Brian Farrell

Dear GWB users, Only 1 seat remaining for the Florence course. If you can attend, please let us know by early tomorrow, August 9. Cheers, Brian

Hi Maki, We've identified a problem with the script editor and with interpreting multi-line command line scripts. One of the programmers is working on fixing these. Script files work fine, so you test your custom rate laws using .bas files. As I mentioned earlier, I don't think Fd, FA, etc. mean anything in your script without being defined first. I'm sorry if the simple example I gave in a different thread confused you. It was only meant to describe the Eh threshold effect you were looking to model, not the complete rate law you would need. The example in Section 5.2 of the Reaction Modeling Guide contains variables like fd, fa, tpf (defined by the user) used to evaluate the custom rate law. FD, FA, and TPF are set to the current values of fd, fa, and tpf for plotting purposes. I think you should take a look at that example. Regards, Brian

Hi Sakambari, You should be able to slide pH when you have a kinetic mineral. Depending on how the rate law is set up, however, the mineral may be dissolving as the pH and solutions chemistry changes. Regards, Brian

Hi Shaofeng, Do you have any clue about the redox state of your system? Do you know whether you have As(V) or As(III) in your system, or maybe both? An Eh measurement perhaps? Do you have measurements for both oxidized and reduced sulfur? Is your system open to the atmosphere? Do you observe any minerals which might buffer the oxidation state? If the answer to any of these questions is yes, you can perform a basis swap. That is, you'll replace O2(aq) in the basis with something that is more convenient for your particular system, such as the Eh or the ratio of SO4-- to H2S. There are a few modifications to your existing example I could suggest, but it might be best to hear more about your system first. Have you made a satisfactory redox-pH diagram yet? In such a diagram the O2(aq) activity is an axis variable, which allows you to determine the effect of the redox state on As speciation. Section 5.3 in the GWB Essentials Modeling Guide might be useful to you. Regards, Brian Farrell Aqueous Solutions LLC

Hi Maki, I'm just working on the script editor for now. Regards, Brian

Hi Jubilee, There is a problem with the way you set your Initial system. You swap 3 minerals into the Basis (Gypsum, Calcite, and Quartz), but then you unswap the Gypsum and Calcite by specifying the concentration of Ca++ and HCO3-. You can specify either equilibrium with a mineral for a particular component, or the concentration of a dissolved species, but not both. Later you use the commands "react 20 volume% Gypsum/ Calcite/ Quartz". If these 3 minerals are supposed to be in equilibrium with your system, you don't want to use the "react" command. Instead, you would say "Gypsum = 20 volume%". The "react" command is used to modify the Initial system by adding chemical mass to it. Commonly people use the react command to set up kinetic rate laws for non-equilibrium minerals. I would recommend using units such as meq/kg or mol/l instead of just meq. That way the extent of the system doesn't matter when specifying a fluid's chemistry. If you are having trouble getting your model to even start, I would start by creating models in React for the Initial system and the Inlet fluid. Hope this helps, Brian

Hello Sakambari, The three dataset entries you are having trouble with are all written in terms of 4 basis species. This is fine, but the dataset must be formatted so that only a maximum of 3 species appear on one line - the fourth entry must go on a separate line. To see an example, take a look at the entry for (O-phth)-- in thermo.dat. This isn't a huge problem, but I noticed your entry for >CO3FCa is written in terms of the aqueous species CaF+, rather than the basis species Ca++ and F-. Typically it's good practice to balance reactions in thermo and surface datasets in terms of the basis species. You can use Rxn to read in that dataset and rebalance the reaction in terms of Ca++ and F-, then use the resulting log K in your surface dataset. There are a few strategies for dealing with Calcite in your system. One is to set pH, Ca++, and HCO3- such that the solution is in equilibrium with Calcite. Another strategy is to swap Calcite in for one of those species In this case, the mass of Calcite would replace the concentration for one of those species as a constraint in your sytem. Finally, you can specify the pH, Ca++, and HCO3- content of a fluid not in equilibrium with Calcite (either supersaturated or undersaturated), then add Calcite as a kinetic mineral. In the short timescales considered in laboratory sorption experiments, it is possible that the sorption reactions reach equilibrium much faster than the dissolution or precipitation of calcite. Assuming this is what you want, I would make sure your rate law is slow enough so that Calcite dissolution or precipitation doesn't change your fluid chemistry. Hope this helps, Brian

Hi Maki, Thanks for the clarification. I see your problem with the field variable script editor and am trying to figure out whether it requires any special format. Regards, Brian

Hi Jahed, Most thermo datasets compile data from experiments conducted along the steam saturation curve. In other words, water doesn't boil as you go above 100 C because the pressure is just high enough to match the vapor pressure of water. A few examples in the GWB Users Guides describe the process of "steam flooding" of petroleum reservoirs. The steam is actually hot water (200 C in these particular models). Try taking a look at section 3.4 of the GWB Reaction Modeling Guide, and 3.11 and 4.10 in the GWB Reactive Transport Modeling Guide. Hope this helps, Brian Farrell Aqueous Solutions LLC

Dear GWB users, There is still time to register for the Reactive Transport Modeling workshop to be held August 24-25 before the Goldschmidt conference in Florence, Italy. Only 2 seats remain in the class of 30. If you can join us, please let us know as soon as possible. Regards, Brian Farrell Aqueous Solutions LLC

Dear GWB users, There is still time to register for the Reactive Transport Modeling workshop to be held August 24-25 before the Goldschmidt conference in Florence, Italy. Only 2 seats remain in the class of 30. If you can join us, please let us know as soon as possible. Regards, Brian

Hi Maki, When I open your script none of the kinetic parameters (rate constant, initial biomass, etc.) for microbe-Aerobe-2 have been assigned a value. The program does not take values from microbe-Aerobe-1 by default, you need to set these. In section 5.2 of the GWB Reaction Modeling Guide, for example, the command "kinetic Quartz rate_law = My_scripts.bas rate_constant = 10^-16" is used to set the kinetic rate law, as well as the parameters which are used by the rate law. Also, I think part of the reason your rate law script doesn't work is because the values for FD, FA, and TPF are not defined. I think you need to write a script similar to the one that appears later in section 5.2 of the GWB Reaction Modeling Guide. I'm not sure what you mean by an irregular description in the Reactant pane. Can you clarify this? Thanks, Brian Farrell Aqueous Solutions LLC

Hi Chance, GWB can certainly model sorption, but you'll need to search the literature so that you can create a surface dataset for coal. You should follow the format of the FeOH.dat surface dataset installed with the GWB. Basically, graphite would be your sorbing mineral, and you would add a surface basis species which is an uncomplexed site. You would then add a surface species for the CO2 surface complex. IF you don't want to use a full double layer model, you might also find a Langmuir model to be sufficient. You might want to set up some sort of kinetic rate law to describe the formation of CH4. Regards, Brian

Hi chance, It sounds like you can use React's isotope fractionation model, described in Chapter 19 of the Geochemical and Biogeochemical Reaction Modeling text. Graphite should suffice as a proxy for coal in your model. The mineral is included in the default thermo dataset thermo.dat as well as the compilation of fractionation factors isotope.dat. Regards, Brian

Hi Chance, Can you be a little more specific? Coal is more of a rock than a mineral, so the nature of your problem will dictate how to set up your model. If you're interested in the generation of acid mine drainage, for example, you can certainly model the oxidation of the sulfide minerals present in coal. Hope this helps, Brian Farrell Aqueous Solutions LLC

Hi Jubilee, To figure the volume of a nodal block in X1t, just go to the Domain pane and multiply the node length (delta x) by the width (y) and the height (z). If you didn't set delta x, you can calculate it by dividing the total domain length by Nx. If you're specifying the volume of minerals in your system, make sure the sum of all minerals in a single nodal block does not exceed this value. If you still have a problem please post your .x1t file. For transport in flowing groundwater, you should first look at Chapters 20 and 21 in the GBRM text. Regards, Brian

Hi Bob, You can go to File - Open - Thermo Data... to load different thermo datasets. You might choose thermo.com.v8.R6+.dat for this example, since the default dataset thermo.dat does not contain data for Cd++. From the Basis pane of Act2, you set the main species to diagram, then choose the axes, then finally add any complexing species with the "add" button under the "in the presence of" section. You'll probably want to account for the speciation of complexing species in your diagram. Please refer to section 5.3 (Mosaic diagrams) in the GWB Essentials Modeling Guide for details. To account for both acetate and bicarbonate, you might try decoupling all redox pairs involving carbon (type decouple Carbon into the command pane) then separately adding HCO3- and Acetic acid to the Basis and choosing the "speciate over x" option to create a mosaic diagram. Alternatively, you can decoupling all but the HCO3-/Acetic acid pair, add HCO3-, then choose "speciate over x-y". The GWB Essentials Modeling Guide can be accessed from the help menu of any GWB app. You might also take a look at this for creating specialty plots and diagrams. Hope this helps, Brian Farrell Aqueous Solutions LLC P.S. I moved your post from the archive of old posts and made a new topic on the main GWB forum page so that it's more easily visible.

Hi Shaofeng, People sometimes assume that activity is equivalent to molality in dilute fluids. If this assumption is not appropriate, however, it is easy enough to use GSS or SpecE8 to calculate the activity of individual species in solution. Just pick an appropriate pH and oxidation state to use as constraints with the information you provided. The chapters on GSS and SpecE8 in the GWB Essentials Modeling Guide describe how to calculate the activity of free species. I can't comment specifically on where scorodite should be stable, but if I create a mosaic diagram using your input the stability field changes quite a bit. A mosaic diagram accounts for the speciation of complexing ligands in addition to the main species being diagramed. In your case, the SO4-- component can be present as H2S, HS-, and S-- in addition to SO4--, depending on the pH and Eh. The Fe++ component can similarly be present as Fe+++, Hematite, Fe++, Magnetite, etc. You should take a look at section 5.3 of the GWB Essentials Modeling Guide for more on mosaic diagrams. Hope this helps, Brian Farrell Aqueous Solutions LLC

Hi Pia, I ran your original script using version 9.0.7 without a problem. The gypsum dissolves very quickly, but the model continues to 12 minutes as it should. Could you perhaps explain what you expect to see in the model, and while you feel the model is incorrect? What is the purpose of this model? Are you trying to look at Fe++ oxidation? Regards, Brian Farrell Aqueous Solutions LLC

Hello Padhi, I noticed a couple problems with your surface dataset. It looks like the molecular weight for the surface species >CO3Ca+ is incorrect. The mass balance warning you mentioned is the program alerting you that there is a problem with the overall mass balance of the reaction >CO3Ca+ + H+ = >CO3H + Ca++. When you get that error, you should make sure you have added all the necessary basis species with the correct coefficients, and that the molecular weights are correct. The second warning (Exit: React stop: set-basis: bad charge) arises because you have added a negatively charged surface basis species in <CaCO3-. You need to choose an uncharged species to be the surface basis species. In testing your dataset, I chose >CaHCO3 instead of >CaCO3-. I then had to rebalance the surface reactions in terms of >CaHCO3. Because Rxn will read your original dataset without a problem (once you fix the molecular weight of >CO3Ca+), you can rebalance the reaction in Rxn (and calculate the correct log K for that new reaction) then enter this information in the surface dataset. As an example, I changed the original dataset: 2 basis species >CaCO3- charge= -1.0 mole wt.= 100.0892 3 elements in species 1.000 Ca 1.000 C 3.000 O >CO3H charge= 0.0 mole wt.= 61.0171 3 elements in species 1.000 C 3.000 O 1.000 H -end- 1 sorbing minerals Calcite surface area= 0.277 m2/g 2 sorption sites >CaCO3- site density= 0.0002279 mol/mol mineral >CO3H site density= 0.0002279 mol/mol mineral -end- 6 surface species >CaOH2+ charge= 1.0 mole wt.= 58.0873 3 species in reaction 1.000 >CaCO3- -1.000 CO3-- 1.000 H2O log K= 5.2500 dlogK/dT= 0.0000 to this new version with >CaHCO3 as the surface basis species: 2 basis species >CaHCO3 charge= 0 mole wt.= 101.0971 4 elements in species 1.000 Ca 1.000 H 1.000 C 3.000 O >CO3H charge= 0.0 mole wt.= 61.0171 3 elements in species 1.000 C 3.000 O 1.000 H -end- 1 sorbing minerals Calcite surface area= 0.277 m2/g 2 sorption sites >CaHCO3 site density= 0.0002279 mol/mol mineral >CO3H site density= 0.0002279 mol/mol mineral -end- 6 surface species >CaOH2+ charge= 1.0 mole wt.= 58.0873 4 species in reaction 1.000 >CaHCO3 -1.000 CO3-- 1.000 H2O -1.000 H+ log K= 11.6500 dlogK/dT= 0.0000 As for your first question, I don't really know enough about your example to offer anything but a few ideas. Is Calcite at equilibrium with the fluid at each pH, or is it supersaturated? Since you know the concentration of CO3-- in your sytem, and because CO3-- is both a sorbing ion and important to Calcite saturation, I would probably not use it as the charge balancing ion. Use K+ or NO3-, which are much more abundant and less important to the system's chemistry. Also, you should verify whether you want to use the "sorbate exclude" or "sorbate include" option. You can search the GWB Reference Manual for this command, or read this forum post. Hope this helps, Brian

Hi Michal, X2t uses hydraulic potential instead of pressure, so you don't need to specify the direction of gravity. You can use X2t for modeling a vertical cross section as long as there are no sharp density differences in the fluid. If there are large density differences and you need to account for buoyant forces, then you should use an imported flow field. You should look into section 4.3 - 4.5 of the GWB Reactive Transport Modeling Guide for more info. Regards, Brian Farrell Aqueous Solutions LLC

Hi Jubilee, You just need to change your working directory. See this thread for details. Glad to hear you're using X1t now. Regards, Brian

Hi Jubilee, For applying the virial equations outside 25 C, try taking a look at thermo_phrqpitz.dat, which is included with the GWB. You should be aware that the data for temperature extrapolation is incomplete, however. You should see The PHRQPITZ/ PHREEQC documentation for more information on applying the virial methods outside 25 C. You might also take a look at the model of Yuan and Todd (1991), which is mentioned in Chapter 30 of the Geochemical and Biogeochemical Reaction Modeling textbook. There are many chapters in the GBRM textbook which describe mineral precipitation. Once you familiarize yourself with the basics of chemical equilibrium and mass transfer, I would take a look at Chapter 24, Evaporation, and Chapter 27, Weathering. Hope this helps, Brian Farrell Aqueous Solutions LLC

Hi Steph, Not sure what you'll get out of plotting potassic-aluminosilicates on a fO2-pH diagram, but the first two plots you've described should be fine. Could you attach some screenshots, or maybe the .ac2 files (File - Save as...) so that I can take a look? If you tell me what you expect, or what you're trying to do, hopefully I can help you out. You can specify the main diagram species, as well as the additional basis entries (the "in the presence of" field) using either minerals, gases, or aqueous species. Try modifying the Uranium fO2-pH diagram in the User's Guides (Figure 5.1) by adjusting the activity of U++++. For the K minerals, you might take a look at Figure 5.3 as a starting point. Once you get the hang of Act2 you'll have no trouble with Tact. As long as you include the O2 component in your system in one way or another (as an axis, or in the presence of) then the basis entry Fe++ will consider the appropriate forms of iron. In an fO2-pH diagram with Fe++ selected as the main species, you'll see species like Fe+++ and Hematite under oxidizing conditions, and species like Fe++, Magnetite, FeCO3, etc. under more reducing conditions. Without adding O2, you'll only consider ferrous iron. If you're interested in a fO2-pH diagram for S, then you'll need to leave the SO4--/H2S pair coupled. As for salinity, try taking a look at the first example shown in Figure 5.2. Just change the activity of Cl- in the "in the presence of" field to see how salinity affects your diagram. Try taking a look at the pre-calculated diagrams on our website, as well as our slideshows and . You can click on an Act2 icon on our website to bring up the input files which were used to create that plot. Hope this helps you get started. Regards, Brian Farrell Aqueous Solutions LLC P.S. I moved your post from the archive of old topics to the GWB forum front page.

Hi Clint, You'll need to be a little more specific. Which version of GWB are you using? Are you opening Gtplot from GSS? What type of operation are you performing before Gtplot crashes? FYI, unless you are directly replying to a topic or a conversation on the forum, it's best to post a new topic (this is a pretty old thread). Please reply directly to support@gwb.com. Cheers, Brian