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Karen Johannesson

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  1. Hi Jia, Thanks again. I will correct these issues and will looking to the use of the "TEdit" program. I guess I learned GWB back when I was using version 7, and I haven't kept up will all the new programs and so forth. I just started using the rxn program to balance equations and calculate equilibrium constants based on the basis. Wow. That really helped speed up some of my old fashioned writing stuff down and balancing them myself. I wish I had looked into the rxn program when I was balancing those gnarly expression for the various "arsenogoethite" dummy minerals I devised for the 2019 paper. I noticed that the script from that 2015 paper I was trying to modify did not have any mineral phase to have sorption onto, which confounded me. They used a call that read: surface_data = "C:\Program Files (x86)\Gwb\Gtdata\FeOH+.dat" and later in the script that read: "sorbate include" I could provide you with the entire script if you are interested. Best wishes, Karen
  2. Hi Jia, Let's see if this works. Karen thermo_GKD.tdat thermo_ThioOxyanions2.tdat FeOH_Arsenic_HFO.sdat Austin_Chalk_As.x1t Austin_Chalk_As_KJ.x1t
  3. I am trying to modify an x1t script that a colleagued used in a paper published in Applied Geochemistry back in 2015. He sent me the script, which I have renamed “Austin_Chalk_As.x1t”. This script is essentially identical to his script except for the new name, which at the moment doesn't represent the Austin Chalk. The script is from Lazareva et al. (2015). I am also including a modified version of the standard thermo.tdat database, which has a new “dummy mineral” called Arsenopyrite2, which is Arsenopyrite written in terms of SO4--/HS- instead of As(OH)4-/AsH3 to define redox dissolution. The FeOH.sdat called in the script is the standard Dzombak and Morel (1990) SCM database that comes with GWB. The FeOH+.sdat database also works. My question involves my wish to use my modified database “thermo_ThioOxyanion2.tdat”, in which I redefined the arsenic species basis from As(OH)4- to H2AsO3- and so forth, along with my version of the FeOH.sdat database to fit the new arsenic basis and to use the surface complexation constants from Dixit and Morel (2003) that I call “FeOH_Arsenic_HFO.sdat”. I have included these databases along with the script “Austin_Chalk_As_KJ.x1t”. The only difference between the “Austin_Chalk_As.x1t” and the “Austin_Chalk_As_KJ.x1t” scripts is that the later calls my modified aqueous and surface complexation databases. The problem I am having is that when I run the “Austin_Chalk_As_KJ.x1t”, it does not seem to include any of the surface reactions, whereas the “Austin_Chalk_As.x1t” model has no problem picking up the surface reactions. Do you have any clues as to why “Austin_Chalk_As_KJ.x1t” does not pick up the include any of the SCM reactions? It seems to be loading the surface data. I used both the “thermo_ThioOxyanion2.tdat” along with my modified “FeOH_Arsenic_HFO.sdat” in my paper Johannesson et al., (2019), and that model ran again the other day just fine. I am somewhat perplexed. Best wishes, Karen thermo_GKD.tdat thermo_ThioOxyanions2.tdat FeOH_Arsenic_HFO.sdat Austin_Chalk_As.x1t Austin_Chalk_As_KJ.x1t
  4. Hi Brian, I figured it was something like this as the problem I had before was related to spaces or lack of spaces between some of my terms in my dummy minerals. Your colleague was really helpful finding this issue in my database. That said, I was so frustrated, I tried to re-install GWB 14 over the new updates and now I have no idea what version I have on my home computer. When I tried to run my x1t code, it started and then just "flashed out". That is, it was doing something and then just disappeared from view. This suggests that it probably crashed. So now I have made another problem for myself by trying to go back to the GWB 14. I am not sure what to do. I may need to re-install the new version, but no idea where to start with that. I never use the TEdit thing because when I started using GWB back in 2007, it did not exist. It is relatively simple to go in an edit databases and save them as new databases using a text editor like Notepad, which is what I usually use. I have built a number of new databases over the year to allow us to model thiotungstate speciation, thioarsenic species, and lanthanide speciation in waters. I have also built a number of surface complexation databases as well. Karen
  5. Why won't this new release work with my GWB 14 scripts? I have never experienced this before. I wish someone would actually respond to my numerous queries.
  6. I am wondering how to constrain a kinetic mineral dissolution/precipitation reaction to a specific region of a 1-D flow path. I know how to do this for a reaction I want to constrain to the beginning or the end of a flow path, but what if I want to have the reaction only occurring in the middle of the path? Also, what if I want to have the reaction happen at the beginning and then again at the end, but not along the middle of the flow path? For example, the following portion of a script for calcite and dolomite dissolution/precipitation along a specified portion of a flow path does not work (see attached). I know I could write a C++ library to do these kinds of manipulations, but I'd rather not have to do so if I can simple change the syntax of my x1t script.
  7. Hi again Jia, I have another question, which may be very easy to answer. I have been running that script I sent you, and iterating to find mineral dissolution rates that best reproduce my major ion concentrations along the flow path I am studying. For some reason is I chose an "effective" rate constant for anorthite dissolution/precipitation that exceeds 2e-19 mol/cm3/s, the X1t just seems to stop or get hung up. I am attaching a screenshot of X1t where I have set the effective rate constant for anorthite at 2.5e-19 mol/cm3/s. The program will not go any further than this. If I use a larger effective rate constant it stops at an even lower Xi value. I am also attaching my script, again, but note I am still iterating and trying to come up with the best fits to me actual data. Do you have any suggestions that I might try so that the X1t will complete the simulation with larger values of the effective rate constant for anorthite dissolution? For example, changing the tolerances of the numerical iterations.... Best wishes, Karen Carrizo_Weathering_5.x1t
  8. Hi Jia, That fixed it. Thanks again. Now it's on to finding my next hurdle. 🙂 Karen
  9. Hi Jia, Wow. I would have never caught that extra space. I have made a number of databases in the past and never had an issue. I reckon I never added a space there before. I also eliminated the tabs and changed them all to spaces. I'll give the model a run and see what happens. I hope this works. Assuming it does, then the next step will be "tuning" the kinetic mineral rate constants to fit our data as best as possible. Thanks. Karen
  10. Let me try. First is the database. And second is the script. Note that I haven't included the dll file. Although I compiled one, it the script does even get that far. thermo_ionx.tdat Carrizo_Weathering_5.x1t
  11. Dear Jia, I haven't yet tried to use your suggestion because I am perplexed that when I try to run my script, X1t does not seem to recognize either of the pseudo minerals that Park et al. (2009) provide the recipe for adding to the thermo.tdat dataset. I have been able to get the compiling worked out by downloading the compiler for VS 2019. Also, when I try to run my script, the proper database is loaded "thermo_ionx.tdat", which is the thermo.tdat modified by inclusion of the pseudo minerals Na2EX2 and CaEX2 as per Park et al. If I open up the X1t module, and load thermo_ionx.tdat, and add Ca++ or Na+ to the basis, I can swap them for the pseudo minerals CaEX2 and Na2EX2, respectively. But when I try to run my script with kinetic Na2EX2 or CaEX2, I get an error that says "Could not identify reactant species Na2EX2" (see attached). I have attached another script I used in a previous paper where I made up a pseudo mineral that I called Arsenogoethite that runs fine. I am perplexed. I don't know why this is not reading Na2EX2 or CaEX2. Any suggestions would be greatly appreciated. Best wishes, Karen
  12. Hi Jia, I have made pseudo minerals before (e.g., "arsenogoethite" in a paper I published in GCA at the end of 2019), so I was perplexed by the modified thermo.tdat database not seeing it when I tried to run X1t. I like to work from scripts and less so from the GUI, but maybe I'll try this approach you outline above. I wasn't making a surface dataset, because I was following the approach of Park et al. (2009) to add the pseudo minerals Na2EX2 and CaEX2 directly to the thermo.tdat file. I need to be able to "turn on" the cation exchange reaction for only a portion of the flow path because it appears to only begin to become important after about 26 km of flow. This is also why I was following the script of Park et al. Eventually, when I have the model running and doing a good job of simulating the major ion chemistry along the flow path, my final addition to the model will be for simulating the fate and transport along the flow path of a set of trace elements. I have already built the FeOH_trace element.sdat surface database for that. I have done this (make SCM surface databases) before for arsenic species, tungsten, organic matter, and so forth. At the moment I am trying to compile C++ dll files, but haven't had any luck. I used to be able to do these things without any problem when I was just using a clunky old Dell PC clone. Something about using Parallels and compiling C++ codes is truly perplexing to me. I should be able to do this as all my other PC compatible software, including GWB, runs fine on my Mac using Parallels. If I can solve this issue, then I am hoping my question above will be answered once and for all. I had a similar issue when I was running microbial respiration for Fe(III) oxides with GWB. I could compile the C++ code on my Dell, but could never get it to work in my Mac using Parallels. Thanks, Karen
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