Create a ReactionConfiguration

Goal

Define a sequence of molecular geometries and shared quantum-chemistry settings as a ReactionConfiguration for use in Kvantify Qrunch calculations.

Prerequisites

Basic familiarity with molecular geometry and basis sets
Optional: an .xyz file containing multiple geometries (multi-frame concatenated XYZ)

What Is a ReactionConfiguration?

A ReactionConfiguration packages an ordered list of geometries (images) that represent a path or scan (e.g., different bond lengths) plus the settings (basis set, charge, spin difference, units) that apply to all images.

Creation Methods

Choose one of the following ways to build a ReactionConfiguration:

From a list of coordinate lists (per-image)

Supply a Python list where each item is one geometry, itself a list of (symbol, x, y, z) tuples.

import qrunch as qc

reaction_configuration = qc.build_reaction_configuration(
    reaction=[
        [("H", 0.0, 0.0, 0.0), ("H", 0.72, 0.0, 0.0)],
        [("H", 0.0, 0.0, 0.0), ("H", 0.74, 0.0, 0.0)],
        [("H", 0.0, 0.0, 0.0), ("H", 0.76, 0.0, 0.0)],
    ],
    basis_set="sto3g"
)

From multi-frame .xyz file

Pass a path to an XYZ file that contains multiple geometries (concatenated frames):

from pathlib import Path
import qrunch as qc

reaction_configuration = qc.build_reaction_configuration(
    reaction=Path("path/to/reaction_scan.xyz"),
    basis_set="sto3g",
 )

From a list of Molecule objects

See Create a MolecularConfiguration for how to create a Molecule. Then pass a list of them:

import qrunch as qc

reaction_configuration = qc.build_reaction_configuration(
    reaction=molecules,
    basis_set="sto3g",
)

Optional Settings

See Create a MolecularConfiguration for how to set optional settings.

Basis Set Options

See Create a MolecularConfiguration for how to supply basis sets as enums or per-atom-type dictionaries.

Notes on Inputs

Images: ordering matters — it’s the path you intend to sample.

Verify the Result

Print the ReactionConfiguration to check that number of geometries, atoms, basis sets, charge, spin difference, and units are as expected.
Use the reaction_configuration directly in a problem builder.

Troubleshooting

File not found: Ensure the path to your multi-frame .xyz exists and is readable.
Invalid basis set name provided.: Verify that the basis set name is supported.
Unknown atom symbol: Check spelling and capitalization ("Li" not "li").
Inconsistent image sizes: All images should have the same atom ordering and count.

Next Step

You can use the molecular_configuration to build a reaction path problem: Construct a Reaction-Path Problem