Data

Tools

Indexes

Applications

Experiments

Open Source Science

complicator

Estimate thermodynamic properties of aqueous inorganic complexes with monovalent ligands.

https://github.com/worm-portal/complicator

Science Score: 65.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ✓
    CITATION.cff file
    Found CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 4 DOI reference(s) in README
  • ○
    Academic publication links
  • ○
    Academic email domains
  • ✓
    Institutional organization owner
    Organization worm-portal has institutional domain (worm-portal.asu.edu)
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (10.1%) to scientific vocabulary
Last synced: 6 months ago · JSON representation ·

Repository

Estimate thermodynamic properties of aqueous inorganic complexes with monovalent ligands.

Basic Info
  • Host: GitHub
  • Owner: worm-portal
  • Language: Python
  • Default Branch: master
  • Size: 222 KB
Statistics
  • Stars: 0
  • Watchers: 0
  • Forks: 0
  • Open Issues: 0
  • Releases: 2
Created almost 4 years ago · Last pushed 7 months ago
Metadata Files
Readme Citation

README.md

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

dfinput = pd.DataFrame({ "Metal":["Ag+", "Al+3"], "Ligand":["OH-", "OH-"], "BETA1":[2, 9.03], # stability constant for the first association complex "BETA2":[3.97, 17.6], # second stability constant "BETA3":[float('NaN'), 26.4], # third stability constant "BETA4":[float('NaN'), 33.8], # fourth stability constant "Sass1":[float('NaN'), 36.5], # entropy of association for the first complex (cal/mol/K) })

dfout, _, _, _ = complicate(dfin=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.

Owner

  • Name: WORM: Water-Organic-Rock-Microbe Reaction Modeling
  • Login: worm-portal
  • Kind: organization

A free, open-source online workspace with ready-to-go thermodynamic modeling software

Citation (CITATION.cff) 

# YAML 1.2
---
authors: 
  -
    affiliation: "Arizona State University, School of Earth and Space Exploration"
    family-names: Boyer
    given-names: Grayson
    orcid: "https://orcid.org/0000-0002-7670-9273"
  -
    affiliation: "Arizona State University, School of Earth and Space Exploration"
    family-names: Shock
    given-names: Everett
    orcid: "https://orcid.org/0000-0002-4283-0163"
cff-version: "0.1.1"
license: MIT
message: "If you use this software, please cite it using these metadata."
repository-code: "https://github.com/worm-portal/Complicator"
title: "The Complicator"
version: "0.1.1"
date-released: 2024-08-22
...

GitHub Events

Total
  • Push event: 3
Last Year
  • Push event: 3

Dependencies

setup.py pypi
  • pandas *