def test_ionmix_read_write():
# Verify the writeIonmixFile function
abar = 1.0
zmax = 1.0
fh = opp.OpacIonmix(reference_file,
abar / opp.NA,
twot=True,
man=True,
verbose=False)
fracs = (1.0, )
tmp_file = os.path.join(BASE_DIR, 'imx_sample_tmp.cn4')
try:
pars = {key: getattr(fh, key) for key in fields}
opp.writeIonmixFile(tmp_file, (zmax, ), fracs, **pars)
# Open generated file to check there are no errors.
fh_new = opp.OpacIonmix(tmp_file,
abar / opp.NA,
twot=True,
man=True,
verbose=False)
for key in fields:
yield assert_allclose, getattr(fh, key), getattr(fh_new, key)
except:
raise
finally:
if os.path.exists(tmp_file):
os.remove(tmp_file)
def eosDict_toIonmix(self):
# These are the naming conventions translated to ionmix arguments.
imx_conv = {'Znum':'zvals',
'Xnum':'fracs',
'idens':'numDens',
'temp':'temps',
'Zf_DT':'zbar',
'Pi_DT':'pion',
'Pec_DT':'pele',
'Ui_DT':'eion',
'Uec_DT':'eele',
'groups':'opac_bounds',
'opr_mg':'rosseland',
'opp_mg':'planck_absorb',
'emp_mg':'planck_emiss'}
# Initialize ionmix argument dictionary.
imx_dict = {}
# Translating the keys over.
for key in imx_conv.keys():
if key in self.eos_dict.keys():
imx_dict[imx_conv[key]] = self.eos_dict[key]
# Set ngroups if opacity bounds are present.
if 'opac_bounds' in imx_dict:
imx_dict['ngroups'] = len(self.eos_dict['groups']) - 1
# For verbose flag.
if self.args.verbose:
verb_conv = {'zvals':'Atomic numbers',
'fracs':'Element fractions',
'numDens':'Ion number densities',
'temps':'Temperatures',
'zbar':'Average ionizations',
'pion':'Ion pressure',
'pele':'Electron pressure',
'eion':'Ion internal energy',
'eele':'Electron internal energy',
'opac_bounds':'Opacity bounds',
'rosseland':'Rosseland mean opacity',
'planck_absorb':'Absorption Planck mean opacity',
'planck_emiss':'Emission Planck mean opacity',
'ngroups':'Number of opacity groups'}
verb_str = 'Wrote the following data to IONMIX file:\n'
i = 0
for key in imx_dict.keys():
i = i + 1
if i == len(imx_dict.keys()):
verb_str = verb_str + '{}. {}'.format(i, verb_conv[key])
else:
verb_str = verb_str + '{}. {} \n'.format(i, verb_conv[key])
print(verb_str)
# Write the ionmix file based on what data is stored in imx_dict.
opp.writeIonmixFile(self.args.outname + '.cn4', **imx_dict)
def eosDict_toIonmix(self):
# These are the naming conventions translated to ionmix arguments.
imx_conv = {'Znum':'zvals',
'Xnum':'fracs',
'idens':'numDens',
'temp':'temps',
'Zf_DT':'zbar',
'Pi_DT':'pion',
'Pec_DT':'pele',
'Ui_DT':'eion',
'Uec_DT':'eele',
'groups':'opac_bounds',
'opr_mg':'rosseland',
'opp_mg':'planck_absorb',
'emp_mg':'planck_emiss'}
# Initialize ionmix argument dictionary.
imx_dict = {}
# Translating the keys over.
for key in imx_conv.keys():
if key in self.eos_dict.keys():
imx_dict[imx_conv[key]] = self.eos_dict[key]
# Set ngroups if opacity bounds are present.
if 'opac_bounds' in imx_dict:
imx_dict['ngroups'] = len(self.eos_dict['groups']) - 1
# For verbose flag.
if self.args.verbose:
verb_conv = {'zvals':'Atomic numbers',
'fracs':'Element fractions',
'numDens':'Ion number densities',
'temps':'Temperatures',
'zbar':'Average ionizations',
'pion':'Ion pressure',
'pele':'Electron pressure',
'eion':'Ion internal energy',
'eele':'Electron internal energy',
'opac_bounds':'Opacity bounds',
'rosseland':'Rosseland mean opacity',
'planck_absorb':'Absorption Planck mean opacity',
'planck_emiss':'Emission Planck mean opacity',
'ngroups':'Number of opacity groups'}
verb_str = 'Wrote the following data to IONMIX file:\n'
i = 0
for key in imx_dict.keys():
i = i + 1
if i == len(imx_dict.keys()):
verb_str = verb_str + '{}. {}'.format(i, verb_conv[key])
else:
verb_str = verb_str + '{}. {} \n'.format(i, verb_conv[key])
print(verb_str)
# Write the ionmix file based on what data is stored in imx_dict.
opp.writeIonmixFile(self.args.outname + '.cn4', **imx_dict)
def test_writeIonmixFile(self):
try:
pars = {key: getattr(self.eos_data, key) for key in self.fields}
opp.writeIonmixFile(self.tmp_file, (self.zmax,),
self.fracs, **pars)
# Open generated file to check there are no errors.
self.eos_data_new = opp.OpacIonmix(self.tmp_file,
self.abar/opp.NA,
twot=True,
man=True,
verbose=False)
for key in self.fields:
np.testing.assert_array_equal(getattr(self.eos_data, key),
getattr(self.eos_data_new, key))
except:
raise
finally:
if os.path.exists(self.tmp_file):
os.remove(self.tmp_file)
def test_ionmix_read_write():
# Verify the writeIonmixFile function
abar = 1.0
zmax = 1.0
fh = opp.OpacIonmix(reference_file,
abar/opp.NA,
twot=True, man=True, verbose=False)
fracs = (1.0,)
tmp_file = os.path.join(BASE_DIR, 'imx_sample_tmp.cn4')
try:
pars = {key: getattr(fh, key) for key in fields}
opp.writeIonmixFile(tmp_file, (zmax,), fracs, **pars)
# Open generated file to check there are no errors.
fh_new = opp.OpacIonmix(tmp_file, abar/opp.NA, twot=True, man=True, verbose=False)
for key in fields:
yield assert_allclose, getattr(fh, key), getattr(fh_new, key)
except:
raise
finally:
if os.path.exists(tmp_file):
os.remove(tmp_file)
ax.grid(which='major')
# <codecell>
plot_eos_field(eos_data, 'ioncc', 'pres')
# <codecell>
plot_eos_field(eos_data, 'ioncc', 'pres', grad='rho')
# <codecell>
fracs = (1.0,)
filename = 'al-ses-3717.cn4'
numDens = opp.NA * eos_data['ele_dens'] / eos_data["abar"]
opp.writeIonmixFile(filename, (eos_data['zmax'],), fracs,
numDens=numDens, temps=eos_data['ele_temps'],
eion=np.fmax(eos_data["ioncc_eint"],1e-10),
eele=eos_data["ele_eint"],
pion=eos_data["ioncc_pres"],
pele=eos_data["ele_pres"],
zbar=np.fmax(zbar2,1e-3))
ionmix = opp.OpacIonmix(filename, eos_data["abar"]/opp.NA, twot=True, man=True, verbose=False)
# <codecell>
# <codecell>
plot_eos_field(eos_data, 'ioncc', 'pres')
# <codecell>
plot_eos_field(eos_data, 'ioncc', 'pres', grad='rho')
# <codecell>
fracs = (1.0, )
filename = 'al-ses-3717.cn4'
numDens = opp.NA * eos_data['ele_dens'] / eos_data["abar"]
opp.writeIonmixFile(filename, (eos_data['zmax'], ),
fracs,
numDens=numDens,
temps=eos_data['ele_temps'],
eion=np.fmax(eos_data["ioncc_eint"], 1e-10),
eele=eos_data["ele_eint"],
pion=eos_data["ioncc_pres"],
pele=eos_data["ele_pres"],
zbar=np.fmax(zbar2, 1e-3))
ionmix = opp.OpacIonmix(filename,
eos_data["abar"] / opp.NA,
twot=True,
man=True,
verbose=False)
# <codecell>
cond_data_i["zbar_temps"],
denss[jd], temps[jt],
bctmin=opp.BC_EXTRAP_ZERO)
opp.plot_zbar(denss, temps, zbar, cond_data_i['zmax'], plt.figure())
# <codecell>
# write ionmix file with
fracs = (1.0,)
filename = 'al-ses.cn4'
numDens = opp.NA * eos_data['ele_dens'] / eos_data["abar"]
opp.writeIonmixFile(filename, (eos_data['zmax'],), fracs,
numDens=numDens, temps=eos_data['ele_temps'],
eion=eos_data["ioncc_eint"],
eele=eos_data["ele_eint"],
pion=eos_data["ioncc_pres"],
pele=eos_data["ele_pres"])
opp.writeIonmixFile(filename, (eos_data['zmax'],), fracs,
numDens=numDens, temps=eos_data['ele_temps'])
ionmix = opp.OpacIonmix(filename, eos_data["abar"]/opp.NA, twot=True, man=True, verbose=False)
# <codecell>
# <codecell>
print 'Pressure [Bar]: {0:.3e} {1:.3e}'.format(
*[eos_o[el+'_pres'][rho0_idx, temps0_idx]*1e-6 for el in ['ele', 'ioncc']])
print 'Eint [erg] : {0:.3e} {1:.3e}'.format(
*[eos_o[el+'_eint'][rho0_idx, temps0_idx] for el in ['ele', 'ioncc']])
print 'Zbar : {0:.3f}'.format(zbar_tf[rho0_idx, temps0_idx])
print 'A: {0} / {1} Z: {2} / {3}'.format(mat_dict.A, eos_o['abar'], mat_dict.Z, eos_w['zmax'])
print u'dens[0]: {0} g.cm⁻³, temps[0]: {1} eV'.format(eos_o['ele_dens'][0], eos_o['ele_temps'][0])
print eos_o['ioncc_eint'][0,0]
# writing everything to files
numDens = opp.NA * eos_o['ele_dens'] / eos_o['abar']
#print mat_dict.snop.z, mat_dict.snop.fraction
opp.writeIonmixFile(filename, mat_dict.snop.z, mat_dict.snop.fraction,
numDens=numDens, temps=eos_o['ele_temps'],
eion=eos_o["ioncc_eint"],
eele=eos_o["ele_eint"],
pion=eos_o["ioncc_pres"],
pele=eos_o["ele_pres"],
zbar=zbar_tf)
# rereading the output
ionmix = opp.OpacIonmix(filename, eos_o['abar']/opp.NA, twot=True, man=True, verbose=False)
test_dict = {'temps': 'ele_temps', 'dens': 'ele_dens',
'pele': 'ele_pres', 'pion': 'ioncc_pres',
'eele': 'ele_eint', 'eion': 'ioncc_eint'}
print 'Checking: ',
for attr, key in test_dict.iteritems():
print attr,'...',
np.testing.assert_allclose(getattr(ionmix, attr), eos_o[key], atol=1e-5, rtol=1e-5)
def main():
parser = argparse.ArgumentParser(description= """
This script is used to automate EoS/opacity tables generation for FLASH.
""")
parser.add_argument('-d','--dbdir',
action="store", type=str,
default = os.path.abspath(os.curdir),
help='Path to the database. Default: current directory.')
parser.add_argument('-t','--dbtype',
action="store", type=str,
default='sesame',
help='Database type. Default: sesame.')
parser.add_argument('-n','--tablenum',
action="store", type=int,
help='Table id', required=True)
parser.add_argument('-o','--out',
action="store", type=str,
help='Ouput filename',
default=None)
args = parser.parse_args()
if args.out is None:
args.out = '{0}-eos-{1}'.format(args.dbtype, args.tablenum)
else:
args.out = os.path.splitext(args.out)[0]
if args.dbtype == 'sesame':
print "Parsing sesame input files."
eos_sesame = opp.OpgSesame(os.path.join(args.dbdir, "xsesame_ascii"),
opp.OpgSesame.SINGLE, verbose=False)
cond_sesame = opp.OpgSesame(os.path.join(args.dbdir, "sescu_ascii"),
opp.OpgSesame.DOUBLE, verbose=False)
eos_data_i = eos_sesame.data[args.tablenum]
cond_keys = sorted([key for key, val in cond_sesame.data.iteritems()\
if val['zmax'] == eos_data_i['zmax']])
# by default select the last (i.e. newest) table avalable
cond_data_i = cond_sesame.data[cond_keys[-1]]
print 'Presets for sesame table', args.tablenum,
# Merging ele and ion grids
if args.tablenum in opp.presets.SESAME:
eos_data = opp.adapt.EosMergeGrids(eos_data_i,
**opp.presets.SESAME[args.tablenum]['merge'])
fracs = opp.presets.SESAME[args.tablenum]['fracs']
print 'found'
else:
eos_data = opp.adapt.EosMergeGrids(eos_data_i,
filter_dens=lambda x: x>0,
filter_temps=lambda x: x>0)
fracs = (1.0,)
print 'not found'
output_file = args.out+'.cn4'
print 'Generating IONMIX file: {0}'.format(output_file)
numDens = opp.NA * eos_data['ele_dens'] / eos_data["abar"]
print 'Warning: for now zbar is set to 0.'
opp.writeIonmixFile(output_file, (eos_data['zmax'],), fracs,
numDens=numDens, temps=eos_data['ele_temps'],
eion=eos_data["ion_eint"],
eele=eos_data["ele_eint"],
pion=eos_data["ion_pres"],
pele=eos_data["ele_pres"])
print 'Trying to read if back... ',
try:
ionmix = opp.OpacIonmix(output_file, eos_data["abar"]/opp.NA,
twot=True, man=True, verbose=False)
print '[ok]'
except:
print '[failed]'
rho_min = 0.2*state[1]['rho']
rho_max = 5*state[0]['rho']
temp_min = 0.2*state[1]['temp']
temp_max = 20*state[0]['temp']
rho = np.logspace(np.log10(rho_min), np.log10(rho_max),200)
temp = np.logspace(np.log10(temp_min), np.log10(temp_max), 328)
D, T = np.meshgrid(rho, temp, indices='ij')
pres = tab.Pt_DT(D,T)
eint = tab.Ut_DT(D,T)
print(abar, zbar)
numDens = opp.NA * rho / abar
for filename in ['simulations/DavisEos/eos-vdv-davis.cn4', 'setup/eos-vdv-davis.cn4']:
opp.writeIonmixFile(filename, [zbar], [1.0],
numDens=numDens, temps=temp/eV2K_cst,
eion=0.5*eint.T,
eele=0.5*eint.T,
pion=0.5*pres.T,
pele=0.5*pres.T,
zbar=zbar*np.ones(pres.shape))
# rereading the output
ionmix = opp.OpacIonmix(filename, abar/opp.NA, twot=True, man=True, verbose=False)
# Parse the input file, this part is file dependent.
# For OPAC file format the parser might be opacplot2/opg_tabop.py
# otherwise it would have to be implemented.
print dir(opp.OpgSesame)
eos_data = opp.OpgSesame("../../../eos/sesame/xsesame_ascii", opp.OpgSesame.SINGLE, verbose=False).data[5761]
# Write EoS/Opacity data, see opg_ionmix.py for writeIonmixFile class
# definion. When writing EoS file in 3T one has to provide eion, eele,
# pion, pele, zbar arguments. For a IONMIX file containing opacity data,
# following arguments have to be provided: ngroups, opac_bounds, rosseland,
# planck_absorb, planck_emiss. See FLASH4 manual for expected units in
# the IONMIX format.
fracs = (1.0,)
filename = 'he-ses-5761.cn4'
numDens = opp.NA * eos_data['ele_dens'] / eos_data["abar"] # convert from g.cm⁻³ to cm⁻³.
opp.writeIonmixFile(filename, (eos_data['zmax'],), fracs,
numDens=numDens, temps=eos_data['ele_temps'],
eion=eos_data["ioncc_eint"],
eele=eos_data["ele_eint"],
pion=eos_data["ioncc_pres"],
pele=eos_data["ele_pres"],
zbar=np.ones(eos_data["ele_pres"].shape)*2 # full ionization, just as an exemple
)
# Open generated file to check there are no errors.
ionmix = opp.OpacIonmix(filename, eos_data["abar"]/opp.NA, twot=True, man=True, verbose=False)
def opac_hdf2table():
parser = argparse.ArgumentParser(description="""
This script is used to browse various EoS/Opacity tables formats
""")
parser.add_argument('-t',
'--ftype',
action="store",
type=str,
choices=avalable_formats,
default='multi',
help='Output filetype. Default: multi')
parser.add_argument('-o',
'--outfile',
action="store",
type=str,
help='Output file base name/path')
parser.add_argument('input_file',
action="store",
type=str,
help='Path to the input hdf5 file')
args = parser.parse_args()
basedir, filename = os.path.split(os.path.abspath(args.input_file))
basename_in, _ = os.path.splitext(filename)
if args.outfile is not None:
filename_out = args.outfile
else:
filename_out = os.path.join(basedir, basename_in)
op = OpgHdf5.open_file(os.path.abspath(args.input_file))
# ====================== Writing to output format ====================
if args.ftype == 'multi':
from ..opg_multi import OpgMulti, MULTI_EXT_FMT
op = OpgMulti(**op)
op.set_id(3717) # just a random number, shouldn't matter
op.write(os.path.join(basedir, filename_out), floor=None)
elif args.ftype == 'ascii':
outfile = os.path.join(basedir, filename_out) + '.txt'
def repr_grid(arr, label):
out = []
out += ['=' * 80]
out += [' {0}: {1} points'.format(label, len(arr))]
out += ['=' * 80]
out = '\n'.join(out)
return out + '\n' + np.array2string(arr, precision=3, separator='')
print(repr_grid(op['dens'][:], "Density grid [g/cc]"))
print(repr_grid(op['temp'][:], 'Temperature grid [eV]'))
print(repr_grid(op['idens'][:], "Ionic density grid [1/cc]"))
#print repr_grid(op['groups'][:], "Photon energy groups [eV]")
nu = op['groups'][:]
nu = 0.5 * (nu[1:] + nu[:-1])
out_op = np.array([nu] + [
op[key + '_mg'][0, 0] * op['dens'][0]
for key in ['opp', 'opr', 'emp']
])
np.set_printoptions(threshold=1e9)
print(
repr_grid(out_op.T,
'Opacity: nu [eV], opp [1/cm], opr[1/cm], emp [??]'))
elif args.ftype == 'vtk':
outfile = os.path.join(basedir, filename_out)
from ..opg_vtk import opg_op2vtk
f = opg_op2vtk(op, outfile)
elif args.ftype == 'ionmix':
outfile = os.path.join(basedir, filename_out)
opp.writeIonmixFile(outfile,
op['Znum'],
op['Xnum'],
numDens=op['idens'][:],
temps=op['temp'][:],
ngroups=op.Ng,
opac_bounds=op['groups'][:],
planck_absorb=op['opp_mg'][:],
rosseland=op['opr_mg'][:],
planck_emiss=op['emp_mg'][:])
# check that we can read the file back
ionmix = opp.OpacIonmix(outfile,
op["Abar"] / opp.NA,
twot=True,
man=True,
verbose=False)
else:
print('Error: {0} ftype not known!'.format(args.ftype))
print 'Pressure [Bar]: {0:.3e} {1:.3e}'.format(
*[eos_o[el+'_pres'][rho0_idx, temps0_idx]*1e-6 for el in ['ele', 'ioncc']])
print 'Eint [erg] : {0:.3e} {1:.3e}'.format(
*[eos_o[el+'_eint'][rho0_idx, temps0_idx] for el in ['ele', 'ioncc']])
print 'Zbar : {0:.3f}'.format(zbar_tf[rho0_idx, temps0_idx])
print 'A: {0} / {1} Z: {2} / {3}'.format(mat_dict.A, eos_o['abar'], mat_dict.Z, eos_w['zmax'])
print u'dens[0]: {0} g.cm⁻³, temps[0]: {1} eV'.format(eos_o['ele_dens'][0], eos_o['ele_temps'][0])
print eos_o['ioncc_eint'][0,0]
# writing everything to files
numDens = opp.NA * eos_o['ele_dens'] / eos_o['abar']
#print mat_dict.snop.z, mat_dict.snop.fraction
opp.writeIonmixFile(filename, mat_dict.snop.z, mat_dict.snop.fraction,
numDens=numDens, temps=eos_o['ele_temps'],
eion=eos_o["ioncc_eint"],
eele=eos_o["ele_eint"],
pion=eos_o["ioncc_pres"],
pele=eos_o["ele_pres"],
zbar=zbar_tf)
# rereading the output
ionmix = opp.OpacIonmix(filename, eos_o['abar']/opp.NA, twot=True, man=True, verbose=False)
test_dict = {'temps': 'ele_temps', 'dens': 'ele_dens',
'pele': 'ele_pres', 'pion': 'ion_pres',
'eele': 'ele_eint', 'eion': 'ion_eint'}
print 'Checking that file was correctly written: ',
for attr, key in test_dict.iteritems():
print attr,'...',
try:
def opac_hdf2table():
parser = argparse.ArgumentParser(description= """
This script is used to browse various EoS/Opacity tables formats
""")
parser.add_argument('-t','--ftype',
action="store", type=str,
choices=avalable_formats,
default='multi',
help='Output filetype. Default: multi')
parser.add_argument('-o', '--outfile',
action="store", type=str,
help='Output file base name/path')
parser.add_argument('input_file',
action="store", type=str,
help='Path to the input hdf5 file')
args = parser.parse_args()
basedir, filename = os.path.split(os.path.abspath(args.input_file))
basename_in, _ = os.path.splitext(filename)
if args.outfile is not None:
filename_out = args.outfile
else:
filename_out = os.path.join(basedir, basename_in)
op = OpgHdf5.open_file(os.path.abspath(args.input_file))
# ====================== Writing to output format ====================
if args.ftype == 'multi':
from ..opg_multi import OpgMulti, MULTI_EXT_FMT
op = OpgMulti(**op)
op.set_id(3717) # just a random number, shouldn't matter
op.write(os.path.join(basedir, filename_out), floor=None)
elif args.ftype == 'ascii':
outfile = os.path.join(basedir, filename_out)+'.txt'
def repr_grid(arr, label):
out = []
out += ['='*80]
out += [' {0}: {1} points'.format(label, len(arr))]
out += ['='*80]
out = '\n'.join(out)
return out + '\n'+ np.array2string(arr, precision=3, separator='')
print( repr_grid(op['dens'][:], "Density grid [g/cc]") )
print( repr_grid(op['temp'][:], 'Temperature grid [eV]') )
print( repr_grid(op['idens'][:], "Ionic density grid [1/cc]") )
#print repr_grid(op['groups'][:], "Photon energy groups [eV]")
nu = op['groups'][:]
nu = 0.5*(nu[1:]+nu[:-1])
out_op = np.array([nu]+[op[key+'_mg'][0,0]*op['dens'][0] for key in ['opp', 'opr', 'emp']])
np.set_printoptions(threshold=1e9)
print( repr_grid(out_op.T, 'Opacity: nu [eV], opp [1/cm], opr[1/cm], emp [??]') )
elif args.ftype == 'vtk':
outfile = os.path.join(basedir, filename_out)
from ..opg_vtk import opg_op2vtk
f = opg_op2vtk(op, outfile)
elif args.ftype == 'ionmix':
outfile = os.path.join(basedir, filename_out)
opp.writeIonmixFile(outfile,
op['Znum'], op['Xnum'],
numDens=op['idens'][:], temps=op['temp'][:],
ngroups=op.Ng,
opac_bounds=op['groups'][:],
planck_absorb=op['opp_mg'][:],
rosseland=op['opr_mg'][:],
planck_emiss=op['emp_mg'][:])
# check that we can read the file back
ionmix = opp.OpacIonmix(outfile, op["Abar"]/opp.NA, twot=True, man=True, verbose=False)
else:
print( 'Error: {0} ftype not known!'.format(args.ftype) )
def main():
parser = argparse.ArgumentParser(description="""
This script is used to automate EoS/opacity tables generation for FLASH.
""")
parser.add_argument(
'-d',
'--dbdir',
action="store",
type=str,
default=os.path.abspath(os.curdir),
help='Path to the database. Default: current directory.')
parser.add_argument('-t',
'--dbtype',
action="store",
type=str,
default='sesame',
help='Database type. Default: sesame.')
parser.add_argument('-n',
'--tablenum',
action="store",
type=int,
help='Table id',
required=True)
parser.add_argument('-o',
'--out',
action="store",
type=str,
help='Ouput filename',
default=None)
args = parser.parse_args()
if args.out is None:
args.out = '{0}-eos-{1}'.format(args.dbtype, args.tablenum)
else:
args.out = os.path.splitext(args.out)[0]
if args.dbtype == 'sesame':
print("Parsing sesame input files.")
eos_sesame = opp.OpgSesame(os.path.join(args.dbdir, "xsesame_ascii"),
opp.OpgSesame.SINGLE,
verbose=False)
cond_sesame = opp.OpgSesame(os.path.join(args.dbdir, "sescu_ascii"),
opp.OpgSesame.DOUBLE,
verbose=False)
eos_data_i = eos_sesame.data[args.tablenum]
cond_keys = sorted([key for key, val in cond_sesame.data.iteritems()\
if val['zmax'] == eos_data_i['zmax']])
# by default select the last (i.e. newest) table avalable
cond_data_i = cond_sesame.data[cond_keys[-1]]
print('Presets for sesame table', args.tablenum, end='')
# Merging ele and ion grids
if args.tablenum in opp.presets.SESAME:
eos_data = opp.adapt.EosMergeGrids(
eos_data_i, **opp.presets.SESAME[args.tablenum]['merge'])
fracs = opp.presets.SESAME[args.tablenum]['fracs']
print('found')
else:
eos_data = opp.adapt.EosMergeGrids(eos_data_i,
filter_dens=lambda x: x > 0,
filter_temps=lambda x: x > 0)
fracs = (1.0, )
print('not found')
output_file = args.out + '.cn4'
print('Generating IONMIX file: {0}'.format(output_file))
numDens = opp.NA * eos_data['ele_dens'] / eos_data["abar"]
print('Warning: for now zbar is set to 0.')
opp.writeIonmixFile(output_file, (eos_data['zmax'], ),
fracs,
numDens=numDens,
temps=eos_data['ele_temps'],
eion=eos_data["ion_eint"],
eele=eos_data["ele_eint"],
pion=eos_data["ion_pres"],
pele=eos_data["ele_pres"])
print('Trying to read if back... ', end='')
try:
ionmix = opp.OpacIonmix(output_file,
eos_data["abar"] / opp.NA,
twot=True,
man=True,
verbose=False)
print('[ok]')
except:
print('[failed]')
# Write EoS/Opacity data, see opg_ionmix.py for writeIonmixFile class
# definion. When writing EoS file in 3T one has to provide eion, eele,
# pion, pele, zbar arguments. For a IONMIX file containing opacity data,
# following arguments have to be provided: ngroups, opac_bounds, rosseland,
# planck_absorb, planck_emiss. See FLASH4 manual for expected units in
# the IONMIX format.
fracs = (1.0, )
filename = 'he-ses-5761.cn4'
numDens = opp.NA * eos_data['ele_dens'] / eos_data[
"abar"] # convert from g.cm⁻³ to cm⁻³.
opp.writeIonmixFile(
filename,
(eos_data['zmax'], ),
fracs,
numDens=numDens,
temps=eos_data['ele_temps'],
eion=eos_data["ioncc_eint"],
eele=eos_data["ele_eint"],
pion=eos_data["ioncc_pres"],
pele=eos_data["ele_pres"],
zbar=np.ones(eos_data["ele_pres"].shape) *
2 # full ionization, just as an exemple
)
# Open generated file to check there are no errors.
ionmix = opp.OpacIonmix(filename,
eos_data["abar"] / opp.NA,
twot=True,
man=True,
verbose=False)
for jni, nion in enumerate(nions):
for jt, temp in enumerate(temps):
zbar[jni, jt] = z
pion[jni, jt] = nion * opp.KB * temp
pele[jni, jt] = z * pion[jni, jt]
eion[jni, jt] = 1.5 * opp.KB * temp / mpi
eele[jni, jt] = z * eion[jni, jt]
# Compute specific electron entropy as given by the
# Sackur-Tetrode equation:
sele[jni,jt] = (opp.KB * opp.NA * z/a) * \
( 1.5 * log(opp.KB * temp * opp.ME / (opp.PLANCK * opp.HBAR)) -
log(z*mpi*nion/a) + 5.0/2.0 )
# Write the EOS data out to a file: "al-idealgas-001.cn6":
opp.writeIonmixFile("al-idealgas-001.cn6", (z,), (1.0,), nions, temps,
zbar=zbar,
pion=pion, pele=pele,
eion=eion, eele=eele,
sele=sele)
# Read the EOS data back in:
opg_imx = opp.OpacIonmix("al-idealgas-001.cn6", mpi,
twot=True, man=True, hassele=True)
for jni, nion in enumerate(nions):
for jt, temp in enumerate(temps):
print "%6i %6i %15.6e %15.6e %15.6e" % (jni, jt, nion, temp, opg_imx.sele[jni,jt])
rho = np.logspace(np.log10(rho_min), np.log10(rho_max), 200)
temp = np.logspace(np.log10(temp_min), np.log10(temp_max), 328)
D, T = np.meshgrid(rho, temp, indices='ij')
pres = tab.Pt_DT(D, T)
eint = tab.Ut_DT(D, T)
print(abar, zbar)
numDens = opp.NA * rho / abar
for filename in [
'simulations/DavisEos/eos-vdv-davis.cn4', 'setup/eos-vdv-davis.cn4'
]:
opp.writeIonmixFile(filename, [zbar], [1.0],
numDens=numDens,
temps=temp / eV2K_cst,
eion=0.5 * eint.T,
eele=0.5 * eint.T,
pion=0.5 * pres.T,
pele=0.5 * pres.T,
zbar=zbar * np.ones(pres.shape))
# rereading the output
ionmix = opp.OpacIonmix(filename,
abar / opp.NA,
twot=True,
man=True,
verbose=False)
