LAMMPS from scratch · 20 min

The four blocks of every script

Almost every LAMMPS input has the same skeleton: initialization, system, settings, run. You sort the melt lines into the four blocks, then reuse the skeleton for a different system, a two-dimensional crystal of 9 atoms, predict its first line by hand and check it.

The four blocks and which commands belong in each
Sort every line of the melt example into its block
Build a new 2D system from the same skeleton and match its first line by hand

1 · Understand: one skeleton for every script

Block	Answers the question	Typical commands
1 · Initialization	what kind of world? units, 2D or 3D, what an atom carries	`units`, `dimension`, `boundary`, `atom_style`
2 · System	where are the atoms?	`lattice`, `region`, `create_box`, `create_atoms`, or `read_data` (page A.8)
3 · Settings	how do they interact and move, and what is printed?	`mass`, `velocity`, `pair_style`, `pair_coeff`, `neighbor`, `fix`, `compute`, `thermo`
4 · Run	go!	`run`, `minimize`

The order follows the rules of page A.1: block 1 changes the meaning of everything after it, so it comes first; block 3 needs the atom types created in block 2; block 4 uses everything. velocity is strictly an action, but it is usually written with the settings, just before the run.

2 · Sort the melt lines

Choose a block for each line, then check.

units lj

atom_style atomic

lattice fcc 0.8442

region box block 0 10 0 10 0 10

create_box 1 box

create_atoms 1 box

mass 1 1.0

velocity all create 3.0 87287 loop geom

pair_style lj/cut 2.5

pair_coeff 1 1 1.0 1.0 2.5

neighbor 0.3 bin

neigh_modify every 20 delay 0 check no

fix 1 all nve

thermo 50

run 250

1 = Initialization, 2 = System, 3 = Settings, 4 = Run.

3 · Modify: a new system from the same skeleton

Keep the four blocks and change their contents: a flat (2D) crystal of 3 × 3 atoms on a square grid with spacing 1.2, at temperature 0.72, cutoff 1.8. These are the 9 atoms of Lab 3.9.

# 1 · Initialization units lj dimension 2 atom_style atomic # 2 · System: a 3 x 3 square crystal, spacing 1.2 lattice sq $(1/1.2^2) region box block 0 3 0 3 -0.5 0.5 create_box 1 box create_atoms 1 box # 3 · Settings mass 1 1.0 velocity all create 0.72 87287 loop geom pair_style lj/cut 1.8 pair_coeff 1 1 1.0 1.0 1.8 fix 1 all nve fix 2 all enforce2d # 4 · Run run 0

New commands: dimension 2 (atoms move in a plane), lattice sq (a square grid; in LJ units the number is the density 1/1.2² = 0.69444, so the spacing is 1.2) and fix enforce2d (keeps the motion exactly flat).

Predict by hand

Every atom has 4 neighbours at 1.2 and 4 on the diagonals at 1.2√2 = 1.6971; the next ones, at 2.4, are beyond the cutoff 1.8.

u(r) = 4(r⁻¹² − r⁻⁶) u(1.2) = 4(0.11215665 − 0.33489798) = −0.89096529 u(1.6971) = 4(0.00175245 − 0.04186225) = −0.16043920 E_pair = ½ × (4 × u(1.2) + 4 × u(1.6971)) (each pair shared by 2) = 2 × (−0.89096529 − 0.16043920) = −2.102809 in 2D an atom has 2 degrees of freedom; 2 are removed for the whole crystal: KE/N = (2N − 2)/2 × T / N = 8 × 0.72 / 9 = 0.64 TotEng = −2.102809 + 0.64 = −1.462809 area A = 3.6 × 3.6 = 12.96; pressure in 2D = (kinetic + virial)/(2A) kinetic: (2N − 2) × T /(2A) = 16 × 0.72 / 25.92 = 0.44444444 virial : N × ½ × 4 × (rF(1.2) + rF(1.6971)) /(2A) = 9 × 2 × (−2.65403201 − 0.92057644) / 25.92 = −2.48236700 Press = 0.44444444 − 2.48236700 = −2.0379225 (rF = 24(2r⁻¹² − r⁻⁶) = r times the force)

What the new system shows

The skeleton did not change; only the contents of each block did. Every script in this course, and most in research, has this shape.
A change in block 1 (dimension 2) changed rules everywhere: 2 degrees of freedom per atom instead of 3, an area instead of a volume.
The hand calculation is the same method as for melt: shells of neighbours, half of each pair per atom.

Your turn

1. In which block do compute and dump belong?

2. Change the 2D cutoff to 1.5 (both lines). Which neighbours remain, and what is E_pair?

3. Why does the 2D kinetic energy per atom use (2N − 2)/2 and not 3N/2?