.. _dfe_run: Running the Build ----------------- From inside the working directory containing ``4-dfda-fde-epoxy-thermoset.yaml``: .. code-block:: console $ htpolynet run -diag diagnostics.log 4-dfda-fde-epoxy-thermoset.yaml &> console.log & Because the chemistry, ``CURE`` controls, ``precure`` cascade, and ``postcure`` cascade are identical to :ref:`example 3 `, the stage layout and the diagnostic-log shape are also the same. Refer back to tutorial 3 for the per-stage narrative; below are the few items that are specific to this build. Setup ^^^^^ ``setup`` parameterizes the same kind of template set as example 3 — FDE and DFA primitives, the four primary-to-secondary cure products, the eight secondary-to-tertiary products, the cap variants, and the diastereomer pool from FDE's stereocenters. Furan ring perception adds a small overhead compared to the all-carbocycle PACM/DGEBA case, but ``antechamber`` and ``tleap`` still complete cleanly thanks to the atom-mapped SMILES path described in :ref:`monomers `. Densification, precure, CURE, postcure ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ These mirror example 3 exactly — same 300 kg/m³ initial density, same 300 ps NPT densification, same 0.5 nm starting search radius, same 0.95 desired conversion (target 380 of 400 bonds), same 0.85 late threshold, same drag/relax/equilibrate cascades. Expect a similar shape: early iterations grab dozens of bonds; the long tail picks up ones and twos with the search radius growing into the drag regime. The ``CURE.controls.min_bonds_per_iteration`` knob applies the same way here as in :ref:`example 3 `. The default of ``10`` was chosen using measurements on the DGEBA/PACM system (see the table at :ref:`pde_run`); the same chemistry runs through this system so the sweet spot is likely similar. To explore, drop the knob to ``1`` and compare ``profile.json`` between runs to see the cost of the un-batched regime. Final ^^^^^ After postcure, ``htpolynet`` writes ``final.gro``, ``final.top``, ``final.tpx``, ``final.grx``, the VMD viz pair, and the profile report into ``proj-N/systems/final-results/``. The :ref:`next page ` describes what to look at.