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  1. Today
  2. How do I add units for user defined analytes? Also how do I change the units of acidity so they are in mg/L as CaCO3
  3. This works: myGWB.exec_cmd('print react_output.txt') os.rename(r'react_output.txt',r'<whatever name>') Thanks, Helge
  4. Yesterday
  5. Hello Helge, Sorry about the delayed response. If you would like to put the results in a file, you can try exec_cmd with the normal "print" command in combination with the "suffix" command for changing the name just like one would normally do. The file should still get generated. If you would like a file name besides what can be done directly in React ( React_output[SUFFIX].txt ) then you can try a simple file rename in Python. Hope this helps, Jia Wang
  6. Last week
  7. Dear GWB community, i am just getting started with GWB working in the field of geomicrobiology with a microbiology and marine biology background. I want to generate "fields" of gibbs free energy under varying boundary conditions for a specific redox reaction. This includes pH, Eh, temperature and different concentrations of chemical species and gases. What i did so far: I used SpecE8 to determine the chemical species in the aqueous solution. After that i used Rxn to define half-reactions for active redox species and calculated the gibbs free energy for each based on the activities calculated with SpecE8. Now comes the tricky part. How can i perform a screening e.g. starting with changing environmental Eh? In terms of screening pH and concentrations of chemical species, do i have to change them in SpecE8 first and redefine activities in Rxn afterwards? This would create a huge amount of work, especially if several other concentrations would need to be altered as well. Thanks in advance!
  8. Setting to 1 may be a problem. Because in the result, I found that the porosity value will be greater than 1.
  9. Thank you for your reply! I use the latest version of gwb14. Set to 1 because I want to set an open crack in the center of the model.
  10. Earlier
  11. I am trying to model a polarization scan of Mg++ solution (attached). When talking with an electrochemists they were a bit confused to the the electrochemical kinetics used in GWB, is it bulter volmer? Also how is GWB linking electrochemical potential to mols of electrons when sliding the Eh. initial configuration-2.rea
  12. Many thanks! It's just mysticism - after reading your letter I tried it and everything worked out, and before that the program reported an error. I understood about Rnx, thanks again.
  13. Hello Ulagai, Act2 can create stability or solubility diagram for a dominant species that you choose. You can choose the same species for the diagram species as your x or y axis species.You can see examples of this in section 5.2 of the GWB Essentials guide, where solubility diagrams of Uranium and Aluminium are plotted. In both cases, the y-axis is showing the species of interest and the x-axis is pH. There are a couple of things to note though. As mentioned in one of my previous posts above, Act2 cannot simply raise the power of the activity of a species on the x or y axis. Therefore, you would not be able to replicate your exact diagram with log a[F-]^2 in your x-axis. You can obtain the equilibrium equation to plot your diagram manually using Rxn though. Similar to your previous problem above, you can open up Rxn and select fluorite to write out a balanced reaction. Rxn automatically populates the components to balance fluorite in terms of Ca++ and F-. Enter the temperature at which you want to balance this reaction at and run the calculation. In the 'Results' pane, you will find the equilibrium equation written in terms of log a[Ca++] and 2 log a[F-], which are your y and x axes respectively. If you want, you can return to the basis pane and enter in an activity for F- while leaving the activity for Ca++ blank, run the calculation again to have Rxn calculate the activity of Ca++ for you. If you want to calculate activity of F-, then you would enter the activity of Ca++ in the basis pane and run the calculation. Hope this helps, Jia
  14. With Act2, I want to build a simple graph of this kind: What should I enter in the "diagram species" field. I can’t enter Ca or F, because after that I can’t use them on the axles.
  15. Hello everybody, is it possible to pipe what is usually shown as react_output.txt (when you push the button "view results") from a python script into a user defined text file? Cheers, Helge
  16. Hello Yuhan, Sorry for the delay in getting back to you. What release version of the software you are using? While it took a bit of time to complete the simulation, I did not encounter the too large residual error or the progress being stuck error. To start troubleshooting, I would recommend you using the the 'explain steps' and the 'Follow Output' options. By turning on 'explain steps', the GWB apps will report the limiting factor for the size of time steps over the course of the simulation (e.g. intensity of kinetic reaction, user set maximum steps, etc) . To enable 'explain steps', you can go to Config --> Stepping and select the check box for explain steps. Then to see the limiting factor reported by explain steps, make sure you also check the 'Follow Output' option on the Results pane too. You might also want to shorten your run time, maybe to just 1000 years, to check if your model is performing the calculations that you are expecting. Once you confirm that the model is setup correctly for the reactions you are expecting, then extend the simulation time to what you need. I also noticed that your model have a central row of nodes in which porosity is set to 1 and this might be causing issues with your simulation. Can you explain what you're trying to do in this model? Perhaps a 1D dual porosity model might suite your needs and would require less computational power than X2t. Hope this helps, Jia Wang
  17. Hello Kgaugelo, When you create a new GSS spreadsheet, a set of analytes are preloaded onto the spreadsheet and SO4-- should be one of them. In the case that an analyte is added to the spreadsheet, it will not be available to be added again. If SO4-- is not added to the spreadsheet already, you may want to check if the species is available in the thermo database you are using. You can view the thermo file using TEdit by going to 'File' --> 'View' --> select the thermo file with the extension .tdat. Please refer to section 3 Using GSS in the GWB Essentials User's Guide for more information and example. You can open the user's guide by pressing F1 when you have a GSS spreadsheet open or from the GWB dashboard under the Doc's pane. If you would like to have someone to take a closer look, please attach your GSS file. Hope this helps, Jia Wang
  18. Hi people, I am new user of this software. I am currently at the GSS and I am struggling to SO4-- as my analyte. I cannot find it in basis species and I don not know what to do. Please help me
  19. Hi Silvain, As long as you don’t specify “free” or choose a unit that implies a free constraint (e.g. activity or pH), your constraint is for the bulk concentration of a component. To test this out, fire up SpecE8 and enter HCO3- = .001 molal pH = 6 Na+ = 1 molal balance on Cl- go You can look in the text output file to see the concentrations of several carbon species: CO2(aq) has the highest concentration at .0005060 molal, then in decreasing abundance HCO3-, NaHCO3, CO3--, and NaCO3-. Add them up and you’ll find the molal concentrations will sum to .001 molal, which is the bulk constraint you supplied. Scroll down to “Original basis total moles” in the text file and you’ll see HCO3- = .001 moles, which matches your bulk constraint. You can of course look in the plot file as well. The “species concentration” variable type refers to all the individual aqueous species, and the “components in fluid” refers to bulk composition. You could alternatively use the input below and you’d get the same results. swap CO2(aq) for HCO3- CO2(aq) = .001 molal pH = 6 Na+ = 1 molal balance on Cl- go Of course, if you use units like mg/kg you’ll have to account for the mole weight of whatever species is in your basis, or use the “as” setting to specify concentration in terms of mg Carbon, mg CO2, etc. Since we calculated the complete distribution of species, we can take our results from before and test out the “free” constraint setting: swap CO2(aq) for HCO3- CO2(aq) = .0005060 free molal pH = 6 Na+ = 1 molal balance on Cl- go Running this latest version should give equivalent results. For your second question: Act2 calculates the simple type of diagram that geochemists have traditionally drawn by hand. By design, a number of simplifications make the calculation straightforward (but still laborious). For example, you can only have logarithmic axes (log activity, pH, pe or Eh, etc.). There’s no mass balance. You have to work in terms of activity, rather than concentration. The diagrams are in many cases fairly similar, though. If you want a general picture of how chemistry of a particular system works, a traditional calculation might be fine. Certain applications might demand a more rigorous solution. Beyond recreating activity or redox-pH diagrams, though, Phase2 calculates other diagrams that Act2 cannot even contemplate. You can include surface complexes in your calculations, for example. Or, you can diagram how various properties (solubilities, saturation indices, gas pressures, and so on) vary across the diagram using color maps or contours. You can account for isotope fractionation or kinetic reactions. You can plot assemblages (combinations) of stable minerals under different geochemical conditions. Basically, it has all the capabilities of React, so it's almost endlessly configurable. Hope this helps, Brian Farrell Aqueous Solutions LLC
  20. Hello Dirk, Glad to hear you were able to resolve the issue. Best regards, Jia Wang
  21. Thanks Jia, decided to do the old fashioned thing of just a restart, that worked.
  22. Hi Dirk, It sounds like there might be a problem with your configuration file(s). Can you try creating a new folder (for example, make a GWB test folder on the desktop) and set that to be the working directory in X1t (File --> Working Directory --> select the new folder you just created), rerun your model, then see if you can open Xtplot. Alternatively, you can search for the config file(s) in your current working directory (.xtc extensions for Xtplot config files) and delete them, then rerun your model and try to plot. If that doesn't help, can you please attach a screen shot of the error message you receive when you try to plot? This will help us better assist you. Best regards, Jia Wang
  23. Hi, Xtplot keeps crashing when I try to plot a model that I just ran, doesn't matter how you try to start it, from the Run Complete window, from the file folder or from the GWB start up. Anyone else have this problem? It is a largish file, 19.5 Mb but that should not be a problem I would think. Even plots files that I could previously view do not open.
  24. Hello Abelo, GSS uses SpecE8 to calculate the pH and Eh of the system. Unfortunately, there’s not a set equation to calculate these values. If you would like more information on the calculations and the methods used in SpecE8, please refer to the Geochemical and Biogeochemical Reaction Modeling text. Best regards, Jia Wang
  25. Hello Dirk, You can set up sorption reactions by loading in a surface dataset. The dataset holds information needed to perform sorption reactions in your system. Depending on the sorption model you choose, your surface data will consist of slightly different parameters. Very likely, you would need to edit the surface datasets distributed with The GWB specifically to your system. I would recommend you create a duplicate of a surface dataset distributed with The GWB (e.g. IonEx.sdat or FeOH.sdat) and make changes using TEdit. For more information on sorption in the GWB, please refer to section 2.5 Sorption onto mineral surfaces in the GWB Essentials Guide. The surface data files are distributed in a subfolder named ‘Gtdata’ where you installed the software on your computer. It sounds like the ‘flush model’ feature might be what you need to model your experiment. When you enable a flush model, React displaces fluid from the equilibrium system with unreacted fluid. At the start of a simulation, React will equilibrate the fluid composition in your basis pane before any reactions take place. I would recommend you setup the model with the local groundwater composition in the basis pane and then enter the contaminated fluid composition in the Reactant pane. For more information on flush model, please refer to section 3.3 Flush model of the GWB Reaction Modeling User Guide. Hope this helps, Jia Wang
  26. Hi Ulagai, I am glad you are back up and running. Best regards, Jia Wang
  27. Hello Usman, Here are a couple of suggestions that might help. I think you should consider using the SpecE8 app to calculate mineral saturation indices for your fluid. You can input your geochemical data for each of your fluid into the basis pane in SpecE8 and allow it to perform equilibrium calculation. In the Result pane, you can open and view the output file to see a list of mineral saturation indices. For more information and example, please refer to section 7.2 Equilibrium models in the GWB Essentials Guide. Alternatively, you can also calculate mineral saturation for all your fluid at once using a GSS spreadsheet. To do so, you would need to enter your geochemical data into a GSS spreadsheet and select 'Calculate with SpecE8' under '+analyte'. For more information, please refer to section 3.2.5 Calculating analytes in the GWB Essentials Guide. You can also display your data on the Activity diagram you created by using 'Scatter data'. For more information and example, please refer to section 5.6 Scatter data in the Essentials GWB guide. Hope this helps, Jia Wang
  28. Good afternoon. Can you tell me which equation uses GSS for calculating pH and Eh? well appreciated Abel
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