Re: [Pw_forum] Phonon calculation of Silicene: ph.x

[NEELESH GUPTA]

Dear Jagdish,
 Yes sir you are right. Please consider it as a typo
error.

On Thu, Jan 11, 2018 at 10:08 PM, Jagdish verma 
wrote:

> Dear Neelesh,
>
> I don't know about the error. But in scf input , I think you should have
> 36 36 1 0 0 0 k grid because silicene  has 2D structure. It will decrease k
> points in scf.out. Please correct me if I said anything wrong.
>
> On Thu, Jan 11, 2018 at 5:50 PM, NEELESH GUPTA 
> wrote:
>
>> Dear All ,
>>
>> I'm trying to perform a phonon calculation of silicne using using ph.x on
>> QE v 6.0.
>>
>> I running this simulation using parallelzation
>> mpirun -np 32 -hostfile machine ph.x -ndiag4  -nk 2  ph.out
>>
>>
>>
>> Error generated...
>>
>>  %%%
>> %%%
>>  Error in routine set_kplusq (23976):
>>  too many k points
>>  %%%
>> %%%
>>
>>  stopping ...
>>
>> :
>>
>> ##I have done the scf calculation is done with k-points
>>   36  36  36  0 0 0
>>
>> ##  Detailed paramters
>>   ibrav=4,
>>   celldm(1)=7.3321373633d0, celldm(3)=12.8865979381d0,
>>   nat=2,
>>   ntyp=1,
>>
>>
>> ## the ph code is
>> Ph
>>  
>> prefix='calc'
>> outdir='Xe',
>> fildyn='calc.dyn',
>> tr2_ph=1.0d-16,
>> alpha_mix=0.7,
>> verbosity='high',
>> ldisp=.true.,
>> epsil= .false.
>> trans=.true,
>> nq1=4,nq2=4,nq3=1,
>>
>>
>>
>> I have tried with -nimage in mpi run  but it stops and in crash files it 
>> shows error of too many k-points.
>>
>>
>> *Thanks in advance!*
>>
>>
>>
>>
>> Warm regards
>> Neelesh Gupta
>> Research Scholar,ECE
>>
>>
>>
>>
>>
>>
>>
>>
>>
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>>
>
>
>
> --
> With best regards,
> Jagdish Verma,
>
>
>
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[Pw_forum] electric field

[Eliya Asmani]

Dear all,

I want to calculate bandstructure of bilayer graphene in presence of
electric field. is there any example or document can help me. I appreciate
if any one can sent me a paper has been done this calculation in order to
compare my results.

Best,
Eliya

Eliya Asmani,
Postdoctoral Researcher
School of Physics, Institute for Research in Fundamental Sciences (IPM)
Tehran, Iran
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Re: [Pw_forum] Phonon calculation of Silicene: ph.x

[Ari P Seitsonen]

Dear Neelesh,

  Adding to the answer of Jagdish, there is a fixed dimension:

qe-6.2/Modules/parameters.f90:   npk= 4,  &! max number of k-points

(This in version 6.2)
As pointed our in the previous answer, the number of actual k points will 
be reduced significantly if you do not apply k point beyond one value in 
the direction without periodicity (assuming that you have indeed a 
single, isolated layer in question).


Greetings,

   apsi

-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-
  Ari Paavo Seitsonen / ari.p.seitso...@iki.fi / http://www.iki.fi/~apsi/
Ecole Normale Supérieure (ENS), Département de Chimie, Paris
Mobile (F) : +33 789 37 24 25(CH) : +41 79 71 90 935


On Thu, 11 Jan 2018, Jagdish verma wrote:


Dear Neelesh,

I don't know about the error. But in scf input , I think you should have 36 36 
1 0 0 0 k grid because silicene  has 2D structure. It will
decrease k points in scf.out. Please correct me if I said anything wrong. 

On Thu, Jan 11, 2018 at 5:50 PM, NEELESH GUPTA  wrote:
  Dear All ,
   
I'm trying to perform a phonon calculation of silicne using using ph.x on QE v 
6.0.

I running this simulation using parallelzation
mpirun -np 32 -hostfile machine ph.x -ndiag4  -nk 2  ph.out



Error generated...

 %%
 Error in routine set_kplusq (23976):
 too many k points
 %%

 stopping ...

:

##I have done the scf calculation is done with k-points
  36  36  36  0 0 0

##  Detailed paramters
  ibrav=4,
  celldm(1)=7.3321373633d0, celldm(3)=12.8865979381d0,
  nat=2,
  ntyp=1,


## the ph code is
Ph
 
    prefix='calc'
    outdir='Xe',
    fildyn='calc.dyn',
    tr2_ph=1.0d-16,
    alpha_mix=0.7,
    verbosity='high',
    ldisp=.true.,
    epsil= .false.
    trans=.true,
    nq1=4,nq2=4,nq3=1,



I have tried with -nimage in mpi run  but it stops and in crash files it shows error of too many k-points. 


Thanks in advance!



Warm regards
Neelesh Gupta
Research Scholar,ECE









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Jagdish Verma,



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[Pw_forum] XSpectra orbitals

[Andrea Pedrielli]

Dear users,
me and my colleagues have calculated some xanes spectra of nanowires using
xspectra. Now, but I'm not sure if make sense, I would like to know if
there is a way to plot in 3D the orbitals corresponding to specific peaks
in the xanes spectra. Is it possible to access to these orbitals from
xspectra?
A way could be run again the dft calculation with the core hole and many
bands above the fermi level, then to plot the square modulus of the
orbitals corresponding to the xanes spectra peaks, but in this way the
speed up obtained using xspectra with lanczos chain is essentially lost.

Thanks,

Andrea


PhD
FBK-ECT*
Trento
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Re: [Pw_forum] Phonon calculation of Silicene: ph.x

[Jagdish verma]

Dear Neelesh,

I don't know about the error. But in scf input , I think you should have 36
36 1 0 0 0 k grid because silicene  has 2D structure. It will decrease k
points in scf.out. Please correct me if I said anything wrong.

On Thu, Jan 11, 2018 at 5:50 PM, NEELESH GUPTA 
wrote:

> Dear All ,
>
> I'm trying to perform a phonon calculation of silicne using using ph.x on
> QE v 6.0.
>
> I running this simulation using parallelzation
> mpirun -np 32 -hostfile machine ph.x -ndiag4  -nk 2  ph.out
>
>
>
> Error generated...
>
>  %%%
> %%%
>  Error in routine set_kplusq (23976):
>  too many k points
>  %%%
> %%%
>
>  stopping ...
>
> :
>
> ##I have done the scf calculation is done with k-points
>   36  36  36  0 0 0
>
> ##  Detailed paramters
>   ibrav=4,
>   celldm(1)=7.3321373633d0, celldm(3)=12.8865979381d0,
>   nat=2,
>   ntyp=1,
>
>
> ## the ph code is
> Ph
>  
> prefix='calc'
> outdir='Xe',
> fildyn='calc.dyn',
> tr2_ph=1.0d-16,
> alpha_mix=0.7,
> verbosity='high',
> ldisp=.true.,
> epsil= .false.
> trans=.true,
> nq1=4,nq2=4,nq3=1,
>
>
>
> I have tried with -nimage in mpi run  but it stops and in crash files it 
> shows error of too many k-points.
>
>
> *Thanks in advance!*
>
>
>
>
> Warm regards
> Neelesh Gupta
> Research Scholar,ECE
>
>
>
>
>
>
>
>
>
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Jagdish Verma,
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[Pw_forum] Phonon calculation of Silicene: ph.x

[NEELESH GUPTA]

Dear All ,

I'm trying to perform a phonon calculation of silicne using using ph.x on
QE v 6.0.

I running this simulation using parallelzation
mpirun -np 32 -hostfile machine ph.x -ndiag4  -nk 2  ph.out



Error generated...

 %%
 Error in routine set_kplusq (23976):
 too many k points
 %%

 stopping ...

:

##I have done the scf calculation is done with k-points
  36  36  36  0 0 0

##  Detailed paramters
  ibrav=4,
  celldm(1)=7.3321373633d0, celldm(3)=12.8865979381d0,
  nat=2,
  ntyp=1,


## the ph code is
Ph
 
prefix='calc'
outdir='Xe',
fildyn='calc.dyn',
tr2_ph=1.0d-16,
alpha_mix=0.7,
verbosity='high',
ldisp=.true.,
epsil= .false.
trans=.true,
nq1=4,nq2=4,nq3=1,



I have tried with -nimage in mpi run  but it stops and in crash files
it shows error of too many k-points.


*Thanks in advance!*




Warm regards
Neelesh Gupta
Research Scholar,ECE
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Re: [Pw_forum] Is it possible to calculated IR and Raman spectra for molecules adsorbed on metal surfaces

[Ari P Seitsonen]

Dear Jibiao Li,

  A late reply, but: It is not possible to "isolate" the molecule in the 
calculation nor in the experiment, as any photon hitting the system might 
cause an electronic excitation, either at the molecule or the surface, so 
the intensity of the spectrum would be beyond the non-resonant regime.


  The crude approximation is to calculate the vibrational modes and try to 
correlate those with experiments - without the intensity (but maybe with 
the selection rules from symmetry). Next, you might try to move the atoms 
along the normal modes and see if you get something useful from the 
variation/derivative of the dipole/polarisability. But, as said, also in 
the experiment there could be any excitations, thus smearing the 
intensities.


Greetings from Paris,

   apsi

-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-
  Ari Paavo Seitsonen / ari.p.seitso...@iki.fi / http://www.iki.fi/~apsi/
Ecole Normale Supérieure (ENS), Département de Chimie, Paris
Mobile (F) : +33 789 37 24 25(CH) : +41 79 71 90 935


On Tue, 9 Jan 2018, jibiaoli wrote:


Dear All,

I learned from the maillist that pure metallic systems do not have IR and Raman 
active modes, thereby it's meaningless to calculated IR and Raman
spectra for those systems. However, I am very much interested in molecules 
adsorbed on metal surfaces, is it possible to get IR and Raman spectra
for molecules/metal systems through QE calculations?

Best

Jibiao Li

Yangtze Normal University, China

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Re: [Pw_forum] Different Errors of Raman calculations for ZnO and ZnS

[Leonid Kahle]

Dear Jiabao,

regarding the first error, it is self-explaining what happens from the 
error-message that you get: You have to use LDA to compute the Raman 
cross-section, GGA (PBE is a flavor of GGA) is not implemented. You can 
find LDA-pseudos here: http://theossrv1.epfl.ch/Main/Pseudopotentials, 
look for the "pz" in the name.


For the second error, please consider the documentation of the 
phonon-code: 
http://www.quantum-espresso.org/wp-content/uploads/Doc/INPUT_PH.html#idm63
You can't set epsil to true in a metallic system. Analyze the 
occupations in your system, and if you have a sufficient band-gap, turn 
off the smearing for the SCF, and use this new calculation for computing 
the dielectric constant. Also here, you're using PBE for a Raman 
computation, you'd need to switch to LDA.


Best regards,

    Leonid Kahle


On 01/11/2018 07:48 AM, jibiaoli wrote:

Dear All,

I am using NCPP available online to calculate Raman spectra for ZnS 
and ZnO, but the two different errors  appeared respectively for the 
two crystals. Are they highly dependent on crystal structure? How 
should I modify the inputs and make them working ? Can anyone provide 
me a working example for Raman spectra?


Error message for ZnS

     task #     4
     from phq_setup : error #     1
     third order derivatives not implemented with GGA
 

Error message for ZnO

 task # 0
 from phq_readin : error # 1
 no elec. field with metals
 

Jibiao Li

Yangtze Normal University, China

phonon calculation for ZnS
& inputph
tr2_ph=1.0d-12,
prefix='ZnS',
outdir='./',
amass(1)=32.066,
amass(2)=65.409,
epsil=.true.,
lraman=.true.,
trans=.true.,
fildyn='ZnS_IR.dynG',
fildrho='ZnS_IR.drho',
/
0.0 0.0 0.0


calculation = 'scf',
prefix = 'ZnS',
restart_mode = 'from_scratch' ,
outdir = './' ,
pseudo_dir   = "/home/bmllzr/codes/pseudo/",
etot_conv_thr = 1.0d-5 ,
forc_conv_thr = 1.0d-4 ,
tstress = .true. ,
tprnfor = .true. ,
nstep = 100 ,
/

ibrav = 4,
celldm(1) = 7.1928551712,
celldm(3) = 1.6400783135,
nat=4,
ntyp=2,
ecutwfc=80,
/

conv_thr = 1.D-12,
/
ATOMIC_SPECIES
S   32.066   S.pbe-hgh.UPF
Zn  65.409   Zn.pbe-d-hgh.UPF
ATOMIC_POSITIONS crystal
S    0.3   0.7   0.374653315
S   -0.3  -0.7   0.874653315
Zn   0.3   0.7   0.000346685
Zn      -0.3  -0.7   0.500346685
K_POINTS automatic
6 6 6 0 0 0

Normal modes for Wurtzite
 
  tr2_ph=1.0d-14,
  prefix='ZNO',
  outdir='./',
  amass(1)=65.409,
  amass(2)=15.999,
  epsil=.true.,
  lraman=.true.
  trans=.true.,
  asr=.true.
  fildyn='dmat.zno'
 /
 0.0 0.0 0.0


  calculation  = "scf",
  prefix   = "ZNO",
  pseudo_dir   = "/home/bmllzr/codes/pseudo/",
  outdir   = "./",
/

  ibrav=0, celldm(1) =6.330582528, nat=4, ntyp= 2,
  occupations='smearing', smearing='marzari-vanderbilt', degauss=0.02,
  ecutwfc =80.0, !better 140
/

  mixing_mode='plain'
  mixing_beta = 0.5,
  startingwfc='random',
  conv_thr =  1.0d-8
/
CELL_PARAMETERS alat
  1.55820896 0. 0.
  0. 0.86602540 -0.5000
  0. 0. 1.
ATOMIC_SPECIES
  Zn 65.409  Zn.pbe-d-hgh.UPF
  O  15.999  O.pbe-hgh.UPF
ATOMIC_POSITIONS (alat)
Zn   2.010975287   0.487933254  -0.051360548
Zn   1.234717421   0.199473387   0.44837
O    1.051679030   0.488287222  -0.051814333
O    1.830251369   0.199830262   0.448810714
K_POINTS (automatic)
2 2 2 0 0 0




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Re: [Pw_forum] Different Errors of Raman calculations for ZnO and ZnS

[Ilya Ryabinkin]

I replied before to address the first error. The second error is triggered
because at the chosen level of theory ZnO turned out to be a metal. A
dielectric function for metals is negative and conductance electrons screen
external electric field completely -- no Raman intensities.

For better understanding of the theory I would recommend to consult with
Chapter 5.4.2.2 of the book " Quantum Theory of the Solid State: An
Introduction" by Lev Kantorovich (2004 Springer Science+Business Media
Dordrecht
Originally published by Kluwer Academic Publishers in 2004), ISBN
978-1-4020-2153-4, DOI 10.1007/978-1-4020-2154-1

On Thu, Jan 11, 2018 at 1:48 AM, jibiaoli  wrote:

> Dear All,
>
> I am using NCPP available online to calculate Raman spectra for ZnS and
> ZnO, but the two different errors  appeared respectively for the two
> crystals. Are they highly dependent on crystal structure? How should I
> modify the inputs and make them working ? Can anyone provide me a working
> example for Raman spectra?
>
> Error message for ZnS
> 
>  task # 4
>  from phq_setup : error # 1
>  third order derivatives not implemented with GGA
>  
>
> Error message for ZnO
> 
>  task # 0
>  from phq_readin : error # 1
>  no elec. field with metals
>  
>
> Jibiao Li
>
> Yangtze Normal University, China
>
> phonon calculation for ZnS
> & inputph
> tr2_ph=1.0d-12,
> prefix='ZnS',
> outdir='./',
> amass(1)=32.066,
> amass(2)=65.409,
> epsil=.true.,
> lraman=.true.,
> trans=.true.,
> fildyn='ZnS_IR.dynG',
> fildrho='ZnS_IR.drho',
> /
> 0.0 0.0 0.0
>
> 
> calculation = 'scf',
> prefix = 'ZnS',
> restart_mode = 'from_scratch' ,
> outdir = './' ,
> pseudo_dir   = "/home/bmllzr/codes/pseudo/",
> etot_conv_thr = 1.0d-5 ,
> forc_conv_thr = 1.0d-4 ,
> tstress = .true. ,
> tprnfor = .true. ,
> nstep = 100 ,
> /
> 
> ibrav = 4,
> celldm(1) = 7.1928551712,
> celldm(3) = 1.6400783135,
> nat=4,
> ntyp=2,
> ecutwfc=80,
> /
> 
> conv_thr = 1.D-12,
> /
> ATOMIC_SPECIES
> S   32.066   S.pbe-hgh.UPF
> Zn  65.409   Zn.pbe-d-hgh.UPF
> ATOMIC_POSITIONS crystal
> S0.3   0.7   0.374653315
> S   -0.3  -0.7   0.874653315
> Zn   0.3   0.7   0.000346685
> Zn  -0.3  -0.7   0.500346685
> K_POINTS automatic
> 6 6 6 0 0 0
> 
> 
> Normal modes for Wurtzite
>  
>   tr2_ph=1.0d-14,
>   prefix='ZNO',
>   outdir='./',
>   amass(1)=65.409,
>   amass(2)=15.999,
>   epsil=.true.,
>   lraman=.true.
>   trans=.true.,
>   asr=.true.
>   fildyn='dmat.zno'
>  /
>  0.0 0.0 0.0
>
> 
>   calculation  = "scf",
>   prefix   = "ZNO",
>   pseudo_dir   = "/home/bmllzr/codes/pseudo/",
>   outdir   = "./",
> /
> 
>   ibrav=0, celldm(1) =6.330582528, nat=4, ntyp= 2,
>   occupations='smearing', smearing='marzari-vanderbilt', degauss=0.02,
>   ecutwfc =80.0, !better 140
> /
> 
>   mixing_mode='plain'
>   mixing_beta = 0.5,
>   startingwfc='random',
>   conv_thr =  1.0d-8
> /
> CELL_PARAMETERS alat
>   1.55820896 0. 0.
>   0. 0.86602540 -0.5000
>   0. 0. 1.
> ATOMIC_SPECIES
>   Zn 65.409  Zn.pbe-d-hgh.UPF
>   O  15.999  O.pbe-hgh.UPF
> ATOMIC_POSITIONS (alat)
> Zn   2.010975287   0.487933254  -0.051360548
> Zn   1.234717421   0.199473387   0.44837
> O1.051679030   0.488287222  -0.051814333
> O1.830251369   0.199830262   0.448810714
> K_POINTS (automatic)
> 2 2 2 0 0 0
>
>
>
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Re: [Pw_forum] Error from Raman calculation by QE 6.1

[Ilya Ryabinkin]

Raman intensities require polarisation tensor derivatives, which are
formally the third-order properties (mixed (2,1) derivatives wrt E and R),
and program responded:"third order derivatives not implemented with
GGA".

Minimally, you can enforce LDA calculations instead of an inferred from PP
files PBE (of GGA type), but this is generally not recommended. More
systematic approach is to use LDA-PPs, but you may not be satisfied by LDA
anyway.


On Wed, Jan 10, 2018 at 9:25 PM, jibiaoli  wrote:

> Dear All,
>
> I am new to Raman calcualtions and need your help. By using NCPP available
> online, I try to calculate Raman spectra for ZnS, but the following error
> appeared. Is it possible to modify the input to get the Raman spectra? How?
> 
>  task # 4
>  from phq_setup : error # 1
>  third order derivatives not implemented with GGA
>  
>
> Jibiao Li
> Yangtze Normal University, China
>
> phonon calculation for ZnS
> & inputph
> tr2_ph=1.0d-12,
> prefix='ZnS',
> outdir='./',
> amass(1)=32.066,
> amass(2)=65.409,
> epsil=.true.,
> lraman=.true.,
> trans=.true.,
> fildyn='ZnS_IR.dynG',
> fildrho='ZnS_IR.drho',
> /
> 0.0 0.0 0.0
>
> 
> calculation = 'scf',
> prefix = 'ZnS',
> restart_mode = 'from_scratch' ,
> outdir = './' ,
> pseudo_dir   = "/home/bmllzr/codes/pseudo/",
> etot_conv_thr = 1.0d-5 ,
> forc_conv_thr = 1.0d-4 ,
> tstress = .true. ,
> tprnfor = .true. ,
> nstep = 100 ,
> /
> 
> ibrav = 4,
> celldm(1) = 7.1928551712,
> celldm(3) = 1.6400783135,
> nat=4,
> ntyp=2,
> ecutwfc=80,
> /
> 
> conv_thr = 1.D-12,
> /
> ATOMIC_SPECIES
> S   32.066   S.pbe-hgh.UPF
> Zn  65.409   Zn.pbe-d-hgh.UPF
> ATOMIC_POSITIONS crystal
> S0.3   0.7   0.374653315
> S   -0.3  -0.7   0.874653315
> Zn   0.3   0.7   0.000346685
> Zn  -0.3  -0.7   0.500346685
> K_POINTS automatic
> 6 6 6 0 0 0
>
>
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[Pw_forum] vc-relax

[ade wale]

*Dear all,
**I'm trying to perform a "vc-relax" calculation using the smearing*

*method with QE v 6.2.
**The calculation stops running after iteration at forces acting on atoms*

*(atom 54 out of 60 atoms).*

*I have tried with both mv and gauss smearing, but I have the
**same issue.
**Please find attached, the input and output of my work.
*

*Thanks in advance!
*

* Regards,*

*Akeem Adekunle Adewale*

*PhD Candidate*

*Universiti Malaysia Perlis*


tita.out
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tita.in
Description: Binary data
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