Tutorial: verify a molecular geometry
Measure distances and angles using the packaged water example. Copy the examples into a new folder first:
You do not need a source checkout. Use the same steps with your own structure, checking atom order before choosing atom numbers.
1. Establish identity
Confirm formula, charge, multiplicity, energy, and atom count before measuring.
2. Check connectivity
The bond heuristic should identify two O–H connections and one fragment. This is a structural sanity check, not a quantum bond-order result.
3. Measure the structure
openwfn ./openwfn-examples/water.fchk geometry distance 1 2
openwfn ./openwfn-examples/water.fchk geometry distance 1 3
openwfn ./openwfn-examples/water.fchk geometry angle 2 1 3
Atom numbers are one-based. In angle 2 1 3, atom 1 is the vertex. Expect equal O–H distances for this symmetric example and a bent H–O–H angle.
4. Capture structured evidence
JSON avoids scraping decorated terminal text. Preserve the command, version, and fixture identity.
5. Export and inspect
openwfn ./openwfn-examples/water.fchk convert --to xyz --output water.xyz
openwfn ./openwfn-examples/water.fchk workbench water-workbench.html
XYZ preserves structure but not basis functions, orbitals, or density. Use the offline workbench only for optional spatial review and JSON for computation.
Ask whether charge, multiplicity, atom ordering, dimensions, and connectivity all match the intended system. Continue with the geometry methods.