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Melika Sharifi

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Everything posted by Melika Sharifi

  1. Melika Sharifi

    About import GMS Modflow result to GWB

    Hi John, Thanks for sharing your files with us. Here are a couple of points to help you import output files from GMS to X2t: 1. When you run MODFLOW, you supply various input files, including a discretization file. When it runs, the program can write among other datasets a budget file. Your discretization file already has a suffix “.dis”, but you should change the suffix for your “.ccf” file to “.bud”. 2. X2t does not currently support non-uniform columns and rows. Although it appears that your nodal blocks happen to be of equal size, they must be explicitly set up a certain way for X2t. A user constructing a MODFLOW discretization file by hand would use the DELR and DELC variables to hold the nodal block dimensions constant throughout the domain. If you’re using GMS, you’ll need to figure out how to get these two variables into the discretization file. Four examples of input files for importing MODFLOW results to X2t are included in the GWB Professional distribution and installed automatically with the GWB in the “Script” directory, under “Modflow” (e.g., in “\Program Files\GWB\Script\Modflow”). Hope this helps. Bests, Melika Sharifi Aqueous Solutions LLC
  2. Melika Sharifi

    Thermodynamic database

    Dear Foramruber, The thermo.dat (thermo.tdat) is the LLNL thermo database. It was compiled by Thomas Wolery, Joan Delany, Ken Jackson, James Johnson, and other members of the geochemical modeling group at Lawrence Livermore National Laboratories (LLNL). The dataset is based in large part on the SUPCRT data compilation. Bests, Melika Sharifi Aqueous Solutions LLC
  3. Melika Sharifi

    GWB new user needs assistance

    Dear Burna, Thanks for your message. I would suggest that you start with SpecE8 app to calculate the equilibrium state of your system at each temperature. Using SpecE8, you can calculate the equilibrium distribution of aqueous species in a fluid, the fluid's saturation state with respect to minerals, etc. As for your gases, you can set the fugacity, but not the partial pressure, of gases in the current release. At relatively low pressure, however, they are close to the same. If you know the iron mineral that is controlling solubility in your system, you can swap it into the basis. To include inorganic carbon, methane, and glycol constraints in your calculations, you’ll likely need to decouple some redox pairs depending on the thermo dataset you are using . For more information on using SpecE8, basis swapping, and decoupling, please read sections 2.1, 2.2, 2.4, 7.1, 7.2, and 7.3 in the GWB Essentials Guide. You can access the GWB guides from the Help menu of any GWB app. Once you’re comfortable with using SpecE8, you might set up a sliding temperature path in React, which is a very convenient way to scan over a range of temperatures. If you fix the fugacity of your gases as you trace the simple polythermal path, you’ll be able to accomplish in a single React run what you would with several discrete SpecE8 calculations. Bests, Melika Sharifi Aqueous Solutions LLC
  4. Hi ChenYang, Yes, you are right. It was a typo; the correct balanced reaction is: H2S + 2 O2 = 2 H+ + SO4-- Thanks, Melika Sharifi Aqueous Solutions LLC
  5. Melika Sharifi

    About import GMS Modflow result to GWB

    Dear John, I am not really familiar with GMS, but it sounds like a wrapper for Modflow. I believe as long as they can get the discretization input file and the budget output file from the GMS run and follow the guidelines in the manual, using GMS would not be an issue. For more information on importing from Modflow, please read the Appendix "Importing from Modflow" in the Reactive Transport Modeling guide which can be accessed from the Docs pane in the GWB dashboard. Hope this helps. If they still have trouble, please let us know and provide us with more details about the error they are receiving. Bests, Melika Sharifi Aqueous Soltions LLC
  6. Hi Yzdm, That means the ratio of SO4--to HS- would set the redox state. If you look at the reaction between H2S and SO42-: H2S + 2 O2 - = SO42- + 2 H+ At a constant pH, the ratio of activity of the sulfate and hydrogen sulfide may be expressed as function of O2 activity. Bests, Melika Sharifi Aqueous Solutions LLC
  7. Melika Sharifi

    Error: Don't know keyword: (aq)

    Dear Cshort, Thanks for your message. We will address this error in our next maintenance release. A short-term solution is to edit MINTEQ database by removing the space between NH3 and (aq) (i.e. find NH3 (aq), and change NH3 (aq) to NH3(aq)). The TEdit program, which you can access from the Support pane of the GWB Dashboard, will be very helpful for doing so. You can also check out some tutorials on editing thermo datasets on our website. Please let me know if you have any questions. Thanks, Melika Sharifi Aqueous Solutions LLC
  8. Hi Srikaush, In any GWB app only basis species of the loaded thermo dataset are available to add to the basis pane using "Add”. You can use TEdit program, which you can access from the Support pane of the GWB Dashboard, to check the basis species and reactions along with their log Ks at different temperatures included in each thermo dataset. To make a constrain on your system as HCO3-, for example, rather than CO32-, you should swap HCO3- into the the system for CO32-. For more information, please read sections 2.1, 2.2, and 7.2 in the GWB Essentials guide that can be accessed from the Users Guide from the Help menu of any GWB app. Bests, Melika Sharifi Aqueous Solutions LLC
  9. Melika Sharifi

    How to calculate pH of the solution in GWB

    Dear Yousaf, I'm not sure what assumptions your collaborators have made to get those result, but I'm attaching a script for you for sample 2, for example, that I get the same results for pH, ionic strength, and saturation indices as your attached table using the assumptions mentioned in my previous comment. You can set the same script in GSS using the Command option. For more information on Command option in GSS please read section 3.5 Launching SpecE8 and React from the GWB Essentials guide that can be accessed from the Docs pane in the GWB dashboard. Also, there is no downside to measure the pH of your solution in your experiment before or after mixing that way you do not have to make assumptions to calculate the pH. Hope this helps. Bests, Melika Sharifi Aqueous Solutions LLC sample2.sp8
  10. Melika Sharifi

    How to calculate pH of the solution in GWB

    Dear Yousaf, Thanks for providing more info on your system. You can not calculate the pH of your system with the known concentration of Na, Ca, S, Cl, and no info on carbonates. You would need at least two constraints on carbon to be able to calculate the pH of your system. One can be equilibrium of H+ with CO2 fugacity of the air, and the other one can be, for example, charge balance on HCO3-. That is most probably what your collaborators have made an assumption about to calculate the pH, ionic strength, and saturation indices. Hope this helps. Thanks, Melika Aqueous Solutions LLC
  11. Melika Sharifi

    How to calculate pH of the solution in GWB

    Dear Yousaf, If you are able to measure the pH after equilibrium with the atmosphere, you’ll be able to calculate the saturation indices of various calcium carbonates and sulfates. Or, if you know how much inorganic carbon is dissolved in the fluid (you might know the carbonate alkalinity) then you can assume equilibrium with the atmosphere to calculate pH. In the attached script, for example, I've set your sample 3 to be in equilibrium with the atmosphere and picked a random pH to calculate saturation indices of minerals. I would recommend you wait until you are comfortable with the SpecE8 calculation before setting up a batch job in GSS. Bests, Melika Sharifi Aqueous Solutions LLC spece8-Yousaf.sp8
  12. Melika Sharifi

    How to calculate pH of the solution in GWB

    Dear Yousaf, Thanks for providing the additional info on your system. Unfortunately, knowing about the equilibrium between your system and the atmosphere by itself is not going to help you calculate pH. You would need another constrain (need some lab data or assumptions) on the amount of carbonate present in your system, too. That way, you are putting some constrains on the H+, and then GSS/SpecE8 can calculate pH of your system. Hope this helps. Bests, Melika Sharifi Aqueous Solutions LLC
  13. Dear Yzdm, I am not sure whether the change of activity coefficients of water and CO2 and Debye-Huckel parameters with pressure and temperature are considered in anyway in programs making GWB-formatted datasets at arbitrary temperatures and pressures. I would suggest that you check the DBCreate and K2GWB programs to see if they are considering the effect of pressure and temperature on the activity coefficients and Debye-Huckel parameters in producing GWB-formatted thermo datasets. If not, you may check these two papers and see if they have the information you are looking for: 1- Helgeson, H.C., 1969, Thermodynamics of hydrothermal systems at elevated temperatures and pressures. American Journal of Science 267, 853-877 2- Helgeson, H.C. and D.H. Kirkham, 1974, Theoretical prediction of the thermodynamic behavior of aqueous electrolytes at high pressures, and temperatures, II. Debye-Huckel parameters for activity coefficients and relative partial molal properties. American Journal of Science 274, 1199-1261 Also, I think you will find section 8.1.2 of Craig Bethke's Geochemical and Biogeochemical Reaction Modeling text on B-dot model helpful. Hope this helps. Bests, Melika Sharifi Aqueous Solutions LLC
  14. Melika Sharifi

    calculating activities for Act2

    Dear Manuel, Below, please find the answers to your questions: 1. There is no one "correct" way to constrain an activity diagram. It's a very simplified, visual interpretation of a chemical system, and it does not mean that all of the species you see on an Eh-pH plot are actually accessible in that environment. A rough answer might be to put half the concentration of your main element as the activity for Act2. 2. GSS/SpecE8 uses a default temperature (25C) for their calculations, but there are not such a thing s default pH or f O2(g) defined for them. Please note that you do not need to know the pH/Eh of a solution to calculate activities. When you do not supply the software with aH+ or fO2(g) of your system, it simply does not consider any reactions involving those two species. Hope this helps. Bests, Melika Sharifi Aqueous Solutions LLC
  15. Melika Sharifi

    comparing Act2 and Tact

    Dear Manuel, Thanks for attaching your scripts and for your patience. I noticed that in your Act2 script, you have chosen speciate over x-y (pH and f O2(g)) for complexing species (i.e. SO42-- and Zn2++) while in Tact the complexing species are only allowed to speciate over f O2(g). You need to choose speciate over y (f O2(g)) for your Act2 script to be consistent with they way you have set your system in Tact. Regarding the boundaries not being complete, this happens due to the lack of thermodynamic data at temperatures > 25 C in the thermo.tdat for some species, specifically AsS2- and HAsS2. You may check this using TEdit app. The issue here is that the extrapolate option is being used to carry log Ks to temperatures far beyond the temperatures at which they are defined. In this case, stabilities of two arsenic sulfide species are known at 25 C, but those values are used without modification at 100 C or higher temperatures. The reason reaction lines don’t meet up at the edges of the mosaic pieces is that the extrapolation differs somewhat, depending on which ligand species are predominant at a given subdiagram. In the HS- subdiagram, for example, the reaction considered are: (1) HS- + H+ = H2S(aq) (2) AsS2- + 4 H2O = As(OH)4- + 2 H+ + 2 HS- The log Ks for reaction (1) are written over full temperature range, whereas reaction (2) has no log K defined above 25 C. In the H2S(aq) subdiagram, in contrast, the above two reactions are added together to produce (3) AsS2- + 4 H2O = As(OH)4- + 2 H2S(aq) During the addition, log K values for reaction (1) above 25 C cannot be used and hence are discarded. As a result, the reaction’s log K value extrapolated to 100 C is not consistent with that carried in the previous subdiagram. The take home point is the extrapolate option necessarily involves error and should be used only over a small temperature range. If you nevertheless wants a coherent (although not correct) mosaic diagram, you can use the alter command to set the log Ks for AsS2- and HAsS2 at each of the principal temperatures to the value at 25 C by going to Config --> alter Log Ks. The best practice would be to suppress the two species using the “suppress” command or by going to Config -> Suppress. Hope this helps. Bests, Melika Sharifi Aqueous Solutions LLC
  16. Dear Yzdm, Thanks for sharing your files. I believe the plot you have attached is not a regular predominance diagram, but it shows several ones at different temperatures on one graph. You can get the equation of each equilibrium line using Rxn, or plot each one using Act2, and then overlay separate Act2 plots using Power Point. Please see the tutorial titled "How do I overlay my diagrams?" in the "using GWB section". For example, the script I have attached shows the equilibrium lines between SiO2(aq), quartz, and talc at 90 C. You can calculate other equilibrium lines using Act2, and then plot them all on one graph. Also, I noticed you set a pressure of 250 bars for your modeling. The GWB's default thermo dataset, thermo.tdat, is compiled along the steam saturation curve from 0 - 300 C. You cannot set the confining pressure independently from the temperature, but you can certainly set the partial pressure (or strictlyspeaking, the fugacity) of gases. Hope this helps. Bests, Melika Sharifi Aqueous Solutions LLC Yzdm.ac2
  17. Melika Sharifi

    Loading FeOH+.sdat Error

    Dear Bruce, Thanks for sharing your script. As mentioned above, all .sdat datasets include in the Header a reference to the thermo dataset that supplied all the aqueous species and minerals involved in the surface complexation reactions. If you open FeOH+.sdat using TEdit, you will see its reference thermo dataset is thermo.tdat. It does not mean that FeOH+.sdat does not work with other thermo datasets; but all species in the surface dataset must exist in the thermo dataset loaded into the GWB app. The Preamble section of FeOH+.sdat offers as an example guidance for how to use the surface dataset with thermo.com.v8.R6 dataset instead of the default thermo.tdat dataset. The Co-precipitation example in the GWB Academy is using thermo.tdat and FeOH+.sdat, but in your React script, you are using thermo.minteq dataset which does not have all the species and minerals in the surface dataset. The solution to your problem can be any of the ideas mentioned below depending on the components present in your aqueous systems: 1. Change your working surface dataset to FeOH_minteq.sdat 2. Change your working thermo dataset to thermo.tdat or thermo.com.V8.R6 (for this one you have to change a few species names as mentioned in the preamble box in the Header section. 3. If FeOH_minteq.sdat does not have all the species and minerals you are interested in (it has fewer numbers of species and minerals compared to FeOH+.sdat), you can simply modify FeOH_minteq.sdat by adding species and minerals using TEdit app. Sections 9.2.3 and 9.2.4 in the GWB Essentials Guide describe how to add reactions to your thermo dataset using TEdit. All GWB guides can be accessed from the Docs pane of The GWB dashboard. Bests, Melika Sharifi Aqueous Solutions LLC
  18. Melika Sharifi

    Loading FeOH+.sdat Error

    Dear Bruce, My first thought was that you are using a custom-made thermo dataset that does not include As(OH)3. Could you, please, attach your script along with the surface dataset and thermo dataset that you are using, here? Even if you are using the GWB's dataset, please attach them here so I can take a look into them and make sure they are in a correct format. Thanks, Melika Sharifi
  19. Melika Sharifi

    fO2-pH diagram

    Dear Manuel, Thanks for attaching your script. I would suggest you plot H+ species concentration vs. Rxn progress, choose "delta" for the type of graph (where you choose linear or log scale, there is a third option called delta that shows the difference from the starting point) to see the increase/decrease in concentration of different H+ species. As you can see, OH- concentration decreases mainly due to autoionization of water that is happening in your system with high pH value. Authoionization constant = KW= [H+]*[OH-]. Hope this helps. Bests, Melika Sharifi Aqueous Solutions LLC
  20. Melika Sharifi

    fO2-pH diagram

    Dear Manuel, Please attach your script so we can take a look at it. Thanks, Melika Sharifi Aqueous Solutions LLC
  21. Melika Sharifi

    comparing Act2 and Tact

    Dear Manuel, Thanks for sharing your files with us. We are looking into your problem, and will get back to you in the next couple of days. Bests, Melika Sharifi Aqueous Solutions LLC
  22. Melika Sharifi

    comparing Act2 and Tact

    Dear Manuel, Unfortunately, I do not see any attachments to your posts. Please click on "More Reply Options" down the reply box and attach files from there. Thanks, Melika Sharifi Aqueous Solutions LLC
  23. Melika Sharifi

    comparing Act2 and Tact

    Dear Manuel, Could you, please, attach the errors you receive? Thanks, Melika Sharifi Aqueous Solutions LLC
  24. Melika Sharifi

    How to calculate pH of the solution in GWB

    Dear Yousaf, Thanks for sharing your GSS file with us. You’ll need some way to constrain pH in your system in order for GSS to be able to calculate it for you. Your GSS file does not include any constrains on pH. Do you have any other information on pH? Is your system is in equilibrium with the atmosphere, or calcite or any other minerals? Bests, Melika Sharifi Aqueous Solutions LLC
  25. Melika Sharifi

    calculating activities for Act2

    Dear Manuel, Calculations in GSS are done by SpecE8, and SpecE8 does not use a default pH to do the calculation. You can see the detailed results of your activity calculations done by SpecE8 by launching SpecE8 from GSS using Analysis--> Launch. In the Launch Dialog box, choose your samples and hit Apply. SpecE8 will run, and you can see the results from View Results in the Results pane of SpecE8. If here is no H+ component selected as Basis Species in GSS, or no constraint on the H+, there is no way that pH can be calculated. If you don't have a measured pH value to enter, you might assume equilibrium with some species, gas or mineral in place of H+. Hope this helps. Best Regards, Melika Sharifi Aqueous Solutions LLC
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