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Jia Wang

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Everything posted by Jia Wang

  1. Hello, Activity diagram requires user to input the relevant activities or fugacities of species. The program uses a simple method to draw equilibrium lines and calculate stability fields. If you have a fluid analysis, you can use SpecE8 to calculate the distribution of mass amongst species. SpecE8 will also report the activity for each species which can be used to set up your Activity diagram. You may also be interested in the Phase2 application as well. Unlike Act2 and Tact, Phase2 requires the user to set up an initial system and prescribe reaction paths in the x and y axis. The program then solves the solution to a multi-component chemical system at each node numerically and assembles the result in a grid form. If you're interested in Phase2, please refer to chapter 7 of the Reaction Modeling User Guide for more information and examples. Hope this helps, Jia Wang Aqueous Solutions LLC
  2. Hello Christopher, You can overlay data points from a GSS spreadsheet to an Act2 diagram. You would first need to prepare a GSS file that contains the axis variables on your diagram, in this case, Eh and pH. Save the GSS file. In Act2, create your diagram and go to File --> Open --> Scatter Data... --> select the GSS file your had prepared. After you hit Ok or Apply in the Scatter Data dialog, Act2 will read the data points and project them onto the diagram. For more information and example on how to use scatter data, refer to section 5.6 Scatter data in the GWB Essentials User Guide. Hope this helps, Jia Wang Aqueous Solutions LLC
  3. Hello Tanya, Yes, the bulk concentration for HCO3- is specified for the sum of aqueous species and carbonate minerals (if supersaturated). The speciation calculation does not distribute mass to the gas phase but instead will calculate fugacity of that gas in equilibrium with the fluid. Best regards, Jia
  4. Hello Tanya, The GWB accounts for the effect of gas on an aqueous system by gas partial pressure or fugacity in equilibrium with the system. I am not sure what your system is like but you can set up the Basis pane with the initial bulk HCO3- concentration in the fluid and have the GWB calculate the corresponding CO2(g) fugacity. If your system have a super CO2-charged fluid for example, you could use a sliding fugacity path to simulate degassing to the point of equilibrium with some external reservoir (e.g. atmosphere). Under Reactant properties in Gtplot plot, you can find the amount of CO2 gas exsolved (negative value means gas is leaving the system). You can also track the distribution of species under the variable species concentration. For more information on sliding fugacity paths, please refer to section 3.6 of the GWB Reaction Modeling User Guide. Hope this helps, Jia Wang Aqueous Solutions LLC
  5. Hello Wen, You're welcome. The error indicates that the kinetic reaction specified in the Reactants pane is not balanced. I took a quick look in monitor2.rea and that does seem to be the case. In general, it is good practice to double-check your input file when issues like this arise. Best regards, Jia
  6. Hello Wen, Thanks for the clarification. If you change the thermo dataset in the Preferences window, The GWB will then use whatever dataset set when launching a new instance of React (or any other GWB apps other than the plotting apps). Changing the dataset in Preferences, does not change the dataset loaded for your current input file. To change the dataset loaded for your current file, you have to go to File -> Open -> Thermo Data... and then select the file you want. To see the current thermo file loaded for the simulation, you can go to File --> View --> and select the file with the extension .tdat. Hope this helps, Jia
  7. Hello Wen, 1. The power, powerA, and powerD are the power terms for numerator and denominator terms in the generalized rate law for calculating microbial metabolic rate. You can find the equation and terms explained in section 4.7.1. Metabolic rate in the GWB Reaction Modeling User Guide. 2. The redox pair for Fe+++/Fe++ is decoupled so you have to add in both Fe++ and Fe+++ to your system in the Basis pane. 3. You might want to look at the different types of kinetic models that the GWB has to offer to determine which one is suitable for your needs. Please refer to section 4.6 Kinetics of redox reactions and section 4.7 Microbial metabolism and growth in the GWB Reaction Modeling User Guide. In the sections described above, the equation for each type of microbial reaction is described in detail. 4. I am not really sure what you mean here. If you open a saved React input file and go to File -> Open -> thermo file -> thermo+Lactate.tdat, React loads the new thermo dataset. If there are any conflicts within the existing setup, React will display a pop up showing the conflicts and ask if you would like to proceed. Note that Lactate is a redox species in thermo+Lactate.tdat. If you want to constrain it separately in the Basis pane, you would need to decouple the redox reaction first and then you are able to find it under "add" in the Basis pane. For more information on redox disequilibrium, refer to section 7.3 in the GWB Reaction Modeling User Guide. 5. The datasets available on the GWB academy are in the latest format (currently apr20), used in GWB 2021 (or version 15.0.1). If you are using an older version of the GWB, TEdit is not going to be able to open and edit the dataset. You can still open the dataset in a text editor, such as Notepad, to view the reactions. Alternatively, you can obtain a free GWB Community license, which includes the latest version of TEdit and will allow you to open the dataset. Hope this helps, Jia Wang Aqueous Solutions LLC
  8. Hello Johan, I think your rate law is ok when I tried to read in the script with a different dataset. However, I think your command for report Eh(Fe+++/Fe++) is not quite right. For the Nernst Eh value of a redox pair, you would want to use the keyword "Eh" followed by the arguments "couples" and the name of the couple exactly as shown from the report ('couples') command enclosed in double quotes. For example, to retrieve the Nernst Eh value for the redox pair Fe+++/Fe++, it'll be like this: cp.Report1('Eh couples "Fe+++ /Fe++ "') For a more detailed list of keywords and arguments accepted by the report command, please refer to the Appendix: Report Function section in the ChemPlugin User Guide. Hope this helps, Jia Wang Aqueous Solutions LLC
  9. Hello Jason, I am sorry to hear you're having issues with the installation of the new update. That error typically means the file that the installer is trying to write to is in use by another application or anti-virus software. Please try installing again after rebooting your computer. If you still encounter the same errors, try disabling any anti-virus type software briefly and run the installation again. Hope this helps, Jia
  10. Hello Jon, The GWB apps will report the water type based on the highest electrical equivalents of cation and anion species of a sample after calculating speciation. Best regards, Jia Wang Aqueous Solutions LLC
  11. Hello Wen Qiu, The GWB applications themselves do not carry species, minerals, or gasses. The applications draw reactions from the thermo dataset loaded for your calculation. In React, you can go to File -> View -> select the file that ends in .tdat (or .dat for really old datasets) to view the thermo dataset loaded. thermo.tdat, the default dataset in The GWB does not contain Lactate, you can add the reaction using values in literature or copy and paste it from another database to thermo.tdat and save it as a custom dataset with a new name. You might also find the GWB academy lesson on Microbial Population helpful. The dataset used in this example is a modified thermo.tdat with the addition of the Lactate reaction. For more information on how to alter thermo datasets in the GWB, please refer to section 9 in the GWB Essentials User Guide. Hope this helps, Jia Wang Aqueous Solutions LLC
  12. Hello Erik, If a mineral is known to be in equilibrium with the fluid in your system at the start, then you would swap in the mineral in the basis and allow the program to calculate the dissolved concentration in equilibrium with that mineral. You shouldn't convert a mineral into aqueous species and then sum those concentrations into the basis pane. For example, if your fluid is in equilibrium with Quartz, add SiO2(aq) into the basis and then swap it for Quartz and set the volume of quartz. The speciation calculation in the GWB will calculation the dissolved silica component in addition to the mineral you input. In your input file, it'll look like this: swap Quartz for SiO2(aq) Quartz = 1 free cm3 Also, you don't have to keep to mg/kg as the unit. The GWB accepts many units for minerals and dissolve species concentration. To see all units recognized by the GWB, see the GWB Reference Manual. I think it would be really helpful for you to revisit the sections in the Essentials User Guide on how The GWB configures its geochemical system. The best place to start would be in section 2.1 Configuring a calculation and 2.2 Setting and constraining the basis. You can find the commands accepted by each GWB app in the GWB Command Reference. Hope this helps, Jia
  13. Hello Eden, Act2 draws its species, minerals, and gases from the thermodynamic dataset loaded in the run. You can view the thermodynamic dataset loaded by going to File -> View -> open the file that ends in .tdat (or .dat for really old datasets). thermo.tdat is the default dataset used in The GWB apps and does not contain Antimony. You can add in Antimony and the desired reactions to create a customized thermo dataset tailored for your needs. Here is a similar thread which discusses how to do so. Hope this helps, Jia Wang Aqueous Solutions LLC
  14. Hi Erik, You're welcome. I am not sure what you mean by breaking down each input species to basis species. A good example of a free quantity is pH. pH is a measure of the activity of H+ alone. When you enter a pH, you're describing the hydrogen only in the H+ form and not including any H that's part of other aqueous species (e.g. CH4) or minerals. A typical use of a free quantity is when a user is setting the fluid in equilibrium with a mineral. For example, if the silica component in your system is in equilibrium with the mineral quartz, you should swap in Quartz for SiO2(aq) in your system. Minerals like this are typically set as a free unit since the amount entered represents only the silica that exists as quartz not the silicia in dissolved species such as SiO2(aq). On the other hand, most chemical lab analysis of a water sample provides bulk quantities. In natural waters, sodium may exist in fluid as Na+, NaCl, NaHCO3-, NaOH, and more but the measured concentration only reports the total quantity of Na+. When you enter this bulk concentration in the basis, the software solves a set of matrix equations to distribute the total mass of Na+ amongst all Na-bearing species. The bulk concentration is not just the dissolved Na+ ion alone. Please see section 7.2 Equilibrium models in the GWB Essentials User Guide to see a seawater speciation example. Hope this helps, Jia
  15. Hello, I am glad to hear that you were able to copy the reaction for H2(aq) and H2(g) to thermo_minteq. If you like, you can use Rxn to calculate the log K values for the intermediate temperatures, similar to how it is done for H2(aq). You can load thermo.tdat into Rxn and select H2(g) in the "balance reaction for" section. The program by default populates the "in terms of" section with the basis species that reacts to form H2(g). Since you want the log Ks for the reaction H2(g) = H2(aq), swap H2(aq) for O2(aq) to rebalance the reaction. Then enter the desired temperature and run the calculation. You can find the log K at your desired temperature in the Results pane. Hope this helps, Jia Wang Aqueous Solutions LLC
  16. Hello Erik, Please find my response to your earlier post here. I had already included some explanation regarding bulk vs. free quantity there before seeing this post. Best regards, Jia Wang Aqueous Solutions LLC
  17. Hello Erik, The GWB does not account for species that are not defined in the thermo dataset. In a speciation calculation, you supply the composition of your system and the software calculates the distribution of mass amongst species using thermodynamic information provided in the thermo database loaded. For example, if a system’s composition consists of sodium, chloride, and solvent water at a given temperature, then the program will calculate the mass distributed amongst the dissolved species and minerals given the bulk quantity of each component. If we use thermo.tdat with the system above, the software will calculate the amount of the sodium component distributed between the free sodium ion (Na+), NaCl complex, and the halite mineral if it precipitates (assuming that you are using React). NaCl is not part of the basis species in the thermo.tdat but instead a secondary species that forms from reacting the basis species of Na and Cl, you will find it in the Aqueous Species section. You should never see GWB report a species that doesn’t exist within the dataset loaded. Users can easily edit datasets in TEdit or in a text editor, like Notepad, before the run to account for reactions not in the dataset. For more details, please see section 9 TEdit in the GWB Essentials User Guide. You set the composition of your initial system using a set of basis species. The basis is the set of aqueous species that appear at the beginning of the thermodynamic database. You can alter the basis by swapping in aqueous species, minerals, or gases that you wish to use to constrain your geochemical system. For example, if your system is in equilibrium to quartz, you will add the component SiO2(aq) to your basis and then swap it for Quartz. For more information on setting up your basis, please see section 2 Configuring the Programs in the GWB Essentials User Guide. An important point to note is setting a bulk vs. free quantity in the basis. For example, you can constrain the sodium component in your basis pane by setting a bulk quantity, which would include the total amount of sodium present in all sodium bearing species. Alternatively, you can also set a quantity for the free sodium ion, which does not include the mass of sodium in Na-complexes, and have the software calculate bulk composition. For more details and examples, please refer to section 7.2 Equilibrium models in the GWB Essentials User Guide. Hope this helps, Jia Wang Aqueous Solutions LLC
  18. Hello Karen, Johan, I want to let you know that this issue has been fixed with the release of GWB 15.0.1 for all GWB subscribers. Existing 15.0.0 installations should automatically update if auto-update is enabled. If disabled, you can update your installation under the Help menu in any GWB app. Best regards, Jia
  19. Hello again, I want to let you know that this issue has been fixed with the releases of GWB 15.0.1 and GWB 12.0.8. Existing GWB 15 and GWB 12 installations should automatically update if auto-update is enabled. If disabled, you can update your installation under the Help menu in any GWB app. Best regards, Jia
  20. Dear GWB users, We are pleased to announce our latest maintenance release for GWB subscribers, GWB 15.0.1. The 15.0.1 update fixes tab delimiting issue in thermo datasets, improves presentation of some dialogs on high-resolution monitors, improves messaging in TEdit, enables "report" command to list entries in current thermo database, resolves last-digits inconsistency in reported solvent mass, fixes an issue arising when importing some PhreeqC datasets, allows user-defined analytes to share names with basis entries in GSS, and provides fixes for all known issues. Update from 15.0.0 at no charge to ensure you have all the newest features and bug fixes. Existing installations should automatically update to this release, unless auto-update is disabled. In that case, users should update their installations from the Help menu of any GWB app. Best regards, Jia Wang Aqueous Solutions LLC
  21. Hello Juro, The default GWB dataset (thermo.tdat) is based on the Lawrence Livermore National Laboratory database. Thermo.tdat is converted from the file data0.3245r46 from EQ3/6. You can find information regarding the origin of the dataset at the top of the text file and sources cited at the end of the text file. Or, if you open the dataset in TEdit, you can find both sections in the Header pane. You can contact the original authors regarding compilation method and discrepancies. Also, I wasn't able to verify the Log k value for the reaction stated above in thermo.tdat. Perhaps, you are looking at a different dataset? The expanded variant of LLNL dataset, thermo.V8.R6+.tdat, does contain thermo data for H2AsO3- with Log Ks spanning from 0 to 300C. The Log K at 300C is 13.8282 and not 11.92. Perhaps your reaction data was altered at some point? You can download the version installed with the software from the thermo webpage. SUPCRTBL and SUPCRT uses mostly the same data sources for their compilation but they are not entirely the same. You can view a summary of their differences here. If you would like to use a dataset that's consistent with SUPCRTBL, you can convert one of the ready-to-go PhreeqC datasets to GWB format using the TEdit application. There are several default datasets published that you can choose from. Geothermal.dat is compiled from 0 to 300C using the debye huckel b-dot activity model. To convert geothermal.dat to GWB format, you would need to edit the llnl_aqueous_model_parameters block so that there are only 8 principal temperatures spanning the desired range. For more information on converting datasets, please see section 9.3 Importing PhreeqC datasets in the GWB Essential User Guide. Hope this helps, Jia Wang Aqueous Solutions LLC
  22. Hello Zixuan, GWB does not fit surface data to calculate surface reaction equilibrium constants. However, you may be able to use the Alter Log K dialog to manually alter the log k values for your surface reactions to and find the value that best reproduces your data by trial and error. Overlaying your data on your plot may help to visually assess this. For more information on Altering Log Ks, please refer to the alter command in the GWB Command Reference. In GWB applications (except GSS, TEdit, and the plotting apps), you can find the Alter Log K under Config -> Alter Log Ks... For examples of scatter data, please refer to section 6.5 in the GWB Reaction Modeling Guide. Alternatively, you can also write your own scripts and use React's plugin feature to run the models and retrieve the data, assess the fit quality, update your Log K with a better estimate and rerun the model. Please refer to section 7 of the Command Reference for details regarding the Plugin feature. Best regards, Jia
  23. Hello, For your React simulation, you can plot species in concentration to see which aqueous species are forming. On the X-axis tab in Gtplot, you can plot the mass of chalcopyrite reacted (choose Reactant properties as your Variable type). On the Y-axis tab , select "Species in concentration" as your variable type and then filter to on the CN- component to see all species containing CN-. You can highlight and plot your copper cyanide species in your desired unit(e.g mmoles) and export the numerical data by going to Edit --> Copy and paste in an Excel Spreadsheet. You can sum the mass of CN- from all your copper cyanide species, be sure to account for any conversions needed. Repeat the same steps to see your iron cyanide species in solution. Since I don't have your customized dataset, I am not able to reproduce your exact system. You might also want to check whether or not if there are any copper cyanide or iron cyanide minerals that form. For more information regarding plotting, please see section 6 Gtplot in the GWB Reaction Modeling Guide. You can plot species in concentration as a variable in both SpecE8 and X1t. Unlike React, SpecE8 only calculates a fluid's equilibrium state and it does not account for mineral titration as you have described in React. X1t is a reactive transport simulation application that will account for both geochemical reactions and mass transfer in a 1D domain. In the future, please post any new queries to the front page of the forum. We do not get alerts of new post in the GWB archive. Hope this helps, Jia Wang Aqueous Solutions LLC
  24. Hi Johan, You're welcome. Glad to hear it worked. Best, Jia
  25. Hello Scott, Perhaps you set an inert volume for your system? The program will include any inert volume you set as part of the total mineral volume but won't list it in a separate line under "Minerals in system". The output text file should list the invert volume in the first block of text below the line Step #100. If that's not the case, I would need to take a closer look at the file to see why these values differ. Can you attach the input file? If there are issues with attaching files to the thread, please send the input file and the errors to support@gwb.com Hope this helps, Jia Wang Aqueous Solutions LLC
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