Alternative ways for defining the domain¶

The simulation domain doesn't always need to be fully defined through the domain operator itself — it can instead be derived from a particle-generation operator, or already be contained in an external file.

Built-in particles creators¶

lattice: Replicates a unit cell (SC, BCC, FCC, HCP, …) into a pre-existing, fully-defined domain. Unlike bulk_lattice below, it does not derive or resize the domain itself.
Warning

lattice requires domain to be fully defined and init_rcb_grid to be called in between domain and lattice, so the grid is already partitioned across MPI ranks before particles are generated into it:
```
input_data:
  - domain: { ... }
  - init_rcb_grid
  - lattice: { ... }
```
bulk_lattice: The system shape and size is created according to the replication in the 3D space of a unit cell chosen by the user, from which a matching domain is derived (grid_dims, xform, bounds are computed from the lattice and the repeat count). It performs its own grid partitioning internally, so it does not need a separate init_rcb_grid step.

Warning

bulk_lattice unconditionally sets the domain's periodic flag to [true, true, true] — it is designed to generate a perfectly commensurate, fully 3D-periodic domain, and this cannot be overridden through the operator's parameters. If you need non-periodic or mixed boundary conditions, use lattice with a pre-defined domain instead.

See Particles Features → Input for the full set of built-in particle generators.

External file readers¶

read_xyz_file_with_xform: Instead of creating the system from a template, an external .xyz file is read in which the number of atoms, their positions and the simulation cell size and shape are provided. In that case, only the cell_size property of the domain YAML block is needed.
read_dump_atoms: The simulation starts at a specific timestep for which a restart file was generated. That restart file usually contains all information for the simulation domain.
read_dump_molecule: Same as above but for flexible molecules.
read_dump_rigidmol: Same as above but for rigid molecules.

See Particles Features → Input for the full parameter reference of these readers.