[Pw_forum] Avoiding vacuum and obtaining a periodic relaxed structure
Pascal Boulet
pascal.boulet at univ-amu.fr
Fri Jan 16 11:34:28 CET 2015
Hello Naseem,
I had a look at your structure with xcrysden. The structure has some overlapping atoms which probably causes the crash. You have to rebuild the structure properly before you can go on.
Best regards
Pascal
Le 15 janv. 2015 à 11:59, Naseem Hassan <raheskoon at gmail.com> a écrit :
> 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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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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