def main(comm): """ This is a hacked version of MC3's func.py. This function directly call's the modeling function for the BART project. Modification History: --------------------- 2014-04-19 patricio Initial implementation. [email protected] 2014-06-25 patricio Added support for inner-MPI loop. """ # Parse arguments: cparser = argparse.ArgumentParser(description=__doc__, add_help=False, formatter_class=argparse.RawDescriptionHelpFormatter) # Add config file option: cparser.add_argument("-c", "--config_file", help="Configuration file", metavar="FILE") # Remaining_argv contains all other command-line-arguments: args, remaining_argv = cparser.parse_known_args() # Get parameters from configuration file: cfile = args.config_file if cfile: config = ConfigParser.SafeConfigParser() config.optionxform = str config.read([cfile]) defaults = dict(config.items("MCMC")) else: defaults = {} parser = argparse.ArgumentParser(parents=[cparser]) parser.add_argument("--func", dest="func", type=mu.parray, action="store", default=None) parser.add_argument("--indparams", dest="indparams", type=mu.parray, action="store", default=[]) parser.add_argument("--params", dest="params", type=mu.parray, action="store", default=None, help="Model-fitting parameters [default: %(default)s]") parser.add_argument("--molfit", dest="molfit", type=mu.parray, action="store", default=None, help="Molecules fit [default: %(default)s]") parser.add_argument("--Tmin", dest="Tmin", type=float, action="store", default=400.0, help="Lower Temperature boundary [default: %(default)s]") parser.add_argument("--Tmax", dest="Tmax", type=float, action="store", default=3000.0, help="Higher Temperature boundary [default: %(default)s]") parser.add_argument("--quiet", action="store_true", help="Set verbosity level to minimum", dest="quiet") # Input-Converter Options: group = parser.add_argument_group("Input Converter Options") group.add_argument("--atmospheric_file", action="store", help="Atmospheric file [default: %(default)s]", dest="atmfile", type=str, default=None) group.add_argument("--PTtype", action="store", help="PT profile type.", dest="PTtype", type=str, default="none") #choices=('line', 'madhu')) group.add_argument("--tint", action="store", help="Internal temperature of the planet [default: " "%(default)s].", dest="tint", type=float, default=100.0) # transit Options: group = parser.add_argument_group("transit Options") group.add_argument("--config", action="store", help="transit configuration file [default: %(default)s]", dest="config", type=str, default=None) # Output-Converter Options: group = parser.add_argument_group("Output Converter Options") group.add_argument("--filter", action="store", help="Waveband filter name [default: %(default)s]", dest="filter", type=mu.parray, default=None) group.add_argument("--tep_name", action="store", help="A TEP file [default: %(default)s]", dest="tep_name", type=str, default=None) group.add_argument("--kurucz_file", action="store", help="Stellar Kurucz file [default: %(default)s]", dest="kurucz", type=str, default=None) group.add_argument("--solution", action="store", help="Solution geometry [default: %(default)s]", dest="solution", type=str, default="None", choices=('transit', 'eclipse')) parser.set_defaults(**defaults) args2, unknown = parser.parse_known_args(remaining_argv) # Quiet all threads except rank 0: rank = comm.Get_rank() verb = rank == 0 # Get (Broadcast) the number of parameters and iterations from MPI: array1 = np.zeros(2, np.int) mu.comm_bcast(comm, array1) npars, niter = array1 # ::::::: Initialize the Input converter :::::::::::::::::::::::::: atmfile = args2.atmfile molfit = args2.molfit PTtype = args2.PTtype params = args2.params tepfile = args2.tep_name tint = args2.tint Tmin = args2.Tmin Tmax = args2.Tmax solution = args2.solution # Solution type # Extract necessary values from the TEP file: tep = rd.File(tepfile) # Stellar temperature in K: tstar = float(tep.getvalue('Ts')[0]) # Stellar radius (in meters): rstar = float(tep.getvalue('Rs')[0]) * c.Rsun # Semi-major axis (in meters): sma = float(tep.getvalue( 'a')[0]) * sc.au # Planetary radius (in meters): rplanet = float(tep.getvalue('Rp')[0]) * c.Rjup # Planetary mass (in kg): mplanet = float(tep.getvalue('Mp')[0]) * c.Mjup # Number of fitting parameters: nfree = len(params) # Total number of free parameters nmolfit = len(molfit) # Number of molecular free parameters nradfit = int(solution == 'transit') # 1 for transit, 0 for eclipse nPT = nfree - nmolfit - nradfit # Number of PT free parameters # Read atmospheric file to get data arrays: species, pressure, temp, abundances = mat.readatm(atmfile) # Reverse pressure order (for PT to work): pressure = pressure[::-1] nlayers = len(pressure) # Number of atmospheric layers nspecies = len(species) # Number of species in the atmosphere mu.msg(verb, "There are {:d} layers and {:d} species.".format(nlayers, nspecies)) # Find index for Hydrogen and Helium: species = np.asarray(species) iH2 = np.where(species=="H2")[0] iHe = np.where(species=="He")[0] # Get H2/He abundance ratio: ratio = (abundances[:,iH2] / abundances[:,iHe]).squeeze() # Find indices for the metals: imetals = np.where((species != "He") & (species != "H2"))[0] # Index of molecular abundances being modified: imol = np.zeros(nmolfit, dtype='i') for i in np.arange(nmolfit): imol[i] = np.where(np.asarray(species) == molfit[i])[0] # Pressure-Temperature profile: PTargs = [PTtype] if PTtype == "line": # Planetary surface gravity (in cm s-2): gplanet = 100.0 * sc.G * mplanet / rplanet**2 # Additional PT arguments: PTargs += [rstar, tstar, tint, sma, gplanet] # Allocate arrays for receiving and sending data to master: freepars = np.zeros(nfree, dtype='d') profiles = np.zeros((nspecies+1, nlayers), dtype='d') # This are sub-sections of profiles, containing just the temperature and # the abundance profiles, respectively: tprofile = profiles[0, :] aprofiles = profiles[1:,:] # Store abundance profiles: for i in np.arange(nspecies): aprofiles[i] = abundances[:, i] # ::::::: Spawn transit code ::::::::::::::::::::::::::::::::::::: # # transit configuration file: transitcfile = args2.tconfig # FINDME: Find a way to set verb to the transit subprocesses. # Silence all threads except rank 0: # if verb == 0: # rargs = ["--quiet"] # else: # rargs = [] # Initialize the transit python module: transit_args = ["transit", "-c", transitcfile] trm.transit_init(len(transit_args), transit_args) # Get wavenumber array from transit: nwave = trm.get_no_samples() specwn = trm.get_waveno_arr(nwave) # ::::::: Output Converter ::::::::::::::::::::::::::::::::::::::: ffile = args2.filter # Filter files kurucz = args2.kurucz # Kurucz file # Log10(stellar gravity) gstar = float(tep.getvalue('loggstar')[0]) # Planet-to-star radius ratio: rprs = rplanet / rstar mu.msg(verb, "OCON FLAG 10: {}, {}, {}".format(tstar, gstar, rprs)) nfilters = len(ffile) # Number of filters: # FINDME: Separate filter/stellar interpolation? # Get stellar model: starfl, starwn, tmodel, gmodel = w.readkurucz(kurucz, tstar, gstar) # Read and resample the filters: nifilter = [] # Normalized interpolated filter istarfl = [] # interpolated stellar flux wnindices = [] # wavenumber indices used in interpolation for i in np.arange(nfilters): # Read filter: filtwaven, filttransm = w.readfilter(ffile[i]) # Check that filter boundaries lie within the spectrum wn range: if filtwaven[0] < specwn[0] or filtwaven[-1] > specwn[-1]: mu.exit(message="Wavenumber array ({:.2f} - {:.2f} cm-1) does not " "cover the filter[{:d}] wavenumber range ({:.2f} - {:.2f} " "cm-1).".format(specwn[0], specwn[-1], i, filtwaven[0], filtwaven[-1])) # Resample filter and stellar spectrum: nifilt, strfl, wnind = w.resample(specwn, filtwaven, filttransm, starwn, starfl) mu.msg(verb, "OCON FLAG 67: mean star flux: %.3e"%np.mean(strfl)) nifilter.append(nifilt) istarfl.append(strfl) wnindices.append(wnind) # Allocate arrays for receiving and sending data to master: spectrum = np.zeros(nwave, dtype='d') bandflux = np.zeros(nfilters, dtype='d') # Allocate array to receive parameters from MPI: params = np.zeros(npars, np.double) # :::::: Main MCMC Loop :::::::::::::::::::::::::::::::::::::::::: # :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: while niter >= 0: niter -= 1 # Receive parameters from MCMC: mu.comm_scatter(comm, params) #mu.msg(verb, "ICON FLAG 71: incon pars: {:s}". # format(str(params).replace("\n", ""))) # Input converter calculate the profiles: try: tprofile[:] = pt.PT_generator(pressure, params[0:nPT], PTargs)[::-1] except ValueError: mu.msg(verb, 'Input parameters give non-physical profile.') # FINDME: what to do here? # If the temperature goes out of bounds: if np.any(tprofile < Tmin) or np.any(tprofile > Tmax): print("Out of bounds") mu.comm_gather(comm, -np.ones(nfilters), MPI.DOUBLE) continue #mu.msg(verb, "T pars: \n{}\n".format(PTargs)) mu.msg(verb-20, "Temperature profile: {}".format(tprofile)) # Scale abundance profiles: for i in np.arange(nmolfit): m = imol[i] # Use variable as the log10: aprofiles[m] = abundances[:, m] * 10.0**params[nPT+nradfit+i] # Update H2, He abundances so sum(abundances) = 1.0 in each layer: q = 1.0 - np.sum(aprofiles[imetals], axis=0) aprofiles[iH2] = ratio * q / (1.0 + ratio) aprofiles[iHe] = q / (1.0 + ratio) # print("qH2O: {}, Qmetals: {}, QH2: {} p: {}".format(params[nPT], # q[50], profiles[iH2+1,50], profiles[:,50])) # Set the 'surface' level: if solution == "transit": trm.set_radius(params[nPT]) if rank == 1: print("Iteration: {:05}".format(niter)) # Let transit calculate the model spectrum: spectrum = trm.run_transit(profiles.flatten(), nwave) # Output converter band-integrate the spectrum: # Calculate the band-integrated intensity per filter: for i in np.arange(nfilters): if solution == "eclipse": fluxrat = (spectrum[wnindices[i]]/istarfl[i]) * rprs*rprs bandflux[i] = w.bandintegrate(fluxrat, specwn, nifilter[i], wnindices[i]) elif solution == "transit": bandflux[i] = w.bandintegrate(spectrum[wnindices[i]], specwn, nifilter[i], wnindices[i]) # Send resutls back to MCMC: #mu.msg(verb, "OCON FLAG 95: Flux band integrated ({})".format(bandflux)) #mu.msg(verb, "{}".format(params[nPT:])) mu.comm_gather(comm, bandflux, MPI.DOUBLE) #mu.msg(verb, "OCON FLAG 97: Sent results back to MCMC") # :::::: End main Loop ::::::::::::::::::::::::::::::::::::::::::: # :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: # Close communications and disconnect: mu.comm_disconnect(comm) mu.msg(verb, "FUNC FLAG 99: func out") # Close the transit communicators: trm.free_memory() mu.msg(verb, "FUNC FLAG OUT ~~ 100 ~~")
def main(comm):
"""
This is a hacked version of MC3's func.py.
This function directly call's the modeling function for the BART project.
"""
# Parse arguments:
cparser = argparse.ArgumentParser(
description=__doc__,
add_help=False,
formatter_class=argparse.RawDescriptionHelpFormatter)
# Add config file option:
cparser.add_argument("-c",
"--config_file",
help="Configuration file",
metavar="FILE")
# Remaining_argv contains all other command-line-arguments:
args, remaining_argv = cparser.parse_known_args()
# Get parameters from configuration file:
cfile = args.config_file
if cfile:
config = ConfigParser.SafeConfigParser()
config.optionxform = str
config.read([cfile])
defaults = dict(config.items("MCMC"))
else:
defaults = {}
parser = argparse.ArgumentParser(parents=[cparser])
parser.add_argument("--func",
dest="func",
type=mu.parray,
action="store",
default=None)
parser.add_argument("--indparams",
dest="indparams",
type=mu.parray,
action="store",
default=[])
parser.add_argument("--params",
dest="params",
type=mu.parray,
action="store",
default=None,
help="Model-fitting parameters [default: %(default)s]")
parser.add_argument("--molfit",
dest="molfit",
type=mu.parray,
action="store",
default=None,
help="Molecules fit [default: %(default)s]")
parser.add_argument(
"--Tmin",
dest="Tmin",
type=float,
action="store",
default=400.0,
help="Lower Temperature boundary [default: %(default)s]")
parser.add_argument(
"--Tmax",
dest="Tmax",
type=float,
action="store",
default=3000.0,
help="Higher Temperature boundary [default: %(default)s]")
parser.add_argument("--quiet",
action="store_true",
help="Set verbosity level to minimum",
dest="quiet")
# Input-Converter Options:
group = parser.add_argument_group("Input Converter Options")
group.add_argument("--atmospheric_file",
action="store",
help="Atmospheric file [default: %(default)s]",
dest="atmfile",
type=str,
default=None)
group.add_argument("--PTtype",
action="store",
help="PT profile type.",
dest="PTtype",
type=str,
default="none")
group.add_argument("--tint",
action="store",
help="Internal temperature of the planet [default: "
"%(default)s].",
dest="tint",
type=float,
default=100.0)
# transit Options:
group = parser.add_argument_group("transit Options")
group.add_argument(
"--config",
action="store",
help="transit configuration file [default: %(default)s]",
dest="config",
type=str,
default=None)
# Output-Converter Options:
group = parser.add_argument_group("Output Converter Options")
group.add_argument("--filters",
action="store",
help="Waveband filter name [default: %(default)s]",
dest="filters",
type=mu.parray,
default=None)
group.add_argument("--tep_name",
action="store",
help="A TEP file [default: %(default)s]",
dest="tep_name",
type=str,
default=None)
group.add_argument("--kurucz_file",
action="store",
help="Stellar Kurucz file [default: %(default)s]",
dest="kurucz",
type=str,
default=None)
group.add_argument("--solution",
action="store",
help="Solution geometry [default: %(default)s]",
dest="solution",
type=str,
default="None",
choices=('transit', 'eclipse'))
parser.set_defaults(**defaults)
args2, unknown = parser.parse_known_args(remaining_argv)
# Quiet all threads except rank 0:
rank = comm.Get_rank()
verb = rank == 0
# Get (Broadcast) the number of parameters and iterations from MPI:
array1 = np.zeros(2, np.int)
mu.comm_bcast(comm, array1)
npars, niter = array1
# ::::::: Initialize the Input converter ::::::::::::::::::::::::::
atmfile = args2.atmfile
molfit = args2.molfit
PTtype = args2.PTtype
params = args2.params
tepfile = args2.tep_name
tint = args2.tint
Tmin = args2.Tmin
Tmax = args2.Tmax
solution = args2.solution # Solution type
# Dictionary of functions to calculate temperature for PTtype
PTfunc = {
'iso': pt.PT_iso,
'line': pt.PT_line,
'madhu_noinv': pt.PT_NoInversion,
'madhu_inv': pt.PT_Inversion
}
# Extract necessary values from the TEP file:
tep = rd.File(tepfile)
# Stellar temperature in K:
tstar = float(tep.getvalue('Ts')[0])
# Stellar radius (in meters):
rstar = float(tep.getvalue('Rs')[0]) * c.Rsun
# Semi-major axis (in meters):
sma = float(tep.getvalue('a')[0]) * sc.au
# Planetary radius (in meters):
rplanet = float(tep.getvalue('Rp')[0]) * c.Rjup
# Planetary mass (in kg):
mplanet = float(tep.getvalue('Mp')[0]) * c.Mjup
# Number of fitting parameters:
nfree = len(params) # Total number of free parameters
nmolfit = len(molfit) # Number of molecular free parameters
nradfit = int(solution == 'transit') # 1 for transit, 0 for eclipse
nPT = nfree - nmolfit - nradfit # Number of PT free parameters
# Read atmospheric file to get data arrays:
species, pressure, temp, abundances = mat.readatm(atmfile)
# Reverse pressure order (for PT to work):
pressure = pressure[::-1]
nlayers = len(pressure) # Number of atmospheric layers
nspecies = len(species) # Number of species in the atmosphere
mu.msg(verb,
"There are {:d} layers and {:d} species.".format(nlayers, nspecies))
# Find index for Hydrogen and Helium:
species = np.asarray(species)
iH2 = np.where(species == "H2")[0]
iHe = np.where(species == "He")[0]
# Get H2/He abundance ratio:
ratio = (abundances[:, iH2] / abundances[:, iHe]).squeeze()
# Find indices for the metals:
imetals = np.where((species != "He") & (species != "H2") & \
(species != "H-") & (species != 'e-'))[0]
# Index of molecular abundances being modified:
imol = np.zeros(nmolfit, dtype='i')
for i in np.arange(nmolfit):
imol[i] = np.where(np.asarray(species) == molfit[i])[0]
# Pressure-Temperature profile:
if PTtype == "line":
# Planetary surface gravity (in cm s-2):
gplanet = 100.0 * sc.G * mplanet / rplanet**2
# Additional PT arguments:
PTargs = [rstar, tstar, tint, sma, gplanet]
else:
PTargs = None
# Allocate arrays for receiving and sending data to master:
freepars = np.zeros(nfree, dtype='d')
profiles = np.zeros((nspecies + 1, nlayers), dtype='d')
# This are sub-sections of profiles, containing just the temperature and
# the abundance profiles, respectively:
tprofile = profiles[0, :]
aprofiles = profiles[1:, :]
# Store abundance profiles:
for i in np.arange(nspecies):
aprofiles[i] = abundances[:, i]
# ::::::: Spawn transit code :::::::::::::::::::::::::::::::::::::
# # transit configuration file:
transitcfile = args2.tconfig
# Initialize the transit python module:
transit_args = ["transit", "-c", transitcfile]
trm.transit_init(len(transit_args), transit_args)
# Get wavenumber array from transit:
nwave = trm.get_no_samples()
specwn = trm.get_waveno_arr(nwave)
# ::::::: Output Converter :::::::::::::::::::::::::::::::::::::::
ffile = args2.filters # Filter files
kurucz = args2.kurucz # Kurucz file
# Log10(stellar gravity)
gstar = float(tep.getvalue('loggstar')[0])
# Planet-to-star radius ratio:
rprs = rplanet / rstar
nfilters = len(ffile) # Number of filters:
# FINDME: Separate filter/stellar interpolation?
# Get stellar model:
starfl, starwn, tmodel, gmodel = w.readkurucz(kurucz, tstar, gstar)
# Read and resample the filters:
nifilter = [] # Normalized interpolated filter
istarfl = [] # interpolated stellar flux
wnindices = [] # wavenumber indices used in interpolation
for i in np.arange(nfilters):
# Read filter:
filtwaven, filttransm = w.readfilter(ffile[i])
# Check that filter boundaries lie within the spectrum wn range:
if filtwaven[0] < specwn[0] or filtwaven[-1] > specwn[-1]:
mu.exit(message="Wavenumber array ({:.2f} - {:.2f} cm-1) does not "
"cover the filter[{:d}] wavenumber range ({:.2f} - {:.2f} "
"cm-1).".format(specwn[0], specwn[-1], i, filtwaven[0],
filtwaven[-1]))
# Resample filter and stellar spectrum:
nifilt, strfl, wnind = w.resample(specwn, filtwaven, filttransm,
starwn, starfl)
nifilter.append(nifilt)
istarfl.append(strfl)
wnindices.append(wnind)
# Allocate arrays for receiving and sending data to master:
spectrum = np.zeros(nwave, dtype='d')
bandflux = np.zeros(nfilters, dtype='d')
# Allocate array to receive parameters from MPI:
params = np.zeros(npars, np.double)
# :::::: Main MCMC Loop ::::::::::::::::::::::::::::::::::::::::::
# ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
while niter >= 0:
niter -= 1
# Receive parameters from MCMC:
mu.comm_scatter(comm, params)
# Check for the MCMC-end flag:
if params[0] == np.inf:
break
# Input converter calculate the profiles:
try:
tprofile[:] = pt.PT_generator(pressure, params[0:nPT],
PTfunc[PTtype], PTargs)[::-1]
except ValueError:
mu.msg(verb, 'Input parameters give non-physical profile.')
# FINDME: what to do here?
# If the temperature goes out of bounds:
if np.any(tprofile < Tmin) or np.any(tprofile > Tmax):
mu.comm_gather(comm, -np.ones(nfilters), MPI.DOUBLE)
continue
# Scale abundance profiles:
for i in np.arange(nmolfit):
m = imol[i]
# Use variable as the log10:
aprofiles[m] = abundances[:, m] * 10.0**params[nPT + nradfit + i]
# Update H2, He abundances so sum(abundances) = 1.0 in each layer:
q = 1.0 - np.sum(aprofiles[imetals], axis=0)
if np.any(q < 0.0):
mu.comm_gather(comm, -np.ones(nfilters), MPI.DOUBLE)
continue
aprofiles[iH2] = ratio * q / (1.0 + ratio)
aprofiles[iHe] = q / (1.0 + ratio)
# Set the 'surface' level:
if solution == "transit":
trm.set_radius(params[nPT])
# Let transit calculate the model spectrum:
spectrum = trm.run_transit(profiles.flatten(), nwave)
# Calculate the band-integrated intensity per filter:
for i in np.arange(nfilters):
if solution == "eclipse":
fluxrat = (spectrum[wnindices[i]] / istarfl[i]) * rprs * rprs
bandflux[i] = w.bandintegrate(fluxrat, specwn, nifilter[i],
wnindices[i])
elif solution == "transit":
bandflux[i] = w.bandintegrate(spectrum[wnindices[i]], specwn,
nifilter[i], wnindices[i])
# Send resutls back to MCMC:
mu.comm_gather(comm, bandflux, MPI.DOUBLE)
# :::::: End main Loop :::::::::::::::::::::::::::::::::::::::::::
# ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
# Close communications and disconnect:
mu.comm_disconnect(comm)
trm.free_memory()