fitsvsl

This code determines bond stiffness vs bond length relationship for the purpose
of calculating vibrational properties (with the svsl code).

It requires the following files as an input.
1) A lattice file (by default, lat.in, but this can be overridden with the -l option) which 
   allows the code to determine what chemical bonds are present in the system.
   The format is as described in the maps documentation (see maps -h).
2) A list of directories containing structures that will be used to calculate force constants
   (by default strname.in, but this can be overridden with the -dn option).
   Each of the listed directory must contain 
   a) a str.out file containing an ideal unrelaxed structure that will be used to automatically
      determine the nearest neighbor shell,
   b) a str_relax.out file containing the relaxed structure that will be used to calculate
      bond lengths and that the code will perturb in various ways to determine the force constants.

The code can operate in two modes: a structure generation mode and a fitting mode (indicated by the
-f option).

In structure generation mode:

  All the above input files are needed and the option
  -er must be specified in order to indicate the size of the supercells generated.
  The -er option indicates how far from each other a displaced atom must be from
  its periodic images, the code will infer the smallest supercell satisfying this constraint.
  Typically, -er should be 3 or 4 times the nearest neighbor distance. All of these distances
  are measured using the ideal structures (*/str.out).

  The following parameters have reasonable default values which can be overridden:
   -dr specifies the displacement of the perturbed atom, which is 0.2 Angstrom by default.
   -ms specifies the maximum (linear) expansion of the structures for the purpose of
       lengthing the bond lenght. For instance -ms=0.01 (the default) indicates that the
       supercells will be stretched by up to 1% isotropically.
   -ns indicates the number of intermediate lattice parameters sampled (by default 2, which is
       the minimum in order to be able to determine the length dependence of bond stiffness).

After the structure generation step:

  Each of the directory specified in strname.in will contain multiple subdirectories,
  each of which contains
    a) the ideal unrelaxed supercell in a str_ideal.out file.
    b) the relaxed but unperturbed supercell in a str_unpert.out file.
    c) the actual geometry of perturbed supercell calculation in a str.out file.
  The appropriate first-principles calculations can be performed using the other utilities in the atat
  package, such as runstruct_vasp. Of course a corresponding vasp.wrap file must given
  in order to provide the input parameters for the first-principles calculations.
  Make sure that these parameters indicate a static run (no relaxations!).
  After all (or some) of these calculations are done, each subdirectory will contain
    a force.out file containing the forces acting on each atoms
    a str_relax.out file containing the atomic positions (in the same order as in force.out)

The fitting mode (-f option) of ftsvsl then needs to be used.
  The lattice file (e.g. lat.in) must be present and the code will look for all files of the form
  */force.out and */*/force.out   and the corresponding files */str*.out and */*/str*.out .
  The code will then use that information to create the length-dependent force constants
  (this may take a few minutes) and ouputs them in
     slspring.out
  Here is an example of the format of this file:
    Al Al         (gives the type of bond)
    2             (2 parameters: linear fit is used)
    50.28971      \  polynomial coeficients of the stiffness vs length relationship for stretching term
    7.88973       /  (typically, stiffness is in eV/Angstrom^2 and length is in Angstrom)
    2             \
    6.12722        | idem for bending term
    -1.01641      /
    Ti Al          (repeat for each type of chemical bond)
    3
    etc.
  The only option controling this process is -op, which specifies the order of the polynomial
  used to fit the length dependence (by default -op=1 and a linear fit is used).
  (Contact the author for information about the -sf option.)

Diagnostic files are also output:
  fitsvsl.log                     (a log file)
  fitsvsl.gnu and f_*.dat         (to plot the s vs l relationship)