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The XSF Format Specification

Table of Contents

Specification of the XSF Format
    Introduction to XSF format
    Comment lines
    Specification of Molecular Structure
    Specification of Periodic Structures
    Specification of Forces
    Specification of Animated XSF format
        Animated XSF for molecules
        Animated XSF for periodic structures
            Fixed-cell animated XSF
            Variable-cell animated XSF
    Specification of 2D and 3D scalar-fields
        General vs. Periodic grids
        Datagrids
        Bandgrids (visualization of Fermi surfaces)

Specification of the XSF Format

Introduction to XSF format

The XSF format is internal XCrySDen structure format. XSF stands for XCrySDen Structure File. It is used to describe (i) molecular and crystal structure, (ii) forces acting on constituent atoms, and (iii) scalar fields (for example: charge density, electrostatic potential). The main attributes of XSF format are:
  • all records are in free format
  • the XSF formatted file is composed from various sections
  • each sections begins with the keyword
  • there are two types of keywords: (i) single keywords, and (ii) sandwich keywords, which are defined as:
    • single keyword: section begins with a single keyword and ends without an end-keyword
    • sandwich keyword: section begins with a begin-keyword (i.e. BEGIN_keyword) and ends with an end-keyword (i.e. END_keyword), where keyword is one among keywords.
  • all coordinates are in ANGSTROMS units
  • all forces are in Hartree/ANGSTROM units
  • the comment-lines start with the "#" character (see below)

Comment lines

The comment-lines were introduced to the XSF file starting from XCrySDen version 1.4. The comment-lines start with the "#" character; comments are allowed only between sections and not within a given section. Here are two examples (correct and incorrect).

Correct example (comments are bewteen the sections):


 # this is a specification 
 # of ZnS crystal structure

 CRYSTAL

 # these are primitive lattice vectors (in Angstroms)

 PRIMVEC
    2.7100000000    2.7100000000    0.0000000000
    2.7100000000    0.0000000000    2.7100000000
    0.0000000000    2.7100000000    2.7100000000

 # these are convetional lattice vectors (in Angstroms)

 CONVVEC
    5.4200000000    0.0000000000    0.0000000000
    0.0000000000    5.4200000000    0.0000000000
    0.0000000000    0.0000000000    5.4200000000

 # these are atomic coordinates in a primitive unit cell 
 # (in Angstroms)

 PRIMCOORD
 2 1
 16      0.0000000000     0.0000000000     0.0000000000
 30      1.3550000000    -1.3550000000    -1.3550000000
                
Incorrect example (comment is within the section):

 ATOMS
  6    2.325243   -0.115261    0.031711
  1    2.344577   -0.363301    1.077589
#
# this is a comment on the wrong place
#
  6    0.007719   -0.041269    0.244204
  9    0.064656    1.154700    0.824420
  9   -0.042641   -0.911850    1.255074
  8   -1.071578   -0.152842   -0.539134
                

Specification of Molecular Structure

For MOLECULES the XSF format is very simple. The first line begins with the ATOMS keyword and then one specifies the structural data for all atoms. An entry for an atom looks like:
 AtNum   X Y Z
where AtNum stands for atomic number (or symbol), while X Y Z are Cartesian coordinates in ANGSTROMS units. Here is one example:

 ATOMS
  6    2.325243   -0.115261    0.031711
  1    2.344577   -0.363301    1.077589
  9    3.131708   -0.909527   -0.638930
  9    2.736189    1.130568   -0.134093
  8    1.079338   -0.265162   -0.526351
  6    0.007719   -0.041269    0.244204
  9    0.064656    1.154700    0.824420
  9   -0.042641   -0.911850    1.255074
  8   -1.071578   -0.152842   -0.539134
  6   -2.310374    0.036537    0.022189
  1   -2.267004    0.230694    1.077874
  9   -2.890949    1.048938   -0.593940
  9   -3.029540   -1.046542   -0.203665
                

Specification of Periodic Structures

The XSF format allows to specify structures of different periodicity. The keywords MOLECULE, POLYMER, SLAB, and CRYSTAL designate the 0-, 1-, 2-, and 3-dimensional structures (i.e. periodic dimensions are meant here). For crystal structures the file begin with CRYSTAL keyword. Then one needs to specify the lattice vectors and the atoms belonging to the unit cell. XCrySDen accepts two different setting of the unit cell. These are usually called the primitive and the conventional unit cell. The corresponding keywords are PRIMVEC for primitive lattice vectors and PRIMCOORD for atoms belonging to the primitive unit cell. The CONVVEC and CONVCOORD have the analogous meaning for the conventional unit cell. Warning: in XSF file the two settings of the unit cell are supposed to have the same origin. If you want to specify some crystal structure with two settings of the unit cell, that have different origins you will have to create two XSF files. In practice only PRIMVEC, PRIMCOORD and CONVVEC need to be specified, and then "conventional coordinates" (CONVCOORD) are generated by XCrySDen itself, hence it is never needed to specify the CONVCOORD section !!! Here is an example of ZnS crystal structure:

 CRYSTAL                                        see (1)
 PRIMVEC
    0.0000000    2.7100000    2.7100000         see (2)
    2.7100000    0.0000000    2.7100000
    2.7100000    2.7100000    0.0000000
 CONVVEC
    5.4200000    0.0000000    0.0000000         see (3)
    0.0000000    5.4200000    0.0000000
    0.0000000    0.0000000    5.4200000
 PRIMCOORD
 2 1                                            see (4)
 16      0.0000000     0.0000000     0.0000000  see (5)
 30      1.3550000    -1.3550000    -1.3550000

                
Legend:
(1)
this keyword specify the structure is crystal
(2)
specification of PRIMVEC (in ANGSTROMS) like:
         ax, ay, az    (first lattice vector)
         bx, by, bz    (second lattice vector)
         cx, cy, cz    (third lattice vector)
(3)
specification of CONVVEC (see (2))
(4)
First number stands for number of atoms in the primitive cell (2 in this case). The second number is always 1 for PRIMCOORD coordinates.
(5)
Specification of atoms in the primitive cell (the same as for ATOMS section).

Specification of Forces

All that is needed to specify the forces acting on atoms is to supplement the appropriate coordinate section (ATOMS or PRIMCOORD). Now an entry for an atom would look like:
 AtNum   X Y Z   Fx Fy Fz
where Fx Fy Fz stands for force components in X, Y and Z direction, respectively. The force components are expressed in Cartesian coordinate system in Hartree/ANGSTROM unit. Here is an example of water molecule:

 ATOMS
  8   0.00000  0.00000  0.00000   -.05164  .00000 -.03999
  1   0.00000  0.00000  1.00000    .01769  .00000  .03049
  1   0.96814  0.00000 -0.25038    .03395  .00000  .00949
                  
And here is an example for the periodic structure structure:

 SLAB
 PRIMVEC
   5.8859828533     0.0000000000     0.0000000000
   0.0000000000     5.8859828533     0.0000000000
   0.0000000000     0.0000000000     1.0000000000
 PRIMCOORD 
 11 1
  6    3.674759   2.942992  -3.493103     -0.021668   0.000000  -0.057324
  1    4.121990   3.816734  -4.007689     -0.000478   0.001204   0.006657
  1    4.121990   2.069250  -4.007689     -0.000478  -0.001204   0.006657
  6    2.211226   2.942992  -3.493103      0.021668   0.000000  -0.057324
  1    1.763995   3.816734  -4.007689      0.000478   0.001204   0.006657
  1    1.763995   2.069250  -4.007689      0.000478  -0.001204   0.006657
  8    0.000000   0.000000  -2.719012      0.000000   0.000000  -0.050242
 47    4.448147   4.449892  -1.919011     -0.022812  -0.029123   0.007553
 47    4.448147   1.436093  -1.919011     -0.022812   0.029123   0.007553
 47    1.437838   4.449892  -1.919011      0.022812  -0.029123   0.007553
 47    1.437838   1.436093  -1.919011      0.022812   0.029123   0.007553
                  

Specification of Animated XSF format

It is possible to specify several snapshots of a structure in the XSF format. For example: the file can contain the data for all structures that were created during an optimization run or molecular-dynamics run. These structures can be displayed as animation by XCrySDen. The main attributes of the animated XSF format are:
  • the AXSF file begins with the ANIMSTEPS nstep keyword, where nstep stands for number of animation steps.
  • number of atoms for all steps must be the same !!!
  • in fixed-cell animated XSF for crystal structures the unit cell for all steps is taken to be the same
  • in variable-cell animated XSF for crystal structures the unit cell is specified for each animation step
  • the ATOMS and PRIMCOORD keywords are prefixed by an integer number which is the sequential index of a given snapshot. Therefore the syntax is ATOMS istep and PRIMCOORD istep.
  • for variable-cell crystal structure the PRIMVEC and CONVVEC keywords are prefixed with sequential index.

Animated XSF for molecules

Here is an example of AXSF file. It shows different structures during an optimization of water molecule. Note the index prefixes after ATOMS keywords.

 ANIMSTEPS 4
 ATOMS 1
  8    0.0000  0.0000  0.0000     -0.0516  0.0000 -0.0399
  1    0.0000  0.0000  1.0000      0.0176  0.0000  0.0304
  1    0.9681  0.0000 -0.2503      0.0339  0.0000  0.0094
 ATOMS 2
  8   -0.1480  0.0000 -0.1146      0.0020  0.0000  0.0015
  1   -0.0468  0.0000  0.9134     -0.0069  0.0000  0.0069
  1    0.8726  0.0000 -0.2740      0.0049  0.0000 -0.0084
 ATOMS 3
  8   -0.1032  0.0000 -0.0799      0.0013  0.0000  0.0010
  1   -0.0319  0.0000  0.9591      0.0011  0.0000 -0.0028
  1    0.9205  0.0000 -0.2710     -0.0025  0.0000  0.0018
 ATOMS 4
  8   -0.1102  0.0000 -0.0853      0.0001  0.0000  0.0000
  1   -0.0345  0.0000  0.9503     -0.0000  0.0000 -0.0000
  1    0.9114  0.0000 -0.2714     -0.0000  0.0000 -0.0000
                    

Animated XSF for periodic structures

Fixed-cell animated XSF

Here is an example of animated XSF for the ZnS crystal structure with the fixed unit-cell. Note the index prefixes after PRIMCOORD keywords.

 ANIMSTEPS 2
 CRYSTAL
 PRIMVEC
    0.0000000    2.7100000    2.7100000    
    2.7100000    0.0000000    2.7100000
    2.7100000    2.7100000    0.0000000
 PRIMCOORD 1
    2 1                                           
    16      0.0000000     0.0000000     0.0000000 
    30      1.3550000    -1.3550000    -1.3550000
 PRIMCOORD 2
    2 1                                           
    16      0.0000000     0.0000000     0.0000000 
    30      1.2550000    -1.2550000    -1.2550000
                    

Variable-cell animated XSF

Here is an example of animated XSF for the ZnS crystal structure with the variable unit-cell. Note the index prefixes after PRIMVEC, CONVVEC, and PRIMCOORD keywords.

 ANIMSTEPS 2
 CRYSTAL
 PRIMVEC 1
    2.7100000    2.7100000    0.00000000
    2.7100000    0.0000000    2.71000000
    0.0000000    2.7100000    2.71000000
 CONVVEC 1
    5.4200000    0.0000000    0.00000000
    0.0000000    5.4200000    0.00000000
    0.0000000    0.0000000    5.42000000
 PRIMCOORD 1
    2 1
    16      0.0000000     0.0000000     0.00000000
    30      1.3550000    -1.3550000    -1.35500000
 PRIMVEC 2
    2.9810000    2.9810000    0.00000000
    2.9810000    0.0000000    2.98100000
    0.0000000    2.9810000    2.98100000
 CONVVEC 2
    5.9620000    0.0000000    0.00000000
    0.0000000    5.9620000    0.00000000
    0.0000000    0.0000000    5.96200000
 PRIMCOORD 2
    2 1
    16      0.0000000     0.0000000     0.00000000
    30      1.5905000    -1.5905000    -1.59050000
                    

Specification of 2D and 3D scalar-fields

It is possible to specify one or several scalar fields (both 2D and 3D) as an uniform mesh of values in the XSF formatted file. The mesh can be non-orthogonal. This scalar field meshes are called datagrids.

General vs. Periodic grids

Datagrids in XCrySDen are general grids and not periodic one!!! What is meant by this will be explained bellow. A general grid is a uniform grid that is spanned inside some box, which is either non-orthogonal or orthogonal. For a molecule such a box would be a bounding box, while for crystal such a box would be a unit cell. However in a grid that span a whole unit-cell some border points would be redundant due to translational symmetry. Grids that omit these redundant points are called periodic (by this convention a FFT (fast-Fourier transform) mesh would be a periodic mesh). The general vs. periodic grid concept is shown graphically here:
figure: general vs. periodic grid
Note: datagrids in XCrySDen are general grids !!!

Datagrids

The datagrid section is structured and organized in blocks. The grids inside a block can be manipulated among themselves by XCrySDen program. The main attributes of XSF datagrids are:
(1) 
the top datagrid section is called BLOCK_DATAGRID and is sandwiched between BEGIN_BLOCK_DATAGRID_xD and END_BLOCK_DATAGRID_xD keywords, where x stands for the dimensionality of the grid. Currently 2D and 3D scalar grids are supported.
(2)
there can be an arbitrary number of BLOCK_DATAGRID sections.
(3)
there can be an arbitrary number of datagrids inside one BLOCK_DATAGRID section. All datagrids belonging to the same BLOCK_DATAGRID must have the dimensionality as defined by BEGIN_BLOCK_DATAGRID_xD keyword. These datagrids must also share the following properties: (i) they should span the same space (origin and the spanning vectors must be the same), and (ii) they should have the same number of data-points. Each datagrid in a BLOCK_DATAGRID is sandwiched inside BEGIN_DATAGRID_xD_identifier and END_DATAGRID_xD keywords, where x stands for dimensionality of the grid and the identifier is used as an identifier of the datagrid.
(4)
after the BEGIN_BLOCK_DATAGRID_xD keyword and before the first DATAGRID_xD_identifier keyword is a comment, which is used as an identifier for the BLOCK_DATAGRID. It must be a single word!!!
(5)
the values inside a datagrid are specified in column-major (i.e. FORTRAN) order. This means that values are written as:
  • C-syntax:
      for (k=0; k<nz; k++)
      for (j=0; j<ny; j++)
      for (i=0; i<nx; i++)
      printf("%f",value[i][j][k]);
    
  • FORTRAN syntax:
      write(*,*)
      $  (((value(ix,iy,iz),ix=1,nx),iy=1,ny),iz=1,nz)
    
Above specifications may sound very fuzzy, hence let us clarify this by looking at a very simple example. The description of all records follows after the example. Also take a look at schematic presentation of the structure of datagrids of below example.

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 BEGIN_BLOCK_DATAGRID_2D                 
   my_first_example_of_2D_datagrid      
   BEGIN_DATAGRID_2D_this_is_2Dgrid#1           
     5  5                                 
     0.0 0.0 0.0                          
     1.0 0.0 0.0                          
     0.0 1.0 0.0                          
       0.000  1.000  2.000  5.196  8.000  
       1.000  1.414  2.236  5.292  8.062        
       2.000  2.236  2.828  5.568  8.246        
       3.000  3.162  3.606  6.000  8.544        
       4.000  4.123  4.472  6.557  8.944        
   END_DATAGRID_2D                      
   BEGIN_DATAGRID_2D_this_is_2Dgrid#2           
     5  5                                       
     0.0 0.0 0.0                                
     1.0 0.0 0.0                                
     0.0 1.0 0.0                                
       4.000  4.123  4.472  6.557  8.944        
       3.000  3.162  3.606  6.000  8.544        
       2.000  2.236  2.828  5.568  8.246        
       1.000  1.414  2.236  5.292  8.062        
       0.000  1.000  2.000  5.196  8.000        
   END_DATAGRID_2D                      
 END_BLOCK_DATAGRID_2D                  
                                        
 BEGIN_BLOCK_DATAGRID_3D                        
   my_first_example_of_3D_datagrid      
   BEGIN_DATAGRID_3D_this_is_3Dgrid#1           
     5  5  5                              
     0.0 0.0 0.0                          
     1.0 0.0 0.0                          
     0.0 1.0 0.0                                
     0.0 0.0 1.0                          
       0.000  1.000  2.000  5.196  8.000        
       1.000  1.414  2.236  5.292  8.062        
       2.000  2.236  2.828  5.568  8.246        
       3.000  3.162  3.606  6.000  8.544        
       4.000  4.123  4.472  6.557  8.944        
                                        
       1.000  1.414  2.236  5.292  8.062        
       1.414  1.732  2.449  5.385  8.124        
       2.236  2.449  3.000  5.657  8.307        
       3.162  3.317  3.742  6.083  8.602        
       4.123  4.243  4.583  6.633  9.000        
                                        
       2.000  2.236  2.828  5.568  8.246        
       2.236  2.449  3.000  5.657  8.307        
       2.828  3.000  3.464  5.916  8.485        
       3.606  3.742  4.123  6.325  8.775        
       4.472  4.583  4.899  6.856  9.165        
                                        
       3.000  3.162  3.606  6.000  8.544        
       3.162  3.317  3.742  6.083  8.602        
       3.606  3.742  4.123  6.325  8.775        
       4.243  4.359  4.690  6.708  9.055        
       5.000  5.099  5.385  7.211  9.434        
                                        
       4.000  4.123  4.472  6.557  8.944        
       4.123  4.243  4.583  6.633  9.000        
       4.472  4.583  4.899  6.856  9.165        
       5.000  5.099  5.385  7.211  9.434        
       5.657  5.745  6.000  7.681  9.798        
   END_DATAGRID_3D                      
 END_BLOCK_DATAGRID_3D                   
                    
Legend:
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beginning of 2D block of datagrids
l.02
one word comment - used as an identifier for this block
l.03
beginning of the first 2D datagrid in a block
l.04
number of data-points in each direction (i.e. nx ny for 2D grids)
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origin of the datagrid
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first spanning vector of the datagrid
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second spanning vector
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5x5 datagrid values in column-major mode
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end of the first 2D datagrid in a block
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these lines specify second 2D datagrid in a block in totally analogous manner as the first 2D datagrid.
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end of 2D block of datagrids
 
 
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beginning of 3D block of datagrids
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one word comment - used as an identifier for this block
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beginning of the first 3D datagrid in a block
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number of data-points in each direction (i.e. nx ny nz for 3D grids)
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origin of the datagrid
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first spanning vector of the datagrid
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second spanning vector
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third spanning vector
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5x5x5 datagrid values in column-major mode
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end of the first 3D datagrid in a block
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end of 3D block of datagrids
Here is a scheme of the structure of datagrids of above example as displayed by XCrySDen program.
Datagrid Structure

Bandgrids (visualization of Fermi surfaces)

Bandgrids are variation on a theme of datagrids. They were introduced for the visualization of Fermi surfaces and yields a simplified format of datagrids. Please notice that despite their purpose they are still general grids and not periodic ones. The bandgrid for the visualization of Fermi surface should be defined as:
figure: bandgrid for visualization of Fermi surface
Please notice that the bandgrid span the reciprocal unit cell, not the Brillouin zone !!! Points are later translated back to Brillouin zone by XCrySDen and Fermi surface is rendered inside the Brillouin zone. Warning: so far XCrySDen uses bandgrids solely for the visualization of Fermi surfaces (the coresponding files are called BXSF, standing for Band-XSF). If you want to render some other property as contours/isosurfaces you must specify the scalar fields as datagrids. This is because the Fermi surfaces needs some special processing and therefore bandgrids are automatically processed. The main attributes of bandgrids are:
(1)  
the structure of bandgrids is similar to datagrids
(2)
there can only be one BLOCK_BANDGRID section
(3)
there can only be one BANDGRID in BLOCK_BANDGRID
(4)
there can be an arbitrary number of bands inside BANDGRID section, where BAND is ...
(5)
so far only 3D bandgrids are supported
BEWARE:
the values inside a bandgrid are specified in row-major (i.e. C) order. This means that values are written as:
  • C-syntax:
      for (i=0; i<nx; i++)
      for (j=0; j<ny; j++)
      for (k=0; k<nz; k++)
      printf("%f",value[i][j][k]);
    
  • FORTRAN syntax:
      write(*,*)
      $  (((value(ix,iy,iz),iz=1,nz),iy=1,ny),ix=1,nx)
    
Here is a bandgrid example. The description of the records is below the example.

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 BEGIN_INFO
   #
   # this is a sample Band-XCRYSDEN-Structure-File 
   # aimed for Visualization of Fermi Surface 
   #
   # Case:      just an example
   #
   # Launch as: xcrysden --bxsf example.bxsf
   #
   Fermi Energy: 0.83511
 END_INFO

 BEGIN_BLOCK_BANDGRID_3D
   here_we_have_some_examples
   BEGIN_BANDGRID_3D_simple_example
     2
     4 4 4
     0.0 0.0 0.0
     1.0 0.0 0.0
     0.0 1.0 0.0
     0.0 0.0 1.0
   BAND:  3
       0.000  0.192  0.385  0.577 
       0.192  0.272  0.430  0.609 
       0.385  0.430  0.544  0.694 
       0.577  0.609  0.694  0.816 
       
       0.192  0.272  0.430  0.609 
       0.272  0.333  0.471  0.638 
       0.430  0.471  0.577  0.720 
       0.609  0.638  0.720  0.839 
       
       0.385  0.430  0.544  0.694 
       0.430  0.471  0.577  0.720 
       0.544  0.577  0.667  0.793 
       0.694  0.720  0.793  0.903 
       
       0.577  0.609  0.694  0.816 
       0.609  0.638  0.720  0.839 
       0.694  0.720  0.793  0.903 
       0.816  0.839  0.903  1.000 
   BAND:  4
       1.000  0.942  0.885  0.827 
       0.942  0.918  0.871  0.817 
       0.885  0.871  0.837  0.792 
       0.827  0.817  0.792  0.755 
   
       0.942  0.918  0.871  0.817 
       0.918  0.900  0.859  0.809 
       0.871  0.859  0.827  0.784 
       0.817  0.809  0.784  0.748 
   
       0.885  0.871  0.837  0.792 
       0.871  0.859  0.827  0.784 
       0.837  0.827  0.800  0.762 
       0.792  0.784  0.762  0.729 
   
       0.827  0.817  0.792  0.755 
       0.817  0.809  0.784  0.748 
       0.792  0.784  0.762  0.729 
       0.755  0.748  0.729  0.700     
   END_BANDGRID_3D
 END_BLOCK_BANDGRID_3D
                    
Legend:
l.01
beginning of INFO section
l.02-09
a hash "#" character stands for comment
l.10
a "Fermi Energy:" string is a marker for reading the value of Fermi energy
l.11
end of INFO section
 
 
l.13
beginning of 3D block of bandgrids
l.14
one word comment - used as an identifier for this block
l.15
beginning of the 3D bandgrid
l.16
number of bands in the bandgrid
l.17
number of data-points in each direction (i.e. nx ny nz for 3D grids)
l.18
origin of the bandgrid
Warning: origin should be (0,0,0) (i.e. Gamma point)
l.19
first spanning vector of the bandgrid (i.e. first reciprocal lattice vector)
l.20
second spanning vector
l.21
third spanning vector
l.22
beginning of the BAND with label 3
l.23-41
4x4x4 values in row-major mode
l.42
beginning of the BAND with label 4
l.43-61
4x4x4 values in row-major mode
l.62
end of the bandgrid
l.63
end of 3D bandgrid block

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This document was last modified on Wed Oct 7 16:08:43 CEST 2015