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  1. Today
  2. Thanks Jia, it works! (my rate is far too low btw) Thanks for your quick response!
  3. Yesterday
  4. 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
  5. 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
  6. Hi Jia I am playing around with redox couples in chemplugin. See the attached dummy code. The Fe+++ is decoupled but 1) does the model read the specified kinetic rate? Did I wrote it correctly? Looks like there are 2 escape characters........ cp.Config("kinetic redox-1 rxn = \" Fe++ + H+ + .25 O2(aq) -> Fe+++ + .5 H2O \" rate_con = 1e-12 mpower(Fe++) = 1 mpower(O2(aq)) = 1 apower(OH-) = 2 ") 2) It does not want to report Eh(Fe+++/Fe++). Probably because it didnt read the kinetic rate? Do I call it correctly below? cpReport1('Eh(Fe+++/Fe++)') I run it in Ipython in Spyder. I use thermo.com.v8.r6 Thanks! Johan JF_model_redox_to_GWB.py
  7. Last week
  8. Hi there - I am having trouble installing the new update (v.15.01) for GWB Community Edition 2021. I was notified by my prior version (v.15.00) that the update was released, and I dully downloaded it. Prior to the installation, I uninstalled v.15.00 per the GWB instructions. However, now whenever I try to do the install for v.15.01, I get the following error: Error opening file for writing: C:\Program Files (x86)\GWB\Act2_scat.txt The installation is unable to proceed beyond this point. When presented with the options Abort / Retry / Ignore, and I select Ignore, I get the same error repeated for GTplot_scat.txt, Tact_scat.txt, Act2.ac2, etc. I get a new file name every time I click Ignore, and I gave up at 20 times (e.g., 20 different files... which seems like the error is propagating across the whole directory of files). I am trying the installation using my administrative privileges which allow me to do other software installations, so I am befuddled with what I'm doing wrong. I've tried both the 64-bit and 32-bit versions, and I get the same error both times. Has anyone else seen this issue? Thanks for whatever help you can provide, -Jason Addison
  9. 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
  10. Hello GSS classified a groundwater sample that I input as "Ca-HS" (calcium sulfide). Could anyone please point me to a reference that provides the definition (i.e., ion percent boundaries) for this water type? Regards, Jon
  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. Here's an example of how we reduce the input species to basis species and prorate to form the basis: tdat←'c:\Program Files (x86)\Gwb\Gtdata\thermo_coldchem.tdat' gwbLoadTdat tdat 94 1 1 1 1 1 1 gwbAllocToBasis 'H2O' 'Ca++' 'HCl' 'K+' 'K2O' 'Na+' 'SO4--' H2O 94.191244070000 Ca++ 1.000000000000 H+ 0.006246751707 Cl- 0.972351747200 K+ 1.830157433000 Na+ 1.000000000000 SO4-- 1.000000000000 I suppose these concentrations would all be considered "bulk" as we are doing the calculations to determine the total concentration of each basis species. We are doing this b/c HCl and K2O are non-basis species in the thermo_coldchem database. I'm not sure if there's another (or simpler) way to do this.
  14. hey, I want to make a kinetic microbial model about Bacterial Reduction of Goethite. The Chemical equation is follows:I have difificulty in adding lactate in the basis pane. I would appreciate it very much if you can help me. best wishes, Wen.
  15. Well what I mean by breaking down each input species is let's say the inputs to one of our unit ops consists of two species (an oxide and a mineral) and a given quantity of water. In order to specify the basis in mg/Kg we know the mg/Kg of each species and the amount of water but need to specify the basis in terms of mg/Kg of the basis species that the oxide and mineral are composed of, no? Since we know the mole weights of each basis species we can prorate the original densities to each basis species include H2O which is already a basis species and then sum? At that point we can specify the basis and run the go command to obtain our outputs. Is this not the correct approach? Thanks for any add'l insight.
  16. 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
  17. 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
  18. Earlier
  19. Thank you Jia for the quick and detailed reply. If we are breaking down each input species to basis species and aggregating the unique basis species is there a need to use free or should we always be using it? This is still a bit unclear to me as it would seem that the bulk specification of sodium bearing species would be sufficient--makes no sense to me that a bulk specification of the sodium ion would include all sodium in other species...seems like double counting? Perhaps two small examples (one with free and one w/o) would help.
  20. Hey all, I am looking to create a pH-Eh diagram for the element Antimony (Sb), but it seems like I could not find this element in Act2, I wonder if I need subscription to 'unlock' this element? If anyone can help with this it will be much appreciated. Thanks!
  21. 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
  22. 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
  23. 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
  24. I've read the section in one of the manuals regarding this but as a software engineer and not a chemist I'm still a bit unclear. When setting up a basis, we take the set of input species and drill down to get an aggregated set of basis species and then prorate the specified amounts for each species across its subspecies. In this scenario is there a reason to use "free?" Can anyone explain the use of "free" in layman's terms so a software engineer can understand too? LOL
  25. Our application has a series of unit ops that does a mass balance using GWB. A unit op can have one or more species as defined in the currently loaded tdat file (data command). In setting up the basis for the unit op we determine the basis-species for each input species and prorate the amounts. After running the go command we notice that some of the resultant species are not defined in the current tdat. This is a problem as the outputs to a given unit op will be used as inputs to add'l unit ops. Is it normal for some resultant species not to be defined in the current universe of species. Thoughts on how to handle this? Are we forced to have our users ensure that all resultant species are defined (manually?). Thanks for any insight into the most effective way to handle this. P.S. is breaking the input species down into the component basis-species to set up the basis the correct approach?
  26. I was able to follow the direction in Brian's response to add H2 to a copy of the minteq database. I am able to see the water lines now in pe-pH chart. The one piece I left unresolved is k values for the gas entry, H2(g) = H2(aq), at some of the intermediate temperatures, e.g. 12.5 C, 60 C etc. because I was not sure what reaction would work in this case. But I only need 25 C so I am not too worried about it.
  27. I have the same error message: "Reaction for H2(g) is missing; can not plot water limit" when trying to use Act2. This happens on all cases I have tried, including the youtube example of selenium. I am using the thermo_minteq database. But I cannot find any appendix referred to in the reply above. I don't see any Appendix at all in the Reference manual. What is the recommended procedure for adding the reaction of H2(g) to theormo_minteq.dat produce the correct Eh-pH diagram? (I am using 2021 version of GWB and I realize this thread is quite old. So the documentation may have moved somewhere else.)
  28. 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
  29. 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
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