OriVec 0.1.1

Compute orientation order parameters in polycrystals with point cloud ICP method.

OriVec

OriVec provides tools to compute orientation order parameters for local motifs in atomistic point clouds.

Installation

pip install .

Command Line Usage

orivec .\liquid.data .\ref_unit.xyz --element-map 1=Li,2=Mo,3=S --selected-element S --regularize --parallel --output liquid-orientations.xyz

This command reads a LAMMPS data file, aligns local motifs to the reference geometry, stores the resulting orientation vectors in per-atom arrays, and writes the augmented structure to liquid-orientations.xyz.

Python API

from orivec import get_order_parameters
import numpy as np

structure = get_order_parameters(
    "liquid.data",
    "ref_unit.xyz",
    ref_orientation=np.array([0.0, 0.0, 1.0]),
    elements={1: "Li", 2: "Mo", 3: "S"},
    selected_elements=["S"],
    regularize_orientations=True,
    regularize_anchors=np.array([0.0, 0.0, 1.0]),
    parallel=True,
    max_workers=8,
)

The resulting ase.Atoms object stores orientation vectors in structure.arrays['orientation'], structure.arrays['inlier_rmse']