Revision History (prior to Version 13.0.0)

SPECT3D revision summaries are shown below versions prior to 13.0.0:

Version 12.6.1

• Bug fixes :
• PROPACEOS files containing non-LTE energy resolved opacity data are now read correctly.
• Tabular values used to define the line shape of an X-ray scattering source can have negative electron energies relative to line center.
  

Version 12.6.0

•  The 'divide spatial grid into sectors' option is now available for R-Z geometry. Using a relatively large number of sectors (e.g. 100 - 200) can yield large increases in calculation speed depending on the complexity of the spatial grid and portion of the grid needed to construct the detector image.
• SPECT3D now uses the latest version of the XRTS code (version 6.1) for the X-ray scattering calculation; the X-ray scattering user interface has been updated :
  
• New options are available for bound-free normalization, effective electron mass, Doppler broadening. 
  
• The 'Use ion temperature' option is now available in the gui.
• The ion temperature used for each zone in the the X-ray scattering calculation can now be set by multiplying the electron temperature by a user specified fraction.
• The level of continuum lowering can be set to a user-specified value.
  
• Controls have been added to set the bounds for the minimum and maximum number density and electron temperature for which a scattering calculation will be carried out . Upper and lower bound can be switched on and off independently. 
  
• An XRTS input deck containing the run parameters can be generated during the Spect3D calculation. In the case of a multi-cell calculation, files are only generated for those cells where there was a problem with the scattering calculation.
  
• Bug fixes :
• Photon energy points in an external backlighter (e.g. Visrad file) are now added to the continuum grid by default.
• Contour plot slices through 3-D data using the hydro data view now have the correct x and y axis labels.
  
• Detectors can now be activated/de-activated as expected by clicking on the corresponding checkbox. Previously, the 'active' status of a detector could only be changed if it was first selected from the list, and often settings were overwritten with those of another detector.
• VISUALIZER
• The Coordinate and Data buttons on plot toolbars are now working correctly.
  

Version 12.5.0

• Improved support for large-scale, multi-dimensional hydro datasets:
• The LOS-intersection algorithm has been improved and should lead to substantial speed increases for large 3-D data sets.
• Several optimizations have been made to the LOS-opacity calculation to increase execution speed.
  
• Multi-threading support has been added to graphics for generating contour plot slices from 3-D hydro datasets.
• When generating contour plot slices, the algorithm for treating cases in which volume element walls lie in the plane of the slice has been improved.
• Multi-threading support has been added for reading in and storing hydro data.
• A Reset Data Cache button has been added to the widget controlling the display of hydro data. To avoid unnecessary re-reading of hydro data, flags are used to track most recent data read. Resetting the data cache flags forces data to be re-loaded.
• The K-beta emission modeling for M-shell ions (i.e., for ions which typically have > 10 bound electrons) has been updated. A more accurate model for the shift in wavelength of the K-beta lines, which is based on comparisons with results from first-principles atomic structure calculations, has been implemented.
• Multi-threading over detector pixels is now used for calculations that use only opacity lookup tables and have >100 detector pixels.
  
• The progress monitor widget has been modified to update only once per second.
  

Version 12.2.0

• Use of 3-dimensional hydro data is available for all users.
• The option to use spatial sectors in the LOS-intersection calculation for 3-dimensional data is now available for all users.
• There have been numerous improvements to the X-ray scattering calculation - the RPA model works correctly on Windows platforms; the NE_ZF_LOCK option now works correctly. Additional checks are now made to avoid low values of electron number density that previously caused convergence problems in the scattering calculation.
• VISUALIZER:
  • Legends appearing in line plots are kept up-to-date with the list of selected plots and are also updated when any changes are made to the properties of the plotted lines (e.g. line color, plot symbol).
• Bug fixes:
• The spatial sectors option for the LOS-intersection calculation now works correctly for data read from Silo files.
• Hydro data viewer: contour plots are now displayed correctly in cases where a volume element surface lies exactly in the contour slice plane.
• The visual appearance and behavior of the lineout tool has been improved.
• A labeling inconsistency in the Materials widget for 'single cell' calculations has been fixed.
• The working directory for a simulation is now set to be the same as used in the previous calculation (if available) or the same as the directory containing the currently loaded workspace.

Version 12.1.0

• X-ray scattering modeling for multi-cell grids is now available to all users. By utilizing a multi-cell analysis, the range of scattering angles and plasma conditions is treated more accurately, thereby allowing for a more accurate simulation of scattered spectra.

• The option to reflect the plasma grid through planes that lie parallel to the x-y, y-z, or x-z planes is now available to all users. This allows users to take advantage of symmetries utilized in hydrocode simulations. The parameters used for utilizing this option are set on the Geometry widget.
• The number of processors to use for a simulation can now be set when running in batch mode by using the command line parameter "-n" followed by a number. This overrides the number of processors set in preferences.
• Binned spectral output (i.e., intensity integrated for user-specified wavelength bands) can now be written using ascii or binary format:

• Vapor fraction overrides (not available to all users):
  • Overridden vapor fractions (i.e., specified with an analytic expression) can be plotted.
  • The check box to use a hydro variable for the vapor fraction no longer needs to be checked if an override is to be applied.
  • The overridden data has been added to the Hydro Data Extremes dialog.
  • A warning is now issued if vapor fractions are set for some, but not all, materials.
• VISUALIZER:
  • Results from steady state runs for different timesteps can be merged together using a new Merge runs tool. The workspace for each run should be identical apart from the timesteps selected.
• Bug fixes :
• Program crash when attempting to plot data from a NETCDF file when the data values were not written has been fixed.
• VISUALIZER:
  • Fixed crash in Band Intensity Viewer when working with results from a run with a single timestep.

Version 12.0.0

• X-ray scattering modeling: (This model is in beta form, and is not available to all users.)
  • The x-ray scattering library (based on the Oxford University code) has been updated to support easier integration into the SPECT3D package when future modifications are made .
  • There is a new user interface for entering parameters for the x-ray source modeling.

• An aperture can now be used to limit lines-of-sight that extend through the plasma. At present, this can be used to restrict the angular distribution of photons emanating from the x-ray source used when x-ray scattering modeling is employed.

• Detector-Target Orientation Viewer: Support has been added to show the x-ray source location and, if an aperture is used, the region of the target plasma that is irradiated by photons emanating from the x-ray source.

• For 2-D and 3-D plasma grids, the default LOS-Grid Intersection Model has been changed to Evaluate for Individual Elements. For 1-D grids, the Load Entire Spatial Grid option is always used.
• The maximum number of detectors that can be specified has been changed to 99.
• When attempting to run a time-dependent non-LTE atomic kinetics simulation when only non-DCA materials are used in the calculation, a warning is issued and the calculation is terminated.
• Bug fixes:
  • A problem that occurred when including photoionization modeling for inner-shell transitions that produce Ka/Kβ emission from M-shell ionization stages, while also having regions that contain only non-DCA materials, as been fixed.
  • A problem occurring when plotting data for 1-D and 2-D AMR grids has been fixed.
  • In simulations where more than one detector is used and non-local collisional-radiative modeling is employed (i.e., non-LTE modeling including photoionization/photoexcitation), a problem occurring which resulted in the populations not being set correctly when computing the intensity incident on the second and subsequent detectors has been fixed.
  • VISUALIZER
    • Rate Coefficients Table: When displaying results values of photoionization rates for inner-shell transitions that produce Kα/Kb emission from M-shell ionization stages, results are now shown for the correct spatial zone (volume element).
    • A problem occurring when plotting XRD fluxes with data produced during simulations with SPECT3D 11.5.0 has been fixed.

Version 11.5.0

• When including modeling for inner-shell transitions producing Kα/Kβ emission from M-shell ionization stages, the effects of photoionization are included when computing atomic level populations.
• Improvements for 3-D spatial grids:
  • Substantial improvements have been made to algorithms used to compute the intersections of the hydro grid with lines-of-sight (LOSs) extending from the detector through the plasma. The algorithms are applicable when using the LOS-Grid Intersection Model for Individual Elements (set on the Simulation Type widget).
  • The implementation for multi-threading (used on multi-core desktops and nodes of Linux clusters) has been improved. Smaller bundles of LOSs are used to improve load balancing.
  • Volume elements may be grouped into sectors (or sub-domains), and LOS-sector intersections are first performed to determine whether volume elements within a sector need to be evaluated. This option, when available, is set on the Geometry widget.

• The above upgrades have resulted in more than an order of magnitude reduction in computing time for cases with ~ 50 million volume elements.
• Improvements have been made to significantly reduce memory (RAM) requirements when utilizing large-scale multi-dimensional hydrodynamics grids.
• For 2-D and 3-D Cartesian grids, the option to reflect the plasma grid through planes that lie parallel to the x-y, y-z, or x-z planes is now available. The parameters used for utilizing this option are set on the Geometry widget. (This model is in beta form, and is not available to all users.)

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• Plasma Variables Mapping widget:
  • There is an option to automatically set default values for hydro files generated by either HELIOS-CR or PlasmaGEN. To use this, press the Set to Defaults button.
  • Variables to be used for material fractions or partial densities are now selected using check boxes.
• Materials widget: The values from the hydro file can be overridden by selecting one or more materials and clicking on the Override Data... button. (This model is in beta form, and is not available to all users.)

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• The maximum number of Detectors allowed for a simulation has been increased from 5 to 100.
• An x-ray scattering model (based on G. Gregori formalism) has been added. The x-ray scattering source characteristics are specified on the Backlighter widget (This model is in beta form, and is not available to all users.)

• An option has been added to write out the spectral data for each line of sight in a moderate number of photon energy bins. Parameters for this option are specified on the Spectra tab of the Output widget. This option has been added to support generating filtered images in VISUALIZER, where the filter functions are specified in VISUALIZER (s opposed to SPECT3D).

• When utilizing tabulated line profile data, treatment of the He-like 1s2p configuration requires use of an atomic model with either fine structure splitting or term splitting for that configuration (for computing both atomic level populations and spectra). If this is not done, a warning message is displayed and the simulation is terminated.
• The output files containing atomic level populations (*.pop), atomic transition data (*.edt), and zone-dependent data (*.zdt) have been updated to include the isotope index for DCA atoms.
• Modeling involving inner-shell transitions producing Ka/Kβ emission from M-shell ionization stages has been updated to support parallel simulations.
• The dense plasma Stark line width modeling for K-shell ion resonance lines has been updated. The updated modeling, which is based on fits to detailed Stark broadening simulation results, has been extended to cover elements with Z up to 32.
• VISUALIZER: Rate coefficients are available for virtual atomic levels as well as explicit levels.
• Bug fixes:
  • The species fractions for situations where different isotopes of the same element are present in different materials are now calculated correctly.
  • A problem that could occur when using tabulated line profile data in which different photon energy grids existed at different density points has been fixed.
  • For single volume element simulations involving backlighters, the backlighter is now utilized for all detectors. (The backlighter in single volume element calculations had been ignored since support for multiple detectors was added.)
  • VISUALIZER:
    • Isotope names are now displayed correctly and the correct populations are now displayed in drilldown. Previously the populations for the same atom in a different material might have displayed.
    • Drilldown plots showing atomic level population data when only one volume element is present are now displayed correctly. Previously no plot was shown.
    • A crash that sometimes occurred in drilldown plots showing atomic level population data when more than one element was present has been fixed.

Version 11.0.0

• Support has been added to post-process results from FLASH radiation-hydrodynamics simulations (http://flash.uchicago.edu/site/) when an AMR grid is used.
• Support has been added to post-process results from HYDRA radiation-hydrodynamics simulations in which SILO-PDB files (https://wci.llnl.gov/codes/silo) are generated. This is supported only on Windows 64 and Linux systems.
• The values of all plasma variables and node positions for a volume element can now be displayed for any hydro dataset utilizing 2-D geometry (2-D Cartesian or 2-D cylindrical r-z). Images of the hydro data are displayed by selecting the Display | Hydro Data menu item. To show the data, select the Data icon on the tool bar and click on a point in the plot. The selected zone is highlighted, and a dialog showing the data is displayed (see right image).

 

         

• Simulation Times widget: Controls have been added to aid in the selection of hydro times to be processed in a SPECT3D simulation. The controls for selecting the times at which spectra and images are computed in a time-dependent calculation are similar.

• If a workspace created with a later version of SPECT3D is read in, a message will only be shown if the workspace fails to read.
• When an error is encountered which will prevent all time steps from running correctly, the entire SPECT3D calculation is now aborted.
• The index of the hydro file time has been added added to the *.sim file. The *.sim file format ID is now 2.
• Bug fixes
  • A problem associated with computing the populations of virtual autoionization levels of M-shell ions (i.e., atomic levels having a single K-shell vacancy for ionization states having more than 10 bound electrons) has been fixed. This bug affected SPECT3D versions greater than 8.1.0.
• Fixed problem occurring when using the menu bar and tool bars when displaying hydro data on the Mac.
• In the Display Hydro/PIC File Data widget, the unit in the label for the Hot Electron Energy Bins has been changed from MeV to eV.
• Fixed bug that caused a crash when computing LOS-grid intersections when using the Individual Elements model in 2-D Cartesian geometry.
• Fixed problem that occurred when writing very small numbers for XRD detectors.
• Fixed crash that could occur when selected output cells were shown for an AMR grid.
• Fixed problem occurring when displaying grid extremes for 2-D cylindrical R-Z geometry. Incorrect values were being shown.
• Fix for crash that could occur if changes were made to the plots of hydro data while stepping the plots through time.
• Fixed a problem which resulted in levels with a very low population controlling the convergence. The bug only showed in multiple element simulations when one of the elements had most of the population concentrated in one level.
• Filter names are now written correctly to the image data file (*.dti).
• Fixed a bug that occurred when when the first photon energy in a detector response function file is zero.
• VISUALIZER
  • Plots of XRD filter fluxes vs. time are now correct. Previously only a single point was shown.
  • Time-gated radial plots now update correctly on change of time.
  • Fixed problem that occurred in a time-dependent simulation when using an EXODUS file containing only one time step.
  • Fixed crash that occurred if drilldowns are run on more than one detector simultaneously.
  • Fixed problem for a crash that could occur if changes were made to the plots of time-gated data while stepping the plots through time.

Version 10.1.0

• Support has been added for performing multi-threaded calculation of line-of-sight/grid intersections when selecting the LOS-Grid Intersection Model which computes intersections with volume elements individually (selected on the Simulation Type widget). This, along with other efficiency enhancements, resulted in a reduction in CPU time of a factor of ~ 20 for a 3-D test calculation with 20 million volume elements on a desktop PC with an Intel i7 processor.
• There is an option for time dependent calculations to choose between using LSODE to solve for the populations or the standard solver. The standard solver potentially converges in a shorter time, but may be less accurate, depending on the number of sub-steps specified. The option can be found on the Populs. solution method tab of the Advanced settings on the Kinetics Model widget.

• The minimum and maximum values of the grid data, the temperature data and the density data from a hydro file can be viewed. To view the data, click on the View Data Extremes button on the Hydro File Information dialog. The View Grid Bounds button on the Detector - Target View Settings dialog has been removed.
• The description for using multipliers for rate coefficients when computing atomic kinetics has been clarified.
• VISUALIZER:
  • Noise can be artificially added to image data to better compare with experimental images.
  • Support has been added for viewing hot electron densities per energy group in Drilldown plots.
• Bug fixes:
  • Selected plots of the hydro data have been updated to show the correct units.
  • A bug which required NetCDF/EXODUS files to contain nodal variable names has been fixed.
  • A bug associated with performing multi-threaded (desktop, non-MPI, parallel) calculations where photoionization and photoexcitation rates are computed for non-LTE, non-zero thickness plasmas has been fixed.
  • Problems on Mac OS X arising from starting SPECT3D or VISUALIZER with an expiring or expired license have been fixed.
  • A bug which prevented spatially resolved spectra options being set correctly for any detector except the first has been fixed.
  • A crash which could occur when using the option to compute the contribution to the detector intensity from each volume element has been fixed.
  • Field for writing statistical weight in population files was extended to support correct output for heavily collapsed levels.
  • A bug associated with initializing the isotope index for elements in PROPACEOS files with format < 4 has been fixed.
  • VISUALIZER:
    • A bug associated with the spatial resolution applied to a rectangular detector image has been fixed.

Version 10.0.0

• Multiple detectors now can be specified within a single SPECT3D simulation.
  • Properties for each detector are independently specified, including detector location and viewing volume, number of pixels, and framing camera/XRD filters.
  • A maximum of five detectors can be specified on the Detector widget.
  • There is an option to apply a backlighter to one or more detectors.
  • The Spherical Crystal Projection Model, if needed, can be specified for just one detector.
  • The orientation and positioning of each detector can be viewed on the Detector-Target Orientation viewer.

• More detailed output for individual volume elements can now be saved to output files and displayed with VISUALIZER. Data written for volume elements specified by the user currently include: mean charge state, ionization fractions, and atomic level populations. Data from different times steps can be saved and plotted as a function of time.
• All output parameters are now specified together on a new Output widget.
  • The settings for writing spatially resolved spectra have been moved from the Detector widget to the Spectra tab of the new Output widget.
  • The settings for Additional Graphics Photon Energies and Optical Depth Iso-Surface Values have been moved from the Spectral Grid widget to the Photon Energies and Optical Depths tabs of the new Output widget.

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• The settings for the LOS-Grid Intersection Model have been moved from the Detector widget to the Simulation Type widget.
• VISUALIZER:
  • Support for viewing results from multi-detector calculations has been added.
  • Transitions window:
    • Sliders are now used to set filtering ranges for the photon energy and the oscillator strength.
    • An Update button has been added to apply the changes.
    • The table showing the transitions has been upgraded to significantly reduce the time taken to load, sort and filter a large number of transitions.

    

• Volume element-specific data from a simulation can be viewed by clicking on the Zone Specific Data button on the main window.
• A streaked spectrum can now be convolved in time as well as wavelength. The resolution time is set in the Resolution Parameters Dialog.
• Drilldown plots showing quantity values of volume elements along a line-of-sight are now shown in histogram form (i.e., quantity values are constant through a volume element and change at the volume element boundaries).
• Bug fixes:
  • A problem was fixed that sometimes caused a crash in MPI pixel parallelization calculations when special photon energies are used for detectors.
  • A problem associated with adding frequency grid points for Doppler shifting effects when all fluid velocities are negative has been fixed.
  • Detector-Target Orientation viewer:
    • Fixed problem for 1-D cylindrical plasmas where sometimes view was shown with the wrong origin in the z-direction.
    • Disk detectors now show as disks, not rectangles.

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