Running the Build

From inside 1-polystyrene/, launch htpolynet run:

$ htpolynet run -diag diagnostics.log pSTY.yaml &> console.log &

The -diag flag writes per-iteration diagnostic data to diagnostics.log (used later for plotting). Redirecting stdout/stderr to console.log lets you monitor progress with tail -f console.log.

Build stages

htpolynet works through the following stages in order. Each is visible in console.log.

  1. Template parameterization — htpolynet parameterizes the monomer STY and automatically generates and parameterizes all chain-expanded dimer, trimer, and tetramer templates using AmberTools (antechamber, parmchk2, tleap) and Gromacs (energy minimization).

  2. System assembly — 200 STY molecules are placed in a cubic box at the requested initial density of 300 kg/m3.

  3. Densification — a short minimization followed by NVT (10 ps, 300 K) and NPT (200 ps, 300 K, 10 bar) MD simulations compress the box to near the ambient density.

  4. Pre-cure equilibration — an NPT MD run at 1 bar and 300 K is followed by two annealing cycles (300 → 600 → 300 K) and a final 100 ps NPT equilibration.

  5. CURE iterations — the CURE algorithm searches for reactive C1–C2 pairs within the current search radius, optionally drags distant pairs closer, deletes sacrificial H atoms, forms new bonds, relaxes bond lengths, and runs a short NPT equilibration. The radius expands by 0.25 nm whenever no new bonds are found. This repeats until 95% conversion is reached or 150 iterations are exhausted.

  6. Cap reactions — unreacted STY monomers have their C1–C2 bond restored to a double bond.

  7. Post-cure equilibration — two more annealing cycles followed by a final NPT equilibration produce the finished proj-0/ output.

Monitoring progress

To watch the build in real time:

$ tail -f console.log

To check how many CURE iterations have completed:

$ grep "^INFO> Iteration" console.log

When the build finishes successfully, the last lines of console.log will indicate that post-cure equilibration has completed and the final top and gro files have been saved to proj-0/.