LAMMPS ReaxFF Setup

What it does

When your agent uses it

• Setting up a reactive molecular dynamics run with a ReaxFF force field
• Getting a working, commented input.lammps template for a new system
• Fixing charge equilibration or atom type mapping in an existing ReaxFF input
• Adding species analysis to a ReaxFF simulation

Example prompts

• “Write an NVT ReaxFF input for data.system using the force field file ffield.reax.cho.”
• “Why does my LAMMPS ReaxFF run complain about missing charges? Check the atom style and the qeq fix.”
• “Map atom types 1 to 3 in data.system to C, H and O in pair_coeff.”
• “Add species analysis to the ReaxFF script I already have.”

Requirements

• A LAMMPS build with the REAXFF package enabled
• A ReaxFF force field file such as `ffield.reax.*`
• `uv` and internet access for the online run mode
• Compatibility (from SKILL.md): Requires a LAMMPS build with the REAXFF package enabled (pair_style reaxff and fix qeq/reaxff). Optional acceleration variants: reaxff/omp or reaxff/kk.

Workflow steps

6 steps, taken from the first numbered list in SKILL.md.

1. 1Confirm the ReaxFF force field file (e.g. ffield.reax.*). Do not guess which file is appropriate.
2. 2Confirm the structure/data file (e.g. data.system) and the atom type → element mapping needed by pair_coeff.
3. 3Ensure the input includes charge handling
4. 4Write the LAMMPS input script yourself; keep examples readable and annotated.
5. 5When possible, validate command availability against LAMMPS docs or local lmp -h output before execution.
6. 6Report clearly which command was run, which files were used, and where outputs were written.

What it can do on your machine

Read from SKILL.md and the folder at commit 5c19e75. It shows what the files ask for, not the result of running them.

• Tool permissions

  Pre-approves nothing: there is no allowed-tools line, so your agent's usual permission prompts apply.

  From allowed-tools in the SKILL.md frontmatter.

• Runs code

  Shell commands in SKILL.md call:

  • uvx

  From the folder's file list and the shell code blocks in SKILL.md.

• Network

  Links to these hosts (documentation or services it may open):

  • docs.lammps.org
  • github.com

  From URLs in SKILL.md, links to its own repository left out.

• Credentials

  Names no API keys, tokens, secrets or passwords.

  From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.

• Compatibility

  Requires a LAMMPS build with the REAXFF package enabled (pair_style reaxff and fix qeq/reaxff). Optional acceleration variants: reaxff/omp or reaxff/kk.

  From compatibility in the SKILL.md frontmatter.

Context cost

LAMMPS ReaxFF Setup loads about 1.8k tokens when it runs, and up to ~2.3k if it reads all its reference files. Until then it costs about 105 tokens; SKILL.md has 659 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it

~105

When it runs · the whole SKILL.md, loaded when a task matches

~1.8k

With references · SKILL.md plus every file in references/, read only if the agent opens them

~2.3k

Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.

Safety

Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); files beside SKILL.md are not scanned.

SKILL.md

The full file from jinzhezenggroup/computational-chemistry-agent-skills at commit 5c19e75, republished under its LGPL-3.0-or-later licence (© jinzhezenggroup). 659 words, ~1,814 tokens.

name

lammps-reaxff

description

Run reactive molecular dynamics simulations in LAMMPS with the ReaxFF potential, including preparing input scripts (pair_style reaxff + fix qeq/reaxff), mapping LAMMPS atom types to elements via pair_coeff, choosing ensembles (NVE/NVT/NPT), and adding common ReaxFF diagnostics such as species analysis. Use when the user wants LAMMPS+ReaxFF workflows or needs a working, annotated `input.lammps` template.

compatibility

Requires a LAMMPS build with the REAXFF package enabled (pair_style reaxff and fix qeq/reaxff). Optional acceleration variants: reaxff/omp or reaxff/kk.

license

LGPL-3.0-or-later

metadata.author

njzjz-bot

metadata.version

1.0

metadata.repository

https://www.lammps.org/

metadata.lammps_docs

https://docs.lammps.org/

uvx --from 'lammps[mpi]' lmp -in input.lammps

# --------- user knobs ---------
variable        NSTEPS      equal 200000
variable        THERMO      equal 200
variable        DUMP        equal 1000

variable        TEMP        equal 300.0
variable        TAU_T       equal 100.0

# Timestep (fs for units real). For high-T / reactive runs, 0.1 fs is often safer.
variable        DT          equal 0.25


# QEq parameters
variable        QEQ_EVERY   equal 1
variable        QEQ_TOL     equal 1.0e-6
variable        QEQ_CUTLO   equal 0.0
variable        QEQ_CUTHI   equal 10.0

units           real
boundary        p p p
atom_style      charge

read_data       data.system

neighbor        2.0 bin
neigh_modify    every 1 delay 0 check yes

# ReaxFF potential
pair_style      reaxff NULL
pair_coeff      * * ffield.reax C H O

# Charge equilibration (required for most ReaxFF parameterizations)
fix             fqeq all qeq/reaxff ${QEQ_EVERY} ${QEQ_CUTLO} ${QEQ_CUTHI} ${QEQ_TOL} reaxff
# (`reaxff` here means QEq parameters are extracted from the ReaxFF force field file.)

# Thermo and trajectory
thermo_style    custom step temp pe ke etotal press vol density
thermo          ${THERMO}

dump            1 all custom ${DUMP} traj.lammpstrj id type q x y z

# Dynamics
velocity        all create ${TEMP} 12345 mom yes rot yes dist gaussian
fix             fnvt all nvt temp ${TEMP} ${TEMP} ${TAU_T}

timestep        ${DT}
run             ${NSTEPS}

reset_timestep  0
unfix           fnvt
fix             fnve all nve

# high-T ReaxFF often needs a smaller timestep
# (common choices: 0.1 fs; if needed 0.05 fs)
timestep        0.1
run             2000

© jinzhezenggroup, LGPL-3.0-or-later. Rendered from Markdown: HTML in the file is shown as text, images as links, and headings moved down two levels. Raw file

Files

SKILL.md and 2 other files (references, assets) in molecular-dynamics/lammps-reaxff of jinzhezenggroup/computational-chemistry-agent-skills.

• SKILL.md
• assets/input.reaxff.nvt.lammps
• references/reaxff-workflow.md

Open the folder on GitHubat commit 5c19e75