Brian Farrell

Hi Fernando, I was able to make an Act2 diagram with Enargite using the data you supplied. Perhaps you did not add it to the dataset correctly, or maybe you did not include in your Act2 basis all of the components necessary to form Enargite? If you look at the thermodynamic information you provided above, you'll see the 6 species needed to form it (Cu+, As(OH)4-, SO4--, H2O, O2(aq), and H+). All of those must be present to form Enargite. For example, if I diagram Cu+ on Eh-pH (or O2(aq)-pH) axes, I would additionally need to add As(OH)4- and SO4-- under the "in the presence of" field for Enargite to be considered. If you're still having trouble, you can post your thermo dataset and Act2 script so that I can take a look? You can also email them to me at support@gwb.com. Regards, Brian

Hi, Adding these species will be easy enough, but you'll need to search the literature for reactions (and log K values) between those species and the Basis species (HCO3-, H+, O2(aq), NO3-, and H2O in thermo.dat), Redox species, or Aqueous species in your GWB dataset. Take a look at thermo.com.v8.r6+, thermo_minteq, thermo+Benzene, and thermo+Lactate for different examples of how organic species are added to datasets. The Minteq dataset, you'll notice, has many organic compounds designated as Basis species, while in the others they are added under Redox species. Your application (and the nature of redox equilibrium/ disequilibrium) should dictate your choices. The rules you'll need to follow when modifying thermodynamic datasets can be found in the Appendix to the GWB Reference Manual. Regards, Brian Farrell Aqueous Solutions LLC

Dear GWB Users, Please join us November 29-30 in Seattle for a short course on reactive transport modeling using The Geochemist's Workbench. Then continue to San Francisco for the AGU Annual Meeting. Even if you can’t come, please print and post our flyer for others to see. Regards, Brian Farrell Aqueous Solutions LLC

Hello Arne, With the "diagram species" selection, you choose the main species for which you want information. An Eh-pH diagram of Cu++ show the most stable copper minerals and the predominance of copper species on Eh and pH axes. A similar diagram for SO4-- will consider only sulfur species on the same axes. The "in the presence of field" is used to modify the form of the main species by adding ligands with which the main species can react. If you start with just a diagram of SO4--, the various species formed might include SO4-- and HSO4-, elemental sulfur, H2S(aq), HS-, and S--. By considering Cu++ in the calculation (SO4-- in the presence of Cu++), Brochantite (Cu4(SO4)(OH)6) and Chalcocite (Cu2S) become stable. If you start by diagramming Cu++ with SO4--, on the other hand, many more minerals appear stable on the diagram. Tenorite (CuO), Cuprite (Cu2O), and metallic Copper (Cu) appear in this Cu++ with SO4-- diagram, but not in the SO4-- with Cu++ diagram, since they do not contain any sulfur. The "speciate over x-y" option is used to consider the speciation of the ligand ("in the presence of" species) on the axes chosen, Eh-pH here. For example, if SO4-- is chosen as the ligand, only the SO4-- ion is considered by default. By speciating over x-y, the SO4-- component can be present as SO4-- under oxidizing conditions and as H2S(aq) in reducing conditions, for example. For more information, see the Mosaic Diagrams section (5.3) in the GWB Essentials Guide. Activity diagrams can be quite useful, but keep in mind that they are simplified representations of system chemistry. For a more complete analysis, you might use SpecE8 or React. These will show the predominance of all species at equilibrium, not just the most stable phases of the main species considered. Please let me know if this does not make sense. Regards, Brian Farrell Aqueous Solutions LLC

Hello Maki, There is no H+ component selected in the current basis, so there is no way that pH can be calculated. If you look at the results, without a pH value all carbon is present as HCO3-/CaHCO3+/MgHCO3+/NaHCO3 but not as CO2(aq) or CO3--. To consider pH in your calculation, you'll need to add H+ to the basis. If you don't have a measured pH value to enter, you might assume equilibrium with some species, gas or mineral in place of H+. If your solution is open to the atmosphere, for example, you could use the following commands to calculate a pH value based on the reaction CO2(g) + H2O = HCO3- + H+: HCO3- = 3000 mg/L swap CO2(g) for H+ log fugacity CO2(g) = -3.5 On the other hand, if you believe your fluid is in equilibrium with Calcite, the reaction Calcite + H+ = HCO3- + Ca++ might fix pH: HCO3- = 3000 mg/L swap Calcite for H+ 1 free gram Calcite These are two different assumptions that are commonly used. You'll need to decide what sort of assumptions are appropriate for your particular system. Hope this helps, Brian Farrell Aqueous Solutions LLC

Hi Jim, One thing I would recommend is to decouple the redox couples in your redox reaction (H2(aq)/H+ and CH4(aq)/HCO3-) so that GWB can calculate the voltage for each half cell reaction. You can then solve for the deltaGr from the deltaEh. The decouple Carbon command will be useful to decouple all redox pairs with HCO3- (this prevents species like CH3COO- and O-phth from being considered in your calculation). After decoupling, you can add entries for both HCO3- and CH4(aq) (a very small amount). You'll want to get rid of the O2(aq) and add H2(aq), then swap in H2(g). If you want to add S-- and NH4+, you'll probably want to decouple those redox pairs as well, not swap them. What sort of pH value have you measured for your media? I find a pH of 5.848 if I swap in CO2(g) and balance on the HCO3-. If your colleague has the Geochemical Reaction Modeling text, you should look at the chapter on Redox disequilibria for some helpful information. Hope this helps, Brian Farrell Aqueous Solutions LLC

Hi Nixie, The Geochemist's Workbench is designed for modeling equilibria in aqueous solutions, so it doesn't sound like it will be appropriate for this particular problem. Regards, Brian Farrell Aqueous Solutions LLC

Hi Kawal, I'm not sure about this but I think earlier versions of the code would not work with the Minteq database unless you unchecked the "water limits" option. Now you just get a warning message that you can't include the water limits when using the unmodified Minteq database. You can still toggle water limits on/ off (and modify many other aspects of your plot) by right-clicking your plot and choosing View... or going to Plot - View... In Gtplot and Xtplot there is a little more flexibility in moving around the locations of line labels, but in Act2 and Tact they are placed in the center of the fields which they represent. You can try shrinking the font a little to help distinguish one field from another, and expanding the plot range to pH 16 will also clear things up. You can also just paste your plot into PowerPoint or Illustrator and edit it there. Hope this helps, Brian

Hi Kawal, It looks like you also had the issue discussed here. Calling the species whatever you want (O2 (g) and H2 (g)) will work for most calculations, but I think Act2 and Tact look for O2(g) and H2(g) (with no spaces) when they attempt to draw the water stability limits. You need to be very careful when editing thermo datasets. The default thermo.dat is defined from 0-300 C, while the Minteq database only goes to 100 C, so the values you copied into the Minteq database don't match up. The topic referenced above contains instructions for estimating the log K values at the proper principal temperatures. You also need to update the counts of basis, redox, aqueous, minerals, and gases in the dataset as you add species. I think you may have done this for H2(g) but not for H2(aq). The Thermo datasets Appendix to the GWB Reference Manual will come in handy when analyzing and modifying thermo datasets. Regards, Brian

Hi Kawal, Can you please post your modified database so that I can take a look? Thanks, Brian Farrell Aqueous Solutions LLC

Hi, I think I can identify the source of error in your script. First, though, I want to go over how the specified reaction paths (in the Reactants pane) are affecting your run. Pyrite oxidation in a closed system will stop as soon as oxygen runs out. In a system open to the atmosphere, the reaction will likely continue until the Pyrite is completely dissolved. In the absence of a pH buffer, some variant of the reaction Pyrite + 2 H2O + 3.75 O2(aq) = .5 Hematite + 2 SO4-- + 4 H+ will occur, generating acid. In the experiment, however, f O2(g) and pH are manipulated to remain fixed. In the model, pH is fixed by removing H+ from the system. Since SO4-- keeps accumulating as Pyrite dissolves, Cl- (default charge balancing ion) must be adjusted (lowered) to maintain charge balance. Eventually it disappears completely and causes (I believe) the error you are experiencing. Turning charge balance off helps here (although a plot of charge imbalance error vs. time shows quite a large error, which isn't exactly desirable). Since pH is controlled in the experiment by addition of NaOH, you can use Na+ as the charge balancing ion to more accurately simulate the experiment and get a model that runs. Note that if you remove the pH stat, using Cl- for charge balance works just fine. The other (smaller) issue appears to be the value for the rate constant (or rather, the product of the rate constant, Pyrite's surface area, and any promoting/ inhibiting species if included in the rate law). The reaction (with fixed O2(g), charge balanced by Na+) appears to reach completion extremely quickly (about 8 minutes). I don't know how quickly the reaction proceeded in the experiment, but if I assume that 24 h was chosen for the length of the simulation because that's how long it took the Pyrite to completely dissolve, then a smaller rate constant would be more reasonable. You should check to make sure the units are correct for your kinetic parameters, and whether any promoting/ inhibiting species are supposed to be included. Hope this helps, Brian Farrell Aqueous Solutions LLC

Hello, I'm trying to look at your script, but I notice a few issues/ omissions in the script. What unit are you using to constrain the mass of Pyrite? The time units of your simulation were not saved correctly (it says hou in your script). Perhaps GWB isn't saving your script correctly. Which version are you using? Thanks, Brian Farrell Aqueous Solutions LLC

Hi Zach, If you do not specify redox state, SpecE8 will not consider any of the redox species (redox species are basis species in alternative oxidation states). Section 2.4 (Redox couples) of the GWB Essentials Guide lists the oxidation state of all basis and redox species. In thermo.dat, Fe++ and SO4-- are the basis species, and Fe+++ and HS- are the redox species. Fe++ is reduced, and SO4-- oxidized, so there is no assumption about water being fully oxidized or fully reduced. By omitting Eh, pe, O2(aq), etc., you are instructing SpecE8 to only consider species in the same oxidation state as the basis species (Fe as Fe(II) and S as S(VI)). No Hematite can form, nor will H2S(g), for example. Omitting oxidation state is similar to assuming redox disequilibrium for all couples, except you are only constraining one of the couples. The fugacity is in effect the partial pressure in atm. Hope this helps, Brian

Hi Zach, If you're just calculating things like SI within GSS, SpecE8 handles the actual calculations. You can also launch SpecE8 from GSS for a more complete analysis (for example, SI of every possible mineral, not just what you specify, etc.) Actually launching SpecE8 gives you a little more flexibility in constraining your system, as you can swap equilibrium minerals, gases, or activity ratios (like SO42-/ HS- or Fe+++/ Fe++) into the basis when you have missing analytical data. Redox state is an important variable in speciation calculations. Without any mention of redox state in your input, all iron is assumed to be Fe(II). You might try adding Eh to your spreadsheet (or O2(aq)) and just rerun the simulation with a range of oxidation states. If your water samples comes from deep below the surface, then it's probably a good bet that the O2(g) fugacity is lower than a water sample in equilibrium with the atmosphere. This of course depends on how long it's been since the water was recharged into the subsurface and what sort of reductants (and catalysts) are present in the water or along the flowpath. Cheers, Brian

Hi Dimitri, We try to limit changes to the datasets that we distribute with GWB, especially the default thermo.dat, so as not to affect our users' model outputs. The thermo.com.V8.R6+.dat dataset (distributed with GWB) is based on a later release of the LLNL dataset and includes many organic species. Perhaps other users on the forum will have more knowledge of databases with organic species. Regards, Brian Farrell Aqueous Solutions LLC

Hi Zach, Depending on your needs, you have a few options. You can create a User defined analyte for Ti within GSS. By entering the molecular weight and ionic charge of the Ti species you choose, you'll be able to perform simple operations like unit conversions. See section 3.3.4 (User defined analytes) of the GWB Essentials Guide. For more advanced analyses, like calculating the distribution of Ti species in solution or the saturation state of Ti minerals, you'll need to make a custom thermo dataset with Ti. The Thermo dataset Appendix to the GWB Reference Manual has instructions for adding species to thermo datasets. You can also try some of the other datasets included with GWB, to see if they have the species and minerals which might be important in your system. Hope this helps, Brian Farrell Aqueous Solutions LLC

Hi, I moved your post from the archive of old posts to the main GWB page (for new posts). I'm not exactly sure what you're asking. It doesn't look like Enargite is included in any of the default databases distributed with GWB, but it would be easy enough to add it according to the procedure in the Appendix to the GWB Reference Manual. As for whether Act2 (and the other GWB programs) account for Enargite, all minerals, species, and gases which can be created from the current basis set will be considered. In an Act2 diagram, however, only the most stable species and minerals will end up being plotted. Hope this helps, Brian Farrell Aqueous Solutions LLC

Hi Zach, Are you trying to launch SpecE8 or React from GSS? It sounds like in GSS you have Fe++ in mg/l (as Fe). The (as __) designation does not refer to oxidation state (or the lack of one, rather) but is useful for defining the concentration of compounds like SO4-- or SiO2 when analytical concentration is reported as the mass of the element S or Si, but not the molecule as a whole. For basis species like Fe++ the (as Fe) designation is not necessary, and SpecE8 does not like this. You should use the default setting (as Fe++). Making this change will allow you to launch SpecE8, but you'll notice that only ferrous iron species are loaded, since there is no oxygen in the Basis from which to form ferric iron species. Do you have any measure of redox state like DO or Eh? Can you assume an O2(g) fugacity corresponding to equilibrium with the atmosphere? Equilibrium with a mineral? Perhaps if you have measures of SO4-- and HS- you can swap in that ratio for O2(aq)? You should check out the Redox Couples section of the GWB Essentials Guide, or consult Chapter 7 of the Geochemical and Biogeochemical Reaction Modeling textbook. Hope this helps. Brian Farrell Aqueous Solutions LLC

Hi, I'm taking a look at your script but I don't see the amount of Quartz mentioned in the Initial system. It also looks like you're using a custom thermo dataset. Would you mind posting that or sending it to support@gwb.com? You might be interested in this earlier forum discussion about gas fugacities. Thanks, Brian Farrell Aqueous Solutions LLC

Hi, I don't know too much about the Ag-Cl system specifically, but perhaps you are expecting a higher degree of complexation in your fluid? In general, the ionic strength is a good indicator of whether fluid components like Ag+ and Cl- will be present as free ions or associated as ion pairs/ complexes. Your fluid is very dilute, so it would make sense that the Ag+ and Cl- would be present almost entirely as free ions. In a system with more Cl-, a larger percentage of the Ag+ will be present as complexes. Perhaps you should compare the log K for the reaction AgCl = Ag+ + Cl- in the databases distributed with GWB and in the literature. Another thing to keep in mind, for future reference, is that SpecE8 does not enforce charge balance by default. Adding two components (with different molecular weights) of 1 mg/kg each produces a fluid that cannot exist. For rough calculations this may be fine, of course, but it is something to consider. Hope this helps, Brian Farrell Aqueous Solutions LLC

Hi, A simpler solution would be to use React to titrate K-feldspar into your solution as a simple reactant, rather than as a kinetic mineral. Since you want pure water, start with an initial system with very small concentrations of K+, Al+++, and SiO2(aq), and a pH of 7. Then add K-feldspar to your system (Reactants pane: Add - Simple - Mineral...). Since the dilute solution is initially undersaturated with respect to K-feldspar, it will dissolve. Once enough dissolves (and other saturated minerals form) to the point where K-feldspar is in equilibrium, the mineral will begin to accumulate without further dissolution. Keep in mind that the pH, [K+], [Al+++], and [siO2] of your fluid are not determined solely by equilibrium with K-feldspar. In this example, equilibrium with K-feldspar, Muscovite, and Quartz do not even fully constrain the system - they fix the activity ratio of K+/H+. You should take a look at Chapters 11.3.1 and Chapter 13 in Craig Bethke's Geochemical and Biogeochemical Reaction Modeling text. Hope this helps, Brian Farrell Aqueous Solutions LLC

Hi Maki, I would like to spend some more time looking at your problem, but here a few things to consider right away. The second script is much closer to what is needed for a fully constrained model. Because you have Pyrite in your model, you need to include Fe++ and SO4-- in your Initial system and Inlet fluid (in order to form the Pyrite). As for charge balance, people commonly add both Na+ and Cl- (to balance each other initially) in a concentration much higher than you have here, but not so high as to have a large effect on activity coefficients (by increasing ionic strength). If you make these changes you'll get a simulation that runs (and has lower pH near the inlet), but it could still use some work. You might experiment with swapping minerals into the Initial system (i.e. Pyrite or Hematite) rather than just assuming a very small concentration of Fe++, for example. Hope this helps, Brian

Hi, It looks like your initial step size (set to the default value) is the problem. Oftentimes the initial stages of a reaction process see the most change. If the steps taken by the program are too big then very small differences in chemistry between 37 C and 38 C end up having a large effect on the final solution. If you follow output in the Results pane (Run pane in older versions), you'll see that the solution at 38 C is much "easier" (fewer iterations per step, fewer swaps) than at 37 C. If you lower the step size delxi, however, you'll see that the results at 37 C and 38 C begin to look more alike. Try plotting the minerals formed (and their saturation state) vs. Reaction progress (or mass reacted) to see how step size influences the solution. Since you're interested in CO2(aq) concentration, try plotting that too. What is initially a blocky solution at 37 C begins to look more like the smooth curve at 38 C when you use smaller step sizes. I would recommend you look into the delxi and dx_init variables in the GWB User's Guides. You might try uniform small steps, or small initial steps that get bigger as the reaction proceeds (you can change the step size linearly or logarithmically). Hope this helps, Brian Farrell Aqueous Solutions LLC

Hi Maki, Could you please post your script (.x1t file) so people can take a look? It's always a good idea to start with a simple system and add complexity as you go. Starting with a reaction path model (mixing two fluids) also helps quite a bit. I would use the pickup command in React to model mixing of an initial and inlet fluid. Setting up this system may help you with constraining your reactive transport simulation. Hope this helps, Brian Farrell Aqueous Solutions LLC

Dear GWB users, We are pleased to announce a major maintenance release, GWB 9.0.1. Update from 9.0 to 9.0.1 at no charge to get great new features, install a faster 64 bit version, elect to get automatic software updates, and fix all known issues. Among other things, you’ll be able to set the colors of individual lines in X-Y plots, and represent TDS in Piper, Durov, and ternary diagrams as circles of varying radius. Regards, Brian Farrell Aqueous Solutions LLC