LEGO - Lattice Elemental Geometry Operations

Crystal structure generator for molecular dynamics simulations. Creates arbitrarily rotated and cut crystal structures in IMD and LAMMPS data formats.

Originally by Erik Bitzek (2000-2011). Rewritten 2026.

Building

Requires a C compiler, zlib, and optionally OpenMP.

Linux

make

GCC with OpenMP is typically available out of the box.

macOS

The default Apple Clang does not support OpenMP. LEGO builds without it (single-threaded counting pass), which is fine for smaller systems:

make

For OpenMP support (recommended for large systems), install GCC via Homebrew:

brew install gcc
make CC=gcc-15 OMP_FLAG="-fopenmp"

Replace gcc-15 with the version Homebrew installed (check with ls /opt/homebrew/bin/gcc-*).

Custom Compiler

make CC=icc CFLAGS="-O3 -xHost"

The build produces a lego binary in the project root. The structures/ directory must be accessible at runtime (see Structure Search Path).

Quick Start

1. Create a parameter file Cu_fcc.param:

structure fcc
lattice_const 3.615
mass 63.546
new_x 1 -1 0
new_z 1 1 1
box_x 50
box_y 50
box_z 50
box_mode periodic
output_format imd
outfile Cu_fcc_111.imd

2. Run LEGO:

./lego Cu_fcc.param

This generates a (111)-oriented FCC copper crystal with periodic box dimensions of approximately 50 Angstrom in each direction.

Parameter Reference

Parameters are specified one per line in the form keyword value. Lines starting with # are comments.

Required Parameters

Parameter	Description
structure	Crystal structure name (see Built-in Structures) or poscar for custom
outfile	Output filename
box_x	Target box size in x (Angstrom)
box_y	Target box size in y (Angstrom)
box_z	Target box size in z (Angstrom)

Crystal Definition

Parameter	Default	Description
structure	(required)	Built-in name or poscar
structure_file		Path to POSCAR file (required when structure poscar)
lattice_const	from POSCAR	Override lattice constant a (Angstrom)
lattice_const_b	from POSCAR	Override lattice constant b
lattice_const_c	from POSCAR	Override lattice constant c
mass	from POSCAR	Override mass for type 0 (AMU)
mass1	from POSCAR	Override mass for type 1 (AMU)

Rotation

Three methods are available (highest priority first):

Parameter	Description
rotmat1_x	Explicit rotation matrix row 1 (3 values)
rotmat1_y	Explicit rotation matrix row 2 (3 values)
rotmat1_z	Explicit rotation matrix row 3 (3 values)
new_x	Crystallographic direction for x-axis (3 Miller indices)
new_y	Crystallographic direction for y-axis (3 Miller indices)
new_z	Crystallographic direction for z-axis (3 Miller indices)
axis1	Rotation axis for first rotation (3 values)
angle1	Rotation angle for first rotation (degrees)
axis2	Rotation axis for second rotation (3 values)
angle2	Rotation angle for second rotation (degrees)

When using new_x/new_z, specify any two of the three directions. The third is computed automatically via cross product.

Box and Output

Parameter	Default	Description
box_mode	periodic	periodic (round to repeat distance) or exact
output_format	imd	imd or lammps
compress	no	Gzip LAMMPS output (yes/no)
epsilon	1.0e-6	Tolerance for boundary checks
startnr	1	Starting atom ID number
atomtype	(none)	Override all atom types to this value

Cut Planes

Two independent cut planes are available. Each requires a normal vector, a distance or point, and a direction:

Parameter	Description
cut_norm1	Normal vector of cut plane 1 (3 values)
plane_distance1	Signed distance from origin to plane 1
plane_point1	Point on plane 1 (alternative to distance)
cutdir1	Cut direction: +1 remove far side, -1 remove near side, 0 disable
cut_norm2	Normal vector of cut plane 2
plane_distance2	Signed distance from origin to plane 2
plane_point2	Point on plane 2
cutdir2	Cut direction for plane 2

Miscellaneous

Parameter	Description
shiftvec	Shift all atoms by this vector (3 values, pre-rotation Cartesian)

Built-in Structures

Name	POSCAR File	Description
sc	sc.poscar	Simple cubic
fcc	fcc.poscar	Face-centered cubic
bcc	bcc.poscar	Body-centered cubic
hex / hcp	hex.poscar	Hexagonal close-packed
L12	L12_Ni3Al.poscar	L1_2 ordered (e.g. Ni3Al)
B2	B2_NiAl.poscar	B2 ordered (e.g. NiAl)
D011	D011_Fe3C.poscar	D0_11 ordered (e.g. Fe3C)

Custom structures can be used by setting structure poscar and providing a structure_file path to any valid VASP POSCAR file.

Structure Search Path

LEGO searches for built-in POSCAR files in this order:

1. $LEGO_STRUCTURES environment variable
2. structures/ relative to the current working directory
3. structures/ relative to the executable location

Output Formats

IMD

The default format. Produces plain text files with an orthogonal box header:

#F A 1 1 1 3 0 0
#C number type mass x y z
#X box_x 0 0
#Y 0 box_y 0
#Z 0 0 box_z
##
#E
id type mass x y z
...

Masses are converted to IMD internal units (eV ps^2 / Angstrom^2).

LAMMPS

Produces LAMMPS data files in atomic style:

LEGO generated structure: ...
N atoms
M atom types
0.0 box_x xlo xhi
0.0 box_y ylo yhi
0.0 box_z zlo zhi
Masses
1 mass1
...
Atoms # atomic
id type x y z
...

LAMMPS types are 1-based. Masses are in AMU. Gzip compression is available via the compress parameter.

Python Wrapper

A Python wrapper is provided in python/lego.py:

fromlegoimportLego# Initialize (finds the binary automatically)lego=Lego()
# Run with a parameter fileresult=lego.run("params.param")
print(result.total_atoms, result.box)
# Run with keyword arguments (generates a temp parameter file)result=lego.run(
structure="fcc",
lattice_const=3.615,
mass=63.546,
box_x=100, box_y=100, box_z=100,
new_x="1 1 0", new_z="0 0 1",
output_format="lammps",
outfile="Cu_fcc.lmp"
)
# Convert CIF to POSCAR (requires pymatgen)Lego.cif_to_poscar("structure.cif", "structure.poscar")
# Convert any format to POSCAR (requires ASE)Lego.ase_to_poscar("structure.xyz", "structure.poscar")

The LegoResult object provides:

• total_atoms -- number of atoms generated
• box -- tuple of (box_x, box_y, box_z)
• repeat_dist -- tuple of minimum repeat distances
• success -- whether the run succeeded
• stdout / stderr -- raw output

Examples

See the examples/ directory for ready-to-run parameter files:

• W_bcc_100.param -- BCC tungsten, default (100) orientation
• W_bcc_110.param -- BCC tungsten, (110) orientation
• Cu_fcc_111.param -- FCC copper, (111) orientation
• Cu_fcc_lammps.param -- FCC copper, LAMMPS output
• Ni3Al_L12.param -- L1_2 Ni3Al ordered alloy
• NiAl_B2.param -- B2 NiAl ordered alloy
• custom_poscar.param -- Using a custom POSCAR file

License

GPLv3. See LICENSE.

Citation

If you use LEGO in your research, please cite it. See CITATION.cff for metadata.