def from_dir(cls, top, walk=True):
"""
This classmethod builds a robot by scanning all files located within directory `top`.
Note that if walk is True, directories inside `top` are included as well.
This method should be invoked with a concrete robot class, for example:
robot = GsrRobot.from_dir(".")
Args:
top (str): Root directory
"""
top = os.path.abspath(top)
from abipy.abilab import abiopen
items = []
if walk:
for dirpath, dirnames, filenames in os.walk(top):
filenames = [f for f in filenames if f.endswith(cls.EXT + ".nc") or f.endswith(cls.EXT)]
for f in filenames:
ncfile = abiopen(os.path.join(dirpath, f))
if ncfile is not None: items.append((ncfile.filepath, ncfile))
else:
filenames = [f for f in os.listdir(top) if f.endswith(cls.EXT + ".nc") or f.endswith(cls.EXT)]
for f in filenames:
ncfile = abiopen(os.path.join(top, f))
if ncfile is not None: items.append((ncfile.filepath, ncfile))
return cls(*items)
def _open_files_in_dir(cls, top, walk):
"""Open files in directory tree starting from `top`. Return list of Abinit files."""
if not os.path.isdir(top):
raise ValueError("%s: no such directory" % str(top))
from abipy.abilab import abiopen
items = []
if walk:
for dirpath, dirnames, filenames in os.walk(top):
filenames = [
f for f in filenames if cls.class_handles_filename(f)
]
for f in filenames:
abifile = abiopen(os.path.join(dirpath, f))
if abifile is not None:
items.append((abifile.filepath, abifile))
else:
filenames = [
f for f in os.listdir(top) if cls.class_handles_filename(f)
]
for f in filenames:
abifile = abiopen(os.path.join(top, f))
if abifile is not None:
items.append((abifile.filepath, abifile))
return items
def test_coxp(self):
"""Test files based on the GaAs lobster test. Extracted from abinit calculation."""
# Test COHPCAR
with abiopen(os.path.join(lobster_gaas_dir, "GaAs_COHPCAR.lobster.gz")) as cohp:
repr(cohp); str(cohp)
assert cohp.to_string(verbose=2)
assert cohp.nsppol == 1
assert len(cohp.type_of_index) == 2
assert cohp.type_of_index[0] == "Ga" and cohp.type_of_index[1] == "As"
assert cohp.cop_type == "cohp"
self.assert_almost_equal(cohp.fermie, 2.29843, decimal=4)
assert len(cohp.energies) == 401
assert (0, 1) in cohp.partial
assert ("4s", "4p_x") in cohp.partial[(0, 1)]
assert 0 in cohp.partial[(0, 1)][("4s", "4p_x")]
assert len(cohp.partial[(0, 1)][("4s", "4p_x")][0]["single"]) == 401
self.assertAlmostEqual(cohp.partial[(0, 1)][("4s", "4p_x")][0]["single"][200], -0.02075)
assert len(cohp.site_pairs_total) == 2
assert len(cohp.site_pairs_partial) == 2
self.assertAlmostEqual(cohp.functions_pair_lorbitals[(0, 1)][("4s", "4p")][0].values[200], -0.06225)
self.assertAlmostEqual(cohp.functions_pair_morbitals[(0, 1)][("4s", "4p_x")][0].values[200], -0.02075)
self.assertAlmostEqual(cohp.functions_pair[(0, 1)][0].values[200], -0.06124)
#self.check_average(cohp)
if self.has_matplotlib():
assert cohp.plot(title="default values", show=False)
assert cohp.plot_site_pairs_total(from_site_index=[0, 1], what="single", exchange_xy=True, show=False)
assert cohp.plot_site_pairs_partial(from_site_index=[0, 1], what="single", exchange_xy=True, show=False)
assert cohp.plot_average_pairs(with_site_index=[0, 1], what="single", exchange_xy=True, show=False)
#assert cohp.plot_with_ebands(ebands_kpath, show=False)
if self.has_nbformat():
assert cohp.write_notebook(nbpath=self.get_tmpname(text=True))
# Test COOPCAR
with abiopen(os.path.join(lobster_gaas_dir, "GaAs_COOPCAR.lobster.gz")) as coop:
repr(coop); str(coop)
assert coop.to_string(verbose=2)
assert coop.nsppol == 1
assert len(coop.type_of_index) == 2
assert coop.type_of_index[0] == "Ga" and coop.type_of_index[1] == "As"
assert coop.cop_type == "coop"
assert len(coop.energies) == 401
assert (0, 1) in coop.partial
assert ("4s", "4p_x") in coop.partial[(0, 1)]
assert 0 in coop.partial[(0, 1)][("4s", "4p_x")]
assert len(coop.partial[(0, 1)][("4s", "4p_x")][0]["single"]) == 401
self.assertAlmostEqual(coop.partial[(0, 1)][("4s", "4p_x")][0]["single"][200], 0.01466)
#self.check_average(coop)
if self.has_matplotlib():
assert coop.plot(title="default values", show=False)
if self.has_nbformat():
assert coop.write_notebook(nbpath=self.get_tmpname(text=True))
def bsanddos(inputDos,inputBand,outputDos,outputBand,outputBoth,titleBS,titleDOS,show):
ebands = abilab.abiopen(inputBand).ebands
ebandsDos = abilab.abiopen(inputDos).ebands
dos = ebandsDos.get_edos();
fig=dos.plot(title=titleDOS,show=show,savefig=outputBand)
fig=ebands.plot(title=titleBS,show=show,savefig=outputDos)
fig=ebands.plot_with_dos(dos,savefig=outputBoth,show=show)
def bsanddos(inputDos, inputBand, outputDos, outputBand, outputBoth, titleBS,
titleDOS, show):
ebands = abilab.abiopen(inputBand).ebands
ebandsDos = abilab.abiopen(inputDos).ebands
dos = ebandsDos.get_edos()
fig = dos.plot(title=titleDOS, show=show, savefig=outputBand)
fig = ebands.plot(title=titleBS, show=show, savefig=outputDos)
fig = ebands.plot_with_dos(dos, savefig=outputBoth, show=show)
def test_base(self):
"""Test SIGRES File."""
sigres = abiopen(data.ref_file("tgw1_9o_DS4_SIGRES.nc"))
self.assertTrue(sigres.nsppol == 1)
# Markers are initialied in __init__
self.assertTrue(sigres.ebands.markers)
# In this run IBZ = kptgw
self.assertTrue(len(sigres.ibz) == 6)
self.assertTrue(sigres.gwkpoints == sigres.ibz)
kptgw_coords = np.reshape([
-0.25, -0.25, 0,
-0.25, 0.25, 0,
0.5, 0.5, 0,
-0.25, 0.5, 0.25,
0.5, 0, 0,
0, 0, 0
], (-1,3))
self.assert_almost_equal(sigres.ibz.frac_coords, kptgw_coords)
qpgaps = [3.53719151871085, 4.35685250045637, 4.11717896881632,
8.71122659251508, 3.29693118466282, 3.125545059031]
self.assert_almost_equal(sigres.qpgaps, np.reshape(qpgaps, (1,6)))
def test_mgo_becs_emacro(self):
"""
Testing DDB for MgO with with Born effective charges and E_macro.
Large breaking of the ASR.
"""
with abilab.abiopen(abidata.ref_file("mp-1009129-9x9x10q_ebecs_DDB")) as ddb:
assert ddb.structure.formula == "Mg1 O1"
assert len(ddb.qpoints) == 72
assert ddb.has_epsinf_terms()
assert ddb.has_epsinf_terms(select="at_least_one_diagoterm")
assert ddb.has_bec_terms()
if self.has_matplotlib():
plotter = ddb.anacompare_asr(asr_list=(0, 2), chneut_list=(0, 1), dipdip=1,
nqsmall=2, ndivsm=5, dos_method="tetra", ngqpt=None, verbose=2)
str(plotter)
assert plotter.combiplot(show=False)
# Test nqsmall == 0
plotter = ddb.anacompare_asr(asr_list=(0, 2), chneut_list=(0, 1), dipdip=1,
nqsmall=0, ndivsm=5, dos_method="tetra", ngqpt=None, verbose=2)
assert plotter.gridplot(show=False)
plotter = ddb.anacompare_dipdip(chneut_list=(0, 1), asr=1,
nqsmall=0, ndivsm=5, dos_method="gaussian", ngqpt=None, verbose=2)
assert plotter.gridplot(show=False)
def from_files(cls, filenames, labels=None, abspath=False):
"""
Build a Robot from a list of `filenames`.
if labels is None, labels are automatically generated from absolute paths.
Args:
abspath: True if paths in index should be absolute. Default: Relative to `top`.
"""
filenames = list_strings(filenames)
from abipy.abilab import abiopen
filenames = [f for f in filenames if cls.class_handles_filename(f)]
items = []
for i, f in enumerate(filenames):
try:
abifile = abiopen(f)
except Exception as exc:
cprint("Exception while opening file: `%s`" % str(f), "red")
cprint(exc, "red")
abifile = None
if abifile is not None:
label = abifile.filepath if labels is None else labels[i]
items.append((label, abifile))
new = cls(*items)
if labels is None and not abspath: new.trim_paths(start=None)
return new
def abinp_abispg(options):
"""Call Abinit with chkprim = 0 to find space group."""
inp = build_abinit_input_from_file(options, chkprim=0, mem_test=0)
r = inp.abivalidate()
if r.retcode != 0:
print(r.log_file, r.stderr_file)
return r.retcode
try:
out = abilab.abiopen(r.output_file.path)
except Exception as exc:
print("Error while trying to parse output file:", r.output_file.path)
print("Exception:\n", exc)
return 1
#print(out)
structure = out.initial_structure
# Call spglib to get spacegroup if Abinit spacegroup is not available.
# Return string with full information about crystalline structure i.e.
# space group, point group, wyckoff positions, equivalent sites.
print(structure.spget_summary(verbose=options.verbose))
if options.verbose:
print(structure.abi_spacegroup.to_string(verbose=options.verbose))
return 0
def itest_g0w0_flow(fwp, tvars):
"""Test flow for G0W0 calculations."""
scf, nscf, scr, sig = make_g0w0_inputs(ngkpt=[2, 2, 2], tvars=tvars)
flow = abilab.g0w0_flow(fwp.workdir,
scf,
nscf,
scr,
sig,
manager=fwp.manager)
# Will remove output files at run-time.
flow.set_garbage_collector()
flow.build_and_pickle_dump(abivalidate=True)
for task in flow[0]:
task.start_and_wait()
flow.check_status()
flow.show_status()
assert all(work.finalized for work in flow)
assert flow.all_ok
scf_task = flow[0][0]
nscf_task = flow[0][1]
scr_task = flow[0][2]
sig_task = flow[0][3]
# Test garbage)_collector
# The WFK|SCR file should have been removed because we call set_garbage_collector
assert not scf_task.outdir.has_abiext("WFK")
assert not nscf_task.outdir.has_abiext("WFK")
assert not scr_task.outdir.has_abiext("SCR")
assert not scr_task.outdir.has_abiext("SUS")
# The sigma task should produce a SIGRES file.
sigfile = sig_task.outdir.list_filepaths(wildcard="*SIGRES.nc")[0]
assert sigfile
with abilab.abiopen(sigfile) as sigres:
assert sigres.nsppol == 1
# Test SigmaTask inspect method
#if has_matplotlib
#sig_task.inspect(show=False)
# Test get_results for Sigma and Scr
scr_task.get_results()
sig_task.get_results()
# Test SCR.nc file (this is optional)
if scr_task.scr_path:
with scr_task.open_scr() as scr:
print(scr)
assert len(scr.wpts) == 2
assert scr.nwre == 1 and scr.nwim == 1
for iq, qpoint in enumerate(scr.qpoints[:2]):
print(qpoint)
qpt, iqcheck = scr.reader.find_qpoint_fileindex(qpoint)
assert iqcheck == iq
em1 = scr.get_em1(qpoint)
print(em1)
def test_lobsterdos(self):
"""Testing Lobster DOSCAR files."""
with abiopen(os.path.join(lobster_gaas_dir,
"GaAs_DOSCAR.lobster.gz")) as ldos:
repr(ldos)
str(ldos)
assert ldos.to_string(verbose=2)
assert len(ldos.energies) == 401
assert ldos.nsppol == 1
assert ldos.nsites == 2
assert 1 in ldos.pdos
assert "4p_x" in ldos.pdos[1]
assert 0 in ldos.pdos[1]["4p_x"]
self.assert_almost_equal(ldos.fermie, 2.29843, decimal=4)
assert ldos.type_of_index[0] == "Ga" and ldos.type_of_index[
1] == "As"
self.assertAlmostEqual(ldos.pdos[1]["4p_x"][0][200], 0.02694)
self.assertAlmostEqual(ldos.total_dos[0][200], 0.17824)
self.check_average(ldos)
if self.has_matplotlib():
assert ldos.plot(title="default values", show=False)
assert ldos.plot_pdos_site(site_index=0,
title="default values",
show=False)
assert ldos.plot_pdos_site(site_index=[0, 1],
exchange_xy=True,
title="default values",
show=False)
#assert cohp.plot_with_ebands(ebands_kpath, show=False)
if self.has_nbformat():
assert ldos.write_notebook(nbpath=self.get_tmpname(text=True))
def test_vpot_ncfile(self):
"""Testing POT netcdf file."""
with abilab.abiopen(abidata.ref_file("ni_666k_POT.nc")) as ncfile:
repr(ncfile); str(ncfile)
assert ncfile.ebands.nsppol == 2 and ncfile.ebands.nspden == 2
assert ncfile.structure.formula == "Ni1"
assert ncfile.ebands.structure == ncfile.structure
assert str(ncfile.xc) == "PBE"
vks = ncfile.vks
assert vks.netcdf_name == "vtrial"
assert vks.nspinor == 1 and vks.nsppol == 2 and vks.nspden == 2
assert vks.is_potential_like
assert not vks.is_density_like
## Test converters.
#ncfile.write_chgcar(filename=self.get_tmpname(text=True))
#ncfile.write_xsf(filename=self.get_tmpname(text=True, suffix=".xsf"))
#ncfile.write_cube(filename=self.get_tmpname(text=True), spin="total")
if self.has_matplotlib():
assert ncfile.ebands.plot(show=False)
# Test ipython notebooks.
if self.has_nbformat():
ncfile.write_notebook(nbpath=self.get_tmpname(text=True))
def test_phbst_file_with_loto(self):
"""Testing PHBST file with LOTO terms from anaddb.nc."""
with abilab.abiopen(abidata.ref_file("ZnSe_hex_886.out_PHBST.nc")) as ncfile:
phbands = ncfile.phbands
# Phonon frequencies with non analytical contributions, if calculated, are saved
# in the anaddb.nc file produced by anaddb. The results should be fetched from there
# and added to the phonon bands.
phbands.read_non_anal_from_file(abidata.ref_file("ZnSe_hex_886.anaddb.nc"))
nana = phbands.non_anal_ph
assert nana.structure == phbands.structure
str(nana.structure.reciprocal_lattice)
self.assert_almost_equal(nana.directions.ravel(),
[0.1234510847, -0.071274517, 0, 0.1646014463, 0, 0, 0, 0, 0.0751616546])
for i, cart_direc in enumerate(nana.directions):
assert nana.has_direction(cart_direc, cartesian=True)
red_direc = phbands.structure.reciprocal_lattice.get_fractional_coords(cart_direc)
idir, qdir = phbands.qindex_qpoint(red_direc, is_non_analytical_direction=True)
assert i == idir
idir, qdir = phbands.qindex_qpoint(qdir, is_non_analytical_direction=True)
assert i == idir
if self.has_matplotlib():
assert phbands.plot(title="ZnSe with LO-TO splitting", show=False)
red_direc = phbands.structure.reciprocal_lattice.get_fractional_coords(nana.directions[1])
assert phbands.plot_phdispl(qpoint=red_direc, is_non_analytical_direction=True, show=False)
assert phbands.plot_phdispl(qpoint=red_direc, is_non_analytical_direction=True, use_eigvec=True, show=False)
def add_file(self, label, ncfile):
if is_string(ncfile):
from abipy.abilab import abiopen
ncfile = abiopen(ncfile)
self._do_close[ncfile.filepath] = True
self._ncfiles[label] = ncfile
def test_vpot_ncfile(self):
"""Testing POT netcdf file."""
with abilab.abiopen(abidata.ref_file("ni_666k_POT.nc")) as ncfile:
repr(ncfile); str(ncfile)
assert ncfile.ebands.nsppol == 2 and ncfile.ebands.nspden == 2
assert ncfile.structure.formula == "Ni1"
assert ncfile.ebands.structure == ncfile.structure
assert str(ncfile.xc) == "PBE"
vks = ncfile.vks
assert vks.netcdf_name == "vtrial"
assert vks.nspinor == 1 and vks.nsppol == 2 and vks.nspden == 2
assert vks.is_potential_like
assert not vks.is_density_like
## Test converters.
#ncfile.write_chgcar(filename=self.get_tmpname(text=True))
#ncfile.write_xsf(filename=self.get_tmpname(text=True, suffix=".xsf"))
#ncfile.write_cube(filename=self.get_tmpname(text=True), spin="total")
if self.has_matplotlib():
assert ncfile.ebands.plot(show=False)
# Test ipython notebooks.
if self.has_nbformat():
ncfile.write_notebook(nbpath=self.get_tmpname(text=True))
def on_value_change(change):
"""Callback"""
clear_output()
path = change["new"]
#print(change)
with abilab.abiopen(path) as abifile:
print(abifile)
def test_vhxc_ncfile(self):
"""Testing VHXC netcdf file."""
with abilab.abiopen(abidata.ref_file("ni_666k_VHXC.nc")) as ncfile:
repr(ncfile); str(ncfile)
assert ncfile.ebands.nsppol == 2 and ncfile.ebands.nspden == 2
assert ncfile.structure.formula == "Ni1"
assert ncfile.ebands.structure == ncfile.structure
assert str(ncfile.xc) == "PBE"
# Kpoint sampling
#ngkpt 6 6 6 nshiftk 4
#shiftk 1/2 1/2 1/2 1/2 0.0 0.0 0.0 1/2 0.0 0.0 0.0 1/2
assert not ncfile.ebands.kpoints.is_mpmesh
assert not ncfile.ebands.kpoints.is_path
vhxc = ncfile.vhxc
assert vhxc.netcdf_name == "vhxc"
assert vhxc.netcdf_name == "vhxc"
assert vhxc.nspinor == 1 and vhxc.nsppol == 2 and vhxc.nspden == 2
assert vhxc.is_potential_like
assert not vhxc.is_density_like
## Test converters.
#ncfile.write_chgcar(filename=self.get_tmpname(text=True))
#ncfile.write_xsf(filename=self.get_tmpname(text=True, suffix=".xsf"))
#ncfile.write_cube(filename=self.get_tmpname(text=True), spin="total")
if self.has_matplotlib():
assert ncfile.ebands.plot(show=False)
# Test ipython notebooks.
if self.has_nbformat():
ncfile.write_notebook(nbpath=self.get_tmpname(text=True))
def test_ddk_api(self):
"""Testing DDK API"""
with abilab.abiopen(abidata.ref_file("gaas_444_dir1_DDK.nc")) as ddk:
repr(ddk)
str(ddk)
assert ddk.to_string(verbose=2)
assert ddk.structure.formula == "Ga1 As1"
assert ddk.ebands.nsppol == 1 and ddk.ebands.nspden == 1 and ddk.ebands.nspinor == 1
assert ddk.ebands.nband == 20
assert ddk.idir == 1 and ddk.ipert == len(ddk.structure) + 1
assert ddk.kptopt == 2
ksamp = ddk.kpoints.ksampling
self.assert_equal(ksamp.kptrlatt_orig.ravel(),
[4, 0, 0, 0, 4, 0, 0, 0, 4])
self.assert_equal(
ksamp.shifts_orig.ravel(),
[0.5, 0.5, 0.5, 0.5, 0.0, 0.0, 0.0, 0.5, 0.0, 0.0, 0.0, 0.5])
assert ddk.kpoints.is_ibz
ddk.kpoints.check_weights()
assert np.all(ddk.hdr["qptn"] == 0)
#assert ddk.xc == "LDA"
assert ddk.params["nband"] == 20
if self.has_nbformat():
assert ddk.write_notebook(nbpath=self.get_tmpname(text=True))
def test_lobsterdos(self):
"""Testing Lobster DOSCAR files."""
with abiopen(os.path.join(lobster_gaas_dir, "GaAs_DOSCAR.lobster.gz")) as ldos:
repr(ldos); str(ldos)
assert ldos.to_string(verbose=2)
assert len(ldos.energies) == 401
assert ldos.nsppol == 1
assert ldos.nsites == 2
assert 1 in ldos.pdos
assert "4p_x" in ldos.pdos[1]
assert 0 in ldos.pdos[1]["4p_x"]
self.assert_almost_equal(ldos.fermie, 2.29843, decimal=4)
assert ldos.type_of_index[0] == "Ga" and ldos.type_of_index[1] == "As"
self.assertAlmostEqual(ldos.pdos[1]["4p_x"][0][200], 0.02694)
self.assertAlmostEqual(ldos.total_dos[0][200], 0.17824)
self.check_average(ldos)
if self.has_matplotlib():
assert ldos.plot(title="default values", show=False)
assert ldos.plot_pdos_site(site_index=0, title="default values", show=False)
assert ldos.plot_pdos_site(site_index=[0, 1], exchange_xy=True, title="default values", show=False)
#assert cohp.plot_with_ebands(ebands_kpath, show=False)
if self.has_nbformat():
assert ldos.write_notebook(nbpath=self.get_tmpname(text=True))
def from_files(cls, filenames, labels=None, abspath=False):
"""
Build a Robot from a list of `filenames`.
if labels is None, labels are automatically generated from absolute paths.
Args:
abspath: True if paths in index should be absolute. Default: Relative to `top`.
"""
filenames = list_strings(filenames)
from abipy.abilab import abiopen
filenames = [f for f in filenames if cls.class_handles_filename(f)]
items = []
for i, f in enumerate(filenames):
try:
abifile = abiopen(f)
except Exception as exc:
cprint("Exception while opening file: `%s`" % str(f), "red")
cprint(exc, "red")
abifile = None
if abifile is not None:
label = abifile.filepath if labels is None else labels[i]
items.append((label, abifile))
new = cls(*items)
if labels is None and not abspath: new.trim_paths(start=None)
return new
def from_file(cls, filepath):
"""
Generate object from (SIGRES.nc) file. Main entry point for client code.
"""
from abipy.abilab import abiopen
with abiopen(filepath) as ncfile:
return cls(qps_spin=ncfile.qplist_spin, sigres_ebands=ncfile.ebands)
def add_file(self, label, abifile, filter_abifile=None):
"""
Add a file to the robot with the given label.
Args:
label: String used to identify the file (must be unique, ax exceptions is
raised if label is already present.
abifile: Specify the file to be added. Accepts strings (filepath) or abipy file-like objects.
filter_abifile: Function that receives an ``abifile`` object and returns
True if the file should be added to the plotter.
"""
if is_string(abifile):
from abipy.abilab import abiopen
abifile = abiopen(abifile)
if filter_abifile is not None and not filter_abifile(abifile):
abifile.close()
return
# Open file here --> have to close it.
self._do_close[abifile.filepath] = True
if label in self._abifiles:
raise ValueError("label %s is already present!" % label)
self._abifiles[label] = abifile
def test_plot_functions(self):
"""Testing plotting tools for phonons."""
if not self.has_matplotlib():
raise unittest.SkipTest("matplotlib missing")
phbst_filename = abidata.ref_file("trf2_5.out_PHBST.nc")
from abipy import abilab
with abilab.abiopen(phbst_filename) as nc:
phbands = nc.phbands
phb_objects = [
phbands,
phbst_filename,
]
phdos_filename = abidata.ref_file("trf2_5.out_PHDOS.nc")
phdos = PhdosFile(phdos_filename)
phdos_objects = [
phdos,
phdos_filename,
]
fig = phbands_gridplot(phb_objects,
titles=["phonons1", "phonons2"],
phdos_objects=phdos_objects,
show=False)
assert fig is not None
phdos.close()
def test_vhxc_ncfile(self):
"""Testing VHXC netcdf file."""
with abilab.abiopen(abidata.ref_file("ni_666k_VHXC.nc")) as ncfile:
repr(ncfile); str(ncfile)
assert ncfile.ebands.nsppol == 2 and ncfile.ebands.nspden == 2
assert ncfile.structure.formula == "Ni1"
assert ncfile.ebands.structure == ncfile.structure
assert str(ncfile.xc) == "PBE"
# Kpoint sampling
#ngkpt 6 6 6 nshiftk 4
#shiftk 1/2 1/2 1/2 1/2 0.0 0.0 0.0 1/2 0.0 0.0 0.0 1/2
assert not ncfile.ebands.kpoints.is_mpmesh
assert not ncfile.ebands.kpoints.is_path
vhxc = ncfile.vhxc
assert vhxc.netcdf_name == "vhxc"
assert vhxc.netcdf_name == "vhxc"
assert vhxc.nspinor == 1 and vhxc.nsppol == 2 and vhxc.nspden == 2
assert vhxc.is_potential_like
assert not vhxc.is_density_like
## Test converters.
#ncfile.write_chgcar(filename=self.get_tmpname(text=True))
#ncfile.write_xsf(filename=self.get_tmpname(text=True, suffix=".xsf"))
#ncfile.write_cube(filename=self.get_tmpname(text=True), spin="total")
if self.has_matplotlib():
assert ncfile.ebands.plot(show=False)
# Test ipython notebooks.
if self.has_nbformat():
ncfile.write_notebook(nbpath=self.get_tmpname(text=True))
def test_phbst_file(self):
"""Testing PHBST file."""
with abilab.abiopen(abidata.ref_file("trf2_5.out_PHBST.nc")) as ncfile:
assert ncfile.phbands is not None
for iq, qpt in enumerate(ncfile.qpoints):
assert hasattr(qpt, "frac_coords")
assert ncfile.qpoints[ncfile.qindex(qpt)] == qpt
ii = ncfile.qindex(qpt)
#print("iq", iq, "qpt", qpt, "ii", ii, "qpoints[ii]", ncfile.qpoints[ii])
same_ii, same_qpt = ncfile.qindex_qpoint(ii)
assert same_ii == ii and qpt == same_qpt
same_ii, same_qpt = ncfile.phbands.qindex_qpoint(qpt)
assert same_ii == ii and qpt == same_qpt
qpoint = ncfile.qpoints[0]
frame = ncfile.get_phframe(qpoint)
assert frame.qpoint == qpoint
mode0 = ncfile.get_phmode(qpoint, 0)
repr(mode0)
str(mode0)
mode0.to_string(with_displ=True)
assert mode0.qpoint == qpoint
self.serialize_with_pickle(mode0, test_eq=False)
last_mode = ncfile.get_phmode(ncfile.qpoints[0], -1)
assert last_mode > mode0
# Test notebook
if self.has_nbformat():
ncfile.write_notebook(nbpath=self.get_tmpname(text=True))
def test_base(self):
"""Test SIGRES File."""
sigres = abiopen(data.ref_file("tgw1_9o_DS4_SIGRES.nc"))
self.assertTrue(sigres.nsppol == 1)
# Markers are initialied in __init__
self.assertTrue(sigres.ebands.markers)
# In this run IBZ = kptgw
self.assertTrue(len(sigres.ibz) == 6)
self.assertTrue(sigres.gwkpoints == sigres.ibz)
kptgw_coords = np.reshape([
-0.25, -0.25, 0, -0.25, 0.25, 0, 0.5, 0.5, 0, -0.25, 0.5, 0.25,
0.5, 0, 0, 0, 0, 0
], (-1, 3))
self.assert_almost_equal(sigres.ibz.frac_coords, kptgw_coords)
qpgaps = [
3.53719151871085, 4.35685250045637, 4.11717896881632,
8.71122659251508, 3.29693118466282, 3.125545059031
]
self.assert_almost_equal(sigres.qpgaps, np.reshape(qpgaps, (1, 6)))
def test_phbst_file_with_loto(self):
"""Testing PHBST file with LOTO terms from anaddb.nc."""
with abilab.abiopen(abidata.ref_file("ZnSe_hex_886.out_PHBST.nc")) as ncfile:
phbands = ncfile.phbands
# Phonon frequencies with non analytical contributions, if calculated, are saved
# in the anaddb.nc file produced by anaddb. The results should be fetched from there
# and added to the phonon bands.
phbands.read_non_anal_from_file(abidata.ref_file("ZnSe_hex_886.anaddb.nc"))
nana = phbands.non_anal_ph
assert nana.structure == phbands.structure
str(nana.structure.reciprocal_lattice)
self.assert_almost_equal(nana.directions.ravel(),
[0.1234510847, -0.071274517, 0, 0.1646014463, 0, 0, 0, 0, 0.0751616546])
for i, cart_direc in enumerate(nana.directions):
assert nana.has_direction(cart_direc, cartesian=True)
red_direc = phbands.structure.reciprocal_lattice.get_fractional_coords(cart_direc)
idir, qdir = phbands.qindex_qpoint(red_direc, is_non_analytical_direction=True)
assert i == idir
idir, qdir = phbands.qindex_qpoint(qdir, is_non_analytical_direction=True)
assert i == idir
if self.has_matplotlib():
assert phbands.plot(title="ZnSe with LO-TO splitting", show=False)
red_direc = phbands.structure.reciprocal_lattice.get_fractional_coords(nana.directions[1])
assert phbands.plot_phdispl(qpoint=red_direc, is_non_analytical_direction=True, show=False)
assert phbands.plot_phdispl(qpoint=red_direc, is_non_analytical_direction=True, use_eigvec=True, show=False)
def add_file(self, filepath, label=None):
"""Add a filename to the plotter"""
from abipy.abilab import abiopen
sigres = abiopen(filepath)
self._sigres_files[sigres.filepath] = sigres
# TODO: Not used
self._labels.append(label)
# Initialize/check useful quantities.
#
# 1) Number of spins
if not hasattr(self, "nsppol"):
self.nsppol = sigres.nsppol
if self.nsppol != sigres.nsppol:
raise ValueError("Found two SIGRES files with different nsppol")
# The set of k-points where GW corrections have been computed.
if not hasattr(self, "computed_gwkpoints"):
self.computed_gwkpoints = sigres.gwkpoints
if self.computed_gwkpoints != sigres.gwkpoints:
raise ValueError("Found two SIGRES files with different list of GW k-points.")
#self.computed_gwkpoints = (self.computed_gwkpoints + sigres.gwkpoints).remove_duplicated()
if not hasattr(self, "max_gwbstart"):
self.max_gwbstart = sigres.max_gwbstart
else:
self.max_gwbstart = max(self.max_gwbstart, sigres.max_gwbstart)
if not hasattr(self, "min_gwbstop"):
self.min_gwbstop = sigres.min_gwbstop
else:
self.min_gwbstop = min(self.min_gwbstop, sigres.min_gwbstop)
def test_example03_silicon(self):
"""Parsing example02_silicon.wout with DISENTANGLE"""
filepath = os.path.join(abidata.dirpath, "refs", "wannier90", "example03_silicon.wout")
with abilab.abiopen(filepath) as wout:
repr(wout); str(wout)
assert wout.to_string(verbose=2)
assert wout.version == "2.1.0+git"
assert wout.structure.formula == "Si2"
self.assert_almost_equal(wout.structure.frac_coords.ravel(),
[-0.25000, 0.75000, -0.25000, 0.00000, 0.00000, 0.00000])
assert not wout.warnings
for k in ("MAIN", "WANNIERISE", "DISENTANGLE"):
assert k in wout.params_section
assert wout.use_disentangle
assert wout.nwan == 8
assert np.all(wout.grid_size == 4)
assert len(wout.conv_df) == 6 + 1
assert wout.conv_df.O_D[1] == 0.1213986 and wout.conv_df.O_OD[1] == 2.7017701
assert wout.conv_df.O_D.values[-1] == 0.1054702 and wout.conv_df.O_OD.values[-1] == 2.5449106
# numpy array (nwan, nstep, ...)
nstep = len(wout.conv_df.O_D)
assert wout.wf_centers.shape == (wout.nwan, nstep, 3)
self.assert_equal(wout.wf_centers[7, -1], [0.888643, 0.888652, 1.810090 ])
assert wout.wf_spreads.shape == (wout.nwan, nstep)
self.assert_equal(wout.wf_spreads[7, -1], 1.81245236)
if self.has_matplotlib():
assert wout.plot(show=False)
assert wout.plot_centers_spread(show=False)
if self.has_nbformat():
assert wout.write_notebook(nbpath=self.get_tmpname(text=True))
def abiview_log(options):
"""
Print WARNINGS/COMMENTS/ERRORS found in Abinit log file.
"""
with abilab.abiopen(options.filepath) as abo:
print(abo.to_string(verbose=options.verbose))
return 0
def from_file(cls, filepath):
"""
Generate object from (SIGRES.nc) file. Main entry point for client code.
"""
from abipy.abilab import abiopen
with abiopen(filepath) as ncfile:
return cls(qps_spin=ncfile.qplist_spin, sigres_ebands=ncfile.ebands)
def test_plot_functions(self):
"""Testing plotting tools for phonons."""
phbst_filename = abidata.ref_file("trf2_5.out_PHBST.nc")
with abilab.abiopen(phbst_filename) as nc:
phbands = nc.phbands
phb_objects = [
phbands,
phbst_filename,
]
phdos_filename = abidata.ref_file("trf2_5.out_PHDOS.nc")
phdos = PhdosFile(phdos_filename)
phdos_objects = [
phdos,
phdos_filename,
]
if self.has_matplotlib():
assert phbands_gridplot(phb_objects,
titles=["phonons1", "phonons2"],
phdos_objects=phdos_objects,
units="meV",
show=False)
phdos.close()
def test_dryrun_output(self):
"""Testing AbinitOutputFile with file produced in dry-run mode."""
with abilab.abiopen(abidata.ref_file("refs/dryrun.abo")) as abo:
repr(abo); str(abo)
assert abo.to_string(verbose=2)
assert abo.dryrun_mode
assert abo.ndtset == 1
assert abo.has_same_initial_structures
assert abo.has_same_final_structures
assert len(abo.initial_structures) == 1
assert abo.initial_structure.abi_spacegroup is not None
# This to test get_dims_spginfo_dataset with one dataset.
dims_dataset, spg_dataset = abo.get_dims_spginfo_dataset()
assert len(dims_dataset) == 1
dims = dims_dataset[1]
assert dims["nsppol"] == 1
assert dims["nsym"] == 48
assert dims["nkpt"] == 29
self.assert_almost_equal(dims["mem_per_proc_mb"], 3.389)
self.assert_almost_equal(dims["wfk_size_mb"], 0.717)
self.assert_almost_equal(dims["denpot_size_mb"], 0.046)
assert spg_dataset[1]["spg_symbol"] == "Fd-3m"
assert spg_dataset[1]["spg_number"] == 227
assert spg_dataset[1]["bravais"] == "Bravais cF (face-center cubic)"
def test_phbst_file(self):
"""Testing PHBST file."""
with abilab.abiopen(abidata.ref_file("trf2_5.out_PHBST.nc")) as ncfile:
assert ncfile.phbands is not None
for iq, qpt in enumerate(ncfile.qpoints):
assert hasattr(qpt, "frac_coords")
assert ncfile.qpoints[ncfile.qindex(qpt)] == qpt
ii = ncfile.qindex(qpt)
#print("iq", iq, "qpt", qpt, "ii", ii, "qpoints[ii]", ncfile.qpoints[ii])
same_ii, same_qpt = ncfile.qindex_qpoint(ii)
assert same_ii == ii and qpt == same_qpt
same_ii, same_qpt = ncfile.phbands.qindex_qpoint(qpt)
assert same_ii == ii and qpt == same_qpt
qpoint = ncfile.qpoints[0]
frame = ncfile.get_phframe(qpoint)
assert frame.qpoint == qpoint
mode0 = ncfile.get_phmode(qpoint, 0)
repr(mode0); str(mode0)
mode0.to_string(with_displ=True)
assert mode0.qpoint == qpoint
self.serialize_with_pickle(mode0, test_eq=False)
last_mode = ncfile.get_phmode(ncfile.qpoints[0], -1)
assert last_mode > mode0
# Test notebook
if self.has_nbformat():
ncfile.write_notebook(nbpath=self.get_tmpname(text=True))
def test_frohlich_zpr_flow(self):
"""Testing FrohlichZPRFlow"""
# Read structure from DDB file.
from abipy import abilab
ddb_path = abidata.ref_file("refs/mgo_v8t57/mgo_zpr_t57o_DS3_DDB")
with abilab.abiopen(ddb_path) as ddb:
structure = ddb.structure
pseudos = abidata.pseudos("Ca.psp8", "O.psp8")
scf_input = abilab.AbinitInput(structure=structure, pseudos=pseudos)
# Set other input variables. These quantities are system-depedent.
# Here we use parameters similar to https://docs.abinit.org/tests/v8/Input/t57.in
scf_input.set_vars(
nband=12,
nbdbuf=2,
diemac=6,
ecut=30, # Underconverged ecut.
#ecut=15,
nstep=100,
tolvrs=1e-16,
kptrlatt=[-2, 2, 2, # In cartesian coordinates, this grid is simple cubic
2, -2, 2,
2, 2, -2],
)
workdir = self.mkdtemp()
flow = FrohlichZPRFlow.from_scf_input(workdir, scf_input, ddb_node=ddb_path, ndivsm=2, tolwfr=1e-20,
metadata={"mp_id": "mp-149"})
flow.allocate()
flow.check_status()
isok, checks = flow.abivalidate_inputs()
assert isok
def test_example01_gaas(self):
"""Parsing example01_gaas.wout"""
filepath = os.path.join(abidata.dirpath, "refs", "wannier90", "example01_gaas.wout")
with abilab.abiopen(filepath) as wout:
repr(wout); str(wout)
assert wout.to_string(verbose=2)
assert wout.version == "2.1.0+git"
assert wout.structure.formula == "Ga1 As1"
self.assert_almost_equal(wout.structure.frac_coords.ravel(),
[0.00000, 0.00000, 0.00000, 0.25000, 0.25000, 0.25000])
assert not wout.warnings
for k in ("MAIN", "WANNIERISE"):
assert k in wout.params_section
assert not wout.use_disentangle
assert wout.nwan == 4
assert np.all(wout.grid_size == 2)
assert len(wout.conv_df) == 20 + 1
assert wout.conv_df.O_D[0] == 0.0083198 and wout.conv_df.O_OD[0] == 0.5036294
assert wout.conv_df.O_D[20] == 0.0080300 and wout.conv_df.O_OD[20] == 0.5019880
# numpy array (nwan, nstep, ...)
#natom = len(wout.structure)
nstep = 21
assert wout.wf_centers.shape == (wout.nwan, nstep, 3)
self.assert_equal(wout.wf_centers[1, 20], [-0.866253, 0.866253, 0.866253])
assert wout.wf_spreads.shape == (wout.nwan, nstep)
self.assert_equal(wout.wf_spreads[1, 20], 1.11672024)
if self.has_matplotlib():
assert wout.plot(show=False)
assert wout.plot_centers_spread(show=False)
if self.has_nbformat():
assert wout.write_notebook(nbpath=self.get_tmpname(text=True))
def abiview_ddb_ir(options):
"""
Compute infra-red spectrum from DDB. Plot results.
"""
asr = 2
chneut = 1
dipdip = 1
print("""
Computing phonon frequencies for infra-red spectrum with:
asr = {asr}, chneut = {chneut}, dipdip = {dipdip}
""".format(**locals()))
with abilab.abiopen(options.filepath) as ddb:
tgen = ddb.anaget_dielectric_tensor_generator(asr=asr,
chneut=chneut,
dipdip=dipdip,
verbose=options.verbose)
print(tgen.to_string(verbose=options.verbose))
gamma_ev = 1e-4
print(
"Plotting dielectric tensor with constant phonon damping: %s (eV)"
% gamma_ev)
tgen.plot_all(gamma_ev=gamma_ev)
return 0
def abiview_ddb_ifc(options):
"""
Visualize interatomic force constants in real space.
"""
asr = 2
chneut = 1
dipdip = 1
print("""
Computing interatomic force constants with
asr = {asr}, chneut = {chneut}, dipdip = {dipdip}
""".format(**locals()))
with abilab.abiopen(options.filepath) as ddb:
# Execute anaddb to compute the interatomic force constants.
ifc = ddb.anaget_ifc(asr=asr, chneut=chneut, dipdip=dipdip)
#print(ifc)
with MplExpose(slide_mode=options.slide_mode,
slide_timeout=options.slide_timeout) as e:
e(ifc.plot_longitudinal_ifc(title="Longitudinal IFCs", show=False))
e(
ifc.plot_longitudinal_ifc_short_range(
title="Longitudinal IFCs short range", show=False))
e(
ifc.plot_longitudinal_ifc_ewald(
title="Longitudinal IFCs Ewald", show=False))
return 0
def abinp_abispg(options):
"""Call Abinit with chkprim = 0 to find space group."""
inp = build_abinit_input_from_file(options, chkprim=0, mem_test=0)
r = inp.abivalidate()
if r.retcode != 0:
print(r.log_file, r.stderr_file)
return r.retcode
try:
out = abilab.abiopen(r.output_file.path)
except Exception as exc:
print("Error while trying to parse output file:", r.output_file.path)
print("Exception:\n", exc)
return 1
#print(out)
structure = out.initial_structure
# Call spglib to get spacegroup if Abinit spacegroup is not available.
# Return string with full information about crystalline structure i.e.
# space group, point group, wyckoff positions, equivalent sites.
print(structure.spget_summary(verbose=options.verbose))
if options.verbose:
print(structure.abi_spacegroup.to_string(verbose=options.verbose))
return 0
def add_file(self, label, abifile, filter_abifile=None):
"""
Add a file to the robot with the given label.
Args:
label: String used to identify the file (must be unique, ax exceptions is
raised if label is already present.
abifile: Specify the file to be added. Accepts strings (filepath) or abipy file-like objects.
filter_abifile: Function that receives an ``abifile`` object and returns
True if the file should be added to the plotter.
"""
if is_string(abifile):
from abipy.abilab import abiopen
abifile = abiopen(abifile)
if filter_abifile is not None and not filter_abifile(abifile):
abifile.close()
return
# Open file here --> have to close it.
self._do_close[abifile.filepath] = True
if label in self._abifiles:
raise ValueError("label %s is already present!" % label)
self._abifiles[label] = abifile
def __init__(self, parent, filepath, **kwargs):
"""
Args:
parent:
parent window
filepath:
Abinit output file.
"""
filepath = os.path.abspath(filepath)
if "title" not in kwargs:
kwargs["title"] = "Abinit Timer: %s" % os.path.basename(filepath)
super(AbinitTimerFrame, self).__init__(parent, **kwargs)
try:
abifile = abiopen(filepath)
self.timer_data = abifile.timer_data
except Exception as exc:
raise awx.Error(str(exc))
if not self.timer_data:
raise awx.Error("%s does not contain a valid ABINIT TIMER section!" % filepath)
self.BuildUi()
def abiview_log(options):
"""
Print WARNINGS/COMMENTS/ERRORS found in Abinit log file.
"""
with abilab.abiopen(options.filepath) as abo:
print(abo.to_string(verbose=options.verbose))
return 0
def test_dryrun_output(self):
"""Testing AbinitOutputFile with file produced in dry-run mode."""
with abilab.abiopen(abidata.ref_file("refs/dryrun.abo")) as abo:
repr(abo); str(abo)
assert abo.to_string(verbose=2)
assert abo.dryrun_mode
assert abo.ndtset == 1
assert abo.has_same_initial_structures
assert abo.has_same_final_structures
assert len(abo.initial_structures) == 1
assert abo.initial_structure.abi_spacegroup is not None
# This to test get_dims_spginfo_dataset with one dataset.
dims_dataset, spg_dataset = abo.get_dims_spginfo_dataset()
assert len(dims_dataset) == 1
dims = dims_dataset[1]
assert dims["nsppol"] == 1
assert dims["nsym"] == 48
assert dims["nkpt"] == 29
self.assert_almost_equal(dims["mem_per_proc_mb"], 3.389)
self.assert_almost_equal(dims["wfk_size_mb"], 0.717)
self.assert_almost_equal(dims["denpot_size_mb"], 0.046)
assert spg_dataset[1]["spg_symbol"] == "Fd-3m"
assert spg_dataset[1]["spg_number"] == 227
assert spg_dataset[1]["bravais"] == "Bravais cF (face-center cubic)"
def itest_g0w0_flow(fwp, tvars):
"""Test flow for G0W0 calculations."""
scf, nscf, scr, sig = make_g0w0_inputs(ngkpt=[2, 2, 2], tvars=tvars)
flow = abilab.g0w0_flow(fwp.workdir, scf, nscf, scr, sig, manager=fwp.manager)
# Will remove output files at run-time.
flow.set_cleanup_exts()
flow.build_and_pickle_dump()
for task in flow[0]:
task.start_and_wait()
flow.check_status()
flow.show_status()
assert all(work.finalized for work in flow)
assert flow.all_ok
scf_task = flow[0][0]
nscf_task = flow[0][1]
scr_task = flow[0][2]
sig_task = flow[0][3]
# Test set_cleanup_exts
# The WFK|SCR file should have been removed because we call set_cleanup_exts
assert not scf_task.outdir.has_abiext("WFK")
assert not nscf_task.outdir.has_abiext("WFK")
assert not scr_task.outdir.has_abiext("SCR")
assert not scr_task.outdir.has_abiext("SUS")
# The sigma task should produce a SIGRES file.
sigfile = sig_task.outdir.list_filepaths(wildcard="*SIGRES.nc")[0]
assert sigfile
with abilab.abiopen(sigfile) as sigres:
assert sigres.nsppol == 1
def test_readall(self):
for path in abidata.SIGRES_NCFILES:
with abilab.abiopen(path) as sigres:
repr(sigres)
str(sigres)
assert sigres.to_string(verbose=2)
assert len(sigres.structure)
def test_alas_with_third_order(self):
"""
Testing DDB containing also third order derivatives.
"""
with abilab.abiopen(
abidata.ref_file("refs/alas_nl_dfpt/AlAs_nl_dte_DDB")) as ddb:
repr(ddb)
str(ddb)
assert ddb.to_string(verbose=2)
self.assert_almost_equal(ddb.total_energy.to("Ha"),
-0.10085769246152e+02)
assert ddb.cart_forces is not None
stress = ddb.cart_stress_tensor
# Ha/Bohr^3 from DDB
ref_voigt = np.array([
-0.31110177329142E-05, -0.31110177329142E-05,
-0.31110177329146E-05, 0.00000000000000E+00,
0.00000000000000E+00, 0.00000000000000E+00
])
# AbiPy stress is in GPa
self.assert_almost_equal(stress[0, 0],
ref_voigt[0] * abu.HaBohr3_GPa)
self.assert_almost_equal(stress[1, 1],
ref_voigt[1] * abu.HaBohr3_GPa)
self.assert_almost_equal(stress[2, 2],
ref_voigt[2] * abu.HaBohr3_GPa)
self.assert_almost_equal(stress[1, 2],
ref_voigt[3] * abu.HaBohr3_GPa)
self.assert_almost_equal(stress[0, 2],
ref_voigt[4] * abu.HaBohr3_GPa)
self.assert_almost_equal(stress[0, 1],
ref_voigt[5] * abu.HaBohr3_GPa)
for qpoint in ddb.qpoints:
assert qpoint in ddb.computed_dynmat
def setUp(self):
self.sigres = sigres = abilab.abiopen(
abidata.ref_file("tgw1_9o_DS4_SIGRES.nc"))
repr(self.sigres)
str(self.sigres)
assert self.sigres.to_string(verbose=2)
self.qplist = sigres.get_qplist(spin=0, kpoint=sigres.gwkpoints[0])
def on_value_change(change):
"""Callback"""
clear_output()
path = change["new"]
#print(change)
with abilab.abiopen(path) as abifile:
print(abifile)
def test_sigeph_interpolation(self):
"""Test interpolation and TdepElectronBands"""
sigeph = abilab.abiopen(
abidata.ref_file("diamond_444q_full_SIGEPH.nc"))
# Test interpolation without KS bands.
tdep_nopath = sigeph.interpolate(itemp_list=0)
repr(tdep_nopath)
str(tdep_nopath)
assert tdep_nopath.to_string(verbose=2)
assert tdep_nopath.ntemp == 1
#assert not tdep_nopath.has_kpath
#assert not tdep_nopath.ks_ebands_kpath is None
#assert not tdep_nopath.has_kmesh
#assert not tdep_nopath.ks_ebands_kmesh is None
same_tdep_nopath = tdep_nopath.__class__.pickle_load(
tdep_nopath.pickle_dump())
if self.has_matplotlib():
assert tdep_nopath.plot_itemp(itemp=0, fontsize=8, show=False)
assert tdep_nopath.plot_itemp_with_lws_vs_e0(itemp=0,
fontsize=8,
with_ratios=(3, 1),
show=False)
assert tdep_nopath.plot(show=False)
assert tdep_nopath.plot_lws_vs_e0(itemp_list=[0, -1], show=False)
assert tdep_nopath.get_ebands_plotter()
#assert tdep_nopath.get_edos_plotter() is None
# Test interpolation with KS bands.
tdep = sigeph.interpolate(itemp_list=None,
lpratio=5,
ks_ebands_kpath=None,
ks_ebands_kmesh=None,
ks_degatol=1e-4,
vertices_names=None,
line_density=20,
filter_params=None,
only_corrections=False,
verbose=0)
repr(tdep)
str(tdep)
assert tdep.to_string(verbose=2)
assert tdep_nopath.ntemp == 1
#assert not tdep_nopath.ks_ebands_kpath is None
#assert tdep.has_kpath
#assert not tdep_nopath.has_kmesh
#assert not tdep_nopath.ks_ebands_kmesh is None
if self.has_matplotlib():
assert tdep_nopath.plot_itemp(itemp=0, fontsize=8, show=False)
assert tdep_nopath.plot_itemp_with_lws_vs_e0(itemp=0,
fontsize=8,
show=False)
assert tdep_nopath.plot(show=False)
assert tdep_nopath.plot_lws_vs_e0(itemp_list=[0, -1], show=False)
assert tdep.get_ebands_plotter()
#assert tdep.get_edos_plotter() is None
sigeph.close()
def test_fermi_surface(self):
"""Testing Fermi surface tools."""
with abilab.abiopen(abidata.ref_file(
"mgb2_kmesh181818_FATBANDS.nc")) as fbnc_kmesh:
ebands = fbnc_kmesh.ebands
str(ebands)
ebands.to_bxsf(self.get_tmpname(text=True))
# Test Ebands3d
eb3d = ebands.get_ebands3d()
repr(eb3d)
str(eb3d)
assert eb3d.to_string(verbose=2)
if self.has_matplotlib():
assert eb3d.plot_contour(band=4,
spin=0,
plane="xy",
elevation=0,
show=False)
if self.has_skimage():
assert eb3d.plot_isosurfaces(e0="fermie",
verbose=1,
show=False)
# Test Mayavi
if self.has_mayavi():
assert eb3d.mvplot_isosurfaces(verbose=1, show=False)
def abiview_sigeph(options):
"""Plot e-ph self-energy. Requires SIGEPH.nc file."""
with abilab.abiopen(options.filepath) as abifile:
print(abifile.to_string(verbose=options.verbose))
abifile.expose(slide_mode=options.slide_mode, slide_timeout=options.slide_timeout,
verbose=options.verbose)
return 0
def abiview_a2f(options):
"""Plot Eliashberg function. Requires A2F.nc file."""
with abilab.abiopen(options.filepath) as abifile:
print(abifile.to_string(verbose=options.verbose))
abifile.expose(slide_mode=options.slide_mode, slide_timeout=options.slide_timeout,
verbose=options.verbose)
return 0
def abiview_gruns(options):
"""Plot Grunesein parameters. Requires GRUNS.nc file."""
with abilab.abiopen(options.filepath) as abifile:
print(abifile.to_string(verbose=options.verbose))
abifile.expose(slide_mode=options.slide_mode, slide_timeout=options.slide_timeout,
verbose=options.verbose)
return 0
def from_file(cls, filepath):
"""
Generate an instance of `AutomaticScissorsBuilder` from file.
Main entry point for client code.
"""
from abipy.abilab import abiopen
ncfile = abiopen(filepath)
return cls(qps_spin=ncfile.qplist_spin, e_bands=ncfile.ebands)
def abiopen(self):
"""Dump the gridfs data to a temporary file and use `abiopen` to open the file."""
_, filepath = mkstemp(suffix='.' + self.abiext, text=self.abiform == "t")
with open(filepath , "w" + self.abiform) as fh:
fh.write(self.read())
return abilab.abiopen(filepath)
def setUp(self):
with abilab.abiopen(abidata.ref_file("mgb2_kmesh181818_FATBANDS.nc")) as ncfile:
self.mgb2 = ncfile.structure
assert ncfile.ebands.kpoints.is_ibz
self.kibz = [k.frac_coords for k in ncfile.ebands.kpoints]
self.has_timrev = True
#self.has_timrev = has_timrev_from_kptopt(kptopt)
self.ngkpt = [18, 18, 18]
def itest_htc_bandstructure(fwp, tvars):
"""Test band-structure calculations done with the HTC interface."""
structure = abilab.Structure.from_file(abidata.cif_file("si.cif"))
scf_kppa = 20
nscf_nband = 6
ndivsm = 5
dos_kppa = 40
# TODO: Add this options because I don't like the kppa approach
# I had to use it because it was the approach used in VaspIO
#dos_ngkpt = [4,4,4]
#dos_shiftk = [0.1, 0.2, 0.3]
extra_abivars = dict(
ecut=2,
paral_kgb=tvars.paral_kgb,
)
# Initialize the flow.
flow = abilab.AbinitFlow(workdir=fwp.workdir, manager=fwp.manager)
work = bandstructure(structure, abidata.pseudos("14si.pspnc"), scf_kppa, nscf_nband, ndivsm,
spin_mode="unpolarized", smearing=None, dos_kppa=dos_kppa, **extra_abivars)
flow.register_work(work)
flow.allocate()
flow.build_and_pickle_dump()
fwp.scheduler.add_flow(flow)
fwp.scheduler.start()
assert fwp.scheduler.num_excs == 0
assert fwp.scheduler.nlaunch == 3
flow.show_status()
assert flow.all_ok
assert all(work.finalized for work in flow)
# Test if GSR files are produced and are readable.
for i, task in enumerate(work):
gsr_path = task.outdir.list_filepaths(wildcard="*GSR.nc")[0]
gsr = abilab.abiopen(gsr_path)
print(gsr)
assert gsr.nsppol == 1
assert gsr.structure == structure
ebands = gsr.ebands
# TODO: This does not work yet because GSR files do not contain
# enough info to understand if we have a path or a mesh.
#if i == 2:
# Bandstructure case
#assert ebands.has_bzpath
#with pytest.raises(ebands.Error):
# ebands.get_edos()
if i == 3:
# DOS case
assert ebands.has_bzmesh
gsr.bands.get_edos()