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T.C. Onstott

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  1. running the new version of GWB Professional code made my hydrogen isotope problems go away. thanks for the comments though. i am now running a React code with two microbial reactions but the speed is quite slow. is there any multithread options of way of increasing execution speed? thank you attached is code and databases GullfaksSRB120.rea isotopeno3-v3.txt thermo.com.v8.r6++SCisothiolamine-smec.txt
  2. seems like the error message "stop: def_iso: lost element" relates to the species H2O2(aq)
  3. attached is my modified thermo.dat file. also I should mention that I am using version 8 of GWB. thanks, tco thermo.com.v8.r6++SCisothiolamine.txt
  4. We are attempting to use Geochemist work bench to model the radiolysis of water. We can do this by reacting in H2(aq), O2(aq) and H2O2(aq) and react out H2O(aq) using stoichiometrically balanced reaction rates. this seems to work although we have observed some very strong behavior in the calculation of solution density which we do not understand. We then attempted to model the isotopic evolution of the water by assuming isotopic equilibrium between H2 and H2O and O2 and H2O. but all we get is an error message stating H element is lost and the aqueous species H2(aq) and O2(aq) do not appear on the GUI. not sure this error is related to the one above. I have attached the react code and the isotope dat file. any help would be gratefully appreciated. isotopeno3-v2.txt 95_Level_Radiolysis-2.txt
  5. Never mind, I found the .gss filemaker in the GWB directory. this seems to do the trick.
  6. Dear Brian or others, I am trying to make a scatter plot with Gtplot - specifically using the Piper plot option. I have made text files following as best I can the instructions in the manual, but it does not appear that Gtplot is not importing them when I use the scatter plot option. Can someone please instruct me as to how to sue the scatter plot option and the format of the text file that is required? thank you, tco attached are two text files I made. Pipertest2.txt Pipertest.txt
  7. I am trying to plot up groundwater chemistry results using the Piper plot option in GtPlot. I tried to follow the manual's suggested format, but it does not appear that GtPlot is uploading my text file. I have tried two different test versions but neither seem to work. Can anyone send to me a text file or the format that does work on the Piper plot? Thanks, tco Pipertest.txt Pipertest2.txt
  8. Dear Brian, I have been trying to simulate the gas lost from a sediment column using X1t as part of an experimental program where we monitor greenhouse gas production or consumption in the 1L head space of a 1 meter column. I have attached a simplified code. In this case I am just permitting diffusive flux of methane from pore water into overlying water with a 600 mL headspace. Initially there is insignificant methane in the headspace and top water layer. I have taken advantage of the X1t code to define the headspace by specifying a porosity that is 0.4 and in the sediment quartz which is 0.6. so the sediment has no headspace. what I found was that the code simulate diffusion of dissolved methane from the pore space into the water. it then calculates the fugacity of methane in the headspace as a function of the dissolved methane in the water. but X1t does not seem to account for this methane in the total budget. I do not know if there is a special command that permits this to occur (kind of like an include command for sorption) or whether I need to specify a kinetic gas transfer reaction from cell#5 into cell#4 based upon a diffusion constant. I am thinking that it must be the latter. cheers, tco Permafrost3.x1t
  9. HI Brian, Being a luddite at this stuff, I checked with our IT person and it is very simple. You bring up the Parallels window, but before you launch Windows you pull down the menu for Virtual Machine, click on Configure at the bottom and select the number of CPUs and Memory size and you are good to go for multicore operation when you bring up windows. cheers, tco
  10. I am using X1t to model fluxes into and out of the atmosphere in soil zones and I was wondering what is the best way to obtain the flux across X=0 element as a function of time? or in general the flux between any two nodes as a function of time? I have not found anything obvious on X-Y plot pull down menu. cheers, tco
  11. I am running GWB10, X1t and X2t on Windows Parallel for my MacBook Pro which has multiple cores, but when I try to engage them using the GUI menu, it still pops up as one. It doesn't seem to allow me to select multicore operation. Is this because when running Windows Parallel it is restricted to a single core? Any suggestions are greatly appreciated. thanks, tco
  12. greetings, I was wondering if there was a version of the pick up command for X1T or X2T whereby it would pick up all of the species concentrations from the last step of a simulation and import that into the initial basis of a subsequent simulation? if not, what is the simplest way to inputting this data (concentration, x, y) into the initial basis? thanks, tco
  13. We would like to use our measured N2O concentrations with GWB to calculate microbial nitrogen cycling and was wondering if anyone has produced a set of logK values for an N2O(g) reaction???
  14. Dear Tom, I would like to grow biomass using the microbe reaction and monitor depletion of critical carbon substrate, N (i.e. NH3(a) and P (HPO4--) to determine when an environment becomes substrate limited as opposed to energy limited. I am not sure how to do this. I created a mineral phase bioacetate(s) with the formula C36O40H102N9P1 and comprised of 4 species, Acetic_acid(aq), NH3(aq), HPO4-- and H+. this work fine. I then have a microbe reaction that uses Acetic_acid(aq) and calculates biomass. What I then tried to do is to create a custom rate law for C36O40H102N9P1 where the rate is equal to (biomass-biomass0)/Deltat. I thought that the custom rate laws could import these values like they do in the ratelaw_custom4.bas example, but no luck. I just get a can't evaluate the rate error message. Before I beat my head against a wall, I thought I would check in to see if you can offer some advice. If my code reads as follows: kinetic microbe-24 rxn = "Acetate + H2O -> Methane(aq) + HCO3-" rate_law = ratelaw_example5.bas rate_con = 9e-10 kinetic microbe-24 biomass = 2e-14 kinetic microbe-24 growth_yield = 1 kinetic microbe-24 ATP_energy = -6 kinetic microbe-24 ATP_number = 1 kinetic microbe-24 Decay_con = 1e-11 kinetic microbe-24 power(Acetate) = 1 kinetic microbe-24 powerD(Acetate) = 1 kinetic microbe-24 order1 = 1 kinetic microbe-24 order2 = 1 kinetic microbe-24 KD = 8.6e-4 react 0.1 grams of "bioacetate(s)" kinetic "bioacetate(s)" rate_law = ratelaw_bioacetate2.bas rate_con = 3.18e-8 surface = 1 do I need to explicitly state something like kinetic "bioacetate(s)" biomass0 = ??? kinetic "bioacetate(s)" biomass = ??? in order for this ratelaw to be evaluated? Ideally I want to use the same biomass given by microbe-24. Thanks, tco
  15. sure thing Tom, attached is the React code. I have highlighted the call command down about 3/4 of the way through the program.
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