[Pw_forum] Avoiding vacuum and obtaining a periodic relaxed structure
Naseem Hassan
raheskoon at gmail.com
Thu Jan 15 11:59:00 CET 2015
Dear Pascal Boulet,
Thanks for the guidance. You answer is the first ever answer I received on
QE. I selected C-C bond length around 1.5 Angstrom. And tried to execute
the vc-relax using latest version of QE but I got some error. As I can see
from the error I should increase the Cell factor (Increasing cell vectors
to my understanding ?). I am presenting my input and Error file below for
your kind review. Might be you can suggest me something to modify input
file for the improved calculations and to eliminate the error.
*Input file is *
&control
calculation='vc-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
cell_dynamics = 'damp-pr'
! 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
*and the Error show in output file is as follow*
Error in routine scale_h (1):
Not enough space allocated for radial FFT: try restarting with a
larger cell_factor.
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Error in routine scale_h (1):
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Error in routine scale_h (1):
Error in routine scale_h (1):
Not enough space allocated for radial FFT: try restarting with a
larger cell_factor.
Error in routine scale_h (1):
Not enough space allocated for radial FFT: try restarting with a
larger cell_factor.
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Error in routine scale_h (1):
Not enough space allocated for radial FFT: try restarting with a
larger cell_factor.
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Not enough space allocated for radial FFT: try restarting with a
larger cell_factor.
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Error in routine scale_h (1):
Not enough space allocated for radial FFT: try restarting with a
larger cell_factor.
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Error in routine scale_h (1):
Not enough space allocated for radial FFT: try restarting with a
larger cell_factor.
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Not enough space allocated for radial FFT: try restarting with a
larger cell_factor.
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
stopping ...
stopping ...
stopping ...
stopping ...
stopping ...
stopping ...
stopping ...
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
stopping ...
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Error in routine scale_h (1):
Error in routine scale_h (1):
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Error in routine scale_h (1):
Not enough space allocated for radial FFT: try restarting with a
larger cell_factor.
Error in routine scale_h (1):
Not enough space allocated for radial FFT: try restarting with a
larger cell_factor.
Not enough space allocated for radial FFT: try restarting with a
larger cell_factor.
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Not enough space allocated for radial FFT: try restarting with a
larger cell_factor.
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
stopping ...
Error in routine scale_h (1):
stopping ...
Error in routine scale_h (1):
stopping ...
Not enough space allocated for radial FFT: try restarting with a
larger cell_factor.
Many Thanks
Naseem Hassan
On Wed, Jan 14, 2015 at 10:12 PM, Pascal Boulet <pascal.boulet at univ-amu.fr>
wrote:
>
> 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
> Avenue Normandie-Niemen
> F-13397 Marseille Cedex 20
> Tel.: +33 413.55.18.10
> Fax: +33 413.55.18.50
> http://allos.up.univ-mrs.fr/pascal/
>
>
>
>
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