def __init__(self, filepath, read_blocks=False):
super(DdbFile, self).__init__(filepath)
self._header = self._parse_header()
self._structure = Structure.from_abivars(**self.header)
# Add AbinitSpacegroup (needed in guessed_ngkpt)
# FIXME: has_timerev is always True
spgid, has_timerev, h = 0, True, self.header
self._structure.set_abi_spacegroup(
AbinitSpaceGroup(spgid, h.symrel, h.tnons, h.symafm, has_timerev))
frac_coords = self._read_qpoints()
self._qpoints = KpointList(self.structure.lattice.reciprocal_lattice,
frac_coords,
weights=None,
names=None)
self.blocks = []
if read_blocks:
self.blocks = self._read_blocks()
def test_silicon(self):
"""Test silicon space group."""
structure = Structure.from_file(abidata.ref_file("si_scf_WFK.nc"))
assert structure.has_abi_spacegroup
assert structure.abi_spacegroup.is_symmorphic
spgrp = structure.abi_spacegroup
repr(spgrp); str(spgrp)
self.serialize_with_pickle(spgrp, test_eq=True)
# Classes cover the entire group.
assert sum(len(cls) for cls in spgrp.groupby_class()) == len(spgrp)
# Multiplication table.
mtable = spgrp.mult_table
for i, oi in enumerate(spgrp):
for j, oj in enumerate(spgrp):
ij = mtable[i, j]
assert ij is not None
assert oi * oj == spgrp[ij]
# Operation in the same class have the same trace and determinant.
for cls in spgrp.groupby_class():
#print(cls)
op0 = cls[0]
ref_trace, ref_det = op0.trace, op0.det
for op in cls[1:]:
assert op.trace == ref_trace
assert op.det == ref_det
assert spgrp == spgrp
# FIXME: Temporary disabled spgid is set to 0 in the WFK file.
#assert spgrp.spgid == 227
assert spgrp.has_timerev
assert len(spgrp) == 48 * 2
assert spgrp.num_spatial_symmetries == 48
assert spgrp.is_group()
# TODO
#si_symrel =
si_tnons = np.reshape(24 * [0, 0, 0, 0.25, 0.25, 0.25], (48, 3))
si_symafm = np.ones(48, dtype=np.int)
self.assert_almost_equal(si_tnons, spgrp.tnons)
self.assert_almost_equal(si_symafm, spgrp.symafm)
assert not spgrp.afm_symmops
for idx, symmop in enumerate(spgrp):
repr(symmop); str(symmop)
symmop.to_string(verbose=2)
assert symmop in spgrp
assert spgrp.count(symmop) == 1
assert spgrp.find(symmop) == idx
if symmop.det == 1: assert symmop.is_proper
# Test pickle
self.serialize_with_pickle(spgrp[0], protocols=None, test_eq=True)
for idx in range(len(spgrp)-1):
assert spgrp[idx] == spgrp[idx]
assert spgrp[idx] != spgrp[idx+1]
for fmop in spgrp.fm_symmops:
assert fmop.is_fm and not fmop.is_afm
ucell_coords = np.reshape([site.frac_coords for site in structure], (len(structure), 3))
err_msg = ""
for site in structure:
for symop in spgrp:
rot_coords = symop.rotate_r(site.frac_coords, in_ucell=True)
for atom_coords in ucell_coords:
#print (atom_coords - rot_coords)
if np.allclose(atom_coords, rot_coords):
break
else:
err_msg += "Cannot find symmetrical image of %s\n" % str(rot_coords)
assert not err_msg
k1, k2 = [0.5, 0, 0], [0, 0.5, 0]
ktab = spgrp.symeq(k1, k2, atol=None)
assert ktab.isym != -1
self.assert_equal(spgrp[ktab.isym].rotate_k(k1) - np.array(k2), ktab.g0)
k1, k2 = [0.0, 0, 0], [0, 0.5, 0]
ktab = spgrp.symeq(k1, k2, atol=None)
assert ktab.isym == -1
# Test little group with Gamma point.
lg_gamma = spgrp.find_little_group(kpoint=[0, 0, 0])
assert len(lg_gamma) == len(spgrp)
repr(lg_gamma); str(lg_gamma)
assert lg_gamma.is_symmorphic and not lg_gamma.on_bz_border
for o1, (o2, g0) in zip(spgrp, lg_gamma.iter_symmop_g0()):
assert o1 == o2
assert np.all(g0 == 0)
# Little group with X point.
# 'G' : (0.000, 0.000, 0.000),
# 'X' : (0.500, 0.000, 0.500),
# 'W' : (0.500, 0.250, 0.750),
# 'L' : (0.500, 0.500, 0.500),
# 'K' : (0.375, 0.375, 0.750),
# 'U' : (0.625, 0.250, 0.625)
lg_x = spgrp.find_little_group(kpoint=[0.5, 0, 0.5])
assert len(lg_x) == 32
repr(lg_x); str(lg_x)
assert lg_x.is_symmorphic and lg_x.on_bz_border
# This is just to test from_structure but one should always try to init from file.
other_spgroup = AbinitSpaceGroup.from_structure(structure, has_timerev=True)
assert other_spgroup.has_timerev
assert other_spgroup.spgid == 227
assert len(other_spgroup) == 48 * 2
def test_silicon(self):
"""Test silicon space group."""
structure = Structure.from_file(abidata.ref_file("si_scf_WFK.nc"))
assert structure.has_abi_spacegroup
assert structure.abi_spacegroup.is_symmorphic
spgrp = structure.abi_spacegroup
repr(spgrp)
str(spgrp)
self.serialize_with_pickle(spgrp, test_eq=True)
# Classes cover the entire group.
assert sum(len(cls) for cls in spgrp.groupby_class()) == len(spgrp)
# Multiplication table.
mtable = spgrp.mult_table
for i, oi in enumerate(spgrp):
for j, oj in enumerate(spgrp):
ij = mtable[i, j]
assert ij is not None
assert oi * oj == spgrp[ij]
# Operation in the same class have the same trace and determinant.
for cls in spgrp.groupby_class():
#print(cls)
op0 = cls[0]
ref_trace, ref_det = op0.trace, op0.det
for op in cls[1:]:
assert op.trace == ref_trace
assert op.det == ref_det
assert spgrp == spgrp
# FIXME: Temporary disabled spgid is set to 0 in the WFK file.
#assert spgrp.spgid == 227
assert spgrp.has_timerev
assert len(spgrp) == 48 * 2
assert spgrp.num_spatial_symmetries == 48
assert spgrp.get_spglib_hall_number() == 525
assert spgrp.is_group()
# TODO
#si_symrel =
si_tnons = np.reshape(24 * [0, 0, 0, 0.25, 0.25, 0.25], (48, 3))
si_symafm = np.ones(48, dtype=int)
self.assert_almost_equal(si_tnons, spgrp.tnons)
self.assert_almost_equal(si_symafm, spgrp.symafm)
assert not spgrp.afm_symmops
for idx, symmop in enumerate(spgrp):
repr(symmop)
str(symmop)
symmop.to_string(verbose=2)
assert symmop in spgrp
assert spgrp.count(symmop) == 1
assert spgrp.find(symmop) == idx
if symmop.det == 1: assert symmop.is_proper
# Test pickle
self.serialize_with_pickle(spgrp[0], protocols=None, test_eq=True)
for idx in range(len(spgrp) - 1):
assert spgrp[idx] == spgrp[idx]
assert spgrp[idx] != spgrp[idx + 1]
for fmop in spgrp.fm_symmops:
assert fmop.is_fm and not fmop.is_afm
ucell_coords = np.reshape([site.frac_coords for site in structure],
(len(structure), 3))
err_msg = ""
for site in structure:
for symop in spgrp:
rot_coords = symop.rotate_r(site.frac_coords, in_ucell=True)
for atom_coords in ucell_coords:
#print (atom_coords - rot_coords)
if np.allclose(atom_coords, rot_coords):
break
else:
err_msg += "Cannot find symmetrical image of %s\n" % str(
rot_coords)
assert not err_msg
k1, k2 = [0.5, 0, 0], [0, 0.5, 0]
ktab = spgrp.symeq(k1, k2, atol=None)
assert ktab.isym != -1
self.assert_equal(spgrp[ktab.isym].rotate_k(k1) - np.array(k2),
ktab.g0)
k1, k2 = [0.0, 0, 0], [0, 0.5, 0]
ktab = spgrp.symeq(k1, k2, atol=None)
assert ktab.isym == -1
# Test little group with Gamma point.
lg_gamma = spgrp.find_little_group(kpoint=[0, 0, 0])
assert len(lg_gamma) == len(spgrp)
repr(lg_gamma)
str(lg_gamma)
assert lg_gamma.is_symmorphic and not lg_gamma.on_bz_border
for o1, (o2, g0) in zip(spgrp, lg_gamma.iter_symmop_g0()):
assert o1 == o2
assert np.all(g0 == 0)
# Little group with X point.
# 'G' : (0.000, 0.000, 0.000),
# 'X' : (0.500, 0.000, 0.500),
# 'W' : (0.500, 0.250, 0.750),
# 'L' : (0.500, 0.500, 0.500),
# 'K' : (0.375, 0.375, 0.750),
# 'U' : (0.625, 0.250, 0.625)
lg_x = spgrp.find_little_group(kpoint=[0.5, 0, 0.5])
assert len(lg_x) == 32
repr(lg_x)
str(lg_x)
assert lg_x.is_symmorphic and lg_x.on_bz_border
# This is just to test from_structure but one should always try to init from file.
other_spgroup = AbinitSpaceGroup.from_structure(structure,
has_timerev=True)
assert other_spgroup.has_timerev
assert other_spgroup.spgid == 227
assert len(other_spgroup) == 48 * 2
def _get_structures(self, what):
if what == "header":
vars_global, vars_dataset = self.initial_vars_global, self.initial_vars_dataset
elif what == "footer":
vars_global, vars_dataset = self.final_vars_global, self.final_vars_dataset
else:
raise ValueError("Invalid value for what: `%s`" % str(what))
#print("global", vars_global["acell"])
from abipy.abio.abivars import is_abiunit
inigeo = {k: vars_global[k] for k in GEOVARS if k in vars_global}
spgvars = ("spgroup", "symrel", "tnons", "symafm")
spgd_global = {k: vars_global[k] for k in spgvars if k in vars_global}
global_kptopt = vars_global.get("kptopt", 1)
structures = []
for i in self.datasets:
# This code breaks down if there are conflicting GEOVARS in globals and dataset.
d = inigeo.copy()
d.update({
k: vars_dataset[i][k]
for k in GEOVARS if k in vars_dataset[i]
})
for key, value in d.items():
# Must handle possible unit.
fact = 1.0
tokens = [t.lower() for t in value.split()]
if is_abiunit(tokens[-1]):
tokens, unit = tokens[:-1], tokens[-1]
if unit in ("angstr", "angstrom", "angstroms"):
fact = 1.0 / bohr_to_ang
elif unit in ("bohr", "bohrs", "au"):
fact = 1.0
else:
raise ValueError("Don't know how to handle unit: %s" %
unit)
s = " ".join(tokens)
dtype = np.float if key not in ("ntypat", "typat",
"natom") else np.int
try:
#print(key, s)
value = np.fromstring(s, sep=" ", dtype=dtype)
#print(key, value)
if fact != 1.0:
value *= fact # Do not change integer arrays e.g typat!
d[key] = value
except ValueError as exc:
print(key, s)
raise exc
if "rprim" not in d and "angdeg" not in d: d["rprim"] = np.eye(3)
if "natom" in d and d["natom"] == 1 and all(
k not in d for k in ("xred", "xcart", "xangst")):
d["xred"] = np.zeros(3)
#print(d)
abistr = Structure.from_abivars(d)
# Extract Abinit spacegroup.
spgd = spgd_global.copy()
spgd.update({
k: vars_dataset[i][k]
for k in spgvars if k in vars_dataset[i]
})
spgid = int(spgd.get("spgroup", 0))
if "symrel" not in spgd:
symrel = np.reshape(np.eye(3, 3, dtype=np.int), (1, 3, 3))
spgd["symrel"] = " ".join((str(i) for i in symrel.flatten()))
else:
symrel = np.reshape(
np.array([int(n) for n in spgd["symrel"].split()],
dtype=np.int), (-1, 3, 3))
nsym = len(symrel)
assert nsym == spgd.get("nsym", nsym) #; print(symrel.shape)
if "tnons" in spgd:
tnons = np.reshape(
np.array([float(t) for t in spgd["tnons"].split()],
dtype=np.float), (nsym, 3))
else:
tnons = np.zeros((nsym, 3))
if "symafm" in spgd:
symafm = np.array([int(n) for n in spgd["symafm"].split()],
dtype=np.int)
symafm.shape = (nsym, )
else:
symafm = np.ones(nsym, dtype=np.int)
try:
has_timerev = has_timrev_from_kptopt(vars_dataset[i].get(
"kptopt", global_kptopt))
abi_spacegroup = AbinitSpaceGroup(spgid,
symrel,
tnons,
symafm,
has_timerev,
inord="C")
abistr.set_abi_spacegroup(abi_spacegroup)
except Exception as exc:
print(
"Cannot build AbinitSpaceGroup from the variables reported in file!\n",
str(exc))
structures.append(abistr)
return structures
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)
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("# Abinit Structure")
print(structure.abi_string)
print("\n# K-path in reduced coordinates:")
print("# tolwfr 1e-20 iscf -2 getden ??")
print(" ndivsm 10")
print(" kptopt", -(len(structure.hsym_kpoints) - 1))
print(" kptbounds")
for k in structure.hsym_kpoints:
print(" %+.5f %+.5f %+.5f" % tuple(k.frac_coords), "#",
k.name)
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)
from abipy.data.hgh_pseudos import HGH_TABLE
gsinp = factories.gs_input(structure,
HGH_TABLE,
spin_mode="unpolarized",
kppa=options.kppa)
if options.kppa is not None:
print("Calling Abinit to compute the IBZ with kppa:", options.kppa,
"and shiftk:", options.shiftk)
options.ngkpt = None
else:
print("Calling Abinit to compute the IBZ with ngkpt:",
options.ngkpt, "and shiftk", options.shiftk)
ibz = gsinp.abiget_ibz(ngkpt=options.ngkpt,
shiftk=options.shiftk,
kptopt=options.kptopt)
if options.verbose:
print(gsinp)
print("Found %d points in the IBZ:" % len(ibz.points))
for i, (k, w) in enumerate(zip(ibz.points, ibz.weights)):
print("%6d) [%+.3f, %+.3f, %+.3f] weight=%.3f" %
(i, k[0], k[1], k[2], w))
#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)
# TODO
#kstar = structure.get_star_kpoint(options.kpoint, has_timerev=not options.no_time_reversal)
# 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 == "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
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