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Charlie Thornton

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Everything posted by Charlie Thornton

  1. Nawaz, Sure. Porosity in PetraSim is set using the material system. If you wanted to build up alternating layers of porous and less-porous media, the only limit would be the number of material types (ROCK records) you could create. In the original TOUGH2 simulator binaries this limit was set at 27, but in the version shipped with PetraSim we've increased the limit to 100. That's only a problem if each material needs to be unique. If you just want to use two material types, you can make as many layers as you want. The internal boundary system is useful when working with faults. This approach splits up the model and makes it a bit easier to assign different properties to different areas. I think the MINC (multiple interacting continua) system is designed to handle certain types of faults as well, but I am not very familiar with that method. You may have better luck asking one of the others how to approach a particular kind of fault in PetraSim. I am not familiar with the specifics of "CO2 bubble" or "channel flow". The best I can do is refer you to the manual for ECO2N which is the TOUGH2 module designed to model CO2 flow through porous media. http://esd.lbl.gov/tough+/software-tough2-mp.html (look for ECO2N User's Guide) In your PM you asked about price as well, that has not yet been finalized. You would need to talk to Alison for details. - Charlie
  2. You may want to check out the version 5 beta I just posted in this thread: https://www.rockware.com/forum/index.php?showtopic=1385 It has a lot of new features to help work with stratigraphy. It lets you import XYZ and DXF files as the layer boundaries.
  3. We have posted an beta version of the upcoming PetraSim 5. Some important updates include: Z divisions are now controlled by layers, making it easier to work with stratigraphy. Polygonal (Voronoi) meshes are now supported. Polygonal boundaries and boundary editing is now supported. Many major changes "under the hood" which make PetraSim faster and more reliable. Time history plots of accumulated well quantities are now available. A more complete list of new features and bug fixes is available in the release notes: http://www.thunderheadeng.com/petrasim/relnotes.html You can download a free trial from the PetraSim page: http://www.thunderheadeng.com/petrasim/index.html (Link is in the box at upper-right corner.)
  4. In the current version, the only way to reuse materials is to save your model before adding geometry. Then you can use the saved model as a starting point for other models. In the next version, you will be able to modify the boundary - making reuse much easier.
  5. You can make boundary conditions by editing some cells (e.g. all cells on the max-z face) and setting their Type to Fixed State.
  6. Thank you for linking the test file. EOS7: It looks like PetraSim is writing 4 state variables for the "no air" cases. TOUGH2[EOS7] expects 3 -- P, Xb, and T. I've fixed this in our development version and you should be able to use this mode without any trouble with the upcoming version 5 release. EOS7R: Similar problem. This has also been fixed and will function correctly in the version 5 release. I believe (though I haven't tested it) a workaround for the time being is to use the air-enabled modes with a zero air mass fraction.
  7. Your choices in the Change EOS dialog are controlled by the current simulator (TOUGH2, TOUGHREACT, etc). If an EOS option isn't available in the Select an EOS box, it means that EOS isn't available for the current simulator. No other simulation parameters affect the choice - the reason for that is a little painful. When you change EOS, PetraSim resets all of your data that is based on the primary variable configuration in the EOS. This means that all you data for pressure, temperature, CO2, etc. for all wells, sources (boundary conditions), and initial conditions will be reset to simulator defaults. Basically, you retain all of the geometric data, material configuration, and global properties, but the state of the system is reset to default. - Charlie
  8. Ethan, The simulation output gives us data for the cell centers. We use that data to interpolate values for the cell corners. Based on the interpolated corner data, we create the isosurfaces using VTK's ContourFilter class which I believe uses an implementation of the marching cubes algorithm for 3D volumes. The interpolation is linear - based on the distance between the corner and neighboring cell centers. - Charlie
  9. I'm not sure if I understand. Are you encountering a bug (in the Change EOS dialog) that causes the EOS to change to T2VOC when you select ECO2N? - Charlie
  10. Thank you for your suggestion about scales. I've added a note to our issue tracker. The line plots always use 200 evenly-spaced sample points. The increased resolution of the grid in an area will make those samples more accurate, but it will not increase the frequency of the samples. I agree it would be a lot nicer if the data points on the line plots matched the resolution of the underlying grid. - Charlie
  11. Yes, you are correct. The TOUGH2 source code matches the form: RPgas = ((1-S)^2 * (1-S^2)) I've added a note to our bug tracker. - Charlie
  12. The Custom mode is really only useful if you have a custom compile of the simulator. It doesn't give you any capabilities that the others don't, beyond removing some of the validations and giving access to all of the input fields. For users that have a source code license from Berkeley and a FORTRAN compiler, they can use this to get the inputs they want via PetraSim. If the options you want are just not possible via one of the built-in functions, we may be stuck. Could you post the details about the function you're after? Somebody might have a clever idea for a workaround. - Charlie
  13. Ug. I know exactly what you're talking about. I'm convinced that this problem is caused by a design flaw in Intel integrated graphics cards. On and off I've sunk several days at a time trying to find a workaround for this problem. I keep hoping that "this time" I'll have gotten smart enough to fix it. It hasn't happened yet. When using Intel graphics cards, the SetPixelFormat function call will sometimes return false. The accompanying GetLastError() value is garbage (not one of the standard error values, not any other valid value I can track down). The failure of this function call causes a 3rd party library (VTK) used by PetraSim for visualization to exit - which is okay because after the SetPixelFormat error, subsequent 3d calls fail. SetPixelFormat is invoked when PetraSim needs to create a new 3D rendering context (opening results or resizing a 3d window). Here's the spec for the SetPixelFormat function, if you want something to shake your fist at (that's what I use it for): MSDN docs for SetPixelFormat: http://msdn.microsoft.com/en-us/library/dd369049(VS.85).aspx I have never been able to reproduce this problem on an nVidia or ATI graphics card, they seem to work just fine. To find out what kind of graphics card you have: open your Windows Display Settings dialog, and then click Advanced Settings... Your graphics card will be listed in the Adapter Type box. It might be useful to post the exact type of your graphics card here.
  14. I think the suffixes denote charge. So, dolomite-2 = dolomite-- = dolomite2- - Charlie
  15. I was trying to think of a less ugly hack, but...try this: 1. Open up your OUT file in a text editor 2. Find where it says ECO2: EQUATION OF STATE FOR MIXTURES OF WATER/SODIUM CHLORIDE/CO2 in sort of a box. Mine was 310 lines down. 3. Change the ECO2: to ECO2N: Then when PetraSim checks the EOS in the output file it'll get a match. It looks like we didn't catch this one because our test case for this kind of problem wasn't causing PetraSim to actually try to load the OUT file. I've fixed the bug. I've also attached a zip file if you'd like to try to manually patch your PetraSim installation. To install the patch, extract the contents of "eco2n_reader_patch.zip" to your PetraSim install directory. For example, my install directory is C:\Program Files (x86)\PetraSim so after I applied my patch, I had four new files: C:\Program Files (x86)\PetraSim\petrasim\results\ToughResultsReader.class C:\Program Files (x86)\PetraSim\petrasim\results\ToughResultsReader$EOSMismatch.class C:\Program Files (x86)\PetraSim\petrasim\results\ToughResultsReader$NoResultsData.class C:\Program Files (x86)\PetraSim\petrasim\results\ToughResultsReader$RSRFactory.class If you do the use the patch, you'll need to manually remove the files when you install the next version of PetraSim (otherwise the old files take precedence). - Charlie eco2n_reader_patch.zip
  16. I've been delaying my answer in hopes that someone more knowledgeable might come along...I suppose I'll share what little I know. TOUGH2 uses relative permeabilities to manage air and liquid permeability. I've attached a screen shot from PetraSim's Additional Material Data dialog. I don't know anything about acid rock drainage, so I can't give you any suggestions on what values to use. You can learn more about the RP system in PetraSim from the PetraSim manual (chapter 2): http://www.thunderheadeng.com/petrasim/manual/html/ch02.html And from the TOUGH2 manual (Appendices D, G): http://www.thunderheadeng.com/petrasim/man...ugh2_manual.pdf - Charlie
  17. http://www.lib.berkeley.edu/CHEM/properties.html This link will take you to the Physical and Chemical Properties of Chemicals page at the Chemistry and Chemical Engineering Library maintained by UC Berkeley. (Alison found this, but I thought it should be posted here to finish out the topic.)
  18. Sometimes it can be useful to restrict TOUGH to a smaller time step. I know if you try to run one of the TOUGHREACT example problems (CO2 sequestration) without limiting the max time step, the time step will eventually get too big and the simulation will fail. I think the reasoning is that smaller steps make it easier for the simulator to steer around numerical problems. However, when the simulation crashes immediately like that its usually because you've gotten into an invalid physical state in one or more of the cells. What does the bottom of your OUT file say after the simulation stops? Maybe there are some error lines that can give us some hints. - Charlie
  19. We've had trouble with a few users whose computers were incorrectly configured by the manufacturer. There is a concept of junction folders in Windows Vista. PetraSim relies on the "Application Data" folder being properly junctioned to the C:\ProgramData folder. We lean on this so we can use the same code for Vista and XP. To test and see if your Application Data junction is properly configured: In the Windows "search" box, type cmd.exe (this will open a shell window) type cd \ProgramData and press enter (this will navigate to the ProgramData folder) type dir /aL (this lists junction points in the directory) After running this command, you should see the "Application Data" junction point. I've attached an image of what you should see. Do you have the Application Data junction point? If it's missing, you can remove any bad junction, and create the good one with: rmdir "Application Data" mklink /j "Application Data" C:\ProgramData - Charlie
  20. If you activate your license from a file or use the online activation method, PetraSim will try to copy your license (LIC) file to the C:\ProgramData\PetraSim\license\ folder. When logged in as an administrator, can you copy your LIC file to this folder? - Charlie
  21. Those options are only available in Tetrad mode. I suspect they are still visible in the TOUGH2 modes because someone was planning to incorporate them into the way wells were modeled in TOUGH2 but never figured out how to do it. I'll make a note to have those options removed from the TOUGH2 modes in the next version. To change the wellbore radius, I suppose it would have to be done in terms of the other parameters. Since TOUGH2 doesn't actually have wells, we just intersect cells along the well and give them a GENER (source/sink) entry to simulate the desired well behavior - radius isn't taken into account. - Charlie
  22. Is it possible that temperature or some other primary variable may be causing the pressure rise? (I assume the extra cell is "fixed state.") - Charlie
  23. I'm not sure about the proper way to model the air flow. Is it possible that some fixed cells with a particular pressure condition (representing the air-filled tunnel) might be the answer? To add an extra cell: (first you will need a boundary and a grid, then...) (1) Find the IDs of any cells that will be connected to the extra cell. The easiest way to find a cell's ID is to edit the cell's properties in the Grid Editor. (2) On the Model menu, click Add Extra Cell (3) The Edit Cell Data dialog will pop up. This dialog will contain most of the same editing features as the Grid Editor, but with an extra Connected Cells tab. The Connected Cells tab lets you specify how the extra cell will connect to the rest of the model. If you leave this table empty, the cell will not interact with the rest of the model. This is where you will use the IDs from step 1. For details on each of the columns in the connected cells table, you might want to look at the corresponding section of the users manual (http://www.thunderheadeng.com/petrasim/man...07.html#d0e1832). (4) After you fill in all the details, click OK and the extra cell will be created. You can edit it by double-clicking the extra cell in the tree view. - Charlie
  24. I'm not sure. I imagine you could model the concentration of air as it moved through the formation well enough. I don't think you'll be able to actually flow air into the tunnel in a completely intuitive way - but you could inject air into the surrounding media using the well system or some cell-based air sources. The TOUGH2 module EOS3 works with water and air. That would be a good place to start. - Charlie
  25. Me too. We're finishing up a new version that fixes this bug. It'll also include the latest version of TOUGHREACT. - Charlie
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