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READ.me last update: April 4, 2024 - Sanjoy M. Som |

(for study-specific READ.me files, see study_files/) |

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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 |

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  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. |
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FAQ |

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  • 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. |
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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 |

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