Overview

The orochi.phase package is a versatile Python module for managing and manipulating the structural information of diverse materials. It provides a comprehensive toolkit for working with atomic structures, ranging from three-dimensionally periodic crystals to non-periodic systems and finite-sized nanostructures. As a core component of the Orochi framework, it facilitates detailed structural analysis and model construction.

Key Features

• Comprehensive Structure Representation:

  • Handles a wide array of material structures, including 3D bulk crystals,

    2D materials (e.g., nanosheets), nanoparticles, and other aperiodic or finite systems.

• Advanced Crystallographic Tools:

  • Enables the description of crystal structures starting from the asymmetric unit.

  • Automatically generates full atomic coordinates within the unit cell based on

    space group symmetry operations.

  • Allows for the application of constraints on atomic coordinates derived from

    site symmetry information.

• Customizable Periodic Boundary Conditions (PBCs):

  • Offers flexibility in defining periodicity, allowing PBCs to be restricted

    along arbitrary directions. This is particularly useful for modeling systems with reduced dimensionality, such as surfaces or 2D materials.

• Morphology and Nanostructure Modeling:

  • Facilitates the explicit generation of atomic models for materials exhibiting

    specific morphologies (e.g., nanoparticles, thin films, surfaces). These models can be derived from bulk crystalline data, enabling the study of finite-size and surface effects.

Quickstart: Structure Model Generation & Anisotropic PBCs

from orochi.phase import Phase

# 1. Initialize Phase and load structure
phase = Phase()
phase.read_file("PtO2.cif")

# 2. Toggle Anisotropic Periodic Boundary Conditions
# Seamlessly model 2D monolayers, 1D wires, or 3D bulk without building artificial supercells:
phase["pbc"] = [True, True, False]   # 2D monolayer (ab-periodic, non-periodic c)

# 3. Choose morphology representation
# 'analytical' for bulk crystals / analytical spherical envelopes
# 'sphere' / 'cube' for explicit coordination-preserving nanoparticles
phase["shape_type"] = "analytical"

# 4. Enforce space-group Wyckoff symmetry and lattice constraints
phase.set_lattice_constraints()

# 5. Execute structural expansion
phase.run(force=True)

# 6. Access expanded fractional coordinates and atomic species
xyz = phase["xyz"]
elements = phase["element"]
print(f"Total atoms in expanded cluster/cell: {len(elements)}")

pip install orochi.phase

python -c "import orochi.phase; print('Orochi Phase imported successfully')"

git clone https://github.com/Tominaka-Laboratory/orochi.phase.git
cd orochi.phase
pip install -e .

pip install -e .

@article{tominaka2026orochi,
  title   = {Orochi: A Physics-Grounded Python Package for Pair Distribution Function Analysis of Crystalline and Low-Dimensional Materials},
  author  = {Tominaka, Satoshi},
  year    = {2026},
  url     = {https://github.com/Tominaka-Laboratory/orochi}
}