def plotAbundanceProfiles(self,star_grid=[],models=[],force_plot=0,cfg='',\
fn_plt='',molecules=[],per_molecule=0,frac=1):
'''
Plot abundance profiles for all molecules in every model.
@keyword star_grid: List of Star() instances. If default, model ids
have to be given.
(default: [])
@type star_grid: list[Star()]
@keyword models: The model ids, only required if star_grid is []
(default: [])
@type models: list[string]
@keyword force_plot: force a plotting if more than models are requested
(default: 0)
@type force_plot: bool
@keyword cfg: path to the Plotting2.plotCols config file. If default,
the hard-coded default plotting options are used.
(default: '')
@type cfg: string
@keyword fn_plt: A base plot filename. Includes folder. If not, a
default is added
(default: '')
@type fn_plt: string
@keyword molecules: Molecules to be plotted.
(default: [])
@type molecules: bool
@keyword per_molecule: Plot one molecule for all models in one figure.
(default: 0)
@type per_molecule: bool
@keyword per_model: Plot all molecules for one model in one figure.
(default: 0)
@type per_model: bool
@keyword frac: Plot the fractional abundances. If not frac, plot number
densities.
(default: 1)
@type frac: bool
'''
print '***********************************'
print '** Plotting Abundance Profiles'
if not star_grid and models:
star_grid = self.makeStars(models=models)
elif (not models and not star_grid) or (models and star_grid):
print '** Input is undefined or doubly defined. Aborting.'
return
pfns = []
cfg_dict = Plotting2.readCfg(cfg)
if cfg_dict.has_key('filename'):
fn_plt = cfg_dict.pop('filename')
if cfg_dict.has_key('molecules'):
molecules = cfg_dict.pop('molecules')
if cfg_dict.has_key('per_molecule'):
per_molecule = cfg_dict['per_molecule']
if cfg_dict.has_key('per_model'):
per_model = cfg_dict['per_model']
#-- Some general plot settings
extra_pars = dict()
extra_pars['ymin'] = 1e-9
extra_pars['ymax'] = 1e-3
extra_pars['ylogscale'] = 1
extra_pars['xlogscale'] = 1
extra_pars['figsize'] = (12.5, 8.5)
extra_pars['xaxis'] = 'cm'
#-- Dict to keep track of all data
ddata = dict()
for istar, star in enumerate(star_grid):
if not star['LAST_CHEMISTRY_MODEL']: continue
ddata[istar] = dict()
folder = os.path.join(cc.path.cout,'models',\
star['LAST_CHEMISTRY_MODEL'])+'/'
ddata[istar]['rad'] = DataIO.getChemistryPhysPar(folder+\
'csphyspar.out', 'RADIUS')
ddata[istar]['id'] = star['LAST_CHEMISTRY_MODEL']
if frac:
species = DataIO.getChemistryAbundances(folder + 'csfrac.out')
else:
species = DataIO.getChemistryAbundances(folder + 'csnum.out')
for molec in molecules:
ddata[istar][molec] = species[molec]
if not per_molecule:
#-- Collect all data
radii = [ddata[istar]['rad']] * len(molecules)
abuns = [ddata[istar][molec] for molec in molecules]
keytags = molecules
#ids = star['LAST_CHEMISTRY_MODEL']
ids = ddata[istar]['id']
#-- Set the yaxis tag
yaxis = '$n_\mathrm{molec}/n_{\mathrm{H}_2}$'
#-- Set filename
pfn = fn_plt if fn_plt else 'abundance_profiles'
suff = '_'.join(list(set(ids)))
pfn = self.setFnPlt(pfn, fn_suffix=suff)
pfns.append(Plotting2.plotCols(x=radii,y=abuns,cfg=cfg_dict,\
filename=pfn,keytags=keytags,\
plot_title=ids.replace('_','\_'),\
yaxis=yaxis,**extra_pars))
if per_molecule:
#-- Collect all data
#molecs = list(set([molec for istar in ddata.keys()
#for molec in ddata[istar].keys()]))
for molec in molecules:
#-- Collect data
radii = [dstar['rad'] for istar, dstar in ddata.items()]
abuns = [dstar[molec] for istar, dstar in ddata.items()]
keytags = [
dstar['id'].replace('_', '\_')
for istar, dstar in ddata.items()
]
#-- Set the y axis tag
#strmolec = ddata[0][molec]['key']
yaxis = '$n_\mathrm{%s}/n_{\mathrm{H}_2}$' % str(molec)
#-- Make filename
pfn = fn_plt if fn_plt else 'abundance_profiles'
pfn = self.setFnPlt(pfn, fn_suffix=molec)
pfns.append(Plotting2.plotCols(x=radii,y=abuns,yaxis=yaxis,\
filename=pfn,keytags=keytags,\
cfg=cfg_dict,**extra_pars))
if not per_molecule and pfns and pfns[0][-4:] == '.pdf':
pfn = fn_plt if fn_plt else 'abundance_profiles'
pfn = self.setFnPlt(pfn) + '.pdf'
DataIO.joinPdf(old=pfns, new=pfn)
print '** Plots can be found at:'
print pfn
print '***********************************'
else:
print '** Plots can be found at:'
print '\n'.join(pfns)
print '***********************************'
