[Pw_forum] graphene with Li input problem

[Paolo Giannozzi]

On Fri, 2013-06-14 at 16:55 +0200, yelena wrote:

> So I have graphene 

or so you think (I don't, see below)

> I don’t understand why all C atoms are connected 
> with every other C? 

because xcrysden, like most visualization tools, assumes
that two atoms have a bond when they are closer than a
typical bond length. 

Many years ago I wrote a small code calculating interatomic
distances from PWscf input data: PW/tools/dist.f . It reads 
the following input data, as explained in the file header:

 7 0 4.66 0.0 0.0 0.0 0.0 0.0        ! nat, ibrav, celldm(1-6)
CELL_PARAMETERS (alat=4.66000000){hexagonal}
    0.999984012   0.000000000   0.000000000
   -0.499992006   0.866011558   0.000000000
    0.000000000   0.000000000   12.188495864
ATOMIC_POSITIONS (crystal)
C        0.333333000  -0.000000730  -0.024511570
C        0.666665270  -0.000000730  -0.024511570
C        0.000000730   0.333333730  -0.024511570
C        0.000000730   0.666666000  -0.024511570
C        0.333333000   0.333333730  -0.024511570
C        0.666665270   0.666666000  -0.024511570
Li       0.333333000   0.666666000   0.197069420

and this is what you get (* = in another cell):

species: C   - C       0.00 < D <  1.00
 atoms:     1     2  distance =   0.82197 A
 atoms:     3     5  distance =   0.82197 A
 atoms:     3     4  distance =   0.82197 A
 atoms:     5     6  distance =   0.82197 A
 atoms:     1     4* distance =   0.82197 A
 atoms:     2     6* distance =   0.82197 A
 atoms:     1     5  distance =   0.82198 A
 atoms:     2     3* distance =   0.82198 A
 atoms:     4     6* distance =   0.82198 A
C    1:  neighbors at    0.822   0.822   0.822
         d(center): 1.104 A  angles  :   120.0   120.0   120.0
C    2:  neighbors at    0.822   0.822   0.822
         d(center): 1.801 A  angles  :   120.0   120.0   120.0
C    3:  neighbors at    0.822   0.822   0.822
         d(center): 1.104 A  angles  :   120.0   120.0   120.0
C    4:  neighbors at    0.822   0.822   0.822
         d(center): 1.801 A  angles  :   120.0   120.0   120.0
C    5:  neighbors at    0.822   0.822   0.822
         d(center): 1.104 A  angles  :   120.0   120.0   120.0
C    6:  neighbors at    0.822   0.822   0.822
         d(center): 1.801 A  angles  :   120.0   120.0   120.0
Li   7:  neighbors at    2.466   2.466   2.466
         d(center): 6.092 A  angles  :   180.0   120.0    60.0

P.
-- 
 Paolo Giannozzi, Dept. Chemistry&Physics&Environment, 
 Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
 Phone +39-0432-558216, fax +39-0432-558222