Use this Skill for classical molecular dynamics simulations with LAMMPS: force field selection (LJ, EAM, CHARMM), NVT/NPT ensembles, RDF/MSD post-processing, and OVITO visualization.
Instrucciones de origen · Vista previa de solo lectura
name
lammps-md
description
Use this Skill for classical molecular dynamics simulations with LAMMPS: force field selection (LJ, EAM, CHARMM), NVT/NPT ensembles, RDF/MSD post-processing, and OVITO visualization.
TL;DR — Run classical molecular dynamics (MD) simulations with LAMMPS:
choose a force field (LJ, EAM, CHARMM), select an ensemble (NVE/NVT/NPT),
then post-process dump files to compute RDF, MSD, and diffusion coefficients.
Visualize trajectories with OVITO.
When to Use
Use this Skill when you need to:
Simulate atomic or molecular systems at finite temperature using empirical potentials
Compute structural properties (radial distribution function, coordination number)
Below is a complete NVT simulation of liquid argon using the Lennard-Jones potential.
Save as argon_nvt.in:
# ============================================================# LAMMPS input: LJ argon NVT at 94 K# Units: real (energy=kcal/mol, length=Angstrom, time=fs)# ============================================================# --- Initialization ---
units real
atom_style atomic
boundary p p p
# --- System definition ---# FCC lattice, lattice constant 5.26 Å → density ≈ 1.4 g/cm³
lattice fcc 5.260
region box block 0 6 0 6 0 6 # 6×6×6 unit cells = 864 atoms
create_box 1 box
create_atoms 1 box
# --- Masses ---
mass 1 39.948 # Ar atomic mass (g/mol)# --- Force field: LJ with ε=0.238 kcal/mol, σ=3.405 Å ---
pair_style lj/cut 10.0 # cutoff 10 Å
pair_coeff 1 1 0.238 3.405
# --- Settings ---
timestep 2.0 # 2 fs
thermo 100
thermo_style custom step temp press etotal ke pe
# --- Energy minimization (removes bad contacts) ---
minimize 1.0e-4 1.0e-6 1000 10000
# --- Velocity initialization at 94 K ---
velocity all create 94.0 87654 dist gaussian
# --- NVT thermostat: Nosé-Hoover, T=94 K, damping=200 fs ---
fix nvt all nvt temp 94.0 94.0 200.0
# --- Dump trajectory every 500 steps ---
dump traj all atom 500 argon_nvt.dump
dump_modify traj sortid# --- Production run: 50000 steps = 100 ps ---
run 50000
# --- Write final configuration ---
write_data argon_final.data
Run the simulation:
lammps -in argon_nvt.in -log argon_nvt.log
Step 2 — Parse Dump File and Compute RDF
"""
Compute radial distribution function (RDF) from a LAMMPS dump file.
Uses ASE for parsing; numpy for histogram computation.
"""import numpy as np
import matplotlib.pyplot as plt
from ase.io import read
defparse_lammps_dump(dump_file: str, frame_start: int = 50) -> list:
"""
Read LAMMPS dump file using ASE.
Args:
dump_file: Path to the LAMMPS atom dump file.
frame_start: Index of the first frame to include (skip equilibration).
Returns:
List of ASE Atoms objects for the selected frames.
"""
frames = read(dump_file, index=":", format="lammps-dump-text")
return frames[frame_start:]
defcompute_rdf(
frames: list,
r_max: float = 10.0,
n_bins: int = 200,
atom_type_1: int = 0,
atom_type_2: int = 0,
) -> tuple:
"""
Compute the radial distribution function g(r) by averaging over frames.
The RDF is defined as:
g(r) = (V / N²) * dn(r) / (4π r² Δr)
where dn(r) is the number of pairs with separation in [r, r+Δr].
Args:
frames: List of ASE Atoms objects.
r_max: Maximum distance in Angstroms.
n_bins: Number of histogram bins.
atom_type_1: Index of species 1 (0-indexed by ASE species list).
atom_type_2: Index of species 2.
Returns:
Tuple (r_centers, g_r) — bin centers (Å) and RDF values.
"""
bin_edges = np.linspace(0.0, r_max, n_bins + 1)
dr = bin_edges[1] - bin_edges[0]
rdf_accum = np.zeros(n_bins)
for atoms in frames:
n_atoms = len(atoms)
cell = atoms.get_cell()
volume = atoms.get_volume()
positions = atoms.get_positions()
# All pairwise distances with minimum image convention
counts = np.zeros(n_bins)
for i inrange(n_atoms - 1):
diff = positions[i + 1:] - positions[i]
# Minimum imagefor k inrange(3):
diff[:, k] -= np.round(diff[:, k] / cell[k, k]) * cell[k, k]
r = np.sqrt((diff ** 2).sum(axis=1))
r = r[r < r_max]
hist, _ = np.histogram(r, bins=bin_edges)
counts += hist
# Normalize
r_centers = 0.5 * (bin_edges[:-1] + bin_edges[1:])
shell_vol = 4.0 * np.pi * r_centers ** 2 * dr
rho = n_atoms / volume
g_r = 2.0 * counts / (n_atoms * shell_vol * rho)
rdf_accum += g_r
return r_centers, rdf_accum / len(frames)
defplot_rdf(r: np.ndarray, g_r: np.ndarray, output_path: str = "rdf.png") -> None:
"""Plot and save the radial distribution function."""
fig, ax = plt.subplots(figsize=(7, 4))
ax.plot(r, g_r, color="#2196F3", linewidth=1.5, label="Ar-Ar RDF")
ax.axhline(1.0, color="gray", linestyle="--", linewidth=0.8)
ax.set_xlabel("r (Å)")
ax.set_ylabel("g(r)")
ax.set_title("Radial Distribution Function — Liquid Argon (NVT, 94 K)")
ax.legend()
ax.set_xlim(0, r.max())
fig.tight_layout()
fig.savefig(output_path, dpi=150)
print(f"RDF plot saved to {output_path}")
if __name__ == "__main__":
frames = parse_lammps_dump("argon_nvt.dump", frame_start=20)
r, g_r = compute_rdf(frames, r_max=10.0, n_bins=200)
plot_rdf(r, g_r, "argon_rdf.png")
# First peak position gives the nearest-neighbor distance
peak_idx = np.argmax(g_r[10:]) + 10print(f"First RDF peak at r = {r[peak_idx]:.2f} Å (g(r) = {g_r[peak_idx]:.2f})")
Step 3 — MSD and Diffusion Coefficient
"""
Compute mean squared displacement (MSD) and the self-diffusion coefficient
from an NVT trajectory.
Einstein relation:
D = lim_{t→∞} MSD(t) / (6t) [3D system]
D = lim_{t→∞} MSD(t) / (4t) [2D system]
"""import numpy as np
import matplotlib.pyplot as plt
from ase.io import read
defcompute_msd(
dump_file: str,
n_origins: int = 10,
frame_skip: int = 1,
timestep_fs: float = 2.0,
dump_every: int = 500,
) -> tuple:
"""
Compute MSD using multiple time origins for better statistics.
Args:
dump_file: Path to the LAMMPS dump file.
n_origins: Number of time origins to average over.
frame_skip: Stride for reading frames (1 = read all).
timestep_fs: MD timestep in femtoseconds.
dump_every: Dump frequency in steps.
Returns:
Tuple (time_ps, msd_angstrom2) — time axis and MSD values.
"""
frames = read(dump_file, index=f"::{frame_skip}", format="lammps-dump-text")
n_frames = len(frames)
n_atoms = len(frames[0])
dt_ps = timestep_fs * dump_every * frame_skip / 1000.0# fs → ps# Stack positions: shape (n_frames, n_atoms, 3)
positions = np.array([f.get_positions() for f in frames])
# Unwrap PBC using ASE cell info
cell = frames[0].get_cell().diagonal()
for t inrange(1, n_frames):
delta = positions[t] - positions[t - 1]
delta -= np.round(delta / cell) * cell
positions[t] = positions[t - 1] + delta
max_lag = n_frames // 2
msd = np.zeros(max_lag)
counts = np.zeros(max_lag, dtype=int)
origin_stride = max(1, n_frames // n_origins)
origins = range(0, n_frames - max_lag, origin_stride)
for t0 in origins:
for lag inrange(1, max_lag):
if t0 + lag >= n_frames:
break
disp = positions[t0 + lag] - positions[t0]
msd[lag] += np.mean((disp ** 2).sum(axis=1))
counts[lag] += 1
valid = counts > 0
msd[valid] /= counts[valid]
time_ps = np.arange(max_lag) * dt_ps
return time_ps[1:], msd[1:]
deffit_diffusion_coefficient(
time_ps: np.ndarray,
msd: np.ndarray,
fit_start_frac: float = 0.2,
fit_end_frac: float = 0.8,
) -> float:
"""
Fit the linear regime of MSD to extract the self-diffusion coefficient.
Args:
time_ps: Time array in picoseconds.
msd: MSD array in Ų.
fit_start_frac: Fraction of total time to start linear fit.
fit_end_frac: Fraction of total time to end linear fit.
Returns:
Diffusion coefficient D in cm²/s.
"""
n = len(time_ps)
i0 = int(n * fit_start_frac)
i1 = int(n * fit_end_frac)
slope, intercept = np.polyfit(time_ps[i0:i1], msd[i0:i1], 1)
# slope has units Ų/ps; D = slope / 6 (3D)# Convert: 1 Ų/ps = 1e-20 m² / 1e-12 s = 1e-8 m²/s = 1e-4 cm²/s
D_cm2_per_s = slope / 6.0 * 1e-4return D_cm2_per_s
defplot_msd(
time_ps: np.ndarray,
msd: np.ndarray,
D: float,
output_path: str = "msd.png",
) -> None:
"""Plot MSD curve and annotate with diffusion coefficient."""
fig, ax = plt.subplots(figsize=(7, 4))
ax.plot(time_ps, msd, color="#E91E63", linewidth=1.5, label="MSD")
ax.set_xlabel("Time (ps)")
ax.set_ylabel("MSD (Ų)")
ax.set_title(f"Mean Squared Displacement — D = {D:.3e} cm²/s")
ax.legend()
fig.tight_layout()
fig.savefig(output_path, dpi=150)
print(f"MSD plot saved to {output_path}")
if __name__ == "__main__":
time_ps, msd = compute_msd("argon_nvt.dump", n_origins=20)
D = fit_diffusion_coefficient(time_ps, msd)
print(f"Self-diffusion coefficient D = {D:.3e} cm²/s")
print(f" (Literature: Ar at 94 K ≈ 2.4×10⁻⁵ cm²/s)")
plot_msd(time_ps, msd, D, "argon_msd.png")
Advanced Usage
EAM Potential for Metals (Copper)
# Requires: Cu_u3.eam from NIST or LAMMPS potentials directory
units metal
atom_style atomic
boundary p p p
lattice fcc 3.615 # Cu FCC lattice constant (Å)
region box block 0 8 0 8 0 8
create_box 1 box
create_atoms 1 box
mass 1 63.546
pair_style eam
pair_coeff 1 1 Cu_u3.eam
timestep 0.001 # 1 fs (metal units: time in ps)
thermo 200
velocity all create 300.0 12345
fix npt all npt temp 300.0 300.0 0.1 iso 0.0 0.0 1.0
dump traj all atom 1000 cu_npt.dump
run 100000
write_data cu_final.data
OVITO Python API for Visualization
"""
Use OVITO's Python API to load a LAMMPS dump, color by kinetic energy,
and render a PNG snapshot.
"""import ovito
from ovito.io import import_file
from ovito.modifiers import ColorCodingModifier, CommonNeighborAnalysisModifier
from ovito.vis import Viewport, RenderSettings
import ovito.vis
defrender_trajectory_snapshot(
dump_file: str,
frame_index: int = -1,
output_image: str = "snapshot.png",
width: int = 800,
height: int = 600,
) -> None:
"""
Load a LAMMPS dump file in OVITO, apply CNA structure identification,
color atoms by structure type, and render a PNG.
Args:
dump_file: Path to the LAMMPS dump file.
frame_index: Frame to render (-1 = last frame).
output_image: Output PNG file path.
width: Image width in pixels.
height: Image height in pixels.
"""# Import pipeline
pipeline = import_file(dump_file, multiple_frames=True)
# Common Neighbor Analysis to identify FCC/HCP/BCC/other structures
cna = CommonNeighborAnalysisModifier(mode=CommonNeighborAnalysisModifier.Mode.FixedCutoff)
pipeline.modifiers.append(cna)
# Color by structure type
color_mod = ColorCodingModifier(
property="Structure Type",
gradient=ColorCodingModifier.Rainbow(),
)
pipeline.modifiers.append(color_mod)
# Evaluate at the requested frame
n_frames = pipeline.source.num_frames
frame = n_frames - 1if frame_index == -1else frame_index
data = pipeline.compute(frame)
print(f"Frame {frame}: {data.particles.count} atoms")
# Setup viewport and render
vp = Viewport(type=Viewport.Type.Perspective)
vp.zoom_all()
rs = RenderSettings(size=(width, height), filename=output_image)
vp.render_image(settings=rs, frame=frame, pipeline=pipeline)
print(f"Snapshot saved to {output_image}")
if __name__ == "__main__":
render_trajectory_snapshot(
dump_file="argon_nvt.dump",
frame_index=-1,
output_image="argon_snapshot.png",
)
NPT Equation of State Calculation
"""
Run LAMMPS across a grid of (T, P) conditions to build an equation of state.
Uses Python subprocess to launch LAMMPS jobs.
"""import subprocess
import os
import numpy as np
import pandas as pd
LAMMPS_TEMPLATE = """
units real
atom_style atomic
boundary p p p
read_data argon_final.data
pair_style lj/cut 10.0
pair_coeff 1 1 0.238 3.405
timestep 2.0
thermo 500
thermo_style custom step temp press vol density etotal
fix npt all npt temp {T} {T} 200.0 iso {P} {P} 2000.0
run 25000
variable avg_density equal density
variable avg_vol equal vol
print "RESULT density ${{avg_density}} vol ${{avg_vol}}"
"""defrun_eos_point(T: float, P: float, work_dir: str) -> dict:
"""Run a single LAMMPS NPT point and return density and volume."""
os.makedirs(work_dir, exist_ok=True)
script = os.path.join(work_dir, "run.in")
log = os.path.join(work_dir, "run.log")
withopen(script, "w") as f:
f.write(LAMMPS_TEMPLATE.format(T=T, P=P))
result = subprocess.run(
["lammps", "-in", script, "-log", log],
capture_output=True, text=True
)
# Parse log for average density
density = np.nan
for line inopen(log):
if"RESULT density"in line:
parts = line.split()
density = float(parts[parts.index("density") + 1])
return {"T_K": T, "P_atm": P, "density_g_cm3": density}
defcompute_eos(
temperatures: list = [80, 94, 110],
pressures: list = [1, 100, 500],
) -> pd.DataFrame:
"""Compute EOS on a T-P grid."""
records = []
for T in temperatures:
for P in pressures:
wd = f"eos_T{T}_P{P}"
rec = run_eos_point(T, P, wd)
records.append(rec)
print(f"T={T} K, P={P} atm → ρ={rec['density_g_cm3']:.4f} g/cm³")
df = pd.DataFrame(records)
df.to_csv("eos_argon.csv", index=False)
return df
Troubleshooting
Error
Cause
Fix
Dangerous builds are not allowed
Atoms outside simulation box after build
Add boundary p p p and check lattice constant
Out of range atoms - cannot compute PPPM
Atoms flew out of box
Reduce timestep; add fix nve/limit during equilibration
Lost atoms: original N atoms now M
Simulation exploded
Energy-minimize first; check force field parameters
Communication cutoff is shorter than the ghost cutoff
Cutoff > half box length
Increase box size or reduce cutoff
OVITO ImportError
Missing ovito package
pip install ovito or use ovito Pro
ASE cannot read dump
Non-standard dump columns
Add dump_modify traj sort id to LAMMPS script
Diffusion coefficient off by 6x
Wrong dimension factor
Use / 6 for 3D; / 4 for 2D
RDF integrates to wrong coordination number
PBC not applied
Ensure minimum image convention in displacement calculation
Allen & Tildesley, "Computer Simulation of Liquids", 2nd ed. (Oxford)
Examples
Example 1 — Full LJ Argon NVT Pipeline
import subprocess
import os
# 1. Write LAMMPS input
lammps_input = """
units real
atom_style atomic
boundary p p p
lattice fcc 5.260
region box block 0 5 0 5 0 5
create_box 1 box
create_atoms 1 box
mass 1 39.948
pair_style lj/cut 10.0
pair_coeff 1 1 0.238 3.405
timestep 2.0
thermo 200
minimize 1.0e-4 1.0e-6 1000 10000
velocity all create 94.0 42 dist gaussian
fix nvt all nvt temp 94.0 94.0 200.0
dump traj all atom 500 argon.dump
run 20000
write_data argon_eq.data
"""withopen("run_argon.in", "w") as f:
f.write(lammps_input)
# 2. Run LAMMPS
ret = subprocess.run(["lammps", "-in", "run_argon.in"], capture_output=True, text=True)
if ret.returncode != 0:
print("LAMMPS error:", ret.stderr[:500])
else:
print("LAMMPS simulation complete")
# 3. Post-processif os.path.exists("argon.dump"):
from ase.io import read
import numpy as np
frames = read("argon.dump", index="10:", format="lammps-dump-text")
print(f"Loaded {len(frames)} production frames")
r, g_r = compute_rdf(frames, r_max=10.0)
peak = r[np.argmax(g_r[5:])+5]
print(f"Nearest-neighbor distance: {peak:.2f} Å")
Example 2 — EAM Copper Melting Point Estimation
"""
Estimate the melting point of Cu by tracking potential energy vs temperature
in a series of NPT simulations.
"""import numpy as np
import matplotlib.pyplot as plt
# Simulated PE data (replace with actual LAMMPS output from NPT runs)
temperatures = np.array([800, 900, 1000, 1100, 1200, 1300, 1357, 1400, 1500])
# Potential energy per atom (eV) — shows discontinuity at melting
pe_per_atom = np.array([-3.40, -3.35, -3.29, -3.23, -3.16, -3.08, -2.98, -2.71, -2.64])
fig, ax = plt.subplots(figsize=(7, 4))
ax.plot(temperatures, pe_per_atom, "o-", color="#FF5722", linewidth=1.5)
ax.axvline(1357, color="gray", linestyle="--", linewidth=0.8, label="Exp. T_m = 1357 K")
ax.set_xlabel("Temperature (K)")
ax.set_ylabel("Potential Energy per Atom (eV)")
ax.set_title("Cu Melting: Potential Energy vs Temperature (EAM)")
ax.legend()
fig.tight_layout()
fig.savefig("cu_melting.png", dpi=150)
print("Melting point analysis saved to cu_melting.png")
Example 3 — Coordination Number from RDF
"""
Compute coordination number by integrating the first peak of g(r).
The coordination number gives the average number of nearest neighbors.
"""import numpy as np
defcoordination_number(
r: np.ndarray,
g_r: np.ndarray,
r_min: float,
r_max: float,
rho: float,
) -> float:
"""
Integrate g(r) from r_min to r_max to get coordination number.
Z = 4π ρ ∫_{r_min}^{r_max} g(r) r² dr
Args:
r: Radial distance array (Å).
g_r: RDF values.
r_min: Integration lower bound (Å) — start of first peak.
r_max: Integration upper bound (Å) — first minimum after peak.
rho: Number density of the fluid (atoms/ų).
Returns:
Coordination number Z (dimensionless).
"""
mask = (r >= r_min) & (r <= r_max)
dr = r[1] - r[0]
Z = 4.0 * np.pi * rho * np.trapz(g_r[mask] * r[mask] ** 2, r[mask])
return Z
# Example: liquid argon at 94 K, density ≈ 0.021 atoms/ų
rho_Ar = 0.021# atoms/ų# Assuming r, g_r computed from compute_rdf() above# Z = coordination_number(r, g_r, r_min=3.0, r_max=5.5, rho=rho_Ar)# print(f"Coordination number: {Z:.1f} (expected ~12 for liquid Ar)")print("Coordination number formula ready — supply r, g_r from compute_rdf()")
