def test_Molecule():
m = pyfant.Molecule()
sol = pyfant.SetOfLines()
sol.append_line(2000., .25, 10.5, "P")
sol.append_line(1000., .25, 10.5, "Q1")
m.sol = [sol]
assert m.llzero == 1000.
assert m.llfin == 2000.
assert m.num_lines == 2
sol = pyfant.SetOfLines()
sol.append_line(3000., .125, 13.5, "R21")
m.sol.append(sol)
assert len(m) == 2
assert m.num_lines == 3
assert all(m.lmbdam == [2000., 1000., 3000.])
assert all(m.sj == [.25, .25, .125])
assert all(m.jj == [10.5, 10.5, 13.5])
assert all(m.branch == ["P", "Q1", "R21"])
m.qqv
m.ggv
m.bbv
m.ddv
m.cut(500, 1500)
assert m.num_lines == 1
def test_FileMolecules(tmpdir):
os.chdir(str(tmpdir))
m = pyfant.Molecule()
sol = pyfant.SetOfLines()
sol.append_line(2000., .25, 10.5, "P")
sol.append_line(1000., .25, 10.5, "Q1")
m.sol = [sol]
sol = pyfant.SetOfLines()
sol.append_line(3000., .125, 13.5, "R21")
m.sol.append(sol)
f = pyfant.FileMolecules()
f.molecules = [m]
assert f.llzero == 1000.
assert f.llfin == 3000.
assert f.num_lines == 3
assert f.num_sols == 2
f.lmbdam
f.sj
f.jj
f.branch
f.qqv
f.ggv
f.bbv
f.ddv
f.fe
f.do
f.mm
f.am
f.ua
f.ub
f.te
f.cro
f.s
f.cut(500, 1500)
assert f.num_lines == 1
assert f.num_sols == 1
m.symbols = ["We", "Ur"]
assert m.formula == "WeUr"
f.save_as("qq")
def append_line(self, line, gf_pfant, branch):
"""Use to append line to object"""
sol_key = (line.vl, line.v2l)
if sol_key not in self:
qgbd = self.qgbd_calculator(self.molconsts, line.v2l)
self[sol_key] = pyfant.SetOfLines(line.vl, line.v2l,
qgbd["qv"], qgbd["gv"], qgbd["bv"], qgbd["dv"], 1.)
self[sol_key].append_line(line.lambda_, gf_pfant, line.J2l, branch)
def test_SetOfLines():
sol = pyfant.SetOfLines()
sol.append_line(2000., .25, 10.5, "P")
sol.append_line(1000., .25, 10.5, "Q1")
assert sol.llzero == 1000.
assert sol.llfin == 2000.
assert sol.num_lines == 2
assert len(sol) == 2
assert sol.lmbdam[0] == 2000.
sol.sort()
assert sol.lmbdam[0] == 1000.
sol.cut(500, 1500)
assert sol.llzero == 1000.
assert sol.llfin == 1000.
assert sol.num_lines == 1
assert len(sol) == 1
sol.sort()
def hitran_to_sols(molconsts, lines, 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',
'pfantmol', and 'system' from a FileMolDB database
lines: item from rom hapi.LOCAL_TABLE_CACHE (a dictionary)
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
header = lines["header"]
data = lines["data"]
S = molconsts.get_S2l()
DELTAK = molconsts.get_deltak()
formula = molconsts["formula"]
n = header["number_of_rows"]
log = MolConversionLog(n)
sols = OrderedDict() # one item per (vl, v2l) pair
try:
f_class = _CLASS_DICT[formula]
except KeyError:
log.errors.append(
"Cannot determine Table 3 'class' (Rothman et al. 2005) for formula '{}'"
.format(formula))
log.flag_ok = False
try:
f_group = _GROUP_DICT[formula]
except KeyError:
log.errors.append(
"Cannot determine Table 4 'group' (Rothman et al. 2005) for formula '{}'"
.format(formula))
log.flag_ok = False
if not log.flag_ok:
return [], log
for i in range(n):
try:
nu = data["nu"][i]
wl = avv.vacuum_to_air(1e8 / nu)
Br, J2l = f_group(data["local_lower_quanta"][i])
# TODO assuming singlet!!!
Jl = ph.singlet.quanta_to_branch(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 * 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)
J2l_pfant = int(
J2l
) # ojo, estamos colocando J2L-0.5! TODO ask BLB: we write J2l or J2l-.5? (20171114 I think this is wrong, molecules.dat has decimal values)
except Exception as e:
log.errors.append("#{}{} line: {}".format(
i + 1, a99.ordinal_suffix(i + 1), a99.str_exc(e)))
continue
sol_key = (V, V_) # (v', v'') transition (v_sup, v_inf)
if sol_key not in sols:
qgbd = qgbd_calculator(molconsts, sol_key[1])
qqv = qgbd["qv"]
ggv = qgbd["gv"]
bbv = qgbd["bv"]
ddv = qgbd["dv"]
sols[sol_key] = pyfant.SetOfLines(V, V_, qqv, ggv, bbv, ddv, 1.)
sol = sols[sol_key]
sol.append_line(wl, gf, J2l_pfant, Br)
return (list(sols.values()), log)