Computational Chemistry Agent Skills
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packmol-generate-mixture

data-processing
A tool for generating initial packed molecular configurations (XYZ format) from single-molecule structures by calculating box dimensions, writing input scripts, and executing Packmol. USE WHEN you need to randomly pack a specific number of molecules into a simulation box (defined by target density or fixed lengths) to create starting geometries for molecular dynamics or related computational chemistry workflows.
v1.0 Requires uv and internet access (uses `uvx packmol ...`). repository source

Installation

Install folder: packmol-generate-mixture · Repo path: data-processing/packmol-generate-mixture
Copy/paste this message to your OpenClaw agent. 
Please install the OpenClaw skill "packmol-generate-mixture" on the OpenClaw host.

Steps:
- Download: https://skills.computchem.cn/skill-zips/packmol-generate-mixture.zip
- Unzip it to get packmol-generate-mixture/
- Copy packmol-generate-mixture/ into the workspace skills directory (<workspace>/skills/)
- Start a NEW OpenClaw session so the skill is loaded

Then verify:
openclaw skills list --eligible
openclaw skills info packmol-generate-mixture
Prerequisites: Requires uv and internet access (uses `uvx packmol ...`).

packmol-generate-mixture

Use Packmol to generate an initial packed configuration for a molecular mixture.

Agent responsibilities (do these in order)

  1. Collect inputs (ask if missing; do not guess):

    • component structure files (XYZ), one per species (e.g. species1.xyz, species2.xyz)
    • molecule counts for each species (e.g. species1: 100, species2: 650)
    • either target density (g/cm^3) or a fixed cubic box length (Å)
    • Packmol tolerance (Å)
    • output location: output directory + output filename prefix (system name)

  2. Validate inputs:

    • confirm XYZ files exist and are readable
    • confirm the first line (atom count) matches the number of coordinate lines
    • if density-based box estimation is requested: confirm each molecule’s elemental composition can be inferred from the XYZ symbols

  3. Decide box size:

    • If user provides box_length_A: use it.
    • Else compute box_length_A from density (see formula below).

  4. Create a working folder at the requested output location:

    • copy the component XYZ files into it (or reference them with absolute paths)

  5. Write Packmol input ${system_name}.inp:

    • one structure ... end structure block per component
    • all components share the same inside box 0 0 0 L L L

  6. Run Packmol locally:

    • Prefer: uvx packmol -i ${system_name}.inp
    • If you need to force the source package: uvx --from packmol packmol -i ${system_name}.inp

  7. Report results:

    • exact output paths (inp, xyz, log)
    • final box length (Å) and the parameters used (counts, density or fixed L, tolerance)
    • basic sanity checks (total molecules, total atoms)

  8. (Optional) Post-process for LAMMPS

If the user plans to run LAMMPS (especially ReaxFF), they often need a LAMMPS data file with correct box bounds.

  • If you convert XYZ -> LAMMPS data with dpdata, dpdata may write default box bounds (e.g., 0..100 Å).
  • Fix the bounds to match the Packmol cubic box length using lammps-md-tools from PyPI:
uvx --from lammps-md-tools lammps-fix-box \
    --in  input.data \
    --out output.boxfix.data \
    --L 60.690 \
    --wrap

This rewrites xlo/xhi, ylo/yhi, zlo/zhi to 0..L, zeroes tilt factors, and optionally wraps atoms into the box.

What to ask the user (plain language)

If the user didn’t specify them, ask at minimum:

  • Packing counts: how many molecules of each species? (e.g., species1=100, species2=650)
  • Box definition: do you want to estimate a cubic box from a target density (g/cm^3), or do you want to provide a fixed cubic box length L (Å)?
  • Tolerance: what Packmol tolerance (Å) should be used? (common starting point: 2.0 Å)
  • Output location: which directory should receive the results, and what system name / filename prefix should be used?

If the user says “use defaults”, propose defaults:

  • tolerance = 2.0 Å
  • output dir: a packed/ subfolder under the folder containing the input XYZ
  • (density) do not assume; ask for it, but you may suggest a starting value the user can confirm.

Example (replace with your own species/files):

system_name: mixture_pack
output_dir: /path/to/output/packed
# Choose ONE of the following:
density_g_cm3: 0.25
# box_length_A: 60.69

tolerance_A: 2.0
components:
  - name: species1
    structure_file: /path/to/species1.xyz
    number: 100
  - name: species2
    structure_file: /path/to/species2.xyz
    number: 650

Density → cubic box length (Å)

When density_g_cm3 is provided and box_length_A is not, estimate L from total mass:

  • infer each molecule’s elemental composition from its XYZ symbols
  • use standard atomic masses (g/mol)
  • compute total molar mass of the whole configuration (g/mol)
  • convert to mass per configuration: m_cfg = M_total / N_A (g)
  • compute volume in cm^3: V_cm3 = m_cfg / density_g_cm3
  • convert to Å^3: V_A3 = V_cm3 * 1e24
  • cubic length: L_A = V_A3 ** (1/3)

This is an initial packing estimate (geometry construction), not an equilibrated density.

Output contract

The run should produce (within output_dir):

  • ${system_name}.inp (Packmol input)
  • ${system_name}.xyz (packed XYZ output; name may include _packed suffix)
  • packmol.out (stdout log; capture with tee)

Limitations (be explicit)

  • Packed XYZ has coordinates only; no topology, no force-field types, no LAMMPS data.
  • Packing success ≠ physically valid structure; minimization/equilibration still required.