Compatibility

PQ inputs

PQSetup currently writes inputs for the stable PQ v0.6.4 schema. It does not expose unreleased keywords merely because they exist on a development branch.

Selected PQ executable	Input generation	PQ parser validation
Advertises validation schema v1	Available	portable during export and installed from the CLI
Does not advertise the validation contract	Available for v0.6.4 inputs	Not run; local checks remain active
Not detected	Portable export remains available	Not run; the missing executable is reported

Calculator availability is reported separately from PQ parser support.

Structure formats

Format	Extension	Notes
PQ restart	.rst	Preserves atom names, molecule types, and available velocities or forces
CIF	.cif	Read through ASE
XYZ / extended XYZ	.xyz, .extxyz	A centered vacuum cell is generated when no cell is present
Protein Data Bank	.pdb	Read through ASE
MOL / SDF	.mol, .sdf	Read through ASE
ASE trajectory	.traj	The final frame is imported

Uploads are limited to 100 MB.

Generated cells

PQ uses a cell centered on the origin. PQSetup therefore wraps periodic coordinates into fractional coordinates from −0.5 to +0.5, equivalent to −L/2 to +L/2 for an orthorhombic cell.

For a structure without a cell, the import and preparation model:

1. centers the coordinate bounds on the origin;

2. adds 6 Å of padding on each side;

3. assigns a diagonal periodic cell;

4. records the generated-cell provenance in pqproject.json.

QM exports retain this generated cell. MM exports omit the generated Box and write the configured density to the PQ input instead.

QM NPT setup requires an imported physical cell; a generated vacuum cell is not accepted for that workflow.

Platform notes

The local interface is Python-based and does not require Node.js at runtime. Exported launchers require Bash. Calculator and PQ platform support still depends on the selected external software.