[Pw_forum] Avoiding vacuum and obtaining a periodic relaxed structure

[Pascal Boulet]

Hello,

My brute force suggestion:
1. Select a chemically consistent axis so that the bond length is around 1.5 angstrom.
2. Optimize the cell parameters and atomic positions using vc-relax

Pascal


Le 14 janv. 2015 à 09:16, Naseem Hassan <raheskoon at gmail.com> a écrit :

> Dear All
> 
> I have made a structure similar to propylene using chemcraft. Then I picked the Cartesian coordinates and made an input file for relaxation. But I am not sure How long a Cell vector I should select along z-axis (along the Carbon chain). I want this structure to be periodic along the chain only. I selected 9 and 10 Angstrom of lattice vector along Z-axis and obtained C-C distance 5 and 6 Angstrom (Approx) respectively. It seems with 10 Angstrom a little vacuum is added and C-C bonds are elongated more. if I give small lattice vector (say 7 Ang) then C-C bond shrinks. How to obtain an optimized C-C bond length ? What is proper method of avoiding vacuum and obtaining a perfect periodic relaxed structure. 
> 
> Kindly have a look at the input file.
> 
>   &control
>     calculation='relax'
>     restart_mode='from_scratch'
>     pseudo_dir = '/share/QE_pseudo'
>     outdir='./'
>     prefix='Graphane'
>     forc_conv_thr=1.0D-4
>     nstep=3000
> /
>  &system
>     ibrav=  0
>     nat=  24,  ntyp= 2
>     ecutwfc =60.0
>     occupations='smearing'
>     degauss=0.002
>  /
>  &electrons
>     scf_must_converge = .false.
>     mixing_mode='plain'
>  /
>  &ions
>     ion_dynamics = 'damp'
> !   ion_temperature='not_controlled'
>  /
> CELL_PARAMETERS {angstrom}
>   10.00000000000   0.0000000000000000   0.000
>   0.0000000000   10.000000   0.000
>   0.0000000000000000   0.0000000000000000  10.0
> ATOMIC_SPECIES
> H  1.0079 H.pw-mt_fhi.UPF
> C  12.0111 C.pw-mt_fhi.UPF
> ATOMIC_POSITIONS {angstrom}
> C        5.367107970   4.716603635   1.053018481
> C        6.255850131   5.148617707   2.197431688
> C        5.604070962   5.956723221   3.300642187
> C        5.221138074   5.110436404   4.489234599
> C        4.929412403   5.933432549   5.718863005
> C        4.751718300   5.084706368   6.956077606
> C        5.325054303   5.689729332   8.206876709
> C        4.097184203   4.164227727   4.168731293
> H        6.706474032   4.257638763   2.659887322
> H        4.344006686   3.515258124   3.319860376
> H        3.854647824   3.519241858   5.021187742
> H        3.190910142   4.727029043   3.904250319
> H        3.696251345   4.818294626   7.110426161
> H        4.348967601   4.517546557   1.417990955
> H        5.731392495   3.757052353   0.655098847
> H        7.101013257   5.709772742   1.774202810
> H        6.288921269   6.743142271   3.648137411
> H        4.714167633   6.481058689   2.916034182
> H        6.110659580   4.502596625   4.738962908
> H        4.050783951   6.573507244   5.541152210
> H        5.775952152   6.619568616   5.878615758
> H        4.786163229   6.607591885   8.486624196
> H        6.356503452   6.007847752   7.983988564
> H        5.270145007   4.125317908   6.789870671
> K_POINTS {automatic}
>   3 3 1 0 0 0
> Many thanks
> Naseem 
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Pascal Boulet

--
pascal.boulet at univ-amu.fr
Aix-Marseille University
MADIREL Laboratory
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