complicator 0.3.0

Estimate thermodynamic properties of aqueous metal complexes with monovalent ligands.

The Complicator

Code Authors: Grayson Boyer, Everett Shock Data Compilers: GEOPIG Lab, Apar Prasad

This is a Python package for estimating standard state thermodynamic properties and Helgeson-Kirkham-Flowers (HKF) equation of state parameters for aqueous metal complexes with monovalent ligands using published methods from Sverjensky et al. (1997) and Shock et al. (1997)

Installation

This package can be installed through PyPI with: pip install Complicator

Usage

The best way to learn about the Complicator is through the WORM Portal (worm-portal.asu.edu). Check out Jupyter notebook demo 4-2-1 in the WORM Library that is available when you log in.

What follows is a brief example of how the Complicator can be used.

Supply a dataframe containing names of metals, ligands, stability constants for the first through fourth association at 25 °C, and optionally, standard state entropies of association for the first through fourth association complex. An example is assigned to the variable df_input in the example below.

import pandas as pd
from Complicator import complicate

df_input = pd.DataFrame({
        "Metal":["Ag+", "Al+3"],
        "Ligand":["OH-", "OH-"],
        "BETA_1":[2, 9.03], # stability constant for the first association complex
        "BETA_2":[3.97, 17.6], # second stability constant
        "BETA_3":[float('NaN'), 26.4], # third stability constant
        "BETA_4":[float('NaN'), 33.8], # fourth stability constant
        "Sass_1":[float('NaN'), 36.5], # entropy of association for the first complex (cal/mol/K)
        })

df_out, _, _, _ = complicate(df_in=df_input)

df_out

The output is a dataframe containing estimated thermodynamic properties, parameters for the revised Helgeson Kirkham Flowers (HKF) equation of state, and more. The format of the output is explained in more detail here. This Water-Organic-Rock-Microbe (WORM) database format is designed to be compatible with the free and open source online geochemical modeling platform WORM Portal. Estimated thermodynamic properties of complexes from the Complicator can be used in conjunction with the rest of the WORM database to:

• calculate properties of reactions and create activity or predominance diagrams.
• expand the number of aqueous complexes available in geochemical speciation (equilibration) and mass transfer calculations.