set* command

Syntax

set style ID keyword values ...

  • style = atom or type or group or region

  • ID = depends on style

for style = atom, ID = a range of atom IDs
for style = type, ID = a range of numeric types or a single type label
for style = group, ID = a group ID
for style = region, ID = a region ID

  • one or more keyword/value pairs may be appended

  • keyword = x or y or z or diameter or density or mass or outer_mass or outer_diameter or outer_density or biomass or bacillus/inertia or bacillus/pole/random or bacillus/length type or type/fraction or type/ratio or type/subset

x,y,z value = atom coordinate (m)
diameter value = diameter of spherical coccus, or width of rod bacillus (m)
density value = atom density (kg/m3)
mass value = wet mass (kg)
outer_mass value =  EPS shell mass (exclude inner mass)
outer_diameter value  = outer diameter (diameter + EPS shell depth)
outer_density value = EPS shell density
biomass value = dry mass ratio
bacillus/length value = length of bacillus
bacillus/inertia value = ixx iyy izz ixy ixz iyz
 ixx iyy izz ixy ixz iyz = 6 moments of inertia
bacillus/pole/random value = angle seed
 angle = orientation of line segment with respect to one of the 7 directions: x or y or z or xy or yz or xz or xyz
 seed = random # seed (positive integer) for line segment orientations
type value = numeric atom type or type label
 value can be an atom-style variable

Examples

set type 1 z 1e-6
set type 2 diameter 1e-6
set group HET outer_diameter 1.2e-6
set group AOB density 290
set group AOB NOB biomass 0.6
set group Ecoli bacillus/length 3e-6
set group Ecoli diameter 0.8e-6
set group Ecoli bacillus/inertia 0 0 9e-23 0 0 0
set group Ecoli bacillus/pole/random xy 1234

Note

This page describes properties used for atom_style coccus and atom_style bacillus only. Properties for other LAMMPS atom types are detailed in set*.

Set one or more properties of coccus and bacillus atoms. The command can be useful for overriding the default or initial values assigned by the create_atom*, read_data or read_restart* command.

The style atom selects all the atoms in a range of atom IDs.

The style type selects all the atoms in a range of types or type labels. The style type selects atoms in one of two ways. A range of numeric atom types can be specified. Or a single atom type label can be specified, e.g. “C”.

In each of the range cases, the range can be specified as a single numeric value, or a wildcard asterisk can be used to specify a range of values. This takes the form “*” or “*n” or “n*” or “m*n”. For example, for the style type, if N = the number of atom types, then an asterisk with no numeric values means all types from 1 to N. A leading asterisk means all types from 1 to n (inclusive). A trailing asterisk means all types from n to N (inclusive). A middle asterisk means all types from m to n (inclusive). For all the styles except mol, the lowest value for the wildcard is 1; for mol it is 0.

The style group selects all the atoms in the specified group. The style region selects all the atoms in the specified geometric region. See the region*. and group*. for details of how to specify a group or region.

This section describes the keyword options for which properties to change, for the selected atoms.

Keyword type sets the atom type for all selected atoms. A specified value can be either a numeric atom type or an atom type label. When using a numeric type, the specified value must be from 1 to ntypes, where ntypes was set by the create_box* command or the atom types field in the header of the data file read by the read_data* command.

Keywords x, y, z set the coordinates of all selected atoms.

Keyword diameter sets the size of the selected atoms. The value must be positive. Note that this command does not adjust the atom mass.

Keyword density also sets the mass of all selected atoms if they have a positive diameter value. Therefore, the diameter of atoms must already be defined in order to set the mass using this command.

Keyword mass sets the mass of all selected atoms. The value must be positive.

Keyword outer_diameter sets the outer diameter of the selected atoms defined as atom_style coccus with EPS shell. The value is the sum of EPS shell depth and the inner diameter, and must be greater or equal than the inner diameter.

Keyword outer-density sets the EPS shell density of the selected atoms. It also set the outer mass of EPS shell for atoms if they have a positive outer diameter attribute.

Keyword outer_mass sets the mass of the outer EPS shell of the selected atoms. The value must be greater than or equal to 0.

Keyword bacillus/length sets length of the selected atoms defined a atom_style bacillus. Since bacillus is represented as a cylinder with hemispherical caps. The length is the distance between the two hemispherical caps (i.e, the height of the cylinder).

Keyword bacillus/inertia sets the 6 moments of inertia for the atoms defined as atom_style bacillus. The values should be consistent with the current orientation of the bacillus around its center of mass. The values are with respect to the simulation box XYZ axes, not with respect to the principal axes of the particle itself. NUFEB performs the latter calculation internally. The center-of-mass position of the particle is specified by the x,y,z values above.

Keyword bacillus/pole/random sets initial orientation of atoms defined as atom_style bacillus. The orientation corresponds to the line segment with respect to one of the 7 directions:

  • x y z refer to the x-, y-, and z-axes of the box;

  • xy yz xz indicate that the line segment is in parallel to the corresponding surface, while the orientation of the third direction is determined randomly based on seed value;

  • xyz indicates a random orientation with respect to the three axes.