def test_effmassline_work(self):
"""Testing EffMassLineWork."""
si_structure = abidata.structure_from_cif("si.cif")
scf_input = gs_input(si_structure, pseudos=abidata.pseudos("14si.pspnc"), ecut=4, spin_mode="unpolarized")
flow = flowtk.Flow.temporary_flow()
with self.assertRaises(ValueError):
work = EffMassLineWork.from_scf_input(scf_input, k0_list=(0, 0, 0), step=0.01, npts=2)
# Run SCF from scratch.
work = EffMassLineWork.from_scf_input(scf_input, k0_list=(0, 0, 0), step=0.01, npts=9)
t0, t1 = work[0], work[1]
assert t1.depends_on(t0)
assert t1.input["kptopt"] == 0
assert t1.input["iscf"] == -2
flow.register_work(work)
flow.allocate()
flow.check_status()
isok, checks = flow.abivalidate_inputs()
assert isok
# From DEN file
flow = flowtk.Flow.temporary_flow()
work = EffMassLineWork.from_scf_input(scf_input, k0_list=(0, 0, 0), step=0.01, npts=10,
red_dirs=(1, 0, 0),
cart_dirs=[(1, 0, 0), (1, 1, 0)],
den_node=abidata.ref_file("si_DEN.nc"))
flow.register_work(work)
flow.allocate()
flow.check_status()
isok, checks = flow.abivalidate_inputs()
assert isok
def test_gruneisen_work(self):
"""Testing GruneisenWork."""
si_structure = abidata.structure_from_cif("si.cif")
gs_inp = gs_input(si_structure,
pseudos=abidata.pseudos("14si.pspnc"),
ecut=4,
spin_mode="unpolarized")
flow = flowtk.Flow.temporary_flow()
voldelta = gs_inp.structure.volume * 0.02
work = GruneisenWork.from_gs_input(gs_inp,
voldelta,
ngqpt=[2, 2, 2],
with_becs=False)
flow.register_work(work)
assert len(work.relax_tasks) == 3
assert all(t.input["optcell"] == 3 for t in work)
assert all(t.input["ionmov"] == 3 for t in work)
assert all(t.input["ecutsm"] == 0.5 for t in work)
assert all(t.input["dilatmx"] == 1.05 for t in work)
flow.allocate()
flow.check_status()
isok, checks = flow.abivalidate_inputs()
assert isok
with self.assertRaises(ValueError):
GruneisenWork.from_gs_input(gs_inp,
voldelta,
ngqpt=[3, 3, 3],
with_becs=False)
def test_phonopy_work(self):
"""Testing PhononWork."""
self.skip_if_not_phonopy()
si_structure = abidata.structure_from_cif("si.cif")
same_structure = abiph.structure_from_atoms(abiph.atoms_from_structure(si_structure))
assert si_structure == same_structure
# TODO: Spin
gsinp = gs_input(si_structure, pseudos=abidata.pseudos("14si.pspnc"), ecut=4, spin_mode="unpolarized")
#gsinp = gs_input(si_structure, pseudos=abidata.pseudos("14si.pspnc"), ecut=4, spin_mode="polarized")
flow = flowtk.Flow.temporary_flow()
scdims = [2, 2, 2]
phpy_work = abiph.PhonopyWork.from_gs_input(gsinp, scdims=scdims, phonopy_kwargs=None, displ_kwargs=None)
flow.register_work(phpy_work)
self.assert_equal(scdims, phpy_work.scdims)
assert hasattr(phpy_work, "phonon")
assert len(phpy_work.phonopy_tasks) == len(phpy_work)
assert len(phpy_work.phonopy_tasks) == 1
assert len(phpy_work.bec_tasks) == 0
# Gruneisen with phonopy
grun_work = abiph.PhonopyGruneisenWork.from_gs_input(gsinp, voldelta=0.1, scdims=scdims,
phonopy_kwargs=None, displ_kwargs=None)
flow.register_work(grun_work)
self.assert_equal(scdims, grun_work.scdims)
flow.allocate()
flow.check_status()
isok, checks = flow.abivalidate_inputs()
assert isok
def abinp_phonons(options):
"""Build Abinit input for phonon calculations."""
structure = get_structure(options)
pseudos = get_pseudotable(options)
gsinp = factories.gs_input(structure,
pseudos,
kppa=options.kppa,
ecut=None,
pawecutdg=None,
scf_nband=None,
accuracy="normal",
spin_mode=options.spin_mode,
smearing=options.smearing,
charge=0.0,
scf_algorithm=None)
multi = factories.phonons_from_gsinput(gsinp,
ph_ngqpt=None,
qpoints=None,
with_ddk=True,
with_dde=True,
with_bec=False,
ph_tol=None,
ddk_tol=None,
dde_tol=None,
wfq_tol=None,
qpoints_to_skip=None)
# Add getwfk variables.
for inp in multi[1:]:
inp["getwfk"] = 1
return finalize(multi, options)
def itest_phonopy_flow(fwp, tvars):
"""
Testing phonopy flow with the scheduler.
"""
if not has_phonopy():
raise unittest.SkipTest("This test requires phonopy")
#print("tvars:\n %s" % str(tvars))
si_structure = abidata.structure_from_cif("si.cif")
gsinp = gs_input(si_structure,
pseudos=abidata.pseudos("14si.pspnc"),
kppa=10,
ecut=2,
spin_mode="unpolarized")
gsinp["paral_kgb"] = tvars.paral_kgb
flow = flowtk.Flow(workdir=fwp.workdir, manager=fwp.manager)
scdims = [2, 2, 2]
phpy_work = abiph.PhonopyWork.from_gs_input(gsinp,
scdims=scdims,
phonopy_kwargs=None,
displ_kwargs=None)
flow.register_work(phpy_work)
assert hasattr(phpy_work, "phonon")
assert len(phpy_work.phonopy_tasks) == len(phpy_work)
assert len(phpy_work.phonopy_tasks) == 1
assert len(phpy_work.bec_tasks) == 0
nptu.assert_equal(scdims, phpy_work.scdims)
# Will remove output files (WFK)
flow.set_garbage_collector()
flow.use_smartio()
flow.build_and_pickle_dump(abivalidate=True)
scheduler = flow.make_scheduler()
assert scheduler.start() == 0
assert not scheduler.exceptions
flow.show_status()
assert flow.all_ok
assert all(work.finalized for work in flow)
# The WFK files should have been removed because we called set_garbage_collector
for task in flow[0]:
assert not task.outdir.has_abiext("WFK")
out_filenames = set(
[os.path.basename(f) for f in phpy_work.outdir.list_filepaths()])
nmiss = 0
for f in [
"POSCAR", "disp.yaml", "FORCE_SETS", "band.conf", "dos.conf",
"band-dos.conf", "README.md"
]:
if f not in out_filenames:
nmiss += 1
print("Cannot find %s in work.outdir" % f)
assert nmiss == 0
def abinp_gs(options):
"""Build Abinit input for ground-state calculation."""
structure = abilab.Structure.from_file(options.filepath)
pseudos = get_pseudotable(options)
gsinp = factories.gs_input(structure, pseudos,
kppa=None, ecut=None, pawecutdg=None, scf_nband=None,
accuracy="normal", spin_mode="unpolarized",
smearing="fermi_dirac:0.1 eV", charge=0.0, scf_algorithm=None)
return finalize(gsinp, options)
def abinp_gs(options):
"""Build Abinit input for ground-state calculation."""
structure = abilab.Structure.from_file(options.filepath)
pseudos = get_pseudotable(options)
gsinp = factories.gs_input(structure, pseudos,
kppa=options.kppa, ecut=None, pawecutdg=None, scf_nband=None,
accuracy="normal", spin_mode=options.spin_mode,
smearing=options.smearing, charge=0.0, scf_algorithm=None)
return finalize(gsinp, options)
def itest_phonopy_flow(fwp, tvars):
"""
Testing phonopy Gruneisen flow with the scheduler.
"""
if not has_phonopy():
raise unittest.SkipTest("This test requires phonopy")
#print("tvars:\n %s" % str(tvars))
si_structure = abidata.structure_from_cif("si.cif")
gsinp = gs_input(si_structure, pseudos=abidata.pseudos("14si.pspnc"), kppa=10, ecut=2, spin_mode="unpolarized")
gsinp["paral_kgb"] = tvars.paral_kgb
flow = flowtk.Flow(workdir=fwp.workdir, manager=fwp.manager)
scdims = [2, 2, 2]
# Grunesein with phonopy
grun_work = abiph.PhonopyGruneisenWork.from_gs_input(gsinp, voldelta=0.1, scdims=scdims,
phonopy_kwargs=None, displ_kwargs=None)
flow.register_work(grun_work)
assert len(grun_work) == 3
nptu.assert_equal(scdims, grun_work.scdims)
# Will remove output files (WFK)
flow.set_garbage_collector()
flow.use_smartio()
flow.build_and_pickle_dump(abivalidate=True)
scheduler = flow.make_scheduler()
assert scheduler.start() == 0
assert not scheduler.exceptions
flow.show_status()
assert flow.all_ok
# Initialial work + 3 phonopy works.
assert len(flow) == 4
assert all(work.finalized for work in flow)
# The WFK files should have been removed because we called set_garbage_collector
# FIXME: This does not work because new works that have been created.
#for task in flow.iflat_tasks():
# assert not task.outdir.has_abiext("WFK")
for work in flow[1:]:
out_filenames = set([os.path.basename(f) for f in work.outdir.list_filepaths()])
nmiss = 0
for f in ["POSCAR", "disp.yaml", "FORCE_SETS", "band.conf", "dos.conf", "band-dos.conf", "README.md"]:
if f not in out_filenames:
nmiss += 1
print("Cannot find %s in work.outdir" % f)
assert nmiss == 0
def on_gs_input_btn(self):
if self.gs_input_btn.clicks == 0: return
from abipy.abio.factories import gs_input
from abipy.data.hgh_pseudos import HGH_TABLE
gs_inp = gs_input(
self.structure, HGH_TABLE, kppa=self.kppra.value, ecut=8,
spin_mode=self.label2mode[self.spin_mode.value],
smearing=None)
gs_inp.pop_vars(("charge", "chksymbreak"))
gs_inp.set_vars(ecut="?? # depends on pseudos", nband="?? # depends on pseudos")
if self.gs_type.value == "relax":
gs_inp.set_vars(optcell=2, ionmov=2, ecutsm=0.5, dilatmx=1.05)
gs_inp.set_mnemonics(False)
return html_with_copy_to_clipboard(gs_inp._repr_html_())
def abinp_phonons(options):
"""Build Abinit input for phonon calculations."""
structure = get_structure(options)
pseudos = get_pseudotable(options)
gsinp = factories.gs_input(structure, pseudos,
kppa=None, ecut=None, pawecutdg=None, scf_nband=None,
accuracy="normal", spin_mode="unpolarized",
smearing="fermi_dirac:0.1 eV", charge=0.0, scf_algorithm=None)
multi = factories.phonons_from_gsinput(gsinp, ph_ngqpt=None, qpoints=None, with_ddk=True, with_dde=True, with_bec=False,
ph_tol=None, ddk_tol=None, dde_tol=None, wfq_tol=None, qpoints_to_skip=None)
# Add getwfk variables.
for inp in multi[1:]:
inp["getwfk"] = 1
return finalize(multi, options)
def test_infinite_flow(self):
si_structure = abidata.structure_from_cif("si.cif")
gsinp = gs_input(si_structure,
pseudos=abidata.pseudos("14si.pspnc"),
ecut=4)
flow = flowtk.Flow.temporary_flow()
work = flowtk.Work()
gstask = work.register_scf_task(gsinp)
flow.register_work(work)
flow.allocate()
mocks.infinite_flow(flow)
flow.check_status()
assert (t.status == flow.S_INIT for t in flow)
mocks.change_task_start(gstask, mocked_status="Error")
assert gstask.start() == 1 and gstask.status == gstask.S_ERROR
def test_effmass_autodfpt_work(self):
"""Testing EffMassAutoDFPTWork."""
si_structure = abidata.structure_from_cif("si.cif")
scf_input = gs_input(si_structure, pseudos=abidata.pseudos("14si.pspnc"), ecut=4, spin_mode="unpolarized")
flow = flowtk.Flow.temporary_flow()
# Run SCF from scratch.
work = EffMassAutoDFPTWork.from_scf_input(scf_input)
assert len(work) == 2
assert work[1].depends_on(work[0])
flow.register_work(work)
flow.allocate()
flow.check_status()
isok, checks = flow.abivalidate_inputs()
assert isok
def test_phonopy_work(self):
"""Testing PhononWork."""
self.skip_if_not_phonopy()
si_structure = abidata.structure_from_cif("si.cif")
same_structure = abiph.structure_from_atoms(
abiph.atoms_from_structure(si_structure))
assert si_structure == same_structure
# TODO: Spin
gsinp = gs_input(si_structure,
pseudos=abidata.pseudos("14si.pspnc"),
ecut=4,
spin_mode="unpolarized")
#gsinp = gs_input(si_structure, pseudos=abidata.pseudos("14si.pspnc"), ecut=4, spin_mode="polarized")
flow = flowtk.Flow.temporary_flow()
scdims = [2, 2, 2]
phpy_work = abiph.PhonopyWork.from_gs_input(gsinp,
scdims=scdims,
phonopy_kwargs=None,
displ_kwargs=None)
flow.register_work(phpy_work)
self.assert_equal(scdims, phpy_work.scdims)
assert hasattr(phpy_work, "phonon")
assert len(phpy_work.phonopy_tasks) == len(phpy_work)
assert len(phpy_work.phonopy_tasks) == 1
assert len(phpy_work.bec_tasks) == 0
# Gruneisen with phonopy
grun_work = abiph.PhonopyGruneisenWork.from_gs_input(
gsinp,
voldelta=0.1,
scdims=scdims,
phonopy_kwargs=None,
displ_kwargs=None)
flow.register_work(grun_work)
self.assert_equal(scdims, grun_work.scdims)
flow.allocate()
flow.check_status()
isok, checks = flow.abivalidate_inputs()
assert isok
def test_effmass_dfpt_work(self):
"""Testing EffMassDFPTWork."""
si_structure = abidata.structure_from_cif("si.cif")
scf_input = gs_input(si_structure, pseudos=abidata.pseudos("14si.pspnc"), ecut=4, spin_mode="unpolarized")
flow = flowtk.Flow.temporary_flow()
# Run SCF from scratch.
work = EffMassDFPTWork.from_scf_input(scf_input, k0_list=(0, 0, 0), effmass_bands_f90=[2, 4])
assert len(work) == 3
t0, t1, t2 = work
assert t1.input["iscf"] == -2
assert t2.input["kptopt"] == 0
assert t2.input["efmas"] == 1 and t2.input["rfelfd"] == 2
assert t2.depends_on(t1)
flow.register_work(work)
flow.allocate()
flow.check_status()
isok, checks = flow.abivalidate_inputs()
assert isok
def itest_phonopy_gruneisen_flow(fwp, tvars):
"""
Testing phonopy Gruneisen flow with the scheduler.
"""
if not has_phonopy():
raise unittest.SkipTest("This test requires phonopy")
#print("tvars:\n %s" % str(tvars))
si_structure = abidata.structure_from_cif("si.cif")
gsinp = gs_input(si_structure,
pseudos=abidata.pseudos("14si.pspnc"),
kppa=10,
ecut=2,
spin_mode="unpolarized")
gsinp["paral_kgb"] = tvars.paral_kgb
flow = flowtk.Flow(workdir=fwp.workdir, manager=fwp.manager)
scdims = [2, 2, 2]
# Grunesein with phonopy
grun_work = abiph.PhonopyGruneisenWork.from_gs_input(gsinp,
voldelta=0.1,
scdims=scdims,
phonopy_kwargs=None,
displ_kwargs=None)
flow.register_work(grun_work)
assert len(grun_work) == 3
nptu.assert_equal(scdims, grun_work.scdims)
# Will remove output files (WFK)
flow.set_garbage_collector()
flow.use_smartio()
flow.build_and_pickle_dump(abivalidate=True)
scheduler = flow.make_scheduler()
assert scheduler.start() == 0
assert not scheduler.exceptions
flow.show_status()
if not flow.all_ok:
flow.debug()
raise RuntimeError()
# Initialial work + 3 phonopy works.
assert len(flow) == 4
assert all(work.finalized for work in flow)
# The WFK files should have been removed because we called set_garbage_collector
# FIXME: This does not work because new works that have been created.
#for task in flow.iflat_tasks():
# assert not task.outdir.has_abiext("WFK")
for work in flow[1:]:
out_filenames = set(
[os.path.basename(f) for f in work.outdir.list_filepaths()])
nmiss = 0
for f in [
"POSCAR", "disp.yaml", "FORCE_SETS", "band.conf", "dos.conf",
"band-dos.conf", "README.md"
]:
if f not in out_filenames:
nmiss += 1
print("Cannot find %s in work.outdir" % f)
assert nmiss == 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)
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
