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Jia Wang

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Everything posted by Jia Wang

  1. Hello Teng, With your React_output.txt file, you should see two Xi = 0 text blocks any time an initial system contains supersaturated minerals and precipitation is not disabled. The first block shows you the metastable equilibrium state of your aqueous speciation after you have initialized your run, where no supersaturated minerals have been precipitated. You can see in this first block of text, under section of Original basis, you have 15.2 mg/kg for the component UO2++ and the pH is 4.5. In the next Xi = 0 block, React reports the calculations for a true equilibrium state after all
  2. Hello Thais, I can't know for sure what is causing the issue here without seeing the input file. Here are some general tips for troubleshooting. Try a shortened run time to see if the reactions are occurring as you expect before running it for the full length. I would suggest you start with just 1 day and then check your results with Gtplot and see if it is plotting correctly. If you are prescribing many kinetic reactions, you might want to check if one is proceeding much faster than the others. When a reaction's kinetic rate is going much faster than others, it forces the pro
  3. Hello Thais, You can add the glass as a mineral reaction in your thermo database if you want and model its dissolution with kinetics. I am guessing that's what the author of this paper did but can't know for sure. Adding a new mineral into the database typically requires you to provide the mineral reaction, mol weight, and the log ks. You can edit a thermo dataset easily with the TEdit application. A good place for information and examples is the chapter 9. Using TEdit in the GWB Essentials user guide. You can also find some examples our tutorials page. Hope this helps, Jia
  4. Hello Nick, After taking a quick look at your script, I think there are several issues. Suppress is typically used to remove minerals/aqueous species from consideration during simulation. In this case, you are suppressing all the secondary aqueous species in your simulation, which is making it difficult for the program to find the equilibrium state. I would suggest that you start by unsuppressing all the aqueous species and just suppress hematite and ferrihydrite (aged), since your surface dataset contains surbing sites for Ferrihydrite but not Ferrihydrite(aged). You can view y
  5. Hello Thais, To add oxides to a thermo.tdat, you can navigate to the Oxides section and add a new entry. Oxides can be used as a reactant to change the composition of your system but they are different from a mineral (such as albite). You will notice that the there are no places to include log ks in the thermo databse for an oxide entry because they are not thermodynamically stable. Oxides also do not have a surface area associated with its entry. For more information regarding this section in the dataset, please see section 3.4 Species and reactions in the GWB Reference manual. I am
  6. Hi Andrew, I am glad you found the previous post helpful. I took a quick look at your script and see that you are using a sliding temperature path to heat your system. In the examples previously, you were just setting up React to calculate aqueous speciation for a set of initial condition but no reaction path was set to change your system. Therefore, the mineral mass you prescribed in the basis pane should be the same before and after aqueous speciation. However, with a polythermal reaction path, you are changing the system with increasing temperature, which also changes the log k
  7. Hello Jack, The GWB program is an aqueous model and the default solvent is fixed to H2O. Best regards, Jia Wang
  8. Dear GWB users, Some users have reported the following deactivation error after a recent change in our system. Return failed for GPC.... 9999; Error processing the request [Incident #...] To fix this issue, activate with the license code “tsfix” in the GWB Activation Utility and then deactivate this code. After this, users should be able to deactivate his or her GWB license successfully. If you are experiencing other activation or deactivation errors, please check our list of resolutions to common issues. We appreciate your support and hope you enjoy using The Geoche
  9. Hello Mari, Thank you for your message. Some of our users have encountered this issue after a recent change in our system. Please activate the license code “tsfix” in your GWB Activation Utility and then deactivate this code. After this, you should be all set to deactivate your GWB license again. Best regards, Jia Wang
  10. Hello Andrew, Thanks for attaching your file and the explanation. In this case, I believe the first method is what you should use. If you know that dolomite is in equilibrium with your system, then the best approach is to swap mineral for pH and then allow the program to calculate speciation (and pH and pCO2). You input file for the first method specified the constraints in the basis pane and React calculates the aqueous species distribution, gas fugacity, and mineral saturation by solving a set of matrix equations. The exact details of how React does this can be found in chapter 4,
  11. Hello Paige, In general, I would advise caution when extrapolating log K's for temperature beyond the range of validity prescribed for the reaction of interest. The further you extrapolate outside the range prescribed, the less accurate the values become. You can identify the temperature range for the dataset in the Tables pane in TEdit. Some reactions may not have equilibrium constants for the full range. If you are interested in using the Yucca Mountain dataset for you work, I would advise reading through the documentation for this database carefully before doing so. This dataset
  12. Hello Johan, If you can provide a dummy script for the error you encounter, we can take a closer look at what might be causing the issue. Can you send it to support@gwb.com or attach the script below? Thank you for sharing your solution. We currently don't have any plans to allow unfixing buffers during a simulation but I will certainly pass your suggestion onto our development team. Best regards, Jia
  13. Hello Paige, Here are a few quick suggestions to help you get started: With the "diagram species" selection, you choose the main species for which you want information. In this field, you can choose to select an aqueous species, mineral, or gas to diagram. The "in the presence of" field is used to modify the form of the main species by adding species and minerals that the main species can react with. If a mineral is not available in an existing database, you can edit that database to add the reaction for your mineral of interest. There are a couple of ways to do this. I sugges
  14. Hello Johan, There are actually several options with the pickup command. When you do a simple "pickup" (i.e. "pickup system = entire"), ChemPlugin will retain the entire system (both minerals and fluid) at the end of your first simulation and all kinetic reactions that were defined in the original path. If you specify "pickup fluid" (i.e. "pickup system = fluid"), then the system will only carry the solution results and discard the minerals from your previous simulation, but will still preserve the original kinetic redox and aqueous complexations reactions occurring within the fluid. Ther
  15. Hello Scott, I just want to follow up with a little bit more information regarding dataset editing. The improved TEdit app in GWB 2021 will open up a dataset even when it detects errors and incompatibilities. If you like, you can use TEdit to create a custom version of the FeOH_minteq.sdat that draws species and minerals from thermo.com.V8.R6+ by changing the thermo file in the header pane of FeOH_minteq.sdat. When you do that, TEdit's error status window will pop up and show a list of all incompatibilities due to the thermo dataset change. You can work through the errors to complete your
  16. Hello Scott, Thanks for providing the screenshots of the errors and details. I think I know the cause of this issue. When a surface dataset is created for the GWB, the dataset itself draws its species and minerals from a specified thermo dataset. The name of the thermo dataset is included in the surface dataset under the header lines in the beginning of the text file or in the Header pane if you are viewing in TEdit. When a surface dataset is loaded in a calculation, it is best to either use the thermo dataset specified in the surface dataset or make one that's compatible (i.e. includes a
  17. Hello Johan, Unfortunately there's no way to unfix or remove the fugacity as a reactant in the middle of a simulation. According to your screenshot above, it seems like you wish to change the fugacity constraint at about 300 days. I would suggest you try using the pickup command. You can first set the simulation for a 300 day duration under oxic condition and then use the pickup command to use the result at the end as a new starting point. The pickup command does not preserve fugacity values from the previous simulation so you can set a new value that suits the condition for your nee
  18. Hello Teng, Unfortunately, there's no way to know how the authors processed the data in SpecE8 if they don't specify what they did. Even if the parameters were changed so that the model is converging, there's no guarantee that the results would be comparable. If you are trying to replicate their results, then I suggest you email the corresponding author to see what constraints were set in SpecE8. Best, Jia
  19. Hello Wei, I am glad to hear that you were able to solve the issues with incrementing and outputting results. Best regards, Jia
  20. Hello Thais98, I tried your original script again but this time I changed all your kinetic minerals to simple reactants and got results much closer to what you expected in your original post. I would recommend double checking against the paper and perhaps emailing the authors to clarify the constraints on their model. With regards to the porosity, that suggests that the mineral volume is greater than 100% of your node volume. Perhaps you should check your conversion if you are converting from mmol/kg or the composition in the original paper. Best regards, Jia Wang
  21. Hello Teng, Thanks for reattaching your input file and providing the additional details. In my post above, I mentioned that minerals present with the fluid does not necessarily mean that it is in equilibrium with the fluid. When you swap a mineral into your fluid sample, the program is trying to set the mineral in equilibrium with the fluid. If you do that with minerals that are not in equilibrium with your fluid, then the program cannot solve numerically for the equilibrium state. To troubleshoot your script, I recommend that you begin by setting up your initial fluid with the che
  22. Hello Wei, I am no expert in Tcl so perhaps there's a more elegant solution to doing these things. With regards to your first question, it seems like the incr command will only take integer values. A way around it would be to use the expr command instead. Here is a short explanation and a good example for that: https://stackoverflow.com/questions/23653209/how-to-increment-variable-by-0-5-in-using-for-loop I noticed in the example of the Multiple Analysis chapter of the Reference manual, the section of code specifying the txt file for writing output results is placed near the beginni
  23. Hello Teng, Thank you for providing details to your problem and attaching an input file. However, the input file was not available when I try to download it. The convergence error means that the program cannot calculate the equilibrium state of your system. This can mean that the constraints prescribe doesn't describe a model in equilibrium and the a numerical solution cannot be found. Or, the constraints might be entered it in a way that the program does not expect which does not lead to an easy solution. Since I cannot access the input file provided, I can make a couple of general
  24. Hello Scott, I am sorry I missed your post from earlier. To answer your question, you are right that the ion size parameter does not reflect the ionic radius of the ion. In practice, this parameter is obtained by fitting the Debye-Huckel equation to experimental data to account for effects such as hydration sphere surrounding the ion of interest. These values may differ between datasets and whether or not the activity model is using the classic Debye Huckel equation or B-dot model (extension of the classic D-H equation). At moderate ionic strength, the affect of different ion size paramet
  25. Hello, I just want to clarify my post because it might've been unclear. The front page of the paid forum I was referring to is located here: https://forum.gwb.com/forum/23-the-geochemists-workbench/. You are certainly welcome to post topics here and we would receive notifications. There is a GWB archive section within the paid forum that we do not get notified if new topics are posted there. I have moved your other post regarding React to the paid forum. Here is the link for it: Best regards, Jia
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