def __init__(self, model=None, structure=None, atom_disp=0.015, **kwargs):
self.model = model
self.structure = structure
self.atom_disp = atom_disp
self.qpoints, self.vertices = get_qpoints_and_vertices(self.structure)
is_plusminus = kwargs.get('is_plusminus', True)
is_diagonal = kwargs.get('is_diagonal', True)
is_trigonal = kwargs.get('is_diagonal', False)
supercell_matrix = kwargs.get('is_diagonal', None)
ph_structure = get_phonopy_structure(self.structure)
if supercell_matrix is None:
supercell_matrix = np.eye(3) * np.array((1, 1, 1))
self.phonon = Phonopy(unitcell=ph_structure, supercell_matrix=supercell_matrix)
self.phonon.generate_displacements(distance=self.atom_disp,
is_plusminus=is_plusminus,
is_diagonal=is_diagonal,
is_trigonal=is_trigonal)
disp_supercells = self.phonon.get_supercells_with_displacements()
# Perfect supercell structure
init_supercell = self.phonon.get_supercell()
# Structure list to be returned
self.structure_list = [get_pmg_structure(init_supercell)]
for c in disp_supercells:
if c is not None:
self.structure_list.append(get_pmg_structure(c))
forces = self.model.calculate_forces(self.structure_list)
self.phonon.set_forces(forces[1:])
self.phonon.produce_force_constants()
logging.info("Force constant produced")
def run_all(self):
self.phonon = self.read_yaml(self.filename)
self.optimized_structure = get_pmg_structure(
self.phonon.get_unitcell())
self.supercell_matrix = self.phonon.get_supercell_matrix()
self.phonon_band_structure_pymatgen = self._get_bandstructure_calc(
structure=self.optimized_structure,
phonon=self.phonon,
npoints_band=self.npoints_band)
self.phonon_dos_pymatgen = self._get_dos_calc(
structure=self.optimized_structure,
phonon=self.phonon,
kpoint_density=self.kpoint_density)
def test_structure_conversion(self):
s_pmg = PymatgenTest.get_structure("LiFePO4")
s_ph = get_phonopy_structure(s_pmg)
s_pmg2 = get_pmg_structure(s_ph)
coords_ph = s_ph.get_scaled_positions()
symbols_pmg = {e.symbol for e in s_pmg.composition.keys()}
symbols_pmg2 = {e.symbol for e in s_pmg2.composition.keys()}
self.assertAlmostEqual(s_ph.get_cell()[1, 1],
s_pmg.lattice._matrix[1, 1], 7)
self.assertAlmostEqual(s_pmg.lattice._matrix[1, 1],
s_pmg2.lattice._matrix[1, 1], 7)
self.assertEqual(symbols_pmg, set(s_ph.symbols))
self.assertEqual(symbols_pmg, symbols_pmg2)
self.assertArrayAlmostEqual(coords_ph[3], s_pmg.frac_coords[3])
self.assertArrayAlmostEqual(s_pmg.frac_coords[3],
s_pmg2.frac_coords[3])
self.assertEqual(s_ph.get_number_of_atoms(), s_pmg.num_sites)
self.assertEqual(s_pmg.num_sites, s_pmg2.num_sites)
def runSimulation(self):
starting_struct = singleFromFile(self.args)
relaxed_struct = runCalc("all_relax", ["structures"],
[starting_struct], self.args)["structures"][0]
phonopy_struct = get_phonopy_structure(relaxed_struct)
supercell_matrix = 3 * eye(3)
phonon = Phonopy(phonopy_struct, supercell_matrix)
phonon.generate_displacements(distance=0.01)
supercells = phonon.supercells_with_displacements
phonon_structs = [get_pmg_structure(struct) for struct in supercells]
forces = runCalc("all_static", ["forces"], phonon_structs,
self.args)["forces"]
phonon.set_forces(array(forces))
phonon.produce_force_constants()
phonon.symmetrize_force_constants()
self.plotter = PhononBSPlotter(
get_phonon_band_structure_symm_line_from_fc(
relaxed_struct, supercell_matrix, phonon.force_constants))
def abinit_to_phonopy(anaddbnc,
supercell_matrix,
symmetrize_tensors=False,
output_dir_path=None,
prefix_outfiles="",
symprec=1e-5,
set_masses=False):
"""
Converts the interatomic force constants(IFC), born effective charges(BEC) and dielectric
tensor obtained from anaddb to the phonopy format. Optionally writes the
standard phonopy files to a selected directory: FORCE_CONSTANTS, BORN (if BECs are available)
POSCAR of the unit cell, POSCAR of the supercell.
The conversion is performed taking the IFC in the Wigner–Seitz supercell with weights
as produced by anaddb and reorganizes them in a standard supercell multiple of the
unit cell. Operations are vectorized using numpy. This may lead to the allocation of
large arrays in case of very large supercells.
Performs a check to verify if the two codes identify the same symmetries and it gives a
warning in case of failure. Mismatching symmetries may lead to incorrect conversions.
Args:
anaddbnc: an instance of AnaddbNcFile. Should contain the output of the IFC analysis,
the BEC and the dielectric tensor.
supercell_matrix: the supercell matrix used for phonopy. Any choice is acceptable, however
the best agreement between the abinit and phonopy results is obtained if this is set to
a diagonal matrix with on the diagonal the ngqpt used to generate the anaddb.nc.
symmetrize_tensors: if True the tensors will be symmetrized in the Phonopy object and
in the output files. This will apply to IFC, BEC and dielectric tensor.
output_dir_path: a path to a directory where the phonopy files will be created
prefix_outfiles: a string that will be added as a prefix to the name of the written files
symprec: distance tolerance in Cartesian coordinates to find crystal symmetry in phonopy.
It might be that the value should be tuned so that it leads to the the same symmetries
as in the abinit calculation.
set_masses: if True the atomic masses used by abinit will be added to the PhonopyAtoms
and will be present in the returned Phonopy object. This should improve compatibility
among abinit and phonopy results if frequencies needs to be calculated.
Returns:
An instance of a Phonopy object that contains the IFC, BEC and dieletric tensor data.
"""
ifc = anaddbnc.ifc
nac_params = None
becs = None
epsinf = None
if anaddbnc.becs is not None and anaddbnc.epsinf is not None:
becs = anaddbnc.becs.values
epsinf = anaddbnc.epsinf
# according to the phonopy website 14.399652 is not the coefficient for abinit
# probably it relies on the other conventions in the output.
nac_params = {"born": becs, "dielectric": epsinf, "factor": 14.399652}
s = anaddbnc.structure
phon_at = get_phonopy_structure(s)
if set_masses:
phon_at.masses = [anaddbnc.amu[n] for n in phon_at.numbers]
# use phonopy to get the proper supercell given by the primitive and the matrix
# and convert it to pymatgen
phonon = Phonopy(phon_at,
supercell_matrix,
primitive_matrix=np.eye(3),
nac_params=nac_params,
symprec=symprec)
phon_supercell = phonon.get_supercell()
supercell = get_pmg_structure(phon_supercell)
abi_hall_num = s.abi_spacegroup.get_spglib_hall_number()
spglib_hall_num = phonon.symmetry.dataset["hall_number"]
if abi_hall_num != spglib_hall_num:
warnings.warn(
"The hall number obtained based on the DDB symmetries differs "
f"from the one calculated with spglib: {abi_hall_num} versus "
f"{spglib_hall_num}. The conversion may be incorrect. Try changing symprec."
)
# convert to phonopy units
at_cart = ifc.atoms_cart_coord * abu.Bohr_Ang
ifccc = ifc.ifc_cart_coord * abu.Ha_eV / abu.Bohr_Ang**2
weights = ifc.ifc_weights
latt = supercell.lattice
ifcph = np.zeros((len(s), len(supercell), 3, 3))
# loop over the atoms in the primitive cell
# other operations are vectorized using numpy arrays. Some array may require large allocations
for i, (site, c_list, w_list) in enumerate(zip(s, at_cart, weights)):
ind_w = np.where(w_list > 0)
ifccc_loc = ifccc[i, ind_w[0]]
w_list = w_list[ind_w]
c_list = c_list[ind_w]
# align the coordinates of the first atom in the list (the site under consideration)
# with the site in the primitive cell.
c_list = c_list - c_list[0] + site.coords
# convert to fractional coordinates as needed by the Lattice to get the distances
f_list = latt.get_fractional_coords(c_list)
sc_fcoords = supercell.frac_coords
# construct the list of sites of the supercell that are closer to sites in
# the primitive cell
dist_and_img = [
latt.get_distance_and_image(f_list[0], fc) for fc in sc_fcoords
]
# the function gives the translation of the image, but it should be applied to the coordinates.
# Only the positions are needed
nearest_sc_fcoords = [
fc + trasl for (_, trasl), fc in zip(dist_and_img, sc_fcoords)
]
# divide by the corresponding weights. Elements with weights 0 were discarded above
ifccc_loc = np.transpose(ifccc_loc, (0, 2, 1)) / w_list[:, None, None]
# create an array with all the possible pairs
# instantiating this array seems slow but seems still faster than the required loops
coord_pairs = np.array(
list(itertools.product(nearest_sc_fcoords, f_list)))
# find the pairs that match between the coordinates of the modified supercell and the f_list
ind_match = np.where(
np.abs(coord_pairs[:, 0] -
coord_pairs[:, 1]).sum(axis=1) < 1e-6)[0]
# set the ifc for phonopy in the final array corresponding to the matching indices.
n_points_f_list = len(f_list)
ifcph[i, ind_match // n_points_f_list] = ifccc_loc[ind_match %
n_points_f_list]
phonon.set_force_constants(ifcph)
if symmetrize_tensors:
phonon.symmetrize_force_constants()
if output_dir_path:
makedirs_p(output_dir_path)
fc_filepath = os.path.join(output_dir_path,
prefix_outfiles + "FORCE_CONSTANTS")
write_FORCE_CONSTANTS(phonon.get_force_constants(), fc_filepath)
if becs is not None and epsinf is not None:
born_filepath = os.path.join(output_dir_path,
prefix_outfiles + "BORN")
write_BORN(phon_at,
borns=becs,
epsilon=epsinf,
filename=born_filepath,
symmetrize_tensors=symmetrize_tensors)
poscar_filepath = os.path.join(output_dir_path,
prefix_outfiles + "POSCAR")
poscar = Poscar(s)
poscar.write_file(poscar_filepath, significant_figures=15)
supercell_filepath = os.path.join(output_dir_path,
prefix_outfiles + "supercell_POSCAR")
superce_poscar = Poscar(supercell)
superce_poscar.write_file(supercell_filepath, significant_figures=15)
return phonon
def phonopy_to_abinit(unit_cell,
supercell_matrix,
out_ddb_path,
ngqpt=None,
qpt_list=None,
force_constants=None,
force_sets=None,
born=None,
primitive_matrix="auto",
symprec=1e-5,
tolsym=None,
supercell=None,
calculator=None,
manager=None,
workdir=None,
pseudos=None,
verbose=False):
"""
Converts the data from phonopy to an abinit DDB file. The data can be provided
in form of arrays or paths to the phonopy files that should be parsed.
The minimal input should contains the FORCE_CONSTANTS or FORCE_SETS.
If BORN is present the Born effective charges (BEC) and dielectric
tensor will also be added to the DDB.
The best agreement is obtained with supercell_matrix and ngqpt being
equivalent (i.e. supercell_matrix a diagonal matrix with ngqpt as diagonal
elements). Non diagonal supercell_matrix are allowed as well, but the information
encoded in the DDB will be the result of an interpolation done through phonopy.
Phonopy is used to convert the IFC to the dynamical matrix. However, in order to
determine the list of q-points in the irreducible Brillouin zone and to prepare the
base for the final DDB file, abinit will be called for a very short and inexpensive run.
Performs a check to verify if the two codes identify the same symmetries and it gives a
warning in case of failure. Mismatching symmetries may lead to incorrect conversions.
Args:
unit_cell: a |Structure| object that identifies the unit cell used for the phonopy
calculation.
supercell_matrix: a 3x3 array representing the supercell matrix used to generated the
forces with phonopy.
out_ddb_path: a full path to the file where the new DDB will be written
ngqpt: a list of 3 elements indicating the grid of q points that will be used in the DDB.
qpt_list: alternatively to ngqpt an explicit list of q-points can be provided here.
At least one among ngqpt and qpt_list should be defined.
force_constants: an array with shape (num atoms unit cell, num atoms supercell, 3, 3)
containing the force constants. Alternatively a string with the path to the
FORCE_CONSTANTS file. This or force_set should be defined. If both given this
has precedence.
force_sets: a dictionary obtained from the force sets generated with phonopy.
Alternatively a string with the path to the FORCE_SETS file. This or force_constants
should be defined.
born: a dictionary with "dielectric" and "born" keywords as obtained from the nac_params
in phonopy. Alternatively a string with the path to the BORN file. Notice that
the "factor" attribute is not taken into account, so the values should be in
default phonopy units.
primitive_matrix: a 3x3 array with the primitive matrix passed to Phonopy. "auto" will
use spglib to try to determine it automatically. If the DDB file should contain the
actual unit cell this should be the identity matrix.
symprec: distance tolerance in Cartesian coordinates to find crystal symmetry in phonopy.
It might be that the value should be tuned so that it leads to the the same symmetries
as in the abinit calculation.
tolsym: Gives the tolerance to identify symmetries in abinit. See abinit documentation for
more details.
supercell: if given it should represent the supercell used to get the force constants,
without any perturbation. It will be used to match it to the phonopy supercell
and sort the IFC in the correct order.
calculator: a string with the name of the calculator. Will be used to set the conversion
factor for the force constants coming from phonopy.
manager: |TaskManager| object. If None, the object is initialized from the configuration file
pseudos: List of filenames or list of |Pseudo| objects or |PseudoTable| object. It will be
used by abinit to generate the base DDB file. If None the abipy.data.hgh_pseudos.HGH_TABLE
table will be used.
verbose: verbosity level. Set it to a value > 0 to get more information
workdir: path to the directory where the abinit calculation will be executed.
Returns:
a DdbFile instance of the file written in out_ddb_path.
"""
if ngqpt is None and qpt_list is None:
raise ValueError(
"at least one among nqgpt and qpt_list should be defined")
if force_sets is None and force_constants is None:
raise ValueError(
"at least one of force_sets and force_constants should be provided"
)
phon_at = get_phonopy_structure(unit_cell)
if isinstance(force_constants, str):
force_constants = parse_FORCE_CONSTANTS(filename=force_constants)
elif force_constants is not None:
force_constants = np.array(force_constants)
force_sets = None
if isinstance(force_sets, str):
force_sets = parse_FORCE_SETS(filename=force_sets)
# no nac_params here, otherwise they will be used for the interpolation
phonon = Phonopy(phon_at,
supercell_matrix,
primitive_matrix=primitive_matrix,
nac_params=None,
symprec=symprec,
calculator=calculator)
primitive = get_pmg_structure(phonon.primitive)
if isinstance(born, str):
born = parse_BORN(phonon.primitive, filename=born)
if supercell is not None:
ph_supercell = get_pmg_structure(phonon.supercell)
if not np.allclose(supercell.lattice.matrix,
ph_supercell.lattice.matrix):
raise RuntimeError("The lattice of the supercells do not match")
sc_mapping = []
for i, site_orig in enumerate(supercell):
for j, site_ph in enumerate(ph_supercell):
d = supercell.lattice.get_distance_and_image(
site_orig.frac_coords, site_ph.frac_coords)[0]
if d < 1e-5:
sc_mapping.append(j)
break
else:
raise RuntimeError(
f"Could not find a match for site {i} with coords "
f"{site_orig.cart_coords} in the supercell.")
# cross check that the same atom was not matched twice
n_matches = len(set(sc_mapping))
if n_matches < len(supercell):
raise RuntimeError(
f"Found matches for {n_matches} different atoms in the supercell: {sc_mapping}"
)
force_constants = force_constants[:, sc_mapping]
if force_constants is not None:
phonon.set_force_constants(force_constants)
else:
phonon.dataset = force_sets
phonon.produce_force_constants()
if calculator:
units = get_default_physical_units(calculator)
fc_factor = get_force_constant_conversion_factor(
units["force_constants_unit"], None)
phonon.set_force_constants(phonon.force_constants * fc_factor)
if pseudos is None:
from abipy.data.hgh_pseudos import HGH_TABLE
pseudos = HGH_TABLE
inp = minimal_scf_input(primitive, pseudos)
# get the qpoints list if not defined
if qpt_list is None:
inp["ngkpt"] = ngqpt
qpt_list = inp.abiget_ibz(verbose=verbose)[0]
dm_list = get_dm(phonon, qpt_list, primitive)
if born is not None:
# for the conversion of the BEC the zion (i.e. the ionic charge of the pseudo)
# it is an additive factor and should be the same that goes in the header of the DDB,
# so take it from the pseudos used to generate it.
zion = inp.valence_electrons_per_atom
born_data = generate_born_deriv(born, zion, primitive)
else:
born_data = None
inp = minimal_scf_input(primitive, pseudos)
if tolsym is not None:
inp["tolsym"] = tolsym
task = inp.run_in_shell(workdir=workdir, manager=manager, verbose=verbose)
# use the output of abinit to check that the spacegroup identified by
# phonopy and abinit are the same.
with GsrFile(task.opath_from_ext("GSR.nc")) as gsr:
abi_spg = gsr.structure.abi_spacegroup.spgid
spglib_spg = phonon.symmetry.dataset["number"]
if abi_spg != spglib_spg:
warnings.warn(
"The space group number obtained based on the DDB symmetries differs "
f"from the one calculated with spglib: {abi_spg} versus "
f"{spglib_spg}. The convertion may be incorrect. Try changing symprec or tolsym."
)
tmp_ddb_path = task.opath_from_ext("DDB")
ddb = DdbFile(tmp_ddb_path)
# remove the blocks generated by the calculation and that are meaningless
ddb.remove_block(dord=0)
ddb.remove_block(dord=1)
add_data_ddb(ddb, dm_list, qpt_list, born_data)
ddb.write(out_ddb_path)
new_ddb = DdbFile(out_ddb_path)
return new_ddb