def moogsynth(*args, **kwargs):
"""
NAME:
moogsynth
PURPOSE:
Run a MOOG synthesis (direct interface to the MOOG code; use 'synth' for a general routine that generates the non-continuum-normalized spectrum, convolves withe LSF and macrotubulence, and optionally continuum normalizes the output)
INPUT ARGUMENTS:
lists with abundances (they don't all have to have the same length, missing ones are filled in with zeros):
[Atomic number1,diff1_1,diff1_2,diff1_3,...,diff1_N]
[Atomic number2,diff2_1,diff2_2,diff2_3,...,diff2_N]
...
[Atomic numberM,diffM_1,diffM_2,diffM_3,...,diffM_N]
SYNTHEIS KEYWORDS:
isotopes= ('solar') use 'solar' or 'arcturus' isotope ratios; can also be a dictionary with isotope ratios (e.g., isotopes= {'108.00116':'1.001','606.01212':'1.01'})
wmin, wmax, dw, width= (15000.000, 17000.000, 0.10000000, 7.0000000) spectral synthesis limits, step, and width of calculation (see MOOG)
doflux= (False) if True, calculate the continuum flux instead
LINELIST KEYWORDS:
linelist= (None) linelist to use; if this is None, the code looks for a weed-out version of the linelist appropriate for the given model atmosphere; otherwise can be set to the path of a linelist file or to the name of an APOGEE linelist
ATMOSPHERE KEYWORDS:
Either:
(a) modelatm= (None) can be set to the filename of a model atmosphere (needs to end in .mod)
(b) specify the stellar parameters for a grid point in model atm by
- lib= ('kurucz_filled') spectral library
- teff= (4500) grid-point Teff
- logg= (2.5) grid-point logg
- metals= (0.) grid-point metallicity
- cm= (0.) grid-point carbon-enhancement
- am= (0.) grid-point alpha-enhancement
- dr= return the path corresponding to this data release
vmicro= (2.) microturbulence (km/s) (only used if the MOOG-formatted atmosphere file doesn't already exist)
OUTPUT:
(wavelengths,spectra (nspec,nwave)) for synth driver
(wavelengths,continuum spectr (nwave)) for doflux driver
HISTORY:
2015-02-13 - Written - Bovy (IAS)
"""
doflux = kwargs.pop('doflux', False)
# Get the spectral synthesis limits
wmin = kwargs.pop('wmin', _WMIN_DEFAULT)
wmax = kwargs.pop('wmax', _WMAX_DEFAULT)
dw = kwargs.pop('dw', _DW_DEFAULT)
width = kwargs.pop('width', _WIDTH_DEFAULT)
linelist = kwargs.pop('linelist', None)
# Parse isotopes
isotopes = kwargs.pop('isotopes', 'solar')
if isinstance(isotopes, str) and isotopes.lower() == 'solar':
isotopes = {
'108.00116': '1.001',
'606.01212': '1.01',
'606.01213': '90',
'606.01313': '180',
'607.01214': '1.01',
'607.01314': '90',
'607.01215': '273',
'608.01216': '1.01',
'608.01316': '90',
'608.01217': '1101',
'608.01218': '551',
'114.00128': '1.011',
'114.00129': '20',
'114.00130': '30',
'101.00101': '1.001',
'101.00102': '1000',
'126.00156': '1.00'
}
elif isinstance(isotopes, str) and isotopes.lower() == 'arcturus':
isotopes = {
'108.00116': '1.001',
'606.01212': '0.91',
'606.01213': '8',
'606.01313': '81',
'607.01214': '0.91',
'607.01314': '8',
'607.01215': '273',
'608.01216': '0.91',
'608.01316': '8',
'608.01217': '1101',
'608.01218': '551',
'114.00128': '1.011',
'114.00129': '20',
'114.00130': '30',
'101.00101': '1.001',
'101.00102': '1000',
'126.00156': '1.00'
}
elif not isinstance(isotopes, dict):
raise ValueError(
"'isotopes=' input not understood, should be 'solar', 'arcturus', or a dictionary"
)
# Get the filename of the model atmosphere
modelatm = kwargs.pop('modelatm', None)
if not modelatm is None:
if isinstance(modelatm, str) and os.path.exists(modelatm):
modelfilename = modelatm
elif isinstance(modelatm, str):
raise ValueError('modelatm= input is a non-existing filename')
else:
raise ValueError(
'modelatm= in moogsynth should be set to the name of a file')
else:
modelfilename = appath.modelAtmospherePath(**kwargs)
# Check whether a MOOG version exists
if not os.path.exists(modelfilename.replace('.mod', '.org')):
# Convert to MOOG format
convert_modelAtmosphere(modelatm=modelfilename, **kwargs)
modeldirname = os.path.dirname(modelfilename)
modelbasename = os.path.basename(modelfilename)
# Get the name of the linelist
if linelist is None:
linelistfilename = modelbasename.replace('.mod', '.lines')
if not os.path.exists(os.path.join(modeldirname, linelistfilename)):
raise IOError(
'No linelist given and no weed-out version found for this atmosphere; either specify a linelist or run weedout first'
)
linelistfilename = os.path.join(modeldirname, linelistfilename)
elif os.path.exists(linelist):
linelistfilename = linelist
else:
linelistfilename = appath.linelistPath(linelist,
dr=kwargs.get('dr', None))
if not os.path.exists(linelistfilename):
raise RuntimeError(
"Linelist %s not found; download linelist w/ apogee.tools.download.linelist (if you have access)"
% linelistfilename)
# We will run in a subdirectory of the relevant model atmosphere
tmpDir = tempfile.mkdtemp(dir=modeldirname)
shutil.copy(linelistfilename, tmpDir)
# Cut the linelist to the desired wavelength range
with open(os.path.join(tmpDir, 'cutlines.awk'), 'w') as awkfile:
awkfile.write('$1>%.3f && $1<%.3f\n' % (wmin - width, wmax + width))
keeplines = open(os.path.join(tmpDir, 'lines.tmp'), 'w')
stderr = open('/dev/null', 'w')
try:
subprocess.check_call(
['awk', '-f', 'cutlines.awk',
os.path.basename(linelistfilename)],
cwd=tmpDir,
stdout=keeplines,
stderr=stderr)
keeplines.close()
shutil.copy(os.path.join(tmpDir, 'lines.tmp'),
os.path.join(tmpDir, os.path.basename(linelistfilename)))
except subprocess.CalledProcessError:
print("Removing unnecessary linelist entries failed ...")
finally:
os.remove(os.path.join(tmpDir, 'cutlines.awk'))
os.remove(os.path.join(tmpDir, 'lines.tmp'))
stderr.close()
# Also copy the strong lines
stronglinesfilename = appath.linelistPath('stronglines.vac',
dr=kwargs.get('dr', None))
if not os.path.exists(stronglinesfilename):
try:
download.linelist('stronglines.vac', dr=kwargs.get('dr', None))
except:
raise RuntimeError(
"Linelist stronglines.vac not found or downloading failed; download linelist w/ apogee.tools.download.linelist (if you have access)"
)
finally:
if os.path.exists(os.path.join(tmpDir, 'synth.par')):
os.remove(os.path.join(tmpDir, 'synth.par'))
if os.path.exists(os.path.join(tmpDir, 'std.out')):
os.remove(os.path.join(tmpDir, 'std.out'))
if os.path.exists(
os.path.join(tmpDir, os.path.basename(linelistfilename))):
os.remove(
os.path.join(tmpDir, os.path.basename(linelistfilename)))
if os.path.exists(os.path.join(tmpDir, 'stronglines.vac')):
os.remove(os.path.join(tmpDir, 'stronglines.vac'))
os.rmdir(tmpDir)
shutil.copy(stronglinesfilename, tmpDir)
# Now write the script file
if len(args) == 0: #special case that there are *no* differences
args = ([26, 0.], )
nsynths = numpy.array([len(args[ii]) - 1 for ii in range(len(args))])
nsynth = numpy.amax(nsynths) #Take the longest abundance list
if nsynth > 5:
raise ValueError(
"MOOG only allows five syntheses to be run at the same time; please reduce the number of abundance values in the apogee.modelspec.moog.moogsynth input"
)
nabu = len(args)
with open(os.path.join(tmpDir, 'synth.par'), 'w') as parfile:
if doflux:
parfile.write('doflux\n')
else:
parfile.write('synth\n')
parfile.write('terminal x11\n')
parfile.write('plot 1\n')
parfile.write("standard_out std.out\n")
parfile.write("summary_out '../synth.out'\n")
parfile.write("smoothed_out '/dev/null'\n")
parfile.write("strong 1\n")
parfile.write("damping 0\n")
parfile.write("stronglines_in stronglines.vac\n")
parfile.write("model_in '../%s'\n" %
modelbasename.replace('.mod', '.org'))
parfile.write("lines_in %s\n" % os.path.basename(linelistfilename))
parfile.write("atmosphere 1\n")
parfile.write("molecules 2\n")
parfile.write("lines 1\n")
parfile.write("flux/int 0\n")
# Write the isotopes
niso = len(isotopes)
parfile.write("isotopes %i %i\n" % (niso, nsynth))
for iso in isotopes:
isotopestr = iso
for ii in range(nsynth):
isotopestr += ' ' + isotopes[iso]
parfile.write(isotopestr + '\n')
# Abundances
parfile.write("abundances %i %i\n" % (nabu, nsynth))
for ii in range(nabu):
abustr = '%i' % args[ii][0]
for jj in range(nsynth):
try:
abustr += ' %.3f' % args[ii][jj + 1]
except IndexError:
abustr += ' 0.0'
parfile.write(abustr + "\n")
# Synthesis limits
parfile.write("synlimits\n") # Add 0.001 to make sure wmax is included
parfile.write("%.3f %.3f %.3f %.3f\n" %
(wmin, wmax + 0.001, dw, width))
# Now run synth
sys.stdout.write('\r' + "Running MOOG synth ...\r")
sys.stdout.flush()
try:
p = subprocess.Popen(['moogsilent'],
cwd=tmpDir,
stdin=subprocess.PIPE,
stdout=subprocess.PIPE,
stderr=subprocess.PIPE)
p.stdin.write('synth.par\n')
stdout, stderr = p.communicate()
except subprocess.CalledProcessError:
print("Running synth failed ...")
finally:
if os.path.exists(os.path.join(tmpDir, 'synth.par')):
os.remove(os.path.join(tmpDir, 'synth.par'))
if os.path.exists(os.path.join(tmpDir, 'std.out')):
os.remove(os.path.join(tmpDir, 'std.out'))
if os.path.exists(
os.path.join(tmpDir, os.path.basename(linelistfilename))):
os.remove(os.path.join(tmpDir, os.path.basename(linelistfilename)))
if os.path.exists(os.path.join(tmpDir, 'stronglines.vac')):
os.remove(os.path.join(tmpDir, 'stronglines.vac'))
os.rmdir(tmpDir)
sys.stdout.write('\r' + download._ERASESTR + '\r')
sys.stdout.flush()
# Now read the output
wavs = numpy.arange(wmin, wmax + dw, dw)
if wavs[-1] > wmax + dw / 2.: wavs = wavs[:-1]
if doflux:
contdata = numpy.loadtxt(os.path.join(modeldirname, 'synth.out'),
converters={
0: lambda x: x.replace('D', 'E'),
1: lambda x: x.replace('D', 'E')
},
usecols=[0, 1])
# Wavelength in summary file appears to be wrong from comparing to
# the standard output file
out = contdata[:, 1]
out /= numpy.nanmean(out) # Make the numbers more manageable
else:
with open(os.path.join(modeldirname, 'synth.out')) as summfile:
out = numpy.empty((nsynth, len(wavs)))
for ii in range(nsynth):
# Skip to beginning of synthetic spectrum
while True:
line = summfile.readline()
if line[0] == 'M': break
summfile.readline()
tout = []
while True:
line = summfile.readline()
if not line or line[0] == 'A': break
tout.extend([float(s) for s in line.split()])
out[ii] = numpy.array(tout)
os.remove(os.path.join(modeldirname, 'synth.out'))
if doflux:
return (wavs, out)
else:
return (wavs, 1. - out)
def moogsynth(*args,**kwargs):
"""
NAME:
moogsynth
PURPOSE:
Run a MOOG synthesis (direct interface to the MOOG code; use 'synth' for a general routine that generates the non-continuum-normalized spectrum, convolves withe LSF and macrotubulence, and optionally continuum normalizes the output)
INPUT ARGUMENTS:
lists with abundances (they don't all have to have the same length, missing ones are filled in with zeros):
[Atomic number1,diff1_1,diff1_2,diff1_3,...,diff1_N]
[Atomic number2,diff2_1,diff2_2,diff2_3,...,diff2_N]
...
[Atomic numberM,diffM_1,diffM_2,diffM_3,...,diffM_N]
SYNTHEIS KEYWORDS:
isotopes= ('solar') use 'solar' or 'arcturus' isotope ratios; can also be a dictionary with isotope ratios (e.g., isotopes= {'108.00116':'1.001','606.01212':'1.01'})
wmin, wmax, dw, width= (15000.000, 17000.000, 0.10000000, 7.0000000) spectral synthesis limits, step, and width of calculation (see MOOG)
doflux= (False) if True, calculate the continuum flux instead
LINELIST KEYWORDS:
linelist= (None) linelist to use; if this is None, the code looks for a weed-out version of the linelist appropriate for the given model atmosphere; otherwise can be set to the path of a linelist file or to the name of an APOGEE linelist
ATMOSPHERE KEYWORDS:
Either:
(a) modelatm= (None) can be set to the filename of a model atmosphere (needs to end in .mod)
(b) specify the stellar parameters for a grid point in model atm by
- lib= ('kurucz_filled') spectral library
- teff= (4500) grid-point Teff
- logg= (2.5) grid-point logg
- metals= (0.) grid-point metallicity
- cm= (0.) grid-point carbon-enhancement
- am= (0.) grid-point alpha-enhancement
- dr= return the path corresponding to this data release
vmicro= (2.) microturbulence (km/s) (only used if the MOOG-formatted atmosphere file doesn't already exist)
OUTPUT:
(wavelengths,spectra (nspec,nwave)) for synth driver
(wavelengths,continuum spectr (nwave)) for doflux driver
HISTORY:
2015-02-13 - Written - Bovy (IAS)
"""
doflux= kwargs.pop('doflux',False)
# Get the spectral synthesis limits
wmin= kwargs.pop('wmin',_WMIN_DEFAULT)
wmax= kwargs.pop('wmax',_WMAX_DEFAULT)
dw= kwargs.pop('dw',_DW_DEFAULT)
width= kwargs.pop('width',_WIDTH_DEFAULT)
linelist= kwargs.pop('linelist',None)
# Parse isotopes
isotopes= kwargs.pop('isotopes','solar')
if isinstance(isotopes,str) and isotopes.lower() == 'solar':
isotopes= {'108.00116':'1.001',
'606.01212':'1.01',
'606.01213':'90',
'606.01313':'180',
'607.01214':'1.01',
'607.01314':'90',
'607.01215':'273',
'608.01216':'1.01',
'608.01316':'90',
'608.01217':'1101',
'608.01218':'551',
'114.00128':'1.011',
'114.00129':'20',
'114.00130':'30',
'101.00101':'1.001',
'101.00102':'1000',
'126.00156':'1.00'}
elif isinstance(isotopes,str) and isotopes.lower() == 'arcturus':
isotopes= {'108.00116':'1.001',
'606.01212':'0.91',
'606.01213':'8',
'606.01313':'81',
'607.01214':'0.91',
'607.01314':'8',
'607.01215':'273',
'608.01216':'0.91',
'608.01316':'8',
'608.01217':'1101',
'608.01218':'551',
'114.00128':'1.011',
'114.00129':'20',
'114.00130':'30',
'101.00101':'1.001',
'101.00102':'1000',
'126.00156':'1.00'}
elif not isinstance(isotopes,dict):
raise ValueError("'isotopes=' input not understood, should be 'solar', 'arcturus', or a dictionary")
# Get the filename of the model atmosphere
modelatm= kwargs.pop('modelatm',None)
if not modelatm is None:
if isinstance(modelatm,str) and os.path.exists(modelatm):
modelfilename= modelatm
elif isinstance(modelatm,str):
raise ValueError('modelatm= input is a non-existing filename')
else:
raise ValueError('modelatm= in moogsynth should be set to the name of a file')
else:
modelfilename= appath.modelAtmospherePath(**kwargs)
# Check whether a MOOG version exists
if not os.path.exists(modelfilename.replace('.mod','.org')):
# Convert to MOOG format
convert_modelAtmosphere(modelatm=modelfilename,**kwargs)
modeldirname= os.path.dirname(modelfilename)
modelbasename= os.path.basename(modelfilename)
# Get the name of the linelist
if linelist is None:
linelistfilename= modelbasename.replace('.mod','.lines')
if not os.path.exists(os.path.join(modeldirname,linelistfilename)):
raise IOError('No linelist given and no weed-out version found for this atmosphere; either specify a linelist or run weedout first')
linelistfilename= os.path.join(modeldirname,linelistfilename)
elif os.path.exists(linelist):
linelistfilename= linelist
else:
linelistfilename= appath.linelistPath(linelist,
dr=kwargs.get('dr',None))
# We will run in a subdirectory of the relevant model atmosphere
tmpDir= tempfile.mkdtemp(dir=modeldirname)
shutil.copy(linelistfilename,tmpDir)
# Cut the linelist to the desired wavelength range
with open(os.path.join(tmpDir,'cutlines.awk'),'w') as awkfile:
awkfile.write('$1>%.3f && $1<%.3f\n' %(wmin-width,wmax+width))
keeplines= open(os.path.join(tmpDir,'lines.tmp'),'w')
stderr= open('/dev/null','w')
try:
subprocess.check_call(['awk','-f','cutlines.awk',
os.path.basename(linelistfilename)],
cwd=tmpDir,stdout=keeplines,stderr=stderr)
keeplines.close()
shutil.copy(os.path.join(tmpDir,'lines.tmp'),
os.path.join(tmpDir,os.path.basename(linelistfilename)))
except subprocess.CalledProcessError:
print("Removing unnecessary linelist entries failed ...")
finally:
os.remove(os.path.join(tmpDir,'cutlines.awk'))
os.remove(os.path.join(tmpDir,'lines.tmp'))
stderr.close()
# Also copy the strong lines
stronglinesfilename= appath.linelistPath('stronglines.vac',
dr=kwargs.get('dr',None))
if not os.path.exists(stronglinesfilename):
download.linelist('stronglines.vac',dr=kwargs.get('dr',None))
shutil.copy(stronglinesfilename,tmpDir)
# Now write the script file
if len(args) == 0: #special case that there are *no* differences
args= ([26,0.],)
nsynths= numpy.array([len(args[ii])-1 for ii in range(len(args))])
nsynth= numpy.amax(nsynths) #Take the longest abundance list
if nsynth > 5:
raise ValueError("MOOG only allows five syntheses to be run at the same time; please reduce the number of abundance values in the apogee.modelspec.moog.moogsynth input")
nabu= len(args)
with open(os.path.join(tmpDir,'synth.par'),'w') as parfile:
if doflux:
parfile.write('doflux\n')
else:
parfile.write('synth\n')
parfile.write('terminal x11\n')
parfile.write('plot 1\n')
parfile.write("standard_out std.out\n")
parfile.write("summary_out '../synth.out'\n")
parfile.write("smoothed_out '/dev/null'\n")
parfile.write("strong 1\n")
parfile.write("damping 0\n")
parfile.write("stronglines_in stronglines.vac\n")
parfile.write("model_in '../%s'\n" % modelbasename.replace('.mod','.org'))
parfile.write("lines_in %s\n" % os.path.basename(linelistfilename))
parfile.write("atmosphere 1\n")
parfile.write("molecules 2\n")
parfile.write("lines 1\n")
parfile.write("flux/int 0\n")
# Write the isotopes
niso= len(isotopes)
parfile.write("isotopes %i %i\n" % (niso,nsynth))
for iso in isotopes:
isotopestr= iso
for ii in range(nsynth):
isotopestr+= ' '+isotopes[iso]
parfile.write(isotopestr+'\n')
# Abundances
parfile.write("abundances %i %i\n" % (nabu,nsynth))
for ii in range(nabu):
abustr= '%i' % args[ii][0]
for jj in range(nsynth):
try:
abustr+= ' %.3f' % args[ii][jj+1]
except IndexError:
abustr+= ' 0.0'
parfile.write(abustr+"\n")
# Synthesis limits
parfile.write("synlimits\n") # Add 0.001 to make sure wmax is included
parfile.write("%.3f %.3f %.3f %.3f\n" % (wmin,wmax+0.001,dw,width))
# Now run synth
sys.stdout.write('\r'+"Running MOOG synth ...\r")
sys.stdout.flush()
try:
p= subprocess.Popen(['moogsilent'],
cwd=tmpDir,
stdin=subprocess.PIPE,
stdout=subprocess.PIPE,
stderr=subprocess.PIPE)
p.stdin.write('synth.par\n')
stdout, stderr= p.communicate()
except subprocess.CalledProcessError:
print("Running synth failed ...")
finally:
if os.path.exists(os.path.join(tmpDir,'synth.par')):
os.remove(os.path.join(tmpDir,'synth.par'))
if os.path.exists(os.path.join(tmpDir,'std.out')):
os.remove(os.path.join(tmpDir,'std.out'))
if os.path.exists(os.path.join(tmpDir,
os.path.basename(linelistfilename))):
os.remove(os.path.join(tmpDir,os.path.basename(linelistfilename)))
if os.path.exists(os.path.join(tmpDir,'stronglines.vac')):
os.remove(os.path.join(tmpDir,'stronglines.vac'))
os.rmdir(tmpDir)
sys.stdout.write('\r'+download._ERASESTR+'\r')
sys.stdout.flush()
# Now read the output
wavs= numpy.arange(wmin,wmax+dw,dw)
if wavs[-1] > wmax+dw/2.: wavs= wavs[:-1]
if doflux:
contdata= numpy.loadtxt(os.path.join(modeldirname,'synth.out'),
converters={0:lambda x: x.replace('D','E'),
1:lambda x: x.replace('D','E')},
usecols=[0,1])
# Wavelength in summary file appears to be wrong from comparing to
# the standard output file
out= contdata[:,1]
out/= numpy.nanmean(out) # Make the numbers more manageable
else:
with open(os.path.join(modeldirname,'synth.out')) as summfile:
out= numpy.empty((nsynth,len(wavs)))
for ii in range(nsynth):
# Skip to beginning of synthetic spectrum
while True:
line= summfile.readline()
if line[0] == 'M': break
summfile.readline()
tout= []
while True:
line= summfile.readline()
if not line or line[0] == 'A': break
tout.extend([float(s) for s in line.split()])
out[ii]= numpy.array(tout)
os.remove(os.path.join(modeldirname,'synth.out'))
if doflux:
return (wavs,out)
else:
return (wavs,1.-out)
def turbosynth(*args,**kwargs):
"""
NAME:
turbosynth
PURPOSE:
Run a Turbospectrum synthesis (direct interface to the Turbospectrum code; use 'synth' for a general routine that generates the non-continuum-normalized spectrum, convolves withe LSF and macrotubulence, and optionally continuum normalizes the output)
INPUT ARGUMENTS:
lists with abundances:
[Atomic number1,diff1]
[Atomic number2,diff2]
...
[Atomic numberM,diffM]
SYNTHEIS KEYWORDS:
isotopes= ('solar') use 'solar' or 'arcturus' isotope ratios; can also be a dictionary with isotope ratios (e.g., isotopes= {'6.012':'0.9375','6.013':'0.0625'})
wmin, wmax, dw, width= (15000.000, 17000.000, 0.10000000) spectral synthesis limits and step of calculation (see MOOG)
babsma_wmin, babsma_wmax= (wmin,wmax)) allows opacity limits to be different (broader) than for the synthesis itself
costheta= (1.) cosine of the viewing angle
LINELIST KEYWORDS:
air= (True) if True, perform the synthesis in air wavelengths (affects the default Hlinelist, nothing else; output is in air if air, vacuum otherwise); set to False at your own risk, as Turbospectrum expects the linelist in air wavelengths!)
Hlinelist= (None) Hydrogen linelists to use; can be set to the path of a linelist file or to the name of an APOGEE linelist; if None, then we first search for the Hlinedata.vac in the APOGEE linelist directory (if air=False) or we use the internal Turbospectrum Hlinelist (if air=True)
linelist= (None) molecular and atomic linelists to use; can be set to the path of a linelist file or to the name of an APOGEE linelist, or lists of such files; if a single filename is given, the code will first search for files with extensions '.atoms', '.molec' or that start with 'turboatoms.' and 'turbomolec.'
ATMOSPHERE KEYWORDS:
modelatm= (None) model-atmosphere instance
vmicro= (2.) microturbulence (km/s)
modelopac= (None)
(a) if set to an existing filename: assume babsma_lu has already been run and use this continuous opacity in bsyn_lu
(b) if set to a non-existing filename: store the continuous opacity in this file
MISCELLANEOUS KEYWORDS:
dr= data release
saveTurboInput= if set to a string, the input to and output from Turbospectrum will be saved as a tar.gz file with this name; can be a filename in the current directory or a full path
OUTPUT:
(wavelengths,cont-norm. spectrum, spectrum (nwave))
HISTORY:
2015-04-13 - Written - Bovy (IAS)
"""
# Get the spectral synthesis limits
wmin= kwargs.pop('wmin',_WMIN_DEFAULT)
wmax= kwargs.pop('wmax',_WMAX_DEFAULT)
dw= kwargs.pop('dw',_DW_DEFAULT)
babsma_wmin= kwargs.pop('babsma_wmin',wmin)
babsma_wmax= kwargs.pop('babsma_wmax',wmax)
if babsma_wmin > wmin or babsma_wmax < wmax:
raise ValueError("Opacity wavelength range must encompass the synthesis range")
if int(numpy.ceil((wmax-wmin)/dw > 150000)):
raise ValueError('Too many wavelengths for Turbospectrum synthesis, reduce the wavelength step dw (to, e.g., 0.016)')
costheta= kwargs.pop('costheta',1.)
# Linelists
Hlinelist= kwargs.pop('Hlinelist',None)
linelist= kwargs.pop('linelist',None)
# Parse isotopes
isotopes= kwargs.pop('isotopes','solar')
if isinstance(isotopes,str) and isotopes.lower() == 'solar':
isotopes= {}
elif isinstance(isotopes,str) and isotopes.lower() == 'arcturus':
isotopes= {'6.012':'0.9375',
'6.013':'0.0625'}
elif not isinstance(isotopes,dict):
raise ValueError("'isotopes=' input not understood, should be 'solar', 'arcturus', or a dictionary")
# We will run in a subdirectory of the current directory
tmpDir= tempfile.mkdtemp(dir=os.getcwd())
# Get the model atmosphere
modelatm= kwargs.pop('modelatm',None)
if not modelatm is None:
if isinstance(modelatm,str) and os.path.exists(modelatm):
raise ValueError('modelatm= input is an existing filename, but you need to give an Atmosphere object instead')
elif isinstance(modelatm,str):
raise ValueError('modelatm= input needs to be an Atmosphere instance')
else:
# Check temperature
if modelatm._teff > 7000.:
warnings.warn('Turbospectrum does not include all necessary physics to model stars hotter than about 7000 K; proceed with caution',RuntimeWarning)
# Write atmosphere to file
modelfilename= os.path.join(tmpDir,'atm.mod')
modelatm.writeto(modelfilename,turbo=True)
modeldirname= os.path.dirname(modelfilename)
modelbasename= os.path.basename(modelfilename)
# Get the name of the linelists
if Hlinelist is None:
if kwargs.get('air',True):
Hlinelist= 'DATA/Hlinedata' # will be symlinked
else:
Hlinelist= appath.linelistPath('Hlinedata.vac',
dr=kwargs.get('dr',None))
if not os.path.exists(Hlinelist) and not Hlinelist == 'DATA/Hlinedata':
Hlinelist= appath.linelistPath(Hlinelist,
dr=kwargs.get('dr',None))
if not os.path.exists(Hlinelist) and not kwargs.get('air',True):
print("Hlinelist in vacuum linelist not found, using Turbospectrum's, which is in air...")
Hlinelist= 'DATA/Hlinedata' # will be symlinked
linelistfilenames= [Hlinelist]
if isinstance(linelist,str):
if os.path.exists(linelist):
linelistfilenames.append(linelist)
else:
# Try finding the linelist
atomlinelistfilename= appath.linelistPath(\
'%s.atoms' % linelist,
dr=kwargs.get('dr',None))
moleclinelistfilename= appath.linelistPath(\
'%s.molec' % linelist,
dr=kwargs.get('dr',None))
if os.path.exists(atomlinelistfilename) \
and os.path.exists(moleclinelistfilename):
linelistfilenames.append(atomlinelistfilename)
linelistfilenames.append(moleclinelistfilename)
else:
atomlinelistfilename= appath.linelistPath(\
'turboatoms.%s' % linelist,
dr=kwargs.get('dr',None))
moleclinelistfilename= appath.linelistPath(\
'turbomolec.%s' % linelist,
dr=kwargs.get('dr',None))
if not os.path.exists(atomlinelistfilename) \
and '201404080919' in atomlinelistfilename \
and kwargs.get('air',True):
download.linelist(os.path.basename(atomlinelistfilename),
dr=kwargs.get('dr',None))
if not os.path.exists(moleclinelistfilename) \
and '201404080919' in moleclinelistfilename \
and kwargs.get('air',True):
download.linelist(os.path.basename(moleclinelistfilename),
dr=kwargs.get('dr',None))
if os.path.exists(atomlinelistfilename) \
and os.path.exists(moleclinelistfilename):
linelistfilenames.append(atomlinelistfilename)
linelistfilenames.append(moleclinelistfilename)
if linelist is None or len(linelistfilenames) == 1:
os.remove(modelfilename)
os.rmdir(tmpDir)
raise ValueError('linelist= must be set (see documentation) and given linelist must exist (either as absolute path or in the linelist directory)')
# Link the Turbospectrum DATA directory
os.symlink(os.getenv('TURBODATA'),os.path.join(tmpDir,'DATA'))
# Cut the linelist to the desired wavelength range, if necessary,
# Skipped because it is unnecessary, but left in case we still want to
# use it
rmLinelists= False
for ll, linelistfilename in enumerate(linelistfilenames[1:]):
if not _CUTLINELIST: continue #SKIP
if wmin == _WMIN_DEFAULT and wmax == _WMAX_DEFAULT: continue
rmLinelists= True
with open(os.path.join(tmpDir,'cutlines.awk'),'w') as awkfile:
awkfile.write('($1>%.3f && $1<%.3f) || ( substr($1,1,1) == "'
%(wmin-7.,wmax+7.) +"'"+'")\n')
keeplines= open(os.path.join(tmpDir,'lines.tmp'),'w')
stderr= open('/dev/null','w')
try:
subprocess.check_call(['awk','-f','cutlines.awk',
linelistfilename],
cwd=tmpDir,stdout=keeplines,stderr=stderr)
keeplines.close()
except subprocess.CalledProcessError:
os.remove(os.path.join(tmpDir,'lines.tmp'))
os.remove(os.path.join(tmpDir,'DATA'))
raise RuntimeError("Removing unnecessary linelist entries failed ...")
finally:
os.remove(os.path.join(tmpDir,'cutlines.awk'))
stderr.close()
# Remove elements that aren't used altogether, adjust nlines
with open(os.path.join(tmpDir,'lines.tmp'),'r') as infile:
lines= infile.readlines()
nl_list= [l[0] == "'" for l in lines]
nl= numpy.array(nl_list,dtype='int')
nl_list.append(True)
nl_list.append(True)
nlines= [numpy.sum(1-nl[ii:nl_list[ii+2:].index(True)+ii+2])
for ii in range(len(nl))]
with open(os.path.join(tmpDir,os.path.basename(linelistfilename)),
'w') \
as outfile:
for ii, line in enumerate(lines):
if ii < len(lines)-2:
if not lines[ii][0] == "'":
outfile.write(lines[ii])
elif not (lines[ii+2][0] == "'" and lines[ii+1][0] == "'"):
if lines[ii+1][0] == "'":
# Adjust nlines
outfile.write(lines[ii].replace(lines[ii].split()[-1]+'\n',
'%i\n' % nlines[ii]))
else:
outfile.write(lines[ii])
else:
if not lines[ii][0] == "'": outfile.write(lines[ii])
os.remove(os.path.join(tmpDir,'lines.tmp'))
# cp the linelists to the temporary directory
shutil.copy(linelistfilename,tmpDir)
linelistfilenames[ll]= os.path.basename(linelistfilename)
# Parse the abundances
if len(args) == 0: #special case that there are *no* differences
args= ([26,0.],)
indiv_abu= {}
for arg in args:
indiv_abu[arg[0]]= arg[1]+solarabundances._ASPLUND05[arg[0]]\
+modelatm._metals
if arg[0] == 6: indiv_abu[arg[0]]+= modelatm._cm
if arg[0] in [8,10,12,14,16,18,20,22]: indiv_abu[arg[0]]+= modelatm._am
modelopac= kwargs.get('modelopac',None)
if modelopac is None or \
(isinstance(modelopac,str) and not os.path.exists(modelopac)):
# Now write the script file for babsma_lu
scriptfilename= os.path.join(tmpDir,'babsma.par')
modelopacname= os.path.join(tmpDir,'mopac')
_write_script(scriptfilename,
babsma_wmin,babsma_wmax,dw,
None,
modelfilename,
None,
modelopacname,
modelatm._metals,
modelatm._am,
indiv_abu,
kwargs.get('vmicro',2.),
None,None,None,bsyn=False)
# Run babsma
sys.stdout.write('\r'+"Running Turbospectrum babsma_lu ...\r")
sys.stdout.flush()
if kwargs.get('verbose',False):
stdout= None
stderr= None
else:
stdout= open('/dev/null', 'w')
stderr= subprocess.STDOUT
try:
p= subprocess.Popen(['babsma_lu'],
cwd=tmpDir,
stdin=subprocess.PIPE,
stdout=stdout,
stderr=stderr)
with open(os.path.join(tmpDir,'babsma.par'),'r') as parfile:
for line in parfile:
p.stdin.write(line)
stdout, stderr= p.communicate()
except subprocess.CalledProcessError:
for linelistfilename in linelistfilenames:
os.remove(linelistfilename,tmpDir)
if os.path.exists(os.path.join(tmpDir,'DATA')):
os.remove(os.path.join(tmpDir,'DATA'))
raise RuntimeError("Running babsma_lu failed ...")
finally:
if os.path.exists(os.path.join(tmpDir,'babsma.par')) \
and not 'saveTurboInput' in kwargs:
os.remove(os.path.join(tmpDir,'babsma.par'))
sys.stdout.write('\r'+download._ERASESTR+'\r')
sys.stdout.flush()
if isinstance(modelopac,str):
shutil.copy(modelopacname,modelopac)
else:
shutil.copy(modelopac,tmpDir)
modelopacname= os.path.join(tmpDir,os.path.basename(modelopac))
# Now write the script file for bsyn_lu
scriptfilename= os.path.join(tmpDir,'bsyn.par')
outfilename= os.path.join(tmpDir,'bsyn.out')
_write_script(scriptfilename,
wmin,wmax,dw,
costheta,
modelfilename,
None,
modelopacname,
modelatm._metals,
modelatm._am,
indiv_abu,
None,
outfilename,
isotopes,
linelistfilenames,
bsyn=True)
# Run bsyn
sys.stdout.write('\r'+"Running Turbospectrum bsyn_lu ...\r")
sys.stdout.flush()
if kwargs.get('verbose',False):
stdout= None
stderr= None
else:
stdout= open('/dev/null', 'w')
stderr= subprocess.STDOUT
try:
p= subprocess.Popen(['bsyn_lu'],
cwd=tmpDir,
stdin=subprocess.PIPE,
stdout=stdout,
stderr=stderr)
with open(os.path.join(tmpDir,'bsyn.par'),'r') as parfile:
for line in parfile:
p.stdin.write(line)
stdout, stderr= p.communicate()
except subprocess.CalledProcessError:
raise RuntimeError("Running bsyn_lu failed ...")
finally:
if 'saveTurboInput' in kwargs:
turbosavefilename= kwargs['saveTurboInput']
if os.path.dirname(turbosavefilename) == '':
turbosavefilename= os.path.join(os.getcwd(),turbosavefilename)
try:
subprocess.check_call(['tar','cvzf',turbosavefilename,
os.path.basename(os.path.normpath(tmpDir))])
except subprocess.CalledProcessError:
raise RuntimeError("Tar-zipping the Turbospectrum input and output failed; you will have to manually delete the temporary directory ...")
# Need to remove babsma.par, bc not removed above
if os.path.exists(os.path.join(tmpDir,'babsma.par')):
os.remove(os.path.join(tmpDir,'babsma.par'))
if os.path.exists(os.path.join(tmpDir,'bsyn.par')):
os.remove(os.path.join(tmpDir,'bsyn.par'))
if os.path.exists(modelopacname):
os.remove(modelopacname)
if os.path.exists(modelopacname+'.mod'):
os.remove(modelopacname+'.mod')
if os.path.exists(os.path.join(tmpDir,'DATA')):
os.remove(os.path.join(tmpDir,'DATA'))
if os.path.exists(os.path.join(tmpDir,'dummy-output.dat')):
os.remove(os.path.join(tmpDir,'dummy-output.dat'))
if os.path.exists(modelfilename):
os.remove(modelfilename)
if rmLinelists:
for linelistfilename in linelistfilenames[1:]:
os.remove(linelistfilename)
sys.stdout.write('\r'+download._ERASESTR+'\r')
sys.stdout.flush()
# Now read the output
turboOut= numpy.loadtxt(outfilename)
# Clean up
os.remove(outfilename)
os.rmdir(tmpDir)
# Return wav, cont-norm, full spectrum
return (turboOut[:,0],turboOut[:,1],turboOut[:,2])