Specifying Lattice and Site Information with a Site File


Unless you specify otherwise, structural data (lattice and site data) are read by from the STRUC category in the main input file, ctrl.ext.

You can alternatively read lattice structure, or site information, or both from a site file. That file has no predetermined name; it is given in the ctrl file.
Note: The site file is normally read through the file preprocessor.

  • To read lattice information from sname.ext, use the FILE token in STRUC.
  • To read site information from sname.ext, use the FILE token in SITE. The following snippet does both:
SITE   FILE=sname

Note: If you use the file token in the EXPRESS category, it performs the function of both STRUC_FILE and SITE_FILE, and supersedes both of these tags.

In the EXPRESS mode the species labels are determined from the site file; and the number of atoms and species are determined from the site file so that STRUC_NBAS and STRUC_NSPEC are not used. For every species label in the site file there must be a corresponding label in the SPEC category.

The first nonblank, non-preprocessor directive, should begin with:

% site-data vn=#

Note: Version 7 of the Questaal suite writes version 3.0 site files; it can read versions 3.0 and prior versions.

This first line must also contain token io=#.   io=14 tells the reader that minimal information is available in the file:

  • the number of sites in the lattice
  • the lattice vectors
  • the basis vectors and their species ID.

Usually the first line contains the lattice constant as well. Consider the following snippet:

% site-data vn=3.0 xpos fast io=62 nbas=64 alat=7.3956 plat= 2.0 0.0 0.0 0.0 2.0 0.0 1.0 1.0 3.58664656
#                        pos                                vel                     eula              vshft   PL rlx
 K1        0.0000000   0.0000000   0.0000000    0.0000000    0.0000000    0.0000000    0.0000000    0.0000000    0.0000000 0.000000  0 111
 Fe1       0.3750000   0.1250000   0.2500000    0.0000000    0.0000000    0.0000000    0.0000000    0.0000000    0.0000000 0.000000  0 111

The first line tells the parser the following:

  • io=62 indicates that the following information is available for each site, in the order listed:
    • species index (labels must syncrhonise with the SPEC category in the ctrl file.
    • site positions (expressed as multiples of plat because xpos appears in the first line).
    • velocities – used in molecular dynamics.
    • Euler angles. Rotates the spin quantization axis used by noncollinear parts of the ASA code.
    • site potential shifts, which may be used by the ASA.
    • principal layer index used by the layer Green’s function code.
    • three binary integers nnn specifying which of the three Cartesian components are frozen in molecular dynamics or statics.
      1 allows to relax while 0 freezes that coordinate.
  • xpos indicates that the basis vectors are written as fractional multiples of lattice vectors. By default these vectors are written in Cartesian coordinates in units of the lattice constant alat.
  • fast tells the parser to read basis information with FORTRAN read. By default it will parse each element as an algebraic expression. FORTRAN read is much faster, but you lose the capability of using expressions.
  • nbas=64 tells the parser that there are 64 atoms in the crystal.
  • alat=7.3956 specifies the lattice constant, in atomic units.
  • plat=… specifies the lattice vectors, P1, followed by P2 and P3.

The second line in the snippet above is a comment line. Then follows a sequence of 64 lines, one line for each atom. As a minimum, the row must contain a species label and the site position (io=14). In the snippet above (io=62) the extra information is given.

The bottom of the file may contain “map” data similar to the following snippet

#map   4   2   5   3   9   8   6   1   7   4   2   5   3   9   8   6   1   7   4   2   5   3   8   9
#map   6   1   7   4   5   2   3   9   8   6   1   7

This is generated by the supercell maker lmscell. It maps current sites into original sites from which the supercell was constructed. The mapping is needed to generate the density restart file rst.ext of the supercell from the original one, or the GW self-energy file, sigm.ext.

Other resources

Many of the tutorials, e.g. the basic lmf tutorial, make use of site files. The input file maker, blm, typically generates ctrl and site files as a pair.

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