uppasd_tools.uppout

class uppasd_tools.uppout.UppOut(dir_path: str | Path, simid: str | None = None)

Bases: object

Main interface to UppASD simulation outputs.

It scans an output directory, infers the simulation ID, and catalogs which file types are available. When coord and restart files exist, it loads basic metadata (counts and coordinate ranges) for quick access.

dir_path

Path to the simulation output directory.

Type:: Path

prefixes

Sorted list of output file prefixes detected.

Type:: list[str]

simid

Simulation ID inferred from files or provided by user.

Type:: str | None

num_atoms

Total number of atoms in the simulation.

Type:: int | None

num_atoms_cell

Number of atoms in the unit cell.

Type:: int | None

num_atom_types

Number of unique atom types.

Type:: int | None

num_ens

Number of ensembles in the simulation.

Type:: int | None

xrange

(min, max) x-coordinates from coord file.

Type:: tuple[float, float] | None

yrange

(min, max) y-coordinates from coord file.

Type:: tuple[float, float] | None

zrange

(min, max) z-coordinates from coord file.

Type:: tuple[float, float] | None

atom_type(at_num: int) → int: Return the atom type for a given atom number using the coord data.

final_configs() → List[DataFrame]: Get final configurations of all ensembles from a restart file. Parameters: :returns: List of pandas DataFrames, each containing the configuration for an ensemble.

metadata() → dict[str, object]: Return simulation metadata as a dictionary.

read_averages() → DataFrame: Read an UppASD averages file into a pandas DataFrame.

read_coord() → DataFrame: Read an UppASD coord file into a pandas DataFrame.

read_cumulants() → DataFrame: Read an UppASD cumulants file into a pandas DataFrame.

read_energy() → DataFrame: Read UppASD totenergy and stdenergy files into a pandas DataFrame.

read_projavgs() → dict[int, DataFrame]: Read an UppASD projavgs file into a dict of DataFrames keyed by projection index.

read_projcumulants() → dict[int, DataFrame]: Read an UppASD projcumulants file into a dict of DataFrames keyed by projection index.

read_restart() → DataFrame: Read an UppASD restart file into a pandas DataFrame.

read_struct() → DataFrame: Read an UppASD struct file into a pandas DataFrame.

summary() → str: Return a formatted summary string of simulation metadata.