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p.m.berger

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Everything posted by p.m.berger

  1. Well, I think the reaction would be: Phenol(s) + H2O + 4 SO4-- + 2 Fe++ = 2 Pyrite + 2 H+ + 6 HCO3- Peter
  2. Hello, This should finish in a reasonable amount of time. Peter iso_bug.x1t
  3. Hello, It turned out to be an typo in one of my initialization commands, so Ca wasn't being added as a basis species to some of the nodes. An appendix of error messages would be helpful for the ChemPlugin documentation. Thanks, Peter
  4. Hello, I am trying to incorporate Chemplugin into a python based groundwater flow model. As a starting point, I am having it recreate the Steam_2D.x2t script. However, when the program starts running I get: Internal error: transform_comp: lost transform species ChemPlugin abondoning calculation. What is the meaning of this error? I believe I am putting the same basis species in each node, so it shouldn't be an inconsistency between nodes. Also, it doesn't seem like advancetransport or advancechemical are returning an error code. Thanks, Peter
  5. Here are the files, unfortunately, I didn't save the output. Peter iso2.x2t thermo.com.organ.tdat
  6. Hello, As a follow up to this, I can't decouple the phenol reaction because I am trying to look at pyrite dissolution followed by reprecipitation/reduction by an organic material (phenol being the stand in for said organic material). I have gotten a 1D model to converge in a somewhat reasonable time, however, at the end it says there is no isotopic data to plot for anything, including bulk mineral and fluid, except for pyrite. I assume that just means the isotopic model broke down and xtplot is recognizing that the output is gibberish? Thanks, Peter
  7. Hello, Thanks for looking into it. I actually was doing the solid phase organic when I first ran into problems. I switched to the simple reactant for testing and to simplify my script before posting it. I guess I'll just have to play around with it. Peter
  8. Hello, I am using the attached system to model the dissolution and reprecipitation of pyrite as buffered by organic material (phenol in the model). Along with this, I want to look at the change in 34S. I need to ensure I have enough phenol in the system, but when I increase the amount released into the system from 0.1 mmol/m3/yr to 1.0 the stability of the isotopic part of the model goes haywire. Can you confirm that none of the overall model stability constraints limit step size based on isotopic changes? If my only options are really lowering the Courant and step_increase then I'll probably have to drop the model as it will take too long to run. Thanks, Peter iso_test.x1t
  9. Hello, This computer has never had anything but the GWB 17 installed on it, the current version is 17.0.2. Running the dll that instantly returns 0 works fine. If I put the return 0 after: pre = n.rct[0].preexp; it crashes. It seems to work fine if I put: if (c.Xi == 0) return 0; at the beginning so it doesn't make a calculation for the first time step. I assume that means that the first heat transport step is done before the reaction properties are initialized. Thanks, Peter
  10. Hello, I am trying to link the internal heat source to the reaction rate of pyrite to simulate an exothermic reaction. I created a 64 bit library and was able load the function when into X1t. When the simulation starts, the program instantly closes. Any suggestions about how I broke this? Thanks, Peter #X1t input file data = thermo.tdat verify conductivity = conductivity-USGS.dat suppress ALL unsuppress Hematite K-feldspar Pyrite interval start at 0 day, fluid = fluid_1 time end at .25 m.y. length = 250 m width = 1 m height = 1 m Nx = 25 discharge start = .307 m3/m2/yr diffusion_coef = 1e-7 cm2/s temperature = 100 C heat_source = file D:\Model\Teena\Heat\heat.dll:heat J/cm3/yr transient, Tmax = 300 C scope = initial H2O = 1 free kg Na+ = 1 g/kg balance on Cl- Fe++ = 1 mg/kg swap Pyrite for O2(aq) Pyrite = 10 free volume% SO4-- = 20 mg/kg pH = 6.5 scope = fluid_1 H2O = 1 free kg Na+ = 1 g/kg balance on Cl- Fe++ = 1 mg/kg swap e- for O2(aq) Eh = .2 V SO4-- = 20 mg/kg pH = 6 scope kinetic Pyrite pre-exp = 3.02e-12 act_eng = 56900 surface = 1e4 // Heatlib.cpp : Defines the functions for the library. // #define EXPORT extern "C" __declspec(dllexport) #define NOMINMAX #include <stdio.h> #include <math.h> #include "gwb_context.h" // heat: Examine the amount of pyrite oxidized and return a heat source // proportional to the pyrite reaction rate and the time step. EXPORT double heat(int i, Nodal_block &n, GWBcontext &c) { double pre, act_eng, qnk, surf, temp; pre = n.rct[0].preexp; act_eng = n.rct[0].acteng; qnk = n.rct[0].QoverK; surf = n.rct[0].surfac; temp = n.tempc + 273.15; if (qnk > 1.0) return 0.0; //This is the reaction rate in mol/s which needs to be in J/cm3/s //so divide by the domain size and number of nodal blocks //which gets mol/cm3/s and then multiply by the energy of the reaction //in J/mol which I took from https://doi.org/10.3390/min11060565 return pre*surf*(1.0-qnk)*exp(-act_eng/8.314/temp)/c.Length/c.Width/c.Height/c.Nnode*1409000.0; }
  11. Hello, When I am in map view in Xtplot, the vertical axis on the distance scale changes when I move the scale around the window. It only seems to happen if I move it to a y position greater than 6. At that point, I am also no longer able to set the height in the distance scale dialog. Thanks, Peter
  12. Thanks, that seems to have solved it. Peter
  13. It seems there isn't a work around with using standard numbers or scientific notation correct? NO3- mol 9.99999999998440423e-05 and NO3- mol 0.0000999999999998440423 comes out as 0.001 instead of 0.0001. I'm playing around with the GWB libraries to model multicomponent diffusion so I need the high precision. Thanks, Peter
  14. In react, if I issue the command: NO3- 0x3f1a36e2eb1c232c mol which should be 1e-4 mol NO3-. Instead it comes out as 1e-3. If I save the file in hex format the NO3- line is NO3- = 0x3f50624dd2f197f8 mol which equals 1e-3 mol NO3-. So it seems as the input is being read incorrectly. Bug? Thanks, Peter
  15. I now see the difference in the command is really in the direction of the slashes. If the command to read thermo dat uses \ in the path then everything is fine. If it uses / then the file is read in correctly, but the dialog stops working. Peter
  16. In any of the programs, when I specify a new thermo database at the command pane or in a script, the "File->Open->Thermo Data" menu item no longer brings up a file selection dialog box. The menu/dialog box work fine as long as I use them exclusively. Thanks, Peter
  17. Thanks for the reply, So the water activity results are different from the species activity results? The activity reported for species are act_coef*molality and not act_coef*(mole fraction). Aqueous species molality mg/kg sol'n act. coef. log act. --------------------------------------------------------------------------- Na+ 2.265 4.598e+04 0.6761 0.1850 Peter
  18. Hello, I am trying to use SpecE8 to calculate chemical potential and so need the activities of everything in solution, including water. Can someone clarify if the command "report Watact" reports the activity of water as it specifies in the GWB reference or the activity coefficient? The moles of water in 1 kg is roughly 55.5 but the report command for a dilute system returns 0.999... That would imply the 55 moles have an effective concentration of less than one. Or are solvents treated differently? Assumed to have a base activity of one, or scaled to one mole? Thanks, Peter
  19. Hello, I'm trying to run X1t in with some optimization software and it seems to crash when I try using a report command on an simulation that doesn't converge. React gives me "--Error: Run not finished" in a similar situation but X1t just quits. Thanks, Peter
  20. Is the pause "ctrl+break" still functional in X2t if you want to continue a run afterwards? I'm doing simulations and sometimes want to see how they are going early on, but if I pause and plot the early results then hit continue I get several "Newton failed at node..." messages and it abandons the simulation. Thanks, Peter
  21. Is there a way to do kinetic isotopic exchange as in Druhan et al. GCA 2013? I have a system that recrystallizes calcite due to hot fluid circulation and I've read some papers that look at closure temperatures for isotopes. Currently I have a kinetic transformation from a (segregated) low ordered to a (unsegregated) hydrothermal calcite. I was just wondering if there was a cleaner way. Crunchflow, as used in the original paper, doesn't do heat flow for some reason and so isn't an option. Thanks, Peter
  22. There should be an example in the documentation of writing a script that solves for a rate constant of quartz. Peter
  23. Hello, I tried using a library for setting permeability. I can specify the file if it is in the current working directory and I don't have to specify a file path. However, when I do specify a file path I get "Error: can't load library D" where D is the drive that contains the file. This seems to fail if I use either the command line or GUI. Thanks, Peter
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