def cloudy(self):
'''
Computes a Cloudy Model for the parameters specified in
'''
pc.log_.message('Running {0}'.format(self.model_name), calling='test1')
pc.config.cloudy_exe = '~/cloudy/source/sys_gcc/cloudy.exe'
pc.log_.timer('Starting Cloudy', quiet=True, calling='test1')
self.c_input.run_cloudy()
self.Mod = pc.CloudyModel(self.full_model_name)
pc.log_.timer('Cloudy ended after seconds:', calling='test1')
def plot_model(name, models_dir='./', style='-', fig_num=1):
pc.log_.level = 3
M = pc.CloudyModel('{0}/{1}'.format(models_dir, name), read_emis=False)
X = M.radius / 1e19
colors = ['r', 'g', 'b', 'y', 'm', 'c']
plt.figure(fig_num)
plt.subplot(3, 3, 1)
plt.plot(X, M.get_ionic('H', 0), label='H0', linestyle=style, c=colors[0])
plt.plot(X, M.get_ionic('H', 1), label='H+', linestyle=style, c=colors[1])
plt.plot(X,
M.get_ionic('He', 0),
label='He0',
linestyle=style,
c=colors[2])
plt.plot(X,
M.get_ionic('He', 1),
label='He+',
linestyle=style,
c=colors[3])
plt.plot(X,
M.get_ionic('He', 2),
label='He++',
linestyle=style,
c=colors[4])
if style == '-':
plt.legend()
plt.title(name)
for i_plot, elem in enumerate(['N', 'O', 'Ne', 'S', 'Ar']):
plt.subplot(3, 3, i_plot + 2)
for i in np.arange(4):
plt.plot(X, M.get_ionic(elem, i), linestyle=style, c=colors[i])
plt.text(np.max(X) / 2, 0.9, elem)
if i_plot == 0:
plt.title(M.date_model)
plt.subplot(3, 3, 7)
plt.plot(X, M.ne, label=r'N$_e$', linestyle=style, c='blue')
plt.plot(X, M.nH, label='N$_H$', linestyle=style, c='red')
if style == '-':
plt.legend(loc=3)
plt.xlabel(r'R [10$^{19}$cm]')
plt.subplot(3, 3, 8)
plt.plot(X, M.te, label=r'T$_e$', linestyle=style, c='blue')
if style == '-':
plt.legend(loc=3)
plt.subplot(3, 3, 9)
plt.plot(X, M.log_U, label='log U', c='blue')
if style == '-':
plt.legend()
def read_model(self,
doplot=False,
HeI_cut=None,
verbose=True,
cube_size=None,
r_out_cut=None):
self.Mod = pc.CloudyModel('{0}{1}'.format(self.dir_, self.model_name),
read_grains=True)
if "CA_B_587564A" in self.Mod.emis_labels:
i_line = np.where(self.Mod.emis_labels == 'CA_B_587564A')[0][0]
self.Mod.emis_full[i_line] *= correc_He1(self.Mod.te_full,
self.Mod.ne_full, 5876)
if "CA_B_447149A" in self.Mod.emis_labels:
i_line = np.where(self.Mod.emis_labels == 'CA_B_447149A')[0][0]
self.Mod.emis_full[i_line] *= correc_He1(self.Mod.te_full,
self.Mod.ne_full, 4471)
self.Mod.distance = self.distance
if HeI_cut is not None:
if cube_size is None:
print('Needs a cube_size to compute the HeI cut')
self.Mod = None
return
for radius in self.Mod.radius[::-1]:
self.Mod.r_out_cut = radius
self.make_3D(cube_size, doplot=False, verbose=False)
if verbose:
print('R = {:8.2e} HeI dif = {:.2f}'.format(
radius, self.difs['CA_B_587564A']))
if self.difs['CA_B_587564A'] > HeI_cut:
break
elif r_out_cut is not None:
self.Mod.r_out_cut = r_out_cut
if verbose:
self.Mod.print_stats()
if doplot:
f, ax = plt.subplots(figsize=(10, 7))
ax.plot(self.Mod.radius, self.Mod.te, label='Te')
ax.legend(loc=3)
#Show on the screen
#plt.show()
#print to file
#plt.tight_layout(pad=0.2)
name = self.dir_ + self.model_name + '_Te.png'
f.savefig(name, dpi=200)
def __init__(self, name):
"""
Creating an object to manage the Cloudy output and compare to the observations
"""
self.model = pc.CloudyModel(name)
self.set_3D(use=False)
self.m3d = None
self.mask = None
self.profile_defined = False
self.dim_3D = 101
self.mask_ap_center = (0., 3.5)
self.mask_ap_size = (12., 1)
# define a RedCorr object
self.RC = pn.RedCorr(E_BV=0.26, R_V=3.6, law='Fitz 99')
def _pc_load_models(model_name=None,
mod_list=None,
n_sample=None,
verbose=False,
**kwargs):
"""
Return a list of CloudyModel correspondig to a generic name
Parameters:
- model_name: generic name. The method is looking for any "model_name*.out" file.
- mod_list: in case model_name=None, this is the list of model names (something.out or something)
- n_sample: randomly select n_sample from the model list
- verbose: print out the name of the models read
- **kwargs: arguments passed to CloudyModel
"""
if model_name is not None:
mod_list = glob.glob(model_name + '*.out')
if mod_list is None or mod_list == []:
pc.log_.error('No model found', calling='load models')
return None
if n_sample is not None:
if n_sample > len(mod_list):
pc.log_.error('less models {0:d} than n_sample {1:d}'.format(
len(mod_list), n_sample),
calling='load models')
return None
mod_list = random.sample(mod_list, n_sample)
m = []
for outfile in mod_list:
if outfile[-4::] == '.out':
model_name = outfile[0:-4]
else:
model_name = outfile
try:
cm = pc.CloudyModel(model_name, verbose=0, **kwargs)
if not cm.aborted:
m.append(cm)
if verbose:
print('{0} model read'.format(outfile[0:-4]))
except:
pass
pc.log_.message('{0} models read'.format(len(m)),
calling='load_models')
return m
def get_Q02Lum(SED, logg):
"""
Usage: get_Q02Lum('TL', 4)
"""
if SED not in tabs_T:
print('{0} is not in {1}'.format(SED, tabs_T.keys()))
return None
Q02l = {}
lumi = 3
for Teff in tabs_T[SED]:
In = pc.CloudyInput('./M1')
In.set_cste_density(2)
In.set_radius(19)
if SED[0:2] != 'BB':
In.set_star('table star "{0}"'.format(dic_SEDs[SED]),
(Teff, logg, 0), 'luminosity total solar', lumi)
else:
In.set_BB(Teff, 'luminosity total solar', lumi)
In.set_stop('zone 2')
In.print_input()
In.run_cloudy()
Out = pc.CloudyModel('./M1', read_emis=False)
print('{0} : {1:.2f},'.format(Teff, np.log10(Out.Q0) - lumi))
Q02l[Teff] = np.log10(Out.Q0) - lumi
Question 6.1.1
"""
models_dir = 'CloudyModels' #Create this directory if necessary
pc.config.cloudy_exe = '/usr/local/Cloudy/c10.00/cloudy.exe' # point to the location of Cloudy.exe
# Print the Makefile in th emodels_dir directory (only needed one time)
pc.print_make_file(models_dir)
# Print a file containing the line for intensities
ex6_1.print_line_file(models_dir)
# prepare models with different Q(H)
for qH in [43, 44, 45, 46, 47, 48]:
ex6_1.make_mod(models_dir, name='M_61.1_{0}'.format(qH), Teff=5e4, qH=qH, dens=3, r_in=17)
# run all the models in models_dirs starting with M_61.1
pc.run_cloudy(dir_=models_dir, n_proc=3, use_make=True, model_name='M_61.1')
M43 = pc.CloudyModel('{0}/M_61.1_43'.format(models_dir), read_lin = True)
# load all the models in the models list
models = pc.load_models('{0}/M_61.1_'.format(models_dir), read_lin = True)
# make some plots
ex6_1.plot_Hb(models)
for m in models:
# A posteriori cut of the model
# Line intensities are not changed. Integral of Emissivities are changed.
m.r_out_cut = 1.5e17
# make the same plots
ex6_1.plot_Hb(models)
# prepare models with different Teff
for i, Teff in enumerate(np.array([40, 50, 80, 130, 200]) * 1e3):
# Printing some message to the screen
pc.log_.message('Running {0}'.format(model_name), calling = 'test1')
# In[15]:
# Running Cloudy with a timer. Here we reset it to 0.
pc.log_.timer('Starting Cloudy', quiet = True, calling = 'test1')
c_input.run_cloudy()
pc.log_.timer('Cloudy ended after seconds:', calling = 'test1')
# In[16]:
# Reading the Cloudy outputs in the Mod CloudyModel object
Mod = pc.CloudyModel(full_model_name)
# In[17]:
# Use TAB to know all the methods and variables for CloudyModel class
# Mod.TAB
dir(Mod) # This is the online answering way
# Description of this class is available here: http://pythonhosted.org//pyCloudy/classpy_cloudy_1_1c1d_1_1cloudy__model_1_1_cloudy_model.html
# In[18]:
Mod.print_stats()
def run_test_labels(model_name='model_1'):
test_labels(model_name)
M = pc.CloudyModel('{0}{1}'.format(dir_, model_name), read_cont=True)
M.print_lines(norm='CA_B_486133A')
bigCloud_sim.set_other(('cosmic rays background'))
bigCloud_sim.set_other(('CMB'))
bigCloud_sim.set_iterate(2)
bigCloud_sim.set_other(('save last transmitted continuum file = "{}"'.format(transmitted_ext)))
bigCloud_sim.read_emis_file('lines.dat')
bigCloud_sim.print_input(to_file = True, verbose = False)
#Display input code
bigCloud_sim.print_input(verbose=False)
#Run the model
#bigCloud_sim.run_cloudy(dir_=simu_folder)
#Read the simulation data
bigCloud_output = pc.CloudyModel(simu_folder + name_big, read_emis=True)
#bigCloud_output.print_stats()
#Generate 3D grid
bigCloud_sphere = pc.C3D(bigCloud_output, dims=cube_size, center=True, n_dim=1)
arcsec = lambda cm: conv_arc(dist=dist_big/pc_to_cm/1000, dist_proj=cm)
mask = make_mask_slit(arcsec, bigCloud_sphere, ap_center=[0, 0], ap_size=[50, 1.5]) #ap_size=[50, 1.5]
mask_cirleB = make_mask_circle(arcsec, bigCloud_sphere) #ap_size=[50, 1.5]
mask_big = ~np.logical_not(mask) & np.logical_not(mask_cirleB)
mask_small = ~np.logical_not(mask_cirleB)
#plotting_the_mask(mask_big, arcsec, bigCloud_sphere)
#Calculate abundance
big_lines_dict = extract_fluxes_pure_slits(bigCloud_sphere, mask_big)