Skip to content

Latest commit

 

History

History
89 lines (56 loc) · 6.37 KB

README.md

File metadata and controls

89 lines (56 loc) · 6.37 KB
Raw

INTRODUCTION

chEQWRk is a series of wrappers code around EQ3/6 designed to perform batch Water:Rock reactions using the EQ3/6 geochemistry FORTRAN code (written by Tom Wolery). Output files can be easily converted to csv files, and plotting routines call these csv files to visualize results.

"Study files" are built to call these wrappers to solve specific problems. EQ3/6 needs to be installed in the root directory. See installation guidelines.

KEY FILES

executor.py : Program launcher.
evaporation.py : Creates brines.
serpentinization.py : Runs the W:R rock reaction.
saturation.py : Saturates water file with salt.
plotcsv.py : Generates all the plots.
eq36python.py : Function library that act on EQ3/6 input and output files.
Important : Study-specific .py files are in study_files/ including study-specific READ.me files

DEPENDENCIES

The following python libraries are needed to successfull run chEQWRk: os, sys, time, pandas 1.0.3, numpy 1.19.5, scipy 1.5.4, itertools, shutil

INSTALLATION GUIDELINES

To install WSL (Windows System Linux) on Windows 10/11, open the Microsoft Store app in Windows and search for 'Ubuntu.' Click 'Get' and follow the prompts.

Follow this Gist to install EQ3/6 on linux:
https://gist.github.com/sanjoymsom/529d9100b75d5803a4be54903a759167

On April 4, 2024, EQ3/6 could be found at
https://seaborg.llnl.gov/resources/geochemical-databases-modeling-codes

An X-window is required to run the code in WSL. XMing is good:
https://sourceforge.net/projects/xming/

The code is launched by typing in the terminal: python3 executor.py

INITIAL CONSIDERATIONS

  1. If you're simulating water:rock reactions, do you allow cabonates? If so, put a star in front of SIDERITE, HYDROMAGNESITE, ARTINITE, NESQUEHONITE, CALCITE, Calcite-SS, MAGNESITE, ARAGONITE, HUNTITE, DOLOMITE,ORDERED, DOLOMITE,DISORDERED, DOLOMITE in the 3i file
    located in the input_files/ folder (this example assumes use of the mbn database).
  2. It's a good habit to clear everything (option 0) before running a set of computations. You can save your results at any time and load those saved files. Saved files are stored in the /saved_files folder.
  3. Feel free to mess with the source code to improve things. If you screw up and need to revert, the original .py files are also saved in /python_backup of the release corresponding to the manuscript. .

START A NEW STUDY

One of the tenets of chEQWRk is that it can store "studies" that can be easily loaded again. For example, a study can be loaded to recreate data or reproduce figures from a publication that used chEQWRk.

All studies are stored in the study_files/ folder, and each has their own READ.me. To start a new study, create a new folder in the study_files/ folder and the python file of the study needs to have the same name as the folder. It is recommended to use a starting file from a previous study as a template.

FAQ

  • Why is the code called chEQWRk? Well, it has a double-meaning. First, it is read as "checkwork," implying that it can be used to check the science that is presented by using it. A nod to open science. Second, it also can mean 'C'onsiderable 'h'elp when
    running 'EQ'3/6 for 'W'ater:'R'ock 'k'alculations.

Troubleshooting

Setting up Xwindow within Linux in Windows 11 is a bit tricky.
Here is one solution using XMing

WSL1:

in ~/.bashrc, ensure that DISPLAY is exported to localhost:

export DISPLAY=$localhost:0.0

in /etc/ssh/sshd_config
ensure that X11Fowarding is set to yes

Launch X-window directly via the Xming app.

WSL2:

in ~/.bashrc, export the DISPLAY as follows:

export DISPLAY=$(cat /etc/resolv.conf | grep nameserver | awk '{print $2}'):0

in /etc/ssh/sshd_config
ensure that X11Forarding is set to yes, and
ensure that X11UseLocalHost is set to yes

Launch X-window via the Xlaunch app, and ensure "No Access Control" is selected.

END of READ.me