.. _liquid_styrene_run:

Running the Build
-----------------

From inside the working directory containing ``0-liquid-styrene.yaml``:

.. code-block:: console

   $ htpolynet run -diag diagnostics.log 0-liquid-styrene.yaml &> console.log &

This kicks off the full workflow:

1. **Monomer setup.**  ``htpolynet`` reads the SMILES from
   ``constituents.STY.smiles``, builds ``lib/molecules/inputs/STY.mol2``,
   then invokes ``antechamber``/``parmchk2``/``tleap`` to produce the
   parameterized monomer in ``lib/molecules/parameterized/``.
2. **Initial pack.**  1000 copies of styrene are placed into a box sized
   for ``initial_density: 300 kg/m³``.
3. **Densification.**  The cascade under ``densification`` runs:
   minimization, 10 ps NVT, 200 ps NPT at 10 bar.
4. **Anneal cascade.**  The cascade under ``precure`` runs:
   pre-equilibration, two 300/600 K cycles, post-equilibration.

Each stage writes into its own subdirectory under ``proj-N/systems/``,
where ``N`` is the next available index (the line ``Working in new
project proj-N`` near the top of ``diagnostics.log`` tells you which
one was chosen).  For this no-cure build you'll see:

.. code-block:: text

   proj-0/
   └── systems/
       ├── init/             # initial packed box
       ├── densification/    # min + nvt + npt cascade output
       ├── precure/          # preequilibration, anneal, postequilibration
       ├── postcure/         # empty -- no postcure block in this example
       └── final-results/    # the final structure + topology + viz files

There are no ``capping/`` or ``iter-*/`` subdirectories — those are only
produced when a ``CURE`` block is configured.

If you tail ``diagnostics.log`` while the run is going, the major stage
transitions are clearly logged.  A clean finish ends with an
``htpolynet runtime ends`` line and the ``final-results`` directory
populated.