8.3.3. Using distributed grids — LAMMPS documentation

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# 8.3.3. Using distributed grids

Added in version 22Dec2022.

LAMMPS has internal capabilities to create uniformly spaced grids which overlay the simulation domain. For 2d and 3d simulations these are 2d and 3d grids respectively. Conceptually a grid can be thought of as a collection of grid cells. Each grid cell can store one or more values (data).

The grid cells and data they store are distributed across processors. Each processor owns the grid cells (and data) whose center points lie within the spatial subdomain of the processor. If needed for its computations, a processor may also store ghost grid cells with their data.

Distributed grids can overlay orthogonal or triclinic simulation boxes; see the Howto triclinic doc page for an explanation of the latter. For a triclinic box, the grid cell shape conforms to the shape of the simulation domain, e.g. parallelograms instead of rectangles in 2d.

If the box size or shape changes during a simulation, the grid changes with it, so that it always overlays the entire simulation domain. For non-periodic dimensions, the grid size in that dimension matches the box size, as set by the boundary command for fixed or shrink-wrapped boundaries.

If load-balancing is invoked by the balance or fix balance commands, then the subdomain owned by a processor can change which may also change which grid cells they own.

Post-processing and visualization of grid cell data can be enabled by the dump grid, dump grid/vtk, and dump image commands. The latter has an optional grid keyword. The OVITO visualization tool also plans (as of Nov 2022) to add support for visualizing grid cell data (along with atoms) using dump grid output files as input.

Note

For developers, distributed grids are implemented within the code via two classes: Grid2d and Grid3d. These partition the grid across processors and have methods which allow forward and reverse communication of ghost grid data as well as load balancing. If you write a new compute or fix which needs a distributed grid, these are the classes to look at. A new pair style could use a distributed grid by having a fix define it. Please see the section on using distributed grids within style classes for a detailed description.

These are the commands which currently define or use distributed grids:

- fix ttm/grid - store electron temperature on grid

- fix ave/grid - time average per-atom or per-grid values

- compute property/grid - generate grid IDs and coords

- dump grid - output per-grid values in LAMMPS format

- dump grid/vtk - output per-grid values in VTK format

- dump image grid - include colored grid in output images

- pair_style amoeba - FFT grids

- kspace_style pppm (and variants) - FFT grids

- kspace_style msm (and variants) - MSM grids

The grids used by the kspace_style can not be referenced by an input script. However the grids and data created and used by the other commands can be.

A compute or fix command may create one or more grids (of different sizes). Each grid can store one or more data fields. A data field can be a single value per grid point (per-grid vector) or multiple values per grid point (per-grid array). See the Howto output doc page for an explanation of how per-grid data can be generated by some commands and used by other commands.

A command accesses grid data from a compute or fix using a grid reference with the following syntax:

- c_ID:gname:dname

- c_ID:gname:dname[I]

- f_ID:gname:dname

- f_ID:gname:dname[I]

The prefix “c_” or “f_” refers to the ID of the compute or fix; gname is the name of the grid, which is assigned by the compute or fix; dname is the name of the data field, which is also assigned by the compute or fix.

If the data field is a per-grid vector (one value per grid point), then no brackets are used to access the values. If the data field is a per-grid array (multiple values per grid point), then brackets are used to specify the column I of the array. I ranges from 1 to Ncol inclusive, where Ncol is the number of columns in the array and is defined by the compute or fix.

Currently, there are no per-grid variables implemented in LAMMPS. We may add this feature at some point.