def make_eos_flow(structure_file=None):
"""
Build and return a Flow to compute the equation of state
of an isotropic material for different k-point samplings.
"""
scale_volumes = np.arange(94, 108, 2) / 100.
if structure_file is None:
structure = abilab.Structure.from_file(abidata.cif_file("si.cif"))
else:
structure = abilab.Structure.from_file(structure_file)
multi = abilab.MultiDataset(structure=structure,
pseudos=get_pseudos(structure),
ndtset=len(scale_volumes))
# Global variables
multi.set_vars(ecut=16, tolvrs=1e-16)
multi.set_kmesh(ngkpt=[4, 4, 4],
shiftk=[[0.5, 0.5, 0.5], [0.5, 0.0, 0.0], [0.0, 0.5, 0.0],
[0.0, 0.0, 0.5]])
for idt, scal_vol in enumerate(scale_volumes):
new_lattice = structure.lattice.scale(structure.volume * scal_vol)
new_structure = Structure(new_lattice, structure.species,
structure.frac_coords)
multi[idt].set_structure(new_structure)
eos_flow = abilab.Flow.from_inputs("flow_si_relax",
inputs=multi.split_datasets())
eos_flow.volumes = structure.volume * scale_volumes
return eos_flow
def make_relax_si_flow():
# Structural relaxation for different k-point samplings.
scale_volumes = np.arange(94, 108, 2) / 100.
inp = abilab.AbiInput(pseudos=abidata.pseudos("14si.pspnc"), ndtset=len(scale_volumes))
structure = Structure.from_file(abidata.cif_file("si.cif"))
# Global variables
inp.set_variables(
ecut=16,
tolvrs=1e-16
)
inp.set_kmesh(ngkpt=[4, 4, 4], shiftk=[[0.5, 0.5, 0.5], [0.5, 0.0, 0.0], [0.0, 0.5, 0.0], [0.0, 0.0, 0.5]])
for idt, scal_vol in enumerate(scale_volumes):
new_lattice = structure.lattice.scale(structure.volume*scal_vol)
new_structure = Structure(new_lattice, structure.species, structure.frac_coords)
inp[idt+1].set_structure(new_structure)
si_flow = RelaxSiFlow.from_inputs("flow_si_relax", inputs=inp.split_datasets(), task_class=abilab.RelaxTask)
si_flow.volumes = structure.volume*scale_volumes
return si_flow
def test_structure_from_ncfiles(self):
"""Init Structure objects from Netcdf data files"""
ncfiles = ALL_NCFILES
assert ncfiles
for filename in ncfiles:
print("Reading file %s" % filename)
structure = Structure.from_file(filename)
print(structure)
def structure(self):
"""Returns the `Structure` associated to this dataset."""
try:
return self._structure
except AttributeError:
structure = Structure.from_abivars(self.allvars)
self.set_structure(structure)
return self._structure
def test_silicon(self):
"""Test silicon space group."""
structure = Structure.from_file(get_ncfile("si_nscf_WFK-etsf.nc"))
spgrp = structure.spacegroup
print(spgrp)
self.assertTrue(spgrp.spgid == 227)
self.assertTrue(spgrp.has_timerev)
self.assertTrue(len(spgrp) == 48 * 2)
self.assertTrue(spgrp.num_spatial_symmetries == 48)
self.assertTrue(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)
for (idx, symmop) in enumerate(spgrp):
self.assertTrue(symmop in spgrp)
self.assertTrue(spgrp.count(symmop) == 1)
self.assertTrue(spgrp.find(symmop) == idx)
self.assertTrue(abs(symmop.det) == 1)
for idx in range(len(spgrp)-1):
self.assertTrue(spgrp[idx] == spgrp[idx])
self.assertTrue(spgrp[idx] != spgrp[idx+1])
for fmop in spgrp.fm_symmops:
self.assertTrue(fmop.is_fm)
ucell_coords = np.reshape([site.frac_coords for site in structure], (len(structure), 3))
for site in structure:
for symop in spgrp:
rot_coords = symop.rotate_r(site.frac_coords, in_ucell=True)
found = False
for atom_coords in ucell_coords:
#print (atom_coords - rot_coords)
if np.allclose(atom_coords, rot_coords):
found = True
break
self.assertTrue(found)
def visualize(self, *args, **kwargs):
# TODO Here I have to decide if this method should be defined
# in a subclass of Launcher e.g GSLauncher or in the base class
from .utils import find_file
what_visualize = kwargs.get("what_visualize", "crystal")
visualizer = abipy_env.get_uservar("visualizer", kwargs)
# Find the correct output file
out_files = self.odat_files()
gsfname = find_file(out_files, "GSR")
if gsfname is None:
raise RuntimeError("Cannot find GSR file among " % out_files)
if what_visualize == "crystal":
structure = Structure.from_file(gsfname)
structure.visualize(visualizer)()
elif what_visualize == "density":
raise NotImplementedError("den_fname?")
density = Density.from_file(den_fname)
density.visualize(visualizer)()
elif what_visualize in [
"electrons",
"fermisurface",
]:
from ..electrons import ElectronBands
energies = ElectronBands.from_file(gsfname)
if what_visualize == "electrons": energies.plot()
if what_visualize == "fermisurface":
raise RuntimeError("No hanlder found for fermisurface")
#visu = energies.visualize(self, visualizer, structure)
#visu()
else:
raise RuntimeError("No handler found for %s" % what_visualize)
def __init__(self, filepath):
"""
Initialized the object from a Netcdf file.
"""
super(WFK_File, self).__init__(filepath)
# Initialize the structure from file.
self.structure = Structure.from_file(filepath)
# Initialize the band energies.
self.bands = ElectronBands.from_file(filepath)
self.kpoints = kpoints_factory(filepath)
self.nkpt = len(self.kpoints)
with WFK_Reader(filepath) as reader:
assert reader.has_pwbasis_set
assert reader.cplex_ug == 2
self.npwarr = reader.npwarr
self.nband_sk = reader.nband_sk
self.nspinor = reader.nspinor
self.nsppol = reader.nsppol
self.nspden = reader.nspden
# FFT mesh (augmented divisions reported in the WFK file)
self.fft_mesh = Mesh3D(reader.fft_divs, self.structure.lattice_vectors())
# Build G-spheres for each k-point
gspheres = len(self.kpoints) * [None]
ecut = reader.ecut
for k, kpoint in enumerate(self.kpoints):
gvec_k, istwfk = reader.read_gvec_istwfk(k)
gspheres[k] = GSphere(ecut, self.structure.reciprocal_lattice, kpoint, gvec_k, istwfk=istwfk)
self._gspheres = tuple(gspheres)
# Save reference to the reader.
self.reader = reader
def visualize(self, *args, **kwargs):
# TODO Here I have to decide if this method should be defined
# in a subclass of Launcher e.g GSLauncher or in the base class
from .utils import find_file
what_visualize = kwargs.get("what_visualize", "crystal")
visualizer = abipy_env.get_uservar("visualizer", kwargs)
# Find the correct output file
out_files = self.odat_files()
gsfname = find_file(out_files, "GSR")
if gsfname is None:
raise RuntimeError("Cannot find GSR file among " % out_files)
if what_visualize == "crystal":
structure = Structure.from_file(gsfname)
structure.visualize(visualizer)()
elif what_visualize == "density":
raise NotImplementedError("den_fname?")
density = Density.from_file(den_fname)
density.visualize(visualizer)()
elif what_visualize in ["electrons", "fermisurface",]:
from ..electrons import ElectronBands
energies = ElectronBands.from_file(gsfname)
if what_visualize == "electrons": energies.plot()
if what_visualize == "fermisurface":
raise RuntimeError("No hanlder found for fermisurface")
#visu = energies.visualize(self, visualizer, structure)
#visu()
else:
raise RuntimeError("No handler found for %s" % what_visualize)
def test_silicon(self):
"""Test silicon space group."""
structure = Structure.from_file(abidata.ref_file("si_scf_WFK.nc"))
self.assertTrue(structure.has_spacegroup)
self.assertTrue(structure.is_symmorphic)
print(structure)
print("composition:", structure.composition)
self.serialize_with_pickle(structure, test_eq=True)
spgrp = structure.spacegroup
print("spgrp:\n", spgrp)
#print("mult_tables:\n", spgrp.mult_table)
# Classes cover the entire group.
self.assertEqual(sum(len(cls) for cls in spgrp.groupby_class()),
len(spgrp))
# 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:]:
self.assertEqual(op.trace, ref_trace)
self.assertEqual(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)
for (idx, symmop) in enumerate(spgrp):
self.assertTrue(symmop in spgrp)
self.assertTrue(spgrp.count(symmop) == 1)
self.assertTrue(spgrp.find(symmop) == idx)
self.assertTrue(abs(symmop.det) == 1)
# Test pickle
self.serialize_with_pickle(spgrp[0], protocols=None, test_eq=True)
for idx in range(len(spgrp) - 1):
self.assertTrue(spgrp[idx] == spgrp[idx])
self.assertTrue(spgrp[idx] != spgrp[idx + 1])
for fmop in spgrp.fm_symmops:
self.assertTrue(fmop.is_fm)
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)
self.assertFalse(err_msg)
def test_silicon(self):
"""Test silicon space group."""
structure = Structure.from_file(abidata.ref_file("si_scf_WFK.nc"))
self.assertTrue(structure.has_spacegroup)
self.assertTrue(structure.is_symmorphic)
print(structure)
print("composition:", structure.composition)
self.serialize_with_pickle(structure, test_eq=True)
spgrp = structure.spacegroup
print("spgrp:\n", spgrp)
#print("mult_tables:\n", spgrp.mult_table)
# Classes cover the entire group.
self.assertEqual(sum(len(cls) for cls in spgrp.groupby_class()), len(spgrp))
# 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:]:
self.assertEqual(op.trace, ref_trace)
self.assertEqual(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)
for (idx, symmop) in enumerate(spgrp):
self.assertTrue(symmop in spgrp)
self.assertTrue(spgrp.count(symmop) == 1)
self.assertTrue(spgrp.find(symmop) == idx)
self.assertTrue(abs(symmop.det) == 1)
# Test pickle
self.serialize_with_pickle(spgrp[0], protocols=None, test_eq=True)
for idx in range(len(spgrp)-1):
self.assertTrue(spgrp[idx] == spgrp[idx])
self.assertTrue(spgrp[idx] != spgrp[idx+1])
for fmop in spgrp.fm_symmops:
self.assertTrue(fmop.is_fm)
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)
self.assertFalse(err_msg)
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 set_structure_from_file(self, filepath, dtset=0):
"""Set the `Structure` object for the specified dtset (data is read from filepath)."""
structure = Structure.from_file(filepath)
self.set_structure(structure, dtset=dtset)
return structure