Re: [Pw_forum] Negative frequency in phonon calculation

2015-12-13 Thread Sanjeev Gupta 
The reason of negative frequencies are :
1. Look you pseudopotential perhaps use another and see.
2. Your structure is not well optimized.

and many...

wishes
sanjeev


On Sun, Dec 13, 2015 at 8:02 PM, Barnali Bhattacharya <
barnalidgbh...@gmail.com> wrote:

> Dear Sir/Madam
>
>
>
> I am a quantum espresso user and interested in phonon calculation of BN
> doped two dimensional system. For these first of all I have checked the ecut
> off convergence and taking this ecutwfc value checked the K-point
> convergence. After taking this ecutwfc and k-point value, I have optimized
> the structure with ‘VC-relax option’ with convergence criteria
>
> “etot_conv_thr = 1.0D-16,
>
>  forc_conv_thr = 1.0D-16,”.
>
>
>
> Taking the relaxed position and cell parameter I have checked the suitable
> lattice constant for which energy is minimum by using the script…
>
>
>
> …
>
> #!/bin/sh
>
> ….
>
> 
>
> 
>
> for a in `seq -w 0.995 0.001 1.005 `
>
> do
>
> ……..
>
> 
>
> …….
>
> cat > $MOL.$a.in << EOF
>
> 
>
> calculation='relax',
>
> restart_mode='from_scratch',
>
> ……….
>
> …….
>
> …..
>
> ………
>
> /
>
> CELL_PARAMETERS alat
>
> `echo $a*12.901074275 | bc -l` 0.0  0.0
>
> `echo $a*6.45053713| bc -l`  `echo $a*11.1726581| bc -l` 0.0
>
>  0.0   0.0  29.0
>
> ATOMIC_SPECIES
>
> C 12.0107 C.pz-n-rrkjus_psl.0.1.UPF
>
> ATOMIC_POSITIONS (crystal)
>
> .
>
> ……..
>
> …..
>
> 
>
> …
>
> …..
>
> ……
>
>
>
> Then taking the lattice constant for which energy is minimum and the
> atomic position we have calculated phonon dispersion curve, but found
> negative frequency.
>
>
>
> I am confused is there any mistake in my procedure.
>
>
>
> Could anyone please guide me how this negative frequency will be
> disappear? Any help will be thankfully acknowledged.
>
>
>
> Thanking you.
>
>
>
> Sincerely
>
> Barnali Bhattacharya
>
> Ph.D student
>
> Department of physics
>
> Assam University
>
>
>
>
>
>
>
>
>
> 
>  This
> email has been sent from a virus-free computer protected by Avast.
> www.avast.com
> 
> <#1519ea7e51a8ace0_DDB4FAA8-2DD7-40BB-A1B8-4E2AA1F9FDF2>
>
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-- 
With Best Regards,


Dr. Sanjeev Kumar Gupta
Fulbright Post-Doctoral Scholar
Dept. of Physics
Michigan Technological University
1400 Townsend Drive, Houghton
MI 49931, USA

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[Pw_forum] Plot wannier function with cp.x

2015-12-13 Thread CHEN Jinfan 
Dear pw_forum users,I am trying to plot the density of wannier functions 
with cp.x. I couldn't find any example, can someone provide me a sample input 
file? Mine that is edited according to the input parameters description seem 
not correct. Thank you very much.
   Best regard,   Jinfan
---
calculation   = "cp-wf", restart_mode  = "restart", 
nstep = 100,iprint= 100,isave = 100,dt  
  = 4.D0,ndw   = 53,etot_conv_thr = 1.D-16,
ekin_conv_thr = 1.D-16,prefix= "h2o_mol",pseudo_dir= 
"/home/jinfchen/espresso502/pseudo",outdir= "./",   /
ibrav = 1,celldm(1) = 20.0,nat   = 3,ntyp  = 2,
ecutwfc   = 25.D0,nr1b = 10, nr2b = 10, nr3b = 10,/   emass   
  = 350.D0,emass_cutoff  = 3.D0,ortho_eps = 5.D-8,  
  ortho_max = 250,electron_dynamics = "damp",electron_damping  
= 0.15, /ion_dynamics = "none", /  calwf=1nwf=4
adapt  = .true.,nsteps = 10,  /  PLOT_WANNIER 1 2 3 4  
ATOMIC_SPECIES  O  16.D0  O_US.van  H   2.D0  H_US.van  ATOMIC_POSITIONS (bohr) 
 O 10.10.10.000  H 11.7325 9.675710.000  H  
9.675711.732510.000
  
CHEN
 JinfanSchool of Energy and EnvironmentCity University of Hong KongKowloon, 
Hong Kong 
SAR



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[Pw_forum] Negative frequency in phonon calculation

2015-12-13 Thread Barnali Bhattacharya 
Dear Sir/Madam



I am a quantum espresso user and interested in phonon calculation of BN
doped two dimensional system. For these first of all I have checked the ecut
off convergence and taking this ecutwfc value checked the K-point
convergence. After taking this ecutwfc and k-point value, I have optimized
the structure with ‘VC-relax option’ with convergence criteria

“etot_conv_thr = 1.0D-16,

 forc_conv_thr = 1.0D-16,”.



Taking the relaxed position and cell parameter I have checked the suitable
lattice constant for which energy is minimum by using the script…



…

#!/bin/sh

….





for a in `seq -w 0.995 0.001 1.005 `

do

……..



…….

cat > $MOL.$a.in << EOF



calculation='relax',

restart_mode='from_scratch',

……….

…….

…..

………

/

CELL_PARAMETERS alat

`echo $a*12.901074275 | bc -l` 0.0  0.0

`echo $a*6.45053713| bc -l`  `echo $a*11.1726581| bc -l` 0.0

 0.0   0.0  29.0

ATOMIC_SPECIES

C 12.0107 C.pz-n-rrkjus_psl.0.1.UPF

ATOMIC_POSITIONS (crystal)

.

……..

…..



…

…..

……



Then taking the lattice constant for which energy is minimum and the atomic
position we have calculated phonon dispersion curve, but found negative
frequency.



I am confused is there any mistake in my procedure.



Could anyone please guide me how this negative frequency will be disappear?
Any help will be thankfully acknowledged.



Thanking you.



Sincerely

Barnali Bhattacharya

Ph.D student

Department of physics

Assam University









This
email has been sent from a virus-free computer protected by Avast.
www.avast.com

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[Pw_forum] High adsorption energies: CO on Ni-111

2015-12-13 Thread Elliot Menkah 

Hello Everyone,
In trying to validate the computational methods and configuration of my
system for a desired study, the adsorption energies I obtained upon
computation seems to be about twice the value of what i was expecting.

This is adsorption of CO on nickel surface sites on Ni-111 surface
structure.
Literature mentions the adsorption energies on the sites top, bridge,
fcc and hcp to be: -137.9, -159.0, -163.7 and -164.6 kJ/mol
respectively,  whereas i'm getting -305.03, -328.04, -339.56 and -409.55
kJ/mol respectively.

The qualitative trend seems to exists  where the hcp site is the most
energetically favourable site for adsorption in both literature and my
study, however, quantitatively, my values are too larger.

I adsorb the molecule on only one side of the slab.

Do I have to adsorb on both sides of the slab in mirror positions to
handle dipole moment perpendicular to the surface due to adsorption?


What could the reason or problem be?

Please find attached the input files of my hcp site calculation for your
perusal.

Thank you.

Kind Regards,
Elliot


 

-- 
Elliot S. Menkah, AMRSC 
Research Student - Computational Chemistry/ Computational Material Science
Theoretical and Computational Chemistry
Dept. of Chemistry
Kwame Nkrumah UNiversity of Sci. and Tech.
Kumasi
Ghana

Tel: +233 243-055-717

Alt Email: esmen...@knust.edu.gh
   elliotsmen...@gmail.com
   elliotsmen...@hotmail.com




   title = 'Ni-2x2-111-6L-MD-CO-3fold-fcc' ,
   calculation = 'relax' ,
   restart_mode = 'from_scratch' ,
   outdir = './tmp' ,
   pseudo_dir = '/home/eliot/pseudo' ,
   prefix = 'ni-111-2x2-6L-MD-CO-3fold-fcc',
   tstress = .true. ,
   tprnfor = .true. ,
/
 
   ibrav = 0,
   celldm(1) = 1.88972599,
   nat = 98,
   ntyp = 3,
   ecutwfc = 40,
   ecutrho = 480,
   occupations='smearing',
   smearing='mp',
   degauss=0.05,
   nbnd=560,
   nspin=2,
   starting_magnetization(1)=0.5,
/
 
conv_thr = 1.0D-6,
mixing_mode = 'local-TF'
/
 
/
ATOMIC_SPECIES
Ni 58.6934   Ni.pbe-nd-rrkjus.UPF
 C 12.011 C.pbe-rrkjus.UPF
 O 15.999 O.pbe-rrkjus.UPF
ATOMIC_POSITIONS (alat)
Ni   1.245247692   0.718944090   0.0158687830   0   0
Ni   2.490495415   2.875776414   0.0158687830   0   0
Ni   3.735743138   0.718944090   0.0158687830   0   0
Ni   4.980990830   2.875776397   0.0158683550   0   0
Ni   1.245247472   3.594720360   2.0239987780   0   0
Ni   2.490495415   5.751553065   2.0239987780   0   0
Ni   3.735743358   3.594720360   2.0239987780   0   0
Ni   4.980990830   5.751552793   2.0239994310   0   0
Ni   1.245247844   6.470496971   4.0599651320   0   0
Ni   2.490495415   8.627329032   4.0599651320   0   0
Ni   3.735742986   6.470496971   4.0599651320   0   0
Ni   4.980990830   8.627329190   4.0599649790   0   0
Ni   1.246709841   9.346680057   6.089903308
Ni   2.491049866  11.503272365   6.094695989
Ni   3.736309279   9.347499400   6.091839589
Ni   4.981632933  11.503215624   6.094592854
Ni   1.251397606  12.222515270   8.130528230
Ni   2.493872076  14.374876735   8.130574795
Ni   3.736773669  12.222408715   8.121452049
Ni   4.979701257  14.375516889   8.129406603
Ni   1.243830060  15.097651794  10.124780901
Ni   2.490567863  17.254288878  10.125834084
Ni   3.737277529  15.124361083  10.124533866
Ni   4.983701851  17.254644423  10.125942272
Ni   3.735743107   5.032608685   0.0158687830   0   0
Ni   4.980990830   7.189441009   0.0158687830   0   0
Ni   6.226238553   5.032608685   0.0158687830   0   0
Ni   7.471486245   7.189440992   0.0158683550   0   0
Ni   3.735742887   7.908384955   2.0239987780   0   0
Ni   4.980990830  10.065217660   2.0239987780   0   0
Ni   6.226238773   7.908384955   2.0239987780   0   0
Ni   7.471486245  10.065217388   2.0239994310   0   0
Ni   3.735743259  10.784161566   4.0599651320   0   0
Ni   4.980990830  12.940993627   4.0599651320   0   0
Ni   6.226238401  10.784161566   4.0599651320   0   0
Ni   7.471486245  12.940993785   4.0599649790   0   0
Ni   3.736296794  13.660278999   6.094631584
Ni   4.981840953  15.816305949   6.089805212
Ni   6.225869615  13.659635984   6.091567601
Ni   7.472468264  15.816767005   6.089493887
Ni   3.736896631  16.534686190   8.122356924
Ni   4.983572283  18.693711643   8.122423344
Ni   6.227530794  16.536159378   8.121678221
Ni   7.475062891  18.697174708   8.130314215
Ni   3.737430863  19.413420133  10.125793472
Ni   4.981744277  21.571270847  10.124719443
Ni   6.205422793  19.399131231  10.125043022
Ni   7.471688751  21.569920708  10.195553976
Ni   6.226238522   0.718944090   0.0158687830   0   0
Ni   7.471486245   2.875776414