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VALD: prepare model, dictionaries etc for new data (wave &^Citzwave i…
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…n vacuum)
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@ivh
ivh committed Sep 12, 2011
1 parent 2307b95 commit 5029b6a
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112 changes: 56 additions & 56 deletions nodes/vald/mapping_vald3.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -36,14 +36,14 @@ def get_bibtex_dbref(linedata):
def parse_linelist_file(filename):
"""
Helper method for parsing the vald3 linelist wiki file into
a dictionary of entries. This is the only way to propely
a dictionary of entries. This is the only way to propely
match certain properties of linelists that are only present
in this list. Note that no correction for doublet linelist
matches are done here.
matches are done here.
"""
f = open(filename, 'r')
dic = {}
for line in f:
for line in f:
if not line.startswith('||'):
continue
cols = line.split('||')[1:]
Expand All @@ -56,13 +56,13 @@ def parse_linelist_file(filename):
refs = [element.strip().strip(']]').strip().split('|')[1] for element in cols[3].split(',') if element.strip()]
except IndexError:
pass
dic[fil] = (elements, typ, refs)
dic[fil] = (elements, typ, refs)
return dic
LINELIST_DICT = parse_linelist_file(base + "VALD3linelists.txt")

# obs/exp - transition between levels with experimentally known energies
# emp - relativistic Hartree-Fock calculations, normalized to the experimental lifetimes
# pred - transitions between predicted energy levels
# emp - relativistic Hartree-Fock calculations, normalized to the experimental lifetimes
# pred - transitions between predicted energy levels
# calc - relativistic Hartree-Fock calculations of lifetimes and transition probabilities
# mix - mixture of observation times
OBSTYPE_DICT = {'exp':0, 'obs':1, 'emp':2, 'pred':3, 'calc':4, 'mix':5}
Expand Down Expand Up @@ -109,7 +109,7 @@ def get_obstype(linedata):
{'cname':'solariso',
'cbyte':(charrange, 41,47)},
{'cname':'dissen',
'cbyte':(charrange, 48,57)},
'cbyte':(charrange, 48,57)},
{'cname':'ncomp',
'cbyte':(charrange, 132,133)},
{'cname':'atomic',
Expand All @@ -119,21 +119,21 @@ def get_obstype(linedata):
# many2many field "species" handled by separate table
],
}, # end of definition for species file

# State model read 2 lines at a time from vald3 main file term
# files are grouped with 3 lines (lower,upper,transition_inf) for
# every 2 lines (lower, upper) in the vald file

# States output file appended with lower states
{'outfile':outbase + 'lowstates.dat',
'infiles':(vald_file, vald_file, terms_file, terms_file),
'headlines':(2, 2, 0, 0),
'headlines':(2, 2, 0, 0),
'commentchar':('#','#','#','#'),
'linestep':(2, 2, 3, 3), # step lengh in each file
'lineoffset':(0, 1, 0, 2), # start point of step in each file
'errline':("Unknown", "Unknown", "Unknown", "Unknown"),
'linemap':[
{'cname':'charid', #species,coup,jnum,term,energy (lower states)
{'cname':'charid', #species,coup,jnum,term,energy (lower states)
'cbyte':(merge_cols,
(30,36), (124,126), (58,64), (126,212), (44,58))},
{'cname':'species',
Expand All @@ -156,7 +156,7 @@ def get_obstype(linedata):
'cbyte':(charrange, 17,25)},
{'filenum':1,
'cname':'lande_ref',
'cbyte':(charrange, 33,41)},
'cbyte':(charrange, 33,41)},
{'filenum':1,
'cname':'level_ref',
'cbyte':(charrange, 65,73)},
Expand All @@ -168,11 +168,11 @@ def get_obstype(linedata):
'cbyte':(charrange, 350,354)},
{'cname':'level_linelist',
'cbyte':(charrange, 366,370)},

# these are read from 1st open term file
{'filenum':2, # use term file
'cname':'j',
'cbyte':(get_term_val,'J'),
'cbyte':(get_term_val,'J'),
'cnull':'X',},
{'filenum':2, # use term file
'cname':'l',
Expand Down Expand Up @@ -207,39 +207,39 @@ def get_obstype(linedata):
'cbyte':(get_term_val,'Jc'),
'cnull':'X',},
{'filenum':2, # use term file
'cname':'sn',
'cname':'sn',
'cbyte':(get_term_val,'seniority'),
'cnull':'X',},
'cnull':'X',},

# read extra info from 2nd open term file
{'filenum':3, # use 2nd open term file
'cname':'transition_type',
'cname':'transition_type',
'cbyte':(get_term_transtype,'ttype'),
'cnull':'X',},
'cnull':'X',},
{'filenum':3, # use 2nd open term file
'cname':'autoionized',
'cname':'autoionized',
'cbyte':(get_term_transtype,'autoio'),
'cnull':'X',},
'cnull':'X',},
]
}, # end of State model creation - lower states

# upper states
{'outfile':outbase + 'upstates.dat',
# upper states
{'outfile':outbase + 'upstates.dat',
'infiles': (vald_file, vald_file, terms_file, terms_file),
'headlines':(2, 2, 0, 0),
'commentchar': ('#', '#', '#','#'),
'linestep':(2, 2, 3, 3),
'lineoffset':(0, 1, 1, 2), # start point of step
'errline':("Unknown", "Unknown","Unknown"),
'linemap':[
{'cname':'charid', #species,coup,jnum,term,energy (upper states)
{'cname':'charid', #species,coup,jnum,term,energy (upper states)
'cbyte':(merge_cols,
(30,36), (212,214), (78,84), (214,300), (64,78))},
(30,36), (212,214), (78,84), (214,300), (64,78))},
{'cname':'species',
'cbyte':(charrange, 30,36)},
{'cname':'energy',
'cbyte':(charrange, 64,78)},
#{'cname':'j',
#{'cname':'j',
# 'cbyte':(charrange, 77,82),},
{'cname':'lande',
'cbyte':(charrange, 90,96),
Expand Down Expand Up @@ -285,8 +285,8 @@ def get_obstype(linedata):
'cnull':'X',},
{'cname':'p',
'filenum':2, # use term file
'cbyte':(get_term_val,'parity'),
'cnull':'X',},
'cbyte':(get_term_val,'parity'),
'cnull':'X',},
{'cname':'j1',
'filenum':2, # use term file
'cbyte':(get_term_val,'J1'),
Expand All @@ -310,20 +310,20 @@ def get_obstype(linedata):
{'cname':'sn',
'filenum':2, # use term file
'cbyte':(get_term_val,'seniority'),
'cnull':'X',},
'cnull':'X',},
# read extra info from every third line in term file
{'filenum':3, # use 2nd open term file
'cname':'transition_type',
'cname':'transition_type',
'cbyte':(get_term_transtype,'ttype'),
'cnull':'X',},
'cnull':'X',},
{'filenum':3, # use 2nd open term file
'cname':'autoionized',
'cname':'autoionized',
'cbyte':(get_term_transtype,'autoio'),
'cnull':'X',},
'cnull':'X',},
]
}, # end of upper states
# Transition model, using the vald file

# Transition model, using the vald file
{'outfile': outbase + 'transitions.dat',
'infiles':(vald_file,vald_file),
'headlines':(2,2),
Expand All @@ -336,15 +336,15 @@ def get_obstype(linedata):
'cnull':'NULL'},
{'cname':'upstate',
'cbyte':(merge_cols,
(30,36), (212,214), (78,84), (214,300), (64,78))},
(30,36), (212,214), (78,84), (214,300), (64,78))},
#(30,36), (170,172), (77,82), (172,218), (63,77))},
{'cname':'lostate',
'cbyte':(merge_cols,
(30,36), (124,126), (58,64), (126,212), (44,58))},
#(30,36), (122,124), (58,63), (124,170), (44,58))},
{'cname':'vacwave',
{'cname':'ritzwave',
'cbyte':(charrange, 0,15)},
{'cname':'airwave',
{'cname':'wave',
'cbyte':(charrange, 15,30)},
{'cname':'species',
'cbyte':(charrange, 30,36)},
Expand All @@ -359,12 +359,12 @@ def get_obstype(linedata):
'cnull':'0.0'},
{'cname':'gammastark',
'cbyte':(charrange, 109,116),
'cnull':'0.000'},
'cnull':'0.000'},
{'cname':'gammawaals',
'cbyte':(get_gammawaals, 116,124),
'cnull':'0.000',
'debug':False},
{'cname':'sigmawaals', # only filled if raw value > 0.
{'cname':'sigmawaals', # only filled if raw value > 0.
'cbyte':(get_sigmawaals, 116,124),
'cnull':'0.000',
'debug':False},
Expand All @@ -379,14 +379,14 @@ def get_obstype(linedata):
'cbyte':(charrange, 318,334)},
{'cname':'srctag',
'cbyte':(charrange, 300,307),
'skiperror':True},
'skiperror':True},

# read from every second line of the vald file
{'filenum':1,
'cname':'wave_ref',
'cname':'wave_ref',
'cbyte':(charrange, 0,9)},
{'filenum':1,
'cname':'loggf_ref',
'cname':'loggf_ref',
'cbyte':(charrange, 9,17)},
# removed - see comment about lande factor above
#{'filenum':1,
Expand All @@ -399,10 +399,10 @@ def get_obstype(linedata):
'cname':'gammastark_ref',
'cbyte':(charrange, 49,57)},
{'filenum':1,
'cname':'waals_ref',
'cname':'waals_ref',
'cbyte':(charrange, 57,65)},
## These are the old connections to linelists rather than refs directly
{'cname':'wave_linelist',
{'cname':'wave_linelist',
'cbyte':(charrange, 334,338)},
{'cname':'loggf_linelist',
'cbyte':(charrange, 338,342)},
Expand All @@ -412,31 +412,31 @@ def get_obstype(linedata):
'cbyte':(charrange, 354,358)},
{'cname':'gammastark_linelist',
'cbyte':(charrange, 358,362)},
{'cname':'waals_linelist',
{'cname':'waals_linelist',
'cbyte':(charrange, 362,366)},
# obstype is parsed from wave_linelist in post-processing
# but we need to insert NULLs to make the DB accept the file.
# but we need to insert NULLs to make the DB accept the file.
{'cname':'id',
'cbyte':(constant, 'NULL'),
'cnull':'NULL'},
],
}, # end of transitions

# Populate References with bibtex data file (block parsing)
{'outfile':outbase + 'references.dat',
{'outfile':outbase + 'references.dat',
'infiles':ref_file,
'headlines':0,
'headlines':0,
'commentchar':'%',
'startblock':('@article','@book','@techreport','@inproceedings','@misc','@ARTICLE','@phdthesis','@unpublished'),
'endblock':('@article','@book','@techreport','@inproceedings','@misc','@ARTICLE','@phdthesis','@unpublished'),
'linemap':[
'linemap':[
{'cname':'dbref',
'cbyte':(get_bibtex_dbref,)},
{'cname':'bibtex',
'cbyte':(get_bibtex,)},
],
}, # end of bibtex
'cbyte':(get_bibtex,)},
],
}, # end of bibtex

# Populate LineList model from vald_cfg file
{'outfile': outbase + 'linelists.dat',
'infiles':vald_cfg_file,
Expand All @@ -447,7 +447,7 @@ def get_obstype(linedata):
'cbyte':(bySepNr, 1)},
{'cname':'srcfile',
'cbyte':(bySepNr, 0)},
{'cname':'srcfile_ref',
{'cname':'srcfile_ref',
'cbyte':(get_srcfile_ref, 0, 3)},
{'cname':'speclo',
'cbyte':(bySepNr, 2)},
Expand All @@ -457,7 +457,7 @@ def get_obstype(linedata):
'cbyte':(bySepNr, 4)},
{'cname':'obstype',
'cbyte':(get_obstype, ),
'cnull':'X'},
'cnull':'X'},
{'cname':'r1',
'cbyte':(bySepNr, 5)},
{'cname':'r2',
Expand All @@ -480,7 +480,7 @@ def get_obstype(linedata):
'cbyte':(bySepNr, 14)},
],
}, # end of definition for vald_conf file

]

#mapping = [mapping[-1]]
29 changes: 8 additions & 21 deletions nodes/vald/node.atom/dictionaries.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -12,18 +12,6 @@
'SourceURI':'Source.url',
'SourceVolume':'Source.volume',
'SourceYear':'Source.year',
#'MethodID':'"MOBS"',
#'MethodCategory':'"observed"',
#'MethodDescription':'',
############################################################
'MoleculeStateID':'MoleculeState.id',
'MoleculeChemicalName':'Molecule.name',
'MoleculeSpeciesID':'Molecule.id',
'MoleculeInchiKey':'Molecule.inchikey',
'MoleculeInchi':'Molecule.inchi',
'MoleculeStateEnergy':'MoleculeState.energy',
'MoleculeStateEnergyRef':'MoleculeState.energy_ref_id',
'MoleculeStateEnergyUnit':'1/cm',
#############################################################
'AtomStateID':'AtomState.id',
'AtomSymbol':'Atom.name',
Expand All @@ -50,14 +38,11 @@
#############################################################
'RadTransSpeciesRef':'RadTran.species_id',
'RadTransComments':'Wavelength is for vacuum.',
'RadTransWavelength':'RadTran.vacwave',
'RadTransWavelength':'RadTran.wave',
'RadTransWavelengthUnit':u'A',
'RadTransWavelengthRef':'RadTran.wave_ref_id',
'RadTransFinalStateRef':'RadTran.upstate_id',
'RadTransInitialStateRef':'RadTran.lostate_id',
#'RadTransEffectiveLandeFactor':'RadTran.landeff',
#'RadTransEffectiveLandeFactorUnit':'unitless',
#'RadTransEffectiveLandeFactorRef':'RadTran.lande_ref_id',
'RadTransProbabilityLog10WeightedOscillatorStrength':'RadTran.loggf',
#'RadTransProbabilityLog10WeightedOscillatorStrengthAccuracy':'RadTran.accur',
'RadTransProbabilityLog10WeightedOscillatorStrengthUnit':'unitless',
Expand Down Expand Up @@ -88,11 +73,13 @@
'AtomSymbol':'species__name',
'AtomNuclearCharge':'species__atomic',
'AtomIonCharge':'species__ion',
'AtomStateEnergy':'upstate__energy',
'RadTransWavelength':'vacwave',
'RadTransWavenumber':('vacwave',invcm2Angstr),
'RadTransFrequency':('vacwave',Hz2Angstr),
'RadTransEnergy':('vacwave',eV2Angstr),
'AtomStateEnergy':'lostate__energy',
'Initial.AtomStateEnergy':'lostate__energy',
'Final.AtomStateEnergy':'upstate__energy',
'RadTransWavelength':'wave',
'RadTransWavenumber':('wave',invcm2Angstr),
'RadTransFrequency':('wave',Hz2Angstr),
'RadTransEnergy':('wave',eV2Angstr),
'RadTransProbabilityLog10WeightedOscillatorStrength':'loggf',
'RadTransBroadeningNatural':'gammarad',
'RadTransBroadeningPressure':'gammastark',
Expand Down
8 changes: 4 additions & 4 deletions nodes/vald/node.atom/models.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -139,8 +139,8 @@ class Transition(Model):
upstate = ForeignKey(State,related_name='isupperstate_trans',db_column='upstate',null=True, db_index=False)
lostate = ForeignKey(State,related_name='islowerstate_trans',db_column='lostate',null=True, db_index=False)

vacwave = DecimalField(max_digits=20, decimal_places=8, db_index=True)
airwave = DecimalField(max_digits=20, decimal_places=8)
ritzwave = DecimalField(max_digits=20, decimal_places=8)
wave = DecimalField(max_digits=20, decimal_places=8, db_index=True)

species = ForeignKey(Species, db_index=True)
loggf = DecimalField(max_digits=8, decimal_places=3, null=True)
Expand Down Expand Up @@ -168,7 +168,7 @@ class Transition(Model):
gammastark_linelist = ForeignKey(LineList, related_name='isgammastarklinelist_trans', db_index=False)
waals_linelist = ForeignKey(LineList, related_name='iswaalslinelist_trans', db_index=False)

obstype = PositiveSmallIntegerField(null=True, db_index=True) # this is the obstype of the wave_linelist, created in post-processing.
obstype = PositiveSmallIntegerField(null=True, db_index=True) # this is the obstype of the wave_linelist, created in post-processing.

def getWaals(self):
if self.gammawaals: return self.gammawaals
Expand All @@ -183,7 +183,7 @@ def getWaals(self):
# return None

def __unicode__(self):
return u'ID:%s Wavel: %s'%(self.id,self.vacwave)
return u'ID:%s Wavel: %s'%(self.id,self.wave)
class Meta:
db_table = u'transitions'

Expand Down
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