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Simulation Domain

The simulation box — its size, shape, cell decomposition and periodicity — is defined by the domain block, called in the simulation graph before setup_system:

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simulation:
  name: MySimulation
  body:
    - [...]
    - particle_regions
    - preinit_rcut_max
    - domain
    - init_prolog
    - setup_system
    - [...]

The domain block

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domain:
  cell_size: 5.0 ang
  grid_dims: [ 20, 20, 20 ]
  bounds: [ [ 0 ang, 0 ang, 0 ang ], [ 100 ang, 100 ang, 100 ang ] ]
  xform: [ [ 1., 0., 0. ], [ 0., 1., 0. ], [ 0., 0., 1. ] ]
  periodic: [ true, true, true ]
  mirror: []
  expandable: false
Parameters' description
Property Type Default Description
cell_size float 0.0 Size of a grid cell (used for parallel domain decomposition)
grid_dims IJK [0,0,0] Number of cells along each axis; if 0,0,0, deduced from bounds and cell_size
bounds AABB [[0,0,0],[0,0,0]] Domain bounds [[xmin,ymin,zmin],[xmax,ymax,zmax]]
xform Mat3d identity Grid space → physical space transformation matrix (for non-orthorhombic/triclinic domains)
periodic [bool;3] [false,false,false] Periodic boundary conditions along each axis
mirror list [] Mirror (reflective) boundary conditions, e.g. [ "X-", "Z" ] for a mirror at the lower X bound and both Z bounds
expandable bool true Whether the domain is allowed to grow to contain particles that move outside its bounds

Warning

periodic and mirror are mutually exclusive per axis: setting one on a given bound disables the other.

exaStamp's own default (in main-config.msp) leaves cell_size/grid_dims at 0, so they are automatically deduced from the interatomic potential's cutoff radius, and sets expandable: false.

For the full derivation of the physical-space/grid-space transform, more xform examples (orthorhombic, triclinic domains) and alternative ways of defining a domain (from a lattice template, an external file, or a restart), see Simulation Domain in the Domain & Regions reference section.

Expandable domains

If expandable: true and the domain isn't fully periodic, the extend_domain operator (run automatically as part of init_particles and at every full particle update) grows the domain's bounds to keep containing any particle that has drifted outside them, rather than losing it. A fully periodic domain cannot be expandable — exaStamp will disable it and print a warning if both are set together.

Filling the domain

Defining domain only reserves the simulation box — it doesn't create any particle. Populating it (e.g. with the lattice operator, or by reading particles from an external file) is done as part of setup_system, covered on the next page.