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Code cleanup
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@gmatteo
gmatteo committed Sep 12, 2023
1 parent 064cdd2 commit 66f18a1
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Showing 2 changed files with 26 additions and 26 deletions.
4 changes: 2 additions & 2 deletions abipy/ml/aseml.py
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Original file line number Diff line number Diff line change
Expand Up @@ -922,7 +922,7 @@ def pf(*args, **kwargs):
converged = dyn.run(fmax=fmax, steps=steps)
t_end = time.time()
pf('Relaxation completed in %2.4f sec\n' % (t_end - t_start))
if not converged:
if not converged:
raise RuntimeError("ASE relaxation didn't converge")

r1 = AseResults.from_atoms(dyn.atoms)
Expand Down Expand Up @@ -1244,7 +1244,7 @@ class MyAlignnCalculator(_MyCalculator, AlignnAtomwiseCalculator):
"""Add abi_forces and abi_stress"""

model_name = default_path() if self.model_name is None else self.model_name
cls = MyAlignnCalculator if with_delta else AlignnAtomwiseCalculator
cls = MyAlignnCalculator if with_delta else AlignnAtomwiseCalculator
return cls(path=model_name)

#if self.nn_type == "quip":
Expand Down
48 changes: 24 additions & 24 deletions abipy/ml/ml_phonopy.py
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Original file line number Diff line number Diff line change
@@ -1,4 +1,5 @@
"""
Classes to compute vibrational properties with phonopy and ML potentials.
"""
from __future__ import annotations
Expand All @@ -17,7 +18,7 @@
from abipy.core.structure import Structure
from abipy.dfpt.ddb import DdbFile
from abipy.tools.context_managers import Timer
from abipy.ml.aseml import RX_MODE, CalcBuilder, AseResults, MlBase, get_atoms, relax_atoms, dataframe_from_results_list
from abipy.ml.aseml import RX_MODE, CalcBuilder, AseResults, MlBase, relax_atoms, dataframe_from_results_list
try:
import phonopy
from phonopy import Phonopy
Expand Down Expand Up @@ -67,7 +68,7 @@ def get_phonopy(structure: Structure,
a = Atoms(symbols=sc.symbols,
positions=sc.positions,
masses=sc.masses,
cell=sc.cell,
cell=sc.cell,
pbc=True,
calculator=calculator)

Expand All @@ -89,7 +90,7 @@ class MlPhonopyWithDDB(MlBase):
"""
def __init__(self, distance, asr, dipdip, line_density, qppa,
relax_mode, fmax, pressure, steps, optimizer, nn_names,
verbose, workdir, prefix=None,
verbose, workdir, prefix=None,
ddb_filepath=None, supercell=None):
"""
Args:
Expand Down Expand Up @@ -123,21 +124,22 @@ def __init__(self, distance, asr, dipdip, line_density, qppa,
self.optimizer = optimizer
self.nn_names = list_strings(nn_names)
self.verbose = verbose

self.supercell = supercell
self.line_density = line_density
self.qppa = qppa

self.ddb_filepath = ddb_filepath

with DdbFile(self.ddb_filepath) as ddb:
self.initial_atoms = get_atoms(ddb.structure)
self.initial_atoms = ddb.structure.to_ase_atoms()
if self.supercell is None:
# Take supercell from the q-mesh used in the DDB
self.supercell = np.eye(3) * ddb.guessed_ngqpt

if self.supercell is None:
raise ValueError("Supercell must be specified in input!")

self.line_density = line_density
self.qppa = qppa

self.abi_nac_params = {}

def to_string(self, verbose=0):
Expand All @@ -162,10 +164,6 @@ def to_string(self, verbose=0):
nn_names = {self.nn_names}
workdir = {self.workdir}
verbose = {self.verbose}
=== ATOMS ===
{self.initial_atoms}
"""
return s

Expand All @@ -182,7 +180,7 @@ def run(self) -> None:

# ab-initio phonons from the DDB.
with ddb.anaget_phbst_and_phdos_files(
qppa=self.qppa, line_density=self.line_density,
qppa=self.qppa, line_density=self.line_density,
asr=self.asr, dipdip=self.dipdip, verbose=self.verbose) as g:

phbst_file, phdos_file = g[0], g[1]
Expand Down Expand Up @@ -228,7 +226,8 @@ def _run_nn_name(self, nn_name) -> None:
pressure=self.pressure,
steps=self.steps,
traj_path=self.get_path(f"{nn_name}_relax.traj", "ASE relax trajectory"),
verbose=self.verbose,
#verbose=self.verbose,
verbose=1,
)

relax = relax_atoms(atoms, **relax_kws)
Expand All @@ -237,7 +236,8 @@ def _run_nn_name(self, nn_name) -> None:
# Call phonopy to compute phonons with finite difference and ML potential.
# Include non-analytical term if dipoles are available in the DDB file.
with Timer(header=f"Calling get_phonopy with {nn_name=}", footer=""):
phonon = get_phonopy(atoms, self.supercell, calculator, distance=self.distance, primitive_matrix=None)
phonon = get_phonopy(atoms, self.supercell, calculator,
distance=self.distance, primitive_matrix=None, remove_drift=True)
if self.abi_nac_params:
print("Including dipolar term in phonopy using BECS and eps_inf taken from DDB.")
phonon.nac_params = self.abi_nac_params
Expand All @@ -250,18 +250,18 @@ def _run_nn_name(self, nn_name) -> None:
from abipy.dfpt.converters import phonopy_to_abinit
with DdbFile(self.ddb_filepath) as ddb:
zion = ddb.header["zion"]
py_ddb = phonopy_to_abinit(unit_cell=Structure.as_structure(atoms.copy()),
supercell_matrix=self.supercell,
py_ddb = phonopy_to_abinit(unit_cell=Structure.as_structure(atoms.copy()),
supercell_matrix=self.supercell,
out_ddb_path=str(self.workdir / f"{nn_name}_DDB"),
ngqpt=ddb.guessed_ngqpt,
force_constants=force_constants,
force_constants=force_constants,
born=None,
primitive_matrix=np.eye(3),
primitive_matrix=np.eye(3),
verbose=self.verbose,
)
# Call anaddb to compute ab-initio phonons from the DDB.
with py_ddb.anaget_phbst_and_phdos_files(
qppa=self.qppa, line_density=self.line_density,
qppa=self.qppa, line_density=self.line_density,
asr=self.asr, dipdip=self.dipdip, verbose=self.verbose) as g:
phbst_file, phdos_file = g[0], g[1]
Expand All @@ -278,7 +278,7 @@ def _run_nn_name(self, nn_name) -> None:

plt = phonon.plot_band_structure()
plt.savefig(workdir / f"phonopy_{nn_name}_phbands.png")
if show: plt.show()
if show: plt.show()
plt.close()

bands_dict = phonon.get_band_structure_dict()
Expand All @@ -294,18 +294,18 @@ def _run_nn_name(self, nn_name) -> None:
py_displ_cart = np.reshape(py_displ_cart, (nqpt, 3*natom, 3*natom))

# Build abipy phonon bands from phonopy results.
py_phbands = PhononBands(self.abi_phbands.structure, self.abi_phbands.qpoints, py_phfreqs,
py_phbands = PhononBands(self.abi_phbands.structure, self.abi_phbands.qpoints, py_phfreqs,
# FIXME: Use phononopy displacement
self.abi_phbands.phdispl_cart,
non_anal_ph=None,
self.abi_phbands.phdispl_cart,
non_anal_ph=None,
amu=self.abi_phbands.amu,
epsinf=self.abi_phbands.epsinf,
zcart=self.abi_phbands.zcart,
)

# Compute diff stats.
mabs_wdiff_ev = np.abs(py_phbands.phfreqs - self.abi_phbands.phfreqs).mean()

ph_plotter = PhononBandsPlotter(key_phbands=[
(f"phonopy with {nn_name}", py_phbands),
("ABINIT DDB", self.abi_phbands),
Expand Down

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