def _do_load_h(self, h, filename):
r = 0 # counts rows of file
ii = 0
species = None
flag_break = False
try:
while True:
s = h.readline().strip()
if len(s) == 0:
break
# linelistCN1214V130710.dat
#
# Mol vup vlow JLow branch gf wavenumber exc (eV) transition (V=violet, R=red)
# 0 1 2 3 5 6 7
#---BEGIN SAMPLE---
#CN1 11 03 034 + R1 0.4853E-07 40369.070 1.020 V
#CN1 11 03 035 + R1 0.5286E-07 40359.670 1.036 V
#CN1 11 03 036 + R1 0.5757E-07 40349.879 1.052 V
#---END SAMPLE---
tmp = s.split()
species = self.molecules[tmp[0]]
line = PlezMolecularLine()
line.Jl = None
line.vl = int(tmp[1])
line.v2l = int(tmp[2])
line.J2l = float(tmp[3])
line.lambda_ = 1 / float(
tmp[7]) * 1e8 # we assume the wavenumber is in 1/cm
line.branch = tmp[5]
species.lines.append(line)
r += 1
ii += 1
if ii == _PROGRESS_INDICATOR_PERIOD:
# a99.get_python_logger().info(
# "Loading '{}': {}".format(filename, a99.format_progress(r, num_lines)))
ii = 0
except Exception as e:
raise RuntimeError("Error around %d%s row of file '%s': \"%s\"" %
(r + 1, a99.ordinal_suffix(r + 1), filename,
a99.str_exc(e))) from e
def _do_load_h(self, h, filename, num_lines=0):
r = 0 # counts rows of file
ii = 0
try:
self.lines = []
while True:
s = h.readline().strip("\n")
if len(s) == 0:
break
"""
KuruczMolLineOld1 = namedtuple("KuruczMolLineOld1",
["lambda_", "J2l", "Jl", "state2l", "v2l", "spin2l", "statel", "vl",
"spinl", ])
"""
line = KuruczMolLineOld1(
float(s[0:9]),
float(s[9:15]),
float(s[15:21]),
s[22:23],
int(s[23:25]),
int(s[26:27]),
s[28:29],
int(s[29:31]),
int(s[32:33]),
)
self.lines.append(line)
r += 1
ii += 1
if ii == _PROGRESS_INDICATOR_PERIOD:
a99.get_python_logger().info("Loading '{}': {}".format(
filename, a99.format_progress(r, num_lines)))
ii = 0
except Exception as e:
raise RuntimeError("Error around %d%s row of file '%s': \"%s\"" %
(r + 1, a99.ordinal_suffix(r + 1), filename,
a99.str_exc(e))) from e
def _do_load(self, filename):
"""Clears internal lists and loads from file."""
with open(filename, "r") as h:
r = 0 # counts rows of file
edict = {
} # links atomic symbols with Atom objects created (key is atomic symbol)
try:
while True:
line = AtomicLine()
# (EE)(I) --whitespace-- (float) --ignored...--
temp = a99.str_vector(h)
elem, s_ioni = temp[0][:-1], temp[0][-1]
line.lambda_ = float(temp[1])
elem = pyfant.adjust_atomic_symbol(elem)
key = elem + s_ioni # will gb.py elements by this key
if key in edict:
a = edict[key]
else:
a = edict[key] = Atom()
a.elem = elem
a.ioni = int(s_ioni)
self.atoms.append(a)
a.lines.append(line)
r += 1
[line.kiex, line.algf, line.ch, line.gr, line.ge, line.zinf, line.abondr, finrai] = \
a99.float_vector(h)
r += 1
# last element is end-of-file flag "finrai"
if finrai == 1:
break
except Exception as e:
raise type(e)(("Error around %d%s row of file '%s'" %
(r + 1, a99.ordinal_suffix(r + 1), filename)) +
": " + str(e)).with_traceback(sys.exc_info()[2])
def _do_load_h(self, h, filename, num_lines=0):
r = 0 # counts rows of file
ii = 0
try:
self.lines = []
while True:
s = h.readline().strip("\n")
if len(s) == 0:
break
line = KuruczMolLineOld(
float(s[0:10]),
float(s[10:15]),
float(s[15:20]),
int(s[20:22]),
int(s[22:24]),
s[24:25],
int(s[25:27]),
s[27:28],
int(s[28:29]),
s[32:33],
int(s[33:35]),
s[35:36],
int(s[36:37]),
)
self.lines.append(line)
r += 1
ii += 1
if ii == _PROGRESS_INDICATOR_PERIOD:
a99.get_python_logger().info("Loading '{}': {}".format(
filename, a99.format_progress(r, num_lines)))
ii = 0
except Exception as e:
raise RuntimeError("Error around %d%s row of file '%s': \"%s\"" %
(r + 1, a99.ordinal_suffix(r + 1), filename,
a99.str_exc(e))) from e
def _do_load(self, filename):
"""Clears internal lists and loads from file."""
with open(filename, "r") as h:
r = 0 # counts rows of file
try:
number = int(h.readline()) # not used (see below)
r += 1
self.titm = a99.readline_strip(h)
r += 1
nv = a99.int_vector(
h) # number of transitions=sets-of-lines for each molecule
r += 1
# Uses length of nv vector to know how many molecules to read (ignores "number")
num_mol = len(nv)
for im in range(num_mol):
nvi = nv[im]
m = Molecule()
self.molecules.append(m)
m.titulo = a99.readline_strip(h)
a99.get_python_logger().debug(
'Reading %d%s molecule \'%s\'' %
(im + 1, a99.ordinal_suffix(im + 1), m.titulo))
parts = [s.strip() for s in m.titulo.split("#")]
m.description = parts[0]
if len(parts) > 1:
# Found 'structure' in m.titulo
m.symbols = [
basic.adjust_atomic_symbol(s) for s in [
s.strip() for s in parts[1].split(" ")
if len(s.strip()) > 0
]
]
else:
# Will try to guess molecule by m.titulo's contents
temp = basic.description_to_symbols(parts[0])
m.symbols = temp or []
transitions = []
if len(parts) > 2:
numbers = [
int(float(x))
for x in re.findall('([0-9.]+)', parts[2])
]
transitions = list(zip(numbers[0::2], numbers[1::2]))
r += 1
m.fe, m.do, m.mm, m.am, m.bm, m.ua, m.ub, m.te, m.cro = a99.float_vector(
h)
r += 1
h.readline() # Skips line which is blank in file
# In readers.f90 the variables are ise, a0, a1, a2 a3, a4, als
# but the pfant does not use them.
r += 1
m.s = float(h.readline())
r += 1
# These vectors must have nvi elements
s_v, r_inc = a99.multirow_str_vector(h, nvi, r)
r += r_inc
qqv = list(map(float, s_v))
s_v, r_inc = a99.multirow_str_vector(h, nvi, r)
r += r_inc
ggv = list(map(float, s_v))
s_v, r_inc = a99.multirow_str_vector(h, nvi, r)
r += r_inc
bbv = list(map(float, s_v))
s_v, r_inc = a99.multirow_str_vector(h, nvi, r)
r += r_inc
ddv = list(map(float, s_v))
s_v, r_inc = a99.multirow_str_vector(h, nvi, r)
r += r_inc
fact = list(map(float, s_v))
for name in ["qqv", "ggv", "bbv", "ddv", "fact"]:
v = eval(name)
if len(v) != nvi:
raise RuntimeError(
'Attribute %s of molecule #%d must be a vector with %d elements (has %d)'
% (name, im + 1, nvi, len(v)))
# creates sets of lines and appends to molecule
for isol, (q, g, b, d,
f) in enumerate(zip(qqv, ggv, bbv, ddv, fact)):
o = SetOfLines()
o.qqv = q
o.ggv = g
o.bbv = b
o.ddv = d
o.fact = f
if isol < len(transitions):
o.vl, o.v2l = transitions[isol]
m.sol.append(o)
# Now reads lines
sol_iter = iter(
m.sol
) # iterator to change the current set-of-lines with the "numlin" flag
o = next(sol_iter) # current set-of-lines
# o.lmbdam, o.sj, o.jj, o.branch = [], [], [], []
while True:
# Someone added "*" signs as a 6th column of some lines
# which was causing my reading to crash.
# Therefore I read the line and discard beyond the 5th column before
# converting to float
temp = a99.str_vector(h)
lmbdam = float(temp[0])
sj = float(temp[1])
jj = float(temp[2])
# Alphanumeric now iz = int(temp[3])
iz = temp[3]
numlin = int(temp[4])
r += 1
o.lmbdam.append(lmbdam)
o.sj.append(sj)
o.jj.append(jj)
o.branch.append(iz)
if numlin > 0:
if numlin == 9:
break
o = next(sol_iter)
a99.get_python_logger().info("Loading '{}': {}".format(
filename, a99.format_progress(im + 1, num_mol)))
if im + 1 == num_mol:
break
# im += 1
except Exception as e:
raise type(e)(("Error around %d%s row of file '%s'" %
(r + 1, a99.ordinal_suffix(r + 1), filename)) +
": " + str(e)).with_traceback(sys.exc_info()[2])
def _do_load(self, filename):
def strip(s):
return s.decode("ascii").strip()
def I(s):
return s.decode("ascii") # Identity
my_struct = struct.Struct(
"14s 13s 12s 4s 6s 6s 3s 12s 4s 6s 6s 3s 13s 2x 3s 1x 1s 1x 1s 6s 2x"
)
func_map = [
float, float, float, int, float, float, int, float, int, float,
float, int, float, strip, I, I, strip
]
filesize = os.path.getsize(filename)
num_lines = float(filesize) / 120
if num_lines != int(num_lines):
raise RuntimeError(
"Fractionary number of lines: {}, not a FilePlezTiO".format(
num_lines))
num_lines = int(num_lines)
with open(filename, "rb") as h:
try:
r = 0 # counts rows of file
ii = 0 # progress feedback auxiliary variable
while True:
s = h.readline()
# print(s)
# break
if len(s) == 0:
break # # EOF: blank line or references section
# Filtering part
gf = float(s[14:27])
J2l = float(s[43:49])
vl = int(s[70:74])
v2l = int(s[49:53])
# gf = float(bits[1])
# J2l = float(bits[4])
# vl = float(bits[8])
# v2l = float(bits[3])
# gf = args[1]
# J2l = args[4]
# vl = args[8]
# v2l = args[3]
if not (gf >= self.min_gf and J2l <= self.max_J2l
and vl <= self.max_vl and v2l <= self.max_v2l):
r += 1
continue
bits = my_struct.unpack_from(s)
args = [func(x) for func, x in zip(func_map, bits)]
line = PlezTiOLine(*args)
self.lines.append(line)
r += 1
# args = [func(x) for func, x in zip(func_map, bits)]
# line = PlezTiOLine(*bits)
# self.lines.append(line)
# 1 2 3 4 5 6 7 8 9 10 11
# 01234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678
#
# lambda_air(A) gf Elow(cm-1) vl Jl Nl syml Eup(cm-1) vu Ju Nu symu gamrad mol trans branch
# 3164.8716 0.769183E-11 3459.6228 0 5.0 5.0 0 35047.3396 15 6.0 6.0 0 1.821557E+07|'TiO a f R '
# 12345678901234 | 12345678901234
# 0 1234567890123 |
# 1 123456789012 |
# 2 1234 |
# 3 123456 |
# 4 123456 |
# 5 123 |
# 6 123456789012 |
# 7 1234 |
# 8 123456 |
# 9 123456 |
# 10 123 |
# 11 1234567890123|
# 12 2x
# 123 1 1 123456
# 13 141516
ii += 1
if ii > 12345:
a99.get_python_logger().info("Loading '{}': {}".format(
filename, a99.format_progress(r + 1, num_lines)))
ii = 0
except Exception as e:
raise type(e)(("Error around %d%s row of file '%s'" %
(r + 1, a99.ordinal_suffix(r + 1), filename)) +
": " + str(e)).with_traceback(sys.exc_info()[2])
def append_error(msg):
log.errors.append("#{}{} line: {}".format(i + 1, a99.ordinal_suffix(i + 1), str(msg)))
def vald3_to_sols(molconsts, file_vald3, qgbd_calculator):
"""
Converts HITRAN molecular lines data to PFANT "sets of lines"
Args:
molconsts: a dict-like object combining field values from tables 'molecule', 'state',
and 'pfantmol' from a FileMolDB database
file_vald3: FileVald3 instance with only one species
qgbd_calculator: callable that can calculate "qv", "gv", "bv", "dv",
e.g., calc_qbdg_tio_like()
Returns: (a list of ftpyfant.SetOfLines objects, a MolConversionLog object)
"""
def append_error(msg):
log.errors.append("#{}{} line: {}".format(i + 1, a99.ordinal_suffix(i + 1), str(msg)))
# C BAND (v',v'')=(VL,V2L)
# C WN: vacuum wavenumber WL : air wavelength
# C J2L: lower state angular momentum number
# C iso: isotope/ 26: 12C16O, 36: 13C16O, 27: 12C17O, 28: 12C18O
# C ramo: branch, for P: ID=1, for R: ID=2
# C name: file name/ coisovLv2L
# C HL: Honl-London factor
# C FR: oscillator strength
if not isinstance(file_vald3, pyfant.FileVald3):
raise TypeError("Invalid type for argument 'file_vald3': {}".format(type(file_vald3)))
if len(file_vald3) > 1:
raise ValueError("Argument 'file_vald3' must have only one species, but it has {}".format(len(file_vald3)))
lines = file_vald3.speciess[0].lines
n = len(lines)
S = molconsts.get_S2l()
DELTAK = molconsts.get_deltak()
sols = OrderedDict() # one item per (vl, v2l) pair
log = MolConversionLog(n)
for i, line in enumerate(lines):
assert isinstance(line, pyfant.Vald3Line)
try:
wl = line.lambda_
# Br, J2l = f_group(data["local_lower_quanta"][i])
# Jl = _Jl(Br, J2l)
# V = f_class(data["global_upper_quanta"][i])
# V_ = f_class(data["global_lower_quanta"][i])
# A = data["a"][i]
# A seguir normalizacion de factor de Honl-london (HLN)
Normaliza = 1/((2.0*line.J2l+1)*(2.0*S+1)*(2.0-DELTAK))
# A seguir teremos a forca de oscilador
# mas q sera normalizada segundo o programa da Beatriz
# gf = Normaliza*1.499*(2*Jl+1)*A/(nu**2) <-- this was for HITRAN
gf_pfant = Normaliza*10**line.loggf
J2l_pfant = int(line.J2l) # ojo, estamos colocando J2L-0.5!
except Exception as e:
log.errors.append("#{}{} line: {}".format(i+1, a99.ordinal_suffix(i+1), str(e)))
continue
sol_key = "%3d%3d" % (line.vl, line.v2l) # (v', v'') transition (v_sup, v_inf)
if sol_key not in sols:
qgbd = qgbd_calculator(molconsts, line.v2l)
qqv = qgbd["qv"]
ggv = qgbd["gv"]
bbv = qgbd["bv"]
ddv = qgbd["dv"]
sols[sol_key] = pyfant.SetOfLines(line.vl, line.v2l, qqv, ggv, bbv, ddv, 1.)
sol = sols[sol_key]
# TODO assuming singlet!!!
sol.append_line(wl, gf_pfant, J2l_pfant, ph.singlet.quanta_to_branch(line.Jl, line.J2l))
return (list(sols.values()), log)
def _do_load_h(self, h, filename):
# ---SAMPLE FILE---
# Lande factors Damping parameters
# Elm Ion WL_air(A) log gf* E_low(eV) J lo E_up(eV) J up lower upper mean Rad. Stark Waals
# 'OH 1', 16401.409, -8.587, 4.0602, 39.5, 4.8160, 39.5,99.000,99.000,99.000, 0.000, 0.000, 0.000,
# ' Hb 2s2.3s2.1p3 X,2,1,f,40,3'
# ' Hb 2s2.3s2.1p3 X,2,1,f,39,7'
r = 0 # counts rows of file
self.speciess = defaultdict(lambda: defaultdict(lambda: []))
try:
# Uses header as "magic characters"
s = h.readline().strip("\n")
if s != " Lande factors Damping parameters":
raise RuntimeError(
"This doesn't appear to be a VALD3 extended-format atomic/molecular lines file"
)
r += 1
h.readline()
r += 1
while True:
# Line 1/4
# ========
#
s = h.readline().strip()
if len(s) == 0 or not s.startswith("'"):
# EOF: blank line or references section
break
fields = s.split(",")
formula, s_ioni = fields[0][1:-1].split(" ")
if formula in _symbols:
r += 1
# Atom, skips altogether (skips next three lines and loops)
for _ in range(3):
h.readline()
r += 1
continue
line = Vald3MolecularLine(
lambda_=float(fields[1]),
loggf=float(fields[2]),
Jl=float(fields[6]), # J_up
J2l=float(fields[4]) # J_lo
)
r += 1
# Line 2/4 and 3/4
# ================
#
# Parses "molecular system" TODO rename this term later
# TODO dunno what comes first, vl or v2l, but if it follows the file header,
# v2l (v lower) should come first, because "J lo" comes before "J up" in the file header
s = h.readline().strip()
r += 1
sys00, sys01, sys02, v2l = _parse_system(s)
s = h.readline().strip()
r += 1
sys10, sys11, sys12, vl = _parse_system(s)
species_key = (formula, int(s_ioni))
sol_key = Vald3SolKey(vl, v2l, sys00, sys01, sys02, sys10,
sys11, sys12)
self.speciess[species_key][sol_key].append(line)
# Line 4/4 (citation line (skips))
# ================================
#
h.readline()
r += 1
except Exception as e:
raise type(e)(("Error around %d%s row of file '%s'" %
(r + 1, a99.ordinal_suffix(r + 1), filename)) +
": " + str(e)).with_traceback(sys.exc_info()[2])
def vald3_to_atoms(file_obj):
"""
Converts data from a VALD3 file into a FileAtoms object.
Args:
file_obj: file-like object, e.g., returned by open()
Returns: a FileAtoms object
VALD3 website: http://vald.astro.uu.se/
"""
_logger = a99.get_python_logger()
def log_skipping(r, reason, row):
_logger.info("Skipping row #%d (%s)" % (r, reason))
_logger.info(str(row))
reader = csv.reader(file_obj)
ret = pyfant.FileAtoms()
edict = {
} # links atomic symbols with Atom objects created (key is atomic symbol)
r = 0
num_skip_ioni, num_skip_mol = 0, 0
try:
for row in reader:
r += 1
if len(row) <= 12: # Condition to detect row of interest
continue
elem = row[0][1:row[0].index(" ")]
if not elem in _Symbols:
# skips molecule
num_skip_mol += 1
continue
# # Collects information and creates atomic line object.
# Note: Variable names follow Fortran source variable names.
s_ioni = row[0][-2]
ioni = int(s_ioni) # not used, stays as file validation
if ioni > 2:
# log_skipping(r, "ionization > 2", row)
num_skip_ioni += 1
continue
_waals = float(row[12])
if _waals > 0:
# If the van der Waals damping parameter is > 0, it means
# something else, see the documentation at
# http://www.astro.uu.se/valdwiki/Vald3Format:
# "if >0 : two parameters as defined in Barklem et al.
# 2000A&AS..142..467B : integer part is cross-section sigma,
# fractional part is velocity parameter alpha"
# Therefore, we fall back.
_waals = 0
line = pyfant.AtomicLine()
line.lambda_ = float(row[1])
line.algf = float(row[2])
line.kiex = float(row[3])
if _waals == 0:
line.ch = 0.3e-31
else:
try:
# Formula supplied by Elvis Cantelli:
# extracted from cross-entropy code by P. Barklem
line.ch = 10**(2.5 * _waals - 12.32)
except:
# Catches error to log _waals value that gave rise to error
_logger.critical("Error calculating ch: waals=%g" % _waals)
raise
# Setting gr to zero will cause PFANT to calculate it using a formula.
# See pfantlib.f90::read_atoms() for the formula.
line.gr = 0.0
# ge is not present in VALD3 file.
# it enters as a multiplicative term in popadelh(). The original
# atom4070g.dat and atoms.dat all had ge=0 for all lines.
line.ge = 0.0
# Attention: zinf must be tuned later using tune-zinf.py
line.zinf = 0.5
# Never used in PFANT
line.abondr = 1
# # Stores line in object
elem = pyfant.adjust_atomic_symbol(elem)
key = elem + s_ioni # will group elements by this key
if key in edict:
a = edict[key]
else:
a = edict[key] = pyfant.Atom()
a.elem = elem
a.ioni = int(s_ioni)
ret.atoms.append(a)
a.lines.append(line)
except Exception as e:
raise type(e)(("Error around %d%s row of VALD3 file" %
(r, a99.ordinal_suffix(r))) + ": " +
str(e)).with_traceback(sys.exc_info()[2])
_logger.debug("VALD3-to-atoms conversion successful!")
_logger.info("Number of lines skipped (molecules): %d" % num_skip_mol)
_logger.info("Number of lines skipped (ioni > 2): %d" % num_skip_ioni)
_logger.debug("Number of (element+ioni): %s" % len(ret))
_logger.debug("Total number of atomic lines: %d" %
(sum(len(a) for a in ret.atoms), ))
return ret
def _do_load_h(self, h, filename, num_lines=0):
r = 0 # counts rows of file
ii = 0
try:
self.lines = []
while True:
s = h.readline().strip("\n")
if len(s) == 0:
break
# Kurucz: "negative energies are predicted or extrapolated"
# (http: // kurucz.harvard.edu / linelists.html)
E2l = float(s[22:32])
if E2l < 0:
E2l = -E2l
El = float(s[37:48])
if El < 0:
El = -El
try:
spin2l = int(s[57:58])
except ValueError:
spin2l = 0
try:
spinl = int(s[65:66])
except ValueError:
spinl = 0
line = KuruczMolLine(
float(s[0:10]) * 10,
float(s[10:17]),
float(s[17:22]),
E2l,
float(s[32:37]),
El,
int(s[48:50]),
int(s[50:52]),
s[53:54],
int(s[54:56]),
s[56:57],
spin2l,
s[61:62],
int(s[62:64]),
s[64:65],
spinl,
int(s[68:70]),
)
self.lines.append(line)
r += 1
ii += 1
if ii == _PROGRESS_INDICATOR_PERIOD:
a99.get_python_logger().info("Loading '{}': {}".format(
filename, a99.format_progress(r, num_lines)))
ii = 0
except Exception as e:
# f = type(e)(("Error around %d%s row of file '%s'" %
# (r + 1, a99.ordinal_suffix(r + 1), filename)) + ": " + str(
# e)).with_traceback(sys.exc_info()[2])
raise RuntimeError("Error around %d%s row of file '%s': \"%s\"" %
(r + 1, a99.ordinal_suffix(r + 1), filename,
a99.str_exc(e))) from e
def turbospectrum_to_atoms(file_obj):
"""
Converts data from a TurboSpectrum file into a FileAtoms object.
Args:
file_obj: file-like object, e.g., returned by open()
Returns: a FileAtoms object
"""
_logger = a99.get_python_logger()
def log_skipping(r, reason, row):
_logger.info("Skipping row #%d (%s)" % (r, reason))
_logger.info(str(row))
ret = pyfant.FileAtoms()
edict = {} # links atomic symbols with Atom objects created (key is atomic symbol + ionization)
r = 0 # number of current row
num_skip_ioni, num_skip_mol = 0, 0
state = _X_EL0
try:
for row in file_obj:
r += 1
if state < _X_LINE_OR_EL0:
if row[0] != "'":
raise ParseError("Expecting element specification, but found something else")
if state == _X_EL0:
#' 3.000 ' 1 110
#0123456
elem = _Symbols[int(row[1:3])]
ioni = int(row[4:7])+1
state = _X_EL1
elif state == _X_EL1:
state = _X_LINE_OR_EL0
elif state == _X_LINE_OR_EL0:
if row[0] == "'":
elem = _Symbols[int(row[1:3])]
ioni = int(row[4:7]) + 1
state = _X_EL1
else:
if ioni > 2:
# log_skipping(r, "ionization > 2", row)
num_skip_ioni += 1
continue
#'Li I '
# 4601.843 1.848 -5.804 2.50 6.0 5.01E+07 'p' 'f' 0.0 1.0 'Li I 2p 2P 4f 2F SEN '
#0 1 2 3
#01234567890123456789012345678901234567890
rr = row.split()
_waals = float(rr[3])
if _waals > 0:
_waals = 0
line = pyfant.AtomicLine()
line.lambda_ = float(rr[0])
line.kiex = float(rr[1])
line.algf = float(rr[2])
if _waals == 0:
line.ch = 0.3e-31
else:
try:
# Formula supplied by Elvis Cantelli:
# extracted from cross-entropy code by P. Barklem
line.ch = 10**(2.5*_waals-12.32)
except:
# Catches error to log _waals value that gave rise to error
_logger.critical("Error calculating ch: waals=%g" % _waals)
raise
# Setting gr to zero will cause PFANT to calculate it using a formula.
# See pfantlib.f90::read_atoms() for the formula.
line.gr = 0.0
# ge is not present in VALD3 file.
# it enters as a multiplicative term in popadelh(). The original
# atom4070g.dat and atoms.dat all had ge=0 for all lines.
line.ge = 0.0
# Attention: zinf must be tuned later using tune-zinf.py
line.zinf = 0.5
# Never used in PFANT
line.abondr = 1
key = f"{elem:2}{ioni:1}" # will group elements by this key
if key in edict:
a = edict[key]
else:
a = edict[key] = pyfant.Atom()
a.elem = pyfant.adjust_atomic_symbol(elem)
a.ioni = ioni
ret.atoms.append(a)
a.lines.append(line)
except Exception as e:
raise type(e)(("Error around %d%s row of TurboSpectrum file" %
(r, a99.ordinal_suffix(r)))+": "+str(e)).with_traceback(sys.exc_info()[2])
_logger.debug("VALD3-to-atoms conversion successful!")
_logger.info("Number of lines skipped (molecules): %d" % num_skip_mol)
_logger.info("Number of lines skipped (ioni > 2): %d" % num_skip_ioni)
_logger.debug("Number of (element+ioni): %s" % len(ret))
_logger.debug("Total number of atomic lines: %d" % (sum(len(a) for a in ret.atoms),))
return ret
def _do_load_h(self, h, filename):
r = 0 # counts rows of file
ii = 0
expr_branch = re.compile(
"[PQRS]\d*") # regular expression to find the branch
# states
EXP_SPECIES = 0 # expecting species definition
EXP_NAME = 1 # expecting name of species
EXP_ANY = 2
state = EXP_SPECIES
is_atom = None
species = None
flag_break = False
try:
while True:
s = h.readline().strip()
if len(s) == 0:
flag_break = True
if not flag_break:
if s[0] == "'":
if state == EXP_SPECIES or state == EXP_ANY:
# New species to come
# Determine whether atom or molecule
atnumber = int(s[1:s.index(".")])
is_atom = atnumber <= 92
state = EXP_NAME
elif EXP_NAME:
name = s.strip("'")
species = self.atoms[
name] if is_atom else self.molecules[name]
a99.get_python_logger().info(
"Loading '{}': species '{}'".format(
filename, name))
state = EXP_ANY
else:
if state != EXP_ANY:
raise RuntimeError("Not expecting line right now")
# It is a line
# Read 6 numeric values then something between quotes
line = PlezAtomicLine(
) if is_atom else PlezMolecularLine()
line.lambda_, line.chiex, line.loggf, line.gu, line.fdamp, line.raddmp = \
[float(x) for x in s[:s.index("'")].split()]
if not is_atom:
# Get the branch
tmp = s[s.index("'"):].strip("'").split()
_branch = tmp[0]
line.branch = expr_branch.search(_branch).group()
line.Jl = float(tmp[2])
line.vl = int(tmp[1])
line.v2l = int(tmp[6])
line.J2l = float(tmp[7])
species.lines.append(line)
if flag_break:
break
r += 1
ii += 1
if ii == _PROGRESS_INDICATOR_PERIOD:
# a99.get_python_logger().info(
# "Loading '{}': {}".format(filename, a99.format_progress(r, num_lines)))
ii = 0
except Exception as e:
raise RuntimeError("Error around %d%s row of file '%s': \"%s\"" %
(r + 1, a99.ordinal_suffix(r + 1), filename,
a99.str_exc(e))) from e
