Particle list

Neighbor list

class NeighborList(all_info, r_cut, r_buffer)

Constructor of a neighbor list object

Parameters:

• all_info (AllInfo) – System information

• r_cut (float) – Cut-off radius

• r_buffer (float) – Buffer distance

setRCut(float r_cut, float r_buffer)

specifies the cut-off and buffer distance.

setRCutPair(string typi, string typj, float r_cut)

specifies the cut-off per unique pair of particle types.

setNsq()

switches on the method of searching all particle to build up list.

setDataReproducibility()

switches on the data reproducibility.

addExclusionsFromBonds()

adds 1-2 exclusion into exclusion list.

addExclusionsFromAngles()

adds 1-3 exclusion into exclusion list.

addExclusionsFromDihedrals()

adds 1-4 exclusion into exclusion list.

addExclusionsFromBodies()

adds body exclusion into exclusion list.

setFilterDiameters()

considers the radius of particle in neighbor list which includes the particles within r_cut + (diameter_i + diameter_j)/2.

Example:

neighbor_list = gala.NeighborList(all_info, 3.0 ,0.4)

Cell list

class CellList(all_info)

Constructor of a cell list object

Parameters:

all_info (AllInfo) – System information

setNominalWidth(float width)

specifies the length of cell.

setNominalDim(unsigned int x, unsigned int y, unsigned int z)

specifies the dimensions of grid in ‘X’, ‘Y’, and ‘Z’ directions.

setDataReproducibility()

switches on data reproducibility function.

Example:

cell_list = gala.CellList(all_info)