Changelog

All notable changes to this project are documented here. To ensure that they are using the most up-to-date version of the PyGCC software, users should update PyGCC on their local computers using the following command:

pip install --upgrade pygcc

v1.5.3 (27/06/2026)

Added

  • outputfmt (polycoeffs mode): when only two temperature bounds [Tmin_K, Tmax_K] are supplied via *TK_range, the GWB and PHREEQC blocks now expand them to an 8-point grid internally so curve_fit has enough data for the 6- and 5-parameter polynomials respectively.

  • outputfmt (polycoeffs mode): TminK/TmaxK in GWB output are now derived from the valid (non-placeholder) temperature range rather than the full grid extent.

  • _build_message now reports supplemental minerals that were injected from built-in thermodynamic data in read_db.py (Fluorapatite, Hydroxyapatite, Ankerite, Acmite, Annite, Phlogopite, Molybdenite, Molybdite), grouped by their reference source.

  • solidsolution_thermo (solidsolution_type='All'): basaltic glass calculation is now included and optional — skipped when glass_oxide_wt is not supplied, instead of raising a ValueError.

  • readSourcePHREEQCdb: get_phases now handles LLNL-style PHREEQC databases (e.g. llnl.dat) where a commented-out alternative formula line appears between the mineral name and the actual reaction. The parser skips comment and blank lines to reach the real reaction.

Changed

Fixed

  • Fixed write_database crashing with KeyError when using llnl.dat as a PHREEQC source database. Three sub-fixes were required: (1) sourcedic_logK now preserves original (un-normalized) keys for species that appear in both SOLUTION_SPECIES/SOLUTION_MASTER_SPECIES and PHASES (60+ dual-membership species in llnl.dat such as AlF3, Sb(OH)3); (2) write_PHREEQCdb’s minerals loop wraps calcRxnlogK in a try/except KeyError — when a mineral’s solid-state data is absent from the direct-access database (e.g. because speq21.dat only has the aqueous complex), the mineral is silently skipped rather than crashing; (3) all curve_fit calls throughout write_PHREEQCdb and outputfmt are now guarded by an n_valid >= n_params check (5 for PHREEQC analytic, 6 for GWB polycoeffs) so a single-temperature database (T=[25]) no longer crashes — when too few valid logK points exist the closest-to-25 °C value is written as log_k only, without the -analytic expression.

  • Fixed header garbling when a pygcc-generated GWB database is reused as the source for a subsequent write_database call. The writer was appending (degC) and (bar) directly to the marker strings without a space (temperatures(degC), pressures(bar)), which the reader’s in [...] check did not match — causing the search loop to consume up to 1000 lines into the species section before giving up. Fixed in both the writer (now emits temperatures (degC) / pressures (bar)) and the reader (accepts both forms for backward compatibility). Same fix applied to the EQ36 writer.

  • Fixed calclogKclays producing all-NaN logK for 7Å (serpentine) and 14Å (chlorite) clay minerals when Int_Mg_fract defaulted to 1. The default moved all Mg to the interlayer site, making octahedral Mg zero and producing a divide-by-zero in the R1+1 denominator. I_Mg is now capped at Tot_Oxy (0 for non-smectite minerals), keeping all Mg in the octahedral/brucitic site where it belongs.

  • Fixed write_database(T=[0, 300], P=..., clay_thermo=True, logK_form='polycoeffs') raising ValueError: ydata must not be empty!. The rhoEG size mismatch when T was internally expanded from 2 to 8 points was corrected, and the Int_Mg_fract cap (above) prevented all-NaN clay logK that left curve_fit with no valid data.

Removed

v1.5.2 (12/05/2026)

Added

  • can now handle newer dataset format of GWB, such as ‘jul22’, ‘jan26’

Changed

Fixed

  • fixed compilation error in v.1.5.1 and associated water equation of state issues.

Removed

v1.5.1 (08/10/2025)

Added

Changed

Fixed

  • fixed compilation error in v.1.5.0 and associated water equation of state issues.

Removed

v1.5.0 (29/09/2025)

Added

  • We added PHREEQC integration with pygcc, including the following databases distributed with the program (‘llnl.dat’, ‘phreeqc.dat’,and ‘pitzer.dat’).

Changed

Fixed

Removed

v1.4.0 (05/06/2025)

Added

  • We introduced the keyword heatcap_approx to allow users to specify either ‘Maier-Kelley’ or ‘constant’ for heat capacity calculations in clay mineral thermodynamic properties. This provides flexibility in choosing between a temperature-dependent Maier-Kelley formulation or a constant heat capacity approximation.

Changed

Fixed

  • fixed error in writing ptizer database for Toughreact, particularly in source database, like data0.hmw with no lamda values.

Removed

v1.3.7 (11/05/2025)

Added

Changed

Fixed

  • fixed compilation error in v.1.3.7.

Removed

v1.3.6 (11/05/2025)

Added

Changed

Fixed

  • we fixed calculation errors in logK values and reaction parameters for clay thermodynmanics and introduced partitioning parameters such as “Int_Mg_fract” and “Int_Li_fract” to help users specify the fraction of Mg and Li in the interlayer sheet.

Removed

v1.3.5 (12/04/2025)

Added

Changed

Fixed

  • we have fixed the dimer error enforced on other mineral databases.

  • we revised concentration_converter function

Removed

v1.3.3 (25/01/2025)

Added

Changed

Fixed

  • we have fixed the extrapolation error at higher pressures related to Helgeson_activity function.

Removed

v1.3.1 (11/11/2024)

Added

  • we added flexible direct-access modifying option that reads a csv file and makes a new direct-access database. Test = dbaccess_modify(in_filename = ‘geotpd_data_block_cr.csv’, dbaccess = ‘./speq23.dat’)

Changed

Fixed

  • we have fixed the calculation error when generating pflotran databased with GWB source database (starting from mar21 format).

Removed

v1.3.0 (03/05/2024)

Added

  • we have incorporated the NaCl-H2O phase relationship equations of Driesner and Heinrich (2007) which was utilized in the Syverson, et al. (2023) Geology paper for geothermobarometer calculation.

Changed

Fixed

Removed

v1.2.0 (10/09/2023)

Added

  • we have included the thermodynamic databases speq23 and speq23_dimer. To utilize these databases in pygcc, users are now required to specify their selection. For example, users can set “dbaccessdb = speq21_dimer”, “dbaccessdb = speq23”, “dbaccessdb = speq23_dimer”.

Changed

  • modified the default speq21 database to reinstate the thermodynamics data for SiO2(aq) to the values presented in Shock et al. (1989)

  • modified the database creation to include dimer - Si2O4(aq) - for scenarios where SiO2(aq) from Sverjensky et al. (2014) - speq21_dimer.dat is used. Users who intend to utilize speq21_dimer or speq23_dimer databases should verify that the dimer reaction is present in their source database. Note that source databases, including the default ‘thermo.com.tdat’ and ‘thermo_latest.tdat’ have been updated to include dimer reactions.”

Fixed

  • In previous versions, errors related to deprecated functionality were encountered when using Python versions greater than 3.9.6.

Removed

v1.1.4 (25/11/2022)

Added

  • Mineral “Graphite” was added to the thermo.2021.dat database. Other modifications were made to the formula of some carboxylic acids in the database

  • A debug message has been added to the write_database class, with a default value of False, to print out options included in generating the database. The print option can be turned on by specifying “print_msg = True”

  • The source databases included with pygcc downloads can now be specified using the file names rather their full paths, such as “sourcedb = thermo.com”, “sourcedb = thermo.2021”, “sourcedb = thermo_latest”, etc.

  • Pitzer activity model format for ToughReact is now included

  • Created an option to use the GWB source database to generate the EQ36 database, i.e., convert GWB database to EQ36 database.

Changed

  • modified the default output database for ToughReact from “thermo_ToughReact%sbars” to “thermo%sbars”

  • modified the creation of output folder to specify subfolders for ToughReact, GWB, EQ36 and PFLOTRAN

  • modified the code so that the density extrapolation prompt message is only activated in cases where the density is less than 350 g/cm3

Fixed

  • v1.1.2 and v1.1.3 have errors that are now fixed

Removed

v1.1.1 (19/09/2022)

Added

Changed

  • modified the naming of log10_co2_gamma in the Henry_duan_sun and drummondgamma functions to activity coefficients

  • corrected dielectric constants units in water_dielec class implementation of water dielectric constants

  • modified pressure region for Helgeson_activity function to include pressures above 5 kbar

Fixed

Removed

v1.1.0 (21/06/2022)

Added

Changed

  • modified db_reader function to support jul17 and jan19 gwb legacy formats

Fixed

Removed

v1.0.6 (15/05/2022)

Added

  • Added the Holland and Power heat capacity equation using the SUPCRTBL database, tagged as heatcaphp.

  • A supcrtaq function option has been added, allowing users to specify input units for direct-access or sequential-access thermodynamic databases. The keyword “InUnit” can take ‘cal’ or ‘KJ’ and convert to ‘cal’ which is used in the supcrtaq function.

  • Added “supcrtbl.dat”, a sequential-access thermodynamic database containing Holland and Power datasets
    documented in SUPCRTBL by Zimmer et al. (2016) SUPCRTBL: A revised and extended thermodynamic dataset and software package of SUPCRT92. Computer and Geosciences 90:97-111.

  • Added an option in calcRxnlogK to automatically identify species class based on species’ last letter/ number. This means that species ending with ‘(aq)’, ‘+’, ‘-’ or last letter/number isdigit are classified as aqueous species whereas others are gases or mineral species. This is used in case the user does not provide a specielist, which has become an optional input into the calcRxnlogK class function

  • Added the capability to generate the most recent database version of GWB (mar21) formats.

  • Added an option in solidsolution_thermo class function “Al_Si” to allow the user to specify how Al and Si will be expressed in the solid solution reactions. The keyword can take ‘Arnorsson_Stefansson’ which expresses them as ‘Al(OH)4-’ and ‘H4SiO4(aq)’ while ‘pygcc’ expresses them as ‘Al3+’ and ‘SiO2(aq)’

Changed

  • modified mineral_eos keyword to heatcap_method

  • modified Mintype keyword to ClayMintype

  • combined functions like heatcaphp, heatcap_Berman and heatcapusgscal into a single class function heatcap

  • updated the online documentation to reflected the functions removed

Fixed

Removed

  • The heatcap, heatcap_Berman and heatcapusgscal functions are no longer in use

v1.0.5 (22/03/2022)

Added

Changed

  • Issues with polycoeffs logK in GWB database generation have been resolved. The polynomial coefficients were rounded off to shorter significant factors in the previous implementation, which hampered the ability to generate the correct logK values. This update fixed that by extending the significant factors.

Fixed

v1.0.4 (10/03/2022)

Added

  • A new option was implemented to automatically specify the structuring layer for calclogKclays with the goal of achieving charge balance of 14 for the ‘7A’ group, 22 for the ‘10A’ group and 28 for the ‘14A’ group.

Changed

Fixed

v1.0.3 (17/02/2022)

Added

  • Added the importlib_metadata dependencies.

Changed

Fixed

v1.0.2 (02/02/2022)

Added

Changed

  • Modified the iapws95 class function because the previous implementation had issues with using fsolve solver to solve for an array of data to find the roots of any function.

Fixed

v1.0.1 (01/02/2022)

Added

  • Python tutorial files have been added.

Changed

Fixed

v1.0.0 (31/01/2022)

  • This is the first release of pygcc!