Here is a description of the most important parts of the LAMMPS input file for Lab 1. We will go through more of them for Lab 3.
boundary p p p
Here we say that we want to perform a simulation that is periodic in all three directions.
lattice fcc 4.080
region bulkau block 0 10 0 10 0 10
#region vacancy block -0.01 0.01 -0.01 0.01 -0.01 0.01
create_box 1 bulkau
create_atoms 1 box
#delete_atoms region vacancy
- The lattice command tells LAMMPS to create a set of points in space corresponding to an fcc arrangement with a lattice constant of 4.08 angstroms. We haven't created any atoms yet!
- The first "region" command creates a region called "bulkau" (you could name it anything) with a "block" shape (you can create spheres, etc.) spanning space from x=0 to x=10, y=0 to y=10, z=0 to z=10fractional coordinates (in Cartesian coordinates, the box is 40.8x40.8x40.8 angstroms!)
- The region command preceded by # is commented, which means that LAMMPS will ignore it until you delete the #. You can use this tiny box region to select an atom (or atoms) for deletion.
- create_box tells LAMMPS we want to use the bulkau region as our simulation cell. "1" is the number of atom types in the simulation.
- create_atoms is when we finally decorate our fcc lattice with atom type 1 (defined as Au by the Au_u3.eam potential file).
- If we uncommented the delete_atoms line, all the atoms (in this case 1) in the region "vacancy" would be deleted.
pair_coeff * * Au_u3.eam
Now we tell LAMMPS to use an EAM potential and to find the needed parameters (remember, projected electron densities!) in the file Au_u3.eam.
minimize 1e-4 1e-6 100 1000
Finally, we want to minimize energy with respect to atomic coordinates.
- First number: unitless energy tolerance criterion
- Second number: force convergence criterion, in force units (eV/angstrom in this simulation)
- Third number: maximum number of iterations for the minimizer
- Fourth number: maximum total number of energy and force calculations