Brian Farrell

Hi Ian, In Gtplot, does Quartz show up in the "minerals" section, or only in the "mineral saturation" category? If it's the latter there is no problem, since a mineral need not be present to have a saturation index. Is the output being updated after each run? Could you post your script so we can take a look? Thanks, Brian Farrell Aqueous Solutions LLC

Hi Akram, I figured this was a little tricky, and since we're currently setting up an instructional YouTube channel I made an experimental video walkthrough for you. The video describes how you should move the entry for HgCO3(aq) from thermo_minteq.dat to thermo.com.V8.R6+.dat. I hope this helps. GWB YouTube channel: https://www.youtube.com/user/GeochemistsWorkbench/videos?flow=grid&view=1 Please let us know what you think about the channel as a whole. If you subscribe, you'll be able to follow our new content as soon as its posted. Cheers, Brian

Hi Maki, Rate laws are typically derived to fit experimental data, and when their forms change it is often interpreted that the mechanism of the reaction changes. This is the case with the three rate laws mentioned for albite. pH < 1.5: ralb=ASk+aH+(1-Q/K) rate = surface * rate_con * (activity("H+")^1) * (1 - Q/K) 1.5 < pH < 8: ralb=ASk+(1-Q/K) rate = surface * rate_con * (1 - Q/K) pH > 8: ralb=ASk+aH+-.5(1-Q/K) rate = surface * rate_con * (activity("H+")^-1/2) * (1 - Q/K) I don't think you can simply exclude promoting and inhibiting species from a rate law. In the first rate law, for example (pH < 1.5), the H+ activity will be different for pH 0.5, 1.0, and 1.5, so the rate is not constant - it will decrease from pH 0.5 to 1.5. Above pH 1.5 this rate won't change much until you get to pH 8. As you get to pH > 8, the rate will increase with higher pH. In other words, the rate is variable below pH 1.5, constant between 1.5 and 8, and variable above pH 8. If you eliminated the promoting/ inhibiting species, then you would only have three distinct rates. Of course, this is slightly more complicated since surface area and the (1-Q/K) term can be affected by the system's chemistry as well. In some cases, it might be possible to have a single reaction mechanism across a wide pH range. In this case, a rate law like ralb=ASk+aH+(1-Q/K) could possibly be used by itself - the effect of pH upon the rate might be entirely accounted for by the activity of H+ in the rate law. There is no guarantee of this, however. Hope this helps, Brian

Hi Maki, I think there are a few items to consider here. These include the form of the kinetic rate laws, the effects of approaching equilibrium on the rate of a reaction (the thermodynamic limits), and the microbial population dynamics (i.e. a microbe dying out when conditions become inhospitable). Chapter 16 (Kinetics of dissolution and precipitation) in the Geochemical and Biogeochemical Reaction Modeling text describes three different rate laws for albite dissolution. Each of these is valid under a different pH range. You can set different rate laws (rate constants, promoting and inhibiting species, etc.) for different pH conditions using the Custom rate law capabilities of React, X1t, and X1t. As described in the GBRM text, you might consider adding H+ or OH- as promoting/ inhibiting species in some of your rate laws. A recent forum post discussed a similar topic, and more information can be found in section 5.1 of the GWB Reaction Modeling Guide. Since you're considering microbial kinetics, I think the available/ usable energy for a particular metabolism will come into play in the thermodynamic term of the kinetic rate law. The Thermodynamic ladder paper you referenced in another post (Bethke et al. (2011) American Journal of Science Vol. 311 pp.183-210.) describes the effect of pH, among other variables, on the ability of a microbe to carry out its metabolic reaction. If you decide on using multiple rate laws, you might consider different growth yields or decay constants under different conditions for a particular type of microbe. Just a few ideas. Hope this helps, Brian Farrell Aqueous Solutions LLC

Hi Ian, I think Dawsonite precipitates so quickly that it is effectively at equilibrium, so I would probably do it all in one reaction path. You could break it up into distinct stages and pick up your results, but this would be more work. Since you're running it both ways, you should be able to check how good of an assumption that is. Do you mean something similar to setting a target pH in a sliding pH path (or activity, fugacity, etc.)? I don't believe there is any way to make the run stop when a certain molality is reached. Just figuring out how much to titrate it by trial and error. Regards, Brian

Hi Ian, You are correct - the much faster rate for Dawsonite precipitation forces React to take very small timesteps. In taking a look at your original script, I see that Q/K for Dawsonite quickly reaches 1. Shortly afterward (around 200 years into the simulation), the program crashes. Since Dawsonite precipitates so much faster than the silicate minerals, you should allow Dawsonite to precipitate as an equilibrium mineral. In doing so, I get results that look exactly the same. If you were only running this model for a few days, on the other hand, you might use a kinetic rate law for Dawsonite, but suppress the silicate minerals. In general, it's a good idea to divide chemical reactions into three groups: 1) Reactions that proceed quickly over the time span of the calculation, use an equilibrium model. 2) Reactions that proceed negligibly over the time span of the calculation, suppress the reaction. 3) Reactions that proceed slowly, but measurably, use a kinetic rate law. For more information, please see Chapter 16 of the Geochemical and Biogeochemical Reaction Modeling text. Hope this helps, Brian Farrell Aqueous Solutions LLC

Hi Kirk, Do you have thermo_minteq.dat loaded (which has CO3-- as the Basis species), but are trying to read a script which was written with HCO3- as the Basis species? This might be a simple fix. Could you please post the script that is giving you problems? Thanks, Brian Farrell Aqueous Solutions LLC

Hi Akram, I believe thermo.com.v8.R6+.dat has FeCO3(aq), and thermo_minteq.dat has an entry for HgCO3(aq) at 25 C. Since you're already using v8.R6+ (as far as I can tell), you might try to add the entry for HgCO3 from the minteq database to v8.R6+. That reaction (HgCO3 (aq) + 2 H2O = 2 H+ + Hg(OH)2 + CO3--), which is valid at 25 C, will have to be rewritten in terms of the Basis species in v8.R6+, so that it looks like HgCO3 (aq) + H+ = Hg++ + HCO3-. You can do this in Rxn by performing Basis swaps (swap the Hg(OH)2 out for Hg++, and the CO3-- out for HCO3-). You'll need the equilibrium constant for that reaction calculated at 25 C. Assuming you add this species to v8.R6+, you'll be able to create an Eh-pH diagram for Fe which considers C complexes, or one for Hg which considers C complexes. You won't be able to consider Fe and Hg together, however, unless you create a diagram with C as the main system, in the presence of both Fe and Hg complexes. That being said, your FeCO3(aq) or MgCO3(aq) complexes will not necessarily show up on your diagram unless they are the most stable species for any given conditions. You can consider surface complexes with Rxn, SpecE8, React, X1t, and X2t. Rxn will allow you to balance reactions involving surface complexes and is a great place to start. You'll want to try surface datasets like FeOH.dat (to be used with thermo.dat, or thermo.com.v8.R6+.dat- please note you may need to edit the names of a few species when using it with v8.R6+) or FeOH_minteq.dat (to be used with thermo_minteq.dat). Try taking a look at Sections 2.5 and 7.5 in the GWB Essentials Guide or Sectoin 3.6 in the Reaction Modeling Guide. Browsing through chapters 9, 10, and 11 in the Geochemical and Biogeochemical Reaction Modeling textbook will also be helpful. Regards, Brian

Hi Alexis, Thanks for reporting this. It should be fixed in the next maintenance release, 9.0.4. Please check the forum for an announcement. BTW, when you install the software, you can choose to check for updates automatically. This will ensure that you are always made aware when new releases come out. Regards, Brian Farrell Aqueous Solutions LLC

Hi Christiane, You are correct in that Th(CO3)5(6-) is the source of the problem. When the HMW calculations were originally coded into the GWB, it was a safe bet that species with charges of +/- 6 wouldn't be seen, but since that time the applications of the ion interaction models have expanded significantly. We'll include a fix in our next maintenance release of version 9. By the way, you might want to set a free constraint for OH-, instead of a total concentration. Regards, Brian Farrell Aqueous Solutions LLC

Hi Johan, It looks like there were a few keywords that weren't recognized or that were used incorrectly. First, you should use rate_con instead of rate_const. The other issues is that you used the "powerD() parameter. This is for use with the half saturation term of the electron donating reaction in the microbial rate law. If you want the activity of the H+ ion raised to a certain exponent, you can just use the "^" symbol. If you save the block of text into a .bas file your script will run. You should ensure that it is doing what you want it to, however. IF pH > 6.3 THEN 20 ELSE 40 rate = rate_con * surface * (1 - Q/K) GOTO 60 40: rate = 3.235936569E+05 * rate_con * surface * (1 - Q/K) * (activity("H+")^1) 60: RETURN rate Regards, Brian

Hi Suma, It sounds like you might have your Working Directory set to Program files/ Program files (x86), or some other restricted folder. Windows prevents users from writing to these folders. To change your directory, you should open up React and go to File - Working Directory... and select a different folder. You might work under Users/, the Desktop, or a "GWB_scripts" folder. for example. For more info, look up the "chdir" command in the GWB Reference Manual. Hope this helps, Brian Farrell Aqueous Solutions LLC

Hi, Could you post your entire React script (the .rea file), and a BASIC file (.bas) if you're using one, so that I can take a look? Thanks, Brian Farrell Aqueous Solutions LLC P.S. I moved your post from the archive of old posts to the main GWB forum page.

Hi, This is not an error, but part of the solution procedure. The Eh you specify is used to constrain the initial system, but as the reaction path progresses the program may need to adapt the Basis to match the current system. Try browsing through Chapter 5. Changing the basis and Chapter 6. Equilibrium models of natural waters (specifically section 6.1.4) in the Geochemical and Biogeochemical Reaction Modeling text for more on Basis swapping. If the oxidation state of the system you are trying to model is controlled in some way, and you are concerned that the Eh changes over the course your simulation, perhaps you should set a fixed Eh path. Hope this helps, Brian Farrell Aqueous Solutions LLC

Hi Maki, Regarding question 1, I think I agree with some of your logic. In the 2005 paper, m and X for hydrogentrophic sulfate reduction (m = 1/3, X = 2) are written in terms of 1 H2 (or 2 e-, or 1/4 SO4--). If the reaction is written in terms of 4 H2 (or 8 e-, or 1 SO4--), then I think the m and X values would be 4/3 and 8, respectively. Without looking into either reference too closely I can't say why the 2011 paper (written in terms of 8 e-) has slightly different values for m and X (m = 1, X = 6). It looks like the values assumed for the methanogens are slightly different as well. Perhaps the physiology described is slightly different? I think you should take note of the relative values for m and X corresponding to the various functional groups (iron reducers, sulfate reducers, and methanogens) in the 2011 paper. Since this is an area of active research, I might go with the more recent paper's values. You might also search out more references by Qusheng Jin. I believe he has a new paper which describes some more of this material in detail . Regards, Brian Farrell Aqueous Solutions LLC

Hi Sakambari, In taking a look at your surface dataset, it looks like there are mistakes in how a few of the surface reactions are written. >(s)FeH2AsO4 and >(s)FeHAsO4- are balanced in terms of >(w)FeOH instead of >(s)FeOH, and the opposite is true for >(w)FeAsO4--. When I fix these I get results much closer to the original paper and the Visual Minteq runs. Hope that takes care of it. Regards, Brian Farrell Aqueous Solutions

Hi Michael, Your conversion seems fine, as far as I can tell. I think an important question to ask yourself is whether the conditions of your model are similar to the experiment(s) from which the kinetic parameters were derived. Since you're using the Arrhenius equation, the rate constant is going to increase with temperature - is your temperature too high? Perhaps you've specified a very large initial mass for Barite, which means it has a very high surface area, and thus a very high dissolution rate. Were pH or headspace gases controlled in the experiment, but not fixed in your model? Are there any differences between the promoting or inhibiting species used in your model and those used in the original reference? Hope this helps, Brian Farrell Aqueous Solutions LLC

Hi Sanjoy, Are you looking at the activity of the free H+ ion, or the concentration? If the difference is not due to leaving out the activity coefficient, could you post your script so I can take a look? Thanks, Brian Farrell Aqueous Solutions LLC

Dear GWB Users, We hope you can attend our pre-Goldschmidt workshop in Florence, Italy. If not, please consider our upcoming short course May 23-24 in Stockholm, Sweden. Regards, Brian Farrell Aqueous Solutions LLC

Hi Akram, Are you still interested in an Eh-pH diagram? The Eh is just another way to think about the oxidation state of your system. Could you please post one of the species or minerals that you would like to add, along with its thermodynamic data? Thanks, Brian

Hi, You don't need to calculate the activity ratios yourself. Just calculate the activity of each individual species you're interested in (SiO2, K+, and H+ for the diagram you mentioned) using GSS, then save your spreadsheet. Go to File - Open - Scatter Data and select your spreadsheet. Act2 will use the activities in the spreadsheet to calculate the activity ratios and plot the scatter points. Keep in mind that the diagram is created for a single temperature, but your samples cover a range of temperatures. Only samples whose temperature falls within a limited range will plot as scatter data on your diagram. Hope this helps, Brian

Hi, I opened it up in GWB 8.0.12 and it seems to work fine. Can you please try updating to the latest version of 8? After updating, try opening the spreadsheet again. You might need to resave it in the new version. Are you using the same exact spreadsheet that you've posted here, or are there any analytes you've already calculated? Regards, Brian

Hi, Can you please attach your GSS spreadsheet? Thanks, Brian Farrell Aqueous Solutions LLC

Dear GWB Users, Please join us May 23-24 in Stockholm, Sweden for a short course on reactive transport modeling using the GWB. Can’t make it? Consider our pre-Goldschmidt workshop in Florence, Italy on August 24-25. Regards, Brian Farrell Aqueous Solutions LLC

Hi, We recommend that you update to version 9.0.3, available from our website. You can also check for updates from the Help menu of any GWB application. You can use the "reactants times" option to continuously add your reactant fluid into an initial system. You might also be interested in the "flush" configuration built into the GWB. With this option, your (unreacted) reactant fluid enters the equilibrium system, which contains a unit volume of an aquifer and its pore fluid, and displaces the reacted fluid (rather than simply accumulating). I would check Section 2.2 of Craig Bethke's Geochemical and Biogeochemical Reaction Modeling textbook, as well as some of the examples in the Sediment Diagenesis and Petroleum Reservoirs chapters. Since you generally specify total component concentrations in the Basis pane, you don't need to add both CO2 and HCO3-. In fact, by specifying both, you simply overwrite the first input constraint. Try taking a look at Section 2 and Section 7 in the GWB Essentials Modeling Guide. If you take a look at the output from some of the examples, you'll see that the HCO3- component that you specify actually goes into forming all of the various possible carbonate species, including the free HCO3- and CO3-- ions and CO2(aq). If you look at Seawater example in Chapter 6 of the GBRM, you may ask why CO2 and HCO3- can both be in the Basis. In this case, CO2(g) is swapped in for the H+ component (not HCO3-). The reaction H+ + HCO3- = CO2(g) + H2O is used to fix pH (rather, the negative log activity of H+ ion), since the CO2(g) fugacity is known, and the activities of H2O and free HCO3- ion are calculated. This is different from what you appear to be trying. Simply assuming 1 mg/kg for all of your analytes is not typically the best thing to do. If you're considering Al in a dilute fluid, for example, you might want to specify a smaller concentration. Keep in mind too that the concentration of the oxygen component that you specify can have a large effect on your results - while 1 mg/kg O2(aq) may seem like a trivial value it actually denotes a specific redox state. Do you have any estimate of the redox state of your system? Is it open to the atmosphere? Any mineral buffer perhaps? Hope this helps, Brian