Known issues and patches
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    (updated 07/29/15) (updated 08/18/16)    

New issues from Xspec 12.9.0

Frequently Asked Questions

List of currently outstanding issues.


Patches:

latest update 12.9.0s Aug 19, 2016

Requires patch installer v4.7

To apply patches, you'll need to have downloaded and already built the source code distribution of XSPEC. For details about the patch installer including options available with the latest v4.7, click here. Otherwise, just follow the instructions below.


(Note: This assumes you have already set your HEADAS environment variables with the headas-init script, as you would if you were running XSPEC.)

To make sure your XSPEC installation is up to date with ALL listed patches:

1.    If you don't already have the patch installer tcl script (v4.7), download and place it in the XSPEC src directory. This directory should be at heasoft-[ver]/Xspec/src from the source code distribution.

2.    Download the latest patchfile into the same directory. There is no need to unzip/untar the patchfile since the installer will do that.

3.    At the command line, launch the script by typing 'tclsh patch_install_[ver].tcl', and that's all.


The script should detect which patches you've installed previously, copy the new code files to the necessary directories, determine whether complete or only partial rebuilds are necessary, and finally perform the rebuilds. Numbers listed in red indicate that the patch modifies the interface to one or more of XSPEC's libraries. These patches will generally cause longer rebuilds. If you have a local model library, it is recommended (though not always necessary) that you rebuild it with initpackage after applying red patches.


12.9.0a This fixes a bug in the calculation of agauss/zagauss models. Our thanks to Doug Burke for pointing this out. Report added on Aug 05, 2015.

This patch modifies heasoft-6.17/Xspec/src/XSFunctions/ calcGaussianLine.cxx

12.9.0b The (b)vvapec model calculation exits early with an "Unrecognized value of itype" error. Our thanks to Doug Burke for pointing this out. Report added on Aug 06, 2015.

This patch modifies heasoft-6.17/Xspec/src/XSFunctions/ smdem2.cxx

12.9.0c If a link expression is entered during the parameter prompting stage when initially defining a model, AND the link uses the new 'p' format specifier AND the link is to a parameter within the same model and data group, XSPEC will improperly reject the link as invalid. Note: This is mostly likely to occur when reloading a model from an XSPEC save file, as save files now use the 'p' format when storing link expressions. Our thanks to Kenji Hamaguchi for pointing this out. Report added on Aug 14, 2015.

This patch modifies heasoft-6.17/Xspec/src/XSModel/Parameter/ ParameterLink.cxx

12.9.0d The lmod command is not working when called from an xspec.rc start-up file. To load local models from the .rc file, XSPEC is requiring that you use the Tcl 'load < /path/to/liblocalMod.so >' command rather than the lmod shortcut. Our thanks to Eric Miller for pointing this out. Report added on Aug 31, 2015.

This patch modifies heasoft-6.17/Xspec/src/XSUser/Handler/ xsLmod.cxx

12.9.0e The 12.9.0 enhancements which allow the data and back commands to handle files with multiple SPECTRUM extensions should not be applied to OGIP type-II files. Otherwise this can cause loading difficulties when the background is from another row within the same file as the spectrum. Our thanks to Kim Page for pointing this out. Report added on Oct 15, 2015.

This patch modifies heasoft-6.17/Xspec/src/XSUser/Handler/ xsBackgrnd.cxx

12.9.0f The files used by NEI v2 models are not installed correctly. Note that if you previously downloaded these files using the link at the bottom of the heasoft downloads page you should discard them and use only the files included in the distribution. Our thanks to Svet Zhekov for drawing this to our attention. Report added on Nov 5, 2015.

This patch modifies heasoft-6.17/Xspec/src/spectral/modelData/ Makefile

12.9.0g An error was introduced in v12.9.0 when interpreting levels given in the plot contour command. This fix restores the old behavior. Our thanks to Kim Page for spotting this. Report added on Nov 5, 2015.

This patch modifies heasoft-6.17/Xspec/src/XSPlot/Commands/ ContourPlot.h, XSPlot/Plot/ CreateContourPlotGroups.cxx, and .h

12.9.0h This restores the ability to read in XFLT keywords whose values are numbers encoded as strings. Previously 12.9.0 could only read XFLT strings of format "< key> :< val> ". Our thanks to Nora Troja for bringing this to our attention. Report added on Nov 19, 2015.

This patch modifies heasoft-6.17/Xspec/src/XSModel/Data/ OGIP-92aData.cxx

12.9.0i Fix to the compPS additive model for the case of using cylindrical geometry. The model was retrieving the H/R value from parameter 10 rather than parameter 8. Our thanks to Yuki Yoshida for bringing this to our attention. Report added on Dec 17, 2015.

This patch modifies heasoft-6.17/Xspec/src/XSFunctions/ compps.f

12.9.0j The renorm operation fails and may crash when performed on a mixing model with one or more of its norms frozen. This can also appear during fitting and the error command when performed in auto-renorm mode. Our thanks to Alessandro Paggi for bringing this to our attention. Report added on Feb 16, 2016.

This patch modifies heasoft-6.18/Xspec/src/XSFit/Fit/ StatMethod.cxx

12.9.0k When using xsatbl or addTableCalc to access an additive table model the redshift is restricted to greater than zero. This patch changes the behavior to allow negative redshifts greater than minus one. Our thanks to Mike Nowak for bringing this to our attention. Report added on Feb 25, 2016.

This patch modifies heasoft-6.18/Xspec/src/XSModel/Model/Component/OGIPTable/ TableModel.cxx

12.9.0l A crash may occur when running the xset command with a model loaded but no data. Our thanks to Maxim Markevitch for bringing this to our attention. Report added on Mar 21, 2016.

This patch modifies heasoft-6.18/Xspec/src/XSModel/GlobalContainer/ DataContainer.cxx

12.9.0m PyXspec enhancement. This adds 2 new attributes to the Chain class: Chain.walkers and Chain.algorithm. The first is for setting the walkers value for Goodman-Weare chains. The second is to allow toggling between chain algorithm types: 'gw' (Goodman-Weare, the default) and 'mh' (Metropolis-Hastings).

As with other Chain attributes, the default values for these are set through their corresponding attributes in the AllChains chain container: AllChains.defWalkers, AllChains.defAlgorithm. They may also be reset for new chains individually by passing them as arguments to the Chain object constructor:

c1 = Chain("chain.fits", runLength=48, walkers=6) # Creates a G-W chain using 6 walkers
c2 = Chain("chain.fits", algorithm="mh") # Creates a chain using Metropolis-Hastings.

This patch also fixes a bug which was preventing the resetting of the Metropolis-Hastings temperature parameter. Report added on Mar 29, 2016.

This patch modifies heasoft-6.18/Xspec/src/XSUser/Python/xspec/ PyFit.cxx and chain.py

12.9.0n PyXspec enhancement. This adds a new tclLoad method to the AllModels container. It provides a lower-level alternative to the lmod method for loading local model libraries. It is intended to be the equivalent of doing a "load /path/to/lib_your_mod.so" call from standard Xspec. The proper usage is:

AllModels.tclLoad("/path/to/lib_your_mod.so").

Our thanks to Roderick Johnstone for this suggestion. Report added on Apr 27, 2016.

This patch modifies heasoft-6.18/Xspec/src/XSUser/Handler/ XSinterface.h, xsLmod.cxx, XSUser/Python/xspec/ PyModel.cxx, .h and model.py

12.9.0o The various apec models have incorrect normalization dependence on redshift in v12.9.0 (the fitted normalization is a factor ~(1+z) too small). In v12.8.1 and 12.8.2 (but not in 12.9.0) there is also an incorrect abundance dependence on redshift (the fitted abundance is a factor ~(1+z) too small). Versions earlier than v12.8.1 had the correct redshift dependence for both normalization and abundance. These problems are solely in the XSPEC code and are not due to anything in AtomDB. Our thanks to Keita Miyaoka and Adam Mantz for noticing this. Report added on Jun 15, 2016.

This patch modifies heasoft-6.19/Xspec/src/XSFunctions/ Aped.cxx

12.9.0p It is not currently possible to unlink an already linked parameter in a Python-coded local model in PyXspec. This patch is needed to add that functionality. Our thanks to Christian Schneider for bringing this to our attention. Report added on Jul 27, 2016.

This patch modifies heasoft-6.19/Xspec/src/XSModel/Parameter/ Parameter.cxx

12.9.0q There is a subtle problem in simftest which could cause parameters used in the simulations to random walk away from those of the best fit rather than be distributed around it. This became notable when running many simulations when the model moved into an invalid region of parameter space. Our thanks to Simone Lotti for bringing this to our attention. Report added on Aug 19, 2016.

This patch modifies heasoft-6.19/Xspec/src/scripts/ lrt.tcl and simftest.tcl

12.9.0r When using the GW method for MCMC the initial walkers can be incorrect if the hard limits for a parameter are very restrictive. Our thanks to Mariano Mendez for reporting this. Report added on Aug 19, 2016.

This patch modifies heasoft-6.19/Xspec/src/XSFit/Fit/ Fit.cxx

12.9.0s When making a 2-D contour plot in the same session from which an earlier 1-D contour plot was run, Xspec still attempts to draw the 1-D plot's horizontal bar showing the minimum statistic. Our thanks to Laura Brenneman for bringing this to our attention. Report added on Aug 19, 2016.

This patch modifies heasoft-6.19/Xspec/src/XSPlot/Commands/ ContourPlot.h


Older Versions:

Final issues/patches pages:
    12.8.2
    12.8.1
    12.8.0
   
Links to v11 bugs pages:
       v11 Bugs       v11 Bug reporters

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Last modified: Thursday, 18-Aug-2016 14:54:33 EDT