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Brian Farrell

Geochemist's Workbench
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Everything posted by Brian Farrell

  1. Hi Thomas, In the Al solubility example, you must have the mineral swapped into the Basis before its activity can be set. As for what you are attempting to do with your Gold example, I believe this is not possible at the moment, at least without altering log K values. This limited ability to specify mineral activity might be useful to some users, but it is not a true solid solution model in any way. We will consider your ideas along with those of other users as we begin the next stages of development. Sorry for any confusion this may have caused. Sincerely, Brian P.S. Are you using the alter command to change your log K values, or are you manually changing the thermo datasets and reloading them every time? The alter command provides a quick way to search through minerals, gases, and species and alter log Ks in your run without permanently changing the dataset (though you can save your altered settings for future runs). Hope this helps.
  2. Hi, Sure you can edit the database if you feel changes are warrented. Take a look at the Appendix to the GWB Reference Manual for info on editing thermo datasets. You might remove minerals or species which appear in the high pH region of your plots, or change the stability (log K value) of Ettringite. You can also do this from within GWB in a less permanent fashion, using the Suppress and Alter commands. A few things to consider before doing this, though. Do other minerals appear on your plot? If not, make sure that the field for "minerals" is checked in the View dialog box. Also make sure that Ettringite is not undersaturated in your system, and that it is indeed the most stable Al species. Hope this helps, Brian
  3. Hi Thomas, You have to set the activity of a mineral like Quartz using the GUI, or with the command "activity Quartz = 0.4," for example. As I mentioned above, it is not possible at this time to save a script with a nonunity mineral activity, so I can't post the exact script. Give that a shot in your examples. You might have an issue with your Gold example, however, depending on how you want to set up your problem. I believe for a solubility diagram, the main species must match one of the axes (you can't have Au(s) and Au+ both as the Gold component) and you can't make mineral activity one of the axes. Let me know how that works for you. Hope to help, Brian
  4. Hi FER, It sounds like you are either working from a restricted directory (like c:\program files\gwb) or the directory was changed when you loaded the hmw dataset. Type the command 'cd' (no quotess) to see which directory you are in, and 'chdir "..."' to change your directory (i.e. chdir "c:\users\bfarrell"). Typing 'chdir ~' will take you to your home directory, as defined by your operating system. You can also use the GUI by going to File - Working Directory. Most people work from their user directory - this will give you write permission and should fix your problem. As for running the patch, when I click on the Download link I get the option to either run or save the patch. The easiest thing to do is select run, but if that doesn't come up, you can try right-clicking and looking for "Save target as" or something to that effect (save to the Desktop, perhaps). Then you should be able to double-click on that and run. If you can't get the patch to work, please let me know what internet browser and version you are using, as well as the version of GWB you are running. Hope this helps, Brian Farrell Aqueous Solutions LLC
  5. Hi, The method Thomas mentioned will work for any GWB program. Act2, however, does have some ability to handle nonunity mineral activities much more easily. I've attached two plots which demonstrate this. The first plot is an example taken from the GWB Essentials Guide and the second is the same example with Quartz activity set to 0.4. Lowering the activity of Quartz, the Kaolinite field decreases (hard to tell - take a look at the printed output) and eventually Gibbsite replaces Kaolinite. Unfortunately at this time you cannot save nonunity mineral activities in your scripts, but you can easily edit your input files before running. Hope this helps, Brian Solubility.ac2
  6. Hi Jeff, Assuming you've equilibrated 1kg of a fluid, picked it up and made it a reactant, and are mixing that into your other fluid, just add the line reactants times 10, for example, to the command line (or from the GUI), set the end time to 10 minutes, perhaps, and the fluid will be added continuously at a rate of 1 kg per minute. Just specify a kinetic rate law for Fe++ oxidation, and you should be all set. The program will move toward overall equilibrium with each step of the reaction path, incrementally adding your fluid, evaluating your kinetic rate law for Fe++, and attaining equilibrium for the rest of the species at each step. Hope this helps, Brian
  7. Hi, A few things. Your assumption of an activity coefficient close to 0.5 for O2(aq) is not the best, although in the grand scheme of where that plots on your diagram (on a log scale), it is insignificant. Activity coefficients for electrically neutral, nonpolar species like O2(aq) actually go above 1 with incresing salinity, according to the "B-dot" activity model used within GWB programs. You may be familiar with the "salting out" effect in which gas solubility decreases with increasing salinity. As for the range of log a O2(aq) values, keep in mind that any redox reaction can be written in terms of O2, whether or not it is actually involved in the reaction, or even whether there is actually O2 present at all. It is simply a measure of the redox state of the system, useful in understanding equilibrium models of real systems, and not necessarily a measure of the true dissolved O2 concentration. I assume by greater than -30 you mean more negative (more reducing, less oxygen, etc.). This is possible, either in terms of actual concentration being very low, or in a more theoretical thermodynamic context in which the environment is very reducing. You should look into Chapter 8 of Craig Bethke's Geochemical and Biogeochemical Reaction Modeling text for information about calculation of activity coefficients, and any thermodynamics or geochemistry text for a discussion of oxygen activity/fugacity and redox state. Chapter 12 in Greg Anderson's Thermodynamics of Natural Systems, for example, has some explantations you may find useful. Let me know if I haven't answered your questions. Hope this helps, Brian Farrell Aqueuos Solutions
  8. Hi Jeff, It's probably a good idea to start with an equilibrium model, as you are doing, and then add complexity (like kinetic rate laws) as you gain more understanding of your system. As for "dumping" minerals to prevent them from redissolving, there are several reaction configurations within React that may prove useful. There is in fact a "dump" configuration, but I think the flow-through option would be best for the problem you are describing. From Craig Bethke's Geochemical and Biogeochemical Reaction Modeling text: "In a flow-through reaction path, the model isolates from the system minerals that form over the course of the calculation, preventing them from reacting further... In the dump option, once the equilibrium state of the initial system is determined, the minerals in the system are jettisoned. The minerals present in the initial system, then, are not available over the course of the reaction path. The dump option differs from the flow-through model in that while the minerals present in the initial system are prevented from back-reacting, those that precipitate over the reaction path are not." You should take a look at Section 2.2.5 of GBRM or Chapter 3 of the GWB Reaction Modeling Guide (Release 8) for more discussion and examples. Hope this helps, Brian Farrell Aqueous Solutions
  9. Hi, Act2 does not have any capabilities for calculations involving isotopes. If you know the values for these isopleths you could always add scatter data to your plot, however. As for your solubility contours, you cannot make these types of diagrams directly in Act2, but they are easy to assemble in a program like Powerpoint by overlaying several diagrams. You'll need to create several plots (each with a different activity for your main species, perhaps), copy them as enhanced metafiles, then paste into Powerpoint. You can then ungroup each image, and copy and paste into a single plot. Hope this helps, Brian Farrell Aqueous Solutions
  10. Hi Mathew, Glad that worked out. You can keep it as a reactant if that works, or try adding a fixed CH4(g) fugacity from the Reactants pane. Alternatively, you could decouple the Methane(aq)/HCO3- redox pair and add Methane to the Initial pane. If you think that the Methane will not react with other carbon species, then just constrain Methane. If you think methane is reacting with other carbon (slow enough to not assume equilibrium, but fast enought that it matters), you might set a kinetic rate law for Methane generation or production on the Reactants pane, in addition to setting its initial value from the Initial pane. Hope that helps, Brian
  11. Hi Mathew, It should be coming out very soon hopefully, perhaps within a few weeks. Brian
  12. Hi Mathew, I think there are some issues with the GUI in GWB8 that aren't allowing you to select volume% as a unit (GWB9 has a brand new GUI that is much improved). You can enter the volume% directly from the Command pane, however. Use the volume% or vol% commands (i.e. Quartz = 20 vol%). You can make the mineral volumes and porosity add up to 100, or less than 100 and the remainder will be taken up by "inert volume." Rock mass includes minerals and the "inert volume." If you look at the variable mass H2O or Solution mass (set to wt %) you will find that this equals 100% I think. The rock mass, then, is 30 times the mass of the water. In your case, rock volume is 92% and solution volume (porosity) is 8%. This means that the rock's volume is 11.5 times greater than that of the water. Taking a density value of 2.65 g/cm3, the rock mass is approximately 30 times that of water. So I think that is where the rock mass = 3000% comes from. You might be getting a lot of inert volume if the values you entered for each minerals wt% (or mass, volume, etc.) don't match up with the porosity and amount of water. Using mineral volume% should help to clear that up. The rest of your results are probably pretty close to where they should be, because the mass of equilibrium minerals only matters in the case of sorption, if a mineral is consumed by some bufering reaction, perhaps, or if the permeability is tied to the mineral volume. Let me know how that works out, Brian
  13. Hi Duc, All you need to do is calculate species activity (either go to Data - Calculate..., or + analyte - Calculate...), then right-click the cell in your spreadsheet where it says "activity" and select "log." Hope to help, Brian Farrell Aqueous Solutions
  14. Hi Mathew, It sounded from your original post that you want these minerals to make up the rock composition of your domain (ie the 92% that is not water). If this is the case, those minerals should be swapped into the Initial pane, not added in as Reactants. Give this a shot. Make sure to take a look at the User's Guide for info on setting up your domain. See section 2.8 (Initial conditions) and 2.12 (Porosity evolution) from The Reactive Transport Modeling Guide (Release 8). Hope this helps, Brian
  15. Hi Mathew, Although you can set the mass of equilibrium minerals in X1t and X2t, it is generally easier to set the volume% instead. This way, if you change the dimensions or nodal block spacing of your domain you won't have to adjust the amount of minerals in your system. I have a feeling the problem may be that your input is not the same as what you are conceptualizing. Could you please post a script so I can take a closer look at your problem? Hope to help, Brian Farrell Aqueous Solutions
  16. Hi Elisabeth, Your problem was that you didn't put the range of values for each sample in a single cell. I've made you a GSS spreadsheet that will show you how to enter in your data. You'll want a row for each analyte (pH and Temperature) and columns for each sample. You can enter in three values in a single cell, separated by a vertical bar (|), to represent the data point itself and the ends of the error bar. If you enter in two values separated by a double bar (||) you will get just the error bar. Of course, entering a single value per cell will give you a standard data point. Hope this helps, Brian Nov pH T with ST DEV.gss
  17. Hi Elisabeth, Can you post your GSS and React files so I can take a look at your problem? Thanks, Brian
  18. Hi Elisabeth, All you need to do to set errors bars is enter a triplet of values separated by vertical bars in each cell of your GSS spreadsheet. For pH, put in 6.3|6.5|6.7, for example, to create error bars of standard deviation 0.2 about a measured pH value of 6.5. Unfortunately you cannot just enter a standard deviation value once and have it apply for all your datapoints. This may be a bit tedious, but that is how the program is set up right now. Hope this helps, Brian Farrell Aqueous Solutions LLC
  19. Hi, A few things. The species listed after Subdiagram #7,8 etc. are the Basis species for that particular subdiagram. You have chosen to account for the speciation of all your complexing species. The Ca++ component, for example, appears as CaOH+ in #7 and as Portlandite in #8. This does not mean that CaOH+ or Portlandite are present in any amount, however. It simply means that any reaction within that subdiagram with Ca++ is written in terms of CaOH+ or Portlandite. If you scroll down a little bit (from Subdiagram - Basis species - Species and minerals in main system - Line equation - Main Diagram) you will find the species and minerals which actually have predominance over the subdiagram, and will appear in the main diagram. Keep in mind that Act2 generates predominance diagrams, meaning only the most stable mineral or species will appear. Furthermore, you are diagramming the Fe system, so every mineral or species on the diagram must have Fe in it. You can use SpecE8 or React to calculate the concentrations of other aqueous species, mineral saturation, etc if that is what you are interested in. Finally, I noticed that you have decoupled several Fe and Mn redox pairs. Because you decoupled Fe+++/Fe++ and chose to diagram Fe+++ without specifying any Fe++, you have prevented Fe++ minerals and species from being considered in your diagram. You should make sure this is what you really want. Let me know if you want anything explained better. Hope this helps, Brian Farrell Aqueous Solutions LLC
  20. Hi Trevor, You can certainly assume equilibrium with an Al mineral to solve for the concentration of dissolved Al species. Just swap in your mineral (microcline) for Al+++ from the Basis pane and specify its mass (though the actual amount will not affect your results). Generally for minerals you specify a free mass. Hope this helps, Brian Farrell Aqueous Solutions LLC
  21. Hi DL, I didn't get your message. As for your question, you should decouple redox pairs when you believe your system is not in redox equilibrium (low temperature natural waters, perhaps), or when you have analytical data for the same element in several redox states. If you set Eh (or pe, f O2(g), O2(aq)) and leave Fe2+/Fe3+ coupled then the equilibrium between Fe2+/Fe3+ is determined by that Eh value. However, if you decouple Fe2+/Fe3+, then the redox equilibrium between them is set by constraining each component separately (Fe2+ and Fe3+). In this case, the system Eh has no effect on Fe speciation. If you decouple the pair and only specify Fe2+, then no Fe3+ species will form (similarly decoupling the pair and only constraining Fe3+ will prevent Fe2+ from forming), so be careful with this. You should check out Section 7.3 of the GWB Essentials Guide (Release 8) or Chapter 7 of Craig Bethke's Geochemical and Biogeochemical Reaction Modeling text for more on redox disequilibrium. Hope this helps, Brian
  22. From Craig Bethke's Geochemical and Biogeochemical Reaction Modeling text, Section 8.1.2: "The B-dot equation...is considered reasonably accurate in predicting the activities of Na+ and Cl- ions to concentrations as large as several molal, and of other species to ionic strenghts up to about 0.3 to 1 molal." You should take a look at Chapter 8 of that text, or Section 7.4 of the GWB Essentials Guide for more on the implementation of activity coefficients and activity models in GWB. As for your specific problem, I would use thermo.dat. Hope this helps, Brian
  23. Hi, For this example, I would stick with the thermo.dat dataset. Your initial solution does not have a very high ionic strength and you are only evaporating about a third of the water. Running this example, the highest ionic strength reached is about 0.05 molal, so the B-dot equation (extended form of Debye-Huckel) works just fine. Thermo.dat also has the advantage of being parameterized from 0-300 C, unlike the phrqpitz dataset, which is defined at 25 C, though it has a limited (and largely untested) provision for calculations at other temperatures. Unfortunately you cannot just add thermodynamic data for Al and Si to the phrqpitz dataset (which uses the virial activity model), without adding appropriate virial coefficients to the bottom section of the dataset. And if you are editing a database, be sure to follow the conventions outlined in the Appendix to the GWB Reference Manual. (Elements added in alphabetical order by name (Oxygen is always first, however), the list of Basis species must begin with H2O, etc.) Hope this helps, Brian Farrell Aqueous Solutions
  24. Hi DL, SpecE8 solves for the equilibrium distribution of aqueous species in a fluid and on surfaces, as well as mineral saturation state and the fugacity of dissolved gases. If you want to know how pH affects your equilibrium system, just change the pH value a small amount, rerun your SpecE8 model, and repeat again and again. This is where React makes things easy, as it is a program for modeling reaction paths. What you need to do is start with an initial system just like in SpecE8, then go to the reactants pane. You can titrate in aqueous species like HCl or NaOH (as simple reactants) to vary the pH, or you can use a sliding pH path. You will do the same thing for Fe and P (sliding paths are calculated in terms of activity, but if you're interested in concentation just add in Fe and P as simple reactants. The GWB Reaction Modeling Guide has sections on Titration paths (section 3.1 in Release 8.0) and Sliding activity and fugacity paths (3.6) with examples that should help you figure out how to set up your calculations. You might also try diagramming Fe in Act2, choosing pH and Fe or P activity as axes. This will give you a simple predominance diagram, rather than a complete analysis that you would get from a SpecE8 or React simulation. Hope this helps, Brian Farrell
  25. Hi Stefan, The Thermo Datasets Appendix to the GWB Reference Manual has a section on Virial coefficients. From section A.1.10 (Release 8), "Any omitted entries for the polynmial are treated as zero values." So it looks like you don't have to worry about manually entering zero values for these coefficients. Hope this helps, Brian Farrell Aqueous Solutions LLC
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