docs/guide: Update to refer to the right config.spec

Delete the old outdated one.

2 files changed, 2 insertions, 496 deletions

diff --git a/docs/fg21sim.conf.spec b/docs/fg21sim.conf.spec
deleted file mode 100644
index 9477dd7..0000000
--- a/docs/fg21sim.conf.spec
+++ /dev/null
@@ -1,495 +0,0 @@
-# Configurations for "fg21sim"
-# -*- mode: conf -*-
-#
-# Syntax: `ConfigObj`, https://github.com/DiffSK/configobj
-#
-
-# Foreground components to be simulated
-[foregrounds]
-# Diffuse Galactic synchrotron emission (unpolarized)
-galactic/synchrotron = boolean(default=False)
-
-# Diffuse Galactic free-free emission
-galactic/freefree = boolean(default=False)
-
-# Galactic supernova remnants emission
-galactic/snr = boolean(default=False)
-
-#  Extragalactic clusters of galaxies emission
-extragalactic/clusters = boolean(default=False)
-
-# Emission from multiple types of extragalactic point sources
-# NOTE: This component is not well integrated and tested at the moment
-extragalactic/pointsources = boolean(default=False)
-
-
-# Simulation sky/region configurations
-[sky]
-# Type of the input/output simulation sky
-# + patch:
-#       Input/output sky template is only a (square) patch of the sky.
-#       The simulated output maps have the same coverage/field as the
-#       input template, as well as the coordinate projection.
-# + healpix:
-#       Input/output sky template covers (almost) all sky, and stored
-#       in HEALPix format.  The simulated output maps will also be
-#       all-sky using the HEALPix projection.
-type = option("patch", "healpix", default="patch")
-
-  # Configurations for input/output sky patch
-  [[patch]]
-  # The (R.A., Dec.) coordinate of the sky patch center
-  # Unit: [deg]
-  # (MWA EoR0 field center: (0, -27))
-  xcenter = float(default=0.0, min=0.0, max=360.0)
-  ycenter = float(default=-27.0, min=-90.0, max=90.0)
-
-  # The image dimensions (i.e., number of pixels) of the sky patch,
-  # along the X (R.A./longitude) and Y (Dec./latitude) axes.
-  # Default: 1800x1800 => 10x10 [deg^2] (20 arcsec/pixel)
-  xsize = integer(default=1800, min=1)
-  ysize = integer(default=1800, min=1)
-
-  # Pixel size [arcsec]
-  pixelsize = float(default=20.0, min=0.0)
-
-  # Configurations for input/output HEALPix sky
-  [[healpix]]
-  # HEALPix Nside value, i.e., pixel resolution
-  nside = integer(default=1024, min=128)
-
-
-# Frequencies specification of the simulation products
-[frequency]
-# How to specify the frequencies
-# + custom:
-#       directly specify the frequency values using the "frequencies" config
-# + calc:
-#       calculate the frequency values by "start", "stop", and "step"
-type = option("custom", "calc", default="custom")
-
-# The frequency values to be simulated if above "type" is "custom".
-# Unit: [MHz]
-frequencies = float_list(default=list())
-
-# Parameters to calculate the frequencies
-# NOTE: "start" and "stop" frequencies are both inclusive.
-# Unit: [MHz]
-start = float(default=None, min=0.0)
-stop = float(default=None, min=0.0)
-step = float(default=None, min=0.0)
-
-
-# Configuration for output products
-[output]
-# Filename pattern for the output products, which will be finally
-# formatted using `str.format()`.
-filename_pattern = string(default="{prefix}_{frequency:06.2f}.fits")
-
-# Use single-precision float instead of double (to save spaces)
-float32 = boolean(default=True)
-
-# Whether to calculate the checksum for the output FITS file?
-# NOTE: May cost significantly more time on writing FITS file.
-checksum = boolean(default=False)
-
-# Whether to overwrite existing files (e.g., maps, catalogs, manifest, ...)
-clobber = boolean(default=False)
-
-# Filename of the simulation products manifest (JSON format), which
-# records all output products together with their sizes and MD5 hashes.
-# Do not create such a manifest if this option is not specified.
-manifest = string(default=None)
-
-
-# Cosmological parameters
-# References: Komatsu et al. 2011, ApJS, 192, 18; Tab.(1)
-[cosmology]
-# Hubble constant at z=0; [km/s/Mpc]
-H0 = float(default=71.0, min=0.0)
-# Density of non-relativistic matter in units of the critical density at z=0
-OmegaM0 = float(default=0.27, min=0.0, max=1.0)
-# Density of the baryon at present day
-Omegab0 = float(default=0.046, min=0.0, max=1.0)
-# Present-day CMB temperature; [K]
-Tcmb0 = float(default=2.725)
-# Present-day rms density fluctuations on a scale of 8 h^-1 [Mpc]
-sigma8 = float(default=0.81, min=0.0)
-# Scalar spectral index
-ns = float(default=0.96, min=0.0)
-
-
-# Configurations for initialization/reconfiguration of the `logging` module
-[logging]
-# debug:    Detailed information, typically of interest only when diagnosing
-#           problems.
-# info:     Confirmation that things are working as expected.
-# warning:  An indication that something unexpected happended, or indicative
-#           of some problem in the near future (e.g., "disk space low").
-#           The software is still working as expected.
-# error:    Due to a more serious problem, the software has not been able to
-#           perform some function.
-# critical: A serious error, indicating that the program itself may be unable
-#           to continue running.
-level = option("debug", "info", "warning", "error", "critical", default="info")
-
-# Set the format of displayed messages
-format = string(default="%(asctime)s [%(levelname)s] <%(name)s:%(lineno)d> %(message)s")
-
-# Set the date/time format in messages
-datefmt = string(default="%H:%M:%S")
-
-# Set the logging filename (will create a `FileHandler`)
-# If set to "" (empty string), then the `FileHandler` will be disabled.
-filename = string(default="")
-
-# Set the stream used to initialize the `StreamHandler`
-# If set to "" (empty string), then the `StreamHandler` will be disabled.
-stream = option("stderr", "stdout", "", default="stderr")
-
-
-# Options corresponding the Galactic emission components, which currently
-# includes the following components:
-# - synchrotron
-# - freefree
-# - snr
-
-[galactic]
-
-  # Synchrotron emission component (unpolarized)
-  [[synchrotron]]
-  # The template map for the simulation, e.g., Haslam 408 MHz survey.
-  # Unit: [K] (Kelvin)
-  template = string(default=None)
-  # The frequency of the template map.
-  # Unit: [MHz]
-  template_freq = float(default=None, min=0.0)
-
-  # Spectral index map
-  indexmap = string(default=None)
-
-  # Whether add fluctuations on the small scales according the angular
-  # power spectrum prediction?
-  add_smallscales = boolean(default=False)
-  # Range of multipole moments (l) of the angular power spectrum.
-  # The power spectrum will be cut off to a constant for multipole l < lmin.
-  # NOTE: Update the ``lmax`` accordingly w.r.t. ``sky/healpix/nside``.
-  #       Generally, lmax = 3 * nside - 1
-  lmin = integer(min=0, default=10)
-  lmax = integer(min=1, default=3071)
-
-  # Filename prefix for this component
-  prefix = string(default="gsync")
-  # Output directory to save the simulated results
-  output_dir = string(default=None)
-
-  # Free-free bremsstrahlung emission component
-  [[freefree]]
-  # The Hα map from which to derive the free-free emission
-  # Unit: [Rayleigh]
-  halphamap = string(default=None)
-
-  # The 100-μm dust map used to correct Hα dust absorption
-  # Unit: [MJy/sr]
-  dustmap = string(default=None)
-
-  # Effective dust fraction in the LoS actually absorbing Halpha
-  dust_fraction = float(default=0.33, min=0.1, max=1.0)
-
-  # Halpha absorption threshold:
-  # When the dust absorption goes rather large, the true Halpha
-  # absorption can not well determined.  This configuration sets the
-  # threshold below which the dust absorption can be well determined,
-  # while the sky regions with higher absorption are masked out due
-  # to unreliable absorption correction.
-  # Unit: [mag]
-  halpha_abs_th = float(default=1.0)
-
-  # The electron temperature assumed for the ionized interstellar medium
-  # that generating H{\alpha} emission.
-  # Unit: [K]
-  electron_temperature = float(default=7000.0, min=1000)
-
-  # Filename prefix for this component
-  prefix = string(default="gfree")
-  # Output directory to save the simulated results
-  output_dir = string(default=None)
-
-  # Supernova remnants emission
-  [[snr]]
-  # The Galactic SNRs catalog data (CSV file)
-  catalog = string(default=None)
-  # Output the effective/inuse SNRs catalog data (CSV file)
-  catalog_outfile = string(default=None)
-
-  # Resolution for simulating each SNR template, which are finally
-  # mapped to the all-sky HEALPix map if used.
-  # Unit: [arcsec]
-  resolution = float(default=30.0, min=5.0)
-
-  # Filename prefix for this component
-  prefix = string(default="gsnr")
-  # Output directory to save the simulated results
-  output_dir = string(default=None)
-
-
-# Options corresponding the extragalactic emission components, which
-# currently includes the following components:
-# - clusters: halos
-# - pointsources
-
-[extragalactic]
-  #
-  # Press-Schechter formalism to determine the cluster distributions
-  # with respect to mass and redshift, from which to further determine
-  # the total number of clusters within a sky patch and to sample the
-  # masses and redshifts for each cluster.
-  #
-  [[psformalism]]
-  # The model of the fitting function for halo/cluster mass distribution
-  # For all models and more details:
-  # https://hmf.readthedocs.io/en/latest/_autosummary/hmf.fitting_functions.html
-  model = option("smt", "jenkins", "ps", default="ps")
-
-  # The minimum (inclusive) and maximum (exclusive!) cluster mass
-  # within which to calculate the halo mass distribution.
-  # Unit: [Msun]
-  M_min = float(default=1e12, min=1e10, max=1e14)
-  M_max = float(default=1e16, min=1e14, max=1e18)
-  # The logarithmic (base 10) step size for the halo masses; therefore
-  # the number of intervals is: (log10(M_max) - log10(M_min)) / M_step
-  M_step = float(default=0.01, min=0.001, max=0.1)
-
-  # The minimum and maximum redshift within which to calculate the
-  # halo mass distribution; as well as the step size.
-  z_min = float(default=0.01, min=0.001, max=1.0)
-  z_max = float(default=4.0, min=1.0, max=100)
-  z_step = float(default=0.01, min=0.001, max=1.0)
-
-  # Output file (NumPy ".npz" format) to save the calculated halo mass
-  # distributions at every redshift.
-  #
-  # This file packs the following 3 NumPy arrays:
-  # * ``z``:
-  #   Redshifts where the halo mass distribution is calculated.
-  # * ``mass``:
-  #   (Logarithmic-distributed) masses points.
-  #   Unit: [Msun] (the little "h" is folded into the values)
-  # * ``dndlnm``:
-  #   Shape: (len(z), len(mass))
-  #   Differential mass function in terms of natural log of M.
-  #   Unit: [Mpc^-3] (the little "h" is folded into the values)
-  dndlnm_outfile = string(default=None)
-
-
-  #
-  # Extended emissions from the clusters of galaxies
-  # The configurations in this ``[[clusters]]`` section may also be
-  # used by the following ``[[halos]]`` section.
-  #
-  [[clusters]]
-  # Output CSV file of the cluster catalog containing the simulated
-  # mass, redshift, position, shape, recent merger info, etc.
-  catalog_outfile = string(default=None)
-
-  # Whether to dump the raw data of the simulated cluster catalog in
-  # Python native pickle format (i.e., ".pkl") to a file with the same
-  # basename as the above ``catalog_outfile``?
-  # The dumped data can be easily loaded back for reuse.
-  dump_catalog_data = boolean(default=True)
-
-  # Whether to directly use the (previously simulated) catalog data as
-  # specified by the above "catalog_outfile" and ``dump_catalog_data``
-  # options?
-  # NOTE:
-  # By using an existing catalog, the steps to derive these data are
-  # simply skipped.
-  # Due to the small number density of the galaxy clusters, the simulated
-  # results within a small patch of sky (e.g., 100 [deg^2]) show
-  # significant fluctuations (several or even several tens of times
-  # of differences between simulations).  Therefore, one may run many
-  # tests and only create images at some frequencies necessary for
-  # testing, then select the satisfying one to continue the simulation
-  # to generate images at all frequencies.
-  use_dump_catalog_data = boolean(default=False)
-
-  # Output CSV file of the halos catalog containing the calculated
-  # properties of the simulated halos.
-  halos_catalog_outfile = string(default=None)
-
-  # Whether to dump the whole data of the simulated halos in Python
-  # native pickle format (i.e., ".pkl") to a file with the same basename
-  # as the above ``halos_catalog_outfile``?
-  # The dumped data also includes the derived electron spectrum for
-  # each halo, therefore this file can be reloaded back in order to
-  # calculate the emissions at other frequencies.
-  dump_halos_data = boolean(default=True)
-
-  # Whether to directly use the (previously dumped) halos data (".pkl")
-  # as specified by the above ``halos_catalog_outfile`` and
-  # ``dump_halos_data`` options?
-  # In this way, the radio emissions at additional frequencies can be
-  # easily (and consistently) calculated.
-  use_dump_halos_data = boolean(default=False)
-
-  # The minimum mass for clusters when to determine the galaxy clusters
-  # total counts and their distributions.
-  # Unit: [Msun]
-  mass_min = float(default=1e14, min=1e13)
-
-  # Boost the number of expected cluster number within the sky coverage
-  # by the specified times.
-  # WARNING: for testing usage.
-  boost = float(default=1.0, min=0.1, max=1e4)
-
-  # Minimal elongated fraction for creating the images of radio halos
-  # The ``felong`` is defined as ``felong = b/a``, similar to the Hubble
-  # classification for the elliptical galaxies.  ``felong_min = 1.0``
-  # means no elongation, and ``felong_min = 0.6`` is a good choice as
-  # the observed radio halos are generally regular.
-  felong_min = float(default=1.0, min=0.1, max=1.0)
-
-  # Number of most powerful halos to be dropped out.
-  halo_dropout = integer(default=0, min=0)
-
-  # Minimum mass change of the main cluster to be regarded as a merger
-  # event instead of an accretion event.
-  # Unit: [Msun]
-  merger_mass_min = float(default=1e13, min=1e11, max=1e14)
-
-  # The trace back time when to stop tracing the merging history of
-  # clusters.  ~2-3 Gyr should be enough since the turbulence acceleration
-  # effective time ~<1 Gyr and the halo lifetime is also short compared
-  # to mergers.
-  # Unit: [Gyr]
-  time_traceback = float(default=3.0, min=1.0, max=5.0)
-
-  # The fraction of the magnetic field energy density w.r.t. the ICM
-  # thermal energy density, which is used to determine the mean magnetic
-  # field strength within the ICM and is also assumed to be uniform.
-  # * ~< 0.4% (Ref: Pfrommer & Ensslin 2004, MNRAS)
-  # * ~0.3%-1% (Ref: Bohringer et al. 2016, A&A)
-  eta_b = float(default=0.001, min=1e-5, max=0.1)
-
-  # The temperature of the outer gas surrounding the cluster.  Accretion
-  # shocks form near the cluster virial radius during the cluster formation,
-  # which can heat the cluster ICM to have a higher temperature than the
-  # virial temperature:
-  #     kT_icm ~ kT_vir + 1.5 * kT_out,
-  # with: kT_out ~ 0.5 [keV]
-  # Reference: Fujita et al. 2003, ApJ, 584, 190; Eq.(49)
-  # Unit: [keV]
-  kT_out = float(default=0.0, min=0.0)
-
-  # Filename prefix for this component
-  prefix = string(default="cluster")
-  # Output directory to save the simulated results
-  output_dir = string(default=None)
-
-
-  #
-  # Giant radio halos
-  #
-  [[halos]]
-  # A custom parameter to tune the turbulent acceleration efficiency.
-  # NOTE: The smaller this parameter, the shorter the acceleration
-  #       timescale, therefore more efficient acceleration.
-  f_acc = float(default=1.0, min=0.1, max=10)
-
-  # The turbulence is generally injected at the cluster center during
-  # a merger.  This option parameterize the turbulence injection scale
-  # to be a fraction of the virial radius of the cluster, which is also
-  # used to determine the radio halo size.
-  f_lturb = float(default=0.33, min=0.1, max=1.0)
-
-  # An efficiency factor describing the effectiveness of plasma
-  # instabilities (e.g., due to spatial or temporal intermittency).
-  zeta_ins = float(default=0.1, min=0.1, max=1.0)
-
-  # The fraction of merger energy transferred into the turbulence.
-  eta_turb = float(default=0.1, min=0.1, max=0.5)
-
-  # The fraction of the thermal energy injected into the cosmic-ray
-  # electrons during the cluster life time.
-  eta_e = float(default=0.003, min=0.001, max=0.1)
-
-  # The ratio of cosmic ray (including protons and electrons) energy
-  # density (i.e., pressure) to the thermal energy density.
-  # NOTE: Fermi-LAT has placed an upper limit of ~1.25%-1.4%
-  #       (Ackermann et al. 2014, ApJ, 787, 18)
-  # NOTE: The energy ratio of cosmic-ray electrons to protons K_ep ~0.01
-  #       for our Galaxy (Pinzke et al. 2017, MNRAS, 465, 4800)
-  x_cr = float(default=0.015, min=0.001, max=0.1)
-
-  # Electron injection, which is assumed to have a constant injection
-  # rate and a power-law spectrum.
-  injection_index = float(default=2.3, min=2.1, max=3.0)
-
-  # Minimum and maximum Lorentz factor (i.e., energy) of the relativistic
-  # electron spectrum.
-  gamma_min = float(default=1)
-  gamma_max = float(default=1e5)
-  # Number of cells on the logarithmic momentum grid used to solve the
-  # Fokker-Planck equation.
-  gamma_np = integer(default=200)
-
-  # Number of cells used as the buffer regions near both the lower
-  # and upper boundaries, within which the values will be replaced by
-  # extrapolating from the inner-region data, in order to avoid the
-  # unphysical particle pile-ups.
-  # It is suggested to be about 5%-10% of the above ``gamma_np``.
-  # NOTE: * set to 0 to disable boundary fixes;
-  #       * otherwise, set to a number >= 2.
-  buffer_np = integer(default=10, min=0)
-
-  # Time step for solving the Fokker-Planck equation
-  # Unit: [Gyr]
-  time_step = float(default=0.02, min=1e-4, max=0.1)
-
-  # How long the period before the merger begins, which is used to derive
-  # an approximately steady initial electron spectrum.  During this period,
-  # the acceleration is turned off and only leaves energy loss mechanisms.
-  # Unit: [Gyr]
-  time_init = float(default=1.0, min=0)
-
-
-  #
-  # Extragalactic point sources
-  #
-  [[pointsources]]
-  # Output directory to save the simulated catalog
-  output_dir = string(default="PS_tables")
-  # PS components to be simulated
-  pscomponents = string_list(default=list())
-  # Resolution [arcmin]
-  resolution = float(default=0.6, min=0.0)
-
-    [[[starforming]]]
-    # Number of samples
-    numps = integer(default=1000)
-    # Prefix
-    prefix = string(default="SF")
-
-    [[[starbursting]]]
-    # Number of samples
-    numps = integer(default=1000)
-    # Prefix
-    prefix = string(default="SB")
-
-    [[[radioquiet]]]
-    # Number of samples
-    numps = integer(default=1000)
-    # Prefix
-    prefix = string(default="RQ")
-
-    [[[FRI]]]
-    # Number of samples
-    numps = integer(default=1000)
-    # Prefix
-    prefix = string(default="FRI")
-
-    [[[FRII]]]
-    # Number of samples
-    numps = integer(default=1000)
-    # Prefix
-    prefix = string(default="FRII")
diff --git a/docs/guide.rst b/docs/guide.rst
index d1a4d5d..ff5e4ab 100644
--- a/docs/guide.rst
+++ b/docs/guide.rst
@@ -30,7 +30,8 @@ There are two types of configuration options:
 *required* (which require the user to explicitly provide the values)
 and *optional* (which already have sensible defaults, however, the user
 can also override them).
-Please refer to the `configuration specification file <fg21sim.conf.spec>`_
+Please refer to the
+`configuration specification file <../fg21sim/configs/config.spec>`_
 for more information on the available options.
 Also there is a brief `test configuration file <fg21sim-test.conf>`_
 which may be useful to test whether this package is correctly installed