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XSPEC_EMCEE ----------- This is a program to use emcee to do MCMC analyses of X-ray spectra in xspec. This program has the advantage over the built-in Goodman Weare sampler in xspec of being able to run multiple xspec processes simultaneously, speeding up the analysis. It can also switch to parameterizing norm parameters in log space. ** Please acknowledge use of this code by Jeremy Sanders in any publications. ** As described on their website, emcee is an extensible, pure-Python implementation of of Goodman & Weare's Affine Invariant Markov chain Monte Carlo (MCMC) Ensemble sampler. REQUIREMENTS: Python: 2.x (2.5 or better) argparse: http://pypi.python.org/pypi/argparse (for Python < 2.7) h5py: http://www.h5py.org/ emcee: http://danfm.ca/emcee/ xspec: http://heasarc.nasa.gov/xanadu/xspec/ USAGE: The program will run using an input XCM file (loading data+model). It writes out an xspec-compatible chain file, plus a HDF5 data file containing the chains and log likelihoods. You need to choose the number of iterations, length of burn in period and number of walkers. Remember that for every iteration you get the number of walkers points in the output chain file. The chains from the walkers are flattened in the output .chain file, with all the results from one walker, followed by the next. The walkers are started clustered around the parameters of the XCM file given, using the delta value of the parameter as the width of a normal distribution (clipped to the hard bounds of the parameter range). Make sure that the delta values of parameters are set to values smaller than the uncertainties on each parameter. Note, however, that xspec_emcee will do a fit on the model, and if the 0.1 * sigma of the parameter (as calculated from the covariance matrix) is bigger than this delta, then 0.1 * sigma is used instead. This is a safety mechanism as xspec has poorly chosen deltas for some inbuilt models. We don't always use sigma, as it can be very wrong (usually too large). The program can run multiple copies of xspec simultaneously. By default it runs one copy on a local machine. You can run multiple copies by providing a list of systems with the --systems option. The name localhost runs on the local system without ssh. For instance --systems="localhost localhost" runs two local copies of xspec. You may also use the syntax --systems='localhost*8' to run N copies on a system (here localhost). You can run remote copies over ssh by using a different system name. Note that you will probably need to edit start_xspec.sh for non-remote systems to run appropriate initialisation files. The program prints out the number of times the xspec model has been evaluated as it runs (and the likelihood value -statistic/2). The program will flush the contents of the chain and likelihoods to the HDF5 file every 10 minutes after the burn-in period. Pressing Ctrl+C will also save the current state of the chain and exit. The chain can be continued with the --continue-run option. $ ./xspec_emcee.py --help usage: xspec_emcee.py [-h] [--niters N] [--nburn N] [--nwalkers N] [--systems LIST] [--output-hdf5 FILE] [--output-chain FILE] [--continue-run] [--debug] [--no-chdir] [--initial-parameters FILE] [--log-norm] XCM Xspec MCMC with EMCEE. Jeremy Sanders 2012-2016. positional arguments: XCM Input XCM file optional arguments: -h, --help show this help message and exit --niters N Number of iterations (default: 5000) --nburn N Number of burn iterations (default: 500) --nwalkers N Number of walkers (default: 50) --systems LIST Space-separated list of computers to run on (default: localhost) --output-hdf5 FILE Output HDF5 file (default: emcee.hdf5) --output-chain FILE Output text file (default: None) --continue-run Continue from an existing chain (in HDF5) (default: False) --no-fit Disable fit after loading model (default: False) --debug Create Xspec log files (default: False) --no-chdir Do not chdir to XCM file directory before execution (default: False) --initial-parameters FILE Provide initial parameters (default: None) --log-norm Use priors equivalent to using log norms (default: False) --chunk-size N Currently ignored (default: 4) --link EXPR Link two parameters in model (default: None) TODO: - Use local xspec to find remote xspecs automatically?