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Merge pull request #243 from phonopy/pypolymlp
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Update pypolymlp feature
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@atztogo
atztogo authored Jun 29, 2024
2 parents 9eb95a7 + 4f95be3 commit 628b4fb
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Showing 7 changed files with 274 additions and 167 deletions.
218 changes: 159 additions & 59 deletions phono3py/api_phono3py.py
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Original file line number Diff line number Diff line change
Expand Up @@ -303,6 +303,8 @@ def __init__(
# MLP
self._mlp = None
self._mlp_dataset = None
self._phonon_mlp = None
self._phonon_mlp_dataset = None

# Setup interaction
self._interaction = None
Expand Down Expand Up @@ -700,22 +702,25 @@ def mlp_dataset(self) -> Optional[dict]:

@mlp_dataset.setter
def mlp_dataset(self, mlp_dataset: dict):
if not isinstance(mlp_dataset, dict):
raise TypeError("mlp_dataset has to be a dictionary.")
if "displacements" not in mlp_dataset:
raise RuntimeError("Displacements have to be given.")
if "forces" not in mlp_dataset:
raise RuntimeError("Forces have to be given.")
if "supercell_energy" in mlp_dataset:
raise RuntimeError("Supercell energies have to be given.")
if len(mlp_dataset["displacements"]) != len(mlp_dataset["forces"]):
raise RuntimeError("Length of displacements and forces are different.")
if len(mlp_dataset["displacements"]) != len(mlp_dataset["supercell_energies"]):
raise RuntimeError(
"Length of displacements and supercell_energies are different."
)
self._check_mlp_dataset(mlp_dataset)
self._mlp_dataset = mlp_dataset

@property
def phonon_mlp_dataset(self) -> Optional[dict]:
"""Return phonon displacement-force dataset.
The phonon supercell matrix is equal to that of usual displacement-force
dataset. Only type 2 format is supported. "displacements", "forces", and
"supercell_energies" should be contained.
"""
return self._phonon_mlp_dataset

@phonon_mlp_dataset.setter
def phonon_mlp_dataset(self, mlp_dataset: dict):
self._check_mlp_dataset(mlp_dataset)
self._phonon_mlp_dataset = mlp_dataset

@property
def band_indices(self) -> list[np.ndarray]:
"""Setter and getter of band indices.
Expand Down Expand Up @@ -950,18 +955,18 @@ def phonon_displacements(self):
shape=(supercells, natom, 3), dtype='double', order='C'
"""
if self._phonon_supercell_matrix is None:
raise RuntimeError("phonon_supercell_matrix is not set.")

dataset = self._phonon_dataset
if "first_atoms" in dataset:
num_scells = len(dataset["first_atoms"])
if self._phonon_dataset is None:
raise RuntimeError("phonon_dataset is not set.")
if "first_atoms" in self._phonon_dataset:
num_scells = len(self._phonon_dataset["first_atoms"])
natom = len(self._phonon_supercell)
displacements = np.zeros((num_scells, natom, 3), dtype="double", order="C")
for i, disp1 in enumerate(dataset["first_atoms"]):
for i, disp1 in enumerate(self._phonon_dataset["first_atoms"]):
displacements[i, disp1["number"]] = disp1["displacement"]
elif "forces" in dataset or "displacements" in dataset:
displacements = dataset["displacements"]
elif (
"forces" in self._phonon_dataset or "displacements" in self._phonon_dataset
):
displacements = self._phonon_dataset["displacements"]
else:
raise RuntimeError("displacement dataset has wrong format.")

Expand Down Expand Up @@ -1045,6 +1050,16 @@ def grid(self):
"""
return self._bz_grid

@property
def mlp(self):
"""Return MLP instance."""
return self._mlp

@property
def phonon_mlp(self):
"""Return MLP instance for fc2."""
return self._phonon_mlp

def init_phph_interaction(
self,
nac_q_direction=None,
Expand Down Expand Up @@ -1214,48 +1229,56 @@ def generate_displacements(
):
"""Generate displacement dataset in supercell for fc3.
This systematically generates single and pair atomic displacements
in supercells to calculate fc3 considering crystal symmetry.
When this method is called, existing cache of supercells with
displacements for fc3 are removed.
For fc3, two atoms are displaced for each configuration
considering crystal symmetry. The first displacement is chosen
in the perfect supercell, and the second displacement in the
displaced supercell. The first displacements are taken along
the basis vectors of the supercell. This is because the
symmetry is expected to be less broken by the introduced first
displacement, and as the result, the number of second
displacements may become smaller than the case that the first
atom is displaced not along the basis vectors.
Systematic displacements
------------------------
Unless number_of_snapshots is specified, this method systematically
generates single and pair atomic displacements in supercells to
calculate fc3 considering crystal symmetry.
For fc3, two atoms are displaced for each configuration considering
crystal symmetry. The first displacement is chosen in the perfect
supercell, and the second displacement in the displaced supercell. The
first displacements are taken along the basis vectors of the supercell.
This is because the symmetry is expected to be less broken by the
introduced first displacement, and as the result, the number of second
displacements may become smaller than the case that the first atom is
displaced not along the basis vectors.
Random displacements
--------------------
Unless number_of_snapshots is specified, displacements are generated
randomly. There are several options how the random displacements are
generated.
Note
----
When phonon_supercell_matrix is not given, fc2 is also
computed from the same set of the displacements for fc3 and
respective supercell forces. When phonon_supercell_matrix is
set, the displacements in phonon_supercell are generated unless
those already exist.
When phonon_supercell_matrix is not given, fc2 is also computed from the
same set of the displacements for fc3 and respective supercell forces.
When phonon_supercell_matrix is set, the displacements in
phonon_supercell are generated unless those already exist. If a specific
set of displacements for fc2 is expected, generate_fc2_displacements
should be called.
Parameters
----------
distance : float, optional
Constant displacement Euclidean distance. Default is 0.03.
cutoff_pair_distance : float, optional
This is used as a cutoff Euclidean distance to determine if
each pair of displacements is considered to calculate fc3 or not.
Default is None, which means cutoff is not used.
This is used as a cutoff Euclidean distance to determine if each
pair of displacements is considered to calculate fc3 or not. Default
is None, which means cutoff is not used.
is_plusminus : True, False, or 'auto', optional
With True, atomis are displaced in both positive and negative
directions. With False, only one direction. With 'auto',
mostly equivalent to is_plusminus=True, but only one direction
is chosen when the displacements in both directions are
symmetrically equivalent. Default is 'auto'.
directions. With False, only one direction. With 'auto', mostly
equivalent to is_plusminus=True, but only one direction is chosen
when the displacements in both directions are symmetrically
equivalent. Default is 'auto'.
is_diagonal : Bool, optional
With False, the second displacements are made along the basis
vectors of the supercell. With True, direction not along the basis
vectors can be chosen when the number of the displacements
may be reduced.
vectors can be chosen when the number of the displacements may be
reduced.
number_of_snapshots : int or None, optional
Number of snapshots of supercells with random displacements. Random
displacements are generated displacing all atoms in random
Expand Down Expand Up @@ -1362,14 +1385,6 @@ def generate_fc2_displacements(
value.
"""
if self._phonon_supercell_matrix is None:
msg = (
"phonon_supercell_matrix is not set. "
"This method is used to generate displacements to "
"calculate phonon_fc2."
)
raise RuntimeError(msg)

if number_of_snapshots is not None and number_of_snapshots > 0:
self._phonon_dataset = self._generate_random_displacements(
number_of_snapshots,
Expand Down Expand Up @@ -2214,6 +2229,75 @@ def evaluate_mlp(self):
self.supercell_energies = energies
self.forces = forces

def develop_phonon_mlp(
self, params: Optional[Union[PypolymlpParams, dict, str]] = None
):
"""Develop MLP of pypolymlp for fc2.
Parameters
----------
params : PypolymlpParams or dict, optional
Parameters for developing MLP. Default is None. When dict is given,
PypolymlpParams instance is created from the dict.
"""
if self._phonon_mlp_dataset is None:
raise RuntimeError("MLP dataset is not set.")

if params is not None:
_params = parse_mlp_params(params)
else:
_params = params

disps = self._phonon_mlp_dataset["displacements"]
forces = self._phonon_mlp_dataset["forces"]
energies = self._phonon_mlp_dataset["supercell_energies"]
n = int(len(disps) * 0.9)
train_data = PypolymlpData(
displacements=disps[:n], forces=forces[:n], supercell_energies=energies[:n]
)
test_data = PypolymlpData(
displacements=disps[n:], forces=forces[n:], supercell_energies=energies[n:]
)
self._phonon_mlp = develop_polymlp(
self._phonon_supercell,
train_data,
test_data,
params=_params,
verbose=self._log_level - 1 > 0,
)

def evaluate_phonon_mlp(self):
"""Evaluate the machine learning potential of pypolymlp.
This method calculates the supercell energies and forces from the MLP
for the displacements in self._dataset of type 2. The results are stored
in self._dataset.
The displacements may be generated by the produce_force_constants method
with number_of_snapshots > 0. With MLP, a small distance parameter, such
as 0.001, can be numerically stable for the computation of force
constants.
"""
if self._mlp is None and self._phonon_mlp is None:
raise RuntimeError("MLP is not developed yet.")

if self.phonon_supercells_with_displacements is None:
raise RuntimeError(
"Displacements are not set. Run generate_fc2_displacements."
)

if self._phonon_mlp is None:
mlp = self._mlp
else:
mlp = self._phonon_mlp
energies, forces, _ = evalulate_polymlp(
mlp, self.phonon_supercells_with_displacements
)
self.phonon_supercell_energies = energies
self.phonon_forces = forces

###################
# private methods #
###################
Expand Down Expand Up @@ -2569,3 +2653,19 @@ def _generate_random_displacements(
)
dataset["displacements"] = d
return dataset

def _check_mlp_dataset(self, mlp_dataset: dict):
if not isinstance(mlp_dataset, dict):
raise TypeError("mlp_dataset has to be a dictionary.")
if "displacements" not in mlp_dataset:
raise RuntimeError("Displacements have to be given.")
if "forces" not in mlp_dataset:
raise RuntimeError("Forces have to be given.")
if "supercell_energy" in mlp_dataset:
raise RuntimeError("Supercell energies have to be given.")
if len(mlp_dataset["displacements"]) != len(mlp_dataset["forces"]):
raise RuntimeError("Length of displacements and forces are different.")
if len(mlp_dataset["displacements"]) != len(mlp_dataset["supercell_energies"]):
raise RuntimeError(
"Length of displacements and supercell_energies are different."
)
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