Saturday, December 29, 2007

Webspec for Chandra Cycle 10

Updated Webspec with the Chandra cycle 10 responses.

Wednesday, December 19, 2007

Suzaku XIS response generator

Checked in xsl_suzaku_xis_makeresp, an automated script to build the XIS rmf and arf by calling xisrmfgen and xissimarfgen. Three speed options (fast, medium, slow) use different channel and energy binning schemes as well as different accuracies in the xissimarfgen run. The accuracies probably need a little more tweaking.

The point source option assumes that the source is in the center of the WMAP. Other possibilities here are to use ftstat on the WMAP to get the pixel with the highest value or the centroid of the map. It's not clear which is the best thing to do.

I would like to be able to use the algorithm found by Randall and implemented in xissmooth. This requires turning xissmooth into a general purpose ftool.

first xspec v12.4 patches

A couple of minor patches are now up

12.4.0a This fixes some cases where invalid input leads to segmentation faults: The model command crashes for certain forms of invalid model syntax. The tclout command crashes for some of its options when the invalid spectrum number 0 is specified while there are data sets loaded. Our thanks to Jeremy Sanders for pointing this out. Report added on Dec 10, 2007.

This patch modifies headas/Xspec/src/XSUser/Handler/HandlerUtils.cxx, XSUtil/Parse/Expression.cxx, and XSPlot/Plot/Plot.cxx

12.4.0b For the model command, entering the abbreviated name bkn should select the bknpower component and not the bkn2pow component. Our thanks to Davide Donato for pointing this out. Report added on Dec 18, 2007.

This patch modifies headas/Xspec/src/manager/model.dat

Wednesday, December 12, 2007

MJDREF precision and time filter file in extractor

Craig Markwardt spotted that when extractor writes out MJDREF it is only in single precision while it can be read in at double precision. Modified this to preserve precision as v4.80.

Craig also noted that the time filter file can be specified as just the filename or the filename with a numerical HDU specifier but not with a named HDU eg filename[STDGTI]). This is now fixed in v4.81.

Monday, December 10, 2007

XSPEC wiki and some notes for Suzaku

I've added notes for the Suzaku meeting in San Diego to the new XSPEC wiki.

Friday, December 07, 2007

Friday, November 30, 2007

running xspec as a shell

John Baker just came up with a way of running xspec which hadn't occurred to me. Create a file of xspec commands with the first line as


This has the advantage that arguments can be used eg

cat > testscript.xcm
data $argv

chmod +x testscript.xcm

testscript.xcm file.pha

Thursday, November 29, 2007

model.dat entry for refsch in xspec v12

The refsch model.dat entry has a unit on one parameter of "erg cm/s". This is not interpreted correctly by xspec v12 with the result that the default input parameter values end up strange. The fix is to change the unit definition to ergcm/s.

Monday, November 26, 2007

bad error in gabs model

Takao Kitaguchi and colleagues at the University of Tokyo point out that the gabs, gaussian absorption, model gives a result dependent on the energy bin size. This has been fixed in v11.3.2aj and v12.4.0.

Wednesday, November 14, 2007


Wrote a handy XSPEC Tcl procedure to multiply the covariance matrix used in an MCMC chain proposal distribution by a factor. Use after defining a proposal distribution by eg
 XSPEC12>chain proposal cauchy fit
XSPEC12>source rescalecov.tcl
XSPEC12>rescalecov 0.5
which divides all elements in the covariance matrix by 2.


Created a new ftool to correct the XMM RGS response for an extended source. This uses Andy Rasmussen's code included in the xspec v11 model rgsxsrc. Since that model has no free parameters it seems easier just to modify the response matrix before reading it into xspec and that is what this new tool does. This replaces the need to add rgsxsrc to xspec v12.


Flegal et al. discuss error estimation methods for MCMC computations.

Clifford Will notes that if there are stars in highly eccentric short period orbits (<~0.1 year) around Sgr A* they could be used to test the no-hair theorem. Cen & Fang show that GRBs may be biased tracers of star formation.

Eckert et al. use Integral IBIS imaging of the Coma cluster to find a hard X-ray source extending in the direction of the sub-cluster and co-incident with 1.4 GHz emission.

Ajith et al. construct a template bank for the GW signal from coalescing non-spinning BHs.

Ishak et al. show that gravitational lensing has a dependence on the cosmological constant and that current observations place an upper limit which is competitive with values determined from cosmology.

Davison & Sartori present their approach to the "Banff Challenge" of finding a signal in noisy particle physics data.

Dimopoulos et al. propose GW detection using atom interferometry which has the potential to be more sensitive than LIGO from the ground and LISA from space.

Tuesday, November 13, 2007

xspec plot contour

The contour information being passed from xspec to PLT was not at a high enough precision leading to problems when there are many (>10000) data channels and hence a large value of chi-squared. Fixed this for the 12.4 release.

Thursday, November 08, 2007

fluxerror and linked parameters

Robert Dunn pointed out that fluxerror.tcl doesn't work correctly if there are linked parameters. I made a simple fix to correct that. It does require the xspec 12.3.1an patch.

Friday, November 02, 2007


Jasra et al. present a population-based Reversible Jump MCMC method and argue that it works better than other MCMC methods on high dimension problems.

Hardcastle et al. report on an accumulated 700ksec observation of the Cen A jet which shows that the outer part of the jet requires an as yet unknown distributed acceleration mechanism.

Gierlinski et al. argue that the high frequency end of the power density spectrum in the hard states of BH sources is invariant in shape and the amplitude provides an estimate of the mass.

Snowden et al. present a catolog of 70 XMM cluster observations with a detailed description of their handling of background.

Lang & Hughes investigate the ability of GW observations to localize a SMBH-SMBH merger.

Narayan et al. fit Novikov-Thorne thin disk models to X-ray transients in the thermal state and estimate black hole rotation rates.

Mahdavi et al. compare weak lensing and X-ray measures of mass and find evidence for non-thermal pressure support.

Bianchi et al. use XMM and optical observations of NGC3147 to show that it has no intrinsic X-ray absorption but also no optical broad lines.

Thursday, November 01, 2007

XSPEC bug fixes for tclout plink and fakeit

A couple of recent minor bug fixes...

12.3.1an For the tclout plink option, it is more useful to output the link string in a format which can be used as input for other parameter commands, such as newpar. Our thanks to Jeremy Sanders for pointing this out. Report added on Oct 15, 2007.

The fix is to replace headas/Xspec/src/XSUser/Handler/xsTclout.cxx, and rebuild xspec.

12.3.1ao When a fakeit run is using a response with first legal channel number (TLMIN4) = 0, and is NOT based on an already existing spectrum, the last channel is erroneously ignored and always ends up with 0 counts. Our thanks to David Morris for pointing this out. Report added on Oct 31, 2007.

The fix is to replace headas/Xspec/src/XSModel/Data/SpectralData.cxx, and rebuild xspec.

Monday, October 22, 2007

rbnrmf bug in energy binning

I made an error in the new energy binning option - I should be averaging the response rather than summing it so the resulting responses were too large by the binning factor. Also, there was a one-off problem for responses with zero-based channels. Checked in fixes.

Friday, October 19, 2007


Franz discusses confidence regions on ratios.

Hague et al. discuss statistical tests for deviations from the power-law for the cosmic ray energy spectrum.

Lang & Hughes investigate the ability to localize SMBH mergers from the GW signal.

Comastri & Brusa review AGN results from X-ray surveys and their multiwavelength follow-up and consider that case for 2-3 Msec XMM survey.

Rapetti & Allen consider what it would take to use X-ray observations of cluster of galaxies to determine dark energy parameters with a precision comparable to other methods.

Brunetti et al estimate hard X-ray fluxes from clusters of galaxies and relate them to prospective observations with SIMBOL-X.

Thursday, October 18, 2007


Spent some time working on webspec. Main changes are to the look : the front page is more compact so I don't have to scroll down to hit the button; the advanced page allows up to 9 components; the basic and advanced pages both read the list of missions from the same file so they won't fall out of step as in the past; the page to set exposure and parameters has been tidied up a bit; the results page now has the plot next to the set of options to change plotting parameters.

I would like to have the replot option simply change the plot on the current results page rather than opening a new page however this would involve substantial programming changes. Another nice option would be the ability to make contour plots (by running steppar) however this is a potentially huge cpu hog and I'm not sure we want to do this on the main web servers. Perhaps this would be better as part of heraspec.

UPDATE: Fixed a problem that appeared under Safari - the check box for background was not coming up checked by default because I put checked inside double quotes in the html input tag.

Monday, October 15, 2007


gcc 4.2 and later now includes support for the OpenMP shared-memory parallelization API. This would be a good way of adding support to xspec for multi-core machines. This can be used in C/C++ or Fortran and provides a simple way of parallelizing loops.

Wednesday, September 26, 2007

xselect and directory paths with spaces

Eric Miller points out that xselect runs into problems on the Mac if the directory path has a space in it even if a soft link is used to produce a path without a space. This occurs because xselect calls getcwd to return the current working directory and getcwd resolves any links to give the absolute path. This then runs into the customary problems with directory paths containing spaces.

The best workaround seems to be to change xsel_utils.f and replace

call XPICWD(wrkdir)


wrkdir = "./"
call XSL_EXPAND_DIR(wrkdir,status)

since the xsl_expand_dir routine in xsel_unix_c.c spawns a shell and runs pwd to get the current directory path. This method does preserve links.

Note that having an explicit directory path with a space (ie no links) fails in all sorts of ways and will be very hard to work around.

Thursday, September 20, 2007

Linking parameters in xspec

There is a subtle issue when linking parameters in xspec. If you do something like

XSPEC12> newpar 5 = 12

then the hard limits used for parameter 12 are those of parameter 5. This is not usually a problem however if parameter 12 is part of a table model and its tabulated parameters cover a smaller range than parameter 5 it is possible for the fit to reach a point outside the available tabulated data. This will generate a warning message in v11 and an error message in v12.

The best workaround is to always make sure that table model parameters are linked to rather than from so that the hard limits in use will be those from the table model.

Thursday, September 06, 2007

bad channels in the Suzaku XIS

Koji just spotted that xselect sets the channels 1-81 bad for the Suzaku XIS and this ought to be 0-81. Checked in a fix to xselect.mdb.

Thursday, August 30, 2007

Removing values of names set using xset

Jeremy Sanders enquires how to return to the default after having used xset to change APECROOT. Doing
actually works although this is undocumented and is misleading because doing an xset then shows APECROOT still existing but with no value. Fixed so that the name no longer shows up as existing.

Tuesday, August 28, 2007

Abundances in NEI models

Frank Haberl pointed out that the documentation on the NEI models is wrong. The documentation states that abundances are wrt Anders & Grevesse while in fact they are relative to whatever is set by the abund command. This was a change in code from June 2005 which was never documented. Updated all the relevant files (11.3.2ai).

Thursday, August 23, 2007

PGPLOT PS driver

Phil Evans reports occasionally losing a few pixels from text labels due to the bounding box being set too small. Made a simple fix in grtext.f to add 2% in each direction.

rdblur model

The hard lower limit on the Rin parameter for rdblur should be 6, not 0 as currently set. If Rin < 6 then the model returns zero.

Monday, August 20, 2007

xspec updates

Bug fixes/updates from Craig. These are all listed on the bugs page.

12.3.1ak This fixes dummyrsp so it can be applied to any model for a given spectrum, and can now take advantage of XSPEC's recently added multiple sources capability in the same way as the response command. Previously dummyrsp only worked properly for the standard single source cases. This also fixes a Solaris specific bug, which could cause NaN calculation errors when folding a model with a dummy response. Report added on Aug 20, 2007.

The fix is to replace headas/Xspec/src/XSModel/Data/ SpectralData.cxx, src/XSModel/Data/Detector/ UserDummyResponse.cxx, src/XSModel/GlobalContainer/ DataContainer.cxx, src/XSUser/Handler/ xsDummyrsp.cxx, xsResponse.cxx, and rebuild xspec.

12.3.1al Using delcomp to remove a table model component causes a segmentation fault. If editmod is used on a model with a table component, and the component is written with an abbreviated form of "atable", "mtable", etc., editmod erroneously considers it a modified component. Report added on Aug 20, 2007.

The fix is to replace headas/Xspec/src/XSModel/Model/ Model.cxx, src/XSModel/Model/Component/ Component.cxx, and rebuild xspec.

12.3.1am A couple of output formatting improvements: lumin output should be in standard "d.ddde+EE" format and not written as "d.ddd x 10^EE". The margin command output should switch from fixed to scientific format for a wider range of exponent values. Our thanks to Jeremy Sanders for pointing this out. Report added on Aug 20, 2007.

The fix is to replace headas/Xspec/src/XSFit/MCMC/ MarginGrid.cxx, src/XSModel/Model/ Model.cxx, and rebuild xspec.

Thursday, August 16, 2007

building lisatools

Building lisatools using the instructions provided by Michele. A few things to note :

1. The correct svn command is
svn co lisatools

2. The build of synthLISA fails with a C++ error. This is because python2.5 requires the
SWIGged files to have been created by swig 1.3.31, not the swig 1.3.29 in lisatools. Grabbed
the new gzipped swig from sourceforge and replaced in lisatools/Packages. Then edited to use 1.3.31 instead of 1.3.29.

3. This still fails because the SWIGged files are not created in the standard build. Deleted
lisasim/{lisasim-swig_wrap.cpp,} then built synthLISA using the in
synthLISA-1.3.3. Note that if I rerun the it reextracts the contents of the
tarfile and puts back the two files I just deleted.

Monday, August 13, 2007

xspec lumin command

Jeremy Sanders points out that the lumin command doesn't write the number in standard computer notation (x.xxxxxe+yy) unlike every other output number in xspec. So, modified Model.cxx appropriately.

xselect array sizes

Kenji ran into a problem with xselect trying to use a large number of MKFs. Since the cost in memory is low I increased most of the sizes in the file.

Saturday, July 28, 2007

Ubuntu network problem

I ran into a problem with avahi that appears to be relatively common. My version is that the wireless networking fails and Network Tools shows a network device called eth1:avahi which shows a few transmitted and received bytes (with errors) but no interface information. This device appears to have preempted the correct eth1 device. I killed this rogue device using
sudo avahi-autopid --kill eth1
then after a while wireless works again as the eth1 device shows a connection.

At the suggestion of omingo I have done a
sudo apt-get --purge install avahi-autoipd --reinstall
to make sure the latest version of avahi-autopid is in use.

Update: this doesn't seem to have helped. Another possible workaround seems to be to go to Wireless Connections Properties using the Network Settings tool and switch from DHCP to Zeroconf, click on OK, wait for the tool to finish resetting the connection, then go back into Properties and switch back to DHCP.

Update: this may actually be a problem with network-manager. I've made the fix to NetworkManager.conf for bug 40125. Did a suspend then restart and the wireless connection came up correctly which it has not done before.

Thursday, July 26, 2007

HEAsoft built under Ubuntu

Successfully built the HEAsoft distribution on my new Dell with Ubuntu Feisty Fawn. I had to get a number of packages...

sudo apt-get install gfortran g++
sudo apt-get install libncurses5-dev
sudo apt-get install x-dev libx11-dev libxt-dev

Just to be on the safe side (and under bash) I did a

export F77
export CC
export CXX

Then the configure and build is

./configure > config.out 2>&1 &amp;
make > build.log 2>&1 &
make install > install.log 2>&1 &

Wednesday, July 25, 2007

Cisco VPN client and Ubuntu Feisty Fawn

Working on setting up my new Dell laptop which came preinstalled with Ubuntu Feisty Fawn. A little work needed with the Cisco VPN client - the version downloaded from Goddard CNE needs patching for recent versions of Linux. Fortunately, there are really helpful instructions on using the VPN client available. Tricks I had to do were
sudo chmod 4111 /opt/cisco-vpnclient/bin/cvpnd
/etc/init.d/vpnclient_init restart

to get round the error messages
privsep: unable to drop privileges: group set failed.
The application was unable to communicate with the VPN sub-system.

then I got
Initializing the VPN connection.
Initiating TCP to, port 10005
Secure VPN Connection terminated locally by the Client
Reason: Failed to establish a VPN connection.
There are no new notification messages at this time.

This occurs if both the wireless and ethernet connections are enabled at the same time. I turned off the ethernet connection by going to Network Settings selecting Wired Connection then clicking on Properties followed by checking the Enable Roaming Mode box.

Friday, July 20, 2007

update of fluxerror.tcl for multiple datasets

Shao Li noted that fluxerror.tcl doesn't work if multiple datasets have been read in. An immediate workaround is just to change "tcloutr flux" to "tcloutr flux 1" in the script. I have checked in a new version of the script which returns an error range for each dataset - note that the flux ranges will only actually be different if the datasets are members of different datagroups.

Thursday, July 19, 2007

xspec v12 gain fit parameters

Craig has fixed the gain fit parameters so they can be individually frozen during a fit (other than just having both parameters fixed or free). This makes the behavior similar to that available in v11. v12.3.1ae.

swind1 model update

Chris Done supplied modified model.dat information for her swind1 model which is currently available through the new models website. The only change is to the allowed range in the column parameter.

Wednesday, July 18, 2007

Unable to save file in xspec v11

Glenn Morris reported that when xspec v11 is built using gcc4 then the save command will not allow an existing filename to be overwritten. This turned out to be because in this case the Fortran OPEN command returns an IOSTAT=1, not IOSTAT=128 as per gcc3. This breaks the code in OPENWR in sys.lnx and sys.darwin. Fixed in v11.3.2ah by using an INQUIRE in these two files to check for a pre-existing file.

Note that the sys.* options are labelled by operating system however all those running gcc should be the same (eg sys.lnx and sys.darwin).

Friday, July 13, 2007

invalid filter expressions in extractor

Extractor was silently ignoring invalid filters attached to filenames eg infile.fits[pi>100]. Now it at least generates an error message. Note that the only allowed filters are of form name=#:#. v4.79

xspec v11 bug in HEAsoft 6.3

One of my minor mods to xspec v11 to support the use of the gfortran compiler introduced a bug in the addcomp command - inserting a component into the model caused the name of the final component to be changed to CPCMOD. Thanks to a report from Lisa Winter we caught this within a week of the HEAsoft 6.3 release and have updated the tar files.

Monday, June 04, 2007

xspec v11 on 64-bit Linux

Glenn Morris reported the very strange error "Fit parameter*** belongs to no model" when running xspec v11 on a 64-bit machine with RHEL4. We have established that this is a function of compiling using gcc/g77 3.4.6 and upgrading to gcc/gfortran 4 (ie RHEL5) solves the problem.

Tuesday, May 29, 2007


Roelofs et al. derive parallaxes for a set of AM CVn binaries and predict LISA GW signals.

Dietrich et al. describe BLOX, a program to select galaxy clusters based on optical, X-ray and weak lensing shear.

Percival et al. measure the baryon oscillation signal at z=0.2 and z=0.35 using SDSS and 2dFGRS to constrain w=-1.004 +/- 0.089 for a flat model including the supernova and CMB constraints.

Wallin et al. place limits on deviations from Newtonian gravity in the outer Solar System through observations of the orbits of TNOs.

Markevitch points out that X-ray emission from clusters of galaxies depends on the He abundance in their cores which is unknown (and may be enhanced due to sedimentation). Combining SZ measurements with distances determined using other techniques can be used to estimate the He abundance.

Ruiter et al. calculate the LISA foreground due to mass-transferring binaries and find that it becomes significant at frequencies above ~7 mHz.

Bickel et al. develop methods for searching for periodicity in photon event times with application in the gamma-ray regime.

Prix & Whelan apply F-statistic methods developed for LIGO to the MLDC binary challenges.

srcut and sresc seg fault in xspec v12

Heather Matheson at U.Manitoba reported that srcut seg faults in v12. This turned out to be due to an error in the C++ to Fortran conversion for the power-law routine that is called by srcut and sresc.

Tuesday, May 22, 2007

another seg fault in compps

I had a slight error in the dynamic memory allocation for the compps model which caused a potential seg fault if the response had < 88 energy bins. This is patched in both v11 and v12.

Thursday, May 17, 2007


Jee et al. use weak-lensing analysis of Cl0024+17 and find a ring of dark matter which they interpret as the result of a high-velocity line-of-sight collision.

Tsalmantza et al. present the first results from a program to generate a library of synthetic galaxy spectra to be used to classify the several million unresolved galaxies whose spectra will be acquired by Gaia.

Wu & Wang calculate Fe K line shapes from relativistic accreting disks including the effects of self-shadowing.

Tornatore et al. use hydro simulations to investigate chemical evolution in clusters of galaxies.

Trimble et al. summarize astrophysics in 2006.

Padmanabhan reviews dark energy cosmology, argues that only a cosmological constant makes sense and that the problem cannot be satisfactorily solved at our current level of (mis)understanding.

Fiore et al. combine optical, IR, and X-ray observations of the Chandra Deep Field South to identify the Compton-thick AGN that have so far been missing from deep Chandra observations.

Kelly describes a Bayesian approach using Gaussian mixtures for linear regression in the presence of measurement errors, non-detections, and selection effects.

Eckert et al. analyze a 1.1Ms Integral ISGRI observation of the Coma cluster to find an extended hard X-ray excess in the direction of the infalling cluster A1376.

Sanders & Fabian continue their analysis of the very deep Chandra observation of the Perseus cluster finding a) the ripples interpreted as sound waves carry a significant fraction of the energy lost to radiative cooling b) the distribution of metals peaks at 40 kpc and is clumpy on scales of 5 kpc c) there is no evidence for thermal emission from the radio bubbles.

Repin et al. give analytic approximations for the relativistic Fe K line shape from accretion disks. A table is available.

Friday, May 04, 2007


Jeremy Sanders provides a faster version of the gsmooth model which precalculates an array of erf values then interpolates on them.

Thursday, May 03, 2007


Stanek proposes a an alternative history version of astro-ph for failed telescope and other proposals. Probably should have come out on Apr 1.

Feroz & Hobson describe an efficient sampling method for multimodel and/or degenerate distributions when calculating Bayesian evidence.

Hallman et al. use numerical simulations to show that using beta-model fits to X-ray data in the analysis of SZE observations leads to systematic biases and suggest a simple correction.

Miller reviews relativistic X-ray lines from the inner regions of accretion disks.

Magliocchetti & Bruggen combine X-ray data from the REFLEX and NORAS samples and radio data from the NVSS to investigate the effects of radio sources on the cluster L_X-T relation.

Kitaura & Ensslin survey Bayesian reconstruction schemes for large-scale structure.

Kerkyacharian et al. present a new estimation method for the inverse problem building on SVD decomposition.

Wednesday, May 02, 2007

building with gfortran

Successfully built headas on my Mac using the gfortran from the installer supplied at This places the gfortran library files in /usr/local/gfortran/lib so configure has to be altered so that F77LIBS4C in hmakerc includes this directory. If the gfortran plug-in for Xcode is used then the gfortran library files end up in /usr/local/lib which is in the link path anyway so need not be specified in F77LIBS4C. Also had to update cctools to avoid an undefined dso_handle. Had to add DHAVE_ETIME=1 to DEFS in hmakerc to ensure that etime is not defined again in xanlib/sysdep/sysc.c.

Not directly connected to gfortran but we discovered cod.dhf was not being built - this requires running hlpdhf on cod.hlp which means ensuring ia/doc is built ahead of qdp.

Tuesday, May 01, 2007

udmget : Too many blocks error

Both Roderick Johnstone and Ewan O'Sullivan have reported getting "Too many blocks" errors when using xspec v11 with complicated models. MAXBLK is set to 100 in udmget.c and there is no good reason why this should be so small. I've changed this to 1000 for the next release which should solve these problems.

Note that Bryan has updated xspec/src/tcl/Makefile so that it will rebuild libxantcl* when changes are made in the libxanlib* library. I really should be building libxantcl under the xanlib tree rather than the somewhat bizarre way it is done at present under the xspec tree.

Monday, April 30, 2007

hk file extension numbers in xselect

Change requested by Suzaku XIS team to allow multiple extensions in HK files. The read hk command now allows an extension to be given eg filename+3. This entire name plus extension is passed to maketime when doing a select hk. The code change does in principle allow the same syntax to be used when reading an event file however this is disabled because in some places xselect appends a +1 extension descriptor to the event file name.

Thursday, April 12, 2007

xspec v11 and gfortran block data problem

Put in workarounds for the block data initialization problem with gfortran. None of these should have any discernible effect but we shall see. The changes were in the default values for genfit, the default names for model components, the default gain parameters in response, and the atdata.f routine used by the NEI models.

This latter has been changed in xspec v12 as well.

Errors on fluxes of model components

A frequently requested enhancement for xspec is to be able to estimate the error on the flux from part of the model eg the model without Galactic absorption. I've now written a more detailed explanation and provided a helpful Tcl script. It should be possible to incorporate this functionality within xspec itself.

Monday, April 09, 2007

gfortran compiler and BLOCK DATA

The gfortran compiler appears to have a known issue with intializing common variables in a BLOCK DATA. This leads to problems in xparse with the XPRSBD block and causes msetup to fail. The workaround is to create a dummy routine which calls XPRSBD and insert a call in any xparse routine that uses variables in the BLOCK DATA. This fixes the problem and xspec v11 builds and runs the session/xspec.xcm script successfully. However, there are other BLOCK DATA in HEAsoft so we need to make similar fixes for them. Note that in Fortran 90 and later code BLOCK DATA is supposed to be replaced by MODULE.

Wednesday, April 04, 2007

xspec background models

I wrote a slightly longer explanation of the v12 replacement for v11 /b models. I also added a link from the xspec FAQ.


Evans et al. describe the on-line database of Swift GRB lightcurves.

Tombesi et al. find a variable redshifted Fe K line with a modulation timescale of 27 ksec using XMM observations of NGC3783.

Bonavita & Desidera note from a literature search that there appears to be no difference between planet detection rates in single and binary star systems.

Migliori et al. analyze XMM observations of the radio lobes of Pictor A and finds that the particle energy is above the equipartition value and that spacial changes in radio flux are due to magnetic field variation.

Zhang et al. discuss how to test standard gravity on cosmological scales by comparing matter overdensity to gravitational lensing.

Kurucz argues that the exoplanets detected so far are "cryptoplanets" formed from matter ejected by protostars.

Bryan et al. (the CMU astrostatisticians) present a new method to determine multidimensional confidence intervals and apply it to the cosmological data.

Porter & Ferland discuss the addition of He I like lines to Cloudy and their use for diagnostics.

Afshordi considers the accuracy of mass estimates from SZ surveys of clusters.

Erickcek et al. note that the X-ray quantum calorimeter (XQC) rocket flight can be used to place strong constraints on interaction cross-sections between baryons and dark matter.

Rudnick et al. point out that the WMAP cold-spot corresponds to a dip in the number counts of NVSS sources. If this is Sachs-Wolfe effect it would require a void of radius 140 Mpc.

Werner et al. analyze XMM and Suzaku observations of Sersic 159-03 and find a central soft excess but no evidence for lines ruling out thermal sources.

Wednesday, March 28, 2007

long hk and mkf selection expressions in xselect

The Suzaku XIS team ran into a problem with a really long hk selection expression in xselect. I've increased the relevant strings to 4098 characters which should be enough for the moment.

swind1 fix

The swind1.f source file available on the extra models page had an error reported by Roderick Johnstone - lenact was not declared. Fixed this.

Monday, March 26, 2007

gfortran and mac

Just for future reference here is the link for the gfortran plug-in to Xcode.

Friday, March 16, 2007

hardcopy in xspec v12

The hardcopy command is implemented through a script hardcopy.tcl in Xspec/src/scripts. This script had an error and didn't work. Note that implementing a command through a script means that abbreviating the command doesn't work.

uninitialized string in xinfix

Glenn Morris reported bizarre behaviour in xspec11 when giving setplot an invalid argument. This turned out to be an uninitialized string in xanlib/xparse/xinfix.f which has somehow avoided detection before now. Note that we really need to fix the Makefile in xspec11/src/tcl so that libxantcl*.a is rebuilt if libxanlib*.a is changed.

Tuesday, March 13, 2007

compps model

Hiromitsu Takahashi reports that the compps model in xspec seg faults when using the Suzaku XIS response. This is because there were hard-wired array sizes in xscompps.f. I replaced these by dynamic arrays using the standard method as well as removing some unused variables. This change in is v11.3.2ae and will be in v12 shortly.


Gliozzi et al. describe Chandra observations of three Sy IIs whose variability and spectral properties are similar to Sy Is implying these may be AGN without a BLR.

Heavens et al. extend the Fisher Matrix to provide a way of estimating how good a planned experiment will be at distinguishing between different models.

Gilmore reviews the six types of stellar populations in the Galaxy and what can be learned from their study.

Liddle et al reply to a critique of Bayesian model selection by Linder & Miquel noting that the latter authors have made three serious errors in understanding the conceptual underpinnings of the method.

Ignatiev discusses a possible terrestrial test for MOND !

Mahdavi et al. present a joint X-ray, SZ, and weak-lensing analysis of A478.

Ebeling et al. provide a statistically complete subset of the 12 most massive clusters at z>0.5 found in MACS.

Micic et al. estimate the evolution of seed BHs to IMBH and SMBH using cosmological N-body simulations.

Boehringer et al. introduce a survey with XMM of a representative sample of clusters which is designed to investigate the uncertainties in determining cosmological parameters from X-ray cluster surveys.

Smith et al. investigate biassing effects in measuring the baryonic acoustic signature.

Maughan uses his sample of 116 clusters observed using Chandra to investigate the Lx-Yx relation and finds that excludes cores produces a tight relation with 11% scatter in Lx.

Padmanabhan et al. achieve a ~1% photometric calibration of the SDSS.

Wednesday, March 07, 2007

extractor bug in Intel Mac

Jamie Kennea reports problems with extractor on Intel Mac when filtering on a region. If an indirect file was in use for the input event files it was being opened multiple times and not closed. Eventually this generated an error in the fortran open statement. Also moved the ADDFN routine from extractor.f to wstdky.f because it was only being called from WSTDKY. These fixes are v4.76 and go out with HEAsoft 6.2.

Followed up with a whole bunch of mainly cosmetic changes to eliminate most of the compiler warning messages from g95. This is v4.77 and is not part of HEAsoft 6.2.

Another iteration for 4.78 which simplifies the code for reading the file containing the names of input event files and ensures that this file is not opened again when it is already open.

Monday, March 05, 2007


Russell et al. use MCMC to do a joint analysis of Chandra and ROSAT data on the cool core group NGC 4325.

Holder et al. estimate the SZ background and consider the limits on SZ cluster measurements due to confusion effects.

Zhang et al. look at the X-ray properties and scaling relations for 12 z~0.2 clusters observed by XMM-Newton and note that if the central cores are excluded then normalizations agree to 10% irrespective of cluster morphology.

Chartas et al. analyze Chandra and XMM observations of the gravitationally lensed low ionization broad absorption line quasar H1413+117 and detect emission lines.

Fujita et al. look at MHD Alfven waves as a heating method for cool cores in clusters and note that they would also create longitudinal (sound) waves observable as ripples.

Bogdanovic et al. argue that torques during galaxy mergers will tend to align the spins of their MBHs thus reducing gravitational radiation kicks when the MBHs merge.

Ciotti & Ostriker perform high-res hydro simulations with photoionization and Compton heating to investigate the effects of an AGN on the ISM of an isolated early type galaxy.

Trotta presents a new procedure for estimating the Bayes factor of future observation to help with experiment design.

Scharf considers the effects of parallax on exoplanet timing measurements.

Giommi et al. use Swift to measure the X-ray fluxes of blazars which are CMB foreground sources and show that there is a tight correlation between X-ray and microwave fluxes.

Maughan et al. present a summary of the analysis of ACIS-I observations of 116 clusters from z of 0.1 to 1.3.

The HiRes Collaboration detect the GZK cut-off at 6e19 eV, precisely as predicted.

Monday, February 26, 2007

chandra response matrix generation in xselect

Updated the perl script xsl_chandra_acis_makeresp to replace old ftools with new heatools and improve the search for the bad pixel file. Outstanding issues are that mkacisrmf doesn't work with old event files (fails to find a relevant CALDB file) presumably because these event files have to be reprocessed in CIAO 3.4; the current advice is to use mkarf for point sources and mkwarf for extended sources - at present we use mkwarf for all sources; there should be a mechanism for the user to give their own bad pixel file.

bug in kerrbb

There is a memory handling bug in kerrbb (due to my error) which can cause a seg fault if multiple response matrices are in use and the first one does not have the largest number of energy bins. This is fixed in both v11 and v12.

Thursday, February 22, 2007

filter intensity in xselect

Another iteration on the filter intensity perl script in xselect. Replaced most of the calls to old ftools with their heatools analogs. This seems to fix a problem with long filenames.

Wednesday, February 14, 2007

bug in extractor when combining event files

Fixed bug reported by Phil Evans when creating a new event file from multiple input event files with different WCS values. If the sky X and Y columns were integers the new values were calculated as an INT after doing the transformation instead of a NINT causing a possible one pixel shift. Also did some optimization of the code. v4.74.

Update: Also found that the goodfwcs logical variable in EXTWCS was not being initialized which was causing the position recalculation not to occur in some circumstances. v4.75

Keywords: HEAsoft, extractor.

Tuesday, February 13, 2007

xspec error with the migrad method

There was a bug in xspec v12 when using the error command with the migrad method. If there were frozen parameters the wrong parameter number was being passed to the MINOS command.

A useful tip to know when using migrad is that the standard MINUIT output is written to the file mn_output.log in the current directory.

Handy C++ tip: there is a function, distance, associated with maps to return the distance in the first index of the map between two iterators. So if we have a map called mymap and an iterator called iter then the position in the map list of iter is 1+distance(mymap.begin(),iter).

Keywords: HEAsoft, xspec

keV-Angstrom conversion factor in xspec

Both v11 and v12 xspec use a conversion factor from keV to Angstrom of 12.39854. Using the current standard values of constants (CODATA(2002) via NIST) this factor should be 12.3984191. Apparently the difference is noticeable when plotting grating spectra in wavelengths. Made this change in both v11 (bug fix 11.3.2ac) and v12.

Keywords: HEAsoft, xspec

text size in the PGPLOT PS driver

Another tweak of the new PGPLOT PS driver to get the text size closer to that appearing on the screen with other drivers. Also, moved the code to calculate the correction to the string length from grlen to the driver.

Keywords: HEAsoft, pgplot

Saturday, February 10, 2007

ranlux in xspec11

xspec11 crashes when compiled using gfortran apparently due to a problem with ranlux. So replaced xanlib/sysdep/ranlux.f with C code based on the gsl version but with gsl-specific parts stripped out. Note that only the RLUXGO and RANLUX Fortran calls are supported and that RLUXGO ignores the final two arguments (K1 and K2) ie the restart option is not supported.

Keywords: HEAsoft, xspec

Tuesday, February 06, 2007


Portegies Swart et al. test using modern Graphics Processing Units to perform N-body calculations and conclude they show some cost and reliability benefits over specialised hardware.

Brownstein & Moffatt argue that the bullet cluster results are consistent with modified gravity and not with dark matter.

Evrard et al. use an ensemble of heirarchical clustering simulations to argue that sigma_8 = 0.8 in contrast to the best-fit number of 0.69 favored by recent WMAP and SDSS analysis.

Lodato & Natarajan derive the seed function of mass BHs at z~15.

Krongold et al. use an XMM observation of NGC4051 to track changes in the ionization state of the warm absorber and deduce that it comes from an accretion disk wind not the dusty torus.

Schafer provides a statistically rigorous method of estimating luminosity function using truncated data.

Rossetti & Molendi fire back in the controversy over the existence of a non-thermal tail in the X-ray spectrum of the Coma cluster.

Medvedev examines evaporation rates of hot gas from clusters as a possible explanation of recent S-Z results and concludes that for the mechanism to work magnetic fields must be non-existent or highly ordered.

Seto & Cooray discuss a technique for placing limits on primordial BH densities by using pulsar timing measurements to look for impulsive accelerations on the Earth.

Linder & Miquel warn against applying model selection procedures in cosmology without adequate thought about physics.

Hickox & Markevitch look at Chandra deep field data excluding all known HST and Spitzer sources to provide a limit on X-ray emission from the WHIM.

Fusco-Femiano et al. continue the data about the Coma hard X-ray emission.

Chen et al. use ROSAT and ASCA observations of HIFLUGCS clusters to investigate the statistical properties of cooling cores.

Zavlin reviews what is known about thermal emission from neutron stars.

Johnstone et al. analyze the Spitzer 10-37 micron spectra from off-nuclear regions in NGC1275 and 4696.

Monday, February 05, 2007

extractor and string columns

Phil Evans reported a problem that when combining two event files a string column in the output was garbage for all rows copied from the second input file. This happened because the input files had differing WCS so the slow copy method had to be used and this read all columns as doubles. Fixed the problem by checking for string columns and reading/writing them as strings. Note that strings can have a maximum length of 256 characters. Fix is v4.73.

Keywords: HEAsoft, extractor

Tuesday, January 30, 2007

r1mach routine in xspec v11

An internal change to allow compilation using gfortran : the fortran r1mach routine which was included in the file functions/cont.f has been replaced by a C version (with appropriate cfortran macro) in the new file functions/r1mach.c. This should have no effect visible to users. The analogous change has already been made in v12.

Keywords: HEAsoft, xspec

Thursday, January 25, 2007

chatter in xselect

Binbin Zhang asks a question about using chatter in xselect. The chatter command is handled through the xpi gtcom2 call but was not defined in xselect.key and so was rejected as an unknown command. Modified these files so that chatter is now recognised. However, all output from xselect is at chatter=5 so unless we make changes to the xselwrite calls we can either see all the output or none of it.

Keywords: xselect, HEAsoft


Roncarelli et al. calculate the thermal and kinetic SZ signals from a large cosmology simulation and look at correlations with the soft X-ray signal.

Bolton et al. use strong lensing data to replace the surface brightness with mass density in the fundamental plane relation for ellipticals and show that the variance decreases and the tilt is removed implying that early type galaxies are an homologous sequence varying in mass-to-light ratio.

Mathews & Brighenti describe how cosmic rays produced by an AGN generate the cavities and radio sources seen in X-ray emitting clusters.

Edmondson et al. discuss frequentist and Bayesian estimation of photometric redshifts.

Krivinos et al. present results from the Integral/IBIS all-sky survey in the 17-60 keV band.

Ghosh & Raychaudhuri discuss the effect of systematic errors on time series data.

Shaw et al. describe a more efficient scheme for Bayesian inference in cosmology and make available their code.

Kalirai et al. use HST images to measure the proper motion of the globular cluster NGC6397 with respect to the population of background galaxies in the field.

Markevitch & Vihklinin review shocks and cold fronts in the ICM.

Friday, January 12, 2007

Old PS driver

At Andy Beardmore's suggestion put old PS driver back into the distribution available as /OPS, /OVPS, /OCPS, /OVCPS plot types.

Keywords: HEAsoft, pgplot

nsa model in xspec

Slava Zavlin supplied updated versions of the files used by the nsa model. These files are identical to the current versions except that the energy range is extended to 12 keV.

Keywords: HEAsoft, xspec

Thursday, January 11, 2007


Koester et al. create a catalog of 13,823 clusters of galaxies in the SDSS. The algorithm used is described in another preprint.

Collister et al. use a neural network to generate a photometric redshift catalog of over one million luminous red galaxies from the SDSS. The training set is a 15,000 galaxy spectroscopic catalog from Cannon et al.

Houck & Allen describe models for non-thermal photon emission.

Sato et al. measure temperature and abundance profiles in A1060 using Suzaku.

Done & Nayakshin argue that the AGN soft excess is more likely to be due to absorption in a wind than reflection from a disk since the latter, unlike the former, requires fine tuning of the ionization state.

Temi et al. find extended far IR emission from ellipticals using Spitzer and interpret it as due to cold gas buoyantly transported from a reservoir in the core.

Corasaniti et al. note that a new generation of big telescopes and very high resolution spectrographs will be able to measure the change in redshift in quasar absorption line systems over a ten-year baseline and hence constrain models for the cosmic expansion history.

Blasi et al. review expected gamma-ray emission from clusters of galaxies.

Kocsis et al. provide a Fourier decomposition method of determining the position of SMBH binary inspiral observed using LISA.

Ng argues that if spacetime undergoes quantum fluctuations then an EM wavefront acquires uncertainties in direction which will show up in interferometric observations of distant quasars.

Poole et al. use a suite of simulations to investigate the effects of mergers on cluster parameter relations.

de Plaa et al. use XMM observations of abundances in 22 clusters to test SN models.

Sesana et al. consider the prospects for using LISA observations to constrain models of the build-up of SMBHs.

Wednesday, January 10, 2007

bug in rbnrmf

Stephane Paltani reports an array overwrite warning message when running rbnrmf on JEM-X response matrix. It turns out to be due to these matrices having a starting channel of 0 for the EBD extension but 1 for the MATRIX extension. This shouldn't be a problem except that rbnrmf was incorrectly using the number from the EBD extension when rebinning the data from the MATRIX extension. Fixed this as version 5.0.1.

Keywords: HEAsoft, Integral

Monday, January 08, 2007


Bauer et al. use XMM RGS and EPIC observations to investigate the starburst outflow from NGC253. They use cross-dispersion profiles to map the distribution of prominent ions.

Dimopolous et al. propose various laboratory tests of GR using atom interferometry.

Liddle et al. discusses Bayesian evidence for techniques for dark energy.

Petrosian et al. report on RXTE observations of the "bullet cluster".

Clowe et al. present weak lensing results on the cluster 1E0657-558 which shows that the baryon (X-ray emitting) peak is not at the same position as the dark matter peak.

Wheatley & Kallman note the striking similarity between the X-ray spectra of the symbiotic star CH Cyg and Seyfert II - the soft component in both is due to scattering off a photoionized medium.

Dravina reviews quantum optical effects which may be of interest in astronomy.

Ford & Gregory discuss Bayesian model selection in planet searches.

Coble et al. present results on 28.5 GHz radio sources in 90 cluster fields. They find 9 times more sources in cluster cores than in the outskirts which themselves are 3 times overdense in sources relative to the field.

Barnes et al. present the S2PLOT 3-D graphics library.

Churazov et al. use Earth-occulting INTEGRAL observations to measure the CXB from 5-100 keV. They find results consistent to HEAO-1 but with a 10% higher normalization.

Wednesday, January 03, 2007

cstat with background files and low counts

There are bugs in both v11 and v12 which prevent correct convergence for some datasets with low counts in both the source and background files. The v11 fix is available as 11.3.2ab and the v12 fix will be available shortly.

However, it appears that the eventual best fit is still biased - this is likely a statistical rather than computational problem. The model seems to be be biased systematically below the data so a possible approach is to add another term which pushes the total number of model and data counts to be the same.

Keywords: HEAsoft, xspec

Monday, January 01, 2007


Gruzinov estimates molecular viscosity in the ICM due to magnetic fields and finds a value large enough to noticeably damp turbulence.

von der Linden et al. construct a sample of 625 brights group and cluster galaxies from the SDSS and compare their properties with other ellipticals.

Best et al. use their sample of BCGs to show that BCGs are preferentially radio-loud and consider the consequences for cooling cores.

Pfrommer et al. calculate the effects of cosmic rays on the X-ray luminosity and S-Z decrement of clusters of galaxies.

Mix et al. present a primer on astrobiology.

Gilli et al. detail their latest CXB synthesis.

Scargle et al. discuss the problem of testing quantum gravity with timing data on GRBs.

Liddle reviews approaches to the problem of selecting between competing models.

Takei et al. claim a detection of the WHIM in the direction of X Comae both in absorption using the XMM RGS and emission using EPIC.

Nevaleinen et al. look at XMM observations of 4 clusters with previous claims of soft excesses and conclude that there are still significant calibration problems at low energies in either the MOS or PN (or perhaps) both which make it impossible to conclude whether or not there is a soft excess.

Kallman & Palmeri review atomic data sources of relevance for astronomy.