Notebooks · posts/molecular-dynamics-2d

A Lennard-Jones liquid by molecular dynamics in two dimensions

Adam Zettel · September 22, 2026 · written with an agent

100 atoms in a periodic box, velocity Verlet, no thermostat. The total energy never moves from its starting value by more than a thousandth of the kinetic energy, the speeds settle onto the Maxwell distribution at the temperature the kinetic energy says, and the pair correlation peaks where the potential is deepest.

V (r) = 4 ε [(\frac{σ}{r})^{12} - (\frac{σ}{r})^{6}]

Atoms interact by the Lennard-Jones potential $u (r) = 4 ε [(σ / r)^{12} - (σ / r)^{6}]$ , in units where $σ = ε = m = 1$ . The box is periodic with the minimum-image rule, there is no cutoff (every pair, $N$ small), and the integrator is velocity Verlet, which is symplectic: the energy wobbles but does not drift.

What is checked

Momentum stays at zero to rounding, because every force has an equal and opposite partner. The total energy never moves from its starting value by more than a thousandth of the kinetic energy (velocity Verlet's error is second order in the step; halve DT and it drops fourfold). And the speeds, collected over the second half of the run, follow the two-dimensional Maxwell distribution $f (v) = (v / T) e^{- v^{2} /2 T}$ at the temperature $T = ⟨ v^{2} ⟩ /2$ that equipartition gives, averaged over the same half — the histogram against that curve is the second figure, and the test checks that their mean speeds agree to two percent.

The pair correlation $g (r)$ is the third figure: near zero inside the core, a first peak close to $2^{1/6} σ = 1.12$ where the potential is deepest, then ripples that fade toward 1. The fourth test checks the position and height of that peak.

The force loop is written with arrays: for each atom, the displacements to all the others are one array, the minimum image is one line, and the pair forces are a pow and two products. The post also shows a recorded run of the same program at 400 atoms and three times the steps (the large setting), compiled to C and run natively; 100 atoms takes a few seconds in a browser tab.

Look inside this program

Atlas
The program’s map: every function and which calls which.
There’s no recorded run of this program yet.

Shift+Enter in a cell runs it and moves to the next. Running a cell runs every cell above it too, as one program.

[1]lines 41–220

N = 100            #: N      atoms
STEPS = 2000       #: STEPS  time steps
DT = 0.005         #: DT     time step
T0 = 0.5           #: T0     starting temperature (kinetic energy per atom)
BINS = 30
pi = 3.141592653589793

# a square box at reduced density 0.7, atoms started on a square lattice
DENSITY = 0.7
L = sqrt(N / DENSITY)
SIDE = ceil(sqrt(N))
SPACING = L / SIDE

X = zeros(N)
Y = zeros(N)
for i to N {
    X[i] = (mod(i, SIDE) + 0.5) * SPACING
    Y[i] = (floor(i / SIDE) + 0.5) * SPACING
}

# random velocities, zero total momentum, then scaled to T0
srand(3.0)
VX = zeros(N)
VY = zeros(N)
for i to N {
    VX[i] = rand() - 0.5
    VY[i] = rand() - 0.5
}
VX = VX - sum(VX) / N
VY = VY - sum(VY) / N
scale = sqrt(2.0 * T0 * N / sum(VX * VX + VY * VY))
VX = scale * VX
VY = scale * VY

#| Minimum-image displacement: wrap a difference into (-L/2, L/2].
def wrap(d) {
    return d - L * round(d / L)
}

#| The force on atom i from every other atom, and its potential energy: [fx, fy, u].
def force_on(i) {
    dx = wrap(X - X[i])
    dy = wrap(Y - Y[i])
    r2 = dx * dx + dy * dy
    r2[i] = 1.0e30
    inv6 = pow(r2, -3.0)
    f_over_r = 24.0 * (2.0 * inv6 * inv6 - inv6) / r2
    u = 4.0 * (inv6 * inv6 - inv6)
    return [-sum(f_over_r * dx), -sum(f_over_r * dy), 0.5 * sum(u)]
}

#| Fill FX and FY with the force on every atom, and return the total potential energy.
FX = zeros(N)
FY = zeros(N)
def compute_forces() {
    u = 0.0
    for i to N {
        f = force_on(i)
        FX[i] = f[0]
        FY[i] = f[1]
        u = u + f[2]
    }
    return u
}

#| The total kinetic energy of the atoms.
def kinetic() {
    return 0.5 * sum(VX * VX + VY * VY)
}

# the run: velocity Verlet, sampling speeds and g(r) over the second half
potential = compute_forces()
E0 = kinetic() + potential
SPEEDS = zeros(N * (STEPS / 2))
G_BINS = 60
R_MAX = 0.5 * L
gcount = zeros(G_BINS)
nsample = 0.0
worst_drift = 0.0
temp_acc = 0.0
FRAME_EVERY = 40
stage("100 Lennard-Jones atoms, periodic box", -0.5, L + 0.5, -0.5, L + 0.5)
segment("bottom", 0.0, 0.0, L, 0.0)
segment("top", 0.0, L, L, L)
segment("left", 0.0, 0.0, 0.0, L)
segment("right", L, 0.0, L, L)
dots("atoms", X, Y, 0.35)
for s to STEPS {
    VX = VX + 0.5 * DT * FX
    VY = VY + 0.5 * DT * FY
    X = X + DT * VX
    Y = Y + DT * VY
    X = X - L * floor(X / L)
    Y = Y - L * floor(Y / L)
    potential = compute_forces()
    VX = VX + 0.5 * DT * FX
    VY = VY + 0.5 * DT * FY
    e = kinetic() + potential
    worst_drift = max(worst_drift, abs(e - E0))
    if s >= STEPS / 2 {
        k = s - STEPS / 2
        speed = sqrt(VX * VX + VY * VY)
        temp_acc = temp_acc + sum(speed * speed) / (2.0 * N)
        for i to N {
            SPEEDS[k * N + i] = speed[i]
        }
        if mod(k, 10) == 0.0 {
            for i to N {
                dx = wrap(X - X[i])
                dy = wrap(Y - Y[i])
                r = sqrt(dx * dx + dy * dy)
                r[i] = 2.0 * R_MAX
                gcount = gcount + histogram(r, 0.0, R_MAX, G_BINS)
            }
            nsample = nsample + 1.0
        }
    }
    if mod(s, FRAME_EVERY) == 0.0 {
        dots("atoms", X, Y, 0.35)
        frame(DT * FRAME_EVERY)
    }
}

momentum = sqrt(sum(VX) * sum(VX) + sum(VY) * sum(VY))
temperature = temp_acc / (STEPS / 2)
mean_speed = sum(SPEEDS) / len(SPEEDS)
maxwell_mean = sqrt(pi * temperature / 2.0)
show E0
show worst_drift
show momentum
show temperature
show mean_speed
show maxwell_mean

# the speed histogram, as a density, against the Maxwell curve at the measured T
V_MAX = 4.0 * sqrt(temperature)
counts = histogram(SPEEDS, 0.0, V_MAX, BINS)
width = V_MAX / BINS
centers = linspace(0.5 * width, V_MAX - 0.5 * width, BINS)
density = counts / (len(SPEEDS) * width)
maxwell = (centers / temperature) * exp(-centers * centers / (2.0 * temperature))
figure("Speeds over the second half of the run, against Maxwell at the measured temperature", "speed", "density")
bars(centers, density, "measured")
plot(centers, maxwell, "Maxwell, 2-D")

# the pair correlation: counts per shell over the ideal-gas expectation
shell_width = R_MAX / G_BINS
r_centers = linspace(0.5 * shell_width, R_MAX - 0.5 * shell_width, G_BINS)
ideal = DENSITY * 2.0 * pi * r_centers * shell_width * N
g = gcount / (nsample * ideal)
peak_r = 0.0
peak_g = 0.0
for b to G_BINS {
    if g[b] > peak_g {
        peak_g = g[b]
        peak_r = r_centers[b]
    }
}
show peak_r
show peak_g
figure("The pair correlation g(r)", "r", "g")
plot(r_centers, g, "g(r)")
plot(r_centers, zeros(G_BINS) + 1.0, "an ideal gas")

test "momentum stays at zero to rounding" {
    assert_lt(momentum, 1.0e-9)
}
test "the total energy never moves from its starting value by more than a thousandth of the kinetic energy" {
    assert_lt(worst_drift, 1.0e-3 * kinetic())
}
test "the mean speed matches the 2-D Maxwell distribution at the measured temperature to two percent" {
    assert_near(mean_speed, maxwell_mean, 0.02 * maxwell_mean)
}
test "g(r) peaks near 2^(1/6) sigma, the bottom of the potential, and is above 1 there" {
    assert_near(peak_r, 1.122, 0.1)
    assert_gt(peak_g, 1.5)
}

# SPDX-License-Identifier: MIT OR Apache-2.0
# SPDX-FileCopyrightText: 2026 The Viv authors

N = 100            #: N      atoms
STEPS = 2000       #: STEPS  time steps
DT = 0.005         #: DT     time step
T0 = 0.5           #: T0     starting temperature (kinetic energy per atom)
BINS = 30
pi = 3.141592653589793

# a square box at reduced density 0.7, atoms started on a square lattice
DENSITY = 0.7
L = sqrt(N / DENSITY)
SIDE = ceil(sqrt(N))
SPACING = L / SIDE

X = zeros(N)
Y = zeros(N)
for i to N {
    X[i] = (mod(i, SIDE) + 0.5) * SPACING
    Y[i] = (floor(i / SIDE) + 0.5) * SPACING
}

# random velocities, zero total momentum, then scaled to T0
srand(3.0)
VX = zeros(N)
VY = zeros(N)
for i to N {
    VX[i] = rand() - 0.5
    VY[i] = rand() - 0.5
}
VX = VX - sum(VX) / N
VY = VY - sum(VY) / N
scale = sqrt(2.0 * T0 * N / sum(VX * VX + VY * VY))
VX = scale * VX
VY = scale * VY

#| Minimum-image displacement: wrap a difference into (-L/2, L/2].
def wrap(d) {
    return d - L * round(d / L)
}

#| The force on atom i from every other atom, and its potential energy: [fx, fy, u].
def force_on(i) {
    dx = wrap(X - X[i])
    dy = wrap(Y - Y[i])
    r2 = dx * dx + dy * dy
    r2[i] = 1.0e30
    inv6 = pow(r2, -3.0)
    f_over_r = 24.0 * (2.0 * inv6 * inv6 - inv6) / r2
    u = 4.0 * (inv6 * inv6 - inv6)
    return [-sum(f_over_r * dx), -sum(f_over_r * dy), 0.5 * sum(u)]
}

#| Fill FX and FY with the force on every atom, and return the total potential energy.
FX = zeros(N)
FY = zeros(N)
def compute_forces() {
    u = 0.0
    for i to N {
        f = force_on(i)
        FX[i] = f[0]
        FY[i] = f[1]
        u = u + f[2]
    }
    return u
}

#| The total kinetic energy of the atoms.
def kinetic() {
    return 0.5 * sum(VX * VX + VY * VY)
}

# the run: velocity Verlet, sampling speeds and g(r) over the second half
potential = compute_forces()
E0 = kinetic() + potential
SPEEDS = zeros(N * (STEPS / 2))
G_BINS = 60
R_MAX = 0.5 * L
gcount = zeros(G_BINS)
nsample = 0.0
worst_drift = 0.0
temp_acc = 0.0
FRAME_EVERY = 40
stage("100 Lennard-Jones atoms, periodic box", -0.5, L + 0.5, -0.5, L + 0.5)
segment("bottom", 0.0, 0.0, L, 0.0)
segment("top", 0.0, L, L, L)
segment("left", 0.0, 0.0, 0.0, L)
segment("right", L, 0.0, L, L)
dots("atoms", X, Y, 0.35)
for s to STEPS {
    VX = VX + 0.5 * DT * FX
    VY = VY + 0.5 * DT * FY
    X = X + DT * VX
    Y = Y + DT * VY
    X = X - L * floor(X / L)
    Y = Y - L * floor(Y / L)
    potential = compute_forces()
    VX = VX + 0.5 * DT * FX
    VY = VY + 0.5 * DT * FY
    e = kinetic() + potential
    worst_drift = max(worst_drift, abs(e - E0))
    if s >= STEPS / 2 {
        k = s - STEPS / 2
        speed = sqrt(VX * VX + VY * VY)
        temp_acc = temp_acc + sum(speed * speed) / (2.0 * N)
        for i to N {
            SPEEDS[k * N + i] = speed[i]
        }
        if mod(k, 10) == 0.0 {
            for i to N {
                dx = wrap(X - X[i])
                dy = wrap(Y - Y[i])
                r = sqrt(dx * dx + dy * dy)
                r[i] = 2.0 * R_MAX
                gcount = gcount + histogram(r, 0.0, R_MAX, G_BINS)
            }
            nsample = nsample + 1.0
        }
    }
    if mod(s, FRAME_EVERY) == 0.0 {
        dots("atoms", X, Y, 0.35)
        frame(DT * FRAME_EVERY)
    }
}

momentum = sqrt(sum(VX) * sum(VX) + sum(VY) * sum(VY))
temperature = temp_acc / (STEPS / 2)
mean_speed = sum(SPEEDS) / len(SPEEDS)
maxwell_mean = sqrt(pi * temperature / 2.0)
show E0
show worst_drift
show momentum
show temperature
show mean_speed
show maxwell_mean

# the speed histogram, as a density, against the Maxwell curve at the measured T
V_MAX = 4.0 * sqrt(temperature)
counts = histogram(SPEEDS, 0.0, V_MAX, BINS)
width = V_MAX / BINS
centers = linspace(0.5 * width, V_MAX - 0.5 * width, BINS)
density = counts / (len(SPEEDS) * width)
maxwell = (centers / temperature) * exp(-centers * centers / (2.0 * temperature))
figure("Speeds over the second half of the run, against Maxwell at the measured temperature", "speed", "density")
bars(centers, density, "measured")
plot(centers, maxwell, "Maxwell, 2-D")

# the pair correlation: counts per shell over the ideal-gas expectation
shell_width = R_MAX / G_BINS
r_centers = linspace(0.5 * shell_width, R_MAX - 0.5 * shell_width, G_BINS)
ideal = DENSITY * 2.0 * pi * r_centers * shell_width * N
g = gcount / (nsample * ideal)
peak_r = 0.0
peak_g = 0.0
for b to G_BINS {
    if g[b] > peak_g {
        peak_g = g[b]
        peak_r = r_centers[b]
    }
}
show peak_r
show peak_g
figure("The pair correlation g(r)", "r", "g")
plot(r_centers, g, "g(r)")
plot(r_centers, zeros(G_BINS) + 1.0, "an ideal gas")

test "momentum stays at zero to rounding" {
    assert_lt(momentum, 1.0e-9)
}
test "the total energy never moves from its starting value by more than a thousandth of the kinetic energy" {
    assert_lt(worst_drift, 1.0e-3 * kinetic())
}
test "the mean speed matches the 2-D Maxwell distribution at the measured temperature to two percent" {
    assert_near(mean_speed, maxwell_mean, 0.02 * maxwell_mean)
}
test "g(r) peaks near 2^(1/6) sigma, the bottom of the potential, and is above 1 there" {
    assert_near(peak_r, 1.122, 0.1)
    assert_gt(peak_g, 1.5)
}

# SPDX-License-Identifier: MIT OR Apache-2.0
# SPDX-FileCopyrightText: 2026 The Viv authors