[Pw_forum] Should we use a double bond or 2 H atoms to saturate the system?

Hongsheng Zhao zhaohscas at yahoo.com.cn
Tue Apr 26 14:15:36 CEST 2011


On 04/25/2011 07:04 AM, O. Baris Malcioglu wrote:
> Dear Hongsheng Zhao,
>
> Unless you are asking if someone ever tried forcing a particular
> "bond" or aromaticity in PW explicitly (one can try to constrain some
> number of KS states trying to estimate a particular bond, but I don't
> think this is a good idea to do in a pw DFT code), I think you might
> be a little confused by the concepts.
>
> Beware that in literature they tend to do assume hydrogens implicitly
> in order not to complicate figure presentation. Also, please notice
> that you add hydrogens not just to saturate, but to put the atom in a
> particular "bonding state" (i.e. sp3 or sp2 hybridization etc.). That
> "bonding state" is handled by PW with no additional constraints (i.e.
> when you input the coordinates of Carbon and Hydrogen atoms in
> Benzene, with a suitable XC kernel, the electronic structure will
> assume aromaticity without you explicitly mentioning it, and if you
> want to see explicit proof of aromaticity using the nomenclature of
> theoretical chemistry, you can, for example, project the ks states in
> terms of atom centered pi levels)
Thanks a lot for your kindly reply.  In fact, I want to know how to do 
the corresponding adding operations in the input file for pwscf.

Say, for example, the following is the model input file for graphene 
nanoribbon including 7 primitive unit cell of armchair graphene 
nanoribbon (8), which is described and used in the following paper: 
http://tinyurl.com/3nz3xz9 ,

---------------
&CONTROL
calculation = 'scf'
prefix='block_1'
pseudo_dir = './'
outdir='./'
tstress=.true.
tprnfor = .true.
forc_conv_thr=1.0d-4
nstep=200
/
&SYSTEM
ibrav=0
celldm(1)=1.889726
nat=112
ntyp=1
ecutwfc=36
/
&ELECTRONS
mixing_beta=0.7
conv_thr =  1.0d-8
electron_maxstep=200
/
&IONS
trust_radius_max=0.2
/
&CELL
cell_dynamics='bfgs'
/
ATOMIC_SPECIES
    C  12.0110   C.UPF

CELL_PARAMETERS (alat)
   16.5000000000    0.0000000000    0.0000000000
    0.0000000000    8.0000000000    0.0000000000
    0.0000000000    0.0000000000   30.8203000000

ATOMIC_POSITIONS (crystal)
  C       0.128008000     0.500000000     0.050828000
  C       0.128008000     0.500000000     0.092030000
  C       0.197928000     0.500000000     0.023239000
  C       0.197929000     0.500000000     0.119619000
  C       0.273757000     0.500000000     0.047731000
  C       0.273757000     0.500000000     0.095127000
  C       0.349589000     0.500000000     0.023674000
  C       0.349589000     0.500000000     0.119183000
  C       0.425569000     0.500000000     0.047753000
  C       0.425570000     0.500000000     0.095104000
  C       0.501414000     0.500000000     0.023700000
  C       0.501414000     0.500000000     0.119157000
  C       0.577255000     0.500000000     0.048189000
  C       0.577255000     0.500000000     0.094668000
  C       0.647174000     0.500000000     0.020600000
  C       0.647174000     0.500000000     0.122256000
  C       0.128008000     0.500000000     0.193686000
  C       0.128008000     0.500000000     0.234887000
  C       0.197928000     0.500000000     0.166096000
  C       0.197929000     0.500000000     0.262476000
  C       0.273757000     0.500000000     0.190588000
  C       0.273757000     0.500000000     0.237984000
  C       0.349589000     0.500000000     0.166531000
  C       0.349589000     0.500000000     0.262040000
  C       0.425569000     0.500000000     0.190611000
  C       0.425570000     0.500000000     0.237961000
  C       0.501414000     0.500000000     0.166557000
  C       0.501414000     0.500000000     0.262014000
  C       0.577255000     0.500000000     0.191046000
  C       0.577255000     0.500000000     0.237525000
  C       0.647174000     0.500000000     0.163457000
  C       0.647174000     0.500000000     0.265113000
  C       0.128008000     0.500000000     0.336543000
  C       0.128008000     0.500000000     0.377744000
  C       0.197928000     0.500000000     0.308953000
  C       0.197929000     0.500000000     0.405334000
  C       0.273757000     0.500000000     0.333445000
  C       0.273757000     0.500000000     0.380842000
  C       0.349589000     0.500000000     0.309389000
  C       0.349589000     0.500000000     0.404897000
  C       0.425569000     0.500000000     0.333468000
  C       0.425570000     0.500000000     0.380818000
  C       0.501414000     0.500000000     0.309414000
  C       0.501414000     0.500000000     0.404871000
  C       0.577255000     0.500000000     0.333903000
  C       0.577255000     0.500000000     0.380382000
  C       0.647174000     0.500000000     0.306315000
  C       0.647174000     0.500000000     0.407970000
  C       0.128008000     0.500000000     0.479400000
  C       0.128008000     0.500000000     0.520601000
  C       0.197928000     0.500000000     0.451810000
  C       0.197929000     0.500000000     0.548191000
  C       0.273757000     0.500000000     0.476302000
  C       0.273757000     0.500000000     0.523699000
  C       0.349589000     0.500000000     0.452246000
  C       0.349589000     0.500000000     0.547755000
  C       0.425569000     0.500000000     0.476325000
  C       0.425570000     0.500000000     0.523675000
  C       0.501414000     0.500000000     0.452271000
  C       0.501414000     0.500000000     0.547729000
  C       0.577255000     0.500000000     0.476760000
  C       0.577255000     0.500000000     0.523239000
  C       0.647174000     0.500000000     0.449172000
  C       0.647174000     0.500000000     0.550827000
  C       0.128008000     0.500000000     0.622257000
  C       0.128008000     0.500000000     0.663458000
  C       0.197928000     0.500000000     0.594667000
  C       0.197929000     0.500000000     0.691048000
  C       0.273757000     0.500000000     0.619159000
  C       0.273757000     0.500000000     0.666556000
  C       0.349589000     0.500000000     0.595103000
  C       0.349589000     0.500000000     0.690612000
  C       0.425569000     0.500000000     0.619182000
  C       0.425570000     0.500000000     0.666532000
  C       0.501414000     0.500000000     0.595128000
  C       0.501414000     0.500000000     0.690586000
  C       0.577255000     0.500000000     0.619617000
  C       0.577255000     0.500000000     0.666096000
  C       0.647174000     0.500000000     0.592029000
  C       0.647174000     0.500000000     0.693684000
  C       0.128008000     0.500000000     0.765114000
  C       0.128008000     0.500000000     0.806316000
  C       0.197928000     0.500000000     0.737525000
  C       0.197929000     0.500000000     0.833905000
  C       0.273757000     0.500000000     0.762016000
  C       0.273757000     0.500000000     0.809413000
  C       0.349589000     0.500000000     0.737960000
  C       0.349589000     0.500000000     0.833469000
  C       0.425569000     0.500000000     0.762039000
  C       0.425570000     0.500000000     0.809389000
  C       0.501414000     0.500000000     0.737985000
  C       0.501414000     0.500000000     0.833443000
  C       0.577255000     0.500000000     0.762475000
  C       0.577255000     0.500000000     0.808953000
  C       0.647174000     0.500000000     0.734886000
  C       0.647174000     0.500000000     0.836542000
  C       0.128008000     0.500000000     0.907971000
  C       0.128008000     0.500000000     0.949173000
  C       0.197928000     0.500000000     0.880382000
  C       0.197929000     0.500000000     0.976762000
  C       0.273757000     0.500000000     0.904873000
  C       0.273757000     0.500000000     0.952270000
  C       0.349589000     0.500000000     0.880817000
  C       0.349589000     0.500000000     0.976326000
  C       0.425569000     0.500000000     0.904896000
  C       0.425570000     0.500000000     0.952246000
  C       0.501414000     0.500000000     0.880842000
  C       0.501414000     0.500000000     0.976300000
  C       0.577255000     0.500000000     0.905332000
  C       0.577255000     0.500000000     0.951810000
  C       0.647174000     0.500000000     0.877743000
  C       0.647174000     0.500000000     0.979399000
K_POINTS {automatic}
  4 4 4  1 1 1
---------------

In that paper, we can find the following description on page two:

---------
The carbon atoms at the edges are saturated with H atoms.
----------

So, according to the above description, what should I revise the input 
file in order to saturating the edges with H atoms?

Attached please find the snapshot for this structure.

Regards.
-- 

Hongsheng Zhao<zhaohscas at yahoo.com.cn>
School of Physics and Electrical Information Science,
Ningxia University, Yinchuan 750021, China

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