def to_string(self, verbose=0):
"""
Human-readable string with useful information on the object.
Args:
verbose: Verbosity level.
"""
lines = []; app = lines.append
app(self.structure.to_string(verbose=verbose, title="Structure"))
app("")
app(marquee(r"Fullfilment of \int dw g_ij(w) = \delta_ij", mark="="))
app("")
from scipy.integrate import simps
for iatom, site in enumerate(self.structure):
d = simps(self.values[iatom], x=self.wmesh)
app("For site: %s" % site)
app(str(d))
app("Trace: %.4f, determinant: %.4f" % (d.trace(), np.linalg.det(d)))
app("")
for fmt in ("cartesian", "cif"):
df = self.get_dataframe(temp=300, view="inequivalent", fmt=fmt, verbose=verbose)
s = print_dataframe(df, title="Format: %s" % fmt, file="string")
lines.extend(s.splitlines())
title = marquee("Constraints on tensor components in reduced coords induced by site symmetries", mark="=")
s = print_dataframe(self.structure.site_symmetries.get_tensor_rank2_dataframe(), file="string", title=title)
lines.extend(s.splitlines())
#if verbose > 1:
#max_err = self.check_site_symmetries(verbose=verbose)
return "\n".join(lines)
def print_results(self, fmt="abivars", verbose=0, file=sys.stdout):
"""
Print pandas dataframe, structures using format `fmt`, and data to file `file`.
`fmt` is automaticall set to `cif` if structure is disordered.
Set fmt to None or empty string to disable structure output.
"""
print("\n# Found %s structures in %s database (use `verbose` to get further info)\n"
% (len(self.structures), self.dbname), file=file)
if self.dataframe is not None: print_dataframe(self.dataframe, file=file)
if verbose and self.data is not None: pprint(self.data, stream=file)
# Print structures
print_structures = not (fmt is None or str(fmt) == "None")
if print_structures:
for i, structure in enumerate(self.structures):
print(" ", file=file)
print(marquee("%s input for %s" % (fmt, self.ids[i]), mark="#"), file=file)
print("# " + structure.spget_summary(verbose=verbose).replace("\n", "\n# ") + "\n", file=file)
if not structure.is_ordered:
print(structure.convert(fmt="cif"), file=file)
else:
print(structure.convert(fmt=fmt), file=file)
print(2 * "\n", file=file)
if len(self.structures) > 10:
# Print info again
print("\n# Found %s structures in %s database (use `verbose` to get further info)\n"
% (len(self.structures), self.dbname), file=file)
def print_results(self, fmt="abivars", verbose=0, file=sys.stdout):
"""
Print pandas dataframe, structures using format `fmt`, and data to file `file`.
`fmt` is automaticall set to `cif` if structure is disordered.
Set fmt to None or empty string to disable structure output.
"""
print("\n# Found %s structures in %s database (use `verbose` to get further info)\n"
% (len(self.structures), self.dbname), file=file)
if self.dataframe is not None: print_dataframe(self.dataframe, file=file)
if verbose and self.data is not None: pprint(self.data, stream=file)
# Print structures
print_structures = not (fmt is None or str(fmt) == "None")
if print_structures:
for i, structure in enumerate(self.structures):
print(" ", file=file)
print(marquee("%s input for %s" % (fmt, self.ids[i]), mark="#"), file=file)
print("# " + structure.spget_summary(verbose=verbose).replace("\n", "\n# ") + "\n", file=file)
if not structure.is_ordered:
print(structure.convert(fmt="cif"), file=file)
else:
print(structure.convert(fmt=fmt), file=file)
print(2 * "\n", file=file)
if len(self.structures) > 10:
# Print info again
print("\n# Found %s structures in %s database (use `verbose` to get further info)\n"
% (len(self.structures), self.dbname), file=file)
def summarize(self, acc=4):
self._consistency_check()
for segment in self.segments:
df = segment.get_dataframe_with_accuracies(acc_list=[acc])
title = "k: %s, spin: %s, nbands: %d" % (repr(
segment.k0), segment.spin, segment.nb)
#label="direction: %s" % segment.kdir.tos(m="fracart") if ib == 0 else None)
print_dataframe(df, title=title)
def to_string(self, verbose=0):
"""String representation."""
lines = [
"ndtset: %d, completed: %s" % (self.ndtset, self.run_completed)
]
app = lines.append
# Different cases depending whether final structures are available
# and whether structures are equivalent.
if self.run_completed:
if self.has_same_final_structures:
if self.initial_structure != self.final_structure:
# Structural relaxation.
df = dataframes_from_structures(
[self.initial_structure, self.final_structure],
index=["initial", "final"])
app("Lattice parameters:")
app(str(df.lattice))
app("Atomic coordinates:")
app(str(df.coords))
else:
# initial == final. Print final structure.
app(self.final_structure.to_string(verbose=verbose))
else:
# Final structures are not available.
if self.has_same_initial_structures:
app(self.initial_structure.to_string(verbose=verbose))
else:
df = dataframes_from_structures(
self.initial_structures,
index=[i + 1 for i in range(self.ndtset)])
app("Lattice parameters:")
app(str(df.lattice))
app("Atomic coordinates:")
app(str(df.coords))
# Print dataframe with dimensions.
dims_dataset, spginfo_dataset = self.get_dims_spginfo_dataset(
verbose=verbose)
rows = []
for dtind, dims in dims_dataset.items():
d = OrderedDict()
d["dataset"] = dtind
d.update(dims)
d.update(spginfo_dataset[dtind])
rows.append(d)
from abipy.tools.printing import print_dataframe
df = pd.DataFrame(rows, columns=list(rows[0].keys()) if rows else None)
df = df.set_index('dataset')
strio = cStringIO()
print_dataframe(df, file=strio)
strio.seek(0)
app("")
app(marquee("Dimensions of calculation", mark="="))
app("".join(strio))
return "\n".join(lines)
def to_string(self, verbose=0):
"""String representation."""
lines = ["ndtset: %d, completed: %s" % (self.ndtset, self.run_completed)]
app = lines.append
# Different cases depending whether final structures are available
# and whether structures are equivalent.
if self.run_completed:
if self.has_same_final_structures:
if self.initial_structure != self.final_structure:
# Structural relaxation.
df = dataframes_from_structures([self.initial_structure, self.final_structure],
index=["initial", "final"])
app("Lattice parameters:")
app(str(df.lattice))
app("Atomic coordinates:")
app(str(df.coords))
else:
# initial == final. Print final structure.
app(self.final_structure.to_string(verbose=verbose))
else:
# Final structures are not available.
if self.has_same_initial_structures:
app(self.initial_structure.to_string(verbose=verbose))
else:
df = dataframes_from_structures(self.initial_structures,
index=[i+1 for i in range(self.ndtset)])
app("Lattice parameters:")
app(str(df.lattice))
app("Atomic coordinates:")
app(str(df.coords))
# Print dataframe with dimensions.
dims_dataset, spginfo_dataset = self.get_dims_spginfo_dataset(verbose=verbose)
rows = []
for dtind, dims in dims_dataset.items():
d = OrderedDict()
d["dataset"] = dtind
d.update(dims)
d.update(spginfo_dataset[dtind])
rows.append(d)
from abipy.tools.printing import print_dataframe
df = pd.DataFrame(rows, columns=list(rows[0].keys()) if rows else None)
df = df.set_index('dataset')
strio = cStringIO()
print_dataframe(df, file=strio)
strio.seek(0)
app("")
app(marquee("Dimensions of calculation", mark="="))
app("".join(strio))
return "\n".join(lines)
def to_string(self, verbose=0):
"""String representation."""
lines = [
"ndtset: %d, completed: %s" % (self.ndtset, self.run_completed)
]
app = lines.append
# Different cases depending whether final structures are available
# and whether structures are equivalent.
if self.run_completed:
if self.has_same_final_structures:
if self.initial_structure != self.final_structure:
# Structural relaxation.
df = dataframes_from_structures(
[self.initial_structure, self.final_structure],
index=["initial", "final"])
app("Lattice parameters:")
app(str(df.lattice))
app("Atomic coordinates:")
app(str(df.coords))
else:
# initial == final. Print final structure.
app(self.final_structure.to_string(verbose=verbose))
else:
# Final structures are not available.
if self.has_same_initial_structures:
app(self.initial_structure.to_string(verbose=verbose))
else:
df = dataframes_from_structures(
self.initial_structures,
index=[i + 1 for i in range(self.ndtset)])
app("Lattice parameters:")
app(str(df.lattice))
app("Atomic coordinates:")
app(str(df.coords))
# Print dataframe with dimensions.
df = self.get_dims_spginfo_dataframe(verbose=verbose)
from abipy.tools.printing import print_dataframe
strio = StringIO()
print_dataframe(df, file=strio)
strio.seek(0)
app("")
app(marquee("Dimensions of calculation", mark="="))
app("".join(strio))
return "\n".join(lines)
def print_dataframes(self, with_spglib=False, file=sys.stdout, verbose=0):
"""
Print pandas dataframe to file `file`.
Args:
with_spglib: True to compute spacegroup with spglib.
file: Output stream.
verbose: Verbosity level.
"""
print_dataframe(self.dataframe, file=file)
if verbose:
from abipy.core.structure import dataframes_from_structures
dfs = dataframes_from_structures(self.structures, index=self.mpids, with_spglib=with_spglib)
print_dataframe(dfs.lattice, title="Lattice parameters:", file=file)
if verbose > 1:
print_dataframe(dfs.coords, title="Atomic positions (columns give the site index):", file=file)
def print_dataframes(self, with_spglib=False, file=sys.stdout, verbose=0):
"""
Print pandas dataframe to file `file`.
Args:
with_spglib: True to compute spacegroup with spglib.
file: Output stream.
verbose: Verbosity level.
"""
print_dataframe(self.dataframe, file=file)
if verbose:
from abipy.core.structure import dataframes_from_structures
dfs = dataframes_from_structures(self.structures, index=self.mpids, with_spglib=with_spglib)
print_dataframe(dfs.lattice, title="Lattice parameters:", file=file)
if verbose > 1:
print_dataframe(dfs.coords, title="Atomic positions (columns give the site index):", file=file)