jinzhezenggroup/computational-chemistry-agent-skills/lammps-reaxff

LAMMPS + ReaxFF

Use this skill when the user wants to run molecular dynamics in LAMMPS with a ReaxFF force field, prepare or explain an input.lammps file, and set up charge equilibration (QEq) correctly.

Agent responsibilities

1. Confirm the ReaxFF force field file (e.g. ffield.reax.*). Do not guess which file is appropriate.

• If the user does not have a force field yet, point them to known sources (e.g. LAMMPS potentials/ffield.reax.* at https://github.com/lammps/lammps/tree/develop/potentials).

1. Confirm the structure/data file (e.g. data.system) and the atom type → element mapping needed by pair_coeff.
2. Ensure the input includes charge handling:

• Use a charge-capable atom style, such as atom_style charge or atom_style full, and ensure charges are initialized either from the data file (with a charge column compatible with the chosen atom_style) or via explicit commands (e.g. set or equal-style variables). Do not rely on fix property/atom q as a substitute for a real charge field used by ReaxFF/QEq.
• Add one charge equilibration fix, typically fix qeq/reaxff, unless the user explicitly requests otherwise.

1. Write the LAMMPS input script yourself; keep examples readable and annotated.
2. When possible, validate command availability against LAMMPS docs or local lmp -h output before execution.
3. Report clearly which command was run, which files were used, and where outputs were written.

Minimum information to collect

Ask only for what is missing:

• LAMMPS data file path (or structure + how to generate a data file)
• ReaxFF force field file path (ffield.reax...)
• Atom types present and their element mapping (for pair_coeff * * ffield ...)
• Ensemble (NVE / NVT / NPT)
• Temperature, pressure (if NPT), timestep, run length
• Execution mode: online provisioning vs user-specified LAMMPS binary

Execution mode

Online mode (only if internet access + uv is available)

Use:

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

Notes:

• If you see error while loading shared libraries: libmpi.so..., you likely installed an MPI-linked lmp without MPI runtime libraries. Prefer uvx --from 'lammps[mpi]' ... (bundles MPI runtime), or load/install MPICH/OpenMPI via system packages/conda/HPC module.

Offline mode (common / HPC)

Do not invent the executable. Ask which command should be used, e.g.:

• lmp -in input.lammps
• mpirun -np 32 lmp_mpi -in input.lammps
• srun lmp -in input.lammps

Example: annotated NVT input (ReaxFF + QEq)

See also assets/input.reaxff.nvt.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}

Notes on the example

• units real is a common choice for ReaxFF (time in fs). Many published ReaxFF workflows use real, but the correct choice depends on the parameterization and your conventions.
• Timestep: 0.25 fs may be fine for moderate temperatures, but for high-temperature ReaxFF (especially with H present) it is common to reduce to `0.1 fs` (or even 0.05 fs if needed). A quick sanity check is a short NVE segment to verify total-energy drift before running long NVT/NPT.
• atom_style charge is used because ReaxFF and QEq require per-atom charges.
• pair_style reaxff NULL uses default ReaxFF control settings. If you have a ReaxFF control file, replace NULL with its filename.
• pair_coeff * * ffield.reax C H O:
• The trailing symbols define the element mapping for LAMMPS atom types (type 1->C, type 2->H, type 3->O in this example). Adjust to match your data file.
• fix qeq/reaxff ... reaxff uses QEq parameters extracted from the ReaxFF force field file.

Sanity checks (recommended before long runs)

1. Short NVE stability check (no thermostat/barostat)

• Run 1–5 ps NVE and check that etotal drift is reasonable (and that the run does not blow up).

Example (units real):

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

• If it blows up: reduce timestep (e.g. 0.25 fs → 0.1 fs → 0.05 fs), check the initial geometry, and ensure QEq converges.

1. QEq convergence

• If QEq hits max iterations often, consider better initial charges, looser timestep, or maxiter (see LAMMPS fix qeq/reaxff).

Optional: species analysis

If the user wants reaction product tracking, add fix reaxff/species (see references/reaxff-workflow.md). This writes time series counts of detected molecular species using bond-order cutoffs.

Output checklist

After a run, report at least:

• executed command
• input script path
• data file path
• ffield path and element mapping used
• whether QEq was enabled and with which settings
• main log path (log.lammps)
• trajectory/species output paths (if any)

References

• pair_style reaxff: https://docs.lammps.org/pair_reaxff.html
• fix qeq/reaxff: https://docs.lammps.org/fix_qeq_reaxff.html
• fix reaxff/species: https://docs.lammps.org/fix_reaxff_species.html