ProbingMC 2.9.0.post1

Core tools for crystal structures, CIF/XYZ I/O, and Quantum ESPRESSO input/output

ProbingMC (Python package: Structure)

A lightweight, ASE‑style toolkit for crystal structures, molecules, and I/O to/from CIF/XYZ and Quantum ESPRESSO (pw.x) files.

ProbingMC exposes a single importable package named Structure. You install the PyPI project ProbingMC, then import like:

from Structure import Structure

---

Key features

• Core Structure class for loading structures from CIF, Quantum ESPRESSO outputs (vc-relax, relax, scf), QE inputs (.in), and XYZ/MOPAC; includes coordinate transforms, supercells, rotations/reflections, atom insertion, and multiple writers (CIF/XYZ/MOP/QE input).
• CIF I/O: parses _cell_* parameters and atomic positions; if CIF symmetry operations (_symmetry_equiv_pos_as_xyz) are present, atoms are duplicated accordingly (basic symmetry expansion). Writing uses a CIF template.
• Quantum ESPRESSO I/O: reads vc-relax and relax outputs (including final cell, positions, and total energy when available), reads .in files, and writes QE inputs from templates.
• Atom utilities: van der Waals/covalent radii, masses, simple overlap checks (vdW/covalent), neighbor handling, and pseudopotential name maps used when writing QE inputs.
• ASE interoperability: convert to/from ase.Atoms (get_ase, add_ase_structure) for quick visualization or downstream workflows.

Note on scope: this project focuses on pragmatic structure manipulation. CIF symmetry handling is limited to duplicating positions from provided operations; it does not perform full symmetry analysis/reduction.

---

Install

From PyPI:

pip install ProbingMC

From source (editable dev install):

git clone https://github.com/Andrey-Tokarev/probingmc.git
cd probingmc
pip install -e .

The package on import is Structure even though the distribution name is ProbingMC.

---

Quickstart

from Structure import Structure

# Load a CIF
s = Structure("examples/data/graphene.cif")   # reads cell + atoms and expands symmetry if present
print(s.number_of_atoms())

# Make a 2×2 supercell and export
s.super_cell(2, 2, 1)                          # builds supercell
s.write_structure_to_xyz(modifier="2x2")       # writes <name>_2x2.xyz next to the input

The Structure class supports .cif, QE .out/.in, and .xyz/MOPAC sources; writers include CIF/XYZ/MOP/QE‐input. See write_structure_to_cif, write_structure_to_xyz, write_structure_to_qe_in, rotations/reflections, and more in the source.

With ASE (optional):

ase_atoms = s.get_ase()                        # to ASE
# ... visualize or process with ASE ...

---

Quantum ESPRESSO notes

• Readers: load_structure_from_qe_relax (also captures total energy), load_structure_from_qe_vc_relax, and load_structure_from_qe_in.
• Writer: write_structure_to_qe_in(...) populates a QE input file using templates and pseudopotential maps declared in Atom. Ensure your pseudopotential filenames match the entries in Atom.PPs_ONCV_PBE or adjust them.
• Template path: the current writer uses a hard‑coded templates folder path in QEIO.dump_structure_to_qe (marked as a “quick fix”). Update that constant or refactor to load templates from a project‑relative templates/ directory before publishing.

---

CIF notes

• CIF reader (load_structure_from_cif) parses cell parameters and atomic sites; when _symmetry_equiv_pos_as_xyz is present, it expands atoms by applying the listed operations. The CIF writer fills a sample.cif template—adjust the template location as needed.

---

API overview

• Structure.Structure: load/write, coordinate transforms, supercells, rotations (rotate_structure_from_a_to_b, bond‑to‑bond), atom add/copy/remove, double‑layer builder, surface/volume/composition utilities.
• Structure.Atom: radii, masses, overlap checks, relaxed DOF flags, distance with/without periodic images.
• Structure.CIFIO / Structure.QEIO: file readers/writers for CIF and QE formats.
• Structure.controls: simple error helper used across modules.

---

Examples

The examples/ folder is the best place to start. Recommended examples to include:

1. CIF → XYZ: load a CIF, expand symmetry if present, export to XYZ.
2. QE relax parse: parse a QE relax output, print final energy and export to CIF.
3. Supercell + rotation: build a supercell, align a bond along a target vector, and write QE input.
4. ASE interop: convert to ase.Atoms, visualize or run quick operations, then round‑trip back.

It’s okay if you haven’t chosen the exact files yet—list them here and commit small inputs in examples/data/ so readers can run them end‑to‑end.

---

Requirements

• Python 3.10+ (pattern‑matching syntax is used in the QE input reader).
• Runtime deps: numpy and ase.

---

Contributing

PRs and issues are welcome. Please:

• Add a minimal example and/or unit test for new features.
• Keep I/O templates project‑relative and configurable.
• Avoid committing large generated files (dist/, build/, *.out, *.xyz)—see .gitignore.

---

License

MIT — see LICENSE for details.