Advanced settings

The Advanced dialog in the Method section exposes the optional PQ keywords that apply to the selected calculator or force field. Every value is written verbatim as keyword = value;; leaving a field blank keeps PQ’s default and writes nothing. The keywords in force are echoed next to the button so the Method section reads like the input file.

The dialog offers exactly what the PQ v0.7.x input parsers accept (src/input/inputFileParser/*.cpp and inputValidation.cpp at the targeted release). The same table lives in pqsetup/keywords.py and drives validation: values PQ would refuse are reported as errors before anything is written, with the same wording PQ’s parser uses for its option lists.

QM calculators

Program	Keywords	Notes
ASE · xTB	xtb_method	GFN2-xTB (default), GFN1-xTB, IPEA1-xTB
ASE · DFTB+	slakos, slakos_path, third_order, hubbard_derivs, dispersion	slakos = custom requires slakos_path. PQ enables third order for 3ob when the key is absent and disables it otherwise; Hubbard derivatives (El: value, …) are only offered — and only accepted — with third order on. D3 dispersion is on by default.
MACE-MP, MACE-OFF	mace_model, mace_model_path, mace_mode, dispersion	MACE-OFF ships only small/medium/large; mace_model = custom needs mace_model_path and the path is refused without it. mace_mode: accurate (e3nn) or fast (cuequivariance). D3 dispersion off by default.
DFTB+, PySCF, Turbomole	qm_script_full_path	Runs your own script instead of the bundled qm_script. The physics (Hamiltonian, basis, SCC settings) lives in the DFTB+ template or the script itself, not in the PQ input.
all	remove_net_force, qm_loop_time_limit	Net-force removal after each call; wall-time cap per QM call in seconds (≤ 0 = unlimited)
all (Constraints)	shake, shake-tolerance, shake-iter, rattle-tolerance, rattle-iter, distance-constraints	SHAKE/RATTLE and distance constraints run in every PQ MD job. In a QM run they freeze bonds (typically X–H) so the timestep can move past 0.5 fs. The bonds come from a topology file, so switching them on adds a required Topology slot to the Files row below. M-SHAKE is not offered for QM: its reference geometries refer to molecule types.

Molecular mechanics

Group	Keywords	Notes
Potentials	noncoulomb (GUFF modes), long_range, wolf_param, rf_epsilon, virial	noncoulomb chooses how guff.dat is read: GUFF, Lennard-Jones, Buckingham, Morse (a parameter file declares its own type in its nonCoulombics header). long_range: none/shifted, Wolf (wolf_param ≥ 0 Å⁻¹), reaction field (rf_epsilon ≥ 1). virial: molecular (intramolecular correction from the molecule descriptor, default) or atomic.
Neighbour search	cell-list, cell-number	Cell list replaces the brute-force pair loop; needs rcoulomb > 0 and is refused by PQ for pure QM runs
Constraints (topology modes)	shake, shake-tolerance, shake-iter, rattle-tolerance, rattle-iter, mshake-tolerance, mshake-iter, distance-constraints	Same as for QM, plus M-SHAKE. shake: off, SHAKE + RATTLE (on), or M-SHAKE rigid bodies plus SHAKE (mshake). Choosing M-SHAKE adds a required M-SHAKE geometries file (mshake_file) to the Files row below, one reference geometry per molecule type. Bond and distance constraints themselves come from the topology file.

Run › Steps › Resets

These keywords are not calculator settings: PQ applies them in its MD engine (MDEngine::takeStepAfterForces) for every MD run, QM or MM, whatever the runner. They therefore live under Run › Steps behind the Resets button, next to the step count they refer to, and are echoed there.

• Temperature rescaling — nscale (first n steps), fscale (every n steps): hard velocity scaling to the target temperature. Offered for NVT and NPT only; PQ would scale an NVE run to 0 K, so the keys are refused there.

• Drift removal — nreset / freset (total momentum), nreset_angular / freset_angular (angular momentum), freset_forces (net force): as a number of initial steps or an interval.

Blank means never. Optimisations ignore all of them.

What validation checks

• Option lists (xtb_method, slakos, mace_model, mace_mode, noncoulomb, long_range, virial, shake) and boolean tokens (on/off, true/false, yes/no).

• Ranges: tolerances > 0, iteration counts ≥ 1, cell-number ≥ 1, wolf_param ≥ 0, rf_epsilon ≥ 1, reset counters ≥ 0.

• Combinations PQ’s inputValidation.cpp rejects: custom Slater–Koster set without a path, Hubbard derivatives without third order, custom MACE model without a path (and a path without custom), MACE-OFF with a MACE-MP-only model, reaction field without rf_epsilon, constraints without a topology file, M-SHAKE without its file (or in a QM run), a cell list without a Coulomb cutoff or in a QM run, temperature rescaling without a target temperature.

• Spelling: cell-list and cell_list are the same keyword to PQ, so setting both is refused; a keyword PQSetup writes itself is refused too.

Keywords that do not apply to the current job (MM keywords in a QM run, a calculator-specific keyword for another calculator) raise a warning; the page strips them from the input regardless. Keywords PQSetup does not know pass through with a warning — PQ has the final say.

Keywords PQSetup manages itself

jobtype, nstep, timestep, start_file, restart_file, file_prefix, output_freq, overwrite_output, random_seed, init_velocities, temp, start_temp, temp_ramp_steps, thermostat and its parameters, manostat, pressure and its parameters, isotropy, qm_prog, qm_script, dftb_file, moldescriptor_file, guff_file, topology_file, parameter_file, intra-nonbonded_file, mshake_file, force-field, rcoulomb, density. These come from the visible controls (output_freq from Write every in Output, file names from the Files row) and cannot be overridden from the dialog.

Not exposed

PQ also accepts, and PQSetup does not present: FeNNol as a calculator (fennol_model_path, gpu_preprocessing), the integrator choice (PQ has only velocity Verlet), per-file output names, dim and floating_point_type, ring-polymer MD (rpmd_n_replica), the mm-opt optimizer and mm-hessian controls, and the hybrid QM/MM keywords, whose names changed after v0.7.1. Water models and rnoncoulomb exist only on PQ’s development branch.