Annealing

An "annealing" simulation heats up a crystal to a high temperature before rapidly cooling it to a low temperature. This allows its atoms to move around somewhat before settling in more realistic positions.

It is accessible in the "LAMMPS - Anneal" tab of the simulation generator dialog:

Annealing tab of the simulation builder dialog

Requirements

In order to build an annealing simulation, a structure with a non-zero bounding box must already be set up in the viewer:

Bounding box example

General Options

The first set of options involve basic information about the simulation and structure:

Screenshot of the general options area in the dialog

Field Description
Working Directory Location to generate the files to
Secondary Name Name of simulation. This will decide the name of the output directory
Structure Name Name of structure. Used in deciding file names of simulation outputs
Mass Table Atomic masses to use in the simulation. Defaults to the masses defined in the atom styles table
Bounding Box Bounding box of the structure. Defaults to the bounding box already defined for the structure

Potentials Options

The next set of options controls the potential coefficients and potential style used in the simulation.

Screenshot of the potentials options area in the dialog

Field Description
Pair Coefficients Coefficients used in the pair potentials
Potential Style Style to use for the potential

In order for a simulation to be considered valid, you must have enough potentials for all elements:

Potential coefficient table with all required pair potentials Potential coefficient table with that's missing some required pair potentials

For convenience, both potential coefficients and styles can be saved and loaded. More information on saving/loading potential coefficients can be found here. Additionally, more information on saving/loading/creating potential styles can be found here.

Slurm Options

The next set of options controls some variables used by slurm.

Screenshot of the slurm options area in the dialog

Field Description
Memory Amount of memory, in megabytes, to allocate per job

LAMMPS Options

The next set of options are those specific to LAMMPS:

Screenshot of the LAMMPS options area in the dialog

Field Description
LAMMPS Version LAMMPS module name for slurm to load
KSpace Solver Name of long-range force solver for LAMMPS to use. For more information on kspace styles, see here
KSpace Accuracy Accuracy of kspace solver
Timestep Timestep used in simulations. Measured in picoseconds by default
Unit System Unit system used by LAMMPS. For more information on LAMMPS unit systems, see here. Note: unit systems besides metal have not been tested, use at your own risk!

Annealing Options

The final set of options controls the annealing process:

Screenshot of the annealing options area in the dialog

Field Description
Steps Number of timesteps the annealing takes place over.
Starting Temperature Initial temperature, in kelvin, for the annealing process.
Ending Temperature Final temperature, in kelvin, for the annealing process to cool to.
Simulation Mode Which parameters to hold constant. Options are NPT (isothermal-isobaric ensemble) and NVT (canonical ensemble)