This is an update for the PetraSim 5 beta release.

• Added remaining TOUGH2-MP EOS support (simulator executables).
• The TOUGH2-MP EOS9 executable is not currently recommended. It originated from a different code base and has not yet been made consistant with the other simulator versions.
• Material can now be specified by layer (in addition to global, region, and cell).
• Fixed a bug in the mesh creator that occurred when using an auto-fit boundary.
• Fixed a bug in the Polygonal mesh creator UI that sometimes caused the cell count estimate to be negative.
• Fixed a bug in the layer manager that prevented color and top/base changes from correctly propagating through the event system.
• The Tree View will no longer become too thin when PetraSim is run at 800x600 resolution.
• Made the FOFT/GOFT output options more consistant across cell and well editing.
• Wells with no print flags enabled will no longer appear in the Well Results dialog.
• Fixed a bug that caused items in the tree to sometimes become unselectable.
• When a TOUGH2-MP simulator is launched, all previous COFT, FOFT, and GOFT multi-files (e.g. coft_001.csv) will be deleted. This prevents mixing results with the current run with previous runs.
• In the Boundary editor, the quick set feature will now initialize to the current boundary.
• Regions can now be named.
• Initial conditions can now be loaded from a TOUGH2-MP-generated SAVE file
• Fixed a bug that caused PetraSim to crash if the splash screen was clicked before native libraries had finished loading.
• Fixed a bug preventing EOS7 brine data from being saved.
• Added delete to the right-click menu for wells.
• Fixed a crash that would occur when creating a new mesh in a model with "extra" cells.
• It is now possible to delete a mixed set of items all at once (e.g. wells and materials).

This is an update for the PetraSim 5 beta release.

• Added TOUGH2-MP support. The EOS3 module is included with this release.
• TOUGH2-MP options have been added to the Simulation Parameters dialog.
• TOUGHREACT EXEs have been rolled back to the build deployed with PetraSim 4.2. This fixes a convergence bug caused by compiler optimizations.
• When switching EOS modules, variable format data will be reset. State variables may still be re-interpreted to invalid values.
• Fixed a bug that caused PetraSim to fail to import old SIM files that did not contain a mesh.
• A warning is now shown when creating a new mesh will destroy existing cell data.
• Improved the performance of the tree view when working with large numbers of cells.
• The Show Vectors UI component is now properly linked to vector visibility in the 3D results.
• Fixed a bug that caused PetraSim to be locale-sensitive when selecting the decimal character for TOUGH2 input files (e.g. sometimes use commas instead of periods).
• Improved the performance of the input file writer. This is most noticeable when using large meshes.
• Restored the model outline display to the 3D Results view.
• Partial results can now be read while the simulation is running.
• The results reader is now much more memory efficient.
• When changing the number of z-divisions, PetraSim will now issue a warning if the mesh is out of sync.
• The Set/Remove Top Image actions are now in the Model menu.
• Improved the performance of cell and region coloring. This is most noticeable in complex models.
• Limited the range of the RP parameter Sls to <= 1.
• Injection enthalpy is no longer required to be greater than 0.0.
• Fixed an off-by-one error in the simulation time step display.
• Fixed a bug that caused the 3D font engine to use too much memory.
• The PetraSim User Manual is now bundled with the software.

This is an update for the PetraSim 5 beta release.

• Fixed a bug that caused PetraSim to sometimes omit relative permeability data when generating the ROCKS record of the TOUGH2 input file. ROCKS records 1.1-3 are now always written.
• Fixed a bug in the cell connection area calculation for RZ meshes.
• PetraSim now clamps the maximum number of GOFT entries at 100 this matches the TOUGH2 specification.
• Models loaded from PetraSim v4 SIM files will now use less memory.
• Fixed a bug that caused PetraSim to crash when starting a TOUGH2 simulation if a cell had a BC specified using a table.
• Fixed a bug that caused incorrect INCON values to be written for TMVOC simulations that used a gas/NAPL or three-phase specification format.
• Fixed a bug that caused TMVOC models loaded from v4 SIM files to lose BC data.
• Improved 3D results performance when using a background images.
• Setting axis scale will no longer reset the camera position.
• Updated VTK to version 5.6.0. VTK is used by PyroSim to compute 3D contours, slice planes, etc.
• Vertex buffers and 3D context sharing are now disabled by default - improving reliability at the cost of 3D rendering performance. These options can be enabled via the Preferences dialog.
• Fixed a bug that sometimes caused incorrect lighting to be used when displaying the background image.
• The Recent Files menu now updates immediately when opening a file.
• Added an action to select the regions between internal boundaries to help select fault regions. To use this feature, the user must select two internal boundaries, right-click one of them and click "Select Regions In between".
• In the boundary editor, the Quick Set Min/Max action is now initialized with the current bounding box.
• Improved the quantitative data displayed in the simulation run dialog: the time remaining field is now more accurate, current time step is now listed, and the update frequency was reduced to eliminate flicker.
• Fixed a bug that caused the log in the simulation run dialog to consume excessive memory when the Log is not showing.
• The updated the icon used by PetraSim to be the arrow icon, rather than the grid icon.
• Improved the reliability of the surface testing and intersection algorithms used to handle triangulated surfaces.
• Fixed a bug that cause triangulated surfaces to be incorrectly displayed.
• Added a Regenerate Conceptual Model action to the Model menu. This action can be used to "clean up" the underlying data model after complex surfaces have been deleted.
• Global initial conditions can once more be set by a function of x,y, and z, rather than just x and y.
• Fixed a bug that caused the COFT writer to generate an invalid TOUGH2 input record.
• When opening a PetraSim 4 file, users will now be prompted to create a backup of the old file. Use of this feature is encouraged since PetraSim 5 SIM files cannot be used by PetraSim 4.
• The contour (CTR file) reader can now detect loops and will not add a constrained edges between loops. This prevents errors when loading CTR files that have <contour> sections that contain disconnected polygons.
• Added a From File... option to the boundary editor that allows initialization from a list of (x,y) points.
• The current SIM file name is now displayed in the title bar for the results windows.
• The 3D Results view now hides disabled cells when displaying the mesh.
• Fixed a bug that caused PetraSim to sometimes crash while updating the graph in the simulation run dialog.
• XYZ files that contain duplicate x,y coordinates will no longer crash during import.
• The boundary editor now includes a convex hull option when auto sizing the boundary to layer data.

This is a minor update for the PetraSim 5 beta release.

• A Select Cells action is now available on the context menu for regions, layers, and wells. This action will select all cells in the element.
• Fixed a bug that occured when importing old models that contained wells. Well cell IDs will will no longer be increased by one.

This version is a major update to PetraSim 4. All users are encouraged to work though the short Getting Started guide on the support page to learn how some of the new features operate.

New features in PetraSim 5 include:

• The 2D cell editor has been replaced by cell editing in the main 3D view.
• 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.
• The Run dialog now includes a Log tab which shows selected simulator output.

Additional changes include:

• Simulator run time can now be specified with units (e.g. 10 years)
• XYZ and DXF files are now supported for contoured boundaries
• The New dialog now allows simulator selection and model boundary specification
• Tree selection now correctly tracks model selection and additional model elements are now in the tree
• When opening a model, PetraSim will now automatically switch to the correct simulator mode
• Fixed a bug with EOS7 and EOS7R that caused PetraSim to create an invalid input file when the air component was disabled
• It is now possible to "drape" an image over the top of the model
• Added a workaround for a bug in ATI graphics cards that caused crashes in the 3D display
• Added a Safe Mode shortcut which displays console output while PetraSim is running
• Added a Remove License action to make it easier to transfer licenses between computers
• In the 3D results, vectors are now rooted at the cell centers rather than the corners
• Fixed a bug that caused a crash while editing diffusion coefficients in TMVOC
• Fixed a typo in the relative permeability equation for Corey's curves
• In TOUGHREACT, fixed several dialog issues relating to additional mechanism specification
• Fixed a bug where cells could appear in GOFT that were not in GENER
• Fixed a bug that caused a crash in the Initial Conditions Cell Panel for TMVOC
• Removed unused parameters from the Edit Well dialog
• Added an action to the Edit menu that selects all cells
• Fixed a input file generation bug in EOS3: in TWO-PHASE mode, Sg was being output as [0...1] rather than [10...11]
• Improved the performance of the Line Plot results feature

The following items are no longer supported:

• Non-CSV output from unmodified LBNL source is no longer supported.
• The Tetrad simulator is no longer supported.
• The confining beds feature is no longer supported.

Known issues in beta release:

• TOUGH-MP is not yet supported. If all goes well, the official release of PetraSim 5 will support TOUGH-MP.

Changes since PetraSim 4.2.1006 include:

• In TMVOC, cells will no longer switch to local (non-auto) state variables when edited via the multiple cell editor.
• Models containing confining beds will no longer cause the results reader to crash.
• Fixed a bug that caused PetraSim to interfere with double-click application launching. PetraSim will no longer cause a long double-click launch delay.
• In TOUGHREACT, added support for water zone option ICON=2: concentration will be calculated s.t. log(Q/K) = QKSAT[NAMEQ]
• In TOUGHREACT, fixed a bug that caused the water zone panel to crash when switching between zones.
• Fixed some typographical errors in the van Genuchten relative permeability and cappillary pressure functions.
• TOUGHREACT users can now select ECO2N using the Switch EOS function in the Global Options dialog.

Changes since PetraSim 4.2.0919 include:

• Reworked TOUGHREACT example problem 5 (CO₂ Disposal in Deep Saline Aquifers, ECO2N) to work with TOUGHREACT v1.2
• Fixed a bug that caused a menu separator in the TOUGHREACT menu to have a different look and feel than the separators in other menus.
• Fixed a bug that caused the value 0 (zero) to be displayed in edit boxes as "0.0" - even when the correct localization was "0,0". This issue was causing fields that contained zero values to fail validation in locales where the decimal point was not represented as "."
• Fixed a bug in the Export CSV function of the 2D results view. Now the Export CSV will only save the data that is currently displayed. In some cases, this sometimes tried to write all data using a single, incomplete data set - causing a crash.
• Fixed a bug that caused results not to load properly for simulations that used the restart feature (where the results time steps did not begin at t=0).
• The Run Simulation dialog will now display status times in seconds, days, and years when appropriate (rather than only seconds).
• It is now possible to enable gaseous species transport (NGAS1) for ECO2N simulations. This was not allowed under TOUGHREACT v1.0, but changed in TOUGHREACT v1.2.

Changes since PetraSim 4.2.0912 include:

• Fixed a bug that prevented new features in TOUGHREACT from being initialized when an old SIM file was loaded. This was causing the Restart option to be enabled when an old file was loaded - which prevented the simulation from running properly.
• Added information to the users manual about additional internal boundary features.
• Updated the TMVOC Buckley Leverette example problem.

Changes since PetraSim 4.1 include:

• The TOUGHREACT simulator executables have been updated to version 1.2.
• The new ECO2N TOUGHREACT EOS has been added. The old ECO2 TOUGHREACT EOS has been removed. PetraSim will automatically convert ECO2 SIM files to ECO2N as they are loaded.
• Add support for iTOUGH2 input file generation has been added.
• Added support for EOS4 (TOUGH2, TOUGHREACT).
• Fixed a bug that could cause the Edit Cell Dialog to crash while editing a cell's Source/Sink information (TOUGH2,TOUGHREACT).
• Fixed a bug that prevented extra cells from working in TOUGHREACT.
• Improved the performance and reliability of results file processing. Also reduced the memory requirements during results visualization. This is a substantial improvement that involves re-mapping the simulator results files to a streamable binary format and re-working the visualization algorithms.
• Improved the licensing system. PetraSim now uses a file-based licensing system that should have far fewer problems with licensing ending prematurely.
• Added an online activation feature for licenses.
• Added TOUGHREACT restart capability. It is now possible to load the SAVE and savechem files which will be written out as INCON and inchem. The INCON portion of the flow input file will be omitted if the restart feature is enabled.
• It is now possible to include the legend in a 3D results screen shot.
• The 3D results viewer now remembers custom scalar ranges for a variable after switching to a different variable.
• It is now possible to use a triangulated mesh as an internal boundary using DXF, XYZ, and CTR files.
• PetraSim (TOUGH2) will now prevent values larger than 9999 from being used for MSEC.
• Fixed a bug that caused a crash when the last well (in the well list) was deleted from a TETRAD model.
• Reduced memory usage and repaired some memory leaks.
• Reduced the file size of PetraSim save files.
• Now the tree selection is synchronized with the 3D selection display. In some cases this makes region editing much easier. Also, internal regions can now be edited.
• Added options for TOUGH2 and TOUGHREACT to enable cell-based plot data for wells.
• Fixed a bug that was preventing input validation in the cell editor.
• Fixed a bug that was causing the additional mechanisms dialog to fail to save data (TOUGHREACT).
• Fixed a bug that caused the editor panel of the additional mechanisms dialog to be enabled even though no mechanism was selected (TOUGHREACT).
• Fixed a bug that caused punctuation characters (e.g. "!") to be read as "null" when importing an intersim file (TETRAD).
• Deleting a well will now cause that well's label to be deleted. Also, moving a well will now cause that well's label to move.
• Added auto naming for well cells to help with 2D data analysis. If a cell has not been manually named, well cells will be given a name based on the well's name (e.g. "Well (1)"). These names are properly maintained if the well is moved or deleted.
• Fixed a bug that caused extra cells to be omitted from solute.inp (TOUGHREACT).
• Fixed a bug that caused some properties for disabled cells to be written to solute.inp.
• PetraSim no longer crashes when CO2TAB cannot be located (TOUGH2, TOUGHREACT).
• The thermodynamic database is now stored in the simulation save file. This makes sharing TOUGHREACT models considerably easier. Also, the default thermodynamic database file name (thermxu4.dat) can now be edited in the PROPS file.
• Fixed a bug that was causing some table values to not be saved in the sources/sinks tab of the Edit Cell dialog (TOUGH2, TOUGHREACT).
• Attempting to load a SIM file that uses the wrong simulator mode (e.g. attempting to load a TOUGHREACT model while in the TOUGH2 mode) will now produce an error message.
• Fixed a bug in TETRAD's 2D results comparison function that caused cells to receive incorrect names and values if the two results files contained different numbers of cells.
• In the 2D results, cell selection color now matches line plot color (TETRAD).
• Extra cell names are now properly displayed in the cell time history list (TOUGH2, TOUGHREACT).
• In the Grid Editor, it is now possible to edit DZ and TOP for multiple cells at the same time.
• Fixed a bug in the TOUGH simulation monitor that caused the dialog to stop updating after the time step exceeded 9999.
• Added a more specific simulation completion message for PetraSim. It now differentiates between steady state and end time.
• In the 3D Results view in TETRAD, the Z direction now goes down in the front and side views.
• Changing/resetting the view in the Grid Editor will no longer reset the axis scaling.
• For radial grids, the flux results will now be calculated using the r-theta-h cross-sectional area rather than the approach used for rectangular grids (TOUGH2, TOUGHREACT).
• Deactivated 2D menu rendering optimizations to fix menu flicker on some computers.
• TOUGHREACT data now survives the Change EOS feature. Previously, changing the EOS would reset all TOUGHREACT data.
• Fixed a bug in the results reader that caused files with ELEM=0 to be read incorrectly (TOUGH2, TOUGHREACT).
• When editing a well, the differences between min/max well dimensions and the min/max completion depths are now checked and (if needed) users are prompted to reconcile them.
• Fixed a bug that caused some chemical zone indices to be written as -1 to chemical.inp (TOUGHREACT).
• Fixed a bug that was preventing PetraSim from releasing the write lock on simulation output files. This was preventing deletion of sim_name.out (TOUGH2) and flow.out (TOUGHREACT) while PetraSim will running.
• The license agreement will now be copied into the installation directory for later reference.
• Updated the TOUGHREACT example problem for EOS9: Aqueous Transport with Adsorption and Decay.

Changes since PetraSim 4.0 (Beta) include:

• When loading Tetrad results, PetraSim will no longer crash when it encounters unexpected newlines.
• Fixed a bug that caused PetraSim to crash when adding grid lines in the cell editor.
• Fixed a bug that prevented the CSV results files from being created in TOUGHREACT simulations if reactive chemistry was disabled.
• Fixed a bug that caused initial conditions to be incorrectly loaded when using the TOUGH EWASG module.
• Isosurfaces will no longer cause long delays when used with data sets that have a small range.

Changes since PetraSim 3 include:

• TOUGH2 and TOUGHREACT now output comma separated value (CSV) files in addition to the normal simulator-specific output. The CSV files provide a consistent format that can be used by both PetraSim and external tools such as MS Excel.
• TOUGHREACT now supports 3D vector data.
• 3D line plots are now available in the 3D results view. Line plots allow you to visualize results along a line between any two points. In the 3D Results view, click the File menu, then click Line Plot...
• It is now possible to view 3D results in a grayscale color model. This improved the quality of black and white reproductions of results data (for publication and printing).
• PetraSim will now detect models with too many cells or connections and issue a warning.
• The color scheme system has been updated to support gradient backgrounds.
• The users manual has been updated to include information about new features.