def __init__(self, parent, filepath, **kwargs):
super(AbinitEventsPanel, self).__init__(parent, -1, **kwargs)
self.filepath = os.path.abspath(filepath)
parser = EventsParser()
self.events = events = parser.parse(self.filepath)
main_sizer = wx.BoxSizer(wx.VERTICAL)
vbox = wx.BoxSizer(wx.VERTICAL)
panel1 = awx.Panel(self, -1)
panel2 = awx.Panel(self, -1)
self.tree = tree = wx.TreeCtrl(panel1, 1, wx.DefaultPosition, (-1, -1),
wx.TR_HIDE_ROOT | wx.TR_HAS_BUTTONS)
root = self.tree.AddRoot('Events')
err_tree = tree.AppendItem(root, "%d Errors" % events.num_errors)
warn_tree = tree.AppendItem(root, "%d Warnings" % events.num_warnings)
com_tree = tree.AppendItem(root, "%d Comments" % events.num_comments)
for e in self.events.errors:
tree.AppendItem(err_tree,
"line: " + str(e.lineno),
data=wx.TreeItemData(e.message))
for w in self.events.warnings:
tree.AppendItem(warn_tree,
"line: " + str(w.lineno),
data=wx.TreeItemData(w.message))
for c in self.events.comments:
tree.AppendItem(com_tree,
"line: " + str(c.lineno),
data=wx.TreeItemData(c.message))
tree.Bind(wx.EVT_TREE_SEL_CHANGED, self.OnSelChanged, id=1)
self.display = wx.StaticText(panel2,
-1,
'', (10, 10),
style=wx.ALIGN_LEFT)
vbox.Add(self.tree, 1, wx.EXPAND)
main_sizer.Add(panel1, 1, wx.EXPAND)
main_sizer.Add(panel2, 1, wx.EXPAND)
panel1.SetSizerAndFit(vbox)
self.SetSizerAndFit(main_sizer)
self.Centre()
def read_mainlog_ewc(self):
"""
Read errors, warnings and comments from the main output and the log file.
:return: Two namedtuple instances: main, log.
The lists of strings with the corresponding messages are
available in main.errors, main.warnings, main.comments, log.errors etc.
"""
from pymatgen.io.abinit.events import EventsParser
parser = EventsParser()
main_events = parser.parse(self.last_output())
log_events = parser.parse(self.log_name)
return main_events, log_events
def read_mainlog_ewc(self):
"""
Read errors, warnings and comments from the main output and the log file.
:return: Two namedtuple instances: main, log.
The lists of strings with the corresponding messages are
available in main.errors, main.warnings, main.comments, log.errors etc.
"""
from pymatgen.io.abinit.events import EventsParser
parser = EventsParser()
main_events = parser.parse(self.last_output())
log_events = parser.parse(self.log_name)
return main_events, log_events
def events(self):
"""
List of ABINIT events reported in the file.
"""
# Parse the file the first time the property is accessed or when mtime is changed.
stat = os.stat(self.filepath)
if stat.st_mtime != self._last_mtime or not hasattr(self, "_events"):
self._events = EventsParser().parse(self.filepath)
return self._events
def __init__(self, parent, filepath, **kwargs):
super(AbinitEventsPanel, self).__init__(parent, -1, **kwargs)
self.filepath = os.path.abspath(filepath)
parser = EventsParser()
self.events = events = parser.parse(self.filepath)
main_sizer = wx.BoxSizer(wx.VERTICAL)
vbox = wx.BoxSizer(wx.VERTICAL)
panel1 = awx.Panel(self, -1)
panel2 = awx.Panel(self, -1)
self.tree = tree = wx.TreeCtrl(panel1, 1, wx.DefaultPosition, (-1, -1), wx.TR_HIDE_ROOT | wx.TR_HAS_BUTTONS)
root = self.tree.AddRoot('Events')
err_tree = tree.AppendItem(root, "%d Errors" % events.num_errors)
warn_tree = tree.AppendItem(root, "%d Warnings" % events.num_warnings)
com_tree = tree.AppendItem(root, "%d Comments" % events.num_comments)
for e in self.events.errors:
tree.AppendItem(err_tree, "line: " + str(e.lineno), data=wx.TreeItemData(e.message))
for w in self.events.warnings:
tree.AppendItem(warn_tree, "line: " + str(w.lineno), data=wx.TreeItemData(w.message))
for c in self.events.comments:
tree.AppendItem(com_tree, "line: " + str(c.lineno), data=wx.TreeItemData(c.message))
tree.Bind(wx.EVT_TREE_SEL_CHANGED, self.OnSelChanged, id=1)
self.display = wx.StaticText(panel2, -1, '', (10, 10), style=wx.ALIGN_LEFT)
vbox.Add(self.tree, 1, wx.EXPAND)
main_sizer.Add(panel1, 1, wx.EXPAND)
main_sizer.Add(panel2, 1, wx.EXPAND)
panel1.SetSizerAndFit(vbox)
self.SetSizerAndFit(main_sizer)
self.Centre()
def main():
def str_examples():
examples = """\
Usage example:
abiinsp.py OUTFILE status ==> Report the list of Warning, Commments, Errors
abiinsp.py OUTFILE plot ==> Plot results of the GS Scf cycle, Phonon Scf cycle...
abiinsp.py OUTFILE timer ==> Visualize timing data with matplotlib.
"""
return examples
def show_examples_and_exit(err_msg=None, error_code=1):
"""Display the usage of the script."""
sys.stderr.write(str_examples())
if err_msg: sys.stderr.write("Fatal Error\n" + err_msg + "\n")
sys.exit(error_code)
parser = argparse.ArgumentParser(epilog=str_examples(), formatter_class=argparse.RawDescriptionHelpFormatter)
parser.add_argument('-V', '--version', action='version', version="%(prog)s version " + abilab.__version__)
parser.add_argument('--loglevel', default="ERROR", type=str,
help="set the loglevel. Possible values: CRITICAL, ERROR (default), WARNING, INFO, DEBUG")
parser.add_argument('filepath', nargs="?", help="File to inspect (output file or log file)")
# Create the parsers for the sub-commands
subparsers = parser.add_subparsers(dest='command', help='sub-command help', description="Valid subcommands")
# Subparser for status command.
p_status = subparsers.add_parser('status', help="Check the status of the run (errors, warning, completion)")
#p_status.add_argument('format', nargs="?", default="cif", type=str, help="Format of the output file (ciff, POSCAR, json).")
# Subparser for plot command.
p_plot = subparsers.add_parser('plot', help="Plot data")
#p_plot.add_argument('visualizer', nargs="?", default="xcrysden", type=str, help="Visualizer.")
p_timer = subparsers.add_parser('timer', help="Show timing data.")
p_pseudo = subparsers.add_parser('pseudo', help="Show info on pseudopotential file.")
# Parse command line.
try:
options = parser.parse_args()
except Exception:
show_examples_and_exit(error_code=1)
# loglevel is bound to the string value obtained from the command line argument.
# Convert to upper case to allow the user to specify --loglevel=DEBUG or --loglevel=debug
import logging
numeric_level = getattr(logging, options.loglevel.upper(), None)
if not isinstance(numeric_level, int):
raise ValueError('Invalid log level: %s' % options.loglevel)
logging.basicConfig(level=numeric_level)
if options.command == "status":
# Parse the Abinit Events in filepath.
parser = EventsParser()
report = parser.parse(options.filepath)
print(report)
elif options.command == "plot":
# TODO: At present only GS runs are supported by plottable_from_outfile
obj = plottable_from_outfile(options.filepath)
if obj is not None:
obj.plot()
else:
raise ValueError("Don't know how to extract plottable data from %s" % options.filepath)
elif options.command == "timer":
parser = abilab.AbinitTimerParser()
parser.parse(options.filepath)
elif options.command == "pseudo":
from pymatgen.io.abinit.pseudos import PseudoParser
pseudo = PseudoParser().parse(options.filepath)
print(pseudo)
else:
raise ValueError("Unsupported command %s" % options.command)
return 0
def main():
def str_examples():
examples = """
Usage example:\n
abiinsp.py OUTFILE status ==> Report the list of Warning, Commments, Errors
abiinsp.py OUTFILE plot ==> Plot results of the GS Scf cycle, Phonon Scf cycle...
abiinsp.py OUTFILE timer ==> Visualize timing data with matplotlib.
"""
return examples
def show_examples_and_exit(err_msg=None, error_code=1):
"""Display the usage of the script."""
sys.stderr.write(str_examples())
if err_msg: sys.stderr.write("Fatal Error\n" + err_msg + "\n")
sys.exit(error_code)
parser = argparse.ArgumentParser(epilog=str_examples(), formatter_class=argparse.RawDescriptionHelpFormatter)
parser.add_argument('filepath', nargs="?", help="File to inspect (output file or log file)")
# Create the parsers for the sub-commands
subparsers = parser.add_subparsers(dest='command', help='sub-command help', description="Valid subcommands")
# Subparser for status command.
p_status = subparsers.add_parser('status', help="Check the status of the run (errors, warning, completion)")
#p_status.add_argument('format', nargs="?", default="cif", type=str, help="Format of the output file (ciff, POSCAR, json).")
# Subparser for plot command.
p_plot = subparsers.add_parser('plot', help="Plot data")
#p_plot.add_argument('visualizer', nargs="?", default="xcrysden", type=str, help="Visualizer.")
subparsers.add_parser('timer', help="Show timing data.")
subparsers.add_parser('pseudo', help="Show info on pseudopotential file.")
# Parse command line.
try:
options = parser.parse_args()
except Exception:
show_examples_and_exit(error_code=1)
if options.command == "status":
# Parse the Abinit Events in filepath.
parser = EventsParser()
report = parser.parse(options.filepath)
print(report)
elif options.command == "plot":
# TODO: At present only GS runs are supported by plottable_from_outfile
obj = plottable_from_outfile(options.filepath)
if obj is not None:
obj.plot()
else:
raise ValueError("Don't know how to extract plottable data from %s" % options.filepath)
elif options.command == "timer":
parser = AbinitTimerParser()
parser.parse(options.filepath)
#parser.plot_pie(key="wall_time", minfract=0.05)
#parser.plot_efficiency),
#parser.plot_stacked_hist),
elif options.command == "pseudo":
from pymatgen.io.abinit.pseudos import PseudoParser
pseudo = PseudoParser().parse(options.filepath)
print(pseudo)
else:
raise ValueError("Unsupported command %s" % options.command)
return 0
