10.157. Write LAMMPS File
Group (Subgroup)
IO (Output)
Description
This filter writes atom coordinates from a Vertex Geometry (a point cloud, where each point is one atom) into an input file for LAMMPS. LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator) is an open-source molecular-dynamics code from Sandia National Laboratories that simulates the motion of atoms and molecules.
The typical workflow first builds an atomistic representation of a microstructure with the Insert Atoms filter. Given a microstructure, Insert Atoms follows the crystallographic orientation of each Feature (grain) to place atoms inside it and stores the resulting atom positions in a Vertex Geometry. This Write LAMMPS File filter then reads that Vertex Geometry and writes a LAMMPS data file that LAMMPS can use to initialize the atom coordinates of a simulation.
Atom coordinates are written in the physical units of the Vertex Geometry (the same units as the vertex positions, typically Angstroms or nanometers for atomistic data). The Atom Feature Labels array assigns each atom an atom type, so atoms belonging to different grains can be distinguished in the simulation.
Example Output
A LAMMPS data file begins with header lines giving the atom and type counts and the simulation box bounds, followed by an Atoms section listing, for each atom, its ID, type, and x/y/z coordinates:
Number of Atoms
8000 atoms
25 atom types
0.0 100.0 xlo xhi
0.0 100.0 ylo yhi
0.0 100.0 zlo zhi
Atoms
1 1 0.000000 0.000000 0.000000
2 1 1.500000 0.000000 0.000000
3 2 3.000000 0.000000 0.000000
..
Required Input Sources
Vertex Geometry – the atom positions to export, typically produced by the Insert Atoms filter.
Atom Feature Labels – a per-atom integer array (one value per vertex) giving each atom’s type, also produced by Insert Atoms.
Input Parameter(s)
Parameter Name |
Parameter Type |
Parameter Notes |
Description |
|---|---|---|---|
Output File Path |
FileSystemPath |
The path to the output file |
Input Data Objects
Parameter Name |
Parameter Type |
Parameter Notes |
Description |
|---|---|---|---|
Input Vertex Geometry |
Geometry Selection |
Vertex |
The vertex geometry holding the arrays to write |
Atom Feature Labels |
Array Selection |
Allowed Types: int32 Comp. Shape: 1 |
Data Array that specifies to which Feature each Element belongs |
License & Copyright
Please see the description file distributed with this Plugin
DREAM3D-NX Help
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