.. _liquid_styrene_configuration: Configuration ------------- The full ``0-liquid-styrene.yaml`` is short — no ``reactions``, no ``CURE``, no ``postcure``. It is just enough to parameterize a single monomer, build a low-density box, and run the densification + anneal cascade. .. literalinclude:: ../../../../src/htpolynet/resources/example_depot/0-liquid-styrene.yaml :language: yaml A block-by-block walk-through: ``Title`` A free-text label for the run; appears in logs and in the title field of generated topology/structure files. ``gromacs`` Tells ``htpolynet`` how to invoke GROMACS. ``gmx_options`` are passed to every ``gmx`` invocation; ``mdrun_options`` are passed to ``mdrun`` only. The ``gpu_id: 0`` line is left in by default and the runtime will automatically strip it (with a warning) if the ``gmx`` build is not GPU-capable or no GPU is visible. ``ambertools`` Selects the partial-charge method for ``antechamber``; ``gas`` is Gasteiger and is fast and good enough for a non-reactive densification. ``constituents`` Declares the molecular species in the box. Here, one species (``STY``, 1000 copies) generated from SMILES. See :ref:`monomer ` for the atom-mapping details. ``densification`` The post-pack equilibration cascade. Starts at ``initial_density: 300 kg/m³`` (deliberately loose so the pack succeeds without overlaps) and runs minimization → 10 ps NVT at 300 K → 200 ps NPT at 300 K, 10 bar. The deliberately high pressure accelerates compaction. ``precure`` Despite the name, ``precure`` is not chemically a curing step — it is the post-densification equilibration that ``htpolynet`` runs whether or not a cure is configured. Here it is: * ``preequilibration`` — 200 ps NPT at 300 K, 1 bar (relax the pressure jolt from densification); * ``anneal`` — two 300 K → 600 K → 300 K cycles, 80 ps per cycle, useful for shaking the liquid out of any pack-induced local traps; * ``postequilibration`` — 100 ps NPT at 300 K, 1 bar. The comment block at the top of the YAML also sketches an ``htpolynet analyze`` configuration (``ck.yaml``) you can run after the build to compute free volume and similar properties; see :ref:`results ` and the :doc:`postsim` section.