cell Module

class cell.CellLayerSort

Bases: object

cell_occupancy_counter()

Array containing the number of atoms per cell

cell_occupancy_matrix = None

Get the cell occupancy matrix.

num_layers = None

Maximum number of layers in use.

particle_layers = None

Get the particle layer index.

setup(list_in=None, openmp=False)
update()
version_id = None

version id for cell layer

class cell.CellList

Bases: object

Class to handle cell lists for a given domain.

cell_contents_count
Returns:The cell contents count lookup
cell_list
Returns:The held cell list.
cell_reverse_lookup
Returns:The Reverse lookup map.
cell_width

Return the cell width used to setup the cell structure. N.B. cells may be larger than this.

check()

Check if the cell_list needs updating and update if required. :return:

create()
domain
Returns:The domain used.
get_setup_parameters()

Get the values/function handles used to setup the cell list. :return:

halo_version_id = None

halo version id incremented when halo cell list is updated.

num_particles

Get the number of particles in the cell list

offset

Get the offset required to find the starting position of the cells in the cell list.

Returns:int start of cells in cell list.
post_halo_exchange()
prepare_halo_sort(total_size)
reset_callbacks()
setup(n_func, positions, domain)

Setup the cell list with a set of positions and a domain. :param n_func: Function handle to get number of local particles. :param positions: Positions to use to sort into cells using. :param domain: Domain to setup with cell array. :param cell_width: Cell width to use for domain partitioning. :return:

setup_callback_on_update(func)

Setup a function to be ran after the cell list if updated. :param func: Function to run. :return:

setup_pre_update(func)
setup_update_tracking(func)

Setup an automatic cell update. :param func:

sort()

Sort local particles into cell list. :return:

sort_halo_cells(local_cell_indices_array, cell_contents_recv, npart, total_size)
total_num_particles

Number of local particles + halo particles.

trigger_update()

Trigger an update of the cell list.

version_id = None

Version id, incremented when the list is updated.

class cell.GroupByCell

Bases: object

Class to group dats based on the cells particles reside in.

group_by_cell()

Run library to group data by cell.

setup(state_in)

Setup library to group data in the state particle dats such that data for particles in the same cell are sequential. :param state state_in: State containing particle dats.

class cell.NeighbourList(list=None)

Bases: object

setup(n, positions, domain, cell_width)
update(_attempt=1)
version_id = None

Update tracking of neighbour list.

class cell.NeighbourListHaloAware(list=None)

Bases: object

halo_update(_hattempt=1)
setup(n, positions, domain, cell_width)
update(_attempt=1, _hattempt=1)
version_id = None

Update tracking of neighbour list.

class cell.NeighbourListLayerBased

Bases: object

neighbour_matrix = None

Neighbour matrix (host.Array)

num_neighbours_per_atom = None

maxmium_number of neighbours per atom

setup(layer_method_instance, cell_list_instance, openmp=False)
update()
version_id = None

version id for neighbour matrix

class cell.NeighbourListNonN3(list=None)

Bases: cell.NeighbourList

setup(n, positions, domain, cell_width)
update()
class cell.NeighbourListPairIndices(list=None)

Bases: object

setup(n, positions, domain, cell_width)
update(_attempt=1)
version_id = None

Update tracking of neighbour list.

class cell.NeighbourListv2(list=None)

Bases: cell.NeighbourList

setup(n, positions, domain, cell_width)
class cell.NeighbourMatrix(list=None)

Bases: object

setup(n, positions, domain, cell_width)
update(_attempt=1)
version_id = None

Update tracking of neighbour list.

cell.reset_cell_list()

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