LAMMPS, and the input script

The shape of it

One text fileis the whole simulation

LAMMPS has no project format and no session. You write an input script, you run it, and everything that happens is in that file.

Declarative, then run

Commands build up a state, and run executes it. Order matters, because later commands see earlier ones.

Particles, not molecules

Atoms, coarse-grained beads, grains of sand. LAMMPS does not assume biology, which is why materials work lives here.

Everything is a package

Potentials, fixes and computes ship as optional modules, so two builds can genuinely differ in what they accept.

Reading a script

Six commandsin a fixed order

Almost every input script says the same six things. Once you can see them, unfamiliar scripts stop being unfamiliar.

in.copper

units       metal
atom_style  atomic
lattice     fcc 3.615
region      box block 0 10 0 10 0 10
create_box  1 box
create_atoms 1 box
pair_style  eam
pair_coeff  1 1 Cu_u3.eam
velocity    all create 300.0 4928459
fix         1 all nve
thermo      100
run         10000

units · atom_styleWhat the numbers mean, and what an atom carries — just a position, or charges and bonds as well.

region · create_box · create_atomsThe geometry, the box built from it, and the particles placed inside on a lattice or at random.

pair_style · pair_coeffThe physics. EAM for metals, Tersoff for covalent solids, Lennard-Jones plus Coulomb for liquids.

fix · runThe ensemble and anything applied during integration, then how many steps to take.

Units

Choose once,and never think again

The units command decides what every number in the file means. Getting it wrong produces results that look plausible and are not.

metal

eV, ångström, picoseconds. The default for solids, alloys and anything using an EAM potential.

real

kcal/mol, ångström, femtoseconds. What biomolecular work and organic-liquid simulations use.

Dimensionless reduced units. Used for polymers and studies of generic behaviour, not a real material.

There is no conversion layer. If you write a Lennard-Jones epsilon in kcal/mol into a script declared units metal, LAMMPS will read it as electronvolts and run happily to completion.

Output

Dump files,and what opens them

LAMMPS writes snapshots and thermodynamic output. Everything downstream — pictures, analysis, papers — comes from those two streams.

dumpSnapshotspositions every N steps

thermoNumbersenergy, temperature, pressure

OVITOOpened byor ParaView, on the same machine

A dump command writes atom positions every N steps. Choose N carefully: too frequent and the file outgrows the disk you are paying for; too sparse and the event you were watching for happens between frames. OVITO and ParaView both read the standard dump formats, and ParaView is here as a workflow if you want it on the same machine.

The status

LAMMPS isbeing built

The image and its definition are being verified. When they are done, it deploys by name like the rest.

Ask for itSay so on the community tracker, and it moves up the list.Or build itOpen a pull request on the hub, following a published one.

Read it, then run itPrepaid and by the hour, on a machine that is yours about a minute after you ask.

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