Particle list¶
Neighbor list¶
- class NeighborList(all_info, r_cut, r_buffer)¶
Constructor of a neighbor list object
- Parameters:
- 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)