def test_vibrational_levels_labelling(verbose=True, *args, **kwargs):
# If verbose: print some
if verbose:
printm("Some vibrational level formats:")
printm("... CO, HITRAN format (v):\t\t", vib_lvl_name_hitran_class1(10))
printm(
"... CO2, HITRAN format (v1,v2,l2,v3):\t\t",
vib_lvl_name_hitran_class5(2, 1, 1, 3),
)
printm(
"... CO2, HITRAN format, short (v1v2l2v3):\t",
vib_lvl_name_hitran_class5_short(2, 1, 1, 3),
)
printm("... CO2, CDSD format (p,c):\t\t", vib_lvl_name_cdsd_pc(14, 1))
printm("... CO2, CDSD format (p,c,N):\t\t", vib_lvl_name_cdsd_pcN(14, 1, 1))
# Do the tests
assert vib_lvl_name_hitran_class1(10) == "(10)"
assert vib_lvl_name_hitran_class5(2, 1, 1, 3) == "(2,1,1,3)"
assert vib_lvl_name_hitran_class5_short(2, 1, 1, 3) == "21`1`3"
assert vib_lvl_name_cdsd_pc(14, 1) == "(14,1)"
assert vib_lvl_name_cdsd_pcN(14, 1, 1) == "(14,1,1)"
return
def _add_levels(self, df):
viblvl_label = self.viblvl_label
if viblvl_label == "p":
df["viblvl"] = vib_lvl_name_cdsd_p(df.p,)
elif viblvl_label == "pc":
df["viblvl"] = vib_lvl_name_cdsd_pc(df.p, df.c)
elif viblvl_label == "pcN":
df["viblvl"] = vib_lvl_name_cdsd_pcN(df.p, df.c, df.N)
elif viblvl_label == "pcJN":
df["viblvl"] = vib_lvl_name_cdsd_pcJN(df.p, df.c, df.j, df.N)
elif viblvl_label is None:
# dont label the levels. Wont be able to use the EnergyDatabase to fetch
# vibrational energies for lines, however it can still be used to
# calculate Partition functions independently from a Spectrum calculation
pass
else:
raise ValueError("Unexpected viblvl_label value: {0}".format(viblvl_label))
return df
def vib_lvl_name_cdsd(p, c, N):
return vib_lvl_name_cdsd_pc(p, c)
def add_bands(df, dbformat, lvlformat, verbose=True):
''' Assign all transitions to a vibrational band:
Add 'band', 'viblvl_l' and 'viblvl_u' attributes for each line to allow
parsing the lines by band with::
df0.groupby('band')
Parameters
----------
df: pandas Dataframe
Line (transitions) database
dbformat: one of :data:`~radis.lbl.loader.KNOWN_DBFORMAT` : ``'cdsd```, ``'hitemp'``
format of Line database
lvlformat: 'cdsd`, 'hitemp'
format of
Returns
-------
None
input df is changed
Examples
--------
Add transitions in a Dataframe based on CDSD (p, c, j, n) format::
add_bands(df, 'cdsd')
Notes
-----
Performance with test case (CDSD CO2 2380-2400 cm-1):
- Initial: with .apply() 8.08 s ± 95.2 ms
- with groupby(): 9s worse!!
- using simple (and more readable) astype(str) statements: 523 ms ± 19.6 ms
'''
# Check inputs
if not dbformat in KNOWN_DBFORMAT:
raise ValueError('dbformat ({0}) should be one of: {1}'.format(
dbformat, KNOWN_DBFORMAT))
if not lvlformat in KNOWN_LVLFORMAT:
raise ValueError('lvlformat ({0}) should be one of: {1}'.format(
lvlformat, KNOWN_LVLFORMAT))
if verbose:
t0 = time()
print('... sorting lines by vibrational bands')
# Calculate bands:
id = list(pd.unique(df['id']))
if len(id) > 1:
raise ValueError('Cant calculate vibrational bands for multiple ' +
'molecules yet') # although it's an easy fix. Just
# groupby id
molecule = get_molecule(id[0])
if molecule == 'CO2':
vib_lvl_name_hitran = vib_lvl_name_hitran_class5
if lvlformat in ['cdsd-pc', 'cdsd-pcN', 'cdsd-hamil']:
# ensures that vib_lvl_name functions wont crash
if dbformat not in ['cdsd', 'cdsd4000', 'hitran']:
raise NotImplementedError(
'lvlformat {0} not supported with dbformat {1}'.format(
lvlformat, dbformat))
# Use vibrational nomenclature of CDSD (p,c,j,n) or HITRAN (v1v2l2v3J)
# depending on the Level Database.
# In both cases, store the other one.
# ... note: vib level in a CDSD (p,c,j,n) database is ambiguous.
# ... a vibrational energy Evib can have been defined for every (p, c) group:
if lvlformat in ['cdsd-pc']:
viblvl_l_cdsd = vib_lvl_name_cdsd_pc(df.polyl, df.wangl)
viblvl_u_cdsd = vib_lvl_name_cdsd_pc(df.polyu, df.wangu)
# ... or for every (p, c, N) group:
elif lvlformat in ['cdsd-pcN']:
viblvl_l_cdsd = vib_lvl_name_cdsd_pcN(df.polyl, df.wangl,
df.rankl)
viblvl_u_cdsd = vib_lvl_name_cdsd_pcN(df.polyu, df.wangu,
df.ranku)
# ... or for every level (p, c, J ,N) (that's the case if coupling terms
# are used taken into account... it also takes a much longer time
# to look up vibrational energies in the LineDatabase, warning!):
elif lvlformat in ['cdsd-hamil']:
viblvl_l_cdsd = vib_lvl_name_cdsd_pcJN(df.polyl, df.wangl,
df.jl, df.rankl)
viblvl_u_cdsd = vib_lvl_name_cdsd_pcJN(df.polyu, df.wangu,
df.ju, df.ranku)
else:
raise ValueError(
'Unexpected level format: {0}'.format(lvlformat))
band_cdsd = viblvl_l_cdsd + '->' + viblvl_u_cdsd
df.loc[:, 'viblvl_l'] = viblvl_l_cdsd
df.loc[:, 'viblvl_u'] = viblvl_u_cdsd
df.loc[:, 'band'] = band_cdsd
# Calculate HITRAN format too (to store them))
if all_in(['v1l', 'v2l', 'l2l', 'v3l'], df):
viblvl_l_hitran = vib_lvl_name_hitran(df.v1l, df.v2l, df.l2l,
df.v3l)
viblvl_u_hitran = vib_lvl_name_hitran(df.v1u, df.v2u, df.l2u,
df.v3u)
band_hitran = viblvl_l_hitran + '->' + viblvl_u_hitran
df.loc[:, 'viblvl_htrn_l'] = viblvl_l_hitran
df.loc[:, 'viblvl_htrn_u'] = viblvl_u_hitran
df.loc[:, 'band_htrn'] = band_hitran
# 'radis' uses Dunham development based on v1v2l2v3 HITRAN convention
elif lvlformat in ['radis']:
if dbformat not in ['hitran', 'cdsd']:
raise NotImplementedError(
'lvlformat `{0}` not supported with dbformat `{1}`'.format(
lvlformat, dbformat))
# Calculate bands with HITRAN convention
viblvl_l_hitran = vib_lvl_name_hitran(df.v1l, df.v2l, df.l2l,
df.v3l)
viblvl_u_hitran = vib_lvl_name_hitran(df.v1u, df.v2u, df.l2u,
df.v3u)
band_hitran = viblvl_l_hitran + '->' + viblvl_u_hitran
df.loc[:, 'viblvl_l'] = viblvl_l_hitran
df.loc[:, 'viblvl_u'] = viblvl_u_hitran
df.loc[:, 'band'] = band_hitran
else:
raise NotImplementedError(
'Cant deal with lvlformat={0} for {1}'.format(
lvlformat, molecule))
elif molecule in HITRAN_CLASS1: # includes 'CO'
# Note. TODO. Move that in loader.py (or somewhere consistent with
# classes defined in cdsd.py / hitran.py)
if lvlformat in ['radis']:
# ensures that vib_lvl_name functions wont crash
if dbformat not in ['hitran']:
raise NotImplementedError(
'lvlformat {0} not supported with dbformat {1}'.format(
lvlformat, dbformat))
vib_lvl_name = vib_lvl_name_hitran_class1
df.loc[:, 'viblvl_l'] = vib_lvl_name(df['vl'])
df.loc[:, 'viblvl_u'] = vib_lvl_name(df['vu'])
df.loc[:, 'band'] = df['viblvl_l'] + '->' + df['viblvl_u']
else:
raise NotImplementedError(
'Lvlformat not defined for {0}: {1}'.format(
molecule, lvlformat))
else:
raise NotImplementedError(
'Vibrational bands not yet defined for molecule: ' +
'{0} with database format: {1}. '.format(molecule, dbformat) +
'Update add_bands()')
if verbose:
print(('... lines sorted in {0:.1f}s'.format(time() - t0)))
return
