LAMMPS Molecular Dynamics Simulation
You are executing LAMMPS molecular dynamics simulations on this workstation.
CRITICAL: Finding Your Own Parameters
You must find force field parameters yourself. They are NOT provided.
How to Find Force Field Parameters
Step 1: Identify what you need
- What material? (argon, water, copper, etc.)
- What property? (diffusion, structure, thermal conductivity)
- What conditions? (temperature, pressure)
Step 2: Search literature
Good search queries:
- "[material] lennard-jones parameters molecular dynamics"
- "[material] force field molecular dynamics"
- "[material] interatomic potential parameters"
- "[water model] parameters" (for TIP3P, TIP4P, SPC/E, etc.)
- "[metal] EAM potential"Step 3: Find authoritative sources
| Material | Seminal Paper | Key Values |
|---|---|---|
| Liquid Argon | Rahman 1964, Phys. Rev. 136, A405 | ε/kB=119.8 K, σ=3.405 Å |
| TIP4P Water | Jorgensen 1983, J. Chem. Phys. 79, 926 | See paper Table I |
| TIP3P Water | Jorgensen 1983 (same paper) | ε=0.1521 kcal/mol, σ=3.1507 Å |
| SPC/E Water | Berendsen 1987, J. Phys. Chem. 91, 6269 | qO=-0.8476e, ε=0.1553 kcal/mol |
Step 4: Download supplementary materials if needed Use Playwright or WebFetch to get SI with parameter tables.
Step 5: Convert units
kJ/mol → kcal/mol: divide by 4.184
eV → kcal/mol: multiply by 23.06
K → kcal/mol: multiply by 0.001987 (kB)Step 6: Document source in input file
# Lennard-Jones parameters for liquid argon
# Source: Rahman, Phys. Rev. 136, A405 (1964)
# ε/kB = 119.8 K = 0.238 kcal/mol, σ = 3.405 Å
pair_coeff 1 1 0.238 3.405Binary Location
LAMMPS is configured via environment variable (set in .claude/settings.json or shell):
# From environment variable
LMP="${LMP:-lmp}" # Falls back to 'lmp' in PATH
# Or check your config
echo $LMPExecution Commands
CPU:
$LMP -in input.lmpGPU (for large systems):
$LMP -sf gpu -pk gpu 1 neigh yes -in input.lmpComplete Workflow (Agentic)
Example: Liquid Argon Diffusion
Given only: "Calculate the self-diffusion coefficient of liquid argon"
You do:
- Search literature for argon MD parameters
- Find Rahman 1964 as seminal paper - Extract: ε/kB = 119.8 K, σ = 3.405 Å - Note conditions: T = 94.4 K (triple point), ρ = 1.374 g/cm³
- Convert parameters
- ε = 119.8 K × 0.001987 kcal/(mol·K) = 0.238 kcal/mol
- Calculate system size
- N = 864 atoms (Rahman's choice, or 256-500 for faster) - Box size from density: L = (N × M / (ρ × Nₐ))^(1/3)
- Create input file with citations
# Liquid Argon MD - Self-diffusion calculation # Parameters from Rahman, Phys. Rev. 136, A405 (1964) units real atom_style atomic boundary p p p # Create FCC lattice, will melt to liquid lattice fcc 5.26 # ~1.374 g/cm³ region box block 0 6 0 6 0 6 create_box 1 box create_atoms 1 box mass 1 39.948 # Argon # LJ potential - Rahman 1964 parameters pair_style lj/cut 10.0 pair_coeff 1 1 0.238 3.405 # ε=0.238 kcal/mol, σ=3.405 Å # Initialize velocities at target temperature velocity all create 94.4 12345 # Equilibration fix 1 all nvt temp 94.4 94.4 100.0 timestep 2.0 thermo 100 run 10000 # Production with trajectory for MSD reset_timestep 0 dump 1 all custom 100 trajectory.lammpstrj id type x y z run 50000 - Run simulation
$LMP -in input.lmp - Analyze MSD and extract D
- Use LAMMPS compute msd or post-process trajectory - D = lim(t→∞) MSD(t) / (6t)
- Compare to literature
- Rahman 1964: D ≈ 2.43 × 10⁻⁵ cm²/s - Your result should be within ~10%
Common Pair Styles and When to Use
| Pair Style | Use For | Notes |
|---|---|---|
lj/cut | Noble gases, simple fluids | Need ε, σ from literature |
lj/cut/coul/long | Molecular systems with charges | Combine with kspace |
eam | Metals | Download.eam file from literature |
tersoff | Covalent (Si, C, etc.) | Use published parameter files |
reaxff | Reactive systems | Requires force field file |
Finding EAM Potentials for Metals
- Search: "[metal] EAM potential LAMMPS"
- Check NIST Interatomic Potentials Repository: https://www.ctcms.nist.gov/potentials/
- Download the.eam.alloy or.eam.fs file
- Reference in input:
pair_style eam/alloy pair_coeff * * Cu_Zhou04.eam.alloy Cu
Input File Structure
- Units and style -
units realfor most molecular systems - Structure -
read_dataor create withlattice/create_atoms - Force field -
pair_styleandpair_coeff(YOU FIND THESE) - Dynamics -
fix nvt/npt/nve,timestep - Output -
thermo,dump - Run -
minimizeorrun
Common Issues and Solutions
- "Unknown pair style" - Style not compiled in. Check
$LMP -hfor available. - "Bond atom missing" - Topology error in data file
- "Out of range atoms" - Timestep too large or bad parameters
- Wrong temperature/energy - Check unit consistency (real vs metal vs lj)
Property Calculations
Diffusion Coefficient
compute msd all msd
fix msd_out all ave/time 100 1 100 c_msd[4] file msd.datThen: D = slope(MSD vs t) / 6
Radial Distribution Function
compute rdf all rdf 100
fix rdf_out all ave/time 100 1 100 c_rdf[*] file rdf.dat mode vectorTemperature/Pressure
Already in thermo output by default.
Key Principle
Don't use placeholder parameters. Every pair_coeff line should have a citation in the comments. If you can't find parameters, search harder or report that the parameters aren't available in literature.