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READ.me
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READ.me
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#######################################################################
# READ.me last update: April 4, 2024 - Sanjoy M. Som |
# (for study-specific READ.me files, see study_files/) |
# |
#######################################################################
# INTRODUCTION |
#######################################################################
chEQWRk is a series of wrappers code around EQ3/6 designed to perform |
Water:Rock reactions. "Study files" are built that call these wrappers|
to solve specific problems. chEQWRk is designed to be as robust and |
flexible as possible, but you may encounter errors/bugs. Sorry. Thanks|
for understanding that anticipating every contingency is next to |
impossible. 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 August 31, 2023, 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) prior to running a|
set of computations. You can save your results at any time with |
option 9, and load those saved files with option 1. Saved file 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 released at |
manuscript publication 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 have 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=$localhost:0.0 |
|
in /etc/ssh/sshd_config |
ensure that X11Fowarding is set to yes |
|
WSL2: in ~/.bashrc, export the DISPLAY as follows: \-------------
export DISPLAY=$(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 |
|
#######################################################################
# END of READ.me |
#######################################################################