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Version history

0.5 [beta]

Switches from Autograd to JAX for faster automatic differentiation and JIT compilation.

0.5.2 (31 Aug 2021)

Changes in v0.5.2

  • Fixed calculation error in convert.solvent_to_solution.
  • Added more ions in properties.ion_to_mass.

0.5.1 (17 Aug 2021)

Changes in v0.5.1

  • Fixed pz.convert.solvent_to_solution to take and return pK values instead of K values, and to replace any NaNs in the input with 0.
  • Added pz.equilibrate.stoichiometric.get_constants() to calculate stoichiometric equilibrium constants for the carbonic acid equilibria when total dissolved inorganic carbon is zero.

0.5.0 (9 Aug 2021)

Changes in v0.5.0

  • Switched from Autograd to JAX for faster automatic differentiation and JIT compilation.
  • Renamed and reorganised virtually everything.

0.4 [beta]

Adds solvers to determine the equilibrium composition of aqueous solutions. This version was demonstrated at the AGU/ASLO/TOS Ocean Sciences Meeting (San Diego, Feb 2020).

0.4.3 (11 Sep 2019)

Changes in v0.4.3

  • Added osm function for osmotic coefficient to matrix module;
  • Added io module functions to roughly convert between molinity (mol/kg-solution) and molality (mol/kg-H2O);
  • Added salinity2mols function in io module to estimate molalities from salinity for MZF93 artificial seawater;
  • Switched assemble function in matrix module to use the MarChemSpec parameter library by default.

0.4.2 (6 Sep 2019)

Changes in v0.4.2

  • Removed pressure input from thermodynamic equilibrium constant functions;
  • Converted copies from shallow to deep in parameter library modules;
  • Added plot module with some meta-analytical visualisation tools (not yet documented).

0.4.1 (13 Aug 2019)

Changes in v0.4.1

  • Added carbonic acid and boric acid equilibrium solving;
  • Eliminated module tables;
  • Updated functions and parameter libraries noting that ['Cl', 'CO3'] gets sorted to ['CO3', 'Cl'];
  • Fixed incorrect alph1 values for all HMW 1:(>1) electrolytes;
  • Added several new interaction parameter functions;
  • Testing MIAMI parameter library against PM16's model:
    • Adjusted numerical values to fix errors in some parameter functions:
      • bC_Ca_BOH4_SRM87;
      • bC_K_OH_MP98;
      • bC_Mg_BOH4_SRM87;
      • bC_Na_Br_MP98;
      • bC_Na_F_MP98;
      • bC_Na_HSO4_MP98;
      • bC_Sr_Cl_MP98;
      • theta_K_Sr_MP98;
    • Added new MP98 functions until numerical conflicts can be resolved:
    • bC_K_CO3_MP98 should follow SRG87;
    • theta_H_K_MP98 and theta_H_Na_MP98 should follow CMR93.

0.4.0 (3 Aug 2019)

Changes in v0.4.0

  • Module dissociation added with functions to evaluate thermodynamic dissociation constants;
  • Module equilibrate added with an equilibrium solver and associated functions;
  • Added blackbox_equilibrate function to demonstrate equilibration procedure;
  • Fixed indexing error in matrix.assemble for the zeta coefficient matrix;
  • Module jfuncs renamed as unsymmetrical;
  • As a general terminology change, the Pitzer model interaction coefficients are now instead referred to as parameters, for better consistency with the published literature. As a consequence:
    • Module coefficients renamed as parameters;
    • Module cflibs renamed as libraries;
    • Class CoefficientLibrary renamed as ParameterLibrary, and its abbreviation cflib to prmlib;
  • Parameter libraries can now be stored in separate script files.
  • Added complete HMW84 parameter library;
  • Added all interaction coefficients to MIAMI parameter library - but its calculation results have not yet been tested;
  • Fixed multiplier error for Cphi values in PM73_TableVI in tables module;
  • Added presumably missing *1e-3 multiplier to Cphi values in all SRRJ87 binary interaction functions;
  • Added meta-analysis functions in meta module.

0.3 [beta]

Adds pressure as an input variable. However, most of the interaction coefficients are still not yet pressure-sensitive.

0.3.1 (16 Jul 2019)

Changes in v0.3.1

  • Module props renamed as properties;
  • Module coeffs renamed as coefficients;
  • Class CoeffLib renamed as CoefficientLibrary;
  • Added docstrings to all functions in coefficients module;
  • Added matrix module with alternative, matrix-based Pitzer model implementation;
  • Added none function to jfuncs module to ignore unsymmetrical mixing;
  • Fixed Aϕ bug in CoefficientLibrary method print_coeffs;
  • In preparation for equilibration calculations:
    • Added gettots function to io module.

0.3.0 (12 Apr 2019)

Changes in v0.3.0

  • Moved Debye-Hückel functions (for Aϕ) from coeffs into new module debyehueckel;
  • Added Archer and Wang (1990) calculation of Aϕ;
  • Added pressure input (pres in dbar) to all relevant functions in coeffs, debyehueckel, model, io and blackbox functions;
  • Added teos10 module to calculate various properties of pure water;
  • Added Seawater coefficient library - like MarChemSpec, but with pressure-dependent Aϕ term (following Archer and Wang, 1990), and other general improvements;
  • Made cflib input optional for all model functions (default = Seawater);
  • Fixed loop index correction for n-n' interactions;
  • Eliminated unnecessary arrays for constant values in coeffs;
  • Adjusted model.B and model.CT function inputs to reduce number of cflib function calls;
  • Rewrote CRP94 Aosm function to make it autograd-able;
  • Added docstrings throughout (except for functions in coeffs).

0.2 [beta]

Includes calculation of solute activity coefficients, water activity and osmotic coefficients, as a function of temperature and composition, at a constant pressure of 1 atmosphere.

0.2.7 (4 Mar 2019)

Changes in v0.2.7

  • Transposed all inputs to the excess Gibbs energy function and its derivatives, giving about a 5× speed-up;
  • For consistency with Pitzer.jl:
    • Simplified osmotic coefficient calculation approach;
    • Added direct calculation of water activity by differentiation;
    • Changed both T and temp to tempK in input files and all functions;
    • Renamed coefficient "dictionary" as "library":
      • CoefficientDictionary class becomes CoeffLib;
      • cfdict function inputs become cflib;
    • Updated documentation to reflect these changes;
  • Added io.saveall function to create CSV file for results;
  • Switched CoeffLib.get_contents() to use dict key names, not function names, to find ions.

0.2.6 (20 Feb 2019)

Changes in v0.2.6

  • Continuing to build MIAMI (i.e. MP98) coefficient dictionary:
    • Added bC_ functions for borate interactions from SRM87;
    • Added bC_ functions for bisulfide interactions from HPM88;
    • Added new tables of PM73 data, and a new type of coefficient function in bC_PM73(T,iset) to use them (not yet compatible with all CoefficientDictionary methods);
  • Updated pytzer.blackbox:
    • Changed output filename extension to _py;
    • Saving results to file now optional (with default behaviour to save);
    • Can also optionally use a different CoefficientDictionary (default remains MarChemSpec);
  • Added numerical integral approach for unsymmetrical mixing J function to jfuncs (not yet differentiable by autograd).

0.2.5 (6 Feb 2019)

Changes in v0.2.5

  • Testing MarChemSpec05 against FastPitz at 278.15 K - perfect agreement to 6 significant figures;
  • Added theta_Ca_H_MarChemSpec to combine RGO82 and WM13 equations;
  • Added new module pytzer.tables to store long lists of coefficients found in tables;
  • Added basic tables page to documentation, and new ions to the name conventions lists;
  • Updated bC_ functions for Ca-SO4, Ca-HSO4 and K-HSO4:
    • Used data from new pytzer.tables module;
    • Relabelled from P91 to WM13, to better reflect their provenance;
  • Added Aosm_MarChemSpec, which adds a small offset to Aosm_CRP94 to make it consistent with AW90 and FastPitz;
  • Created new MarChemSpec CoefficientDictionary, with temperature-varying Aosm_MarChemSpec;
  • Added equations and usage examples to documentation for pytzer.model;
  • Wrote pytzer.blackbox function and quick-start documentation, for easy end-user testing.

0.2.4 (31 Jan 2019)

Changes in v0.2.4

  • Testing activity coefficients against Prof D.R. Turner's and Prof S.L. Clegg's implementations (GIVAKT and FastPitz respectively):
    • Assembled new CoefficientDictionary WM13_MarChemSpec25 for testing;
    • Corrected alph1 for bC_Ca_OH_HMW84 to 2;
    • Fixed temperature units for theta_H_Na_CMR93 and theta_H_K_CMR93;
    • Deleted duplicate MP98 functions in coeffs;
    • Added functions with temporary values for 298.15 K for λ(tris, tris), ζ(tris, Na, Cl) and μ(tris, tris, tris) to MarChemSpec25 CoefficientDictionary;
    • pytzer activity and osmotic coefficients agree perfectly (to 6 significant figures) with FastPitz at 298.15 K with the MarChemSpec25 CoefficientDictionary;
  • Continued adding coefficient functions to cfdicts.MIAMI:
    • All from PP82 (Na-CO3 and Na-HCO3 interactions);
  • Added equations for neutral-neutral interactions (lambda coefficient) to model.Gex_nRT and also to cfdicts.add_zeros method;
  • Changed to evaluating all neutral interactions (including with ions) even at zero ionic strength;
  • Updated nomenclature for consistency with P91, MP98 and others: eta (η) is now zeta (ζ).

0.2.3 (30 Jan 2019)

The build of v0.2.3 had errors that prevented installation. These were fixed by v0.2.3.3, which is otherwise identical.

Changes in v0.2.3

  • Verified both jfuncs.P75_eq47 and jfuncs.Harvie, and their derivatives, against Prof D.R. Turner's and Prof S.L. Clegg's implementations (GIVAKT and FastPitz respectively):
    • P75_eq47 returns identical results (to >10 significant figures) in every case;
    • Harvie agrees perfectly (to >10 significant figures) with GIVAKT, but FastPitz differs from both by up to 5%;
  • Began assembling MIAMI CoefficientDictionary following MP98;
  • Added constant Aϕ function for 25 °C following P91 to coeffs.Aosm_25 for MarChemSpec project testing.

0.2.2 (28 Jan 2019)

Changes in v0.2.2

  • Added temperature to the file produced by print_coeffs;
  • Improved documentation:
    • Added neutrals, and made other updates, for pytzer.coeffs;
    • Updated for pytzer.cfdicts;
    • Added pytzer.meta page;
    • Updated installation instructions;
    • Documented new Izero=False input to model.Gex_nRT;
  • Fixed zero ionic strength error for model.Gex_nRT;
  • Removed Jp outputs from all jfuncs, and set up correct differentiation for Harvie;
  • Corrected functions in CoefficientDictionary WM13 following intercomparison with Prof S.L. Clegg's Fortran implementation:
    • bC_Mg_SO4_PP86ii: eliminated difference of two large numbers error, by substitution;
    • bC_Na_HSO4_HPR93: fixed incorrect charge for HSO4;
    • bC_Na_OH_PP87i: fixed typos in coefficients;
  • Switched MarChemSpec CoefficientDictionary to not use GT17simopt for Na-Cl interaction (stick with M88 instead);
  • Fixed function for H-Na-HSO4 interaction in WM13 CoefficientDictionary;
  • Added external package requirements (i.e. numpy and autograd) to the;
  • Fixed CoefficientDictionary.get_contents to include neutral species;
  • Added input Izero=False to model.Gex_nRT and its derivatives, to allow calculations for solutions with zero ionic strength.

0.2.1 (24 Jan 2019)

Changes in v0.2.1

  • Fixed fatal indexing error in model.Gex_nRT;
  • Added CoefficientDictionary WM13 for the Waters and Millero (2013) model;
  • Added CoefficientDictionary MarChemSpec for MarChemSpec project testing;
  • Added some coefficient values from Gallego-Urrea and Turner (2017);
  • Added equations for neutral solute interactions to model.Gex_nRT, along with supporting functions in pytzer.cfdicts;
  • Added CoefficientDictionary methods:
    • print_coeffs, to evaluate all model coefficients at a given temperature, and print them to file;
    • get_contents, to generate lists of all ions and all references within the dictionary;
  • Updated documentation on coefficient dictionaries to reflect these changes;
  • Added meta module as single-source-of-truth for package version;
  • Updated documentation with basic information on neutral solutes.

0.2.0 (23 Jan 2019)

The first beta release, including full documentation on

0.1 [alpha]


Versions 0.1.X were used for alpha development. Changes are not documented.