Running the Build

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

$ 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:

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.