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View Code? Open in Web Editor NEWC++ version of the SED fitting code FAST (Kriek et al. 2009); it's faster, uses less memory, and has more features.
License: MIT License
C++ version of the SED fitting code FAST (Kriek et al. 2009); it's faster, uses less memory, and has more features.
License: MIT License
Running some initial tests and noticed an issue with the valid dust laws in fast++-read_input.cpp:
note: this is FAST++ version '1.2'
error: unknown dust law 'mw'
error: possible values: {calzetti, mz, noll, kc}
Hi Corentin,
Would it be possible to add a small section on the documentation on adding new filters? It seems there are some minor differences between the IDL and C++ versions in how the filters are identified from the database?
Hi!!!
In the download script for the models the final names are in the format of
*.ised_ASCII
However, when the code is executed libraries are still expected in this format:
fastpp/share/libraries/ised_exp.hr/bc03_hr_ch_z004_ltau8.5.ised
when I try to install the code in strw desktops I get the following error:
is this a quick fix?
[ 93%] Performing build step for 'fast++'
Scanning dependencies of target fast++-sfh2sed
[ 7%] Building CXX object CMakeFiles/fast++-sfh2sed.dir/fast++-sfh2sed.cpp.o
/data2/themiya/softwares/fastpp/src/fast++-sfh2sed.cpp: In function ‘int phypp_main(int, char**)’:
/data2/themiya/softwares/fastpp/src/fast++-sfh2sed.cpp:58:9: error: ‘end_with’ was not declared in this scope
if (end_with(sfh_file, ".fits")) {
^~~~~~~~
make[5]: *** [CMakeFiles/fast++-sfh2sed.dir/build.make:63: CMakeFiles/fast++-sfh2sed.dir/fast++-sfh2sed.cpp.o] Error 1
make[4]: *** [CMakeFiles/Makefile2:68: CMakeFiles/fast++-sfh2sed.dir/all] Error 2
make[3]: *** [Makefile:130: all] Error 2
make[2]: *** [CMakeFiles/fast++.dir/build.make:113: fast++-prefix/src/fast++-stamp/fast++-build] Error 2
make[1]: *** [CMakeFiles/Makefile2:143: CMakeFiles/fast++.dir/all] Error 2
make: *** [Makefile:130: all] Error 2
kuider [524] $
Hi,
I am trying to install fast++, but I am getting an error (see below). I have a Dell XPS15 with Ubuntu 22.04 OS. I also installed cmake
with sudo apt install cmake
.
Error:
...
[ 81%] Performing build step for 'fast++'
[ 7%] Building CXX object CMakeFiles/fast++.dir/fast++-read_input.cpp.o
In file included from /home/tomas/fastpp/external/include/vif/core/vec.hpp:1236,
from /home/tomas/fastpp/src/fast++.hpp:5,
from /home/tomas/fastpp/src/fast++-read_input.cpp:1:
/home/tomas/fastpp/external/include/vif/core/bits/operators.hpp:155:15: error: invalid use of incomplete type ‘struct vif::impl::op_mul_t’
155 | VECTORIZE(*, *=)
| ^
/home/tomas/fastpp/external/include/vif/core/bits/operators.hpp:26:56: note: in definition of macro ‘OP_TYPE’
26 | #define OP_TYPE(op) decltype(impl::op_node_t{} op impl::op_node_t{})
| ^~
/home/tomas/fastpp/external/include/vif/core/bits/operators.hpp:155:5: note: in expansion of macro ‘VECTORIZE’
155 | VECTORIZE(*, *=)
| ^~~~~~~~~
/home/tomas/fastpp/external/include/vif/core/bits/operators.hpp:12:16: note: forward declaration of ‘struct vif::impl::op_mul_t’
12 | struct op_mul_t;
| ^~~~~~~~
/home/tomas/fastpp/external/include/vif/core/bits/operators.hpp:78:56: error: template argument 1 is invalid
78 | vec<Dim,typename impl::op_res_t<OP_TYPE(op),T,U>::type> operator op (const vec<Dim,T>& v, const vec<Dim,U>& u) { \
| ^
/home/tomas/fastpp/external/include/vif/core/bits/operators.hpp:155:5: note: in expansion of macro ‘VECTORIZE’
155 | VECTORIZE(*, *=)
| ^~~~~~~~~
/home/tomas/fastpp/external/include/vif/core/bits/operators.hpp:78:57: error: ‘<declaration error>’ is not a template [-fpermissive]
78 | vec<Dim,typename impl::op_res_t<OP_TYPE(op),T,U>::type> operator op (const vec<Dim,T>& v, const vec<Dim,U>& u) { \
| ^~
/home/tomas/fastpp/external/include/vif/core/bits/operators.hpp:155:5: note: in expansion of macro ‘VECTORIZE’
155 | VECTORIZE(*, *=)
| ^~~~~~~~~
/home/tomas/fastpp/external/include/vif/core/bits/operators.hpp:78:63: error: template argument 2 is invalid
78 | vec<Dim,typename impl::op_res_t<OP_TYPE(op),T,U>::type> operator op (const vec<Dim,T>& v, const vec<Dim,U>& u) { \
| ^
/home/tomas/fastpp/external/include/vif/core/bits/operators.hpp:155:5: note: in expansion of macro ‘VECTORIZE’
155 | VECTORIZE(*, *=)
| ^~~~~~~~~
/home/tomas/fastpp/external/include/vif/core/bits/operators.hpp: In function ‘int vif::operator*(const vif::vec<Dim, Type>&, const vif::vec<Dim, U>&)’:
/home/tomas/fastpp/external/include/vif/core/bits/operators.hpp:155:15: error: invalid use of incomplete type ‘struct vif::impl::op_mul_t’
155 | VECTORIZE(*, *=)
| ^
/home/tomas/fastpp/external/include/vif/core/bits/operators.hpp:26:56: note: in definition of macro ‘OP_TYPE’
26 | #define OP_TYPE(op) decltype(impl::op_node_t{} op impl::op_node_t{})
| ^~
/home/tomas/fastpp/external/include/vif/core/bits/operators.hpp:155:5: note: in expansion of macro ‘VECTORIZE’
155 | VECTORIZE(*, *=)
| ^~~~~~~~~
/home/tomas/fastpp/external/include/vif/core/bits/operators.hpp:12:16: note: forward declaration of ‘struct vif::impl::op_mul_t’
12 | struct op_mul_t;
| ^~~~~~~~
compilation terminated due to -fmax-errors=5.
make[5]: *** [CMakeFiles/fast++.dir/build.make:76: CMakeFiles/fast++.dir/fast++-read_input.cpp.o] Error 1
make[4]: *** [CMakeFiles/Makefile2:87: CMakeFiles/fast++.dir/all] Error 2
make[3]: *** [Makefile:136: all] Error 2
make[2]: *** [CMakeFiles/fast++.dir/build.make:86: fast++-prefix/src/fast++-stamp/fast++-build] Error 2
make[1]: *** [CMakeFiles/Makefile2:168: CMakeFiles/fast++.dir/all] Error 2
make: *** [Makefile:136: all] Error 2
would be helpful if the header in best_fits *.input_res.fit
files state the column names in the file itself or in the param file
Hello! I'm really excited to use fastpp, but I'm really confused as to a few things with respect to the comparison between the results from fastpp and FAST-IDL. When I use the same parameter file with both FAST-IDL and fastpp, I get similar masses, but vastly different ages, tau values, and SFRs (the tau values and ages don't have any correlation), even when I set:
C_INTERVAL=68
BEST_AT_ZPHOT=1
ZPHOT_CONF=68
as suggested in the README. The chi-square values are larger for FAST-IDL by quite a bit than for fastpp, as well. For this test, I'm running with N_SIM = 0
, for quick usage.
In addition, I'm confused as to what the fitting redshifts correspond to. In the .param file, I set:
NAME_ZPHOT = 'z_peak'
and the output redshifts in the .fout file don't seem to correspond to z_peak values, even with BEST_AT_ZPHOT = 1
. Here, both the z_spec value in the .zout and .cat files are set to -9999.
Perhaps I am not understanding how the code works, but I just don't know why I can't seem to get fast to try to fit at the z_peak values.
Hey, How do you get higher significant figures for your output columns? Can you add a feature where we can define that?
I am trying to run FAST++ on some JWST photometry and every time I run the parameter file it always aborts.
I use the new FILTERS.RES file from EAZY that includes the JWST filters.
Here is the parameter file (most of them are the default parameters and I use absolute paths):
#... FAST++ V1.2: parameter file .......................................
#--- GENERAL INFORMATION -----------------------------------------------
#
# Please read this parameter file in detail, you can find all relevant
# information here. Note that you have to adjust your input catalogs
# accordingly, otherwise FAST++ may not work properly!
#
# o Requirements:
# - about 30 MB of free RAM memory
# - at least one CPU core
#
# o The current directory should contain the following files:
# - This parameter file
# - [CATALOG].cat If you fit broadband photometry
# - [CATALOG].zout If you input photometric redshifts
# - [CATALOG].lir If you input infrared luminosities
# - [CATALOG].translate If you input a translate file
# - [SPECTRUM].spec If you fit spectra
#
# o FAST++ runs from the command line.
# The first argument is the parameter file. Default is 'fast.param'
# $ fast++
# $ fast++ my_fast.param
#
# o VERBOSE: set to 0 to disable output in the terminal (except for
# warnings and errors, which are always shown)
#
# o PARALLEL: sets which part of the code should be executed in parallel.
# - 'none': (default) no parallelization, the code will execute on
# one CPU.
# - 'generators': each model will be generated and adjusted to the
# photometry in a separate thread. Good when you have a huge number
# of models and very few galaxies to fit. Will fallback to 'models'
# if a model cache exists.
# - 'models': each model will be adjusted to the photometry in a
# separate thread, but models are generated in the main thread only.
# Good when you have many models and few galaxies to fit, or when
# the models were already generated and cached on the disk.
# - 'sources': the input catalog will be split into equal parts, and
# each part will be analyzed in a separate thread. Good when you
# have few models but lots of galaxies.
#
# o N_THREAD: sets the maximum number of threads the program can use at
# once. This should be close to (or equal to) the number of available
# cores on your CPU, or one less than the number of nodes available on a
# cluster. Setting this to zero will disable parallelization. Note that,
# to enable parallel execution, you also need to change PARALLEL to
# something other than 'none'.
#
# o MAX_QUEUED_FITS: sets the maximum number of fits that are queued and
# waiting to be executed by the worker threads. Increasing this value
# will make the code run faster, but will also increase memory usage.
# For a run on a desktop computer with no more than 10 threads, a value
# of 1000 provides a good compromise; larger values do not improve
# performances significantly (no more than 10%).
#
#-----------------------------------------------------------------------
VERBOSE = 1 # 0 / 1
PARALLEL = 'generators' # 'none', 'generators', 'models', or 'sources'
N_THREAD = 4 # 0, 1, 2, 3, 4, etc
MAX_QUEUED_FITS = 10000
#--- BROADBAND PHOTOMETRIC INFORMATION ---------------------------------
#
# o [CATALOG].cat (similar as for EAzY):
# - Example catalog: hdfn_fs99.cat
# - FAST++ recognizes columns with names {id,ID,z_spec,F[n],E[n],
# TOT[n]} with n the number of the filter
# - If z_spec is not given or any negative value, no z_spec is assumed
# - Give a negative error or "NaN" if the object has no coverage in a
# certain band
#
# o [CATALOG].zout (preferably generated with EAzY):
# - Example catalog: hdfn_fs99.zout
# - If NAME_ZPHOT is not defined, FAST reads columns with labels "z_phot"
# as best-fit photometric redshifts "l68/l95/l99" and "h68/h95/h99"
# for the confidence intervals
# - If input photo-z is a negative value, the photo-z will be ignored
# - If [CATALOG].zout is not available, and no z_specs are given in
# [CATALOG].cat, then the redshifts are allowed to float
# - You can also read in spectroscopic redshifts from [CATALOG].zout.
# The corresponding column should be labeled "z_spec". However, if you
# list them in [CATALOG].cat, FAST++ will ignore those in [CATALOG].zout
#
# o [CATALOG].translate:
# - Example file: hdfn_fs99.translate
# - Translates the column names in [CATALOG].cat to the required
# F[n],E[n],etc formats
# - Will only be used when available
#
# o AB_ZEROPOINT: m_AB = AB_ZEROPOINT - 2.5*log(F[n])
# - Default: AB_ZEROPOINT = 23.9
# - fluxes in micro Janskys: AB_ZEROPOINT = 23.9
# - fluxes in erg sec^{-1} cm^{-2} Hz^{-1}: AB_ZEROPOINT = 48.6
#
# o FILTERS_RES: similar as for EAzY
#
# o FILTER_FORMAT: tells the program in the response curves provided in
# filters_res file are determined for energy-counting (=0) or photon-
# counting (=1) detectors (Default: 1)
#
# o TEMP_ERR_FILE: Template error function. The photometric errors are
# in rest-frame multiplied by this function.
#
# o NAME_ZPHOT: Header name of the column in your [CATALOG].zout file
# that you want to use for your photometric redshifts. If not defined,
# FAST will look for 'z_phot'
#
# o FORCE_ZPHOT: if set to 1, tells the program to treat the photometric
# redshifts as spectroscopic redshifts.
#
# o BEST_AT_ZPHOT: if set to 1, tells the program to force the best-fit
# solution to match the photometric redshift obtained by EAzY, but the
# confidence intervals will still account for the uncertainty on the
# redshift (note that these intervals may not be centered on the best-
# fit solution if this option is enabled).
#
# o ZPHOT_CONF: tells which confidence interval of the photometric
# redshifts should be used to limit the grid for each galaxy.
# Redshifts outside of this confidence interval will not be considered.
#
# o USE_LIR: if set to 1 and [CATALOG].lir exists, FAST++ will read
# infrared luminosities from this file and use them to constrain the
# fit. Must contain columns: id, lir and elir. The observed luminosities
# (given in units of total solar luminosity) are compared to the
# modelled difference of bolometric luminosity before and after dust
# attenuation is applied to the model. This can help break degeneracies,
# but requires that the redshift is well known. The file can contain a
# fourth column, labelled 'log', which is a 0/1 flag that determines if
# the LIR value is given in log10 units or in natural units. This
# changes the way the uncertainty is interpreted: with log=0 the
# uncertainty is assumed to be Gaussian (additive), but with log=1 the
# uncertainty is assumed to be log-normal (multiplicative). Therefore
# when log=1, the 'elir' column must contain the 1-sigma uncertainty on
# log10(LIR).
#
#-----------------------------------------------------------------------
CATALOG = '/Users/nikhilgaruda/Documents/Astronomy_Research/G165/fast/img_fam'
AB_ZEROPOINT = 0.
FILTERS_RES = '/Users/nikhilgaruda/Documents/Astronomy_Research/G165/Photometry/EAZYpy/eazy/data/filters/FILTER.RES.latest'
FILTER_FORMAT = 1
TEMP_ERR_FILE = ''
NAME_ZPHOT = 'z_m1'
FORCE_ZPHOT = 0 # 0 / 1
BEST_AT_ZPHOT = 0 # 0 / 1
ZPHOT_CONF = 68 # 68 / 95 / 99
USE_LIR = 0 # 0 / 1
#--- SPECTROSCOPIC INFORMATION -----------------------------------------
#
# o SPECTRUM:
# - Example file: "1030_gnirs.spec"
# - The file should have the following format:
# # bin wl_low wl_low F[id1] E[id1] F[id2] E[id2] ...
# - bin: ID of the bin in which the spectral element falls
# - wl_low: lower wavelength of the spectral element in Angstrom
# - wl_up: upper wavelength of the spectral element in Angstrom
# - (e)fl: in 10^-19 ergs s-1 cm-2 Angstrom-1 (these units do not
# matter if AUTO_SCALE is set to 1)
# - id[.]: should be an ID in the flux catalog
# - Missing values can be signaled with negative errors or "NaN".
#
# o AUTO_SCALE: This option automatically adjusts the spectrum to the
# model separately from the rest of the photometry. The spectrum thus
# does not participate in determining the best amplitude of the
# model, but still participates in the chi2. This can account for
# uncertain flux calibration of the spectrum, and will emphasize more
# the features of the spectrum rather than it's absolute flux level.
# Note that when this feature is enabled, the template error function,
# if used, will not be applied to the spectral data.
#
# o APPLY_VDISP: Velocity dispersion of the spectral templates. Setting
# this parameter to a non-zero value will broaden the templates with
# a fixed velocity dispersion before the fit. This is only relevant
# when fitting spectra, and has an impact on performances (a couple
# seconds of extra delay), so it is disabled by default.
#
#-----------------------------------------------------------------------
SPECTRUM = ''
AUTO_SCALE = 0 # 0 / 1
APPLY_VDISP = 0 # km/s
#--- OUTPUT INFORMATION -----------------------------------------------
#
# o OUTPUT_DIR: output directory for results
#
# o OUTPUT_FILE: output file for results.
# If not given: [CATALOG]_[SPECTRUM].fout
#
# o N_SIM: The number of Monte Carlo simulations used to determine the
# confidence levels. If zero or not defined, only best-fit values will
# be given.
#
# o C_INTERVAL: Percentage of confidence intervals, choose from 68% (1
# sigma), 95% (2 sigma), or 99% (3 sigma)
#
# o BEST_FIT: output best-fit SPS model in the 'best_fits' directory
#
# o BEST_FROM_SIM: use the median of the Monte Carlo simulation as
# best-fit instead of the model with the smallest chi squared on
# the original (unperturbed) photometry.
#
# o INTERVAL_FROM_CHI2: use the chi2 grid directly to compute confidence
# intervals on the fit parameters, instead of using Monte Carlo
# simulation. This will force setting 'SAVE_BESTCHI' to a value large
# enough to encompass the chosen confidence intervals.
#
# o SAVE_SIM: save the best-fit parameters for each Monte Carlo
# simulation for all sources in the "best_fits" directory.
#
# o SFR_AVG: output the SFR as the average of the 'SFR_AVG' last million
# years. If set to zero (the default) FAST++ will output the
# instantaneous SFR.
#
# o INTRINSIC_BEST_FIT: if BEST_FIT=1, setting this option to 1 will also
# output the intrinsic best-fit SED of the galaxy, as it would be seen
# without dust obscuration. This intrinsic SED is saved as a third
# column in the best-fit SED file.
#
# o BEST_SFHS: if set to 1, the program will output the best-fit star
# formation history along with the best fit SEDs. If Monte Carlo
# simulations are enabled, the confidence intervals of the SFH will
# also be written.
#
# o SFH_OUTPUT_STEP: if BEST_SFHS=1, sets the time step of the output SFH
# in million years. The default is 10 Myr.
#
# o SFH_OUTPUT: 'sfr' will output the evolution of the star formation rate
# with time, while 'mass' will show the total stellar mass (including
# mass loss).
#
# o REST_MAG: list of filter ID to use to compute rest-frame magnitudes.
# These absolute magnitudes are then given at 10pc in the AB system,
# using AB_ZEROPOINT, and are not corrected for attenuation.
#
# o CONTINUUM_INDICES: file listing the continuum indices (absorption
# line equivalent-width, Dn4000, ...) to compute from each model
# spectrum. See examples in the "share/continuum_indices" directory.
#
# o SFH_QUANTITIES: list of SFH quantities to compute for each model.
# These quantities are computed directly on the SFH functional form
# of each model, and are thus non-parametric. Available quantites:
# - 'tsf': shortest time interval over which 68% of SFR took place
# (= duration of star formation).
# - 'past_sfr': average SFR during the above time interval
# (= mean past SFR).
# - 'sfr'X : average SFR over the last 'X' Myr.
# - 'brate'X : 'sfr'X / 'past_sfr' (= birth-rate parameter).
# - 'tquench'X : elapsed time since the SFR dropped below a factor
# 'X' of the 'past_sfr' (= time since quenching).
# - 'tform'X : elapsed time since the galaxy had formed 'X'% of its
# current mass (= time since formation).
#
# o OUTPUT_COLUMNS: define here what columns to write in [CATALOG].fout
# Available columns: id, metal, lage, Av, lmass, lsfr, lssfr, lldust,
# llion, lmform and chi2. If using the "standard" FAST templates, two
# additional columns are available: ltau and la2t. If using custom SFH,
# you can also choose any of your custom SFH parameter. Rest-frame
# magnitudes specified in 'REST_MAG' are also available, the format is
# "M[...]" where "[...]" is the filter ID. If this variable is set to
# an empty array (default), then all available parameters are written
# in the file (except lldust, llion, and lmform).
#
#-----------------------------------------------------------------------
OUTPUT_DIR = '/Users/nikhilgaruda/Documents/Astronomy_Research/G165/fast/OUTPUT'
OUTPUT_FILE = ''
N_SIM = 100
C_INTERVAL = [68 ,95] # 68 / 95 / 99 or [68,95] etc
BEST_FIT = 1 # 0 / 1
BEST_FROM_SIM = 0 # 0 / 1
INTERVAL_FROM_CHI2 = 0 # 0 / 1
SAVE_SIM = 1 # 0 / 1
SFR_AVG = 0 # 0, 100 Myr, 300 Myr etc
INTRINSIC_BEST_FIT = 0 # 0 / 1
BEST_SFHS = 1 # 0 / 1
SFH_OUTPUT_STEP = 1 # 10 Myr, 100 Myr etc
SFH_OUTPUT = 'sfr' # 'sfr' or 'mass'
REST_MAG = [] # [140,142,161] for UVJ colors
CONTINUUM_INDICES = ''
SFH_QUANTITIES = ['tsf','past_sfr','sfr10','brate10','tquench10','tform50'] # ['tquench10','tform50','brate10', ...]
OUTPUT_COLUMNS = ['id','Av','lmass','lsfr', 'metal', 'chi2'] # ['id','Av','lmass','lsfr', ...]
#--- CHOOSE STELLAR POPULATIONS LIBRARY --------------------------------
#
# o LIBRARY_DIR: directory containing the stellar population libraries
# of the form: ised_[SFH].[resolutions].
# The binaries in these directories are of the following form:
# [library]_[resolution]_[imf]_z[metallicity]_ltau[ltau/yr].ised
#
# o All binary inputs are made using "csp_galaxev"
# ("galaxev" software by Bruzual & Charlot 2003) on the SSP models
# "bc2003_[RESOLUTION]_[metal]_[IMF]_ssp.ised" and assuming no dust
# law (and no recycling of gas ejected by stars for exponentially
# declining star formation history)
#
# o LIBRARY: choose from Bruzual & Charlot 2003 ('bc03'),
# Maraston 2005 ('ma05'), and FSPS by Conroy et al. ('co11')
#
# o RESOLUTION: Choose 'hr' for spectral fitting, and 'pr' (photometric
# resolution) or 'lr' for medium and broadband filters. Not all
# resolutions are standard available for all SFHs or libraries or IMFs
#
# o IMF (stellar initial mass function), choose from
# - 'ch'(abrier)
# - 'sa'(lpeter)
# - 'kr'(oupa)
#
# o SFH: parametrization of the star formation history (SFH), choose from
# - 'exp': exponentially declining SFH; sfr ~ exp(-t/tau)
# - 'del': delayed exponentially declining SFH; sfr ~ t exp(-t/tau)
# - 'tru': truncated SFH, with constant star formation between
# t_onset and t_onset+tau
# For all SFH you can specify the range tau in the grid
#
# o DUST_LAW: parametrization of the dust attenuation curve. You can
# choose from the following options
# - 'calzetti': Calzetti (2000) dust law
# - 'mw': Milky Way, following parametrization by Cardelli et al. (1989)
# - 'kc': Kriek & Conroy (2013). Average dust law. We use the
# parametrization by Noll et al. with E_B = 1 and delta = -0.1
# - 'noll': For this law you have to parametrize E_b and delta.
# You can only pick one value for each, arrays are not allowed.
#
# o MY_SFH: if you define this option, FAST++ will not fit a range of
# star-formation histories, but just one model (so LOG_TAU_XXX will
# be ignored). For this option you can only read in one custom star
# formation history, for which you have to make the ISED file
# yourself using "csp_galaxev". The naming of the ised file has to
# be as follows:
# [library]_[resolution]_[imf]_z[metallicity]_[MY_SFH].ised
# This file needs to be placed directly in 'LIBRARY_DIR'
#
# o CUSTOM_SFH: if you define this option, FAST++ will build a grid of
# templates on the fly using SSP models, instead of reading the
# composite models from "csp_galaxev". You can therefore fit any
# star formation history. The SFH must be a mathematical expression
# which returns the SFR as a function of the time 't' since the galaxy
# was born (the unit of the SFR doest not matter). Custom grid parameters
# can be referenced in this function (see below) but not the age or the
# dust attenuation.
#
# o CUSTOM_PARAMS: when using CUSTOM_SFH, define here the names of your
# grid parameters (e.g., log_tau). For each of these parameters you
# must provide the _MIN, _MAX and _STEP values, as for the other
# grid parameters.
#
# o CUSTOM_SFH_LOOKBACK: changes the meaning of the time 't' in the SFH
# expression, so that 't' refers to the lookback time. The instant t=0
# then refers to the moment where the galaxy is observed, and larger
# values correspond to earlier times in the past. This is equivalent
# to substituting 't' for '10^lage - t' in the SFH expression.
#
#-----------------------------------------------------------------------
LIBRARY_DIR = '/Users/nikhilgaruda/Documents/Documents/Astronomy_Research/Software/fastpp/share/libraries/'
LIBRARY = 'co11' # 'bc03' / 'ma05' / 'co11'
RESOLUTION = 'hr' # 'pr' / 'lr' / 'hr'
IMF = 'ch' # 'ch' / 'sa' / 'kr'
SFH = 'del' # 'exp' / 'del' / 'tru'
DUST_LAW = 'kc' # 'calzetti' / 'mw' / 'kc' / 'noll'
# E_B = 1 # only define for 'noll' dust law
# delta = -0.2 # only define for 'noll' dust law
MY_SFH = ''
CUSTOM_SFH = '' # '(1 + t)^alpha'
CUSTOM_PARAMS = [] # ['alpha', ...]
CUSTOM_SFH_LOOKBACK = 0 # 0 / 1
# ALPHA_MIN = -2 # define these for each parameter
# ALPHA_MAX = 2 # define these for each parameter
# ALPHA_STEP = 0.1 # define these for each parameter
#--- DEFINE GRID -------------------------------------------------------
#
# o Choose only values for tau and metallicity that are in your library.
# Otherwise extend your library.
#
# o If EAzY is used, make sure Z_MIN, Z_MAX are similar.
#
# o METAL: the options differ per stellar population library
# ma05: Z=0.001, Z=0.01, Z=0.02 [solar], and Z=0.04
# bc03: Z=0.004, Z=0.008, Z=0.02 [solar], and Z=0.05
# co11: Z=0.0008, Z=0.0031, Z=0.0096, Z=0.019 [solar], and Z=0.03
# You can choose more than one by defining an array.
#
# o If a grid has already been made for a specific LIBRARY, RESOLUTION,
# IMF, tau, age, z, A_v, A_v_bc, metallicity, and filter set and/or
# spectral elements, the grid will be automatically read from the cache
# unless the NO_CACHE option is set to "1". This option will also
# prevent the code from writing this cache in the first place.
#
# o DIFFERENTIAL_A_V: By default (0), all stars suffer the same amount
# of extinction by dust. If DIFFERENTIAL_A_V is set to "1", young
# stars will be place under a thicker screen of dust, as controlled by
# A_V_BC_MIN, A_V_BC_MAX, A_V_BC_STEP, and LOG_BC_AGE_MAX.
#
# o LOG_BC_AGE_MAX: When DIFFERENTIAL_A_V is set to "1", stars in their
# birth cloud will be given extra attenuation. Only stars younger than
# LOG_BC_AGE_MAX are considered to be in their birthcloud. The default
# of 10 Myr is taken from Charlot&Fall (2001).
#
# o NO_MAX_AGE: By default (0), ages that exceed the age of the universe
# are not allowed. However, when NO_MAX_AGE is put to "1" you can have
# older ages.
#
#-----------------------------------------------------------------------
LOG_TAU_MIN = 8.5 # log [yr]
LOG_TAU_MAX = 10. # log [yr]
LOG_TAU_STEP = 0.5 # log [yr], min 0.1
LOG_AGE_MIN = 8.0 # log [yr]
LOG_AGE_MAX = 10.0 # log [yr]
LOG_AGE_STEP = 0.05 # log [yr]
NO_MAX_AGE = 0 # 0 / 1
Z_MIN = 0.01 # Cannot be 0.0
Z_MAX = 14.00
Z_STEP = 0.01
Z_STEP_TYPE = 1 # 0: Z_STEP, 1: Z_STEP*(1+z)
A_V_MIN = 0. # [mag]
A_V_MAX = 3. # [mag]
A_V_STEP = 0.1 # [mag]
A_V_BC_MIN = 0. # [mag]
A_V_BC_MAX = 0. # [mag]
A_V_BC_STEP = 0.1 # [mag]
DIFFERENTIAL_A_V = 0 # 0 / 1
LOG_BC_AGE_MAX = 7.0 # log [yr]
METAL = [0.02] # [0.0096,0.019,0.03]
NO_CACHE = 1 # 0 / 1
#--- COSMOLOGY ---------------------------------------------------------
#
#-----------------------------------------------------------------------
H0 = 70.0 # Hubble constant
OMEGA_M = 0.3 # Omega matter
OMEGA_L = 0.7 # Omega lambda
NO_IGM = 0 # 0 / 1
#--- SAVE INTERMEDIATE PRODUCTS ----------------------------------------
#
# o SAVE_CHI_GRID: if "1" then the chi2 grid for all objects will be
# saved in a ".grid" file in the output directory.
#
# o SAVE_BESTCHI: if anything else than "0", the models with a chi2
# less than SAVE_BESTCHI different from the best chi2 will be
# saved in a ".grid" file in the "best_chi2" directory, for each
# object separately. This will occupy less disk space than the
# SAVE_CHI_GRID option. Usual values are "1" to have 68% chance of
# including the "true" model, "2.71" for 90% and "6.63" for 99%.
# SAVE_CHI_GRID and SAVE_BESTCHI can be enabled together.
#
#-----------------------------------------------------------------------
SAVE_CHI_GRID = 1 # 0 / 1
SAVE_BESTCHI = 1 # 1 (68%) / 2.71 (90%) / 6.63 (99%) / etc
Here is the error I get while running the program:
❯ ./fast++ /Users/nikhilgaruda/Documents/Astronomy_Research/G165/fast/fast.param
note: this is FAST++ version '1.3.0-ecf74e2'
note: using instantaneous SFRs
note: applying Madau+1995 IGM absorption
note: computing SFH quantities: {tform50, tsf, past_sfr, tquench10, sfr10, brate10}
note: reading fluxes from '/Users/nikhilgaruda/Documents/Astronomy_Research/G165/fast/img_fam.cat'
note: using column translation file '/Users/nikhilgaruda/Documents/Astronomy_Research/G165/fast/img_fam.translate'
note: ... translated 16 column names
note: reading filters from '/Users/nikhilgaruda/Documents/Astronomy_Research/G165/Photometry/EAZYpy/eazy/data/filters/FILTER.RES.latest'
note: found 417 filters in the database, will use 8 of them
note: reading fluxes...
note: fitting 2 sources with 8 fluxes each
note: reading photometric redshifts from '/Users/nikhilgaruda/Documents/Astronomy_Research/G165/fast/img_fam.zout'
note: define grid...
note: fitting a grid of 599912 templates (ntau=4,nmetal=1,nage=41,nav=31,navbc=1,nz=118)
note: identify zspecs and redshift bounds in the grid...
note: initializing chi2 grid on disk... (expected size 77.8084 MB)
libc++abi: terminating due to uncaught exception of type std::length_error: vector
[1] 47262 abort ./fast++ /Users/nikhilgaruda/Documents/Astronomy_Research/G165/fast/fast.para
Hi, I'm wondering if it's possible to define a custom SFH using something similar to the piecewise constant model of Leja et al. 2019, section 2.1 and 2.2.1. Essentially the SFH is parameterized as a series of uncorrelated "bursts" with fixed time edges, where the SFR is constant between those time edges, creating a kind of step function.
Reading the available documentation, I'm not sure how I could go about doing this, as the SFR isn't exactly described by a smoothly varying function of time.
Any insight or help would be appreciated!
I am trying to fit a galaxy SED using fast but the code seems to not be able to estimate some parameter values correctly. For example the value which I get for Av is always equal to maximum or minimum possible value for Av. I attaching all the relevant files here.
can I follow up on the new build regarding Z? :)
METAL = [0.004, 0.02, 0.05, 0.008]
In the past commit this would use all SSPs in this array, but now it seems it uses only the first value specified in the array.
Dear Corentin,
I'm running Fast++ on the photometry (with and without spectroscopy) for a single source with a simple set of standard parameters. When I run it with bc03 models, I encounter a "Segmentation fault: 11" error either while fitting or at the end, right after saving catalogs and best fits. This does not occur when I model the same galaxy with co11 models.
I've tried reducing the number of templates, excluding or including spectroscopy, fixing parameters, but the error keeps appearing.
I've refreshed the Fast++ installation, but the error keeps appearing.
Would you have any ideas of how to fix this?
Thank you in advance for your help!
Francesco
Machine: macOS Big Sur (11.7.9)
.param file: with bc03
#... FAST++ V1.2: parameter file .......................................
#--- GENERAL INFORMATION -----------------------------------------------
#
# Please read this parameter file in detail, you can find all relevant
# information here. Note that you have to adjust your input catalogs
# accordingly, otherwise FAST++ may not work properly!
#
# o Requirements:
# - about 30 MB of free RAM memory
# - at least one CPU core
#
# o The current directory should contain the following files:
# - This parameter file
# - [CATALOG].cat If you fit broadband photometry
# - [CATALOG].zout If you input photometric redshifts
# - [CATALOG].lir If you input infrared luminosities
# - [CATALOG].translate If you input a translate file
# - [SPECTRUM].spec If you fit spectra
#
# o FAST++ runs from the command line.
# The first argument is the parameter file. Default is 'fast.param'
# $ fast++
# $ fast++ my_fast.param
#
# o VERBOSE: set to 0 to disable output in the terminal (except for
# warnings and errors, which are always shown)
#
# o PARALLEL: sets which part of the code should be executed in parallel.
# - 'none': (default) no parallelization, the code will execute on
# one CPU.
# - 'generators': each model will be generated and adjusted to the
# photometry in a separate thread. Good when you have a huge number
# of models and very few galaxies to fit. Will fallback to 'models'
# if a model cache exists.
# - 'models': each model will be adjusted to the photometry in a
# separate thread, but models are generated in the main thread only.
# Good when you have many models and few galaxies to fit, or when
# the models were already generated and cached on the disk.
# - 'sources': the input catalog will be split into equal parts, and
# each part will be analyzed in a separate thread. Good when you
# have few models but lots of galaxies.
#
# o N_THREAD: sets the maximum number of threads the program can use at
# once. This should be close to (or equal to) the number of available
# cores on your CPU, or one less than the number of nodes available on a
# cluster. Setting this to zero will disable parallelization.
#
# o MAX_QUEUED_FITS: sets the maximum number of fits that are queued and
# waiting to be executed by the worker threads. Increasing this value
# will make the code run faster, but will also increase memory usage.
# For a run on a desktop computer with no more than 10 threads, a value
# of 1000 provides a good compromise; larger values do not improve
# performances significantly (no more than 10%).
#
#-----------------------------------------------------------------------
VERBOSE = 1 # 0 / 1
PARALLEL = 'generators' # 'none', 'generators', 'models', or 'sources'
N_THREAD = 4
MAX_QUEUED_FITS = 1000
#--- BROADBAND PHOTOMETRIC INFORMATION ---------------------------------
#
# o [CATALOG].cat (similar as for EAzY):
# - Example catalog: hdfn_fs99.cat
# - FAST++ recognizes columns with names {id,ID,z_spec,F[n],E[n],
# TOT[n]} with n the number of the filter
# - If z_spec is not given or any negative value, no z_spec is assumed
# - Give a negative error or "NaN" if the object has no coverage in a
# certain band
#
# o [CATALOG].zout (preferably generated with EAzY):
# - Example catalog: hdfn_fs99.zout
# - If NAME_ZPHOT is not defined, FAST reads columns with labels "z_phot"
# as best-fit photometric redshifts "l68/l95/l99" and "h68/h95/h99"
# for the confidence intervals
# - If input photo-z is a negative value, the photo-z will be ignored
# - If [CATALOG].zout is not available, and no z_specs are given in
# [CATALOG].cat, then the redshifts are allowed to float
# - You can also read in spectroscopic redshifts from [CATALOG].zout.
# The corresponding column should be labeled "z_spec". However, if you
# list them in [CATALOG].cat, FAST++ will ignore those in [CATALOG].zout
#
# o [CATALOG].translate:
# - Example file: hdfn_fs99.translate
# - Translates the column names in [CATALOG].cat to the required
# F[n],E[n],etc formats
# - Will only be used when available
#
# o AB_ZEROPOINT: m_AB = AB_ZEROPOINT - 2.5*log(F[n])
# - Default: AB_ZEROPOINT = 23.9
# - fluxes in micro Janskys: AB_ZEROPOINT = 23.9
# - fluxes in erg sec^{-1} cm^{-2} Hz^{-1}: AB_ZEROPOINT = 48.6
#
# o FILTERS_RES: similar as for EAzY
#
# o FILTER_FORMAT: tells the program in the response curves provided in
# filters_res file are determined for energy-counting (=0) or photon-
# counting (=1) detectors (Default: 1)
#
# o TEMP_ERR_FILE: Template error function. The photometric errors are
# in rest-frame multiplied by this function.
#
# o NAME_ZPHOT: Header name of the column in your [CATALOG].zout file
# that you want to use for your photometric redshifts. If not defined,
# FAST will look for 'z_phot'
#
# o FORCE_ZPHOT: if set to 1, tells the program to treat the photometric
# redshifts as spectroscopic redshifts.
#
# o BEST_AT_ZPHOT: if set to 1, tells the program to force the best-fit
# solution to match the photometric redshift obtained by EAzY, but the
# confidence intervals will still account for the uncertainty on the
# redshift (note that these intervals may not be centered on the best-
# fit solution if this option is enabled).
#
# o ZPHOT_CONF: tells which confidence interval of the photometric
# redshifts should be used to limit the grid for each galaxy.
# Redshifts outside of this confidence interval will not be considered.
#
# o USE_LIR: if set to 1 and [CATALOG].lir exists, FAST++ will read
# infrared luminosities from this file and use them to constrain the
# fit. Must contain columns: id, lir and elir. The observed luminosities
# (given in units of total solar luminosity) are compared to difference
# of bolometric luminosity before and after dust attenuation is applied
# to the models. This can help break degeneracies, but requires that
# the redshift is well known.
#
#-----------------------------------------------------------------------
CATALOG = 'psb'
AB_ZEROPOINT = 23.9
FILTERS_RES = 'FILTER.RES.latest'
FILTER_FORMAT = 1
TEMP_ERR_FILE = '/Users/fvalenti/bin/fastpp/share/TEMPLATE_ERROR.fast.v0.2'
NAME_ZPHOT = 'z_phot'
FORCE_ZPHOT = 1 # 0 / 1
BEST_AT_ZPHOT = 0 # 0 / 1
ZPHOT_CONF = 68 # 68 / 95 / 99
USE_LIR = 0 # 0 / 1
#--- SPECTROSCOPIC INFORMATION -----------------------------------------
#
# o SPECTRUM:
# - Example file: "1030_gnirs.spec"
# - The file should have the following format:
# # bin wl_low wl_low F[id1] E[id1] F[id2] E[id2] ...
# - bin: ID of the bin in which the spectral element falls
# - wl_low: lower wavelength of the spectral element in Angstrom
# - wl_up: upper wavelength of the spectral element in Angstrom
# - (e)fl: in 10^-19 ergs s-1 cm-2 Angstrom-1 (these units do not
# matter if AUTO_SCALE is set to 1)
# - id[.]: should be an ID in the flux catalog
# - Missing values can be signaled with negative errors or "NaN".
#
# o AUTO_SCALE: This option automatically adjusts the spectrum to the
# model separately from the rest of the photometry. The spectrum thus
# does not participate in determining the best amplitude of the
# model, but still participates in the chi2. This can account for
# uncertain flux calibration of the spectrum, and will emphasize more
# the features of the spectrum rather than its absolute flux level.
# Note that when this feature is enabled, the template error function,
# if used, will not be applied to the spectral data.
#
# o APPLY_VDISP: Velocity dispersion of the spectral templates. Setting
# this parameter to a non-zero value will broaden the templates with
# a fixed velocity dispersion before the fit. This is only relevant
# when fitting spectra, and has an impact on performances (a couple
# seconds of extra delay), so it is disabled by default.
#
#-----------------------------------------------------------------------
SPECTRUM =''
AUTO_SCALE = 0 # 0 / 1
APPLY_VDISP = 266 # km/s ; 300 km/s for the first run
#--- OUTPUT INFORMATION -----------------------------------------------
#
# o OUTPUT_DIR: output directory for results
#
# o OUTPUT_FILE: output file for results.
# If not given: [CATALOG]_[SPECTRUM].fout
#
# o N_SIM: The number of Monte Carlo simulations used to determine the
# confidence levels. If zero or not defined, only best-fit values will
# be given.
#
# o C_INTERVAL: Percentage of confidence intervals, choose from 68% (1
# sigma), 95% (2 sigma), or 99% (3 sigma)
#
# o BEST_FIT: output best-fit SPS model in the 'best_fits' directory
#
# o BEST_FROM_SIM: use the median of the Monte Carlo simulation as
# best-fit instead of the model with the smallest chi squared on
# the original (unperturbed) photometry.
#
# o SAVE_SIM: save the best-fit parameters for each Monte Carlo
# simulation for all sources in the "best_fits" directory.
#
# o SFR_AVG: output the SFR as the average of the 'SFR_AVG' last million
# years. If set to zero (the default) FAST++ will output the
# instantaneous SFR.
#
# o INTRINSIC_BEST_FIT: if BEST_FIT=1, setting this option to 1 will also
# output the intrinsic best-fit SED of the galaxy, as it would be seen
# without dust obscuration. This intrinsic SED is saved as a third
# column in the best-fit SED file.
#
# o BEST_SFHS: if set to 1, the program will output the best-fit star
# formation history along with the best fit SEDs. If Monte Carlo
# simulations are enabled, the confidence intervals of the SFH will
# also be written.
#
# o SFH_OUTPUT_STEP: if BEST_SFHS=1, sets the time step of the output SFH
# in million years. The default is 10 Myr.
#
# o SFH_OUTPUT: 'sfr' will output the evolution of the star formation rate
# with time, while 'mass' will show the total stellar mass (including
# mass loss).
#
# o REST_MAG: list of filter ID to use to compute rest-frame magnitudes.
# These absolute magnitudes are then given at 10pc in the AB system,
# using AB_ZEROPOINT, and are not corrected for attenuation.
#
# o CONTINUUM_INDICES: file listing the continuum indices (absorption
# line equivalent-width, Dn4000, ...) to compute from each model
# spectrum. See examples in the "share/continuum_indices" directory.
#
# o SFH_QUANTITIES: list of SFH quantities to compute for each model.
# These quantities are computed directly on the SFH functional form
# of each model, and are thus non-parametric. Available quantites:
# - 'tsf': shortest time interval over which 68% of SFR took place
# (= duration of star formation).
# - 'past_sfr': average SFR during the above time interval
# (= mean past SFR).
# - 'sfr'X : average SFR over the last 'X' Myr.
# - 'brate'X : 'sfr'X / 'past_sfr' (= birth-rate parameter).
# - 'tquench'X : elapsed time since the SFR dropped below a factor
# 'X' of the 'past_sfr' (= time since quenching).
# - 'tform'X : elapsed time since the galaxy had formed 'X'% of its
# current mass (= time since formation).
#
# o OUTPUT_COLUMNS: define here what columns to write in [CATALOG].fout
# Available columns: id, metal, lage, Av, lmass, lsfr, lssfr, lldust,
# llion, lmform and chi2. If using the "standard" FAST templates, two
# additional columns are available: ltau and la2t. If using custom SFH,
# you can also choose any of your custom SFH parameter. Rest-frame
# magnitudes specified in 'REST_MAG' are also available, the format is
# "M[...]" where "[...]" is the filter ID. By default all available
# parameters are written in the file (except lldust, llion, and lmform).
#
# o OUTPUT_PRECISION: define the numerical precision to use when printing
# values in the output catalog. The default (0) means to use the
# standard precision, which is 1e-4 for the redshift and metallicity,
# and 1e-2 for everything else. If set to any other power of ten
# between zero and one (excluded), this value will be used to round
# the outputs. Note, this only affects the output catalog (.fout);
# all other outputs (including grid files) are always stored in full
# precision.
#
#-----------------------------------------------------------------------
OUTPUT_DIR = 'delayed/bc03_ch/'
OUTPUT_FILE = ''
N_SIM = 100
C_INTERVAL = [68,90,95] # 68 / 95 / 99 or [68,95] etc
BEST_FIT = 1 # 0 / 1
BEST_FROM_SIM = 0 # 0 / 1
SAVE_SIM = 1 # 0 / 1
SFR_AVG = 10 # 0, 100 Myr, 300 Myr etc
INTRINSIC_BEST_FIT = 0 # 0 / 1
BEST_SFHS = 1 # 0 / 1
SFH_OUTPUT_STEP = 10 # 10 Myr, 100 Myr etc
SFH_OUTPUT = 'sfr' # 'sfr' or 'mass'
REST_MAG = [140,142,161,153,155,121,81,414,415,416] # [140,142,161] for UVJ colors
CONTINUUM_INDICES = ''
SFH_QUANTITIES = ['tsf','past_sfr','sfr10','tquench10','tform50','brate10'] # ['tquench10','tform50','brate10',...]
OUTPUT_COLUMNS = ['id','z','ltau','lage','av','lmass','lsfr','lssfr','lldust','lscale','sscale','chi2','tsf','past_sfr','sfr10','tquench10','tform50','brate10','M140','M142','M153','M155','M161','M121','M81','M414','M415','M416','metal'] # ['id','Av','lmass','lsfr', ...]
OUTPUT_PRECISION = 0 # 0 / 0.01 / 0.0001 / 1e-6
#--- CHOOSE STELLAR POPULATIONS LIBRARY --------------------------------
#
# o LIBRARY_DIR: directory containing the stellar population libraries
# of the form: ised_[SFH].[resolutions].
# The binaries in these directories are of the following form:
# [library]_[resolution]_[imf]_z[metallicity]_ltau[ltau/yr].ised
#
# o All binary inputs are made using "csp_galaxev"
# ("galaxev" software by Bruzual & Charlot 2003) on the SSP models
# "bc2003_[RESOLUTION]_[metal]_[IMF]_ssp.ised" and assuming no dust
# law (and no recycling of gas ejected by stars for exponentially
# declining star formation history)
#
# o LIBRARY: choose from Bruzual & Charlot 2003 ('bc03'),
# Maraston 2005 ('ma05'), and FSPS by Conroy et al. ('co11')
#
# o RESOLUTION: Choose 'hr' for spectral fitting, and 'pr' (photometric
# resolution) or 'lr' for medium and broadband filters. Not all
# resolutions are standard available for all SFHs or libraries or IMFs
#
# o IMF (stellar initial mass function), choose from
# - 'ch'(abrier)
# - 'sa'(lpeter)
# - 'kr'(oupa)
#
# o SFH: parametrization of the star formation history (SFH), choose from
# - 'exp': exponentially declining SFH; sfr ~ exp(-t/tau)
# - 'del': delayed exponentially declining SFH; sfr ~ t exp(-t/tau)
# - 'tru': truncated SFH, with constant star formation between
# t_onset and t_onset+tau
# For all SFH you can specify the range tau in the grid
#
# o DUST_LAW: parametrization of the dust attenuation curve. You can
# choose from the following options
# - 'calzetti': Calzetti (2000) dust law
# - 'mw': Milky Way, following parametrization by Cardelli et al. (1989)
# - 'kc': Kriek & Conroy (2013). Average dust law. We use the
# parametrization by Noll et al. with E_B = 1 and delta = -0.1
# - 'noll': For this law you have to parametrize E_b and delta.
# You can only pick one value for each, arrays are not allowed.
#
# o MY_SFH: if you define this option, FAST++ will not fit a range of
# star-formation histories, but just one model (so LOG_TAU_XXX will
# be ignored). For this option you can only read in one custom star
# formation history, for which you have to make the ISED file
# yourself using "csp_galaxev". The naming of the ised file has to
# be as follows:
# [library]_[resolution]_[imf]_z[metallicity]_[MY_SFH].ised
# This file needs to be placed directly in 'LIBRARY_DIR'
#
# o CUSTOM_SFH: if you define this option, FAST++ will build a grid of
# templates on the fly using SSP models, instead of reading the
# composite models from "csp_galaxev". You can therefore fit any
# star formation history. The SFH must be a mathematical expression
# which returns the SFR as a function of the time 't' since the galaxy
# was born (the unit of the SFR doest not matter). Custom grid parameters
# can be referenced in this function (see below) but not the age or the
# dust attenuation.
#
# o CUSTOM_PARAMS: when using CUSTOM_SFH, define here the names of your
# grid parameters (e.g., log_tau). For each of these parameters you
# must provide the _MIN, _MAX and _STEP values, as for the other
# grid parameters.
#
# o CUSTOM_SFH_LOOKBACK: changes the meaning of the time 't' in the SFH
# expression, so that 't' refers to the lookback time. The instant t=0
# then refers to the moment where the galaxy is observed, and larger
# values correspond to earlier times in the past. This is equivalent
# to substituting 't' for '10^lage - t' in the SFH expression.
#
#-----------------------------------------------------------------------
LIBRARY_DIR = '/Users/fvalenti/bin/fastpp/share/libraries/'
LIBRARY = 'bc03' # 'bc03' / 'ma05' / 'co11'
RESOLUTION = 'hr' # 'pr' / 'lr' / 'hr'
IMF = 'ch' # 'ch' / 'sa' / 'kr'
SFH = 'del' # 'exp' / 'del' / 'tru'
DUST_LAW = 'kc' # 'calzetti' / 'mw' / 'kc' / 'noll'
MY_SFH = ''
#--- DEFINE GRID -------------------------------------------------------
#
# o Choose only values for tau and metallicity that are in your library.
# Otherwise extend your library.
#
# o If EAzY is used, make sure Z_MIN, Z_MAX are similar.
#
# o METAL: the options differ per stellar population library
# ma05: Z=0.001, Z=0.01, Z=0.02 [solar], and Z=0.04
# bc03: Z=0.004, Z=0.008, Z=0.02 [solar], and Z=0.05
# co11: Z=0.0008, Z=0.0031, Z=0.0096, Z=0.019 [solar], and Z=0.03
# You can choose more than one by defining an array.
#
# o If a grid has already been made for a specific LIBRARY, RESOLUTION,
# IMF, tau, age, z, A_v, A_v_bc, metallicity, and filter set and/or
# spectral elements, the grid will be automatically read from the cache
# unless the NO_CACHE option is set to "1". This option will also
# prevent the code from writing this cache in the first place.
#
# o DIFFERENTIAL_A_V: By default (0), all stars suffer the same amount
# of extinction by dust. If DIFFERENTIAL_A_V is set to "1", young
# stars will be place under a thicker screen of dust, as controlled by
# A_V_BC_MIN, A_V_BC_MAX, A_V_BC_STEP, and LOG_BC_AGE_MAX.
#
# o LOG_BC_AGE_MAX: When DIFFERENTIAL_A_V is set to "1", stars in their
# birth cloud will be given extra attenuation. Only stars younger than
# LOG_BC_AGE_MAX are considered to be in their birthcloud. The default
# of 10 Myr is taken from Charlot&Fall (2001).
#
# o NO_MAX_AGE: By default (0), ages that exceed the age of the universe
# are not allowed. However, when NO_MAX_AGE is put to "1" you can have
# older ages.
#
#-----------------------------------------------------------------------
LOG_TAU_MIN = 6.5 # log [yr]
LOG_TAU_MAX = 10. # log [yr]
LOG_TAU_STEP = 0.1 # log [yr], min 0.1
LOG_AGE_MIN = 6.5 # log [yr];
LOG_AGE_MAX = 9.2 # log [yr]; max age universe
LOG_AGE_STEP = 0.1 # log [yr]
NO_MAX_AGE = 0 # 0 / 1
Z_MIN = 4.1045 # Cannot be 0.0
Z_MAX = 4.1085
Z_STEP = 0.001
Z_STEP_TYPE = 0 # 0: Z_STEP, 1: Z_STEP*(1+z)
A_V_MIN = 0.0 # [mag]
A_V_MAX = 1.0 # [mag]
A_V_STEP = 0.1 # [mag]
A_V_BC_MIN = 0. # [mag]
A_V_BC_MAX = 0. # [mag]
A_V_BC_STEP = 0.1 # [mag]
DIFFERENTIAL_A_V = 0 # 0 / 1
LOG_BC_AGE_MAX = 7.0 # log [yr]
METAL = [0.02] # BC [0.008,0.02,0.05]
NO_CACHE = 0 # 0 / 1
#--- COSMOLOGY ---------------------------------------------------------
#
#-----------------------------------------------------------------------
H0 = 70.0 # Hubble constant
OMEGA_M = 0.3 # Omega matter
OMEGA_L = 0.7 # Omega lambda
#--- SAVE INTERMEDIATE PRODUCTS ----------------------------------------
#
# o SAVE_CHI_GRID: if "1" then the chi2 grid for all objects will be
# saved in a ".grid" file in the output directory.
#
# o SAVE_BESTCHI: if anything else than "0", the models with a chi2
# less than SAVE_BESTCHI different from the best chi2 will be
# saved in a ".grid" file in the "best_chi2" directory, for each
# object separately. This will occupy less disk space than the
# SAVE_CHI_GRID option. Usual values are "1" to have 68% chance of
# including the "true" model, "2.71" for 90% and "6.63" for 95%.
# SAVE_CHI_GRID and SAVE_BESTCHI can be enabled together.
#
#-----------------------------------------------------------------------
SAVE_CHI_GRID = 0 # 0 / 1
SAVE_BESTCHI = 1 # 1 (68%) / 2.71 (90%) / 3.84 (95%) / 6.63 (99%) / etc
note: this is FAST++ version '1.5.0-dfac27f'
note: averaging SFRs over 10 Myr
note: applying Madau+1995 IGM absorption
note: convolving templates with sigma=266 km/s
note: computing SFH quantities: {tform50, tsf, past_sfr, tquench10, sfr10, brate10}
note: reading fluxes from 'psb.cat'
note: using column translation file 'psb.translate'
note: ... translated 16 column names
note: reading filters from 'FILTER.RES.latest'
note: found 416 filters in the database, will use 8 of them
note: ... plus 10 for rest-frame magnitudes
note: reading fluxes...
note: fitting 1 source with 8 fluxes
note: apply template library error function to photometry '/Users/fvalenti/bin/fastpp/share/TEMPLATE_ERROR.fast.v0.2'
note: define grid...
note: fitting a grid of 55440 templates (ntau=36,nmetal=1,nage=28,nav=11,navbc=1,nz=5)
note: cache file is 'delayed/bc03_ch/bc03_hr_ch_del_kc_dfe63a61ac9a9db8b24a76a4028755bab26660f4.grid'
note: initializing template error function...
note: identify zspecs and redshift bounds in the grid...
note: start fitting...
[--------------------------------] 55441 100%, 7s elapsed, 0ns left, 7s total
note: finding best fits...
note: saving catalog
note: saving best fits
Segmentation fault: 11
The INTRINSIC_BEST_FIT
option is expected to output a text file with wavelength, best-fit SED, and intrinsic best-fit SED. However, fl
and fl_nodust
are both the same and it looks like it is the intrinsic SED that is getting attributed to both the columns here.
Hello, I am doing a combined fit of photometry and spectrum for a galaxy. I set AUTO_SCALE
to 1 and SAVE_CHI_GRID
to 1 but I don't seem to find the scaling factor in FITS file after converting the grid to .FITS.
This was the output I got after using the convert script provided:
found 1 galaxies, with 42 properties, 6 grid parameters and 674016 models
grid names: z, Av, Av_bc, lage, metal, ltau
prop names: lscale, sscale, lmass, lsfr, lssfr, lldust, lldust_bc, llion, lmform, la2t, CN_1, CN_2, Ca4227, G4300, Fe4383, Ca4455, Fe4531, Fe4668, Hbeta, Fe5015, Mg_1, Mg_2, Mg_b, Fe5270, Fe5335, Fe5406, Fe5709, Fe5782, Na_D, TiO_1, TiO_2, Hdelta_A, Hgamma_A, Hdelta_F, Hgamma_F, Halpha, tsf, past_sfr, sfr10, sfr50, brate10, brate50
[--------------------------------] 28982688 100%, 104ms elapsed, 0ns left, 104ms total
Can you please tell me where the scaling factor is located at? Or is it something we will need to extrapolate somehow?
When i specify a filter in REST_MAG
it still does not give the rest-frame magnitude as an output.
When I run FAST++, I get the following error:
error: could not read data in library file '~/Software/fastpp/share/libraries/ised_exp.pr/bc03_pr_ch_z02_ltau7.0.ised'
error: could not open file
error: the file is probably corrupted, try re-downloading it
The libraries available from Mariska Kriek's website are ised_del.lr, ised_del.hr, ised_tru.hr, and ised_exp.hr, but there is no ised_exp.pr as far as I can tell.
There are several galaxies in fastpp which fail to give a reasonably good SED fit to the data. A couple of examples shown below:
Fitting them using similar parameters in FAST (IDL):
Any idea what would cause these discrepancies?
input/output files can be found here: https://www.dropbox.com/sh/otrjvvtfs9k87b4/AABF4qR6cqhFj2y_rq9wJ0UBa?dl=0
Hello,
I am trying to install fast++ on my mac, which has an updated XCode, C++ compiler, git, and CMake. However, while I run the "make install" command, I get an error saying :
".../fastpp/external/cfitsio/group.c:5476:3: error: implicit declaration of function 'getcwd' is invalid in C99 [-Werror,-Wimplicit-function-declaration]"
I wonder whether this error is related to any incompatibility between the recent Mac version (macOS 11.4) and the current fast++ code or there is an issue with my installations.
Any help on this is really appreciated!
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