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When 'contact method' is 'energy', start one MDI engine for the dimer (from the upstream _model_chemistry, like LAMMPS) and, per orientation, find the energy minimum along the approach axis to anchor the surface-gap scan there instead of the vdW contact. Both modes; engine started once and closed in a finally. * _open_energy_engine: build MDIEngine from the model chemistry's get_mdi_engine_command (seamm_mdi imported lazily -- runtime-only dep). * _energy_anchor + _minimize_on_grid: derivative-free 1-D minimum on a grid with a parabolic refine (enough to anchor the scan). Unit-tested with a fake engine. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
* Anchor search now uses a narrower window (seed-0.5 .. seed+3) at a finer step (11 points), so the parabolic refine tracks the real minimum instead of being skewed outward by the steep repulsive wall (verified vs real MOPAC: an H-bond water dimer anchors at ~2.8 A). * When the energy is still falling at the outer edge (a repulsive orientation with no binding well), fall back to the vdW contact anchor. Unit-tested with a monotonic fake engine. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
* Configuration naming 'orientation,distance' now uses a comma (e.g. 2,1) rather than '/', which is reserved for splitting system and configuration names. * When the energy contact method is used, report which model chemistry was called and how many times (via MDIEngine.n_energy_calls) in the step output. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
The sub-flowchart is no longer used -- the 'energy' contact method drives an engine via a model chemistry over MDI -- so drop the Flowchart tab from the dialog (keep Parameters + the base Results tab; tk_subflowchart stays None). Add a note, shown when contact method = energy, that a Model Chemistry step must precede this step. The node keeps its (empty) sub-flowchart for a possible future non-MDI fallback. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
Walk back through the non-graphical nodes (node.previous()) and suppress the 'needs a Model Chemistry step' note when a ModelChemistry node is already upstream. Detected by Python type (class name + module) to avoid an import dependency; defaults to showing the note on any error. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
…2026.7.6 Replace the cookiecutter stub docs with a real User Guide (input modes, the radial scan and spacing, the energy contact method + required Model Chemistry step, fixed/movable subsets, tagged geometry properties, output naming), a proper index tagline, and a developer-guide campaign entry pointing to the seamm_mdi campaign notes. Add the 2026.7.6 HISTORY entry. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
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energycontact method: with a Model Chemistry step before the Dimer Builder step, the contact distance is found from the energy minimum along each approach direction (falling back to the van der Waals estimate for orientations with no binding well). It uses the newseamm_mdiMDI driver to evaluate the energy, and reports which model chemistry was used and how many times it was called.2,1) rather than a slash, which is reserved for separating system and configuration names.