Run packages

PQSetup exports a self-contained ZIP archive. After extracting it into a project directory, a continued NVT plan with equilibration can look like this:

water-nvt/
├── run-eq.in
├── run-01.in
├── run-02.in
├── run-03.in
├── water-example.rst
├── run.sh
└── pqproject.json

Required force-field files or calculator templates are included when the method needs them.

Restart order

The input sequence is explicit:

run-eq.in → run-01.in → run-02.in → run-03.in

Each input writes the restart consumed by the next stage. Filenames use eq for equilibration and zero-padded sampling indices up to 999.

Run launcher

run.sh is an executable Bash script that reads the recorded execution order. Supply the PQ executable as an argument:

./run.sh /opt/pq/bin/PQ

You can also set it once:

PQ_EXECUTABLE=/opt/pq/bin/PQ ./run.sh

The script:

  1. resolves and checks the executable;

  2. runs each input in order;

  3. writes one log per input under run-logs/;

  4. stops at the first non-zero exit or missing PQ ended normally marker.

It does not submit a scheduler job.

Project manifest

pqproject.json records:

  • the PQSetup version and target PQ release;

  • the scientific plan and execution order;

  • input, structure, setup-file, and run-script SHA-256 hashes;

  • structure and preparation provenance;

  • the PQ and calculator environment seen during export;

  • warnings and the result of each PQ validation layer.

The manifest makes it possible to inspect what was prepared without parsing the decorative input header.

Move to another machine

The package is designed to be transferred to the machine that has the required PQ build and calculator. Re-run environment checks there before a long simulation:

pqsetup --pq-executable /cluster/apps/PQ doctor
pqsetup --pq-executable /cluster/apps/PQ validate run-01.in

Then use the package launcher directly or call it from the site’s scheduler script.