def run_chain_parameters():
os.system("rm -rf SPECPAR.log")
logging.basicConfig(filename='SPECPAR.log', format='%(asctime)s : %(message)s', datefmt='%m/%d/%Y %I:%M:%S %p', level=logging.INFO)
logging.info('Started')
path = './'
run_path = 'running_dir/'
save_path = 'save_folder/'
# CREATE folders
# Running ARES
linelist_ew = rp.get_install_dir()+rc.read_config_param('linelists', 'iron_parameters').replace("'", "")
rp.ares_make_mine_opt(run_path, linelist_ew)
logging.info('ARES Started')
rp.run_ares(run_path)
logging.info('ARES Finished')
# Creating moog linelist
filename_lines = rp.get_install_dir()+rc.read_config_param('linelists', 'iron_parameters').replace("'", "")
filename_ares = rc.read_config_param('ares', 'fileout').replace("'", "")
filename_out = 'lines.' + filename_ares
isp.ares_to_lines(run_path+filename_ares, filename_lines, run_path+filename_out, 4000, 9999, 5, 150)
logging.info('Starting AMEBSA for %s', filename_out)
# find_iron_parameters(path,run_path,save_path,filename_out)
find_iron_parameters_tmcalc_prior(path, run_path, save_path, filename_out, filename_ares)
logging.info('Finished')
def run_chain_get_element_abund(moogfile, element):
run_path = 'running_dir/'
save_path = 'save_folder/'
teff, logg, feh, vtur = isp.read_parameters_moogfile(moogfile)
linelist_element = rp.get_install_dir()+rc.read_config_param('linelists', element+'_abund').replace("'", "")
rp.ares_make_mine_opt(run_path, linelist_element)
rp.run_ares(run_path)
filename_ares = rc.read_config_param('ares', 'fileout').replace("'", "")
filename_out = 'lines.' + filename_ares
isp.ares_to_lines(run_path+filename_ares, linelist_element, run_path+filename_out, 4000, 9999, 5, 150)
rp.create_abfind_par(run_path, filename_out)
rp.create_model_kurucz(run_path, teff, logg, feh, vtur)
rp.run_MOOG(run_path, 'abfind.par')
(ele1, ele1_sig, nele1, ele2, ele2_sig, nele2) = rmoog.read_moog_ele_sigma(run_path+'abund_plan_tspec.test', element, 2.)
return (ele1, ele1_sig, nele1, ele2, ele2_sig, nele2)
def find_iron_parameters(path, run_path, save_folder, linesin):
converged = False
owd = os.getcwd()
moog_file = moog_file = 'Out_moog_'+linesin
logging.info('Starting 1st iteration for %s', linesin)
rp.run_amebsa(path, run_path, linesin, 'KURUCZ')
# checking convergency:
if os.path.isfile(run_path+moog_file):
logging.info('First iteration converged for %s', linesin)
else:
logging.warning('First iteration did not converge for %s', linesin)
moog_file = 'Out_moog_b.'+linesin
n_removed_lines = isp.remove_outliers_from_linelist(run_path+linesin,run_path+moog_file,run_path+linesin+'_new',3.)
logging.info('Removed %d outliers lines for %s', n_removed_lines, linesin)
if n_removed_lines > 1:
linesin = linesin+'_new'
moog_file = moog_file = 'Out_moog_'+linesin
logging.info('Starting 2nd iteration for %s', linesin)
rp.run_amebsa(path, run_path, linesin, 'KURUCZ')
if os.path.isfile(run_path+moog_file):
logging.info('Second iteration converged for %s', linesin)
converged = True
else:
logging.error('Final iteration did not converge for %s', linesin)
moog_file = 'Out_moog_b.'+linesin
else:
logging.info('No need for 2nd iteration for %s', filename_lines)
os.system("cp "+run_path+linesin+" "+save_folder)
os.system("cp "+run_path+moog_file+" "+save_folder)
if converged:
logging.info('Computing errors for %s', linesin)
else:
logging.warning('Computing errors for no convergent result of %s', linesin)
# Put a try catch here
moogerr.compute_error(run_path, moog_file, moog_file+'.er', True)
logging.info('Errors computed for %s', linesin)
os.system("cp "+run_path+moog_file+'.er'+" "+save_folder)
os.system("cp "+run_path+moog_file+'.eps'+" "+save_folder)
os.chdir(owd)
os.system("rm -rf "+run_path+"*")
def find_iron_parameters_tmcalc_prior(path, run_path, save_folder,
linesin, filename_ares):
converged = False
owd = os.getcwd()
# Default Starting Values
teff = 5500
logg = 4.0
feh = 0.0
vtur = 1.0
teff, feh = rp.get_tmcalc_teff_feh(run_path+filename_ares)
print teff, feh
if math.isnan(teff):
teff = 5500
if math.isnan(feh):
feh = 0.0
# Ramirez 2013
# vtur = 1.163 + 7.808e-4 * (teff - 5800) - 0.494*(logg - 4.30) - 0.05*feh
# Tsantaki 2013
vtur = 6.932e-4*teff - 0.348*logg - 1.437
logging.info('Using the following parameters as initial: %d %5.2f %5.2f %5.2f', teff, logg, feh, vtur)
moog_file = moog_file = 'Out_moog_'+linesin
logging.info('Starting 1st iteration for %s', linesin)
rp.run_amebsa_prior(path, run_path, linesin, teff, logg, feh, vtur, 'KURUCZ')
# checking convergency:
if os.path.isfile(run_path+moog_file):
logging.info('First iteration converged for %s', linesin)
else:
logging.warning('First iteration did not converge for %s', linesin)
moog_file = 'Out_moog_b.'+linesin
n_removed_lines = isp.remove_outliers_from_linelist(run_path+linesin,run_path+moog_file,run_path+linesin+'_new',3.)
logging.info('Removed %d outliers lines for %s', n_removed_lines, linesin)
if n_removed_lines > 1:
# NEED TO GET THE LAST VALUES FROM MOOG
teff, logg, feh, vtur = isp.read_parameters_moogfile(run_path+moog_file)
linesin = linesin+'_new'
moog_file = moog_file = 'Out_moog_'+linesin
logging.info('Starting 2nd iteration for %s', linesin)
logging.info('Using the following parameters as initial: %d %5.2f %5.2f %5.2f', teff, logg, feh, vtur)
rp.run_amebsa_prior(path, run_path, linesin, teff, logg, feh, vtur, 'KURUCZ')
if os.path.isfile(run_path+moog_file):
logging.info('Second iteration converged for %s', linesin)
converged = True
else:
logging.error('Final iteration did not converge for %s', linesin)
moog_file = 'Out_moog_b.'+linesin
else:
logging.info('No need for 2nd iteration for %s', filename_lines)
os.system("cp "+run_path+linesin+" "+save_folder)
os.system("cp "+run_path+moog_file+" "+save_folder)
if converged:
logging.info('Computing errors for %s', linesin)
else:
logging.warning('Computing errors for no convergent result of %s', linesin)
# Put a try catch here
moogerr.compute_error(run_path, moog_file, moog_file+'.er', True)
logging.info('Errors computed for %s', linesin)
os.system("cp "+run_path+moog_file+'.er'+" "+save_folder)
os.system("cp "+run_path+moog_file+'.eps'+" "+save_folder)
os.chdir(owd)
