avo_ibo

avo_ibo is a plugin for Avogadro 2 (and standalone CLI) that computes and visualizes Intrinsic Bond Orbitals (IBOs) using Psi4 for SCF and wavefunction generation, then performs post-SCF IAO/2014 orbital construction (Knizia, J. Chem. Theory Comput. 2013, 9, 4834) and Pipek-Mezey localization directly in the plugin. Valence-virtual construction follows Derricotte–Evangelista (J. Chem. Theory Comput. 2017, 13, 5984).

Capabilities

• Occupied and valence-virtual IBOs — Pipek-Mezey localization (p=2 warmup + p=4 refinement, conv 1e-12)
• On-atom degeneracy resolution via post-PM Fock diagonalization
• Bond-flat degeneracy resolution — flat {σ, π} planes of symmetric bonds are Fock-diagonalised so distorted geometries yield σ+π (not banana bonds) deterministically
• Valence-virtual IBOs via fixed-count VVO construction (Derricotte–Evangelista, J. Chem. Theory Comput. 2017, 13, 5984): singular-value projection of canonical virtual MOs onto IAO space, PM-localized; bond-flat resolution applies to the virtual block too, so distorted geometries yield σ*+π* deterministically
• IAO-basis Molden export with Fock-diagonal energies for Avogadro rendering
• Analysis table (ibos.txt) — occupancy, energy, bond type, atomic composition, s/p/d hybridization, partial charges, bond orders (density Wiberg decomposed into σ and π, σ+π = total exactly)
• Standalone CLI (python -m avogadro_ibo molecule.xyz) and Avogadro in-app mode
• Full mathematical derivation in mathematics/mathematics.md with paper equation references

New to IBO output? Start with the guide to reading ibos.txt before anything else.

Project notebooks: NOTES.md (open items, design decisions). Release history: CHANGELOG.md.

Validation

We checked our charges against two independent IBO programs (IboView and ORCA) on five molecules. Same minimal basis gives the same numbers to 0.006 electrons; different minimal bases give known, fixed offsets. Details: validation/Validation.md.

Spotlight: a hydrogen bond, quantified

In the water dimer, the acceptor lone pair spills 2.2% onto the donor hydrogen, the donor O–H weakens 0.942 → 0.867, and the H···O contact carries bond order 0.075 — LP→σ* donation read straight off the analysis table. Full writeup: examples/water-dimer.md.

Quick Start

This plugin is developed and CI-tested on Windows. pixi.lock is win-64 only (platforms = ["win-64"] in pyproject.toml); GitHub Actions runs windows-latest with pixi 0.66.0, matching Avogadro 2's bundled pixi. pixi install will not consume this lock on Linux or macOS.

Requires pixi.

Avogadro plugin

git clone https://github.com/exergonic/avo_ibo.git
cd avo_ibo
pixi install

Then symlink so Avogadro finds the plugin (PowerShell as Administrator; replace the target with your clone path):

New-Item -ItemType SymbolicLink -Path "$env:LOCALAPPDATA\OpenChemistry\Avogadro\plugins\avo_ibo" -Target "C:\path\to\avo_ibo"

Restart Avogadro. Extensions → Intrinsic Bond Orbitals → Compute IBOs. Orbitals appear in the Molecular Orbitals panel.

Tests

pixi run test

Standalone CLI

pixi run python -m avogadro_ibo molecule.xyz

Writes to calcs/ (ibo.molden, canonical.molden, ibos.txt, psi4.log). A bare CLI run uses the plugin defaults (wB97X-D / def2-TZVP from Options config). Tests pass --method hf --basis cc-pVDZ explicitly.

pip (no pixi lock)

On Linux or macOS, or if you already have Psi4, install the package with pip. Psi4 must come from conda separately. This is the library/CLI path; the Avogadro symlink above is the Windows plugin location.

pip install git+https://github.com/exergonic/avo_ibo.git

Data location

Each run writes a {molecule}_NNN/ folder under the configured output home (default: the plugin's calcs/ directory). In Avogadro, change it via the Options dialog (Run calculations in); on the CLI pass --output-dir <folder>. The settings file itself always stays in the plugin directory, so moving the output home never orphans the setting. Inside each run folder:

• input.xyz - the input molecule used for calculations
• ibos.txt — analysis table with per-orbital data
• ibo.molden — IAO-basis orbitals for visualization
• canonical.molden — canonical MOs for reference visualization
• psi4.log — Psi4 SCF output

Limitations and Considerations

• Closed-shell only. The IAO/IBO pipeline treats all occupied orbitals as doubly occupied (RHF-style). Open-shell systems (radicals, triplet states, broken-symmetry calculations) are not supported. The SCF will still run, but the orbital construction, analysis, and Molden output will be invalid.

• Symmetric molecules. Pipek-Mezey localization uses fixed sequential Jacobi sweeps. For highly symmetric molecules, symmetry-equivalent orbitals may show small (sub-milliHartree) energy splittings (a known consequence of the orthogonality constraint — see Knizia JCTC 2013 and mathematics.md).

• Analysis Table vs. Isosurface Tails The IBO analysis table (ibos.txt) reports orbital compositions in the IAO basis, where populations are clean and bond assignments are crisp. The Molden isosurfaces are rendered in the full SCF basis via the projection C_AO = C_IAO @ C_IAO_all, which correctly includes the IAO repolarization components.

  These two representations are slightly inconsistent by construction: small density tails visible on non-dominant atoms in the isosurface are physically real repolarization contributions, not rendering artifacts or bugs. The analysis table intentionally omits these for clarity of chemical interpretation. This discrepancy is mathematically unavoidable and is present in all IAO-based implementations.

  These small tails represent the repolarization of each intrinsic atomic orbital in response to the molecular environment. It is the same physics that makes bonds polar and atoms non-spherical in molecules. The analysis table reports populations in the compressed IAO basis for chemical clarity; the isosurface renders the full physical wavefunction including these repolarization contributions.

Learning the output

The examples/ directory holds a section-by-section guide to reading ibos.txt plus worked molecule spotlights — carbocations, aromaticity, bent bonds, hyperconjugation, hydrogen bonding — each with run commands, verified numbers, and orbital images. Start there before the mathematics.

License

BSD 3-Clause. See LICENSE.