Revision History

SPECT3D revision summaries are shown below:

Version 7.0.0

• Viewing and saving plot data has been upgraded to allow users to select either zone centered data or node data for contour plots.
• SpectraPLOT now allows for batch mode

Version 6.4.0

• The spectra per pixel option now works for circular detectors.
• An improved algorithm for non-local calculations reduces the number of iterations required giving a significant speed up.
• An improved algorithm for the photon energy mesh used when computing non-local radiation dependent rates gives a faster calculation.
• The high energy wing of a line does not extend beyond a corresponding bound-free edge. This prevents potential double-counting of emissivity/opacity close to the edge, and may improve computational efficiency.
• VISUALIZER: Graphs of opacity, emissivity and optical depth vs. frequency at a selected depth point in the plasma can be obtained from a drilldown plot.
• Bug fixes:
  • The user input Bragg angle is now saved correctly.
  • VISUALIZER: Fixed a crash that occurred when a finite resolution is applied to a streaked spectrum
  • VISUALIZER: A units conversion problem when applying a finite resolution to a streaked spectrum has been fixed

Version 6.3.0

• A new algorithm for the photon energy grid has been implemented. The new grid has a more efficient treatment of transitions that are close together in energy. Transitions with a line strength less than the user entered minimum line strength and greater than one tenth of the user entered minimum line strength are included with a reduced number of points per line.
• Photon energy points are no longer added at bound free edges.
• VISUALIZER: A choice of photon energy units has been added to all the windows that display spectra.
• Bug fixes:
  • The Detector/Target orientation view now displays 1D spherical plasmas correctly.
  • An error in the path length used to compute escape probabilities in versions 6.0.0 to 6.2.0 has been corrected.
  • The values of 'j' in the *.etd files were too large by a factor of ten.
  • VISUALIZER: For non-LTE simulations, the photon energy grid used in the drilldown plots is now the same as that shown in the time resolved spectrum.

Version 6.1.0

• The filter response functions have been updated:
  • XRD and FFC filter response functions are now specified by two column files in which Column 1 is the photon energy (eV) and Column 2 is the response function value (dimensionless). The reponse function value is exp(-t_F(n)), where t_F(n) is the filter optical depth.
  • XRD output is now expressed in terms of the frequency-integrated flux (convolved with the response function) at the detector.
  • On the XRD tab of the Detector setup widget, areas for entering the Resistance and Effective Area of the detector have been removed.
  • XRD output in SPECT3D Visualizer is now expressed in units of erg/cm²/s
• For many widgets, the hydro data file does not have to exist in order to see the parameters on the widget.
• The Detector/Target orientation view can now be used for 1D netCDF (Exodus) files.
• Documentation:
  • Online documentation has been updated to clarify several features in setting up simulations.
  • A new appendix providing a description of the default atomic models has been added.
  • The appendix on detector intensities and fluxes has been updated to correct typos.
• Atomic model file paths are written to the log file. The levels are not written.
• A default low temperature atomic model file had been added to the available models
• When running interactively, all Physics library error messages from are shown in the log window.
• Some of the image settings on the detector - target view can be changed via a dialog box accessible by double clicking on the image:
  
• The controls for choosing a population model have been changed:

• For 2d cylindrical geometry, a beta version of a multi-angle short characteristics method of calculating the populations may be available. (Not available when running the parallel version.) This method considers radiation transfer over a small number, n, of cells, where the value of n is user determined. For details of the method, please see the Appendix: Short-N Characteristics method:

• Bug fixes:
  • Integration weights used in computing frequency-integrated quantities now properly account for the minimum and maximum of the spectral range (and ignore the effects of adding Additional Graphics Photon Energies).
  • If memory allocation fails, there is a message to that effect (instead of crashing). If another simulation is attempted, it will crash.
  • In a multi time step simulation, there was a potential crash if the first time was aborted during initialization.
  • For a fast calculation run interactively, the updates could be too fast for the window system. The depth progress monitor now only updates approximately every second.

Version 6.0.0

• 3D support has been upgraded. Testing was completed for a 750K volume element hydro dataset (single processor mode).
• Stark line widths can be adjusted by the user by specifying a multiplier to be applied to the calculated value, or by specifying a constant value. Line width modifiers can be specifed for specific:
  • Elements
  • Ions
  • Upper and lower level principal quantum numbers
  • Transition type (e.g., if upper level is an autoioning level).

The user interface for setting the line width parameters (shown below), is accessed in the Transitions tab on the Kinetic Model widget (under Advanced settings).



• Populations files are written for time-dependent, local calculations for times when an image is calculated.
• The detector image can be either rectangular or circular. For a circle, there is a choice between computing all the pixels on the circle or one radial segment.



• When viewing the hydro data, the axes retain the same settings when a different time is chosen.
• There is an option to launch Visualizer at the end of a simulation.
• The spot size for a uniformly distributed backlighter can be specified.



• For the spectral grid, the user set minimum oscillator strength has been changed to the minimum line strength. The line strength depends not only on the oscillator strength but also on the population of the initial level and, for emission, the ratio of the statistical weights of the lower state and the upper state. Thus, a transition involving heavily populated levels may be included, even though the oscillator strength may be small.
• Some default values have changed:
  • Photoionization grid: the default minimum oscillator strength is now 1.0 e-3 and the number of points per transition is now 13 .
  • Spectral grid: the number of points per transition is now 13.
• Bug fixes:
  • Convergence problem for non-LTE at low densities.
  • Potential problems in parallel calculations using tabulated opacities with a non-square opacity grid.
  • Images generated for photon energies added for additional graphics now include the effects of the backlighter.
  • When backlighter frequency-dependent intensities are read from a file, the intensities outside of the range of those contained in the file are set to zero.
  • The atomic weight box on the materials widget now enables correctly following selection of an incorrect hydro file type.
  • Memory allocation no longer accumulates when setting up the hydro grid.
• Physics library:
  • The threshold for including bound-free transitions, based on atomic level populations was adjusted to include more transitions.
  • Computational efficiency:
    • Upgrades were made to photoionization setup routines (~ factor of 5 improvement in test case)
    • Arrays used to track transition indices upgraded to reduce memory requirements (results in ~10x memory reduction in large-scale calculations)
    • Calculation of collapsed transition parameters has been optimized resulting in a significant reduction in initialization time for mid-z elements.
    • Calculation of natural line width parameters has been optimized resulting in a significant reduction in initialization time.
  • A plasma coupling parameter is used as a criterion to switch to LTE population kinetics at high densities to prevent convergence problems due to excessive continuum lowering
  • Added support for a new atomic model file format:
    • Improved consistency for level configuration and term accounting.
  • Improved memory management for repeated calculations.
  • Added an emissivity correction for inner-shell photoionization transitions for which upper states are not explicitly included in the atomic model.
  • Added detailed balancing correction to the effective dielectronic recombination rate coefficient when transitions involving autoionization states are not treated in detail.
  • Added corrections for n-1 (K-alpha, K-beta, K-gamma, etc.) transitions in L-shell ions (Be through F) based on He-like scaling and adjusted to match R. Mancini's calculations for N-, O-, and F-like Al K-alpha lines.
  • Bug fixes:
    • Memory leak fixed in setting up the hydro grid.
    • Fix for incorrect reading of collisional cross-sections. Calculations with non-Maxwellian electron distributions using the latest atomic data format (11) are affected.
    • Bug fix for UTA linewidth. It is now consistently used according to the definition of standard deviation 'sigma' in exp(-x^2/(2*sigma^2)).
    • Fixed bug associated with UTA lineshift. The lineshift correction is now applied only during the opacity/emissivity calculation.
    • Populations of upper levels of implicit channels are scaled to account for missing levels ( upper levels of forbidden transitions ). If statistical weights are wrong ( sum(gupper_impl) .gt. gupper_total), the scaling is not performed, so that populations remain normalized.
    • Bug fix for collapsing of collisional x-sections.
    • Collapsed dielectronic recombination rates are correctly averaged over upper and summed over lower levels.
    • Fix for application crashes when handling memory allocation errors for atomic data.

Version 5.3.0 (October 2005)

• Exodus files without nodal names and values can be read
• The display of contour plots has been speeded up by over an order of magnitude.
• An option has been added to write out a file for the spectrum at each detetector pixel.
• An option has been added to turn off continuum lowering.
• Bug fixes:
  • A problem that occurred on Linux for large grids has been fixed.
  • Default opacity file paths are now correct.
  • Lines of sight now drawn correctly on the LOS/Detector view for all cylindrical geometries.
  • In batch mode, the environment variables written to the copy of the workspace are the values at the time of the simulation
• Physics library:
  • Computational efficiency: upgrades were made to non-DCA opacity calculation routines that result in significant improvements in efficiency. These are particarly relevant to narrow-band (e.g., monochromatic) backlighter simulations.
  • Bug fixes:
    • A bug that occurred for multi-timestep calculations with non-local radiative rates computed in 1-D cylindrical geometry has been fixed.
• ATBASE 5.1
  • Dielectronic recombination rate coefficients have been upgraded to better model rates for L-shell (Be-like to Ne-like) ions.
  • Electron impact excitation cross sections computed from distorted wave calculations are scaled at near-threshold energies consistent with published close-coupling results.
  • All autoionization energy levels for He-like and Li-like satellites are treated explicitly.
  • A flag has been added to identify transitions present in the NIST database.
  • A new configuration string that contains information about parent terms has been added.

Version 5.2.0

• Upgraded to use the new atomic data file structure.
• Improved efficiency in computing bound-bound opacities.
• Angle settings added for 2D r-z geometry.
• Added option to use a convergence algorithm for computing the populations.
• Upgraded line-grid intersection algorithms to work for astrophysical-scale grids.
• Bug fixes:
  • Fixed bug that occurred when deleting elements in the materials panel.

Version 5.1.0

• Maximum number of extra photon energies and iso-optical depth surfaces to 16.
• Added option to set the number of angles used in the photoabsorption calculation. Presently limited to 1D geometries.
• Bug fixes:
  • Check that all materials have a volume fraction assigned.
  • An external radiation source now works correctly for 1D cylindrical geometries.

Version 5.0.0

• Added user set minimum oscillator strength for spectrum
• Added option to include implicit double excited states for non-LTE calculations. This is relevant for ATBASE versions greater than 4.2.

Version 4.2.0

• Support has been added for imaging with finite-size backlighters.
• Support has been added for Spherical Crystal Imaging, including the ability to view the target-crystal-detector configuration.



• Can run a simulation without saving the workspace.
• Support added for utilizing opacity tables with differing frequency group structures.
• User set value for the minumum oscillator strength transitions to include in the photoabsorption grid (non LTE only)
• Added support for pdb files (Linux only).
• Improved algorithm for photon frequency grid with large number of transitions.
• Perspective projection: The effects of the solid angle are treated better, resulting in lower intensities than in previous versions.
• Frequency-gridding:  Points are added in line wings based on minimum oscillator strength (previously true for line cores).
• For Linux systems:
  • Changed preferences to allow the user to set the default location for ATBASE, PROPACEOS and the AtomicModelBuilder.

Version 4.1.1

• Released on the Linux platform.
• Improved algorithm for a photon frequency grid with a large number of transitions.

Version 4.1.0

• Added feature to view the target/lines of sight orientation for 2D cartesian and 2D cylindrical geometries with Exodus files.
• Maximum number of detector pixels in one direction increased to 10,000.
• Kinetics settings:
  • added rate multipliers for atomic processes
  • added parameters for the photoionization grid
• Bug Fixes:
  • Unit conversion for Exodus files defining spatial grid in meters fixed.
  • Frequency-integration algorithm for computing frequency-integrated fluxes/intensities has been improved.
  • Problem associated with "Repeat disk sector about z-axis" in Geometry setup widget fixed.
  • Fixed problem where on some system the simulation thread could freeze.
  • Fixed problem associated with use of 2-D R-Z grids with T-junctions generated by PlasmaGridGenerator.

Version 4.0.0

• SPECT3D Setup rewritten in C++ and renamed SPECT3D.
• SPECT3D multi-time simulations run directly (in a separate thread) with a monitor showing the progress of the simulation.
• Added the ability to run time dependent simulations.
• For time dependent calculations, the time taken for the calculation can be shortened by choosing to calculate only the populations at some of the times (no spectrum or detector image).
• Can include the effects of hot electrons using data from particle-in-cell LSP code.
• Isotopes of hydrogen and helium added to the available atoms to select.

Version 3.0.0

• On the Spectra dialog:
  • Spectral boundary conditions can be specified for 1D geometries.
  • The backlighter, if any, can be defined to be one of the spectral boundary conditions.
  • On the Backlighter tab, for the backlighter type File, the Browse button now appears in a Backlighter Model File table cell while it's being edited.
• On the Detector dialog:
  • Bug fix: Previously, if the detector coordinates were specified with spherical coordinates in degrees, the detector-target orientation scene interpreted the coordinates as if they were specified in radians. Fixed.
  • Changing the image plane coordinate system now causes an automatic conversion of the detector and target fields to the new coordinate system.
• On the Plasma Variables dialog:
  • For convenience, you can now double-click a list item in the Add Material Density Variables child dialog, instead of clicking the OK button.
• Recent file pathnames appearing in the File menu are now abbreviated if they exceed a maximum length.

Version 2.6

• Material libraries are now supported. The Materials tab has buttons supporting import and export of materials to and from material libraries.
• While opening a workspace, if the referenced hydro dataset doesn't exist or isn't readable, a dialog appears asking you either to find it or fix the problem and retry.
• On the main window:
  • The File menu now offers a list of recent workspaces.
  • The menu item Edit->Material Library leads to a dialog in which a material library can be edited.
• On the Plasma Variables dialog:
  • The density model is now configured once, on this dialog, rather than for each material on the Material dialog.
  • Either material density hydro variables or material indices, as appropriate, must now be entered on this dialog. This allows the software to to verify that all hydro material density variables or hydro material indices have been mapped to materials. It also allows the software to provide shorter menus for density variable combo boxes, which allows you to select items from these menus more quickly.
• On the Materials dialog:
  • New buttons allow materials to be copied to and from libraries.
  • Some of the fields in the materials table are now editable.
  • New button Add Z=... provides a shortcut for adding a material consisting of a single DCA element.
  • On the Materials tab, the set of material density hydro variables or material indices is verified upon dialog commit to be the same as that entered on the plasma variables dialog. A warning appears if they are not.
  • On the Materials tab, the mean atomic weights are verified to be positive. A warning appears if they are not.
  • On the DCA Elements tab, the Atomic Model buttons have been replaced by a popup menu accessible via the File button that appears in the Atomic Model File table cell when it's being edited. This provides significantly more space to show atomic model file pathnames.
• On the Material dialog:
  • In the DCA elements table, in the editable atomic number column, you now have the option of entering atomic symbols, in any case, which are translated automatically to the proper atomic number.
  • New button Add Z=... provides an alternative means to add an element.
  • The Material dialog now verifies the readability of the tabulated opacities file, and presents a warning if it cannot be read.
  • Bug fix: For the DCA elements table, when the Add button is pressed, the "Atomic #" cell of the new element now automatically gains keyboard focus.
• On the Detector dialog:
  • Bug fix: On the Detector dialog, verification of the image plane vertical field yielded both false positives and false negatives when the detector coordinate system was spherical. (The verification treated the spherical coordinates as if they were Cartesian.) Fixed.
• Bug fix: Numbers in tables no longer appear rounded to three decimal places.

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