Jia Wang

Hello Yuhan, Sorry for the delay in getting back to you. What release version of the software you are using? While it took a bit of time to complete the simulation, I did not encounter the too large residual error or the progress being stuck error. To start troubleshooting, I would recommend you using the the 'explain steps' and the 'Follow Output' options. By turning on 'explain steps', the GWB apps will report the limiting factor for the size of time steps over the course of the simulation (e.g. intensity of kinetic reaction, user set maximum steps, etc) . To enable 'explain steps', you can go to Config --> Stepping and select the check box for explain steps. Then to see the limiting factor reported by explain steps, make sure you also check the 'Follow Output' option on the Results pane too. You might also want to shorten your run time, maybe to just 1000 years, to check if your model is performing the calculations that you are expecting. Once you confirm that the model is setup correctly for the reactions you are expecting, then extend the simulation time to what you need. I also noticed that your model have a central row of nodes in which porosity is set to 1 and this might be causing issues with your simulation. Can you explain what you're trying to do in this model? Perhaps a 1D dual porosity model might suite your needs and would require less computational power than X2t. Hope this helps, Jia Wang

Hello Kgaugelo, When you create a new GSS spreadsheet, a set of analytes are preloaded onto the spreadsheet and SO4-- should be one of them. In the case that an analyte is added to the spreadsheet, it will not be available to be added again. If SO4-- is not added to the spreadsheet already, you may want to check if the species is available in the thermo database you are using. You can view the thermo file using TEdit by going to 'File' --> 'View' --> select the thermo file with the extension .tdat. Please refer to section 3 Using GSS in the GWB Essentials User's Guide for more information and example. You can open the user's guide by pressing F1 when you have a GSS spreadsheet open or from the GWB dashboard under the Doc's pane. If you would like to have someone to take a closer look, please attach your GSS file. Hope this helps, Jia Wang

Hello Dirk, Glad to hear you were able to resolve the issue. Best regards, Jia Wang

Hi Dirk, It sounds like there might be a problem with your configuration file(s). Can you try creating a new folder (for example, make a GWB test folder on the desktop) and set that to be the working directory in X1t (File --> Working Directory --> select the new folder you just created), rerun your model, then see if you can open Xtplot. Alternatively, you can search for the config file(s) in your current working directory (.xtc extensions for Xtplot config files) and delete them, then rerun your model and try to plot. If that doesn't help, can you please attach a screen shot of the error message you receive when you try to plot? This will help us better assist you. Best regards, Jia Wang

Hello Abelo, GSS uses SpecE8 to calculate the pH and Eh of the system. Unfortunately, there’s not a set equation to calculate these values. If you would like more information on the calculations and the methods used in SpecE8, please refer to the Geochemical and Biogeochemical Reaction Modeling text. Best regards, Jia Wang

Hello Dirk, You can set up sorption reactions by loading in a surface dataset. The dataset holds information needed to perform sorption reactions in your system. Depending on the sorption model you choose, your surface data will consist of slightly different parameters. Very likely, you would need to edit the surface datasets distributed with The GWB specifically to your system. I would recommend you create a duplicate of a surface dataset distributed with The GWB (e.g. IonEx.sdat or FeOH.sdat) and make changes using TEdit. For more information on sorption in the GWB, please refer to section 2.5 Sorption onto mineral surfaces in the GWB Essentials Guide. The surface data files are distributed in a subfolder named ‘Gtdata’ where you installed the software on your computer. It sounds like the ‘flush model’ feature might be what you need to model your experiment. When you enable a flush model, React displaces fluid from the equilibrium system with unreacted fluid. At the start of a simulation, React will equilibrate the fluid composition in your basis pane before any reactions take place. I would recommend you setup the model with the local groundwater composition in the basis pane and then enter the contaminated fluid composition in the Reactant pane. For more information on flush model, please refer to section 3.3 Flush model of the GWB Reaction Modeling User Guide. Hope this helps, Jia Wang

Hi Ulagai, I am glad you are back up and running. Best regards, Jia Wang

Hello Usman, Here are a couple of suggestions that might help. I think you should consider using the SpecE8 app to calculate mineral saturation indices for your fluid. You can input your geochemical data for each of your fluid into the basis pane in SpecE8 and allow it to perform equilibrium calculation. In the Result pane, you can open and view the output file to see a list of mineral saturation indices. For more information and example, please refer to section 7.2 Equilibrium models in the GWB Essentials Guide. Alternatively, you can also calculate mineral saturation for all your fluid at once using a GSS spreadsheet. To do so, you would need to enter your geochemical data into a GSS spreadsheet and select 'Calculate with SpecE8' under '+analyte'. For more information, please refer to section 3.2.5 Calculating analytes in the GWB Essentials Guide. You can also display your data on the Activity diagram you created by using 'Scatter data'. For more information and example, please refer to section 5.6 Scatter data in the Essentials GWB guide. Hope this helps, Jia Wang

Hello Ulagai, I have manually reset Zhanna's activation code and she can try to activate on her computer again. In the future, please do not post activation code(s) in forum post. You can send us the information at support@gwb.com if needed. Best regards, Jia Wang

Hello Usman, To create an Activity-Activity diagram in Act2, you will need to know what the predominant species in your system you wish to diagram and the species for the x and y axes. The predominant species is selected for diagramming under ‘diagram species’ and you would need to enter its activity. For example, to make a redox-pH diagram for iron, you would select Fe++ as the diagram species and then on the x and y axis, select the activity for O2(aq) and pH respectively. The diagram will then show you the predominant species of iron base on the pH and activity of O2(aq). I am not exactly sure what you mean by Fe2+ V activity of O2-, can you clarify on the predominant species you wish to diagram for in Act2? There are a couple of places with good resources to help you get started. Please refer to section 5 Using Act2 in the GWB Essentials Guide for more information regarding calculations and examples. The example I mentioned above is demonstrated in detail in the Stability diagrams lesson at the GWB Academy. Please attach your input file and thermo database file if you want someone to take a further look. Best regards, Jia Wang

Hello Rob, Thank you for the files. The issue here seems having multiple sample entries with same Sample ID. GSS expects each sample to have a unique Sample ID when entered into the spreadsheet. Perhaps you can add a unique identifier to your samples from different dates in the sample ID? Best regards, Jia Wang

Hi Rob, Can you attach a screenshot of your Ternary plot and attach the .xtp file so someone can take a closer look? Thanks, Jia Wang

Hello Rob, You would select samples to plot in the sample pane of your plot of choice. For example, if you're plotting a Piper diagram, you would double click on the center of diagram once it opens from GSS and select the Samples pane. You can select the samples you want to plot by holding down the 'Crtl' button while clicking. Please refer to section 8 Gtplot in the GWB Essentials Guide for more information. Best regards, Jia Wang

Hello Rob, To select samples to display on your Ternary diagram, double click on the diagram to bring up Parameters for Ternary Diagram dialog. Click on the Samples pane and select samples from the available list. You can press 'Crtl' button while clicking to select multiple samples or click on the 'Select All' button if you want to display all samples. If needed, you can add samples to the "Add" or "Add all" button from the Ignore list to the Available list. Please see section 8 Gtplot in the GWB Essentials User Guide for more information. Best regards, Jia Wang

Hello Kevin, Act2 makes calculations for analytical solutions to draw equilibrium lines to show predominant species of the highest activity. Therefore, you should be using the activity of the predominant Fe species in your system for Act2 calculation. Perhaps you might also be interested in Phase2 if you are aiming to investigate a more complex set of reactions? Phase2 draws diagrams that may look similar to Act2 in many cases, but the calculation is a complete solution to the equations describing the distribution of mass, just like in SpecE8 and React. You constrain a fluid in terms of concentration, rather than activity and set up reaction pathways, like in React, along the x and y axis. Please visit the Phase2 webpage for information. Best regards, Jia Wang

Hello Anita, Thank you for the additional information. In Ogata 1970, it was stated that the concentration at x = 0 is maintained at concentration C0 through time to arrive at the analytical solution used in your textbook. Please see example 1 and 2 in the paper for details. Furthermore, the problem prompt from your textbook does not state when the leachate stopped leaking into your system. To accurately treat a solute slug problem, like you described above, you would need that information. Therefore, I think you should approach this problem as if the leachate is leaking continuously for the 1-year duration that you are modeling. A couple of other suggestions that might helpful here. You might want to consider extending the length of your domain by a small distance, maybe by 5 or 10 meters. Dispersion is not evaluated at the boundary condition and therefore introduce a bit of error to the node at the boundary. I would suggest you extend your domain length and look at the concentration at the nearest node to 15 meters. It might also be helpful to increase the number of nodes in your domain. With numerical modeling, there's a certain amount of numerical dispersion associated with grid sizes. Increasing the number of nodes would generally help reduce that numerical dispersion. In your case, I doubled the number of nodes to 300 and it helped. However, at the end of the day, model results will differ slightly from your analytical solution due to the estimations made in the numerical method and also consideration of additional variables that the analytical solution might not. For example, the GWB also considers variables like density changes with varying solute concentration which is not considered in the analytical solution. Hope this helps, Jia Wang

Hello Anita, If you set up your system to have the contaminant flowing into the domain for an interval period of 1 minute, the concentration of Cl- you will see in the system is going to be much lowered than your expected results. To check, you can set the endpoint of your simulation to 10 minutes (before the simulation fails) and see that the maximum concentration of Cl- by plotting the results. You can plot X-position (on X Axis) vs. Cl- in fluid (mg/l) (on Y Axis) and cycle through the time level in the XY configuration dialog. You will see that the concentration of Cl- in your system is only ever as high as 2.18 mg/l. If you are expecting to see a pulse of contaminant in your domain with the Cl- concentration of 725 mg/l, you will need to have a longer interval where the contaminant is flowing into the system. I tried increasing the contaminant interval to 40 days and was able to arrive at 30 mg/l of Cl- at 15 meters from the leaking point. The error you are seeing are associated with stability issues with in your model. You can try to setting your dx_init, initial time step, to a small value (like 1e-5) to help with stability. To change dx_init, go to 'Config' -> 'Stepping' and you will see an option to set a dx_init value. When I tried using 1e-5 for the initial time step, the model ran to completion but again, I am seeing much lower concentration at 15 m than the answer you expected. Can you perhaps clarify what you mean by instantaneous leaking of the contaminant? And is the 30 mg/l of Cl- an analytical solution? Best regards, Jia Wang

Hello Twq, I took a quick look at your script and noticed that all your concentrations besides AsO4--- are extremely low. If you are trying to ask the model to charge balance with such low concentration values concentrations, it might lead to stability issues and I think that is the case here. If you want to preserve charge balance, you might want to set a higher background electrolyte concentration, such as 1 or 0.1 molal for Na+. Alternatively, you can also turn off charge balance. To do so, right click on the unit of a basis species and select 'Do not balance'. You might also want to double check your chemical analysis to make sure your initial system concentrations are correct. I see that you swapped in AsO4--- for As(OH)4- and in doing so, the program calculates the species of other As oxidation states base on redox equilibrium. However, you can disable this by deoupling AsO4--- and adding it as a basis species. By decoupling the redox couple, you can constrained AsO4--- independently in your calculations. You might want to try this if you are interested in the speciation of AsO4--- only. Please refer to section 2.4 Redox Equilibrium for more information on decoupling. In the future, you can also check the equilibrium state of your initial fluid before any reaction path takes place by doing a 'Go initial' run ("Run" --> "Go initial"). This is a useful method to check your basis pane setup before adding in complexities of reactants. If the equilibrated fluid from the initial pane looks correct to you, then issues that occur will likely be due to the reactions from the reaction pathway. Hope this helps, Jia Wang

Hello Dirk, I am glad you got your model up and running. It sounds like your convergence issues might be linked to your model running out of minerals. When you run out of mineral(s) or some other reactant in your system, the model will take smaller time steps to try to calculate the numerical solution, which might explain why you received the error “Step is constrained by rate of increase in length of reaction step at node 0”. In this case, you were trying to sorb solutes onto Fe(OH)3 when it is running out, which is probably why your model couldn’t converge. However, I can’t be sure unless I take a look at your input file but that would be my guess. If you would like someone to help take a closer look, please attach your input and thermo file. Hope this helps, Jia Wang

Hello Rosalyn, Unfortunately, mV is not one of the default available units for Eh in Act2. You can, however, easily make the changes you mentioned above by editing the image in Powerpoint. To do so, you can copy(‘Edit’ -> Copy as ->Enhanced Metafile) and paste the image onto a Powerpoint slide. On your slide, you can right click on the image and ungroup the file and edit the values on the y-axis and change the label to mV. Similarly, you can alter the legend as well to erase any of the sample names and markers you do not want to display. Hope this helps, Jia Wang

Hello Yoshio, Thank you for your question. To calculate Kd' I would use the original sorption isotherm, S = Kd*C, where the sorbed concentration (mole/g dry sediment) is equal to the product of the Kd(cm3/g) and concentration of the free ion (mole/cm3). I would first convert the concentration of dissolved Pb2+ to mole/cm3 which is approximately 10^-8 mole/cm3. Then using the Kd and concentration of dissolved Pb2+, calculate the concentration of Pb sorbed: S = 0.16 [cm3/g] * 10^-8 [mole/cm3] = 1.6 * 10 ^-9 mole of Pb2+ sorbed per gram of sediment. The Kd' term accounts for the activity instead of the concentration. To do so you, you will need to multiply the activity coefficient by the concentration of free ions in solution. Using the activity coefficient (0.66), fraction of free ions in the fluid (0.8), and the concentration of dissolved Pb2+ (~10^-5 molal), you can calculate Kd' like so: 1.6*10^-9 = Kd' * (0.66*0.8*10^-5) where the Kd' is calculated to be approximately 0.0003 mol/g. Hope this helps, Jia Wang

Hello Ulagai, You can enter basis species into the GSS spreadsheet. For your specify question though, HCO3- and CO3-- are both carbonate species. When you enter HCO3- into the database, you are effectively including the sum of the thermodynamic component (e.g. CO2(aq), CO3--, NaHCO3-, etc). If you wish to enter the concentration of HCO3- without the additional species, you will need to enter the species as a free constraint. To do so, you can right click on the unit for HCO3- and select "free". I would not recommend moving CO3-- from aqueous to basis species since components chosen as a basis species must be linearly independent from one another. In this case, HCO3- is the basis species and CO3-- is an aqueous species can be written in terms of HCO3- and H+. You can alternatively add CO3-- as a user defined analyte if you simply want to keep track of how much CO3-- is in your system. But keep in mind, you cannot use user defined analytes in GWB apps for simulations. For more information on how to create your own user analyte, please refer to section 3.3 in the GWB Essentials User guide. Hope this helps, Jia Wang

Hello Ulagai, When you create a new species in the thermo database, in this case H2SiO4, you will need to provide at least one Log K value at one of the 8 principal temperatures. Most commonly, the Log K value is derived at 25 degree Celsius. If you do not enter any Log K values, the GWB programs will not read in the new species you have added. Once you have successfully added in the new species, you should be able to add the species in Rxn and balance reactions. Where the temperature differ from a principal temperature, the application fits non-'500' values to a polynomial. You can expand the results in the Results pane and obtain the temperature polynomial equation the program uses to estimate LogKs with the principal temperature range. While the GWB can extrapolate beyond this range in calculations using the 'extrapolate' option, I would advise to do so cautiously. Please note that starting with GWB14, the thermo database can alternatively carry temperature expansions for log Ks for a range of valid temperature. The method above is for T-table logK approximation for older formatted GWB datasets. Please refer to section 9 in the GWB Essentials Users guide for more information regarding editing thermo datasets in TEdit. Hope this helps, Jia Wang

Hello Anita, I took a quick look at your input file and here are a couple of suggestions to help you get started. It seems like you are trying to model a continuously leaking point source contamination for 1 year. However, I notice that in your Intervals pane, you are only setting a one day reaction interval for the 'contaminated' fluid to enter your system at the inlet and the remaining time flushing the system with dilute fluid. If the goal is to simulate a continuously leaking source of contamination at the inlet, then you should remove the second reaction interval from your simulation and allow for the contaminated fluid flow into the system for a full year. To quickly remove any reaction interval period in your Intervals pane, you can simply click to select it and then click the delete button. I deleted the reaction interval that set the inlet fluid as the dilute fluid (named 'fluid 2') and that allow the model to run to completion. For more information on setting boundary conditions and reaction intervals, please refer to section 2.10 and 2.9 in the Reactive Transport User's Guide. You might also be interested in looking at X1t examples listed in section 3.5. The input file corresponding to each example in section 3.5 is available in the GWB installation subdirectory 'Script'. Hope this helps, Jia Wang

Hello Ulagai, On another thought, I think you will find Rxn useful. You can calculate the equilibrium equation for dolomite (CaMg(CO3)2) using Rxn and make the activity-activity plot manually. To do so, you would open up Rxn and balance the reaction for Dolomite. When you select dolomite, Rxn will automatically balance dolomite in terms of the original basis species, which is Ca++, Mg++, H+, and HCO3-. You can have Rxn write the equilibrium equation in terms of CO3-- by swapping it with HCO3-. If you wish, you can then enter the activity value for CO3-- and have the equation be simplified and solve for log[Mg++] + log[Ca++], which equivalent to the y-axis of the plot you attached. Please refer to section 4.2 Calculating equilibrium equations in the GWB Essential guide for more information and examples. Hope this helps, Jia