def _convert_clicked(self):
self.add_log("===BEGIN===")
try:
errors = self._validate()
if len(errors) == 0:
conv, errors = self._get_conv(errors)
if len(errors) == 0:
lines = self._get_lines()
if lines is None:
errors.append("Molecular lines not specified")
if len(errors) == 0:
fobj, log = conv.make_file_molecules(lines)
self._report_conversion(fobj, log)
if log.flag_ok:
fobj.save_as(self.w_out.value)
self.add_log("File '{}' generated successfully".format(
self.w_out.value))
else:
self.add_log_error(
"Cannot convert:\n - " + ("\n - ".join(errors)), True)
except Exception as e:
a99.get_python_logger().exception("Conversion failed")
self.add_log_error("Conversion failed: {}".format(a99.str_exc(e)),
True)
self.add_log("===END===")
def _populate(self):
self._flag_populating = True
try:
f = self._f = pyfant.FileVald3()
f.load(self.w_file.value)
nr, nc = len(f), 3
t = self.tableWidget
a99.reset_table_widget(t, nr, nc)
t.setHorizontalHeaderLabels(
["VALD3 species", "Number of spectral lines", "Atom/Molecule"])
for i, species in enumerate(f):
item = QTableWidgetItem(str(species))
t.setItem(i, 0, item)
item = QTableWidgetItem(str(len(species)))
t.setItem(i, 1, item)
item = QTableWidgetItem("Atom" if species.formula in
pyfant.symbols else "Molecule")
t.setItem(i, 2, item)
t.resizeColumnsToContents()
except Exception as e:
self._f = None
self.add_log_error(
"Error reading contents of file '{}': '{}'".format(
self.w_file.value, a99.str_exc(e)), True)
raise
else:
self.clear_log()
finally:
self._flag_populating = False
def _calculate(self):
flag_fcf = self.checkbox_fcf.isChecked()
if flag_fcf:
if self.fcfs is None or len(self.fcfs) == 0:
self.add_log_error("FCFs not available", True)
try:
l_text = []
self.status("Calculating...")
molconsts = copy.deepcopy(self.molconsts)
molconsts.None_to_zero()
for vl in range(10):
for v2l in range(10):
l_text.extend(
a99.format_box("vl, v2l = ({}, {})".format(vl, v2l)))
factor = 1.
if flag_fcf:
try:
factor = self.fcfs[(vl, v2l)]
except KeyError:
l_text.append("Franck-Condon Factor not available")
continue
rows, header = [], None
for J in range(40):
mtools = pyfant.kovacs_toolbox(molconsts,
flag_normalize=True)
mtools.populate(vl, v2l, J)
if header is None:
branches = [key[3] for key in mtools.dict_sj]
header = ["J"] + branches + ["Sum"]
vv = mtools.dict_sj.values()
total = sum([
x * factor for x in vv
if x != pyfant.NO_LINE_STRENGTH
])
rows.append([J + .5] + [
"{:.5e}".format(x * factor)
if x != pyfant.NO_LINE_STRENGTH else "-"
for x in vv
] + ["{:.9g}".format(total)])
l_text.append(tabulate.tabulate(rows, header))
l_text.append("")
text = "\n".join(l_text)
self.textEdit.setPlainText(text)
self.status("")
except Exception as E:
self.add_log_error(a99.str_exc(E), True)
a99.get_python_logger().exception("Error calculating HLF")
def _on_run_traprb(self):
if self._id_system is None:
return
row = self._f.get_conn().execute("select * from system where id = ?",
(self._id_system, )).fetchone()
string = pyfant.molconsts_to_system_str(row, SYSTEMSTYLE)
n = len(self._data)
beware = "" if n == 0 else \
"\n\n**Attention**: {} existing FCF{} for this system will be deleted!".\
format(n, "" if n == 1 else "s")
msg = "TRAPRB will be executed to calculate the Franck-Condon factors for system '{}'." \
"{}\n\nDo you wish to continue?".format(string, beware)
r = QMessageBox.question(self, "Calculate FCFs", msg,
QMessageBox.Yes | QMessageBox.No,
QMessageBox.Yes if n == 0 else QMessageBox.No)
if r == QMessageBox.Yes:
r, form = self._show_traprb_parameters_form(r)
if r == QDialog.Accepted:
kwargs = form.get_kwargs()
mc = pyfant.MolConsts()
try:
mc.populate_all_using_system_row(self._f, row)
# TODO maybe intermediate review stage, i.e., allow the user to see the FCFs before inserting
traprb = pyfant.run_traprb(mc, None, None, **kwargs)
traprb.load_result()
output = traprb.result["output"]
pyfant.insert_fcfs(self._f,
self._id_system,
output.fcfs,
flag_replace=True)
self._populate()
n = len(output.fcfs)
self.add_log(
"{} FCF{} successfully inserted".format(
n, "" if n == 1 else "s"), True)
except Exception as e:
self.add_log_error(
"Error calculating FCFs: '{}'".format(a99.str_exc(e)),
True, e)
def _calculate(self):
f = pyfant.FileTRAPRBInput()
try:
f.from_molconsts(self.molconsts, maxv=self.spinBox_vmax.value())
except Exception as e:
self.add_log_error(
"Could not generate TRAPRB input: {}".format(a99.str_exc(e)),
True, e)
else:
text = f.dumps()
self.textEdit.setPlainText(text)
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 _file_changed(self):
f = None
try:
f = self._load_lines()
except Exception as e:
self._flines = None
self._speciess = []
msg = "Error reading contents of file '{}': '{}'".format(
self.w_file.value, a99.str_exc(e))
self.add_log_error(msg, True)
a99.get_python_logger().exception(msg)
# Tries to restore iso without much compromise
self._set_species(self.w_conv.f.obj["species"])
self.w_conv.f.obj["species"] = self._get_species()
self.w_file.flag_valid = f is not None
self.changed.emit()
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
import a99
import logging
# Tests importing packages robobrowser and bs4, requirements for downloaders
flag_ok = True
try:
from robobrowser import RoboBrowser
del RoboBrowser
except ImportError as e:
flag_ok = False
logging.warning("failed to import package robobrowser.Robobrowser: '{}', "
"f311.filetypes.downloaders will not be available".format(
a99.str_exc(e)))
if flag_ok:
try:
import bs4
del bs4
except ImportError as e:
flag_ok = False
logging.warning(
"failed to import package bs4 (Beautiful Soup 4): '{}', "
"f311.filetypes.downloaders will not be available".format(
a99.str_exc(e)))
del a99, logging
if flag_ok:
from .downhitran import *
from .downnist import *
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 _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