Post-build simulations and analyses
-----------------------------------

Polystyrene is a linear polymer rather than a cross-linked network, so a uniaxial-deformation measurement of Young's modulus is not particularly meaningful for the short chains built here.  What we *can* do is anneal and equilibrate the system, then perform a temperature ladder to estimate the glass-transition temperature, and use ``analyze`` to measure the fractional free volume of the equilibrated melt.

The :ref:`pde_tutorial` walks through the full set of postsim and analyze techniques in detail (including deformation, which is well-suited to thermosets); this section adapts that workflow to a linear polymer.

The postsim configuration
^^^^^^^^^^^^^^^^^^^^^^^^^

Create ``postsim.yaml`` in the project base directory:

.. code-block:: yaml

    - anneal:
        input_top: systems/final-results/final.top
        input_gro: systems/final-results/final.gro
        P: 1
        T0: 300
        T1: 600
        ncycles: 2
        T0_to_T1_ps: 10
        T1_ps: 10
        T1_to_T0_ps: 10
        T0_ps: 10
    - equilibrate:
        input_top: systems/final-results/final.top
        input_gro: postsim/anneal/anneal.gro
        T: 300
        ps: 100
    - ladder:
        input_top: systems/final-results/final.top
        input_gro: postsim/equilibrate/equilibrate.gro
        subdir: postsim/ladder-heat
        Tlo: 300
        Thi: 600
        deltaT: 5
        ps_per_rise: 10
        ps_per_run: 90
        warmup_ps: 10
    - ladder:
        input_top: systems/final-results/final.top
        input_gro: postsim/ladder-heat/ladder.gro
        subdir: postsim/ladder-cool
        Tlo: 300
        Thi: 600
        deltaT: -5
        ps_per_rise: 10
        ps_per_run: 90
        warmup_ps: 10

Run it:

.. code-block:: console

    $ htpolynet postsim -cfg postsim.yaml -ocfg 1-polystyrene.yaml -proj proj-0

This produces ``proj-0/postsim/{anneal,equilibrate,ladder-heat,ladder-cool}/`` with the usual Gromacs outputs plus on-the-fly density-vs-time plots.

Density during annealing and equilibration
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

.. admonition:: Placeholder
   :class: caution

   **TODO:** insert the ``rho_v_ns.png`` plots from ``proj-0/postsim/anneal/`` and ``proj-0/postsim/equilibrate/`` here.  Note whether the annealing has actually densified the system (it usually fails to in builds this short) and whether the post-anneal equilibration trace is flat over the second half.

Glass-transition temperature
^^^^^^^^^^^^^^^^^^^^^^^^^^^^

After ``postsim`` has produced the heating and cooling ladders, fit T\ :sub:`g` from the density-vs-temperature traces with:

.. code-block:: console

    $ htpolynet plots post --cfg postsim.yaml --proj proj-0

This emits ``tg.png`` plus per-ladder CSVs in ``proj-0/plots/``.

.. admonition:: Placeholder
   :class: caution

   **TODO:** insert ``proj-0/plots/tg.png`` and report the heating and cooling T\ :sub:`g` values from the console output here.  In simulations this short, expect significant heating/cooling hysteresis — comment on what production-length runs would be needed to get a converged estimate.

Free volume
^^^^^^^^^^^

Use ``htpolynet analyze`` to invoke ``gmx freevolume`` on the equilibration trajectory.  Create ``fv.yaml``:

.. code-block:: yaml

    - command: freevolume

Then:

.. code-block:: console

    $ htpolynet analyze -cfg fv.yaml -proj proj-0

.. admonition:: Placeholder
   :class: caution

   **TODO:** report the fractional free volume (and standard error) from ``proj-0/analyze/freevolume/ffv.dat`` here.  Glassy polystyrene at 300 K typically has FFV in the 0.15–0.20 range.