maki

Hi, Brian, To begin with, I’m working on the problem of ver. 10.0.9. According to your advice, I downloaded and installed the latest one. I think that it got a little faster than previous upgrade. Opening time of files is about two minutes in the case that the files are opened from both saved script and dashboard. Is it normal speed in ver. 10.0.9? The followings are the responses to your questions. Regarding the slowness in 10.0.8, is a new instance of a program like React slow to open from the Dashboard? Or is it only slow when you're trying to open a saved React script? ---> Both of them. Can you please install the latest release and send us a screenshot of the GWB Activation Utility if the program is still slow? Finally, do you have the "Show Announcements" checkbox selected on the Settings pane of the GWB dashboard? If so, does unchecking it make the GWB programs any faster to load? ---> Originally, I haven’t checked "Show Announcements" in any version. In addition, when I select the tab of “Upgrade” on dashboard in 10.0.9, it took about two minutes for opening menu, too. Thanks. Best regards, Maki

Hi, Brian, Thank you for your reply, and sorry for little information. There are two problems. First, opening time of GWB programs got longer after upgrading to 10.0.8. It took several minutes to open in any files. Then, I carried out downgrade from 10.0.8 to 10.0.6. It seems to get back to original speed to open. Second, however, “Save as...” function doesn’t work after downgrading with the message of “Error: Must specify a file to save to”. The followings are the response to your questions. Are you trying to save input files for any of the GWB programs (Rxn, Act2, SpecE8, etc.)? Or one program in particular? ---> Mainly, React, X1t, and X2t. Or by script files are you referring to script files written in the Basic language for use with the Custom Rate Law or Heterogeneity features? ---> In both case with or without referring script files. Have you experienced this problem during the entire time you've been running 10.0.6? Or has the problem only arisen recently? ---> I didn’t have this problem before. I have the problem recently after downgrading. Can you please tell me what Windows OS you're using, whether you're running the 64 bit or 32 bit installer, and any other details that may be important? ---> Windows 7 with 64 bit. Is the dashboard slow to open, or only the individual programs? ---> Both of them in 10.0.8. Calculation works well, and the problems can be avoided by making a new script without renaming in 10.0.6. If you need any other information, could you let me know? Best regards, Maki

Hi I'm using GWB, ver 10.0.6. I haven't been able to save script files by using "Save as ... " with message "Error: Must specify a file to save to", these days. I tried to save the files after renaming in new folder, which was normal way to make new calculation files, since I bought GWB software. I have no idea why it suddenly happened. In addition, I downgraded the software from the latest version to 10.0.6 because handling (ex. opening software, scripts, and so on) got much heavier than before upgrade. Could you give me any idea to handle it? Thank you for your time. Best regards, Maki

Hi Brian, Thank you for your suggestion. I'll adopt that concept. Best regards, Maki

Hi, I hope to describe the microbial reaction catalyzing decomposition of aqueous species like below. Glutamine(aq) + H2O → NH3(aq) + Glutamic_acid(aq) If I set the above reaction in the reactant pane as a microbial kinetics, calculation of equilibrium status seems to be completed in preference to kinetic reaction, and there wasn't any changes in pH, species concentrations, and so on. I am trying some calculations under the below condition, so far. I transferred the information of Glutamine(aq) from Aqueous species to Redox couples in thermodynamic database. The transfer allowed the reaction to depend on microbial kinetics by decoupling Glutamine(aq)/NH3(aq) in trial calculations. The result values seemed to be appropriate. I would like to adopt this modification of thermodynamic database if the concept is correct. I would be grateful if you would give me some suggestions. Best regards, Maki

Hi Brian, Thank you for your reply. As soon as I can, I will upgrade to ver.10. Best regards, Maki

Hi Brian, Thank you for your reply. Although I’m using ver9.0.9 of GWB, the phenomenon appears in the version. How should I handle it? Best regards, Maki

Hi I’m still using ver9 of GWB. I have sometimes encountered the display collapse in Reactants pane of X2t program. ‘Add’ button and “Delete” button spread longitudinally. The phenomenon has been inconvenient to set some parameters in Reactants pane. I, however, could find the procedure causing the collapse. When kinetic reaction of mineral with value of power as ninth reactant is set in X1t and X2t, the problem appears. I have attached the corresponding x2t file. Unless the value of power is add, the problem disappears. I have no idea whether this is my-PC-specific problem or not. In addition, I have not checked it in ver.10, yet. Could you check the procedure of the problem? If my explanation is inadequate, please let me know. Best regards, Maki Example.x2t

Hi Brian, It is useful to export the values from plots to other files (e.g. Excel sheet). On the other hand, although values of volume% could be exported, values of delta volume% could not be exported. I confirmed that the Xtplot had the title of ‘Pyrite (delta volume%)’ in the Y-axis and the XY graph certainly showed the change of delta volume%. Then I chose ‘copy as Spreadsheet (Tab delimited)’ from menu bar and pasted it on the excel sheet. The result, however, was same as ‘volume%’. I’m still using ver.9 of GWB. It would be grateful if you could check it. Thank you for your time. Best regards, Maki

Hi Brian, I’m sorry for delay to reply. Volumes of node in my calculation were set in over 100 m3, and vol% of mineral was very large in each node. Although the dissolution level of them was very small, I needed to obtain precise amount of change. The values, however, were rounded off in X2t_output and X2t_plot. They seem to be four decimal place in both linear and log scales. For the above reason, I have checked the contents of the plot file. It will be very convenient if I may be able to set the digits in X2t_output and X2t_plot. Best regards, Maki

Hi I would like to confirm the units of minerals in the text file of X2t plot. In my calculation, I set four minerals. After the calculation, the text file of X2t plot showed ‘Nmin = 4’ and four numbers below the Nmin’s line. I couldn’t find the explanation in the last paragraph of the text file. What kind of unit do their numbers have? I have no idea whether it is ‘mol/cm3’, ‘mol/bulk volume’, or ‘mol’. e.g. -------------------------------- Nmin = 4 1.4619883e-05 0.014985896 4.676259e-06 0.0055111601 -------------------------------- Do you provide the instruction manual of the text file of X2t plot? Thank you for your consideration. Best regards, Maki

Hi Brian, I have been trying the calculations of kinetic pyrite oxidation under the various conditions according to your advice. I found that the calculation was well converged by setting ‘1’ in ‘power(O2(aq))’ of Kinetic-pyrite in Reactant pane in many cases. The GWB text book says that the exponential number in rate law of kinetic mineral is empirically decided. Indeed, when I set the ‘power = 1’ as the exponent of the relating chemical concentration, reaction rate seems to be larger based on the rate law equation. For example, in pyrite oxidation, O2(aq) is easily imaged as the promoting chemical, and the rule is easy to understand. On the other hand, the calculations in Kinetic Quarts and Kinetic K-feldspar also got converged and got faster by setting “power = 1” of SiO2(aq) and K+, respectively. Their chemicals and ions are put in the right side of their dissolution equations. I think it is unlikely for the dissolution, but the calculations became to be converged. As a technique of GWB calculation, should the ‘power’ be set ‘1’ in chemicals which constitute the mineral and relating chemicals as below when a kinetic-mineral is used? e.g. Kinetic pyrite: O2(aq), Fe++, SO4-- (or only O2(aq)?) --> ‘power = 1’ Kinetic smectite: Al+++, Mg++, SiO2(aq), Fe++ --> ‘power = 1’ Thank you for your consideration. Best regards, Maki

Hi Brian, Thank you for your quick response and help. Best regards, Maki

Hi Brian, Thank you very much for the detailed explanations. I will try the calculations considering the initial equilibrium with pyrite and the fluid in the first model. As I have other cases with actual water analyses, I will apply the advised thinking process to their simulations. Does it seem to take a long time to fix the problem of imported flow fields in ver. 10? In addition, not only in the flow fields, but the other inputs (chemicals in Initial pane, kinetic parameters in Reactants, porosity in Medium and so on) also have same problems. I don’t have so much time to wait for the maintenance in my work. If possible, could you provide the temporary license of ver.9 or the temporary downgrade exe file to ver. 9, please? (I’m not sure if the latest release of ver.9 was 9.0.3 or not, but I am thankful for that you have fixed the same problem of ver.9 before.) If I should send the e-mail about this problem, please let me know that. Thank you for your kind consideration. Best regards, Maki

Hi Brian, In addition to the previous question, I have the other important inquiry. I have tried the calculation that was two dimensional analyses with same chemical composition of Pyrite_oxidation_2. Heterogeneity function in the “importing flow field” didn’t seem to work correctly again. I attached PO_2D.x2t. The calculated flow field was carried out. On the other hand, “node by node” setting and “table file” setting didn't work and the script was compulsorily shut down. Could you check the function, please? It would be great if you could also resolve this matter soon. Best regards, Maki PO_2D.x2t

Hi Brian, Thank you for your advice. Even if discharge, ion concentrations, ion compositions, and numbers of chemicals are modified, the calculations of Pyrite_oxidation_1 aren’t converged with the messages of “N-R didn’t converge ... Largest residual(s): Cl- -2.324e-11 0.0007184 7.987e-6” and so on. In comparison with Pyrite_oxidation_1 and Pyrite_oxidation_2, the only difference is whether the volume of pyrite is set in Initial pane or Reactants pane, simply. As you said, I tried to establish a fluid chemistry using SpecE8. Unfortunately, I couldn’t. If Pyrite_oxidation_2 is correct conceptually in the calculation I posted previously (O2(aq) flows into the rock containing pyrite), I will adopt it in final calculation. In that case, I expect that equilibrium status of chemical composition will be acquired by long time calculation. If my thinking process is incorrect in this case, could you point out that? Best regards, Maki

Hi Brian, I’m sorry for the delay in replying to you. I have tried the further calculations. I attached two scripts that used the thermo.com.V8.R6+.tdat. The concept of my calculation is originally that O2(aq) flows into the rock containing pyrite. While referring to sample script of ‘Infilter’, I carried out Pyrite_oxidation_1. The calculation was not converged. I have no idea how I should handle the calculation condition after the error message ‘N-R didn’t converge after 999 its.,’ appeared. Secondly, I set Pyrite_oxidation_2, which has no mineral in Initial pane and has kinetic of pyrite with 40 volume% in Reactants pane. The calculation proceeded, but I wonder that it was incorrect condition because it was different from my concept. In addition, O2 consumption was not observed. Then, I made new equation (eq.1) for representing pyrite oxidation instead of eq.1 in thermodynamic database (not attached). When I set the mineral volume in Initial pane like Pyrite_oxidation_1, the calculation didn’t converged. On the other hand, only in the case like Pyrite_oxidation_2, the calculation converged. Even if the calculation went through, I’m worried whether the second procedure is incorrect. Do you have any better idea about this problem? Thank you for your consideration. Best regards, Maki pyrite_oxidation_1.x1t pyrite_oxidation_2.x1t Infilter.x1t

Hi I have been trying to calculate kinetic pyrite oxidation. My question is as follows. When I set the kinetic pyrite oxidation in Reactants pane, which should I use “Kinetic -->Mineral...” or “Kinetic --> Redox reaction”? To begin with, I used “Kinetic Mineral... (Pyrite)” by inputting surface area and rate constant derived from some references. I think the eq.1 reaction was automatically used in the thermodynamic database of GWB. Pyrite + H2O = Fe++ + 2*HS- + 0.5*O2(aq) -------------------------eq.1 No relevant results, however, were obtained (pH value increased, dissolution of pyrite didn’t happened so much, and etc), although high concentration of O2(aq) was provided. Secondly, I tried to set eq.1 in “Kinetic redox” without surface area, and with the modified rate constant from mol/cm2 sec to kg/mol sec. Pyrite + 3.5*O2(aq) + H2O = 2*H+ + 2*SO4-- + Fe++ --------------eq.2 The calculation worked out than anticipated. If possible, I’d like to use eq.2, but I am afraid that the second procedure is irrelevant and incorrect. Is the second procedure using “Kinetic Redox reaction” for pyrite oxidation correct? It will be grateful if you could give me any better way to describe pyrite oxidation. Best regards, Maki

Hi Brian, #1 Thank you for your pointing out that. After I tried replacing double quotes with single quotes, the program worked very well! #2 Thank you for your explanation. Of course, I also really think that the suffix function is very useful and helps me. However, in my current case, I have needed to calculate many models at the same time and continuously, which were constructed based on various combinations of changed variables in Initial system, Reactants, Inlet fluid, Flow field, and Medium properties. In addition, the calculation of some models took a few days. So, I have needed to leave every original input file for checking their constraints and have wanted to specify which file were running, for preparing the subsequent one. If there are several the same requests from users besides me and if the concerned maintenance would be easy to carry out for the developers, the maintenance would be grateful. Best regards, Maki

Hi Brian, Thank you for your reply. #1 As we know, five means for setting rate law (Built in, Equation, Script file, Function, and Script) can be used in GWB software. “Script file” works without any problem as you have advised me in the past posts. However, ‘Script’ including same contents of the ‘Script file’ didn’t work, and error messages ‘Error: Don’t know keyword: ***’ were shown. The form of pp. 66-67 of Reaction Modeling Guide was used and same contents of the ‘Script file’ that has worked were pasted to the input window as below. Was it a mistake? --------- aff = QoverK * exp(-ATP_number * ATP_energy / (8.3143 * TK)) aff = aff^order1 IF (aff > 1.0) THEN aff=1.0 . . . return rprime * biomass * --------- When line numbers were added to head of each line as below, it didn’t work either. --------- 10 aff = QoverK * exp(-ATP_number * ATP_energy / (8.3143 * TK)) 20 aff = aff^order1 30 IF (aff > 1.0) THEN aff=1.0 . . . 440 return rprime * biomass * --------- After the error messages were shown, only the first line (aff = QoverK * exp(-ATP_number * ATP_energy / (8.3143 * TK))) remained in both cases. If there is any fundamental mistake throughout the setting, could you point out my mistake? Or, should I input the other commands to deal with microbial kinetics using ‘Script’? #2 I would like to display the name of GWB script file (Input file) on the title bar. When I carry out several calculation derived from Input files of same folder at the same time, it would be helpful to distinguish their running files. Is there any way that I can make it? #3 Thank you for your consideration. Its improvement would be very convenient for extracting data. #4 Thank you for your appropriate advice. Best regards, Maki

Hi I have four inquiries about X2t and Xtplot. Inquiry #1: Script editor of microbial kinetics When I posted the question about custom rate law script on July 24th, 2013, you answered me that the programmer was working on fixing the problem with the script editor of Custom rate law. Could you let me know about the current status of the maintenance? The problem seems to remain even in ver. 9.0.8. If the problem is fixed, it would be very helpful right now. Inquiry #2: File name on title bar In X2t, React, and other programs, the file name is not indicated on the title bar. Folder name of the upper directory is indicated. In the Xtplot file, the file name is indicated. Could you tell me how to indicate the file name on the title bar while opening X2t program? Inquiry #3: Node number on Position tab When I would like to select data of the specific Node with Time (several values at one node) for X axis, I can select them from Position tab (ex. Node 10, 1 (20m, 2m) there). I think it is based on the XY coordinates. On the other hand, I cannot select them by relying on the Node number. Can we make the Node number indicate on Position tab? Inquiry #4: Overlap of objects Even when all of appearances are reset on the X2t map view, the number with Coordinate Axes and the name of Variable partially lie on top of each other. How can we reset objects of Map View including the Coordinate Axes so as not to overlap them? If you need further explanation, please let me know. Best regards, Maki

Hi Brian, Please let me ask one more question. When the mass of H2O of the well in the imported flow field doesn’t need to be taken into consideration, I don’t need to set the discharge well. Or do I have to set the well in the imported flow field? Thank you for your help. Maki

Hi Brian, Thank you for your reply. According to your advice, I tried to set a constant discharge well in the imported flow field. Although the error message ‘Volume imbalance, maximum error of ...’ was shown in the beginning of Results pane, the calculation converged and values of Hydraulic potential in all nodes were zero atm. My understanding is that I don’t need to mind the error message in the above example. Is this right? Best regards, Maki

Hi I’m trying to express the drainage in the heterogeneous flow field in X2t. Simplified example and flow field tables for the import are attached. Please import the table file by using ‘imported’ function on the Domain pane. And I attached the supplements for explanation. Q.1 (the supplements 1 and 2) When the flow field is imported, how should I set the drainage in X2t? Can I set the open node within the domain? In the example, I set the drainage to the central node of the domain having nine nodes. Since the flow field seems to be fixed by the imported value, the function of ‘wells’ cannot be used at the same time and I will not use the function. In the attached file, because all of velocity arrows directs to the central node, the values of Mass H2O, Mass solution, and total moles of node 1, 3, 4, 5, and 7 show much larger than the respective initial ones and the results are not realistic. Their values after the run should be same as initial ones because Bulk volume is not unchanged. On the other hand, the Cl- concentration (molality) calculated by moles in fluid and Fluid volume seems to be correct. I think that approximately no change of Mass H2O and Mass solution compared with the initial values of those is practically desirable. Can I set the ‘realistic’ drainage without using the function of ‘wells’ in the heterogeneous flow field? In other words, because of avoiding such an unrealistic value, can I set the open node within the domain? It will be grateful if you have any good idea to handle this problem. Or, if I need the molality only, should I ignore the unrealistic values of Mass H2O etc. and adopt the calculation result of molality, which seems to be correct, like the attached example? Q.2 (the supplement 3) The scale in Xtplot seems not to show an appropriate range corresponding to pasted values. If the maintenance is needed, could you handle it? In addition, Moles in fluid shows a different value from those output in text file of Xtplot. I guess the value in text file of Xtplot is correct. Is it correct? If my explanation is insufficient, could you let me know? Best regards, Maki drainage.x2t x_dra.txt y_dra.txt the_supplement_drainage_1.pdf the_supplement_drainage_2.pdf the_supplement_drainage_3.pdf

Hi Brian, That is exactly what I looked for! Almost all the problems related with custom rate law have been solved and the task I have been working on will move forward. If the remaining problem (about the script editor of custom rate law) is fixed, could you let us know on this forum? Thank you for your kind support. Best regards, Maki