aqequil

AqEquil is a Python package that interfaces with aqueous speciation software EQ3/6. Quickly build and modify databases of thermodynamic data, perform batch aqueous speciation calculations, and view summarized reports of results.

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

Science Score: 75.0%

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 3 DOI reference(s) in README
✓
Academic publication links
Links to: zenodo.org
○
Academic email domains
✓
Institutional organization owner
Organization worm-portal has institutional domain (worm-portal.asu.edu)
○
JOSS paper metadata
○
Scientific vocabulary similarity
Low similarity (16.4%) to scientific vocabulary

Last synced: 6 months ago · JSON representation ·

Repository

Basic Info

Host: GitHub
Owner: worm-portal
License: mit
Language: HTML
Default Branch: master
Homepage: https://worm-portal.asu.edu/
Size: 5.25 MB

Statistics

Stars: 7
Watchers: 1
Forks: 0
Open Issues: 0
Releases: 9

Created over 4 years ago · Last pushed 7 months ago

Metadata Files

Readme License Citation

README.md

AqEquil

Boyer, G., Robare, J., Park, N., Ely, T., Shock, E.L.

About

AqEquil is a Python 3 package that enables users to rapidly perform aqueous speciation calculations of water chemistry data for multiple samples by interfacing with geochemical speciation software EQ3/6 (Wolery 2013, Wolery 1979). AqEquil uses a modified version of EQ3/6 created by the 39Alpha research team for easy local installation.

Water sample data in CSV format is automatically converted to a format readable by EQ3 and then speciated. Distributions of aqueous species, mineral saturation indices, oxidation reduction potentials, and more are data-mined and returned as Pandas tables and interactive Plotly visualizations.

Speciated fluids can be further reacted with minerals or other fluids in mass transfer calculations to produce tables and interactive diagrams of reaction paths and composition changes as a function of reaction progress.

Requirements

AqEquil has only been tested with Ubuntu 22.04.3 LTS.

This installation requires the Linux version of EQ3/6 v8.0a, which can downloaded here. Installation instructions are provided there.

AqEquil must be installed into an environment with an R installation. See these instructions for installing R with Anaconda.

Additionally, the CHNOSZ package must be installed in R (see instructions below).

Installation

Installing EQ3/6 for Linux

I recommend using this github version of EQ3/6 v.8.0a adapted by the 39Alpha team. Installation instructions are found there.

Create an environment variable called EQ36DO and set it to wherever you installed EQ3/6. (/usr/local/bin by default). Set another environment variable called EQ36DA to the directory containing your data1 thermodynamic database files (if you have one).

Installing CHNOSZ version 1.4.3

Open an R session. Install CHNOSZ version 1.4.3 package with:

install.packages('http://cran.r-project.org/src/contrib/Archive/CHNOSZ/CHNOSZ_1.4.3.tar.gz', repos=NULL, type='source')

Once CHNOSZ is installed you can quit the R session.

Compatibility with CHNOSZ v.2.0.0 is forthcoming.

Installing AqEquil

Install AqEquil using pip:

pip install AqEquil

Usage

See this demo notebook for usage examples.

Owner

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

Website: worm-portal.asu.edu
Repositories: 3
Profile: https://github.com/worm-portal

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 Molecular Sciences"
    family-names: Robare
    given-names: Jordyn
    orcid: "https://orcid.org/0000-0001-9133-8485"
  -
    affiliation: "Arizona State University, School of Earth and Space Exploration"
    family-names: Park
    given-names: Nuri
  -
    affiliation: "University of Minnesota, Department of Soil, Water, and Climate"
    family-names: Ely
    given-names: Tucker
    orcid: "https://orcid.org/0000-0002-2955-4184"
  -
    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: "0.3.0"
license: MIT
message: "If you use this software, please cite it using these metadata."
repository-code: "https://github.com/worm-portal/AqEquil"
title: "AqEquil: Python package for aqueous geochemical speciation"
version: "0.19.0"
date-released: 2024-05-28
...

GitHub Events

Total

Delete event: 1
Push event: 16
Pull request event: 2
Create event: 1

Last Year

Delete event: 1
Push event: 16
Pull request event: 2
Create event: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time

Total issues: 0
Total pull requests: 1
Average time to close issues: N/A
Average time to close pull requests: less than a minute
Total issue authors: 0
Total pull request authors: 1
Average comments per issue: 0
Average comments per pull request: 0.0
Merged pull requests: 1
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 0
Pull requests: 1
Average time to close issues: N/A
Average time to close pull requests: less than a minute
Issue authors: 0
Pull request authors: 1
Average comments per issue: 0
Average comments per pull request: 0.0
Merged pull requests: 1
Bot issues: 0
Bot pull requests: 0

View more stats

Top Authors

Issue Authors

Pull Request Authors

gmboyer (3)

Top Labels

Issue Labels

Pull Request Labels

Dependencies

setup.py pypi

chemparse *
dill *
ipython *
matplotlib *
numpy *
pandas *
periodictable *
plotly *
rpy2 *

ecosyste.ms

Data

Tools

Indexes

Applications

Experiments

Open Source Science