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 = []
app = lines.append
header = 10 * "=" + " Input File " + 10 * "="
app(header)
app(self.string)
app(len(header) * "=" + "\n")
# Print info on structure(s).
if self.structure is not None:
app(self.structure.spget_summary())
else:
structures = [dt.structure for dt in self.datasets]
app("Input file contains %d structures:" % len(structures))
for i, structure in enumerate(structures):
app(boxed("Dataset: %d" % (i + 1)))
app(structure.spget_summary())
app("")
dfs = dataframes_from_structures(
structures, index=[i + 1 for i in range(self.ndtset)])
app(
boxed(
"Tabular view (each row corresponds to a dataset structure)"
))
app("")
app("Lattice parameters:")
app(str(dfs.lattice))
app("")
app("Atomic positions:")
app(str(dfs.coords))
return "\n".join(lines)
def to_string(self, verbose=0):
"""String representation."""
lines = []
app = lines.append
header = 10 * "=" + " Input File " + 10 * "="
app(header)
app(self.string)
app(len(header) * "=" + "\n")
# Print info on structure(s).
if self.structure is not None:
app(self.structure.spget_summary())
else:
structures = [dt.structure for dt in self.datasets]
app("Input file contains %d structures:" % len(structures))
for i, structure in enumerate(structures):
app(boxed("Dataset: %d" % (i+1)))
app(structure.spget_summary())
app("")
dfs = dataframes_from_structures(structures, index=[i+1 for i in range(self.ndtset)])
app(boxed("Tabular view (each row corresponds to a dataset structure)"))
app("")
app("Lattice parameters:")
app(str(dfs.lattice))
app("")
app("Atomic positions:")
app(str(dfs.coords))
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 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))
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)
def get_structure_dataframes(self, abspath=False, filter_abifile=None, **kwargs):
"""
Wrap dataframes_from_structures function.
Args:
abspath: True if paths in index should be absolute. Default: Relative to getcwd().
filter_abifile: Function that receives an ``abifile`` object and returns
True if the file should be added to the plotter.
"""
from abipy.core.structure import dataframes_from_structures
if "index" not in kwargs:
index = list(self._abifiles.keys())
if not abspath: index = self._to_relpaths(index)
kwargs["index"] = index
abifiles = self.abifiles if filter_abifile is not None else list(filter(filter_abifile, self.abifiles))
return dataframes_from_structures(struct_objects=abifiles, **kwargs)
def get_structure_dataframes(self, abspath=False, filter_abifile=None, **kwargs):
"""
Wrap dataframes_from_structures function.
Args:
abspath: True if paths in index should be absolute. Default: Relative to getcwd().
filter_abifile: Function that receives an ``abifile`` object and returns
True if the file should be added to the plotter.
"""
from abipy.core.structure import dataframes_from_structures
if "index" not in kwargs:
index = list(self._abifiles.keys())
if not abspath: index = self._to_relpaths(index)
kwargs["index"] = index
abifiles = self.abifiles if filter_abifile is not None else list(filter(filter_abifile, self.abifiles))
return dataframes_from_structures(struct_objects=abifiles, **kwargs)
def structure_dataframes(self):
"""Pandas dataframes constructed from self.structures."""
from abipy.core.structure import dataframes_from_structures
return dataframes_from_structures(self.structures, index=self.ids, with_spglib=True)
def structure_dataframes(self):
"""Pandas dataframes constructed from self.structures."""
from abipy.core.structure import dataframes_from_structures
return dataframes_from_structures(self.structures,
index=self.ids,
with_spglib=True)
