AtomRelaxTrajectory

class emmet.core.trajectory.AtomRelaxTrajectory(**data)

Bases: BaseModel

Atomistic only, low-memory schema for relaxation trajectories that can interface with parquet, pymatgen, and ASE.

Parameters:

• elements (list[int])

• cart_coords (list[list[tuple[float, float, float]] | None])

• num_ionic_steps (int)

• lattice (list[tuple[tuple[float, float, float], tuple[float, float, float], tuple[float, float, float]]] | None)

• energy (list[float] | None)

• forces (list[list[tuple[float, float, float]]] | None)

• stress (list[tuple[tuple[float, float, float], tuple[float, float, float], tuple[float, float, float]]] | None)

• ionic_step_properties (set[str])

property ionic_step_properties_used: set[str]

Return list of populated fields.

static reorder_sites(structure, ref_z)

Ensure that the sites in a structure match the order in a set of reference Z values.

Quick returns if the structure already matches the reference order.

Return type:

tuple[Structure | Molecule, list[int], bool]

Parameters:

• structure (Structure | Molecule)

• ref_z (list[int])

Parameters

structurepymatgen .Structure or .Molecule

Structure or Molecule to order sites in

ref_zlist of int

List of proton numbers / Z values in the reference structure.

Returns

pymatgen .Structure or .Molecule : structure matching the reference order of sites list of int : indices in the original structure which are reordered bool : Whether the order changed

classmethod from_pmg(traj, **kwargs)

Create a trajectory from a pymatgen .Trajectory.

Return type:

Self

Parameters:

traj (Trajectory)

Parameters

traj : pymatgen.core.trajectory.Trajectory constant_lattice : bool (default = False)

Whether the lattice is constant thoughout the trajectory

lattice_match_tolfloat or None (default = 1e-6)

If a float and constant_lattice is False, this defines the tolerance for determining if the lattice has changed during the course of the trajectory. If None, no check is performed.

Returns

Trajectory

to_arrow(file_name=None, **write_file_kwargs)

Create a PyArrow Table from a Trajectory.

Return type:

Table

Parameters:

file_name (str | Path | None)

Parameters

file_namestr, .Path, or None (default)

If not None, a file to write the parquet-format output to. Accepts any compression extension used by pyarrow.write_table

**write_file_kwargs

If file_name is not None, any kwargs to pass to pyarrow.parquet.write_file

Returns

pyarrow.Table

classmethod from_arrow(pa_table, identifier=None)

Create a trajectory from an arrow Table.

Return type:

Self

Parameters:

• pa_table (Table)

• identifier (str | None)

Parameters

file_namestr or .Path

The parquet file to read from

identifierstr or None (default)

If not None, the identifier of the trajectory to return from a dataset of multiple trajectories.

Returns

Trajectory

classmethod from_parquet(file_name, identifier=None)

Create a Trajectory from a parquet file.

Return type:

Self

Parameters:

• file_name (str | Path)

• identifier (str | None)

Parameters

file_namestr | Path

Path to the parquet file. Can be a remote path, e.g. AWS.

identifierstr | None = None

The string identifier for the task.

to_pmg(frame_props=None, indices=None)

Create a pymatgen Trajectory.

Return type:

Trajectory

Parameters:

• frame_props (Iterable[str] | None)

• indices (int | slice | Iterable[int] | None)

Parameters

frame_propsSequence of str or None (default)

If not None, a list of model fields to populate the frame properties of the pymatgen Trajectory with. If None, defaults to all available fields. If an empty iterable, no frame properties will be returned.

indicesint, slice, iterable of int, or None

If None (default), returns all frames If an int, the index of the frame to return If a slice, returns that range of frames If an iterable of int, returns those specific frames

Frames are always returned in sequential order, even if the user-supplied indices are unsorted.

Returns

pymatgen.core.trajectory.Trajectory

to(file_name=None, fmt=None, **kwargs)

Generic interface to multiple trajectory formats.

file_namestr, .Path, or None (default)

If not None, the name of the file to write to. If fmt is None, the file format will be inferred from this.

fmtTrajFormat, str, or None (default)

The format of the output trajectory. If file_name is None, and fmt is None, defaults to a parquet-compatible PyArrow table.

**kwargs

Any kwargs supported by Trajectory.to_* methods.

Parameters:

• file_name (str | Path | None)

• fmt (TrajFormat | str | None)

model_config: ClassVar[ConfigDict] = {}

Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].