3. Altering the dimensions of the simulation box
3.1. Problem
You wish to adjust the width, length, or heigh of the simulation domain.
3.2. Solution
Edit the appropriate dimensions on lines 6-8 of the atom.in file
1 NUFEB Simulation
2
3 40 atoms
4 2 atom types
5
6 0.0e-04 1e-04 xlo xhi
7 0.0e-04 1e-04 ylo yhi
8 0.0e-04 5e-04 zlo zhi
3.3. Discussion
NUFEB simulations often specify the intial microbial layout, including the simulation dimensions, in an external file by making use of the LAMMPS read_data command. This file is traditionally named atom.in. Lines 6-8 of this file specify the minimum and maximum bounds of the x, y, and z dimensions, with z being the vertical ‘height’ dimension. The values can be given as either plan digits or in scientific notation, and the default SI unit is metres.
Tip
Units are specified in the inpufile using the LAMMPS unit command
It can be easy to mistakenly alter the wrong dimension, it is highly suggested to confirm them in a test run by visualizing results with paraview.
Warning
Altering the simulation box might result in a situation where the diffusion grid voxels specified by the grid_style command in the inputscript may not evenly fit. This will cause an error at runtime and can be fixed by specifing a voxel size which evenly fits within the new dimensions.
See also
- Relevant section of the inputscript documentation:
- Reading data files within LAMMPS
- Specifying the units used in dimensions