[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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