topology command

Warning

GPU support for this command has not been tested and may not work as expected.

Syntax

fix ID group-ID bond/fiber/topology keywords values

ID, is documented in fix command.
addforce/weighted = style name of this fix command
zero or more keyword/value pairs may be appended
keyword = calc_n_fiber_elems_current or mark_root_fibers or calc_n_fiber_elems_orig

calc_n_fiber_elems_current value = yes or no
  yes = do calculate current length of fiber
  no = do not calculate current length of fiber
mark_root_fibers value = yes or no
  yes = mark particles that belong to the root fiber
  no = do not mark particles
calc_n_fiber_elems_orig value = yes or no
  yes = do calculate original length of fiber (when fiber was created)
  no = do not calculate original length of fiber (when fiber was created)

Examples

fix length all bond/fiber/topology calc_n_fiber_elems_current yes calc_n_fiber_elems_orig no
fix length all bond/fiber/topology calc_n_fiber_elems_current yes mark_root_fibers yes calc_n_fiber_elems_orig yes

Description

This command calculates the length of all fiber particles in the simulation, and storing values for the current length (i.e. including all breakage / cutting events) if calc_n_fiber_elems_current is activated and original length (length at fiber creation) if calc_n_fiber_elems_orig is active.

Note

This command requires that all particles in the fiber are ordered, i.e. the particles must be listed in the data file according to their spatial orientation, e.g. starting at the bottom and the last one at the top.

The length of a fiber may thus vary during the simulation, e.g. using a cohesion model fiber.

If mark_root_fibers is active a flag will be set if the particle belongs to the fiber that contains the original root particle (the particle listed first in the particle_template fiber data file). An example usage for this feature is if you want to cut some fibers and see which part of the fiber remains attached to the root. The flag can be accessed via id_root_fiber and is set to one if a particle belongs to a root fiber and zero otherwise.

Restart, fix_modify, output, run start/stop

You can access original and current lengths via id_fiber_n_elems_orig and id_fiber_n_elems_current, respectively. The root particle flag can be accessed using the id_root_fiber property.

This fix does not need to write data to binary restart files. None of the fix_modify options are relevant to this fix. A global vector is stored by this fix for access by various output commands. It contains the x,y,and z component of the force that was actually applied No parameter of this fix can be used with the start/stop keywords of the run command.

Restrictions

This fix is only applicable to fiber particles, as defined via cohesion fiber