def getUNK(file, srcnames=True):
"""returns fields and species found in a hdf5 file.
(species is any unk with a number, plus (n, d, t))
Args:
file(str): path to file.
srcnames(bool): return original names (else d > H2)
Returns:
(str list): field names.
(str list): nuclide codes.
"""
finn = h5py.File(file, "r")
infval = finn['unknown names']
unks = [decode(v[0]) for v in infval]
fields, species = [], []
exceptions = ['n', 'd', 't', 'd', 't']
parsedvals = ['n1', 'H2', 'H3', 'd2', 't3']
for field in unks:
if any(char.isdigit() for char in field):
species.append(field)
elif field.strip() in exceptions:
species.append(field)
else:
fields.append(field)
species = sortNuclides(species)
# once sorted, rename the exceptions
if srcnames:
for i, e in enumerate(parsedvals):
if e in species:
species[species.index(e)] = exceptions[i]
finn.close()
return fields, species
def getFields(flist, srcnames=True):
"""filters flash checkpoint field list, extracting species found
in the checkpoint (including named exceptions, see source).
Args:
flist(tuple list): ds.derived_field_list from yt.
srcnames(bool): return original names for species (n, d, t).
Returns:
fields (list of str): field names in checkpoint.
species (list of str): nuclide codes as in checkpoint.
"""
fields, species = [], []
exceptions = ['n', 'p', 'd', 't']
parsedvals = ['n1', 'p1', 'd2', 't3']
for (t, field) in flist:
if any(char.isdigit() for char in field):
species.append(field)
elif field.strip() in exceptions:
species.append(field)
else:
fields.append(field)
species = sortNuclides(species)
# once sorted, rename the exceptions
if srcnames:
for i, e in enumerate(parsedvals):
if e in species:
species[species.index(e)] = exceptions[i]
return fields, species
def plotDMatMerged(prof, thresh=1e-4, xrange=[0.0, 0.0], byM=True):
"""plots main properties of a profile in only two axes, merging
thermodynamic properties.
Args:
prof (dataMatrix): dataMatrix obj.
thresh (float): ymin for species fraction plot.
xrange (list of float): if set, change the range of the plots.
byM (bool): abundance plot xaxis (by Mass or by Radius).
"""
fig = plt.figure()
skip = ['radius', 'masses', 'density']
plotp = [x for x in prof.bulkprops if x not in skip]
keys = sortNuclides(prof.species)
ncol = 4
labelspace = -0.1
if byM:
xs = prof.masses
xlab = 'Mass ($M_{\odot}$)'
log = False
else:
xs = prof.radius
xlab = 'Radius ($cm$)'
log = True
layout = (2, 2)
# Species
spax = plt.subplot2grid(layout, (0, 0), colspan=2)
skip = plotSpecies(spax, prof, byMass=byM, thresh=thresh, plotall=False)
# remove last(lowest) yticklabel to avoid overlap
spax.get_yticklabels()[1].set_visible(False)
lgd = spax.legend(ncol=ncol, loc='upper left', bbox_to_anchor=(1.00, 1.02),
columnspacing=0.0, labelspacing=0.0, markerfirst=False,
numpoints=3, handletextpad=0.0, edgecolor='k')
spax.axhline(1e0, linewidth=1, linestyle=':', color='black')
spax.set_ylim(thresh, 2.0)
spax.set_ylabel('Mass Frac.($X_{i}$)', size=13, rotation=90, labelpad=0)
spax.yaxis.set_label_coords(labelspace, 0.5)
spax.yaxis.set_minor_formatter(StrMethodFormatter(''))
spax.tick_params(labelbottom=False)
if log:
spax.set_yscale('log')
spax.set_xscale('log')
# Thermodynamical variables (reference is, as always, density)
tdax = plt.subplot2grid(layout, (1, 0), colspan=2, sharex=spax)
tdax.semilogy(xs, prof.density, label='Density')
ylabels = ['$\\frac{g}{cm^3}$']
tdax.yaxis.set_minor_formatter(StrMethodFormatter(''))
tdax.tick_params(labelbottom=False)
for i, p in enumerate(plotp):
u = ut.getUnit(p)
if p=='pressure':
tdax.plot(xs, getattr(prof, p)/1e16, label=p.capitalize())#, color='k')
ylabels.append(u+'$\\times10^{-16}$')
else:
tdax.plot(xs, getattr(prof, p), label=p.capitalize())#, color='k')
ylabels.append(u)
#spacer = labelspace if '\\' in u else labelspace - 0.02
#tdax.set_ylabel('{}({})'.format(p.capitalize(), u), rotation=90, size=13, labelpad=0)
tdax.yaxis.set_minor_formatter(StrMethodFormatter(''))
tdax.tick_params(labelbottom=False)
tdax.set_xlabel(xlab)
tdax.tick_params(labelbottom=True)
tdax.set_ylabel('({})'.format(','.join(ylabels)), size=13, rotation=90, labelpad=0)
tdax.yaxis.set_label_coords(labelspace, 0.5)
lgd = tdax.legend(ncol=1, loc='upper left', bbox_to_anchor=(1.00, 0.50),
columnspacing=0.0, labelspacing=0.0, markerfirst=False,
numpoints=3, handletextpad=0.0, edgecolor='k')
if sum(xrange)!=0.0:
spax.set_xlim(xrange)
plt.subplots_adjust(hspace=0.001, wspace=0.0)
plt.subplots_adjust(left=0.13, right=0.80)
plt.subplots_adjust(top=0.99, bottom=0.10)
fig.set_size_inches(8.5, 7.5, forward=True)
return fig
def plotDMat(prof, thresh=1e-4, xrange=[0.0, 0.0], byM=True):
"""plots main properties of a profile object.
Args:
prof (dataMatrix): dataMatrix obj.
thresh (float): ymin for species fraction plot.
xrange (list of float): if set, change the range of the plots.
byM (bool): abundance plot xaxis (by Mass or by Radius).
"""
fig = plt.figure()
skip = ['radius', 'masses', 'density']
plotp = [x for x in prof.bulkprops if x not in skip]
keys = sortNuclides(prof.species)
ncol = 4
labelspace = -0.15
if byM:
xs = prof.masses
xlab = 'Mass ($M_{\odot}$)'
log = False
else:
xs = prof.radius
xlab = 'Radius ($cm$)'
log = True
layout = (len(plotp)+2, 3)
# Species
ax1 = plt.subplot2grid(layout, (0, 0), colspan=2)
skip = plotSpecies(ax1, prof, byMass=byM, thresh=thresh, plotall=False)
# remove last(lowest) yticklabel to avoid overlap
ax1.get_yticklabels()[1].set_visible(False)
lgd = ax1.legend(ncol=ncol, loc='upper left', bbox_to_anchor=(1.00, 1.05),
columnspacing=0.0, labelspacing=0.0, markerfirst=False,
numpoints=3, handletextpad=0.0)
ax1.axhline(1e0, linewidth=1, linestyle=':', color='black')
ax1.set_ylim(thresh, 2.0)
ax1.set_ylabel('Mass Frac.($X_{i}$)', size=13, rotation=90, labelpad=0)
ax1.yaxis.set_label_coords(labelspace, 0.5)
ax1.yaxis.set_minor_formatter(StrMethodFormatter(''))
ax1.tick_params(labelbottom=False)
if log:
ax1.set_yscale('log')
ax1.set_xscale('log')
ax2 = plt.subplot2grid(layout, (1, 0), sharex=ax1, colspan=2)
ax2.semilogy(xs, prof.density)
ax2.set_ylabel('Density($\\frac{g}{cm^3}$)', size=13, rotation=90, labelpad=0)
ax2.yaxis.set_label_coords(labelspace, 0.5)
ax2.yaxis.set_minor_formatter(StrMethodFormatter(''))
ax2.tick_params(labelbottom=False)
for i, p in enumerate(plotp):
ax3 = plt.subplot2grid(layout, (i+2, 0), sharex=ax1, colspan=2)
for j in range(i+1):
ax3.plot([], [])
ax3.semilogy(xs, getattr(prof, p))#, color='k')
u = ut.getUnit(p)
spacer = labelspace if '\\' in u else labelspace - 0.02
ax3.set_ylabel('{}({})'.format(p.capitalize(), u), rotation=90, size=13, labelpad=0)
ax3.yaxis.set_minor_formatter(StrMethodFormatter(''))
ax3.yaxis.set_label_coords(spacer, 0.5)
ax3.tick_params(labelbottom=False)
ax3.set_xlabel(xlab)
ax3.tick_params(labelbottom=True)
if sum(xrange)!=0.0:
ax1.set_xlim(xrange)
plt.subplots_adjust(hspace=0.001, wspace=0.0)
plt.subplots_adjust(left=0.13, right=0.80)
plt.subplots_adjust(top=0.99, bottom=0.10)
fig.set_size_inches(8.5, 7.5, forward=True)
return fig