Validation¶
PQSetup separates local checks, environment discovery, and PQ parser validation. The interface states which layers actually ran.
Local preflight¶
Local checks run while the setup is edited. They cover:
readable structure data, finite coordinates, and known elements;
periodic-cell geometry and PQ’s centered wrapping convention;
unusually close atom pairs using ASE covalent radii;
ensemble and coupling parameters;
required calculator, topology, parameter, and template files;
restart names and generated-input consistency.
The close-contact scan is a bounded geometric heuristic. It reports up to 200 contacts and does not establish bonding, protonation, or chemical correctness.
Environment discovery¶
pqsetup doctor and the Method step inspect PQ and supported external
calculators. A detected executable means that the command or package was found
and its setup appears complete enough for input generation.
Discovery does not run a reference energy, force, or dynamics calculation. Warnings may therefore accompany an export that is intended for another machine.
PQ parser validation¶
When a selected PQ executable advertises validation schema v1, PQSetup calls PQ’s own parser:
Context |
Scope |
Purpose |
|---|---|---|
Package preview and export |
|
Check syntax and release-level input support without requiring the local calculator |
|
|
Check syntax and the capabilities of the installed PQ build |
PQSetup discovers this support through PQ --capabilities=json. Builds
without the contract continue to receive local checks, and the missing PQ
validation is reported explicitly.
What validation does not prove¶
Passing preflight does not prove:
that the model chemistry or force field is appropriate;
that the timestep and coupling constants are stable;
that equilibration or sampling is long enough;
that the vacuum or periodic cell is converged;
that the structure has the intended bonding, charge, spin, or protonation;
that a detected calculator will produce scientifically meaningful results.
Treat every preset as a starting template. Review the generated inputs and test the protocol on the intended execution environment.
Validate an existing input¶
pqsetup validate run.in
Use --json for structured diagnostics:
pqsetup validate --json run.in
An explicitly configured but unusable PQ executable is an error. A PQ build that does not advertise installed validation produces a warning after local checks.