Demo Notebook

pyEQL is an open-source python library for solution chemistry calculations and ion properties

Documentation

GitHub

Installation

>>> pip install pyEQL

Main feature: The Solution class

from pyEQL import Solution

/home/ryan/mambaforge/envs/pbx/code/pyEQL/src/pyEQL/__init__.py:52: FutureWarning: unitdeprecator is deprecated
The pyEQL UnitRegistry has been renamed from unit to ureg. Change 'from pyEQL import unit' to 'from pyEQL import ureg'!
  globals()["unit"] = unitdeprecator()

s1 = Solution({"Mg+2": "0.2 mol/L", "Cl-1": "0.4 mol/L"}, temperature='20 degC')

WARNING 2023-10-17 09:36:21,530 solution.py _get_property 2089 Partial molar volume for species H[+1] not corrected for temperature
WARNING 2023-10-17 09:36:21,538 solution.py _get_property 2089 Partial molar volume for species OH[-1] not corrected for temperature
WARNING 2023-10-17 09:36:21,788 solution.py _get_property 2089 Partial molar volume for species Mg[+2] not corrected for temperature
WARNING 2023-10-17 09:36:21,818 activity_correction.py _debye_parameter_volume 231 Debye-Huckel limiting slope for volume is approximate when T is not equal to 25 degC

Bulk Properties

s1.density

1.0138757383570756 kg/l

s1.conductivity

WARNING 2023-10-17 09:36:21,869 solution.py viscosity_kinematic 599 Viscosity coefficients for MgCl2 not found. Viscosity will be approximate.
WARNING 2023-10-17 09:36:21,906 solution.py viscosity_kinematic 599 Viscosity coefficients for MgCl2 not found. Viscosity will be approximate.
WARNING 2023-10-17 09:36:21,944 solution.py viscosity_kinematic 599 Viscosity coefficients for MgCl2 not found. Viscosity will be approximate.
WARNING 2023-10-17 09:36:21,970 engines.py get_activity_coefficient 314 Ionic strength too high to estimate activity for species H[+1]. Specify parameters for Pitzer model. Returning unit activity coefficient
WARNING 2023-10-17 09:36:21,985 solution.py viscosity_kinematic 599 Viscosity coefficients for MgCl2 not found. Viscosity will be approximate.
WARNING 2023-10-17 09:36:22,008 engines.py get_activity_coefficient 314 Ionic strength too high to estimate activity for species OH[-1]. Specify parameters for Pitzer model. Returning unit activity coefficient

3.299995263108894 S/m

s1.volume

1 l

s1.pressure

1 atm

s1.temperature

293.15 K

s1.osmotic_pressure

1286752.4185332006 Pa

Composition

s1.components

{'H2O(aq)': 55.221652761186476, 'Cl[-1]': 0.4, 'Mg[+2]': 0.2, 'H[+1]': 1e-07, 'OH[-1]': 1e-07}

s1.solvent

'H2O(aq)'

s1.cations

{'Mg[+2]': 0.2, 'H[+1]': 1e-07}

s1.anions

{'Cl[-1]': 0.4, 'OH[-1]': 1e-07}

s1.neutrals

{'H2O(aq)': 55.221652761186476}

Species Concentrations

s1.get_amount('Mg+2', 'M')

0.20000000000000007 M

s1.get_amount('Cl-', '%')

1.3987118404647676

s1.get_amount('Mg+2', 'eq/L')

0.4 mol/l

s1.get_amount('Mg+2', 'ug/kg')

4886244.60412788 µg/kg

Transport

s1.get_transport_number('Na+')

0.0

s1.get_transport_number('Mg+2')

0.4099879515632778

s1.get_transport_number('Cl-')

0.5900109897851136

Speciation

s1.equilibrate()

s1.components

{'H2O(aq)': 55.238455538403954, 'Cl[-1]': 0.38323989957700755, 'Mg[+2]': 0.18323990520853942, 'MgCl[+1]': 0.016760093825573405, 'H[+1]': 1.2403230417432767e-07, 'OH[-1]': 9.844314720800745e-08, 'HCl(aq)': 5.431780489909693e-09, 'MgOH[+1]': 7.932661202804441e-15, 'O2(aq)': 3.1477649388058775e-26, 'HClO(aq)': 8.450946375546259e-29, 'ClO[-1]': 3.367672345557701e-29, 'H2(aq)': 5.442728186726209e-35, 'ClO2[-1]': 0.0, 'ClO3[-1]': 0.0, 'ClO4[-1]': 0.0, 'HClO2(aq)': 0.0}

Saving Solution to a file

from monty.serialization import dumpfn
dumpfn(s1, 'test_solution.json')

s1.as_dict()

{'@module': 'pyEQL.solution',
 '@class': 'Solution',
 '@version': '0.6.0.post1.dev23+g090ac81',
 'solutes': {'H2O(aq)': '55.238455538403954 mol',
  'Cl[-1]': '0.38323989957700755 mol',
  'Mg[+2]': '0.18323990520853942 mol',
  'MgCl[+1]': '0.016760093825573405 mol',
  'H[+1]': '1.2403230417432767e-07 mol',
  'OH[-1]': '9.844314720800745e-08 mol',
  'HCl(aq)': '5.431780489909693e-09 mol',
  'MgOH[+1]': '7.932661202804441e-15 mol',
  'O2(aq)': '3.1477649388058775e-26 mol',
  'HClO(aq)': '8.450946375546259e-29 mol',
  'ClO[-1]': '3.367672345557701e-29 mol',
  'H2(aq)': '5.442728186726209e-35 mol',
  'ClO2[-1]': '0.0 mol',
  'ClO3[-1]': '0.0 mol',
  'ClO4[-1]': '0.0 mol',
  'HClO2(aq)': '0.0 mol'},
 'volume': '1 l',
 'temperature': '293.15 K',
 'pressure': '1 atm',
 'pH': 6.90646518824501,
 'pE': 8.5,
 'balance_charge': None,
 'solvent': 'H2O(aq)',
 'engine': 'native',
 'database': {'@module': 'maggma.stores.mongolike',
  '@class': 'JSONStore',
  '@version': '0.19.1.post1.dev1792+g0517496',
  'paths': ['/home/ryan/mambaforge/envs/pbx/code/pyEQL/src/pyEQL/database/pyeql_db.json'],
  'read_only': True,
  'serialization_option': None,
  'serialization_default': None,
  'key': 'formula'}}

Units-Aware Calculations

s1.volume.to('mL')

1000.0000000000001 ml

s1.volume.to('gal')

0.26417205235814856 gal

s1.osmotic_pressure.to('bar').magnitude

WARNING 2023-10-17 09:36:22,373 engines.py get_osmotic_coefficient 462 Cannot calculate osmotic coefficient because Pitzer parameters for salt HClO3 are not specified. Returning unit osmotic coefficient
WARNING 2023-10-17 09:36:22,384 engines.py get_osmotic_coefficient 462 Cannot calculate osmotic coefficient because Pitzer parameters for salt HClO2 are not specified. Returning unit osmotic coefficient

12.630074635540739

Contribution Opportunities

Benchmarking - Compiling additional validation data for activity, conductivity, etc. - Quantifying error associated with different models - Refactoring unit tests suite to separate benchmarking

Documentation - Writing tutorials - Writing expanded docs - Cleaning up / updating docstrings

New Features - Better viscosity model - Expanded unit testing (increase test coverage to 90%) - Additional properties - Additional mixing rules / models for mixed electrolytes

Database - Expand database doverage to include additional species - More viscosity coefficients - Add ‘sho’ parameter - More diffusion coefficients

Software Engineering - Additional refactoring (e.g., mypy linting for robustness) - Bugfixes