def main():
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.")
p_timer = subparsers.add_parser('timer', help="Show timing data.")
# Parse command line.
try:
options = parser.parse_args()
except:
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.show_pie(key="wall_time", minfract=0.05)
else:
raise ValueError("Unsupported command %s" % options.command)
return 0
def analyze_data(self, *args, **kwargs):
"""Analyze the collected data."""
# List of SIGRES files computed with different values of nband.
show = kwargs.get("show", True)
from pymatgen.io.abinitio.tasks import Task
from pymatgen.io.abinitio.abiinspect import plottable_from_outfile
out_files = self.all_outfiles(status=Task.S_RUN, op=">=")
figs = []
for out in out_files:
obj = plottable_from_outfile(out)
if obj is not None:
figs.append(obj.plot(title=os.path.relpath(out), show=show))
return figs
def main():
# Decorate argparse classes to add portable support for aliases in add_subparsers
class MyArgumentParser(argparse.ArgumentParser):
def add_subparsers(self, **kwargs):
new = super(MyArgumentParser, self).add_subparsers(**kwargs)
# Use my class
new.__class__ = MySubParserAction
return new
class MySubParserAction(argparse._SubParsersAction):
def add_parser(self, name, **kwargs):
"""Allows one to pass the aliases option even if this version of ArgumentParser does not support it."""
try:
return super(MySubParserAction, self).add_parser(name, **kwargs)
except Exception as exc:
if "aliases" in kwargs:
# Remove aliases and try again.
kwargs.pop("aliases")
return super(MySubParserAction, self).add_parser(name, **kwargs)
else:
# Wrong call.
raise exc
parser = MyArgumentParser(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", aliases=["s", "stat"], 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", aliases=["p"], help="Plot data")
# p_plot.add_argument('visualizer', nargs="?", default="xcrysden", type=str, help="Visualizer.")
subparsers.add_parser("timer", aliases=["t"], help="Show timing data.")
subparsers.add_parser("pseudo", help="Show info on pseudopotential file.")
# Parse command line.
try:
options = parser.parse_args()
except:
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.show_pie(key="wall_time", minfract=0.05)
# parser.show_efficiency),
# parser.show_stacked_hist),
elif options.command == "pseudo":
from pymatgen.io.abinitio.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:
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.show_pie(key="wall_time", minfract=0.05)
#parser.show_efficiency),
#parser.show_stacked_hist),
elif options.command == "pseudo":
from pymatgen.io.abinitio.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:
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.show_pie(key="wall_time", minfract=0.05)
#parser.show_efficiency),
#parser.show_stacked_hist),
elif options.command == "pseudo":
from pymatgen.io.abinitio.pseudos import PseudoParser
pseudo = PseudoParser().parse(options.filepath)
print(pseudo)
else:
raise ValueError("Unsupported command %s" % options.command)
return 0
