The chEQWRk v0.1 code

This dataset represents a series of Python codes that collectively form chEQWRk v0.1 (Pronounced "check work") These codes allow for the recreation of the data and the reproduction of the figures found in "Thermodynamic predictions of hydrogen generation during serpentinization of harzburgite with seawater-derived brines" by Sanjoy Som et al., The Planetary Science Journal, 2024. Installation guidelines and dependencies are listed on GitHub: https://github.com/sanjoymsom/chEQWRk The README file below is also stored in /study_files/som_2024_brines_study: https://github.com/sanjoymsom/chEQWRk/blob/main/study_files/som_2024_brines_study/READ.me 1. Key files eq36python.py :Function library that acts on EQ3/6 input and output files. evaporation.py : Creates brines. executor.py : Program launcher. plotcsv.py : Generates all the plots. saturation.py : Saturates a fluid with salt serpentinization.py : Runs the water:rock reaction. study_files/som_2024_brines_study.py: study file for this study. 2. Initial Considerations 1. Think first of the simulation you want to do. Doing so will allow you to set up the water file correctly. -The water file is swmajp_mbn.3i in /input_files. -In the 'suppress' category of the 3i file (line 115), check whether to suppress or allow carbonate formation _during the evaporation_. The minerals are Aragonite, Artinite, Calcite, Dolomite, Huntite, Hydromagnesite, Lansfordite, Magnesite, Nesquehonite. For all code options except 2, you want to _allow_those minerals (put a star in front of them). 2. If you're simulating water:rock reactions, do you allow carbonates there? If so, put a star in front of SIDERITE, HYDROMAGNESITE, ARTINITE, NESQUEHONITE, CALCITE, Calcite-SS, MAGNESITE, ARAGONITE, HUNTITE, DOLOMITE,ORDERED, DOLOMITE,DISORDERED, DOLOMITE. 3. 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. 4. 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 saved in /python_backup. 3. Manuscript figure reproduction #A1# To generate Fig. 1A, either: - Use option 1 to load 'pure_water_NaCl_sat', then select option 10 and choose 'gH+' as your Y variable and 'Aw' as your X variable. - OR regenerate from scratch: a. Run option 0 to clear files. b. Run option 3. c. Run option 8. d. Run option 10 and choose 'gH+' as your Y variable and 'Aw' as your X variable. #A2# To generate Fig. 1B, either: - Use option 1 to load 'surface_seawater_evaporation.zip', then select option 10, and choose 'pH' as your Y variable and 'Aw' as your X variable. - OR regenerate from scratch: a. In som_2024_brines_study.py, ensure that tophalf_evap (at or near line 196 under option == 2) is set to 'tophalf_mbn_pCO2.evap'. b. Disable lower-case carbonates in the suppress list (which allows them to form) in the seawater file (see 1. above), and run with option 2. c. Enable lower-case carbonates (which in the suppress list suppresses them) in the seawater file (see 1. above), and run with option 2. d. Run option 10, and choose 'pH as your Y variable and 'Aw' as your X variable. #B# To generate Fig. 2, either - Use option 1 to load 'evap_curve_and_brines.zip', then select option 7, and choose either 'TCO2' or 'carbonates_out' as your Y variable and 'Aw' as your X variable. - OR regenerate from scratch: a. Run option 0 to clear files. b. Double-check that the seawater file (/input_files/swmajp_mbn.3i) has a * in front of lower-case carbonates (see 1.). c. Generate the brines with option 6, and ask to run the [s]et. d. Run option 7. e. At the prompt, choose either 'TCO2' or 'carbonates_out' as your Y variable and 'Aw' as your X variable. f. Run option 7 again if desired. #C# To generate Figs 3A, 4A, 5A, 5D, 6A, 6C, 8A, 8C, 8E, 9A, 10A, 10C ("carbonates allowed" cases), either: - Use option 1 to load 'Case1_withcarbonates_WR1', then for... - Fig. 3A: Run option 10, then type 'H2,aq' as your Y variable and 'Temp' as your X variable. - Fig. 4A: Run option 10, then type 'pH' as your Y variable and 'Temp' as your X variable. - Fig. 5A,D: Run option 11, and follow the prompts to remove carbonate minerals and salts. - Fig. 6A,C: Run option 12. - Fig. 7A : Run option 13. - Fig. 8A,C,E: Run option 13. - Fig. 9A: Run option 10, then type 'Aw' as your Y variable and 'Temp' as your X variable. - Fig. 10A: Run option 10, then type 'TFor' as your Y variable and 'Temp' as your X variable. - Fig. 10C: Run option 10, then type 'FORMIC ACID,aq' as your Y variable and 'Temp' as your X variable. - OR regenerate from scratch: a. Run option 0 to clear files. b. Place a star (*) in front of carbonate minerals listed in 2. above in the seawater file, found in /input_files. c. ensure a star is still in front of carbonate minerals listed in 1. above. d. Generate the brines and serpentinize with option 6, and ask to run the [s]et. e. Run option 8 to transform the raw output files into csvs f. Plot figures as above. #D# To generate Figs 3B, 4B, 5B, 5D, 6B, 6D, 8B, 8D, 8F, 9B, 10B, 10D ("carbonates suppressed" cases), either: - Use option 1 to load 'Case2_nocarbonates_WR1', then for... - Fig. 3B, 4B, 5D, 6B, 6D, 7B, 8B, 8D, 8F, 9B, 10B: as above. - Fig. 5C: Run option 10, then type 'MAGNETITE_out' as your Y variable and 'Temp' as your X variable. - OR regenerate from scratch: a. Run option 0 to clear files. b. Remove the star (*) in front of carbonate minerals listed in 2. above in the seawater file, found in /input_files. c. ensure a star is in front of carbonate minerals listed in 1. above. d. Generate the brines and serpentinize with option 6, and ask to run the [s]et. e. Run option 8 to transform the raw output files into csvs. f. Plot figures as #C#. #E# To generate Fig. 11A, 11C ("carbonates allowed" cases), either: - Use option 1 to load either 'withcarbonates_WR0p5.zip or 'withcarbonates_WR10.zip', then - Run option 10, then type 'H2,aq' as your Y variable and 'Temp' as your X variable. - OR regenerate from scratch: a. Run option 0 to clear files. b. Edit the WR_array variable in som_2024_brines_study.py in option 6 (at or near line 233) to either 0.1 or 10. c. Place a star (*) in front of carbonate minerals listed in 2. above in the seawater file, found in /input_files. d. Ensure a star is still in front of carbonate minerals listed in 1. above. e. Generate the brines and serpentinize with option 6, and ask to run the [s]et. f. Run option 8 to transform the raw output files into csvs. e. Plot as in #C# above with 'H2,aq' as your Y variable and 'Temp' as your X variable. #F# To generate Fig. 11B, 11D ("carbonates suppressed" cases), either: - Use option 1 to load either 'nocarbonates_WR0p5.zip or 'nocarbonates_WR10.zip', then - Run option 10, then type 'H2,aq' as your Y variable and 'Temp'| as your X variable. - OR regenerate from scratch: a. Run option 0 to clear files. b. Edit the WR_array variable in som_2024_brines_study.py in option 6 (at or near line 233) to either 0.1 or 10. c. Remove the star (*) in front of carbonate minerals listed in 2. above in the seawater file, found in /input_files. d. Ensure a star is still in front of carbonate minerals listed in 1. above. e. Generate the brines and serpentinize with option 6, and ask to run the [s]et. f. Run option 8 to transform the raw output files into csvs. e. Plot as in #C# above with 'H2,aq' as your Y variable and 'Temp' as your X variable. 4. Manuscript tabular data - Table 2: The data in table 2 comes from the 6o files stored in the plotting_files/brine6o folder. They are extracted from the "Numerical Composition of the Aqueous Solution" section of the 6o file. 5. Other reasonably useful information - The reason for creating a Python wrapper code is to automatically string EQ3 and EQ6 files, which is tedious if done manually. While the plots above are the end-product of the runs, the intermediary files are also available: - The files representing the brines as output of evaporation are in the output_files/ folder, and titled just_the_brine. - The file that represents the brine reacting with rock at the initial temperature (10C in this study) is also found in the output_files/ folder as serp_10C. - The files that represent the result of serpentinization at the initial temperature and heated to 400C are in the plotting_files/raw6o folder. - The 6o files in the plotting_files/raw6o folder are the source data for the csvs in plotting_files/csvs - The colors chosen for the minerals (option 11) are hard-coded in plotcsv.py. Twenty of them are listed there. To see those twenty colors, set the visualize flag to 'True' in study_files/som_2024_brines_study.py (line 255). - 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.