Advanced settings

The Advanced dialog in the Method section exposes 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.

ASE · xTB’s electronic model is a primary Method control. Other advanced settings in the dialog offer PQ v0.7.x input keywords (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.

PQSetup requires output_freq >= 1 because it packages output and restart files for the selected run sequence. PQ itself also accepts 0 for a dry run that writes no output files.

QM calculators

Program	Keywords	Notes
ASE · xTB	xtb_method	GFN2-xTB (default), GFN1-xTB, IPEA1-xTB; selected in Method
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 applies hard velocity scaling for the first n steps; fscale repeats it every n steps. These controls are available for NVT and NPT. PQ would scale an NVE run to 0 K, so the keys are refused there.

Drift removal

nreset / freset remove total momentum, nreset_angular / freset_angular remove angular momentum, and freset_forces removes net force. Each value is 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.