def abiview_ddb_ifc(options):
"""
Visualize interatomic force constants in real space.
"""
asr = 2
chneut = 1
dipdip = 1
print("""
Computing interatomic force constants with
asr = {asr}, chneut = {chneut}, dipdip = {dipdip}
""".format(**locals()))
with abilab.abiopen(options.filepath) as ddb:
# Execute anaddb to compute the interatomic force constants.
ifc = ddb.anaget_ifc(asr=asr, chneut=chneut, dipdip=dipdip)
#print(ifc)
with MplExpose(slide_mode=options.slide_mode,
slide_timeout=options.slide_timeout) as e:
e(ifc.plot_longitudinal_ifc(title="Longitudinal IFCs", show=False))
e(
ifc.plot_longitudinal_ifc_short_range(
title="Longitudinal IFCs short range", show=False))
e(
ifc.plot_longitudinal_ifc_ewald(
title="Longitudinal IFCs Ewald", show=False))
return 0
def expose(self, slide_mode=False, slide_timeout=None, **kwargs):
"""
Shows a predefined list of matplotlib figures with minimal input from the user.
"""
from abipy.tools.plotting import MplExpose
with MplExpose(slide_mode=slide_mode, slide_timeout=slide_mode, verbose=1) as e:
e(self.yield_figs(**kwargs))
def abiview_ddb(options):
"""
Invoke Anaddb to compute phonon bands and DOS from the DDB, plot the results.
"""
with abilab.abiopen(options.filepath) as ddb:
print(ddb.to_string(verbose=options.verbose))
# Don't need PHDOS if phononwebsite
nqsmall = 0 if options.phononwebsite else 10
ndivsm = 20; asr = 2; chneut = 1; dipdip = 1; dos_method = "tetra"; lo_to_splitting = "automatic"
print("""
Computing phonon bands and DOS from DDB file with:
nqsmall: {nqsmall}, ndivsm: {ndivsm},
asr: {asr}, chneut: {chneut}, dipdip: {dipdip}, lo_to_splitting: {lo_to_splitting}, dos_method: {dos_method}
""".format(**locals()))
print("Invoking anaddb ... ", end="")
phbst_file, phdos_file = ddb.anaget_phbst_and_phdos_files(
nqsmall=nqsmall, ndivsm=ndivsm, asr=asr, chneut=chneut, dipdip=dipdip, dos_method=dos_method,
lo_to_splitting=lo_to_splitting, verbose=options.verbose, mpi_procs=1)
print("Calculation completed.\nResults available in:", os.path.dirname(phbst_file.filepath))
phbands = phbst_file.phbands
if options.xmgrace:
outpath = options.filepath + ".agr"
phbands.to_xmgrace(handle_overwrite(outpath, options))
return 0
#elif options.bxsf:
# outpath = options.filepath + ".bxsf"
# phbands.to_bxsf(handle_overwrite(outpath, options))
# return 0
elif options.phononwebsite:
return phbands.view_phononwebsite(browser=options.browser, verbose=options.verbose)
else:
phdos = phdos_file.phdos
units = "mev"
with MplExpose(slide_mode=options.slide_mode, slide_timeout=options.slide_timeout) as e:
#e(phbst_file.expose())
#e(phdos_file.expose())
e(phbands.qpoints.plot(show=False))
e(phbands.plot_with_phdos(phdos, units=units, show=False))
e(phbands.plot_colored_matched(units=units, show=False))
e(phbands.plot_fatbands(units=units, phdos_file=phdos_file, show=False))
e(phdos.plot(units=units, show=False))
e(phdos_file.plot_pjdos_type(units=units, show=False))
#try
# msq_dos = phdos_file.msq_dos
#except RuntimeError:
# msq_dos = None
#if msq_dos is not None:
# e(msq_dos.plot_uiso(show=False))
# e(msq_dos.plot_uiso(show=False))
phbst_file.close()
phdos_file.close()
return 0
def plot(self, tight_layout=True, with_timer=False, show=True):
"""
Plot GS/DFPT SCF cycles and timer data found in the output file.
Args:
with_timer: True if timer section should be plotted
"""
from abipy.tools.plotting import MplExpose
with MplExpose(slide_mode=False, slide_timeout=5.0) as e:
e(self.yield_figs(tight_layout=tight_layout, with_timer=with_timer))
def main():
def show_examples_and_exit(err_msg=None, error_code=1):
"""Display the usage of the script."""
sys.stderr.write(get_epilog())
if err_msg:
sys.stderr.write("Fatal Error\n" + err_msg + "\n")
sys.exit(error_code)
parser = get_parser(with_epilog=True)
# Parse the 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.verbose > 2:
print(options)
if options.mpl_backend is not None:
# Set matplotlib backend
import matplotlib
matplotlib.use(options.mpl_backend)
if options.seaborn:
# Use seaborn settings.
import seaborn as sns
sns.set(context=options.seaborn,
style='darkgrid',
palette='deep',
font='sans-serif',
font_scale=1,
color_codes=False,
rc=None)
if not os.path.exists(options.filepath):
raise RuntimeError("%s: no such file" % options.filepath)
if not options.notebook:
abifile = abilab.abiopen(options.filepath)
if options.print:
# Print object to terminal.
if hasattr(abifile, "to_string"):
print(abifile.to_string(verbose=options.verbose))
else:
print(abifile)
return 0
elif options.expose:
# Generate matplotlib plots automatically.
if hasattr(abifile, "to_string"):
print(abifile.to_string(verbose=options.verbose))
else:
print(abifile)
if hasattr(abifile, "expose"):
abifile.expose(slide_mode=options.slide_mode,
slide_timeout=options.slide_timeout,
verbose=options.verbose)
else:
if not hasattr(abifile, "yield_figs"):
raise TypeError(
"Object of type `%s` does not implement (expose or yield_figs methods"
% type(abifile))
from abipy.tools.plotting import MplExpose
with MplExpose(slide_mode=options.slide_mode,
slide_timeout=options.slide_timeout,
verbose=options.verbose) as e:
e(abifile.yield_figs())
return 0
# Start ipython shell with namespace
# Use embed because I don't know how to show a header with start_ipython.
import IPython
IPython.embed(
header=
"The Abinit file is bound to the `abifile` variable.\nTry `print(abifile)`"
)
else:
# Call specialized method if the object is a NotebookWriter
# else generate simple notebook by calling `make_and_open_notebook`
cls = abilab.abifile_subclass_from_filename(options.filepath)
if hasattr(cls, "make_and_open_notebook"):
if hasattr(cls, "__exit__"):
with abilab.abiopen(options.filepath) as abifile:
return abifile.make_and_open_notebook(
foreground=options.foreground)
else:
abifile = abilab.abiopen(options.filepath)
return abifile.make_and_open_notebook(
foreground=options.foreground)
else:
return make_and_open_notebook(options)
return 0
