fire: The FIRE algorithm

In retistruct: Retinal Reconstruction Program

Description

This is an implementation of the FIRE algorithm for structural relaxation put forward by Bitzek et al. (2006)

Usage

fire(
  r,
  force,
  restraint,
  m = 1,
  dt = 0.1,
  maxmove = 100,
  dtmax = 1,
  Nmin = 5,
  finc = 1.1,
  fdec = 0.5,
  astart = 0.1,
  fa = 0.99,
  a = 0.1,
  nstep = 100,
  tol = 1e-05,
  verbose = FALSE,
  report = message
)

Arguments

r	Initial locations of particles
force	Force function
restraint	Restraint function
m	Masses of points
dt	Initial time step
maxmove	Maximum distance to move in any time step
dtmax	Maximum time step
Nmin	Number of steps after which to start increasing dt
finc	Fractional increase in dt per time step
fdec	Fractional decrease in dt after a stop
astart	Starting value of a after a stop
fa	Fraction of a to retain after each step
a	Initial value of a
nstep	Maximum number of steps
tol	Tolerance - if RMS force is below this value, stop and report convergence
verbose	If TRUE report progress verbosely
report	Function to report progress when verbose is TRUE

Value

List containing x, the positions of the points, conv, which is 0 if convergence as occurred and 1 otherwise, and frms, the root mean square of the forces on the particles.

Author(s)

David Sterratt

References

Bitzek, E., Koskinen, P., G\"ahler, F., Moseler, M., and Gumbsch, P. (2006). Structural relaxation made simple. Phys. Rev. Lett., 97:170201.

retistruct documentation built on April 4, 2020, 5:08 p.m.