def read_doses(self):
"""
Return a |AttrDict| with the DOSes available in the file. Empty dict if
DOSes are not available.
"""
if "gruns_nomega" not in self.rootgrp.dimensions:
cprint("File `%s` does not contain ph-DOSes, returning empty dict" % self.path, "yellow")
return {}
# Read q-point sampling used to compute DOSes.
qptrlatt = self.read_value("gruns_qptrlatt")
shifts = self.read_value("gruns_shiftq")
qsampling = KSamplingInfo.from_kptrlatt(qptrlatt, shifts, kptopt=1)
frac_coords_ibz = self.read_value("gruns_qibz")
weights = self.read_value("gruns_wtq")
qpoints = IrredZone(self.structure.reciprocal_lattice, frac_coords_ibz,
weights=weights, names=None, ksampling=qsampling)
# DOSes are in 1/Hartree.
d = AttrDict(wmesh=self.read_value("gruns_omega_mesh") * abu.Ha_eV, qpoints=qpoints)
for dos_name in _ALL_DOS_NAMES:
dos_idos = self.read_value(dos_name)
dos_idos[0] *= abu.eV_Ha # Here we convert to eV. IDOS are not changed.
d[dos_name] = dos_idos
return d
def main():
#import m_kpoints
#from m_kpoints import m_kpoints as mod
#print(m_kpoints.__doc__)
#v1 = np.zeros(3)
#v2 = v1 + 1.0
#print(v1, v2)
#ans, g0 = mod.isamek(v1, v2)
#print(ans,g0)
from abipy.core.kpoints import IrredZone, kmesh_from_mpdivs
filename = "/Users/gmatteo/Coding/abipy/abipy/data/runs/data_si_ebands/outdata/si_scf_GSR.nc"
structure = Structure.from_file(filename)
ibz = IrredZone.from_file(filename)
#print(ibz)
mpdivs = [8, 8, 8]
shifts = [0.0, 0.0, 0.0]
#tables = map_mesh2ibz(structure, mpdivs, shifts, ibz)
bz = kmesh_from_mpdivs(mpdivs, shifts)
ktab = slow_map_mesh2ibz(structure, bz, ibz.frac_coords)
def test_irredzone_api(self):
"""Testing IrredZone API."""
structure = abilab.Structure.as_structure(abidata.cif_file("si.cif"))
ibz = IrredZone.from_ngkpt(structure, ngkpt=[4, 4, 4], shiftk=[0.0, 0.0, 0.0], verbose=2)
repr(ibz); str(ibz)
assert ibz.to_string(verbose=2)
assert ibz.is_ibz
assert len(ibz) == 8
assert ibz.ksampling.kptopt == 1
self.assert_equal(ibz.ksampling.mpdivs, [4, 4, 4])
ibz = IrredZone.from_kppa(structure, kppa=1000, shiftk=[0.5, 0.5, 0.5], kptopt=1, verbose=1)
assert ibz.is_ibz
assert len(ibz) == 60
self.assert_equal(ibz.ksampling.mpdivs, [8, 8, 8])
def main():
#import m_kpoints
#from m_kpoints import m_kpoints as mod
#print(m_kpoints.__doc__)
#v1 = np.zeros(3)
#v2 = v1 + 1.0
#print(v1, v2)
#ans, g0 = mod.isamek(v1, v2)
#print(ans,g0)
from abipy.core.kpoints import IrredZone, kmesh_from_mpdivs
filename = "/Users/gmatteo/Coding/abipy/abipy/data/runs/data_si_ebands/outdata/si_scf_GSR.nc"
structure = Structure.from_file(filename)
ibz = IrredZone.from_file(filename)
#print(ibz)
mpdivs = [8, 8, 8]
shifts = [0.0, 0.0, 0.0]
#tables = map_mesh2ibz(structure, mpdivs, shifts, ibz)
bz = kmesh_from_mpdivs(mpdivs, shifts)
ktab = slow_map_mesh2ibz(structure, bz, ibz.frac_coords)
def get_interpolated_ebands_plotter(self,
vertices_names=None,
knames=None,
line_density=20,
ngkpt=None,
shiftk=(0, 0, 0),
kpoints=None,
**kwargs):
"""
Args:
vertices_names: Used to specify the k-path for the interpolated QP band structure
It's a list of tuple, each tuple is of the form (kfrac_coords, kname) where
kfrac_coords are the reduced coordinates of the k-point and kname is a string with the name of
the k-point. Each point represents a vertex of the k-path. ``line_density`` defines
the density of the sampling. If None, the k-path is automatically generated according
to the point group of the system.
knames: List of strings with the k-point labels defining the k-path. It has precedence over `vertices_names`.
line_density: Number of points in the smallest segment of the k-path. Used with ``vertices_names``.
ngkpt: Mesh divisions. Used if bands should be interpolated in the IBZ.
shiftk: Shifts for k-meshs. Used with ngkpt.
kpoints: |KpointList| object taken e.g from a previous ElectronBands.
Has precedence over vertices_names and line_density.
Return: |ElectronBandsPlotter| object.
"""
diff_str = self.has_different_structures()
if diff_str: cprint(diff_str, "yellow")
# Need KpointList object (assume same structures in Robot)
nc0 = self.abifiles[0]
if kpoints is None:
if ngkpt is not None:
# IBZ sampling
kpoints = IrredZone.from_ngkpt(nc0.structure,
ngkpt,
shiftk,
kptopt=1,
verbose=0)
else:
# K-Path
if knames is not None:
kpoints = Kpath.from_names(nc0.structure,
knames,
line_density=line_density)
else:
if vertices_names is None:
vertices_names = [(k.frac_coords, k.name)
for k in nc0.structure.hsym_kpoints]
kpoints = Kpath.from_vertices_and_names(
nc0.structure,
vertices_names,
line_density=line_density)
plotter = ElectronBandsPlotter()
for label, abiwan in self.items():
plotter.add_ebands(label,
abiwan.interpolate_ebands(kpoints=kpoints))
return plotter
def interpolate_ebands(self, vertices_names=None, line_density=20, ngkpt=None, shiftk=(0, 0, 0), kpoints=None):
"""
Build new |ElectronBands| object by interpolating the KS Hamiltonian with Wannier functions.
Supports k-path via (vertices_names, line_density), IBZ mesh defined by ngkpt and shiftk
or input list of kpoints.
Args:
vertices_names: Used to specify the k-path for the interpolated QP band structure
List of tuple, each tuple is of the form (kfrac_coords, kname) where
kfrac_coords are the reduced coordinates of the k-point and kname is a string with the name of
the k-point. Each point represents a vertex of the k-path. ``line_density`` defines
the density of the sampling. If None, the k-path is automatically generated according
to the point group of the system.
line_density: Number of points in the smallest segment of the k-path. Used with ``vertices_names``.
ngkpt: Mesh divisions. Used if bands should be interpolated in the IBZ.
shiftk: Shifts for k-meshs. Used with ngkpt.
kpoints: |KpointList| object taken e.g from a previous ElectronBands.
Has precedence over vertices_names and line_density.
Returns: |ElectronBands| object with Wannier-interpolated energies.
"""
# Need KpointList object.
if kpoints is None:
if ngkpt is not None:
# IBZ sampling
kpoints = IrredZone.from_ngkpt(self.structure, ngkpt, shiftk, kptopt=1, verbose=0)
else:
# K-Path
if vertices_names is None:
vertices_names = [(k.frac_coords, k.name) for k in self.structure.hsym_kpoints]
kpoints = Kpath.from_vertices_and_names(self.structure, vertices_names, line_density=line_density)
nk = len(kpoints)
eigens = np.zeros((self.nsppol, nk, self.mwan))
# Interpolate Hamiltonian for each kpoint and spin.
start = time.time()
write_warning = True
for spin in range(self.nsppol):
num_wan = self.nwan_spin[spin]
for ik, kpt in enumerate(kpoints):
oeigs = self.hwan.eval_sk(spin, kpt.frac_coords)
eigens[spin, ik, :num_wan] = oeigs
if num_wan < self.mwan:
# May have different number of wannier functions if nsppol == 2.
# Here I use the last value to fill eigens matrix (not very clean but oh well).
eigens[spin, ik, num_wan:self.mwan] = oeigs[-1]
if write_warning:
cprint("Different number of wannier functions for spin. Filling last bands with oeigs[-1]",
"yellow")
write_warning = False
print("Interpolation completed in %.3f [s]" % (time.time() - start))
occfacts = np.zeros_like(eigens)
return ElectronBands(self.structure, kpoints, eigens, self.ebands.fermie,
occfacts, self.ebands.nelect, self.nspinor, self.nspden,
smearing=self.ebands.smearing)
def test_irredzone_api(self):
"""Testing IrredZone API."""
structure = abilab.Structure.as_structure(abidata.cif_file("si.cif"))
ibz = IrredZone.from_ngkpt(structure,
ngkpt=[4, 4, 4],
shiftk=[0.0, 0.0, 0.0],
verbose=2)
repr(ibz)
str(ibz)
assert ibz.to_string(verbose=2)
assert ibz.is_ibz
assert len(ibz) == 8
assert ibz.ksampling.kptopt == 1
self.assert_equal(ibz.ksampling.mpdivs, [4, 4, 4])
ibz = IrredZone.from_kppa(structure,
kppa=1000,
shiftk=[0.5, 0.5, 0.5],
kptopt=1,
verbose=1)
assert ibz.is_ibz
assert len(ibz) == 60
self.assert_equal(ibz.ksampling.mpdivs, [8, 8, 8])
def get_interpolated_ebands_plotter(self, vertices_names=None, knames=None, line_density=20,
ngkpt=None, shiftk=(0, 0, 0), kpoints=None, **kwargs):
"""
Args:
vertices_names: Used to specify the k-path for the interpolated QP band structure
It's a list of tuple, each tuple is of the form (kfrac_coords, kname) where
kfrac_coords are the reduced coordinates of the k-point and kname is a string with the name of
the k-point. Each point represents a vertex of the k-path. ``line_density`` defines
the density of the sampling. If None, the k-path is automatically generated according
to the point group of the system.
knames: List of strings with the k-point labels defining the k-path. It has precedence over `vertices_names`.
line_density: Number of points in the smallest segment of the k-path. Used with ``vertices_names``.
ngkpt: Mesh divisions. Used if bands should be interpolated in the IBZ.
shiftk: Shifts for k-meshs. Used with ngkpt.
kpoints: |KpointList| object taken e.g from a previous ElectronBands.
Has precedence over vertices_names and line_density.
Return: |ElectronBandsPlotter| object.
"""
diff_str = self.has_different_structures()
if diff_str: cprint(diff_str, "yellow")
# Need KpointList object (assume same structures in Robot)
nc0 = self.abifiles[0]
if kpoints is None:
if ngkpt is not None:
# IBZ sampling
kpoints = IrredZone.from_ngkpt(nc0.structure, ngkpt, shiftk, kptopt=1, verbose=0)
else:
# K-Path
if knames is not None:
kpoints = Kpath.from_names(nc0.structure, knames, line_density=line_density)
else:
if vertices_names is None:
vertices_names = [(k.frac_coords, k.name) for k in nc0.structure.hsym_kpoints]
kpoints = Kpath.from_vertices_and_names(nc0.structure, vertices_names, line_density=line_density)
plotter = ElectronBandsPlotter()
for label, abiwan in self.items():
plotter.add_ebands(label, abiwan.interpolate_ebands(kpoints=kpoints))
return plotter
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 command line.
try:
options = parser.parse_args()
except Exception as exc:
show_examples_and_exit(error_code=1)
if not options.command:
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.command == "spglib":
structure = abilab.Structure.from_file(options.filepath)
print(structure.spget_summary(symprec=options.symprec, angle_tolerance=options.angle_tolerance,
verbose=options.verbose))
#remove_equivalent_atoms(structure)
elif options.command == "abispg":
structure = abilab.Structure.from_file(options.filepath)
check_ordered_structure(structure)
spgrp = structure.abi_spacegroup
if spgrp is not None:
print(structure.spget_summary(verbose=options.verbose))
else:
# Here we compare Abinit wrt spglib. If spgrp is None, we create a temporary
# task to run the code in dry-run mode.
print("FILE does not contain Abinit symmetry operations.")
print("Calling Abinit in --dry-run mode with chkprim = 0 to get space group.")
from abipy.data.hgh_pseudos import HGH_TABLE
gsinp = factories.gs_input(structure, HGH_TABLE, spin_mode="unpolarized")
gsinp["chkprim"] = 0
abistructure = gsinp.abiget_spacegroup(tolsym=options.tolsym)
print(abistructure.spget_summary(verbose=options.verbose))
diff_structures([structure, abistructure], mode=options.diff_mode,
headers=["Input structure", "After Abinit symmetrization"], fmt="abivars")
# Save file.
save_structure(abistructure, options)
elif options.command == "convert":
fmt = options.format
if fmt == "cif" and options.filepath.endswith(".cif"): fmt = "abivars"
print(abilab.Structure.from_file(options.filepath).convert(fmt=fmt))
elif options.command == "supercell":
structure = abilab.Structure.from_file(options.filepath)
options.scaling_matrix = np.array(options.scaling_matrix)
if len(options.scaling_matrix) == 9:
options.scaling_matrix.shape = (3, 3)
if options.verbose:
print("scaling matrix: ", options.scaling_matrix)
supcell = structure * options.scaling_matrix
#supcell = structure.make_supercell(scaling_matrix, to_unit_cell=True)
print(supcell.convert(fmt=options.format))
elif options.command == "abisanitize":
print("\nCalling abi_sanitize to get a new structure in which:")
print(" * Structure is refined.")
print(" * Reduced to primitive settings.")
print(" * Lattice vectors are exchanged if the triple product is negative\n")
structure = abilab.Structure.from_file(options.filepath)
sanitized = structure.abi_sanitize(symprec=options.symprec, angle_tolerance=options.angle_tolerance,
primitive=not options.no_primitive, primitive_standard=options.primitive_standard)
index = [options.filepath, "abisanitized"]
dfs = abilab.dataframes_from_structures([structure, sanitized], index=index, with_spglib=True)
abilab.print_dataframe(dfs.lattice, title="Lattice parameters:")
abilab.print_dataframe(dfs.coords, title="Atomic positions (columns give the site index):")
if not options.verbose:
print("\nUse -v for more info")
#print(sanitized.convert(fmt="cif"))
else:
#print("\nDifference between structures:")
if len(structure) == len(sanitized):
table = []
for line1, line2 in zip(str(structure).splitlines(), str(sanitized).splitlines()):
table.append([line1, line2])
print(str(tabulate(table, headers=["Initial structure", "Abisanitized"])))
else:
print("\nInitial structure:")
print(structure)
print("\nabisanitized structure:")
print(sanitized)
# Save file.
save_structure(sanitized, options)
elif options.command == "irefine":
structure = abilab.Structure.from_file(options.filepath)
sanitized = structure.copy()
symprec, angle_tolerance = options.symprec, options.angle_tolerance
print("Calling abi_sanitize with increasing tolerances to reach target space group:", options.target_spgnum)
print("Using symprec_step: ", options.symprec_step, ", angle_tolerance_step:", options.angle_tolerance_step,
"ntrial", options.ntrial)
itrial = 0
while itrial < options.ntrial:
print(">>> Trying with symprec: %s, angle_tolerance: %s" % (symprec, angle_tolerance))
sanitized = sanitized.abi_sanitize(symprec=symprec, angle_tolerance=angle_tolerance,
primitive=not options.no_primitive, primitive_standard=options.primitive_standard)
spg_symb, spg_num = sanitized.get_space_group_info(symprec=symprec, angle_tolerance=angle_tolerance)
print(">>> Space-group number:", spg_symb, ", symbol:", spg_num, "for trial:", itrial)
if spg_num == options.target_spgnum:
print(2 * "\n", "# Final structure with space group number:", spg_symb, ", symbol:", spg_num, 2 *"\n")
print(sanitized.convert(fmt="cif"))
break
# Increment counter and tols.
itrial += 1
symprec += options.symprec_step
angle_tolerance += options.angle_tolerance_step
else:
print("Cannot find space group number:", options.target_spgnum, "after", options.ntrial, "iterations")
return 1
# Save file.
#save_structure(sanitized, options)
elif options.command == "conventional":
print("\nCalling get_conventional_standard_structure to get conventional structure:")
print("The standards are defined in Setyawan, W., & Curtarolo, S. (2010). ")
print("High-throughput electronic band structure calculations: Challenges and tools. ")
print("Computational Materials Science, 49(2), 299-312. doi:10.1016/j.commatsci.2010.05.010\n")
structure = abilab.Structure.from_file(options.filepath)
conv = structure.get_conventional_standard_structure(international_monoclinic=True,
symprec=options.symprec, angle_tolerance=options.angle_tolerance)
index = [options.filepath, "conventional"]
dfs = abilab.dataframes_from_structures([structure, conv], index=index, with_spglib=True)
abilab.print_dataframe(dfs.lattice, title="Lattice parameters:")
if options.verbose:
abilab.print_dataframe(dfs.coords, title="Atomic positions (columns give the site index):")
if not options.verbose:
print("\nUse -v for more info")
else:
#print("\nDifference between structures:")
if len(structure) == len(conv):
table = []
for line1, line2 in zip(str(structure).splitlines(), str(conv).splitlines()):
table.append([line1, line2])
print(str(tabulate(table, headers=["Initial structure", "Conventional"])))
else:
print("\nInitial structure:\n", structure)
print("\nConventional structure:\n", conv)
# Save file.
save_structure(conv, options)
elif options.command == "neighbors":
abilab.Structure.from_file(options.filepath).print_neighbors(radius=options.radius)
elif options.command == "interpolate":
initial_structure = abilab.Structure.from_file(options.filepaths[0])
end_structure = abilab.Structure.from_file(options.filepaths[1])
structures = initial_structure.interpolate(end_structure, nimages=options.nimages,
interpolate_lattices=False, pbc=True,
autosort_tol=options.autosort_tol)
structures = list(map(abilab.Structure.as_structure, structures))
for i, s in enumerate(structures):
print(marquee("Structure #%d" % i, mark="="))
print(s.convert(fmt=options.format))
print(" ")
elif options.command == "xrd":
structure = abilab.Structure.from_file(options.filepath)
two_theta_range = tuple(float(t) for t in options.two_theta_range)
structure.plot_xrd(wavelength=options.wavelength, two_theta_range=two_theta_range,
symprec=options.symprec, annotate_peaks=not options.no_annotate_peaks)
elif options.command == "oxistate":
print(abilab.Structure.from_file(options.filepath).get_oxi_state_decorated())
elif options.command == "ipython":
structure = abilab.Structure.from_file(options.filepath)
print("Invoking Ipython, `structure` object will be available in the Ipython terminal")
import IPython
IPython.start_ipython(argv=[], user_ns={"structure": structure})
elif options.command == "notebook":
structure = abilab.Structure.from_file(options.filepath)
structure.make_and_open_notebook(nbpath=None, foreground=options.foreground)
elif options.command == "visualize":
structure = abilab.Structure.from_file(options.filepath)
print(structure)
print("Visualizing structure with:", options.appname)
structure.visualize(appname=options.appname)
elif options.command == "kpath":
structure = abilab.Structure.from_file(options.filepath)
print(structure.get_kpath_input_string(fmt=options.format, line_density=10))
elif options.command == "bz":
abilab.Structure.from_file(options.filepath).plot_bz()
elif options.command == "ngkpt":
d = abilab.Structure.from_file(options.filepath).calc_ksampling(options.nksmall)
print("ngkpt %d %d %d" % (d.ngkpt[0], d.ngkpt[1], d.ngkpt[2]))
print("nshiftk ", len(d.shiftk), "\nshiftk")
for s in d.shiftk:
print(" %s %s %s" % (s[0], s[1], s[2]))
elif options.command == "ktables":
structure = abilab.Structure.from_file(options.filepath)
k = Ktables(structure, options.mesh, options.is_shift, not options.no_time_reversal)
print(k)
print("")
print("NB: These results are obtained by calling spglib with the structure read from file.")
print("The k-points might differ from the ones expected by Abinit, especially if the space groups differ.")
if not options.verbose:
print("\nUse -v to obtain the BZ --> IBZ mapping.")
else:
print()
k.print_bz2ibz()
elif options.command == "abikmesh":
structure = abilab.Structure.from_file(options.filepath)
if options.kppa is None and options.ngkpt is None:
raise ValueError("Either ngkpt or kppa must be provided")
if options.kppa is not None:
print("Calling Abinit to compute the IBZ with kppa:", options.kppa, "and shiftk:", options.shiftk)
ibz = IrredZone.from_kppa(structure, options.kppa, options.shiftk,
kptopt=options.kptopt, verbose=options.verbose)
else:
print("Calling Abinit to compute the IBZ with ngkpt:", options.ngkpt, "and shiftk:", options.shiftk)
ibz = IrredZone.from_ngkpt(structure, options.ngkpt, options.shiftk,
kptopt=options.kptopt, verbose=options.verbose)
print(ibz.to_string(verbose=options.verbose))
#elif options.command == "kmesh_jhu":
# structure = abilab.Structure.from_file(options.filepath)
# ksampling = structure.ksampling_from_jhudb(kppra=1000)
# #print(ksampling)
elif options.command == "lgk":
structure = abilab.Structure.from_file(options.filepath)
spgrp = structure.abi_spacegroup
if spgrp is None:
cprint("Your file does not contain Abinit symmetry operations.", "yellow")
cprint("Will call spglib to obtain the space group (assuming time-reversal: %s)" %
(not options.no_time_reversal), "yellow")
spgrp = AbinitSpaceGroup.from_structure(structure, has_timerev=not options.no_time_reversal,
symprec=options.symprec, angle_tolerance=options.angle_tolerance)
print()
print(marquee("Structure", mark="="))
print(structure.spget_summary(verbose=options.verbose))
print("\n")
print(marquee("Little Group", mark="="))
ltk = spgrp.find_little_group(kpoint=options.kpoint)
print(ltk.to_string(verbose=options.verbose))
elif options.command == "kstar":
structure = abilab.Structure.from_file(options.filepath)
# Call spglib to get spacegroup if Abinit spacegroup is not available.
if structure.abi_spacegroup is None:
structure.spgset_abi_spacegroup(has_timerev=not options.no_time_reversal)
kpoint = Kpoint(options.kpoint, structure.reciprocal_lattice)
kstar = kpoint.compute_star(structure.abi_spacegroup, wrap_tows=True)
print("Found %s points in the star of %s\n" % (len(kstar), repr(kpoint)))
for k in kstar:
print(4 * " ", repr(k))
elif options.command == "keq":
structure = abilab.Structure.from_file(options.filepath)
# Call spglib to get spacegroup if Abinit spacegroup is not available.
if structure.abi_spacegroup is None:
structure.spgset_abi_spacegroup(has_timerev=not options.no_time_reversal)
k1, k2 = options.kpoints[:3], options.kpoints[3:6]
k1tab = structure.abi_spacegroup.symeq(k1, k2)
if k1tab.isym != -1:
print("\nk1:", k1, "and k2:", k2, "are symmetry equivalent k-points\n")
print("Related by the symmetry operation (reduced coords):\n", k1tab.op)
print("With umklapp vector Go = TO(k1) - k2 =", k1tab.g0)
else:
print(k1, "and", k2, "are NOT symmetry equivalent")
elif options.command == "mp_id":
# Get the Structure corresponding to material_id.
structure = abilab.Structure.from_mpid(options.mpid, final=True,
api_key=options.mapi_key, endpoint=options.endpoint)
# Convert to format and print it.
print(structure.convert(fmt=options.format))
elif options.command == "mp_match":
mp = abilab.mp_match_structure(options.filepath)
if not mp.structures:
cprint("No structure found in database", "yellow")
return 1
if options.notebook:
return mp.make_and_open_notebook(foreground=options.foreground)
else:
mp.print_results(fmt=options.format, verbose=options.verbose)
if options.browser:
mp.open_browser(limit=None if options.verbose == 2 else 10)
elif options.command == "mp_search":
mp = abilab.mp_search(options.chemsys_formula_id)
if not mp.structures:
cprint("No structure found in Materials Project database", "yellow")
return 1
if options.select_spgnum: mp = mp.filter_by_spgnum(options.select_spgnum)
if options.notebook:
return mp.make_and_open_notebook(foreground=options.foreground)
else:
mp.print_results(fmt=options.format, verbose=options.verbose)
if options.browser:
mp.open_browser(limit=None if options.verbose == 2 else 10)
elif options.command == "mp_pd":
if os.path.exists(options.file_or_elements):
structure = abilab.Structure.from_file(options.file_or_elements)
elements = structure.symbol_set
else:
elements = options.file_or_elements.split("-")
if options.verbose > 1: print("Building phase-diagram for elements:", elements)
with abilab.restapi.get_mprester(api_key=options.mapi_key, endpoint=options.endpoint) as rest:
pdr = rest.get_phasediagram_results(elements)
pdr.print_dataframes(verbose=options.verbose)
pdr.plot(show_unstable=options.show_unstable)
elif options.command == "cod_search":
cod = abilab.cod_search(options.formula, primitive=options.primitive)
if not cod.structures:
cprint("No structure found in COD database", "yellow")
return 1
if options.select_spgnum: cod = cod.filter_by_spgnum(options.select_spgnum)
if options.notebook:
return cod.make_and_open_notebook(foreground=options.foreground)
else:
cod.print_results(fmt=options.format, verbose=options.verbose)
elif options.command == "cod_id":
# Get the Structure from COD
structure = abilab.Structure.from_cod_id(options.cod_identifier, primitive=options.primitive)
# Convert to format and print it.
print(structure.convert(fmt=options.format))
elif options.command == "animate":
filepath = options.filepath
if any(filepath.endswith(ext) for ext in ("HIST", "HIST.nc")):
with abilab.abiopen(filepath) as hist:
structures = hist.structures
elif "XDATCAR" in filepath:
structures = Xdatcar(filepath).structures
if not structures:
raise RuntimeError("Your Xdatcar contains only one structure. Due to a bug "
"in the pymatgen routine, your structures won't be parsed correctly"
"Solution: Add another structure at the end of the file.")
else:
raise ValueError("Don't know how to handle file %s" % filepath)
xsf_write_structure(sys.stdout, structures)
else:
raise ValueError("Unsupported command: %s" % options.command)
return 0