Python tools for aqueous chemical speciation.
Project description
AqEquil
Grayson Boyer, PhD
GEOPIG Lab, Arizona State University
Tucker Ely, PhD
Toner Lab, University of Minnesota
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 1979). 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 Matplotlib visualizations. Additionally, EQ6 can be called to speciate .6i input files.
Requirements
AqEquil has only been tested with Ubuntu LTS 20.04.
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
Installation instructions are packaged along with the Linux distribution of EQ3/6 v8.0a.
Set the environment variable EQ36DA to the EQ3/6 database directory containing data1 files (the 'db' folder by default). Likewise, set EQ36CO to the directory with the eq3 executable (the 'bin' folder by default).
Installing CHNOSZ
Open an R session. Install the CHNOSZ package with:
install.packages("CHNOSZ")
Once CHNOSZ is installed you can quit the R session.
Installing AqEquil
Install AqEquil using pip:
pip install AqEquil
Usage
See this demo notebook for usage examples.
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