,25 @@
{
- "creators": [
- {
- "affiliation": "Princeton University",
- "name": "Kingsbury, Ryan",
- "orcid": "0000-0002-7168-3967"
- }
- ],
- "rights": [
- {
- "description": {
- "en": ""
- },
- "id": "lgpl-3.0-only",
- "props": {
- "scheme": "spdx",
- "url": "https://www.gnu.org/licenses/lgpl-3.0-standalone.html"
- },
- "title": {
- "en": "GNU Lesser General Public License v3.0 only"
- }
- }
- ],
- "title": "pyEQL: A python library for water chemistry"
+ "creators": [
+ {
+ "affiliation": "Princeton University",
+ "name": "Kingsbury, Ryan",
+ "orcid": "0000-0002-7168-3967"
+ }
+ ],
+ "rights": [
+ {
+ "description": {
+ "en": ""
+ },
+ "id": "lgpl-3.0-only",
+ "props": {
+ "scheme": "spdx",
+ "url": "https://www.gnu.org/licenses/lgpl-3.0-standalone.html"
+ },
+ "title": {
+ "en": "GNU Lesser General Public License v3.0 only"
+ }
+ }
+ ],
+ "title": "pyEQL: A python library for water chemistry"
}
diff --git a/src/pyEQL/database/pyeql_db.json b/src/pyEQL/database/pyeql_db.json
index fde4577..67f0232 100644
--- a/src/pyEQL/database/pyeql_db.json
+++ b/src/pyEQL/database/pyeql_db.json
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+ },
+ "molar_volume_pitzer": {
+ "Beta0": {
+ "data_type": "fitted",
+ "reference": "10.1021/je2009329",
+ "value": "0.001058 dimensionless"
+ },
+ "Beta1": {
+ "data_type": "fitted",
+ "reference": "10.1021/je2009329",
+ "value": "0.0007117 dimensionless"
+ },
+ "Beta2": {
+ "data_type": "fitted",
+ "reference": "10.1021/je2009329",
+ "value": "0.0 dimensionless"
+ },
+ "Cphi": {
+ "data_type": "fitted",
+ "reference": "10.1021/je2009329",
+ "value": "-0.0003739 dimensionless"
+ },
+ "Max_C": {
+ "data_type": "fitted",
+ "reference": "10.1021/je2009329",
+ "value": "1.999 mol/kg"
+ },
+ "V_o": {
+ "data_type": "fitted",
+ "reference": "10.1021/je2009329",
+ "value": "20.0 dimensionless"
+ }
+ },
+ "viscosity_jones_dole": {
+ "B": null
+ }
+ },
+ "molecular_weight": "225.21699999999998 g/mol",
+ "n_atoms": 3,
+ "n_elements": 2,
+ "oxi_state_guesses": {
+ "Br": -1,
+ "Zn": 2
+ },
+ "pmg_ion": {
+ "@class": "Ion",
+ "@module": "pymatgen.core.ion",
+ "@version": null,
+ "Br": 2,
+ "Zn": 1,
+ "charge": 0
+ },
+ "size": {
+ "molar_volume": null,
+ "radius_hydrated": null,
+ "radius_ionic": {
+ "data_type": "experimental",
+ "reference": "pymatgen",
+ "value": "None"
+ },
+ "radius_vdw": {
+ "data_type": "experimental",
+ "reference": "pymatgen",
+ "value": "2.01 \u212b"
+ }
+ },
+ "thermo": {
+ "\u0394G_formation": null,
+ "\u0394G_hydration": null
+ },
+ "transport": {
+ "diffusion_coefficient": null
+ }
+ },
+ {
+ "charge": 0,
+ "chemsys": "Cl-Zn",
+ "elements": [
+ "Zn",
+ "Cl"
+ ],
+ "formula": "ZnCl2(aq)",
+ "formula_hill": "Cl2 Zn",
+ "formula_html": "ZnCl2",
+ "formula_latex": "ZnCl$_{2}$",
+ "formula_pretty": "ZnCl2",
+ "model_parameters": {
+ "activity_pitzer": {
+ "Beta0": {
+ "data_type": "fitted",
+ "reference": "10.1021/je2009329",
+ "value": "0.1872 dimensionless"
+ },
+ "Beta1": {
+ "data_type": "fitted",
+ "reference": "10.1021/je2009329",
+ "value": "1.766 dimensionless"
+ },
+ "Beta2": {
+ "data_type": "fitted",
+ "reference": "10.1021/je2009329",
+ "value": "0.0 dimensionless"
+ },
+ "Cphi": {
+ "data_type": "fitted",
+ "reference": "10.1021/je2009329",
+ "value": "-0.03625 dimensionless"
+ },
+ "Max_C": {
+ "data_type": "fitted",
+ "reference": "10.1021/je2009329",
+ "value": "2.101 mol/kg"
+ }
+ },
+ "diffusion_temp_smolyakov": {
+ "a1": null,
+ "a2": null,
+ "d": null
+ },
+ "molar_volume_pitzer": {
+ "Beta0": {
+ "data_type": "fitted",
+ "reference": "10.1021/je2009329",
+ "value": "0.0001075 dimensionless"
+ },
+ "Beta1": {
+ "data_type": "fitted",
+ "reference": "10.1021/je2009329",
+ "value": "0.01003 dimensionless"
+ },
+ "Beta2": {
+ "data_type": "fitted",
+ "reference": "10.1021/je2009329",
+ "value": "0.0 dimensionless"
+ },
+ "Cphi": {
+ "data_type": "fitted",
+ "reference": "10.1021/je2009329",
+ "value": "0.0001495 dimensionless"
+ },
+ "Max_C": {
+ "data_type": "fitted",
+ "reference": "10.1021/je2009329",
+ "value": "2.03 mol/kg"
+ },
+ "V_o": {
+ "data_type": "fitted",
+ "reference": "10.1021/je2009329",
+ "value": "2.0 dimensionless"
+ }
+ },
+ "viscosity_jones_dole": {
+ "B": null
+ }
+ },
+ "molecular_weight": "136.315 g/mol",
+ "n_atoms": 3,
+ "n_elements": 2,
+ "oxi_state_guesses": {
+ "Cl": -1,
+ "Zn": 2
+ },
+ "pmg_ion": {
+ "@class": "Ion",
+ "@module": "pymatgen.core.ion",
+ "@version": null,
+ "Cl": 2,
+ "Zn": 1,
+ "charge": 0
+ },
+ "size": {
+ "molar_volume": null,
+ "radius_hydrated": null,
+ "radius_ionic": {
+ "data_type": "experimental",
+ "reference": "pymatgen",
+ "value": "None"
+ },
+ "radius_vdw": {
+ "data_type": "experimental",
+ "reference": "pymatgen",
+ "value": "2.01 \u212b"
+ }
+ },
+ "thermo": {
+ "\u0394G_formation": null,
+ "\u0394G_hydration": null
+ },
+ "transport": {
+ "diffusion_coefficient": null
+ }
+ },
+ {
+ "charge": 0,
+ "chemsys": "I-Zn",
+ "elements": [
+ "Zn",
+ "I"
+ ],
+ "formula": "ZnI2(aq)",
+ "formula_hill": "I2 Zn",
+ "formula_html": "ZnI2",
+ "formula_latex": "ZnI$_{2}$",
+ "formula_pretty": "ZnI2",
+ "model_parameters": {
+ "activity_pitzer": {
+ "Beta0": {
+ "data_type": "fitted",
+ "reference": "10.1021/je2009329",
+ "value": "0.526 dimensionless"
+ },
+ "Beta1": {
+ "data_type": "fitted",
+ "reference": "10.1021/je2009329",
+ "value": "2.317 dimensionless"
+ },
+ "Beta2": {
+ "data_type": "fitted",
+ "reference": "10.1021/je2009329",
+ "value": "0.0 dimensionless"
+ },
+ "Cphi": {
+ "data_type": "fitted",
+ "reference": "10.1021/je2009329",
+ "value": "-0.08623 dimensionless"
+ },
+ "Max_C": {
+ "data_type": "fitted",
+ "reference": "10.1021/je2009329",
+ "value": "2.75 mol/kg"
+ }
+ },
+ "diffusion_temp_smolyakov": {
+ "a1": null,
+ "a2": null,
+ "d": null
+ },
+ "molar_volume_pitzer": {
+ "Beta0": {
+ "data_type": "fitted",
+ "reference": "10.1021/je2009329",
+ "value": "6.577e-05 dimensionless"
+ },
+ "Beta1": {
+ "data_type": "fitted",
+ "reference": "10.1021/je2009329",
+ "value": "-0.001513 dimensionless"
+ },
+ "Beta2": {
+ "data_type": "fitted",
+ "reference": "10.1021/je2009329",
+ "value": "0.0 dimensionless"
+ },
+ "Cphi": {
+ "data_type": "fitted",
+ "reference": "10.1021/je2009329",
+ "value": "2.018e-05 dimensionless"
+ },
+ "Max_C": {
+ "data_type": "fitted",
+ "reference": "10.1021/je2009329",
+ "value": "2.892 mol/kg"
+ },
+ "V_o": {
+ "data_type": "fitted",
+ "reference": "10.1021/je2009329",
+ "value": "50.8 dimensionless"
+ }
+ },
+ "viscosity_jones_dole": {
+ "B": null
+ }
+ },
+ "molecular_weight": "319.21794 g/mol",
+ "n_atoms": 3,
+ "n_elements": 2,
+ "oxi_state_guesses": {
+ "I": -1,
+ "Zn": 2
+ },
+ "pmg_ion": {
+ "@class": "Ion",
+ "@module": "pymatgen.core.ion",
+ "@version": null,
+ "I": 2,
+ "Zn": 1,
+ "charge": 0
+ },
+ "size": {
+ "molar_volume": null,
+ "radius_hydrated": null,
+ "radius_ionic": {
+ "data_type": "experimental",
+ "reference": "pymatgen",
+ "value": "None"
+ },
+ "radius_vdw": {
+ "data_type": "experimental",
+ "reference": "pymatgen",
+ "value": "2.01 \u212b"
+ }
+ },
+ "thermo": {
+ "\u0394G_formation": null,
+ "\u0394G_hydration": null
+ },
+ "transport": {
+ "diffusion_coefficient": null
+ }
+ },
+ {
+ "charge": 0,
+ "chemsys": "O-S-Zn",
+ "elements": [
+ "Zn",
+ "S",
+ "O"
+ ],
+ "formula": "ZnSO4(aq)",
+ "formula_hill": "O4 S Zn",
+ "formula_html": "ZnSO4",
+ "formula_latex": "ZnSO$_{4}$",
+ "formula_pretty": "ZnSO4",
+ "model_parameters": {
+ "activity_pitzer": {
+ "Beta0": {
+ "data_type": "fitted",
+ "reference": "10.1021/je2009329",
+ "value": "0.1991 dimensionless"
+ },
+ "Beta1": {
+ "data_type": "fitted",
+ "reference": "10.1021/je2009329",
+ "value": "2.63 dimensionless"
+ },
+ "Beta2": {
+ "data_type": "fitted",
+ "reference": "10.1021/je2009329",
+ "value": "-37.74 dimensionless"
+ },
+ "Cphi": {
+ "data_type": "fitted",
+ "reference": "10.1021/je2009329",
+ "value": "0.02892 dimensionless"
+ },
+ "Max_C": {
+ "data_type": "fitted",
+ "reference": "10.1021/je2009329",
+ "value": "3.5 mol/kg"
+ }
+ },
+ "diffusion_temp_smolyakov": {
+ "a1": null,
+ "a2": null,
+ "d": null
+ },
+ "molar_volume_pitzer": {
+ "Beta0": {
+ "data_type": "fitted",
+ "reference": "10.1021/je2009329",
+ "value": "0.00155 dimensionless"
+ },
+ "Beta1": {
+ "data_type": "fitted",
+ "reference": "10.1021/je2009329",
+ "value": "-0.004269 dimensionless"
+ },
+ "Beta2": {
+ "data_type": "fitted",
+ "reference": "10.1021/je2009329",
+ "value": "0.0965 dimensionless"
+ },
+ "Cphi": {
+ "data_type": "fitted",
+ "reference": "10.1021/je2009329",
+ "value": "-0.0004204 dimensionless"
+ },
+ "Max_C": {
+ "data_type": "fitted",
+ "reference": "10.1021/je2009329",
+ "value": "3.403 mol/kg"
+ },
+ "V_o": {
+ "data_type": "fitted",
+ "reference": "10.1021/je2009329",
+ "value": "-7.6 dimensionless"
+ }
+ },
+ "viscosity_jones_dole": {
+ "B": null
+ }
+ },
+ "molecular_weight": "161.4716 g/mol",
+ "n_atoms": 6,
+ "n_elements": 3,
+ "oxi_state_guesses": {
+ "O": -2,
+ "S": 6,
+ "Zn": 2
+ },
+ "pmg_ion": {
+ "@class": "Ion",
+ "@module": "pymatgen.core.ion",
+ "@version": null,
+ "O": 4,
+ "S": 1,
+ "Zn": 1,
+ "charge": 0
+ },
+ "size": {
+ "molar_volume": null,
+ "radius_hydrated": null,
+ "radius_ionic": {
+ "data_type": "experimental",
+ "reference": "pymatgen",
+ "value": "None"
+ },
+ "radius_vdw": {
+ "data_type": "experimental",
+ "reference": "pymatgen",
+ "value": "2.01 \u212b"
+ }
+ },
+ "thermo": {
+ "\u0394G_formation": null,
+ "\u0394G_hydration": null
+ },
+ "transport": {
+ "diffusion_coefficient": null
+ }
+ },
+ {
+ "charge": 2,
+ "chemsys": "Zn",
+ "elements": [
+ "Zn"
+ ],
+ "formula": "Zn[+2]",
+ "formula_hill": "Zn",
+ "formula_html": "Zn+2",
+ "formula_latex": "Zn$^{+2}$",
+ "formula_pretty": "Zn^+2",
+ "model_parameters": {
+ "activity_pitzer": {
+ "Beta0": null,
+ "Beta1": null,
+ "Beta2": null,
+ "Cphi": null,
+ "Max_C": null
+ },
+ "diffusion_temp_smolyakov": {
+ "a1": null,
+ "a2": null,
+ "d": null
+ },
+ "molar_volume_pitzer": {
+ "Beta0": null,
+ "Beta1": null,
+ "Beta2": null,
+ "Cphi": null,
+ "Max_C": null,
+ "V_o": null
+ },
+ "viscosity_jones_dole": {
+ "B": {
+ "data_type": "fitted",
+ "reference": "https://doi.org/10.1021/cr00040a004",
+ "value": "0.369 dm**3/mol"
+ }
+ }
+ },
+ "molecular_weight": "65.409 g/mol",
+ "n_atoms": 1,
+ "n_elements": 1,
+ "oxi_state_guesses": {
+ "Zn": 2
+ },
+ "pmg_ion": {
+ "@class": "Ion",
+ "@module": "pymatgen.core.ion",
+ "@version": null,
+ "Zn": 1,
+ "charge": 2
+ },
+ "size": {
+ "molar_volume": {
+ "data_type": "experimental",
+ "reference": "Calculation of the Partial Molal Volume of Organic Compounds and Polymers. Progress in Colloid & Polymer Science (94), 20-39.",
+ "value": "-29.2 cm**3/mol"
+ },
+ "radius_hydrated": {
+ "data_type": "experimental",
+ "reference": "Nightingale1959",
+ "value": "4.3 \u212b"
+ },
+ "radius_ionic": {
+ "data_type": "experimental",
+ "reference": "pymatgen",
+ "value": "0.88 \u00c5"
+ },
+ "radius_ionic_marcus": {
+ "data_type": "experimental",
+ "reference": "Marcus2015",
+ "value": "0.75 \u00b1 0.02 \u212b"
+ },
+ "radius_vdw": {
+ "data_type": "experimental",
+ "reference": "pymatgen",
+ "value": "2.01 \u212b"
+ }
+ },
+ "thermo": {
+ "\u0394G_formation": null,
+ "\u0394G_hydration": {
+ "data_type": "experimental",
+ "reference": "10.1021/acs.jpca.9b05140",
+ "value": "-2043.0 \u00b1 10 kJ/mol"
+ }
+ },
+ "transport": {
+ "diffusion_coefficient": {
+ "data_type": "experimental",
+ "reference": "CRC",
+ "value": "7.03e-06 cm**2/s"
+ }
+ }
+ },
+ {
+ "charge": 4,
+ "chemsys": "Zr",
+ "elements": [
+ "Zr"
+ ],
+ "formula": "Zr[+4]",
+ "formula_hill": "Zr",
+ "formula_html": "Zr+4",
+ "formula_latex": "Zr$^{+4}$",
+ "formula_pretty": "Zr^+4",
+ "model_parameters": {
+ "activity_pitzer": {
+ "Beta0": null,
+ "Beta1": null,
+ "Beta2": null,
+ "Cphi": null,
+ "Max_C": null
+ },
+ "diffusion_temp_smolyakov": {
+ "a1": null,
+ "a2": null,
+ "d": null
+ },
+ "molar_volume_pitzer": {
+ "Beta0": null,
+ "Beta1": null,
+ "Beta2": null,
+ "Cphi": null,
+ "Max_C": null,
+ "V_o": null
+ },
+ "viscosity_jones_dole": {
+ "B": null
+ }
+ },
+ "molecular_weight": "91.224 g/mol",
+ "n_atoms": 1,
+ "n_elements": 1,
+ "oxi_state_guesses": {
+ "Zr": 4
+ },
+ "pmg_ion": {
+ "@class": "Ion",
+ "@module": "pymatgen.core.ion",
+ "@version": null,
+ "Zr": 1,
+ "charge": 4
+ },
+ "size": {
+ "molar_volume": null,
+ "radius_hydrated": null,
+ "radius_ionic": {
+ "data_type": "experimental",
+ "reference": "pymatgen",
+ "value": "0.86 \u00c5"
+ },
+ "radius_ionic_marcus": {
+ "data_type": "experimental",
+ "reference": "Marcus2015",
+ "value": "0.72 \u00b1 0.02 \u212b"
+ },
+ "radius_vdw": {
+ "data_type": "experimental",
+ "reference": "pymatgen",
+ "value": "2.23 \u212b"
+ }
+ },
+ "thermo": {
+ "\u0394G_formation": null,
+ "\u0394G_hydration": {
+ "data_type": "experimental",
+ "reference": "Marcus2015",
+ "value": "-6949.0 \u00b1 6 kJ/mol"
+ }
+ },
+ "transport": {
+ "diffusion_coefficient": null
+ }
}
- }
]
diff --git a/src/pyEQL/solution.py b/src/pyEQL/solution.py
index 56b51ff..c4c39d5 100644
--- a/src/pyEQL/solution.py
+++ b/src/pyEQL/solution.py
@@ -194,7 +194,7 @@ def __init__(
if database is None:
# load the default database, which is a JSONStore
db_store = IonDB
- elif isinstance(database, (str, Path)):
+ elif isinstance(database, str | Path):
db_store = JSONStore(str(database), key="formula")
self.logger.debug(f"Created maggma JSONStore from .json file {database}")
else: