def get_atoms_by_conf(extra_file=None, atoms=None):
if atoms is None:
atoms = get_atoms_by_ZmI(extra_file=extra_file)
res = []
gss = {}
for atom in atoms:
gss[remove_iso(atom)] = gsFromAtom(remove_iso(atom))
for gs in ('s1', 's2', 'p1', 'p2', 'p3', 'p4', 'p5', 'p6', 'd1', 'd2',
'd3', 'd4', 'd5', 'd6', 'd7', 'd8', 'd9', 'd10', 'f1', 'f2',
'f3', 'f4', 'f5', 'f6', 'f7', 'f8', 'f9', 'f10', 'f11', 'f12',
'f13', 'f14', 'unknown'):
for atom in atoms:
if gss[remove_iso(atom)] == gs:
res.append(atom)
return res
def get_atoms_by_conf(extra_file=None, atoms=None):
if atoms is None:
atoms = get_atoms_by_ZmI(extra_file=extra_file)
res = []
gss = {}
for atom in atoms:
gss[remove_iso(atom)] = gsFromAtom(remove_iso(atom))
for gs in ('s1', 's2',
'p1', 'p2', 'p3', 'p4', 'p5', 'p6',
'd1', 'd2', 'd3', 'd4', 'd5', 'd6', 'd7', 'd8', 'd9', 'd10',
'f1', 'f2', 'f3', 'f4', 'f5', 'f6', 'f7', 'f8', 'f9', 'f10', 'f11', 'f12', 'f13', 'f14',
'unknown'):
for atom in atoms:
if gss[remove_iso(atom)] == gs:
res.append(atom)
return res
def print_phyat_list(atom,
tem,
den,
cut=1e-3,
cut_inter=1e-5,
ij_ref=None,
filename=None,
up_lev_rule=None,
NLevels=None,
E_cut=20,
log_file=None,
help_file=None,
verbose=False,
Aij_zero=None):
"""
atom: a string e.g. 'O3' or a pn.Atom object
tem in K
den in cm-3
cut: relative intensity (to the master one) for a line to be printed
cut_inter [deprecated]: largest dynamic between ref lines.
ij_ref: None: is computed. Otherwise must be of the form e.g. (4, 2) or ((4, 2), (5, 3))
filename: where to output the result. May be None, a string or a file object
up_lev_rule: 'each': each upper level are used to define a different master line
'all': all the transitions are grouped into a single master line
list, e.g. [2, 3, [4, 5]]: levels 2, 3 and 4-5 together are used to define a master line.
None: default hard coded value is used, see up_levs below
NLevels : max number of levels for the atom
E_cut: max energy in eV for the energy level to give a line
log_file: for the log
help_file: for the comments on the Te, Ne for each ion.
"""
up_levs = {
's1': [[2, 3], 4, 5, 6],
's2': 'each',
'p1': [2, [3, 4, 5], [6, 7]],
'p2': 'each',
'p3': [2, 3, [4, 5]],
'p4': 'each',
'p5': 'each',
'd2': 'split 3',
'd3': 'split 4',
'd4': 'split 5',
'd6': 'split 5',
'd7': 'split 3',
'd8': 'split 3',
'd9': 'split 3'
} # The others are 'all' by default (i.e. only one master line, with all the lines depending on it
ij_refs = {
's1': ((3, 1), ),
'p1': ((3, 1), (7, 1)),
'p3': ((4, 2), ),
'd6': ((4, 2), ),
'd5': (
(2, 1),
(5, 1),
),
'd4': (
(3, 2),
(7, 5),
),
'd3': ((6, 1), ),
'd2': (
(2, 1),
(12, 1),
)
}
str_print = '{}{:02d}{:02d}{:01d}{:01d}0{:03d}{:03d} {:<8s} {:11.3f} 0.000{:10.3e} 1.000 {:02d}{:02d}{:01d}{:01d}0{:03d}{:03d} -1 1.00 {}'
if filename is None:
f = None
else:
str_print += '\n'
if type(filename) is str:
f = open(filename, 'w')
elif hasattr(filename, 'write'):
f = filename
if filename is None:
def myprint(s):
print(s)
else:
def myprint(s):
f.write(s)
if log_file is None:
def logprint(s):
print(s)
elif type(log_file) is str:
lf = open(log_file, 'w')
def logprint(s):
lf.write(s)
elif hasattr(log_file, 'write'):
lf = log_file
def logprint(s):
lf.write(s)
if help_file is None:
def hprint(s):
print(s)
elif type(help_file) is str:
hf = open(log_file, 'w')
def hprint(s):
hf.write(s)
elif hasattr(help_file, 'write'):
hf = help_file
def hprint(s):
hf.write(s)
if type(atom) is str:
atom = pn.Atom(atom=atom, NLevels=NLevels)
try:
atom_str = '{}-{}'.format(atom.atomFile, atom.collFile)
except:
atom_str = ''
if atom.NLevels == 0:
logprint('Atom {} without data.'.format(atom_str))
return None
energies = atom.getEnergy(unit='eV')
N_energies = (energies < E_cut).sum()
if NLevels is not None:
this_NLevels = np.min((NLevels, atom.NLevels, N_energies))
else:
this_NLevels = np.min((atom.NLevels, N_energies))
if this_NLevels <= 1:
if N_energies <= 1:
logprint('Atom {} without level below {} eV'.format(
atom_str, E_cut))
else:
logprint('Atom {} without energy levels'.format(atom_str))
return None
#print('Doing {} with NLevels={}'.format(atom.atom, this_NLevels))
atom = pn.Atom(atom=atom.atom, NLevels=this_NLevels)
if Aij_zero is not None:
for ij in Aij_zero:
atom._A[ij[0] - 1, ij[1] - 1] = 0.0
try:
NIST_gsconf = atom.NIST[0][0].split('.')[-1]
if NIST_gsconf[-1] in ('0123456789'):
NIST_gsconf = NIST_gsconf[-2:]
else:
NIST_gsconf = NIST_gsconf[-1] + '1'
except:
NIST_gsconf = 'unknown'
logprint('{} levels. '.format(this_NLevels))
emis = atom.getEmissivity(tem, den)
emis_max_tot = np.max(emis)
wls = atom.wave_Ang[0:this_NLevels, 0:this_NLevels]
wls_mask = wls < 911.0
emis[wls_mask] = 0.0
gs = gsFromAtom(atom.atom)
if up_lev_rule is None:
if gs in up_levs:
up_lev_rule = up_levs[gs]
else:
up_lev_rule = 'all'
if up_lev_rule == 'each':
up_lev_list = range(2, this_NLevels + 1)
elif up_lev_rule == 'all':
up_lev_list = [range(2, this_NLevels + 1)]
elif 'split' in up_lev_rule:
N_split = int(up_lev_rule.split()[-1])
up_lev_list = [
range(2, N_split + 1),
range(N_split + 1, this_NLevels + 1)
]
else:
up_lev_list = up_lev_rule
if ij_ref is not None:
if type(ij_ref[0]) is not tuple:
ij_ref = (ij_ref, )
else:
if gs in ij_refs:
ij_ref = ij_refs[gs]
#print('up_lev_rule: {}, up_lev_list: {}'.format(up_lev_rule, up_lev_list))
NLevels_max = 0
print_any = False
to_print = []
ion_name = '{:>2s}_{:<5s}'.format(atom.elem,
int_to_roman(atom.spec)).strip()
N_lines = 0
for i_up_lev, up_lev in enumerate(up_lev_list):
if type(up_lev) is int:
up_lev = [up_lev]
emis_ref = 0
i_emis_ref_loc = None
j_emis_ref_loc = None
for i in up_lev:
if i < this_NLevels + 1:
for j in 1 + np.arange(i):
if ij_ref is not None and (i, j) in ij_ref:
i_emis_ref_loc = i
j_emis_ref_loc = j
emis_ref = emis[i - 1, j - 1]
if i_emis_ref_loc is None:
for i in up_lev:
if i < this_NLevels + 1:
for j in 1 + np.arange(i):
if emis[i - 1, j - 1] > emis_ref:
i_emis_ref_loc = i
j_emis_ref_loc = j
emis_ref = emis[i - 1, j - 1]
"""
if emis_ref < cut_inter * np.max(emis):
if verbose:
print('reset emis ref loc {} < {} * {} (emis_ref < cut_inter * np.max(emis))'.format(emis_ref, cut_inter, np.max(emis)))
i_emis_ref_loc = None
"""
if i_emis_ref_loc is not None:
com_ref = '{} {} {:.1f}'.format(
i_emis_ref_loc, j_emis_ref_loc, wls[i_emis_ref_loc - 1,
j_emis_ref_loc - 1])
if ("split" in up_lev_rule) or ("all" in up_lev_rule):
i_emis_ref_loc = i_up_lev + 1
if i_emis_ref_loc > 9:
logprint('Ref line level is {}. '.format(i_emis_ref_loc))
ref_str = str_print.format('9', Z[atom.elem], atom.spec, 3,
i_emis_ref_loc / 10,
i_emis_ref_loc % 10, 0, ion_name,
1.0, emis_ref, 0, 0, 0, 0, 0, 999,
com_ref)
else:
ref_str = str_print.format('9', Z[atom.elem], atom.spec, 3,
i_emis_ref_loc, 0, 0, ion_name, 1.0,
emis_ref, 0, 0, 0, 0, 0, 999,
com_ref)
print_ref = True
for i in up_lev:
print_it = False
if i > this_NLevels:
break
for j in 1 + np.arange(i):
if emis[i - 1, j - 1] > cut * emis_ref and wls[i - 1, j -
1] > 912:
print_it = True
print_any = True
if i > NLevels_max:
NLevels_max = i
if print_it:
for j in 1 + np.arange(i):
if emis[i - 1,
j - 1] > cut * emis_ref and wls[i - 1,
j - 1] > 912:
com = '{} {}'.format(i, j)
ion_name = '{:>2s}_{:<5s}'.format(
atom.elem, int_to_roman(atom.spec)).strip()
if print_ref:
to_print.append(ref_str)
print_ref = False
i_to_print = np.min((i, 9))
i_to_print = i_emis_ref_loc
if i_emis_ref_loc > 9:
to_print.append(
str_print.format(
' ', Z[atom.elem], atom.spec, 3,
i_to_print, i, j, ion_name, wls[i - 1,
j - 1],
emis[i - 1, j - 1] / emis_ref,
Z[atom.elem], atom.spec, 3,
i_emis_ref_loc / 10,
i_emis_ref_loc % 10, 0, com))
else:
to_print.append(
str_print.format(
' ', Z[atom.elem], atom.spec, 3,
i_to_print, i, j, ion_name, wls[i - 1,
j - 1],
emis[i - 1, j - 1] / emis_ref,
Z[atom.elem], atom.spec, 3,
i_emis_ref_loc, 0, 0, com))
N_lines += 1
if print_any:
hprint('# {} - Temp. = {} K, Dens. = {} cm-3 \n'.format(
atom.atom, tem, den))
for str_ in to_print:
myprint(str_)
logprint('{} lines printed. {}'.format(N_lines, atom_str))
else:
logprint('No print. ')
if len(up_lev_list) == 0:
logprint('No up lev. ')
if i_emis_ref_loc is None:
logprint('No ref loc. ')
if type(help_file) is str:
hf.close()
if type(log_file) is str:
lf.close()
def make_phyat_list(filename,
cut=1e-4,
E_cut=20,
cut_inter=1e-5,
verbose=False,
notry=False,
NLevels=50,
atoms=None,
ref_lines_dic=None,
NLevels_dic=None,
up_lev_rule_dic=None,
Aij_zero_dic=None,
Del_ion=None,
phy_cond_file='phy_cond.dat',
extra_file=None):
"""
filename: output file name
cut: relative intensity (to the master one) for a line to be printed
E_cut: max energy in eV for the energy level to give a line
cut_inter: largest dynamic between ref lines.
NLevels: max number of levels for the atom
verbose: set to True of more info needed
notry: set to True to force calling print_phyat_list outside of a try (debug mode)
atoms: a list of strings, e.g. ['C4', 'C3', 'C2', 'O3', 'O2', 'Ne3', 'Ne2', 'Fe3']. If None, all atoms are done
ref_lines_dic: e.g. {'Fe7': ((4, 2),),
'Fe6': ((2, 1), (5, 1),),
'Fe5': ((3, 2), (7, 5),),
'Fe4': ((6, 1),),
'Fe3': ((2, 1), (12, 1),)
}
NLevels_dic: e.g. {'S1': 8,
'Ni2': 17,
'Fe1': 9,
'Ni3': 9,
'Ni4': 17,
'Fe3': 25,
'Fe4': 26,
'Fe5': 20,
'Fe6': 19,
'Fe7': 9,
'Fe8': 2
}
up_lev_rule_dic: e.g. {'Ni2': 'split 3',
'Fe1': 'split 5',
'Ni3': 'split 3',
'Ni4': 'split 4'
}
Aij_zero_dic: e.g. {'C3': ((2,1),)
}
extra_file: a file of pySSN data format containing data to include.
"""
ref_lines_dic_def = {
'Fe7': ((4, 2), ),
'Fe6': (
(2, 1),
(5, 1),
),
'Fe5': (
(3, 2),
(7, 5),
),
'Fe4': ((6, 1), ),
'Fe3': (
(2, 1),
(12, 1),
),
'Fe2': ((2, 1), (14, 6)),
'Ca2': (2, 3, (4, 5), 6),
'Sc2': ((2, 1), ),
'O4': ((3, 1), (6, 3)),
'Si2': ((2, 1), (5, 2), (7, 1)),
'P3': ((2, 1), (5, 2)),
'S4': ((2, 1), (5, 2)),
'Cl5': ((2, 1), (5, 2)),
'Ar6': ((2, 1), (5, 2)),
'Co4': ((2, 1), ),
'Ni5': ((2, 1), ),
'Cu6': ((2, 1), )
}
if ref_lines_dic is None:
ref_lines_dic = ref_lines_dic_def
else:
for k in ref_lines_dic_def:
if k not in ref_lines_dic:
ref_lines_dic[k] = ref_lines_dic_def[k]
NLevels_dic_def = {
'S1': 8,
'Ni2': 17,
'Fe1': 9,
'Ni3': 9,
'Ni4': 17,
'Fe2': 100,
'Fe3': 25,
'Fe4': 26,
'Fe5': 20,
'Fe6': 19,
'Fe7': 9,
'Fe8': 2,
'Fe14': 10,
'F5': 2,
'Mg6': 49,
'Mg4': 45,
'Si7': 45,
'Na3': 45,
'Si6': 45, #25
'Ar10': 45,
'Ar9': 45,
'P9': 3,
'Si10': 3,
'Cl11': 3,
'Al12': 3,
'K13': 3,
'Ca14': 3,
'Mg2': 3,
'Al3': 3,
'Si4': 3,
'Ca7': 5
}
if NLevels_dic is None:
NLevels_dic = NLevels_dic_def
else:
for k in NLevels_dic_def:
if k not in NLevels_dic:
NLevels_dic[k] = NLevels_dic_def[k]
up_lev_rule_dic_def = {
'Fe1': 'split 5',
'Fe2': 'split 9',
'Mn2': 'split 9',
'Sc2': 'split 9',
'Ni2': 'split 3',
'Ni3': 'split 3',
'Ni4': 'split 4',
'Fe3': 'split 5',
'Fe4': 'all',
'Fe5': 'split 5',
'Fe6': 'split 4',
'Fe7': 'split 3',
'P9': 'all',
'Si10': 'all',
'Cl11': 'all',
'Al12': 'all',
'K13': 'all',
'Ca14': 'all'
}
if up_lev_rule_dic is None:
up_lev_rule_dic = up_lev_rule_dic_def
else:
for k in up_lev_rule_dic_def:
if k not in up_lev_rule_dic:
up_lev_rule_dic[k] = up_lev_rule_dic_def[k]
Aij_zero_dic_def = {'C3': ((2, 1), ), 'S5': ((4, 3), )}
if Aij_zero_dic is None:
Aij_zero_dic = Aij_zero_dic_def
else:
for k in Aij_zero_dic_def:
if k not in Aij_zero_dic:
Aij_zero_dic[k] = Aij_zero_dic_def[k]
Del_ion_def = [
'Ne7', 'Na8', 'Mg9', 'Al10', 'Ar7', 'Ca9', 'Ca14', 'Ti16', 'Cr18',
'Zn28', 'Mg11', 'Al12', 'Si13', 'P14', 'S15', 'Zn27', 'Zn29', 'Ni27',
'Fe25', 'Ca19', 'Fe15', 'Ni17', 'Fe22'
]
if Del_ion is None:
Del_ion = Del_ion_def
else:
for ion in Del_ion_def:
if ion not in Del_ion_def:
Del_ion.append(ion)
phycond = np.genfromtxt(phy_cond_file,
dtype='U3, float,U4, float, float',
names='name, value, RC, temp, dens')
dic_temp_ion = {}
dic_dens_ion = {}
tab_ips = []
tab_temps = []
tab_denss = []
for record in phycond:
if 'C' in record['RC']:
if record['name'] == 'IP':
tab_ips.append(record['value'])
tab_temps.append(record['temp'])
tab_denss.append(record['dens'])
else:
dic_temp_ion['{}{}'.format(record['name'], int(
record['value']))] = record['temp']
dic_dens_ion['{}{}'.format(record['name'], int(
record['value']))] = record['dens']
tab_temp_dens = np.array(list(zip(tab_ips, tab_temps, tab_denss)),
dtype=[('IP', float), ('temp', float),
('dens', float)])
tab_temp_dens.sort()
def get_tem_den(atom):
if atom.atom in dic_temp_ion:
temp = dic_temp_ion[atom.atom]
dens = dic_dens_ion[atom.atom]
return temp, dens
else:
for temp_dens in tab_temp_dens:
if temp_dens['IP'] > atom.IP:
temp = temp_dens['temp']
dens = temp_dens['dens']
return temp, dens
f = open(filename, 'w')
#f.write("# liste_phyat automatically generated on {} \n".format(time.ctime()))
log_file = open('log.dat', 'w')
log_file.write("# log_file automatically generated on {} \n".format(
time.ctime()))
help_file = open('help.dat', 'w')
help_file.write("# help_file automatically generated on {} \n".format(
time.ctime()))
# The following is very badly programmed, need to make it better...
if extra_file is not None:
extra_atoms = np.array(get_extra_atoms(extra_file=extra_file))
with open(extra_file, 'r') as fextra:
extra_data = fextra.readlines()
extra_data = np.array(extra_data)
else:
extra_data = []
extra_atoms = []
if atoms is None:
atoms = get_atoms_by_conf(extra_file=extra_file)
else:
atoms.extend(get_extra_atoms(extra_file, uniq=True))
atoms = get_atoms_by_conf(atoms=atoms)
atoms = unique(atoms)
printed_confs = []
#atoms = []
for a in atoms:
if a not in Del_ion:
print(a)
if a in extra_atoms:
n_lines = 0
for line in extra_data[extra_atoms == a]:
if line[0] != '9':
n_lines += 1
f.write(line)
log_file.write('{}, {} lines from file {}\n'.format(
a, n_lines, extra_file))
else:
if a in ref_lines_dic:
ref_lines = ref_lines_dic[a]
else:
ref_lines = None
if a in NLevels_dic:
this_NLevels = NLevels_dic[a]
else:
this_NLevels = NLevels
if a in up_lev_rule_dic:
up_lev_rule = up_lev_rule_dic[a]
else:
up_lev_rule = None
conf = gsFromAtom(a)
log_file.write('{}, conf={}, '.format(a, conf))
if conf not in printed_confs:
printed_confs.append(conf)
atom_str = ''
try:
atom = pn.Atom(atom=a, NLevels=this_NLevels)
try:
atom_str = '{}-{}'.format(atom.atomFile, atom.collFile)
except:
atom_str = 'atom {}, Nlevels {} not build'.format(a)
if atom.NLevels > 0:
do_it = True
else:
do_it = False
except:
log_file.write('Atom not build. {} \n'.format(atom_str))
do_it = False
if do_it:
tem, den = get_tem_den(atom)
if a in Aij_zero_dic:
Aij_zero = Aij_zero_dic[a]
else:
Aij_zero = None
if notry:
print_phyat_list(atom,
tem,
den,
cut=cut,
filename=f,
E_cut=E_cut,
log_file=log_file,
cut_inter=cut_inter,
verbose=verbose,
help_file=help_file,
ij_ref=ref_lines,
up_lev_rule=up_lev_rule,
Aij_zero=Aij_zero)
else:
try:
print_phyat_list(atom,
tem,
den,
cut=cut,
filename=f,
E_cut=E_cut,
log_file=log_file,
cut_inter=cut_inter,
verbose=verbose,
help_file=help_file,
ij_ref=ref_lines,
up_lev_rule=up_lev_rule,
Aij_zero=Aij_zero)
except:
log_file.write('plp error.')
log_file.write('\n')
#f.write('\n')
f.close()
log_file.write('\n')
log_file.close()
def print_phyat_list(atom, tem, den, cut=1e-3, cut_inter=1e-5, ij_ref = None, filename=None, up_lev_rule=None,
NLevels=None, E_cut=20, log_file=None, help_file= None, verbose=False, Aij_zero = None):
"""
atom: a string e.g. 'O3' or a pn.Atom object
tem in K
den in cm-3
cut: relative intensity (to the master one) for a line to be printed
cut_inter [deprecated]: largest dynamic between ref lines.
ij_ref: None: is computed. Otherwise must be of the form e.g. (4, 2) or ((4, 2), (5, 3))
filename: where to output the result. May be None, a string or a file object
up_lev_rule: 'each': each upper level are used to define a different master line
'all': all the transitions are grouped into a single master line
list, e.g. [2, 3, [4, 5]]: levels 2, 3 and 4-5 together are used to define a master line.
None: default hard coded value is used, see up_levs below
NLevels : max number of levels for the atom
E_cut: max energy in eV for the energy level to give a line
log_file: for the log
help_file: for the comments on the Te, Ne for each ion.
"""
up_levs = {'s1': [[2, 3], 4, 5, 6],
's2': 'each',
'p1': [2, [3, 4, 5], [6, 7]],
'p2': 'each',
'p3': [2, 3, [4, 5]],
'p4': 'each',
'p5': 'each'} # The others are 'all' by default (i.e. only one master line, with all the lines depending on it
ij_refs = {'s1': ((3, 1),),
'p1': ((3, 1), (7, 1)),
'p3': ((5, 1),)}
str_print = '{}{:02d}{:02d}{:01d}{:01d}0{:03d}{:03d} {:<8s} {:11.3f} 0.000{:10.3e} 1.000 {:02d}{:02d}{:01d}00{:03d}{:03d} 1 1.00 {}'
if filename is None:
f = None
else:
str_print += '\n'
if type(filename) is str:
f = open(filename, 'w')
elif type(filename) is file:
f = filename
if filename is None:
def myprint(s):
print(s)
else:
def myprint(s):
f.write(s)
if log_file is None:
def logprint(s):
print(s)
elif type(log_file) is str:
lf = open(log_file, 'w')
def logprint(s):
lf.write(s)
elif type(log_file) is file:
lf = log_file
def logprint(s):
lf.write(s)
if help_file is None:
def hprint(s):
print(s)
elif type(help_file) is str:
hf = open(log_file, 'w')
def hprint(s):
hf.write(s)
elif type(help_file) is file:
hf = help_file
def hprint(s):
hf.write(s)
if type(atom) is str:
atom = pn.Atom(atom=atom, NLevels=NLevels)
if atom.NLevels == 0:
logprint('Atom without data. '.format(atom.atom))
return None
energies = atom.getEnergy(unit='eV')
N_energies = (energies < E_cut).sum()
if NLevels is not None:
this_NLevels = np.min((NLevels,atom.NLevels, N_energies))
else:
this_NLevels = np.min((atom.NLevels, N_energies))
if this_NLevels <=1:
if N_energies <= 1:
logprint('Atom without level below {} eV'.format(E_cut))
else:
logprint('Atom without energy levels')
return None
#print('Doing {} with NLevels={}'.format(atom.atom, this_NLevels))
atom = pn.Atom(atom=atom.atom, NLevels=this_NLevels)
if Aij_zero is not None:
for ij in Aij_zero:
atom._A[ij[0]-1, ij[1]-1] = 0.0
try:
NIST_gsconf = atom.NIST[0][0].split('.')[-1]
if NIST_gsconf[-1] in ('0123456789'):
NIST_gsconf = NIST_gsconf[-2:]
else:
NIST_gsconf = NIST_gsconf[-1] + '1'
except:
NIST_gsconf = 'unknown'
logprint('{} levels. '.format(this_NLevels))
emis = atom.getEmissivity(tem, den)
emis_max_tot = np.max(emis)
wls = atom.wave_Ang[0:this_NLevels, 0:this_NLevels]
wls_mask = wls < 911.0
emis[wls_mask] = 0.0
gs = gsFromAtom(atom.atom)
if up_lev_rule is None:
if gs in up_levs:
up_lev_rule = up_levs[gs]
else:
up_lev_rule = 'all'
if up_lev_rule == 'each':
up_lev_list = range(2, this_NLevels+1)
elif up_lev_rule == 'all':
up_lev_list = [range(2, this_NLevels+1)]
elif 'split' in up_lev_rule:
N_split = int(up_lev_rule.split()[-1])
up_lev_list = [range(2, N_split+1), range(N_split+1, this_NLevels+1)]
else:
up_lev_list = up_lev_rule
if ij_ref is not None:
if type(ij_ref[0]) is not tuple:
ij_ref = (ij_ref,)
else:
if gs in ij_refs:
ij_ref = ij_refs[gs]
#print('up_lev_rule: {}, up_lev_list: {}'.format(up_lev_rule, up_lev_list))
NLevels_max = 0
print_any = False
to_print = []
ion_name = '{:>2s}_{:<5s}'.format(atom.elem, int_to_roman(atom.spec)).strip()
N_lines = 0
for i_up_lev, up_lev in enumerate(up_lev_list):
if type(up_lev) is int:
up_lev = [up_lev]
emis_ref = 0
i_emis_ref_loc = None
j_emis_ref_loc = None
for i in up_lev:
if i < this_NLevels+1:
for j in 1+np.arange(i):
if ij_ref is not None and (i, j) in ij_ref:
i_emis_ref_loc = i
j_emis_ref_loc = j
emis_ref = emis[i-1,j-1]
if i_emis_ref_loc is None:
for i in up_lev:
if i < this_NLevels+1:
for j in 1+np.arange(i):
if emis[i-1,j-1] > emis_ref:
i_emis_ref_loc = i
j_emis_ref_loc = j
emis_ref = emis[i-1,j-1]
"""
if emis_ref < cut_inter * np.max(emis):
if verbose:
print('reset emis ref loc {} < {} * {} (emis_ref < cut_inter * np.max(emis))'.format(emis_ref, cut_inter, np.max(emis)))
i_emis_ref_loc = None
"""
if i_emis_ref_loc is not None:
com_ref = '{} {} {:.1f}'.format(i_emis_ref_loc, j_emis_ref_loc, wls[i_emis_ref_loc-1,j_emis_ref_loc-1])
if ("split" in up_lev_rule) or ("all" in up_lev_rule):
i_emis_ref_loc = i_up_lev + 1
if i_emis_ref_loc > 9:
logprint('Ref line level is {}. '.format(i_emis_ref_loc))
ref_str=str_print.format('9', Z[atom.elem], atom.spec,i_emis_ref_loc/10 , i_emis_ref_loc%10, 0, 0, ion_name, 1.0, 1.0, 0, 0, 0, 0, 999, com_ref)
else:
ref_str=str_print.format('9', Z[atom.elem], atom.spec,i_emis_ref_loc , 0, 0, 0, ion_name, 1.0, 1.0, 0, 0, 0, 0, 999, com_ref)
print_ref = True
for i in up_lev:
print_it = False
if i > this_NLevels:
break
for j in 1+np.arange(i):
if emis[i-1,j-1] > cut * emis_ref and wls[i-1,j-1] > 912:
print_it = True
print_any = True
if i > NLevels_max:
NLevels_max = i
if print_it:
for j in 1+np.arange(i):
if emis[i-1,j-1] > cut * emis_ref and wls[i-1,j-1] > 912:
com = '{} {}'.format(i, j)
ion_name = '{:>2s}_{:<5s}'.format(atom.elem, int_to_roman(atom.spec)).strip()
if print_ref:
to_print.append(ref_str)
print_ref = False
i_to_print = np.min((i, 9))
i_to_print = i_emis_ref_loc
if i_emis_ref_loc > 9:
to_print.append(str_print.format(' ', Z[atom.elem], atom.spec, i_to_print, 0, i, j, ion_name,
wls[i-1,j-1], emis[i-1,j-1]/emis_ref, Z[atom.elem], atom.spec, i_emis_ref_loc/10, i_emis_ref_loc%10, 0, com))
else:
to_print.append(str_print.format(' ', Z[atom.elem], atom.spec, i_to_print, 0, i, j, ion_name,
wls[i-1,j-1], emis[i-1,j-1]/emis_ref, Z[atom.elem], atom.spec, i_emis_ref_loc, 0, 0, com))
N_lines += 1
if print_any:
hprint('# {} - Temp. = {} K, Dens. = {} cm-3 \n'.format(atom.atom, tem, den))
for str_ in to_print:
myprint(str_)
logprint('{} lines printed. '.format(N_lines))
else:
logprint('No print. ')
if len(up_lev_list) == 0:
logprint('No up lev. ')
if i_emis_ref_loc is None:
logprint('No ref loc. ')
if type(help_file) is str:
hf.close()
if type(log_file) is str:
lf.close()
def make_phyat_list(filename, tem1=None, den1=None, cut=1e-4, E_cut=20, cut_inter=1e-5,
verbose=False, notry=False, NLevels=50, atoms=None,
ref_lines_dic=None, NLevels_dic=None, up_lev_rule_dic=None, Aij_zero_dic=None,
Del_ion = (), tem_den_dic = None, extra_file=None):
"""
filename: output file name
tem1: temperature in K
den1: density in cm-3
cut: relative intensity (to the master one) for a line to be printed
E_cut: max energy in eV for the energy level to give a line
cut_inter: largest dynamic between ref lines.
NLevels: max number of levels for the atom
verbose: set to True of more info needed
notry: set to True to force calling print_phyat_list outside of a try (debig mode)
atoms: a list of strings, e.g. ['C4', 'C3', 'C2', 'O3', 'O2', 'Ne3', 'Ne2', 'Fe3']. If None, all atoms are done
ref_lines_dic: e.g. {'Fe7': ((4, 2),),
'Fe6': ((2, 1), (5, 1),),
'Fe5': ((3, 2), (7, 5),),
'Fe4': ((6, 1),),
'Fe3': ((2, 1), (12, 1),)
}
NLevels_dic: e.g. {'S1': 8,
'Ni2': 17,
'Fe1': 9,
'Ni3': 9,
'Ni4': 17,
'Fe3': 25,
'Fe4': 26,
'Fe5': 20,
'Fe6': 19,
'Fe7': 9,
'Fe8': 2
}
up_lev_rule_dic: e.g. {'Ni2': 'split 3',
'Fe1': 'split 5',
'Ni3': 'split 3',
'Ni4': 'split 4',
'Fe3': 'split 5',
'Fe4': 'all',
'Fe5': 'split 5',
'Fe6': 'split 4',
'Fe7': 'split 3'
}
Aij_zero_dic: e.g. {'C3': ((2,1),)
}
tem_den_dic: e.g. {0.: (1e4, 1e3),
13.6: (1e4, 1e3),
24.0: (1e4, 1e3),
1e6: (1e4, 1e3)
}
extra_file: a file of pySSN data format containing data to include.
"""
if ref_lines_dic is None:
ref_lines_dic = {'Fe7': ((4, 2),),
'Fe6': ((2, 1), (5, 1),),
'Fe5': ((3, 2), (7, 5),),
'Fe4': ((6, 1),),
'Fe3': ((2, 1), (12, 1),)
}
if NLevels_dic is None:
NLevels_dic = {'S1': 8,
'Ni2': 17,
'Fe1': 9,
'Ni3': 9,
'Ni4': 17,
'Fe3': 25,
'Fe4': 26,
'Fe5': 20,
'Fe6': 19,
'Fe7': 9,
'Fe8': 2
}
if up_lev_rule_dic is None:
up_lev_rule_dic = {'Ni2': 'split 3',
'Fe1': 'split 5',
'Ni3': 'split 3',
'Ni4': 'split 4',
'Fe3': 'split 5',
'Fe4': 'all',
'Fe5': 'split 5',
'Fe6': 'split 4',
'Fe7': 'split 3'
}
if Aij_zero_dic is None:
Aij_zero_dic = {'C3': ((2,1),)
}
if tem_den_dic is None:
tem_den_dic = {0.: (1e4, 1e3),
13.6: (1e4, 1e3),
24.0: (1e4, 1e3),
1e6: (1e4, 1e3)
}
def get_tem_den(IP):
for k in sorted(tem_den_dic.keys()):
if IP < k:
return tem_den_dic[k]
f = open(filename, 'w')
f.write("# liste_phyat automatically generated on {} \n".format(time.ctime()))
log_file = open('log.dat', 'w')
log_file.write("# log_file automatically generated on {} \n".format(time.ctime()))
help_file = open('help.dat', 'w')
help_file.write("# help_file automatically generated on {} \n".format(time.ctime()))
# The following is very badly programmed, need to make it better...
if extra_file is not None:
extra_atoms = np.array(get_extra_atoms(extra_file=extra_file))
with open(extra_file, 'r') as fextra:
extra_data = fextra.readlines()
extra_data = np.array(extra_data)
else:
extra_data = []
extra_atoms = []
if atoms is None:
atoms = get_atoms_by_conf(extra_file=extra_file)
else:
atoms.extend(get_extra_atoms(extra_file, uniq=True))
atoms = get_atoms_by_conf(atoms=atoms)
atoms = unique(atoms)
for ion in Del_ion:
try:
atoms.remove(ion)
except:
pass
printed_confs = []
#atoms = []
for a in atoms:
print(a)
if a in extra_atoms:
n_lines = 0
for line in extra_data[extra_atoms == a]:
if line[0] != '9':
n_lines += 1
f.write(line)
log_file.write('{}, {} lines from file {}\n'.format(a, n_lines, extra_file))
else:
if a in ref_lines_dic:
ref_lines = ref_lines_dic[a]
else:
ref_lines = None
if a in NLevels_dic:
this_NLevels = NLevels_dic[a]
else:
this_NLevels = NLevels
if a in up_lev_rule_dic:
up_lev_rule = up_lev_rule_dic[a]
else:
up_lev_rule = None
conf = gsFromAtom(a)
log_file.write('{}, conf={}, '.format(a, conf))
if conf not in printed_confs:
printed_confs.append(conf)
try:
atom = pn.Atom(atom=a, NLevels=this_NLevels)
if atom.NLevels > 0:
do_it = True
else:
do_it = False
except:
log_file.write('NIST missing. \n')
do_it = False
if do_it:
if tem1 is None:
tem, den = get_tem_den(atom.IP_up)
else:
tem = tem1
den = den1
if a in Aij_zero_dic:
Aij_zero = Aij_zero_dic[a]
else:
Aij_zero = None
if notry:
print_phyat_list(atom, tem, den, cut=cut, filename=f, E_cut=E_cut, log_file=log_file,
cut_inter=cut_inter, verbose=verbose, help_file=help_file, ij_ref=ref_lines,
up_lev_rule=up_lev_rule, Aij_zero=Aij_zero)
else:
try:
print_phyat_list(atom, tem, den, cut=cut, filename=f, E_cut=E_cut, log_file=log_file,
cut_inter=cut_inter, verbose=verbose, help_file=help_file, ij_ref=ref_lines,
up_lev_rule=up_lev_rule, Aij_zero=Aij_zero)
except:
log_file.write('plp error.')
log_file.write('\n')
f.write('\n')
f.close()
log_file.write('\n')
log_file.close()