Particle list

Neighbor list

class NeighborList(all_info, r_cut, r_buffer)

The constructor of neighbor list object

Parameters:
  • all_info (AllInfo) – The system information
  • r_cut (float) – The cut-off radius
  • r_buffer (float) – The 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()

add 1-2 exclusion into exclusion list.

addExclusionsFromAngles()

add 1-3 exclusion into exclusion list.

addExclusionsFromDihedrals()

add 1-4 exclusion into exclusion list.

addExclusionsFromBodys()

add body exclusion into exclusion list.

setFilterDiameters()

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

Example:

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

Cell list

class CellList(all_info)

The constructor of cell list object

Parameters:all_info (AllInfo) – The 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, z directions.

setDataReproducibility()

switches on data reproducibility function.

Example:

cell_list = galamost.CellList(all_info)