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ATOMDB Installation

Initial Preparation

The ATOMDB consists of a number of files that must be installed in a specific place so that the analysis software can find them. After installing ATOMDB, there is a separate procedure to update GUIDE, update Sherpa, and update XSPEC to use the new ATOMDB files.

Installing the ATOMDB files

Currently, approximately 143 MB is required for version 1.3.1. This includes all the publicly available atomic data and the calculated low-density spectral models. We expect that as new data is added to APED, and as higher density models are added to the APEC outputs, the ATOMDB may grow to about 500MB.

In general, the ATOMDB may be installed anywhere on the system. However, if CIAO is already installed on your system then it will set up a system variable ATOMDB that points where the ATOMDB should be installed. The way it is currently set up, GUIDE will look for ATOMDB files in this location only.

Step 1: If CIAO is already installed on your system, activate it and change to the ATOMDB directory by typing:

unix% ciao
CIAO configuration is complete... 
 CIAO version     :  CIAO 2.3 Wednesday, November 6, 2002
 Proposal Toolkit version :  NRA 4.0 Monday, December 10, 2001
 bin dir          :  /soft/ciao/bin
unix% echo $ATOMDB
soft/ciao/ATOMDB
unix% cd $ATOMDB

Step 2: After ensuring that you can write in this directory, ungzip and untar the ATOMDB tar file:

unix% gunzip atomdb_v1.3.1.tar.gz
unix% tar xvf atomdb_v1.3.1.tar
This will expand into number of files along with the APED directory:
  • apec_v1.3.1_line.fits
  • apec_v1.3.1_linelist.fits
  • apec_v1.3.1_coco.fits
  • VERSION
  • Release_Notes.txt
  • apec_v1.3.1.inp
  • apec_v1.3.1.out
  • filemap_v1.3.1
  • APED/
  • apec_linelist.fits (link to apec_v1.3.1_linelist.fits)
  • apec_line.fits (link to apec_v1.3.1_line.fits)
  • apec_coco.fits (link to apec_v1.3.1_coco.fits)
  • filemap (link to filemap_v1.3.1)

Updating GUIDE to use the new ATOMDB

If you are using CIAO 2.3 or higher, you can skip this section. Otherwise, as distributed in CIAO 2.2, GUIDE references the ATOMDB v1.1.0 release only. This can be fixed by following either A or B below (but not both!)

A: If you can overwrite files in the CIAO distribution, then you can update the old GUIDE initialization file guide_init.sl. The old version contains an explicit reference to the version 1.1.0 file; the updated version does not. To install this file:

  • Download guide_init.sl (shift-click to save)
  • Copy guide_init.sl into the CIAO interpreted binary directory: 
    unix% cp guide_init.sl $ASCDS_BIN/interpreted

    • B: If you do not wish to update CIAO (or do not have write access to those files) you can change the links to make the version 1.2.0 files appear to be version 1.2.0 as follows: 

    unix% mv apec_v1.10_line.fits.gz  apec_v1.10_line.fits.gz.orig
unix% mv apec_v1.10_coco.fits.gz  apec_v1.10_coco.fits.gz.orig
unix% mv apec_v1.10_linelist.fits apec_v1.10_linelist.fits.orig 
unix% ln -s apec_line.fits apec_v1.10_line.fits
unix% ln -s apec_line.fits apec_v1.10_coco.fits
unix% ln -s apec_linelist.fits apec_v1.10_linelist.fits

    Updating Sherpa and XSPEC to use the new ATOMDB

    Sherpa and XSPEC predate the creation of the ATOMDB, and store their own versions of the spectral files for the xsapec, xsvapec (sherpa) and apec, vapec (XSPEC) models. To update these, you must have write access to the CIAO and/or HEAsoft directories.

  • To update Sherpa to use the latest ATOMDB: 
    unix% cd $ASCDS_INSTALL/ots/lheasoft/spectral/xspec/manager
unix% mv apec_v1.10_coco.fits apec_v1.10_coco.fits.orig
unix% mv apec_v1.10_line.fits apec_v1.10_line.fits.orig
unix% ln -s $ATOMDB/apec_coco.fits apec_v1.10_coco.fits
unix% ln -s $ATOMDB/apec_line.fits apec_v1.10_line.fits
  • To update XSPEC to use the latest ATOMDB (assuming HEAsoft or XANADU is currently installed): 
    unix% cd $XANADU/spectral/xspec/manager/
unix% mv apec_v1.10_coco.fits apec_v1.10_coco.fits.orig 
unix% mv apec_v1.10_line.fits apec_v1.10_line.fits.orig 
unix% ln -s $ATOMDB/apec_coco.fits apec_v1.10_coco.fits
unix% ln -s $ATOMDB/apec_line.fits apec_v1.10_line.fits

    When updating XSPEC, be sure that you issue the commands in a window where CIAO has not been started. Otherwise, $XANADU will point to $ASCDS_INSTALL/ots/lheasoft, which means that you will be performing the update for Sherpa, not XSPEC.

    Note that currently, APEC nei files (for the XSPEC version 11.2 nei,vnei models) are only available from ATOMDB v1.1.0. We are working on new files for these models using ATOMDB v1.3.1.



    • Last modified: 11 August 2003




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