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_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 _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
combo.conf.opt.pas = PAS
combo.conf.flag_output_to_dir = True
combo.conf.opt.zinf = args.max
combo.conf.opt.no_molecules = True
combo.conf.opt.opa = False
combo.conf.opt.no_h = True
# Note that half of the line (needs to)/(will be) calculated
combo.conf.opt.llzero = line.lambda_ - args.max
combo.conf.opt.llfin = line.lambda_
combos.append(combo)
ll.append(a)
i += 1
ii += 1
if ii == 1000:
print(a99.format_progress(i, n))
ii = 0
# # Runs pfant
logger.info("Running pfant's...")
# FLAG_CLEAN = True
# rm = RunnableManager(flag_auto_clean=FLAG_CLEAN)
rm = pyfant.RunnableManager()
rm.add_runnables(combos)
app = a99.get_QApplication([])
form = pyfant.XRunnableManager(None, rm)
form.show()
# it is good to start the manager as late as possible, otherwise
# the program will hang if, for example, the form fails to be created.