Lammps Simulation

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

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 3.405

Binary 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 $LMP

Execution Commands

CPU:

$LMP -in input.lmp

GPU (for large systems):

$LMP -sf gpu -pk gpu 1 neigh yes -in input.lmp

Complete Workflow (Agentic)

Example: Liquid Argon Diffusion

Given only: "Calculate the self-diffusion coefficient of liquid argon"

You do:

1. 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

2. Convert parameters

   • ε = 119.8 K × 0.001987 kcal/(mol·K) = 0.238 kcal/mol

3. 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)

4. 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
   

5. Run simulation

   $LMP -in input.lmp
   

6. Analyze MSD and extract D

   • Use LAMMPS compute msd or post-process trajectory
   • D = lim(t→∞) MSD(t) / (6t)

7. 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

Finding EAM Potentials for Metals

1. Search: "[metal] EAM potential LAMMPS"
2. Check NIST Interatomic Potentials Repository: https://www.ctcms.nist.gov/potentials/
3. Download the .eam.alloy or .eam.fs file
4. Reference in input:

   pair_style eam/alloy
   pair_coeff * * Cu_Zhou04.eam.alloy Cu
   

Input File Structure

1. Units and style - units real for most molecular systems
2. Structure - read_data or create with lattice/create_atoms
3. Force field - pair_style and pair_coeff (YOU FIND THESE)
4. Dynamics - fix nvt/npt/nve, timestep
5. Output - thermo, dump
6. Run - minimize or run

Common Issues and Solutions

1. "Unknown pair style" - Style not compiled in. Check $LMP -h for available.
2. "Bond atom missing" - Topology error in data file
3. "Out of range atoms" - Timestep too large or bad parameters
4. 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.dat

Then: 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 vector

Temperature/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.