Running marx simulations

The marx Parameter File

The details of a given simulation are controlled by the marx parameter file marx.par. This file currently contains about 270 different parameters which determine everything from the exposure time to the level of scattering off the HRMA surface. Fortunately, only about 30 of these parameters need ever be (or in fact should ever be) modified under most conceivable circumstances. In practice, most typical science simulations can be defined and controlled with less than 10. Template marx parameter files are included as part of the distribution and can be found in the top level of the source directory. The tool plist can be used to print the contents of marx.par in a more readable format while pset can be used to set the values of specific parameters.

marx utilizes an PROS/IRAF–style parameter interface. By default, marx will search for marx.par in the directories specified by the PFILES and UPARM environment variables. The first version of marx.par found will be used. If a valid parameter file is not found in either of these locations, the current directory will be searched. The tool pwhich can be used to check the current parameter file search path.

marx will also assume that the relevant parameter file is named marx.par. An alternative parameter file may be specified by prefixing the file name with @@ and using the resulting expression as argument on the command line, e.g.,

unix% marx  @@/home/user/simulations/marx_cluster.par

The path to the desired parameter file need not be absolute.

Any marx parameters may be set on the command line via the syntax:

unix% marx PARAMETER-NAME=VALUE PARAMETER-NAME=VALUE ...

The program will prompt for a parameter’s value if VALUE is not specified, e.g.,

unix% marx DetectorType=
Reading HRMA optical constants:
        /usr/local/src/marx_5.1.0-dist/marx/data/iridium.dat
Range error occurred while looking at parameter DetectorType.
Select detector type (HRC-S|ACIS-S|HRC-I|ACIS-I|NONE)[]:

Note that there must be no whitespace surrounding the = sign and marx parameters are case sensitive. In the next few sections, we will discuss the various essential parameters the user must adjust to produce a marx simulation.

Simulation Control

By “simulation control”, we specifically refer to any necessary parameter choices which define the execution of the simulation and are not instrument or source related. These include such things as length of exposure, timed versus ray generation execution, and output location and format.

RandomSeed

(default: -1) marx is a Monte-Carlo simulation program, where all parameters (e.g. the energy or position of a photon, the scattering of a mirror or the diffraction in a grating) are drawn from a distribution of possible outcomes by means of a random number. This means that two marx simulations with the same input parameters will give different results, unless they use the same sequence of random numbers. Set this parameter to a positive number to obtain the same sequence of random numbers. The default is -1, which sets the starting number of the random number generator to the current time when the simulation is run.

Exposure Time

marx simulations can be run either in ray generation mode or in timed exposure mode. Timed exposure mode is probably the simulation method most users will employ most of the time.

ExposureTime

(default: 10000) This parameter is used to specify the total integration time in seconds:

unix% marx ExposureTime=10000 ...

would generate a 10 ksec simulation. marx will accumulate photons until the indicated integration time is reached. This mode takes precedence over ray generation mode. If the ExposureTime parameter is set to any positive, non-zero value, the simulation will be run in timed exposure mode. Users wishing to run simulations in ray generation mode, should set ExposureTime=0.

NumRays

(default: 1000000) This parameter sets the number of rays generated in ray generation mode. Note that some rays may be absorbed or scattered outside of the detector, so the detected number of rays will in general be lower than NumRays. To specify the number of detected rays, set NumRays to a negative number. An example for this case is given in Simulating an LETG/ACIS-S observation.

TStart

(default: 2009.5) The sets the time of the observation, e.g. 2014.5 would be the first of July 2014. Some of the calibration files contain a time dependence, e.g. the ACIS detector contamination increases with time. Set this parameter to the time of the observation to reproduce a specific dataset or to the current year for proposal planning.

All numbers below 2100 (when we expect Chandra’s orbit to become unstable) are interpreted as years, all numbers above that are interpreted as “seconds since 1998.0” (the time system of the space craft clock).

Output Directory

Depending on the particular instrument configuration chosen, marx will produce different sets of binary output data files. By default all available information is saved. OutputVectors can modify this, but we recommend not to change this.

In addition to the binary vectors containing the detected event properties, marx also creates an obs.par file in the output directory. The file contains header information about the simulation which marx2fits uses in the creation of the FITS Level 1 event file. This file should not be modified.

OutputDir

(default: point) This parameter specifies the directory where marx output is written. If the directory specified does not exist, marx will create it. Alternatively, if the specified directory does exist, its contents will be overwritten. In addition to the output photon vectors, marx also copies the current version of the marx.par parameter file to the output directory. Note, if the value of OutputDir corresponds to the current directory and the marx.par controlling the simulation resides in this directory, marx will abort with an error message. Output from a marx run can be directed to the current directory, but only if the marx.par file is in another location. This behavior prevents corruption of the marx.par file.

Instrument Configuration

These parameters control the science instruments which are to be used in the simulation as well as which of marx mirror models to use.

MirrorType

(default: HRMA) This parameter can be one of three values: HRMA, EA-MIRROR, or FLATFIELD. The HRMA model is a full raytrace using an accurate physical model of the HRMA’s parabolic and hyperbolic components. Mode details can be found in HRMA model. EA-MIRROR model is a simpler model based on a thin–lens approximation and using tabulated effective area and point spread function data. This simple model is of historical interest only and is no longer accurate or supported. This option should not be selected.

If MirrorType=FLATFIELD, marx will propagate rays to a specified rectangular region in the focal plane parallel to the optical axis. No HRMA vignetting or scattering is applied. The size of the rectangular region which is illuminated is controlled by the parameters listed in Flat Field Model Parameters. Although useful for simulating detector instrumental backgrounds as well as debugging focal plane geometries, simulations created with the FLATFIELD model can not be combined with standard marx simulations employing the default MirrorType=HRMA option.

GratingType

(default: HETG) This parameter can be one of three options: HETG, LETG, or NONE. Chandra carries two sets of diffraction gratings: the Low Energy Transmission Grating (LETG) and the High Energy Transmission Grating (HETG) (see Grating Modules for a full description). The performance of either instrument can be simulated using this parameter. Imaging observations can be simulated by setting GratingType=NONE.

The grating efficiency models in marx currently rely on a set of efficiency tables provided by the HETG and LETG IPI teams. These tables include grating efficiencies for orders -11 to 11 for the HETG and for the LETG, orders from -25 to 25.

An additional parameter has been added to allow the user to disable the grating efficiency calculation. If the parameter Use_Unit_Efficiencies=yes, rays which intersect the HETG or LETG will still be diffracted but no efficiency filter will be applied. Hence all orders will have an equal probability of being populated.

Focal plane detectors

DetectorType

(default: ACIS-S) The user has the choice of all four Chandra focal plane detectors including the ACIS-I, ACIS-S, HRC-I and HRC-S, see Detector Models. DetectorType can also be set to NONE. In this case, marx does not project the rays to the focal plane but stops at the last simulated element, either the HRMA or the gratings if included. This option is useful for producing rayfiles which can be run through marx again e.g. using different detectors.

../_images/chipmap.png

Layout of Chandra flight focal plane detectors. The chips are numbered with their standard Chandra identifications. Note, the ACIS-I nominal aimpoint falls on chip 3 while the aimpoint for the ACIS-S array corresponds to chip 7. For the HRC-S, the nominal aimpoint is near the center of MCP 1. The sizes of the MCPs and CCDs are drawn roughly to scale, the detector separations and chip gaps are not.

marx automatically places the SIM in the appropriate position such that the center of the source coincides with the default aimpoint for the selected detector. For actual Chandra observations using ACIS, any combination of 6 CCDs may be used at one time. However, at present marx simulations with ACIS only include those CCDs which comprise the selected imager (i.e. chips 0-3 for ACIS-I and chips 4-9 for ACIS-S).

HRC-HESF

(default: yes) If the HRC–S detector is selected, users have the option of including a model of the High Energy Suppression Filter (HESF) (a.k.a. The Drake Flat). Setting the parameter HRC-HESF="yes" includes the HESF; however, as we note below, the DetOffsetZ parameter must also be modified to move the HESF into the beam.

DetIdeal

(default: no) The quantum efficiency of the specified detector can be suppressed using the DetIdeal parameter. If DetIdeal="yes", the focal plane geometry of the selected detector is preserved, but the efficiency is assumed to be unity.

Focal Plane Position

The focal plane science instruments on Chandra are mounted on a movable platform called the Science Instrument Module (SIM) that allows the different detectors to be selected. Movement along the optical axis is also possible to adjust the focus. marx simulates the SIM movement with three parameters:

DetOffsetX

(default: 0) Offset in mm from the nominal on-axis, in-focus SIM position.

In the marx coordinate system (which is the same as the Chandra coordinate system), the X axis corresponds to the optical axis (see The marx Coordinate System). Therefore, the DetOffsetX parameter can be used to simulate defocused Chandra observations. The maximum X motion of the SIM is -9 mm and +10 mm. Movements greater than \(\sim 2\) mm from the best focus position produce ring–like images for point sources. This functionality is useful for studying photon pileup in the ACIS CCDs. Defocusing is one possible means of minimizing this effect for a given observation.

DetOffsetZ

(default: 0) Offset in mm from the nominal on-axis, in-focus SIM position.

The sign convention is opposite to the sim_z_offset that can be specified in Chandra observations to move the source onto a different part of the detector (see Fig 6.1 in the Observatory guide ).

For grating observations this parameter can be used to translate the SIM in the direction perpendicular to the grating dispersion. If the HESF (a.k.a. Drake Flat) is to be used, the DetOffsetZ parameter should be set to a value of 7.25 mm. To use the LESF, a value of DetOffsetZ=-6.5 should be used.

Source Definition

Specifying sources in marx is equivalent to choosing a position on the sky, a spectral energy distribution, and a spatial distribution for the incoming photons. For the latter two source characteristics, a number of simple options are built into marx.

Source Position

SourceRA

(default: 2.502316589E+02) RA of source in the sky in decimal degrees. Corresponds on the RA_TARG FITS header keyword in a standard Chandra Level 2 events file.

SourceDEC

(default: -5.375129700E+01) RA of source in the sky in decimal degrees. Corresponds on the DEC_TARG FITS header keyword in a standard Chandra Level 2 events file.

RA_Nom

(default: 250.2134679741175) RA of nominal aimpoint in the sky in decimal degrees. Corresponds on the RA_NOM FITS header keyword in a standard Chandra Level 2 events file.

Dec_Nom

(default: -53.75743813458669) RA of nominal aimpoint in the sky in decimal degrees. Corresponds on the DEC_NOM FITS header keyword in a standard Chandra Level 2 events file.

Roll_Nom

(default: 237.36968458476) Roll angle in the sky in decimal degrees. Corresponds on the ROLL_NOM FITS header keyword in a standard Chandra Level 2 events file.

If the values of SourceRA and SourceDEC are different from RA_Nom and Dec_Nom, the source will be off-axis.

Source Spectrum

This is described in more details in The spectrum and the spatial shape of the X-ray source. Here, we summarize the most important points.

Users have two options for specifying the spectral energy distribution of source photons: a built-in FLAT spectrum model which produces uniform flux over the specified energy range, or a FILE mode which reads the spectrum from an external ASCII file. The SpectrumType parameter selects between these two options. In both cases, further parameters are needed to give details:

SpectrumType Parameter Description
FLAT MinEnergy keV
MaxEnergy keV
SourceFlux phot/s/cm^2
FILE SpectrumFile phot/s/cm^2/keV - see text
SourceFlux < 0 to use data in the file or > 0 to renormalize the spectrum in the file

If the FLAT spectrum is selected, the SourceFlux parameter is used to determine the overall normalization of the spectrum in photons/sec/cm^2. The MinEnergy and MaxEnergy energy parameters determine the energy range in keV over which photons will be generated for the FLAT spectral model. Both parameters may be set to the same value to generate a monochromatic source.

If the FILE mode is selected, the user must specify the name of an input ASCII file containing the spectral energy distribution using the SpectrumFile parameter. The input ASCII file should contain two columns separated by at least one space where the first column gives the energy grid in keV and the second column gives the flux density at that energy in units of photons/sec/cm^2/keV. No limits are placed on the number of points in the input file and the file is assumed to be ordered by increasing energy. marx checks for this criterion by calculating and reporting the integrated flux from the specified file. xspec2marx is a script installed with marx to convert XSPEC output to the right format.

In FILE mode, the SourceFlux parameter can be used to set the overall normalization of the input spectral energy distribution. Setting SourceFlux to a positive, non-zero value will cause marx to renormalize the spectrum read from the ASCII file to the specified total flux. If SourceFlux=-1 (or any number less than 0), marx will use the normalization inherent in the input spectrum. In this manner, several sources with a consistent spectral shape but varying total flux can be simulated using a single input spectrum file.

The shape of the source on the sky

Again, more details on this can be found in The spectrum and the spatial shape of the X-ray source.

The spatial distribution of source photons in marx is determined by the choice of the SourceType parameter.

The following sources are currently available:

  • POINT: Point Source
  • GAUSS: Radially symmetric Gaussian
  • BETA: Cluster Beta model
  • DISK: Disk or annulus (e.g. SN remnant)
  • LINE: Straight line
  • IMAGE: Input from a FITS image file
  • SAOSAC: Input from an SAOSAC FITS rayfile
  • RAYFILE: Input from a marx rayfile
  • USER: Dynamically linked user–supplied model

The IMAGE, SAOSAC`, and ``RAYFILE source options all take an additional parameter specifying the name of the external file to use. With the exception of the SAOSAC and RAYFILE options, all marx source models obey the SourceRA and SourceDEC parameters. For non-point source models, the center of the source will be placed at the coordinates specified by the (SourceRA, SourceDEC) parameters. In the case of the IMAGE source type, the center of the image will be located at the specified position.

The USER source model requires two additional parameters. UserSourceFile specifies the path to the dynamically linked source file and should be the full, absolute pathname due to peculiarities in the manner in which the dynamic linker locates modules. The value of the parameter UserSourceArgs will depend on the specifics of the user model being linked.

All source models are described in detail in The spectrum and the spatial shape of the X-ray source.

Aspect Dither Motion

Once the source characteristics and science instrument configuration have been specified, the only remaining option the user must choose is whether or not to include a simulation of the Chandra aspect motion. marx includes an internal simulation of the standard lissajous dither pattern which Chandra traverses over the course of an observation.

If DitherModel=INTERNAL, marx will apply an internal simulation of the Chandra aspect dither pattern. This motion will result in a blurring of the source image when viewed in focal plane coordinates. If a dither model is applied to the simulation, marx calculates aspect-corrected sky coordinates. These values are ultimately to the FITS events file by marx2fits is used.

For actual Chandra data sets, residual errors in the aspect correction pipeline will introduce uncertainties into the derived Sky X and Y coordinates. marx includes a simulation of these uncertainties through the AspectBlur parameter. Other errors affecting the derived Sky coordinates include the detector pixelization blur (associated with the non-zero size of the pixel, also known as truncation blur), and the pixel randomization blur (induced from conversion of an integer pixel coordinate to a real-valued one). The user has some control over the form of the randomization blur via the marx2fits --pixadj option.

Figure dither shows an example of a simulated ACIS-I observation of a cluster of galaxies with and without aspect motion included.

Example of ACIS-I simulation with and without dither

Simulation showing the effects of the internal dither model in marx. The panel on the left shows a simulated ACIS-I observation of a cluster of galaxies with no dither included in Sky coordinates. The right panel shows the same simulation with marx‘s INTERNAL dither model turned on. Note how the aspect motion has blurred the ACIS chip gaps but not the cluster image since aspect correction has been applied to the Sky coordinates displayed here.

The functional form of the motion model is described in Simulating Aspect with marx. In general, the form of the dither model has been adjusted to correspond to the current parameters used for ACIS observations. HRC observations with dither can be simulated by adjusting the DitherAmp_RA and DitherAmp_Dec parameters from 8 arcsec to 20 arcsec.

Finally, if DitherModel=FILE, marx will use the contents on an aspect solution file (ASPSOL) to specify the dither motion pattern. The name of the ASPSOL file to use is specified by the DitherFile parameter. ASPSOL files can be produced by the CXCDS aspect pipeline or marxasp. The FILE mode can be useful for generating marx simulations which use the same aspect dither motion as an existing Chandra dataset or a previous simulation. The time interval covered by the ASPSOL file must equal or exceed the requested exposure time of the simulation. If the end of the ASPSOL file is reached before the requested exposure time, marx will truncate the simulation at that point.

Running the Simulation

Once your system has been configured appropriately and any desired modifications have been made to the marx.par parameter file, the simulation is ready to run. If the parameters in the marx.par file are already set appropriately, the simulation can be launched simply by typing marx at the shell prompt. marx will print out a number of diagnostic messages as the simulation proceeds indicating which configuration is being used as well as which data files were accessed. Output from an example using the ACIS-I with dither enabled is shown here:

unix% marx
MARX version 4.0.8, Copyright (C) 2002 Massachusetts Institute of Technology

    /usr/local/src/marx_4.0.8-dist/marx/data/hrma/EKCHDOS06.rdb
Reading binary HRMA optical constants:
    /usr/local/src/marx_4.0.8-dist/marx/data/hrma/iridium.dat
    /usr/local/src/marx_4.0.8-dist/marx/data/hrma/corr_1.dat
    /usr/local/src/marx_4.0.8-dist/marx/data/hrma/corr_3.dat
    /usr/local/src/marx_4.0.8-dist/marx/data/hrma/corr_4.dat
    /usr/local/src/marx_4.0.8-dist/marx/data/hrma/corr_6.dat
Reading scattering tables
    /usr/local/src/marx_4.0.8-dist/marx/data/hrma/scat_p1_M.bin
    /usr/local/src/marx_4.0.8-dist/marx/data/hrma/scat_h1_M.bin
    /usr/local/src/marx_4.0.8-dist/marx/data/hrma/scat_p3_M.bin
    /usr/local/src/marx_4.0.8-dist/marx/data/hrma/scat_h3_M.bin
    /usr/local/src/marx_4.0.8-dist/marx/data/hrma/scat_p4_M.bin
    /usr/local/src/marx_4.0.8-dist/marx/data/hrma/scat_h4_M.bin
    /usr/local/src/marx_4.0.8-dist/marx/data/hrma/scat_p6_M.bin
    /usr/local/src/marx_4.0.8-dist/marx/data/hrma/scat_h6_M.bin
Initializing ACIS-I detector...
Reading ACIS-I/S FEF File
    /usr/local/src/marx_4.0.8-dist/marx/data/caldb/acisfef.fits
Reading ACIS-I QE/Filter Files
    /usr/local/src/marx_4.0.8-dist/marx/data/caldb/acisD1997-04-17qeN0004.fits for [CCDID = 0]
    /usr/local/src/marx_4.0.8-dist/marx/data/caldb/acisD1997-04-17qeN0004.fits for [CCDID = 1]
    /usr/local/src/marx_4.0.8-dist/marx/data/caldb/acisD1997-04-17qeN0004.fits for [CCDID = 2]
    /usr/local/src/marx_4.0.8-dist/marx/data/caldb/acisD1997-04-17qeN0004.fits for [CCDID = 3]
[Using INTERNAL dither model]
Initializing source type POINT...
System initialized.

Starting simulation.  Exposure Time set to 3.000000e+04 seconds
Collecting 100000 photons...
    67631 collected.
Reflecting from HRMA
Detecting with ACIS-I

Writing output to directory 'point' ...
Total photons: 67631, Total Photons detected: 18060, (efficiency: 0.267037)
   (efficiency this iteration  0.267037)  Total time: 30000.079736

Once the initialization is complete, marx will begin processing groups of rays. Again, diagnostic messages will be generated which track the simulation’s progress, i.e. Collecting..., Reflecting..., etc. A short synopsis will also be printed at the end of each group of rays indicating the number of rays processed, the number actually “detected”, the efficiency for this iteration, and the total integration time incurred so far. When the number of rays specified have been processed or the indicated integration time has been reached, the simulation will terminate.

Verbose

(default: yes) The diagnostic messages can be quieted by setting the parameter Verbose="no".

marx Native Binary Output Files

Depending on the values of the OutputDir and OutputVectors parameters, marx will by default create a directory containing a number of binary output files. Usually, a user will not use these files directly, but convert them to fits files using marx2fits (see below). The native binary format is discussed in more detail in the description of the parameter Outputvectors.

These native binary vectors provide convenient access to the individual properties of detected photons. For example, to create an ASCII file containing only the times and pulse heights for a set of detected photons, we can use:

unix% marx --dump point/time.dat point/pha.dat > list.txt
unix% more list.txt
#            TIME             PHA
    3.199424e+00             241
    3.702556e+00             302
    3.722314e+00             256
    4.840378e+00             257
    5.336663e+00             284

In this example, the marx simulation directory was assumed to be named “point”. Alternatively, for IDL users, the routine read_marx_file can be used to read these binary output vectors into internal IDL variables. These direct means of accessing the properties of detected photons can be much more efficient than reading individual columns from the equivalent FITS events file, especially for large simulations.

FITS Events Files

The contents of a marx simulation output directory may be recast in a standard CXC Level 1 FITS events file using the marx2fits tool. Events files created in this way contain the standard “detected” event quantities such as pixel position, pulse height, time, etc. In addition, columns are created in the FITS binary events table for the various “simulation” variables (true photon energy, dispersed order, mirror reflection shell, etc.). marx event files can be used transparently with the CIAO extraction tools as well as XSELECT in the FTOOLS software suite available from HEASARC.

Combining multiple marx Simulations

Complex marx simulations can be built using the marxcat tool. This tool concatenates the results of multiple marx runs and takes as input a list of simulation output directories. As output, it creates a new directory containing the merged binary output vectors from the specified component directories. The resulting merged output vectors will be ordered by photon arrival time. marx2fits can of course still be used to convert concatenated simulations into event files.

The marxcat tool works by merging the various binary output vectors contained in the indicated marx output directories. It is the user’s responsibility to ensure that the simulations being concatenated are commensurate. For example, combining simulations with differing pointing positions (as defined by RA_Nom and Dec_Nom) will produce erroneous results. marxcat will compare the contents of the directories being merged and skip any files which do not have counterparts in all the directories.