From 29f999d9cda723adcbd5aa2c3b87260648b16742 Mon Sep 17 00:00:00 2001 From: Ryan Kingsbury Date: Thu, 10 Aug 2023 13:37:45 -0400 Subject: [PATCH] WIP db refresh --- pyproject.toml | 1 + src/pyEQL/__init__.py | 2 +- src/pyEQL/database/pyeql_db.json | 6843 +++++++++++++++++++++++++++++- src/pyEQL/engines.py | 16 +- src/pyEQL/solution.py | 111 +- tests/test_solution.py | 40 + 6 files changed, 6951 insertions(+), 62 deletions(-) create mode 100644 tests/test_solution.py diff --git a/pyproject.toml b/pyproject.toml index 686584e5..ce0cdfb2 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -86,3 +86,4 @@ no_implicit_optional = false [tool.codespell] ignore-words-list = "nd" skip = 'tests/test_files/*' +exclude = 'src/pyEQL/database/pyeql_db.json' diff --git a/src/pyEQL/__init__.py b/src/pyEQL/__init__.py index 08671477..f5156720 100644 --- a/src/pyEQL/__init__.py +++ b/src/pyEQL/__init__.py @@ -47,7 +47,7 @@ unit.default_format = "P~" # this must be imported after instantiating the UnitRegistry() -from pyEQL.database import Paramsdb # noqa +# from pyEQL.database import Paramsdb # initialize the parameters database # paramsDB = Paramsdb() diff --git a/src/pyEQL/database/pyeql_db.json b/src/pyEQL/database/pyeql_db.json index f86b6be9..12bec5fc 100644 --- a/src/pyEQL/database/pyeql_db.json +++ b/src/pyEQL/database/pyeql_db.json @@ -1 +1,6842 @@ -[{"formula": "Br[-1]", "charge": "-1", "molecular_weight": "79.904 g/mol", "elements": "[Element Br]", "chemsys": "Br", "pmg_ion": "Br1 -1", "formula_html": "Br-1", "formula_latex": "Br$^{-1}$", "formula_hill": "Br", "formula_pretty": "Br^-1", "oxi_state_guesses": "({'Br': -1.0},)", "n_atoms": "1", "n_elements": "1", "size": "{'radius_ionic': {'value': '1.82 \u00c5', 'reference': 'pymatgen', 'data_type': 'experimental'}, 'radius_hydrated': {'value': '3.3 \u212b', 'reference': 'Nightingale1959', 'data_type': 'experimental'}, 'radius_vdw': {'value': '1.85 \u212b', 'reference': 'pymatgen', 'data_type': 'experimental'}, 'molar_volume': None, 'radius_ionic_marcus': {'value': '1.96 \u00b1 0.02 \u212b', 'reference': 'Marcus2015', 'data_type': 'experimental'}}", "thermo": "{'\u0394G_hydration': {'value': '-274.0 \u00b1 6 kJ/mol', 'reference': 'Marcus2015', 'data_type': 'experimental'}, '\u0394G_formation': None}", "transport": "{'diffusion_coefficient': {'value': '2.08e-05 cm**2/s', 'reference': 'CRC', 'data_type': 'experimental'}}", "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': {'value': '-0.033 dm**3/mol', 'reference': 'https://doi.org/10.1021/cr00040a004', 'data_type': 'fitted'}}, 'dielectric_zuber': {'value': '7.31 dimensionless', 'reference': 'https://doi.org/10.1016/j.fluid.2014.05.037', 'data_type': 'fitted'}}"}, {"formula": "H[+1]", "charge": "1", "molecular_weight": "1.00794 g/mol", "elements": "[Element H]", "chemsys": "H", "pmg_ion": "H1 +1", "formula_html": "H+1", "formula_latex": "H$^{+1}$", "formula_hill": "H", "formula_pretty": "H^+1", "oxi_state_guesses": "({'H': 1.0},)", "n_atoms": "1", "n_elements": "1", "size": "{'radius_ionic': {'value': 'None', 'reference': 'pymatgen', 'data_type': 'experimental'}, 'radius_hydrated': None, 'radius_vdw': {'value': '1.1 \u212b', 'reference': 'pymatgen', 'data_type': 'experimental'}, 'molar_volume': None}", "thermo": "{'\u0394G_hydration': {'value': '-1108.0 \u00b1 6 kJ/mol', 'reference': 'Marcus2015', 'data_type': 'experimental'}, '\u0394G_formation': None}", "transport": "{'diffusion_coefficient': {'value': '9.311e-05 cm**2/s', 'reference': 'CRC', 'data_type': 'experimental'}}", "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': {'value': '0.068 dm**3/mol', 'reference': 'https://doi.org/10.1021/cr00040a004', 'data_type': 'fitted'}}, 'dielectric_zuber': {'value': '9.55 dimensionless', 'reference': 'https://doi.org/10.1016/j.fluid.2014.05.037', 'data_type': 'fitted'}}"}, {"formula": "Hf[+4]", "charge": "4", "molecular_weight": "178.49 g/mol", "elements": "[Element Hf]", "chemsys": "Hf", "pmg_ion": "Hf1 +4", "formula_html": "Hf+4", "formula_latex": "Hf$^{+4}$", "formula_hill": "Hf", "formula_pretty": "Hf^+4", "oxi_state_guesses": "({'Hf': 4.0},)", "n_atoms": "1", "n_elements": "1", "size": "{'radius_ionic': {'value': '0.85 \u00c5', 'reference': 'pymatgen', 'data_type': 'experimental'}, 'radius_hydrated': None, 'radius_vdw': {'value': '2.23 \u212b', 'reference': 'pymatgen', 'data_type': 'experimental'}, 'molar_volume': None, 'radius_ionic_marcus': {'value': '0.71 \u00b1 0.02 \u212b', 'reference': 'Marcus2015', 'data_type': 'experimental'}}", "thermo": "{'\u0394G_hydration': {'value': '-7118.0 \u00b1 6 kJ/mol', 'reference': 'Marcus2015', 'data_type': 'experimental'}, '\u0394G_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}}"}, {"formula": "Er[+3]", "charge": "3", "molecular_weight": "167.259 g/mol", "elements": "[Element Er]", "chemsys": "Er", "pmg_ion": "Er1 +3", "formula_html": "Er+3", "formula_latex": "Er$^{+3}$", "formula_hill": "Er", "formula_pretty": "Er^+3", "oxi_state_guesses": "({'Er': 3.0},)", "n_atoms": "1", "n_elements": "1", "size": "{'radius_ionic': {'value': '1.03 \u00c5', 'reference': 'pymatgen', 'data_type': 'experimental'}, 'radius_hydrated': None, 'radius_vdw': {'value': '2.29 \u212b', 'reference': 'pymatgen', 'data_type': 'experimental'}, 'molar_volume': None, 'radius_ionic_marcus': {'value': '1.04 \u00b1 0.01 \u212b', 'reference': '10.1021/ic200260r', 'data_type': 'experimental'}}", "thermo": "{'\u0394G_hydration': {'value': '-3627.0 \u00b1 10 kJ/mol', 'reference': '10.1021/acs.jpca.9b05140', 'data_type': 'experimental'}, '\u0394G_formation': None}", "transport": "{'diffusion_coefficient': {'value': '5.85e-06 cm**2/s', 'reference': 'CRC', 'data_type': 'experimental'}}", "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': {'value': '0.657 dm**3/mol', 'reference': 'https://doi.org/10.1021/cr00040a004', 'data_type': 'fitted'}}}"}, {"formula": "HSeO3[-1]", "charge": "-1", "molecular_weight": "127.96614 g/mol", "elements": "[Element H, Element Se, Element O]", "chemsys": "H-O-Se", "pmg_ion": "H1 Se1 O3 -1", "formula_html": "HSeO3-1", "formula_latex": "HSeO$_{3}$$^{-1}$", "formula_hill": "H O3 Se", "formula_pretty": "HSeO3^-1", "oxi_state_guesses": "({'H': 1.0, 'Se': 4.0, 'O': -2.0}, {'H': -1.0, 'Se': 6.0, 'O': -2.0})", "n_atoms": "5", "n_elements": "3", "size": "{'radius_ionic': {'value': 'None', 'reference': 'pymatgen', 'data_type': 'experimental'}, 'radius_hydrated': None, 'radius_vdw': {'value': '1.1 \u212b', 'reference': 'pymatgen', 'data_type': 'experimental'}, 'molar_volume': None}", "thermo": "{'\u0394G_hydration': {'value': 'nan \u00b1 6 kJ/mol', 'reference': 'Marcus2015', 'data_type': 'experimental'}, '\u0394G_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}}"}, {"formula": "TlH(C3O)2.4H2O(aq)", "charge": "0", 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1.0, 'C': 2.0, 'H': -0.1111111111111111, 'O': -2.0}, {'Tl': 1.0, 'C': 2.3333333333333335, 'H': -0.3333333333333333, 'O': -2.0}, {'Tl': 3.0, 'C': 1.6666666666666667, 'H': -0.1111111111111111, 'O': -2.0}, {'Tl': 1.0, 'C': 2.6666666666666665, 'H': -0.5555555555555556, 'O': -2.0}, {'Tl': 3.0, 'C': 2.0, 'H': -0.3333333333333333, 'O': -2.0}, {'Tl': 1.0, 'C': 3.0, 'H': -0.7777777777777778, 'O': -2.0}, {'Tl': 3.0, 'C': 2.3333333333333335, 'H': -0.5555555555555556, 'O': -2.0}, {'Tl': 3.0, 'C': 2.6666666666666665, 'H': -0.7777777777777778, 'O': -2.0}, {'Tl': 1.0, 'C': 3.3333333333333335, 'H': -1.0, 'O': -2.0}, {'Tl': 3.0, 'C': 3.0, 'H': -1.0, 'O': -2.0})", "n_atoms": "22", "n_elements": "4", "size": "{'radius_ionic': {'value': 'None', 'reference': 'pymatgen', 'data_type': 'experimental'}, 'radius_hydrated': None, 'radius_vdw': {'value': '1.96 \u212b', 'reference': 'pymatgen', 'data_type': 'experimental'}, 'molar_volume': None}", "thermo": "{'\u0394G_hydration': None, '\u0394G_formation': None}", 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"n_atoms": "1", "n_elements": "1", "size": "{'radius_ionic': {'value': '0.83', 'reference': 'pymatgen', 'data_type': 'experimental'}, 'radius_hydrated': {'value': '4.04 \u212b', 'reference': 'Nightingale1959', 'data_type': 'experimental'}, 'radius_vdw': {'value': '1.97 \u212b', 'reference': 'pymatgen', 'data_type': 'experimental'}, 'molar_volume': None, 'radius_ionic_marcus': {'value': '0.69 \u00b1 0.02 \u212b', 'reference': 'Marcus2015', 'data_type': 'experimental'}}", "thermo": "{'\u0394G_hydration': {'value': '-2068.0 \u00b1 10 kJ/mol', 'reference': '10.1021/acs.jpca.9b05140', 'data_type': 'experimental'}, '\u0394G_formation': None}", "transport": "{'diffusion_coefficient': {'value': '6.61e-06 cm**2/s', 'reference': 'CRC', 'data_type': 'experimental'}}", "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': {'value': '0.379 dm**3/mol', 'reference': 'https://doi.org/10.1021/cr00040a004', 'data_type': 'fitted'}}}"}, {"formula": "Sb(OH)6[-1]", "charge": "-1", "molecular_weight": "223.80404 g/mol", "elements": "[Element Sb, Element O, Element H]", "chemsys": "H-O-Sb", "pmg_ion": "Sb1 H6 O6 -1", "formula_html": "Sb(OH)6-1", "formula_latex": "Sb(OH)$_{6}$$^{-1}$", "formula_hill": "H6 O6 Sb", "formula_pretty": "Sb(OH)6^-1", "oxi_state_guesses": "({'Sb': 5.0, 'O': -2.0, 'H': 1.0},)", "n_atoms": "13", "n_elements": "3", "size": "{'radius_ionic': {'value': 'None', 'reference': 'pymatgen', 'data_type': 'experimental'}, 'radius_hydrated': None, 'radius_vdw': {'value': '2.06 \u212b', 'reference': 'pymatgen', 'data_type': 'experimental'}, 'molar_volume': None}", "thermo": "{'\u0394G_hydration': None, '\u0394G_formation': None}", "transport": "{'diffusion_coefficient': {'value': '8.49e-06 cm**2/s', 'reference': 'CRC', 'data_type': 'experimental'}}", "model_parameters": "{'activity_pitzer': {'Beta0': None, 'Beta1': None, 'Beta2': None, 'Cphi': None, 'Max_C': None}, 'molar_volume_pitzer': {'Beta0': None, 'Beta1': None, 'Beta2': None, 'Cphi': None, 'V_o': None, 'Max_C': None}, 'viscosity_jones_dole': {'B': None}}"}, {"formula": "Co[+3]", "charge": "3", "molecular_weight": "58.933195 g/mol", "elements": "[Element Co]", "chemsys": "Co", "pmg_ion": "Co1 +3", "formula_html": "Co+3", "formula_latex": "Co$^{+3}$", "formula_hill": "Co", "formula_pretty": "Co^+3", "oxi_state_guesses": "({'Co': 3.0},)", "n_atoms": "1", "n_elements": "1", "size": "{'radius_ionic': {'value': '0.75 \u00c5', 'reference': 'pymatgen', 'data_type': 'experimental'}, 'radius_hydrated': None, 'radius_vdw': {'value': '2.0 \u212b', 'reference': 'pymatgen', 'data_type': 'experimental'}, 'molar_volume': None, 'radius_ionic_marcus': {'value': '0.65 \u00b1 0.02 \u212b', 'reference': 'Marcus2015', 'data_type': 'experimental'}}", "thermo": "{'\u0394G_hydration': {'value': '-4622.0 \u00b1 10 kJ/mol', 'reference': '10.1021/acs.jpca.9b05140', 'data_type': 'experimental'}, '\u0394G_formation': None}", "transport": "{'diffusion_coefficient': None}", "model_parameters": "{'activity_pitzer': {'Beta0': None, 'Beta1': None, 'Beta2': None, 'Cphi': None, 'Max_C': None}, 'molar_volume_pitzer': {'Beta0': None, 'Beta1': None, 'Beta2': None, 'Cphi': None, 'V_o': None, 'Max_C': None}, 'viscosity_jones_dole': {'B': None}}"}, {"formula": "H4NCl(aq)", "charge": "0", "molecular_weight": "53.491460000000004 g/mol", "elements": "[Element N, Element H, Element Cl]", "chemsys": "Cl-H-N", "pmg_ion": "H4 N1 Cl1 (aq)", "formula_html": "H4NCl", "formula_latex": "H$_{4}$NCl", "formula_hill": "Cl H4 N", "formula_pretty": "H4NCl", "oxi_state_guesses": "({'N': -3.0, 'H': 1.0, 'Cl': -1.0}, {'N': -1.0, 'H': 0.5, 'Cl': -1.0}, {'N': 1.0, 'H': 0.0, 'Cl': -1.0}, {'N': 3.0, 'H': -0.5, 'Cl': -1.0}, {'N': 5.0, 'H': -1.0, 'Cl': -1.0})", "n_atoms": "6", "n_elements": "3", "size": "{'radius_ionic': {'value': 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'10.1021/je2009329', 'data_type': 'fitted'}, 'Cphi': {'value': '0.001244 dimensionless', 'reference': '10.1021/je2009329', 'data_type': 'fitted'}, 'Max_C': {'value': '5.0 mol/kg', 'reference': '10.1021/je2009329', 'data_type': 'fitted'}}, 'molar_volume_pitzer': {'Beta0': {'value': '7.096e-05 dimensionless', 'reference': '10.1021/je2009329', 'data_type': 'fitted'}, 'Beta1': {'value': '0.0002329 dimensionless', 'reference': '10.1021/je2009329', 'data_type': 'fitted'}, 'Beta2': {'value': '0.0 dimensionless', 'reference': '10.1021/je2009329', 'data_type': 'fitted'}, 'Cphi': {'value': '-5.2e-06 dimensionless', 'reference': '10.1021/je2009329', 'data_type': 'fitted'}, 'V_o': {'value': '46.0 dimensionless', 'reference': '10.1021/je2009329', 'data_type': 'fitted'}, 'Max_C': {'value': '4.731 mol/kg', 'reference': '10.1021/je2009329', 'data_type': 'fitted'}}, 'viscosity_jones_dole': {'B': None}}" + }, + { + "formula": "H5N2[+1]", + "charge": "1", + "molecular_weight": "33.0531 g/mol", + 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{'value': '0.129 dm**3/mol', 'reference': 'https://doi.org/10.1021/cr00040a004', 'data_type': 'fitted'}}}" + }, + { + "formula": "SrI2(aq)", + "charge": "0", + "molecular_weight": "341.42894 g/mol", + "elements": "[Element Sr, Element I]", + "chemsys": "I-Sr", + "pmg_ion": "Sr1 I2 (aq)", + "formula_html": "SrI2", + "formula_latex": "SrI$_{2}$", + "formula_hill": "I2 Sr", + "formula_pretty": "SrI2", + "oxi_state_guesses": "({'Sr': 2.0, 'I': -1.0},)", + "n_atoms": "3", + "n_elements": "2", + "size": "{'radius_ionic': {'value': 'None', 'reference': 'pymatgen', 'data_type': 'experimental'}, 'radius_hydrated': None, 'radius_vdw': {'value': '2.49 Å', 'reference': 'pymatgen', 'data_type': 'experimental'}, 'molar_volume': None}", + "thermo": "{'ΔG_hydration': None, 'ΔG_formation': None}", + "transport": "{'diffusion_coefficient': None}", + "model_parameters": "{'activity_pitzer': {'Beta0': {'value': '0.3889 dimensionless', 'reference': '10.1021/je2009329', 'data_type': 'fitted'}, 'Beta1': {'value': '2.001 dimensionless', 'reference': '10.1021/je2009329', 'data_type': 'fitted'}, 'Beta2': {'value': '0.0 dimensionless', 'reference': '10.1021/je2009329', 'data_type': 'fitted'}, 'Cphi': {'value': '0.006908 dimensionless', 'reference': '10.1021/je2009329', 'data_type': 'fitted'}, 'Max_C': {'value': '2.0 mol/kg', 'reference': '10.1021/je2009329', 'data_type': 'fitted'}}, 'molar_volume_pitzer': {'Beta0': {'value': '0.001036 dimensionless', 'reference': '10.1021/je2009329', 'data_type': 'fitted'}, 'Beta1': {'value': '-0.005949 dimensionless', 'reference': '10.1021/je2009329', 'data_type': 'fitted'}, 'Beta2': {'value': '0.0 dimensionless', 'reference': '10.1021/je2009329', 'data_type': 'fitted'}, 'Cphi': {'value': '-0.0004075 dimensionless', 'reference': '10.1021/je2009329', 'data_type': 'fitted'}, 'V_o': {'value': '54.2 dimensionless', 'reference': '10.1021/je2009329', 'data_type': 'fitted'}, 'Max_C': {'value': '1.953 mol/kg', 'reference': '10.1021/je2009329', 'data_type': 'fitted'}}, 'viscosity_jones_dole': {'B': None}}" + }, + { + "formula": "UO2[+1]", + "charge": "1", + "molecular_weight": "270.02771 g/mol", + "elements": "[Element U, Element O]", + "chemsys": "O-U", + "pmg_ion": "U1 O2 +1", + "formula_html": "UO2+1", + "formula_latex": "UO$_{2}$$^{+1}$", + "formula_hill": "O2 U", + "formula_pretty": "UO2^+1", + "oxi_state_guesses": "({'U': 5.0, 'O': -2.0},)", + "n_atoms": "3", + "n_elements": "2", + "size": "{'radius_ionic': {'value': 'None', 'reference': 'pymatgen', 'data_type': 'experimental'}, 'radius_hydrated': None, 'radius_vdw': {'value': '2.41 Å', 'reference': 'pymatgen', 'data_type': 'experimental'}, 'molar_volume': None, 'radius_ionic_marcus': {'value': '2.8 ± 0.02 Å', 'reference': 'Marcus2015', 'data_type': 'experimental'}}", + "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}}" + }, + { + "formula": "K2SO4(aq)", + "charge": "0", + "molecular_weight": "174.2592 g/mol", + "elements": "[Element K, Element S, Element O]", + "chemsys": "K-O-S", + "pmg_ion": "K2 S1 O4 (aq)", + "formula_html": "K2SO4", + "formula_latex": "K$_{2}$SO$_{4}$", + "formula_hill": "K2 O4 S", + "formula_pretty": "K2SO4", + "oxi_state_guesses": "({'K': 1.0, 'S': 6.0, 'O': -2.0},)", + "n_atoms": "7", + "n_elements": "3", + "size": "{'radius_ionic': {'value': 'None', 'reference': 'pymatgen', 'data_type': 'experimental'}, 'radius_hydrated': None, 'radius_vdw': {'value': '2.75 Å', 'reference': 'pymatgen', 'data_type': 'experimental'}, 'molar_volume': None}", + "thermo": "{'ΔG_hydration': None, 'ΔG_formation': None}", + "transport": "{'diffusion_coefficient': None}", + "model_parameters": "{'activity_pitzer': {'Beta0': {'value': '0.07424 dimensionless', 'reference': '10.1021/je2009329', 'data_type': 'fitted'}, 'Beta1': {'value': '0.5188 dimensionless', 'reference': '10.1021/je2009329', 'data_type': 'fitted'}, 'Beta2': {'value': '0.0 dimensionless', 'reference': '10.1021/je2009329', 'data_type': 'fitted'}, 'Cphi': {'value': '-0.01057 dimensionless', 'reference': '10.1021/je2009329', 'data_type': 'fitted'}, 'Max_C': {'value': '2.0 mol/kg', 'reference': '10.1021/je2009329', 'data_type': 'fitted'}}, 'molar_volume_pitzer': {'Beta0': {'value': '-0.001179 dimensionless', 'reference': '10.1021/je2009329', 'data_type': 'fitted'}, 'Beta1': {'value': '0.006263 dimensionless', 'reference': '10.1021/je2009329', 'data_type': 'fitted'}, 'Beta2': {'value': '0.0 dimensionless', 'reference': '10.1021/je2009329', 'data_type': 'fitted'}, 'Cphi': {'value': '0.001473 dimensionless', 'reference': '10.1021/je2009329', 'data_type': 'fitted'}, 'V_o': {'value': '32.0 dimensionless', 'reference': '10.1021/je2009329', 'data_type': 'fitted'}, 'Max_C': {'value': '1.05 mol/kg', 'reference': '10.1021/je2009329', 'data_type': 'fitted'}}, 'viscosity_jones_dole': {'B': None}}" + }, + { + "formula": "NaBr(aq)", + "charge": "0", + "molecular_weight": "102.89376928 g/mol", + "elements": "[Element Na, Element Br]", + "chemsys": "Br-Na", + "pmg_ion": "Na1 Br1 (aq)", + "formula_html": "NaBr", + "formula_latex": "NaBr", + "formula_hill": "Br Na", + "formula_pretty": "NaBr", + "oxi_state_guesses": "({'Na': 1.0, 'Br': -1.0},)", + "n_atoms": "2", + "n_elements": "2", + "size": "{'radius_ionic': {'value': 'None', 'reference': 'pymatgen', 'data_type': 'experimental'}, 'radius_hydrated': None, 'radius_vdw': {'value': '2.27 Å', 'reference': 'pymatgen', 'data_type': 'experimental'}, 'molar_volume': None}", + "thermo": "{'ΔG_hydration': None, 'ΔG_formation': None}", + "transport": "{'diffusion_coefficient': None}", + "model_parameters": "{'activity_pitzer': {'Beta0': {'value': '0.1083 dimensionless', 'reference': '10.1021/je2009329', 'data_type': 'fitted'}, 'Beta1': {'value': '0.239 dimensionless', 'reference': '10.1021/je2009329', 'data_type': 'fitted'}, 'Beta2': {'value': '0.0 dimensionless', 'reference': '10.1021/je2009329', 'data_type': 'fitted'}, 'Cphi': {'value': '-0.00104 dimensionless', 'reference': '10.1021/je2009329', 'data_type': 'fitted'}, 'Max_C': {'value': '9.0 mol/kg', 'reference': '10.1021/je2009329', 'data_type': 'fitted'}}, 'molar_volume_pitzer': {'Beta0': {'value': '4.333e-05 dimensionless', 'reference': '10.1021/je2009329', 'data_type': 'fitted'}, 'Beta1': {'value': '0.0002528 dimensionless', 'reference': '10.1021/je2009329', 'data_type': 'fitted'}, 'Beta2': {'value': '0.0 dimensionless', 'reference': '10.1021/je2009329', 'data_type': 'fitted'}, 'Cphi': {'value': '-1.4e-06 dimensionless', 'reference': '10.1021/je2009329', 'data_type': 'fitted'}, 'V_o': {'value': '23.5 dimensionless', 'reference': '10.1021/je2009329', 'data_type': 'fitted'}, 'Max_C': {'value': '8.376 mol/kg', 'reference': '10.1021/je2009329', 'data_type': 'fitted'}}, 'viscosity_jones_dole': {'B': None}}" + }, + { + "formula": "Y[+3]", + "charge": "3", + "molecular_weight": "88.90585 g/mol", + "elements": "[Element Y]", + "chemsys": "Y", + "pmg_ion": "Y1 +3", + "formula_html": "Y+3", + "formula_latex": "Y$^{+3}$", + "formula_hill": "Y", + "formula_pretty": "Y^+3", + "oxi_state_guesses": "({'Y': 3.0},)", + "n_atoms": "1", + "n_elements": "1", + "size": "{'radius_ionic': {'value': '1.04 Å', 'reference': 'pymatgen', 'data_type': 'experimental'}, 'radius_hydrated': None, 'radius_vdw': {'value': '2.32 Å', 'reference': 'pymatgen', 'data_type': 'experimental'}, 'molar_volume': None}", + "thermo": "{'ΔG_hydration': {'value': '-3523.0 ± 10 kJ/mol', 'reference': '10.1021/acs.jpca.9b05140', 'data_type': 'experimental'}, 'ΔG_formation': None}", + "transport": "{'diffusion_coefficient': {'value': '5.5e-06 cm**2/s', 'reference': 'CRC', 'data_type': 'experimental'}}", + "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}}" + }, + { + "formula": "CaBr2(aq)", + "charge": "0", + "molecular_weight": "199.886 g/mol", + "elements": "[Element Ca, Element Br]", + "chemsys": "Br-Ca", + "pmg_ion": "Ca1 Br2 (aq)", + "formula_html": "CaBr2", + "formula_latex": "CaBr$_{2}$", + "formula_hill": "Br2 Ca", + "formula_pretty": "CaBr2", + "oxi_state_guesses": "({'Ca': 2.0, 'Br': -1.0},)", + "n_atoms": "3", + "n_elements": "2", + "size": "{'radius_ionic': {'value': 'None', 'reference': 'pymatgen', 'data_type': 'experimental'}, 'radius_hydrated': None, 'radius_vdw': {'value': '2.31 Å', 'reference': 'pymatgen', 'data_type': 'experimental'}, 'molar_volume': None}", + "thermo": "{'ΔG_hydration': None, 'ΔG_formation': None}", + "transport": "{'diffusion_coefficient': None}", + "model_parameters": "{'activity_pitzer': {'Beta0': {'value': '0.3409 dimensionless', 'reference': '10.1021/je2009329', 'data_type': 'fitted'}, 'Beta1': {'value': '1.928 dimensionless', 'reference': '10.1021/je2009329', 'data_type': 'fitted'}, 'Beta2': {'value': '0.0 dimensionless', 'reference': '10.1021/je2009329', 'data_type': 'fitted'}, 'Cphi': {'value': '0.01034 dimensionless', 'reference': '10.1021/je2009329', 'data_type': 'fitted'}, 'Max_C': {'value': '6.0 mol/kg', 'reference': '10.1021/je2009329', 'data_type': 'fitted'}}, 'molar_volume_pitzer': {'Beta0': {'value': '0.0004783 dimensionless', 'reference': '10.1021/je2009329', 'data_type': 'fitted'}, 'Beta1': {'value': '-0.002234 dimensionless', 'reference': '10.1021/je2009329', 'data_type': 'fitted'}, 'Beta2': {'value': '0.0 dimensionless', 'reference': '10.1021/je2009329', 'data_type': 'fitted'}, 'Cphi': {'value': '-0.0001828 dimensionless', 'reference': '10.1021/je2009329', 'data_type': 'fitted'}, 'V_o': {'value': '31.5 dimensionless', 'reference': '10.1021/je2009329', 'data_type': 'fitted'}, 'Max_C': {'value': '2.595 mol/kg', 'reference': '10.1021/je2009329', 'data_type': 'fitted'}}, 'viscosity_jones_dole': {'B': None}}" + }, + { + "formula": "SO4[-1]", + "charge": "-2", + "molecular_weight": "192.1252 g/mol", + "elements": "[Element S, Element O]", + "chemsys": "O-S", + "pmg_ion": "S2 O8 -2", + "formula_html": "SO4-2", + "formula_latex": "SO$_{4}$$^{-2}$", + "formula_hill": "O8 S2", + "formula_pretty": "SO4^-2", + "oxi_state_guesses": "[]", + "n_atoms": "10", + "n_elements": "2", + "size": "{'radius_ionic': {'value': '1.7 Å', 'reference': 'pymatgen', 'data_type': 'experimental'}, 'radius_hydrated': None, 'radius_vdw': {'value': '1.8 Å', 'reference': 'pymatgen', 'data_type': 'experimental'}, 'molar_volume': None}", + "thermo": "{'ΔG_hydration': None, 'ΔG_formation': None}", + "transport": "{'diffusion_coefficient': {'value': '1.145e-05 cm**2/s', 'reference': 'CRC', 'data_type': 'experimental'}}", + "model_parameters": "{'activity_pitzer': {'Beta0': None, 'Beta1': None, 'Beta2': None, 'Cphi': None, 'Max_C': None}, 'molar_volume_pitzer': {'Beta0': None, 'Beta1': None, 'Beta2': None, 'Cphi': None, 'V_o': None, 'Max_C': None}, 'viscosity_jones_dole': {'B': None}}" + }, + { + "formula": "S2O3[-2]", + "charge": "-2", + "molecular_weight": "112.12819999999999 g/mol", + "elements": "[Element S, Element O]", + "chemsys": "O-S", + "pmg_ion": "S2 O3 -2", + "formula_html": "S2O3-2", + "formula_latex": "S$_{2}$O$_{3}$$^{-2}$", + "formula_hill": "O3 S2", + "formula_pretty": "S2O3^-2", + "oxi_state_guesses": "({'S': 2.0, 'O': -2.0},)", + "n_atoms": "5", + "n_elements": "2", + "size": "{'radius_ionic': {'value': '1.7 Å', 'reference': 'pymatgen', 'data_type': 'experimental'}, 'radius_hydrated': None, 'radius_vdw': {'value': '1.8 Å', 'reference': 'pymatgen', 'data_type': 'experimental'}, 'molar_volume': None}", + "thermo": "{'ΔG_hydration': None, 'ΔG_formation': None}", + "transport": "{'diffusion_coefficient': {'value': '1.132e-05 cm**2/s', 'reference': 'CRC', 'data_type': 'experimental'}}", + "model_parameters": "{'activity_pitzer': {'Beta0': None, 'Beta1': None, 'Beta2': None, 'Cphi': None, 'Max_C': None}, 'molar_volume_pitzer': {'Beta0': None, 'Beta1': None, 'Beta2': None, 'Cphi': None, 'V_o': None, 'Max_C': None}, 'viscosity_jones_dole': {'B': None}}" + }, + { + "formula": "CH3COO[-1]", + "charge": "-1", + "molecular_weight": "59.04402 g/mol", + "elements": "[Element C, Element H, Element O]", + "chemsys": "C-H-O", + "pmg_ion": "H3 C2 O2 -1", + "formula_html": "CH3COO-1", + "formula_latex": "CH$_{3}$COO$^{-1}$", + "formula_hill": "C2 H3 O2", + "formula_pretty": "CH3COO^-1", + "oxi_state_guesses": "({'C': 0.0, 'H': 1.0, 'O': -2.0}, {'C': 1.0, 'H': 0.3333333333333333, 'O': -2.0}, {'C': 2.0, 'H': -0.3333333333333333, 'O': -2.0}, {'C': 3.0, 'H': -1.0, 'O': -2.0})", + "n_atoms": "7", + "n_elements": "3", + "size": "{'radius_ionic': {'value': 'None', 'reference': 'pymatgen', 'data_type': 'experimental'}, 'radius_hydrated': None, 'radius_vdw': {'value': '1.7 Å', 'reference': 'pymatgen', 'data_type': 'experimental'}, 'molar_volume': None}", + "thermo": "{'ΔG_hydration': None, 'ΔG_formation': None}", + "transport": "{'diffusion_coefficient': {'value': '1.089e-05 cm**2/s', 'reference': 'CRC', 'data_type': 'experimental'}}", + "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}}" + } +] diff --git a/src/pyEQL/engines.py b/src/pyEQL/engines.py index d372feb2..4d10ca1a 100644 --- a/src/pyEQL/engines.py +++ b/src/pyEQL/engines.py @@ -222,7 +222,7 @@ def get_activity_coefficient(self, solution, solute): if verbose is True: print("Calculating activity coefficient based on parent salt %s" % Salt.formula) - param = db.get_parameter(Salt.formula, "pitzer_parameters_activity") + param = db.get_property(Salt.formula, "pitzer_parameters_activity") # determine alpha1 and alpha2 based on the type of salt # see the May reference for the rules used to determine @@ -438,7 +438,7 @@ def get_osmotic_coefficient(self, solution): db.search_parameters(item.formula) if db.has_parameter(item.formula, "pitzer_parameters_activity"): - param = db.get_parameter(item.formula, "pitzer_parameters_activity") + param = db.get_property(item.formula, "pitzer_parameters_activity") osmotic_coefficient = ac.get_osmotic_coefficient_pitzer( ionic_strength, @@ -478,7 +478,7 @@ def get_solute_volume(self, solution): Salt = solution.get_salt() # search the database for pitzer parameters for 'salt' - db.search_parameters(Salt.formula) + # db.search_parameters(Salt.formula) solute_vol = 0 * unit("L") @@ -486,9 +486,8 @@ def get_solute_volume(self, solution): pitzer_calc = False - if db.has_parameter(Salt.formula, "pitzer_parameters_volume"): - param = db.get_parameter(Salt.formula, "pitzer_parameters_volume") - + param = solution.get_property(Salt.formula, "pitzer_parameters_volume") + if param is not None: # determine the average molality of the salt # this is necessary for solutions inside e.g. an ion exchange # membrane, where the cation and anion concentrations may be @@ -550,8 +549,9 @@ def get_solute_volume(self, solution): if pitzer_calc is True and solute in [Salt.anion, Salt.cation]: continue - if db.has_parameter(solute, "partial_molar_volume"): - solute_vol += solution.get_parameter(solute, "partial_molar_volume") * mol + part_vol = solution.get_property(solute, "partial_molar_volume") + if part_vol is not None: + solute_vol += part_vol * mol logger.info("Updated solution volume using direct partial molar volume for solute %s" % solute) else: diff --git a/src/pyEQL/solution.py b/src/pyEQL/solution.py index 8261c0f3..5b3eab92 100644 --- a/src/pyEQL/solution.py +++ b/src/pyEQL/solution.py @@ -127,7 +127,7 @@ def __init__( json = Path(database_dir) / "pyeql_db.json" else: json = database if isinstance(database, str) else str(database) - db_store = JSONStore(json) + db_store = JSONStore(json, key="formula") logger.info(f"Created maggma JSONStore from .json file {database}") else: db_store = database @@ -207,7 +207,7 @@ def add_solute(self, formula, amount): # add the new solute quantity = unit.Quantity(amount) - mw = unit.Quantity(self.get_property(formula, "molecular_weight")) + mw = self.get_property(formula, "molecular_weight") # returns a quantity target_mol = quantity.to("moles", "chem", mw=mw, volume=self.volume, solvent_mass=self.get_solvent_mass()) self.components[formula] = target_mol.to("moles").magnitude @@ -222,7 +222,10 @@ def add_solute(self, formula, amount): target_mass = target_vol.to("L").magnitude * self.water_substance.rho * unit.Quantity("1 g") # mw = unit.Quantity(self.get_property(self.solvent_name, "molecular_weight")) mw = self.get_property(self.solvent_name, "molecular_weight") - print(target_mass, mw) + if mw is None: + raise ValueError( + f"Molecular weight for solvent {self.solvent_name} not found in database. This is required to proceed." + ) target_mol = target_mass.to("g") / mw.to("g/mol") self.components[self.solvent_name] = target_mol.magnitude @@ -454,15 +457,16 @@ def dielectric_constant(self) -> Quantity: # ignore water if item != "H2O": # skip over solutes that don't have parameters - try: - fraction = self.get_amount(item, "fraction") - coefficient = self.get_property(item, "dielectric_parameter_water") + # try: + fraction = self.get_amount(item, "fraction") + coefficient = self.get_property(item, "model_parameters.dielectric_zuber") + if coefficient is not None: denominator += coefficient * fraction - except TypeError: - logger.warning("No dielectric parameters found for species %s." % item) - continue + # except TypeError: + # logger.warning("No dielectric parameters found for species %s." % item) + # continue - return di_water / denominator + return unit.Quantity(di_water / denominator, "dimensionless") # TODO - need tests for viscosity @property @@ -1040,7 +1044,6 @@ def get_amount(self, solute, units): # retrieve the number of moles of solute and its molecular weight try: moles = unit.Quantity(self.components[solute], "mol") - mw = unit.Quantity(self.get_property(solute, "molecular_weight"), "g/mol") # if the solute is not present in the solution, we'll get a KeyError # In that case, the amount is zero except KeyError: @@ -1056,6 +1059,7 @@ def get_amount(self, solute, units): # function calls. if units == "fraction": return moles / (self.get_moles_solvent() + self.get_total_moles_solute()) + mw = self.get_property(solute, "molecular_weight").to("g/mol") if units == "%": return moles.to("kg", "chem", mw=mw) / self.mass.to("kg") * 100 if unit.Quantity(units).dimensionality in ( @@ -1324,15 +1328,15 @@ def get_osmolality(self, activity_correction=False): factor = self.get_osmotic_coefficient() if activity_correction is True else 1 return factor * self.get_total_moles_solute() / self.get_solvent_mass().to("kg") - def get_total_moles_solute(self): + def get_total_moles_solute(self) -> Quantity: """Return the total moles of all solute in the solution.""" tot_mol = 0 for item in self.components: if item != self.solvent_name: - tot_mol += self.components[item].moles - return tot_mol + tot_mol += self.components[item] + return unit.Quantity(tot_mol, "mol") - def get_moles_solvent(self): + def get_moles_solvent(self) -> Quantity: """ Return the moles of solvent present in the solution. @@ -1812,7 +1816,7 @@ def get_mobility(self, solute): return mobility.to("m**2/V/s") - def _get_property(self, solute, name): + def _get_property(self, solute: str, name: str) -> Optional[Quantity]: """Retrieve a thermodynamic property (such as diffusion coefficient) for solute, and adjust it from the reference conditions to the conditions of the solution. @@ -1827,45 +1831,47 @@ def _get_property(self, solute, name): Returns: ------- - Quantity: The desired parameter + Quantity: The desired parameter or None if not found """ - # retrieve the base value and the conditions of measurement from the - # database - - # TODO - replace with a Store query to the database. - base_value = None - rform = Ion.from_formula(solute).reduced_formula - if self.database.get(rform): - base_value = self.database[rform].get(name) - # base_value = self.get_property(solute, name) if db.has_parameter(solute, name) else None - base_temperature = unit.Quantity("25 degC") # base_pressure = unit.Quantity("1 atm") + # query the database using the sanitized formula + rform = Ion.from_formula(solute).reduced_formula + data = list(self.database.query({"formula": rform, name: {"$exists": True}}, properties=["formula", name])) + # formulas should always be unique in the database. len==0 indicates no + # data. len>1 indicates duplicate data. + if len(data) != 1: + print(len(data)) + logger.warning(f"Property {name} for solute {solute} not found in database. Returning None.") + return None + data = data[0] + # perform temperature-corrections or other adjustments for certain # parameter types - if name == "diffusion_coefficient": - if base_value is not None: - # correct for temperature and viscosity - # .. math:: D_1 \over D_2 = T_1 \over T_2 * \mu_2 \over \mu_1 - # where :math:`\mu` is the dynamic viscosity - # assume that the base viscosity is that of pure water - return ( - base_value - * self.temperature - / base_temperature - * self.water_substance.mu - * unit.Quantity("1 Pa*s") - / self.get_viscosity_dynamic() - ) + if name == "transport.diffusion_coefficient": + base_value = data.get(name)["value"] + + # correct for temperature and viscosity + # .. math:: D_1 \over D_2 = T_1 \over T_2 * \mu_2 \over \mu_1 + # where :math:`\mu` is the dynamic viscosity + # assume that the base viscosity is that of pure water + return ( + base_value + * self.temperature + / base_temperature + * self.water_substance.mu + * unit.Quantity("1 Pa*s") + / self.get_viscosity_dynamic() + ) - logger.warning("Diffusion coefficient not found for species %s. Assuming zero." % (solute)) - return unit.Quantity("0 m**2/s") + # logger.warning("Diffusion coefficient not found for species %s. Assuming zero." % (solute)) + # return unit.Quantity("0 m**2/s") # just return the base-value molar volume for now; find a way to adjust for # concentration later - if name == "partial_molar_volume": + if name == "size.molar_volume": # calculate the partial molar volume for water since it isn't in the database if solute == "H2O": vol = ( @@ -1876,17 +1882,18 @@ def _get_property(self, solute, name): return vol.to("cm **3 / mol") - if base_value is not None: - if self.temperature != base_temperature: - logger.warning("Partial molar volume for species %s not corrected for temperature" % solute) - return base_value + base_value = unit.Quantity(data["size"]["molar_volume"]["value"]) + if self.temperature != base_temperature: + logger.warning("Partial molar volume for species %s not corrected for temperature" % solute) + return base_value - logger.warning("Partial molar volume not found for species %s. Assuming zero." % solute) - return unit.Quantity("0 cm **3 / mol") + if name == "model_parameters.dielectric_zuber": + return unit.Quantity(data["model_parameters"]["dielectric_zuber"]["value"]) # for parameters not named above, just return the base value - logger.warning("%s has not been corrected for solution conditions" % name) - return base_value + val = data.get(name) if isinstance(data.get(name), str) else data[name].get("value") + # logger.warning("%s has not been corrected for solution conditions" % name) + return unit.Quantity(val) def get_chemical_potential_energy(self, activity_correction=True): """ diff --git a/tests/test_solution.py b/tests/test_solution.py new file mode 100644 index 00000000..c48f7823 --- /dev/null +++ b/tests/test_solution.py @@ -0,0 +1,40 @@ +""" +pyEQL volume and concentration methods test suite +================================================= + +This file contains tests for the volume and concentration-related methods +used by pyEQL's Solution class +""" + +import pytest +from pyEQL import Solution + + +@pytest.fixture() +def s1(): + return Solution(volume="2 L") + + +@pytest.fixture() +def s2(): + return Solution([["Na+", "4 mol/L"], ["Cl-", "4 mol/L"]], volume="2 L") + + +@pytest.fixture() +def s3(): + return Solution([["Na+", "4 mol/kg"], ["Cl-", "4 mol/kg"]], volume="2 L") + + +@pytest.fixture() +def s4(): + return Solution([["Na+", "8 mol"], ["Cl-", "8 mol"]], volume="2 L") + + +def test_db_connect(): + Solution(database=None) + + +def test_serialization(s1, s2, s3): + assert isinstance(s1.as_dict(), dict) + s1_new = Solution.from_dict(s1.as_dict()) + assert s1_new.volume.magnitude == 2