[Pw_forum] Zr supercell

2018-02-13 Thread Krishnendu Mukherjee 
Dear Dr. Mostafa Youssef,

 Thank you very much for your kind reply. I am trying to build a supercell.
I got another reply in this forum that there has to be at least two Nb
atoms as there is no Wyckofff positions having only 1 atom in the space
group 194. If I want to use the Wyckoff positions I have to use the ones
having no x, y, z parameters in them, because at present I have no
crystallographic information about the Zr-Nb alloy. I may assume that Zr
atoms are in the Wyckoff positions, 2b, 2c, 2d and 6g positions (=total 12
Zr atoms) and Nb atoms are in 2a positions (=2 atoms). These are also
assumptions but at present I do not have any other options to start with.
Of course I suppose this will keep the space group intact, i.e., if I put
the atoms in these Wyckoff positions quantum espresso will be able to
determine the space group as 194.

 Please let me know your comments and suggestions regarding building up the
supercell.
Thanking you,
Yours sincerely,
Krishnendu
---

You wrote:

Dear Krishnendu,

If you model the alloy using a unit cell, then you are modeling a very high
Nb concentration ordered alloy.

Take HCP unit cell having two Zr atoms. If you replace one with Nb, then
you get 50%-50% Zr-Nb.

There is no way to avoid forming a supercell of Zr (Say 54 atoms) and then
replace one with Nb.


Regards,
AUC, New Cairo, Egypt

-- 
Dr. Krishnendu Mukherjee,

Principal Scientist,
CSIR-NML,
Jamshedpur.
___
Pw_forum mailing list
Pw_forum@pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum

Re: [Pw_forum] Zr supercell

2018-02-05 Thread Mostafa Youssef 
Dear Krishnendu,

If you model the alloy using a unit cell, then you are modeling a very high
Nb concentration ordered alloy.

Take HCP unit cell having two Zr atoms. If you replace one with Nb, then
you get 50%-50% Zr-Nb.

There is no way to avoid forming a supercell of Zr (Say 54 atoms) and then
replace one with Nb.


Regards,
AUC, New Cairo, Egypt
___
Pw_forum mailing list
Pw_forum@pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum

[Pw_forum] Zr supercell

2018-02-05 Thread Krishnendu Mukherjee 
Dear expert,

 This is in response to the question why do we want to use a Zr supercell.
We are interested in calculating the elastic constants of Zr alloys (for
example Zr containing 1 wt% Nb). We found a paper titled, "Mechanical
properties of zirconium alloys and zirconium hydrides predicted from
density functional perturbation theory". In that paper the authors
constructed a Zr53Nb supercell with 53 Zr atoms and 1 Nb atom to do the
calculations. As a first step we want to replicate the results. To begin,
we just try to make a Zr supercell. When we are successful in creation of
Zr supercell and able to predict the elastic constants of Zr with the
supercell properly we will replace a Zr atom in that supercell with Nb to
get the elastic constants of the alloy.

 Now my question is,  is it possible to calculate the elastic properties of
Zirconium alloy without constructing a supercell, i.e., through an unit
cell? In that can you please let us know what will be the input parameters
to construct such an unit cell?

 Now in case, if construction of supercell is unavoidable can you please
guide us what are the input to construct the supercell. I guess we have to
input the space group (194, P 63/m m c in this case). I guess the other
input is the basis atom positions which is 0,0,0 and 2/3, 1/3, 1/2. Is
there any other input for constructing a supercell. I will use the program
VESTA for creating a supercell.

 I found some previous discussions in the pwscf forum about the space group
194. There I saw ibarv=4 was used, with some other necessary inputs,
e.g., use_all_frac = .true.. But in that case the input for the
ATOMIC_POSITIONS are to be given in crystal_sg. But I do not know how to
get the crystal_sg output from VESTA.

 I will be grateful to you if you can kindly guide us regarding these
matters.

Thanking you,
Yours sincerely,
krish


-- 
Dr. Krishnendu Mukherjee,

Principal Scientist,
CSIR-NML,
Jamshedpur.
___
Pw_forum mailing list
Pw_forum@pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum

Re: [Pw_forum] Zr supercell with ibrav=0

2018-02-02 Thread Marzari Nicola 

Btw, why use a supercell?

Sent from a tiny keyboard... Contact info:
http://theossrv1.epfl.ch/Main/Contact

On 2 Feb 2018, at 10:07, Paolo Giannozzi 
> wrote:

Lines with "/" should be used to close namelists, not cards. Remove the two at 
the end of cards ATOMIC_ POSITIONS and CELL_PARAMETERS

P.

On Fri, Feb 2, 2018 at 8:34 AM, Krishnendu Mukherjee 
> 
wrote:

Dear experts,

 I am interested in calculation of elastic constants of Zr using a supercell of 
2*2*2. I have used ibrav=0. I used the following input:


cat > thermo_control << EOF
 _THERMO
  what='mur_lc_elastic_constants',
  frozen_ions=.FALSE.
 /
EOF

cat > zr.elastic.in << EOF
 
calculation = 'scf'
restart_mode='from_scratch',
prefix='zr',
tstress = .true.,
   tprnfor = .true.,
pseudo_dir = '$PSEUDO_DIR/',
outdir='$TMP_DIR/'
 /
 
ibrav= 0,
nat= 16,
ntyp= 1,
ecutwfc=50.0,
   ecutrho = 430,
   occupations='smearing',
   smearing='marzari-vanderbilt',
   degauss=0.02
   starting_magnetization(1) = 0.7,
 /
 
conv_thr =  1.0d-12
  /
ATOMIC_SPECIES
 Zr  91.22  Zr.pz-spn-kjpaw_psl.1.0.0.UPF
ATOMIC_POSITIONS (angstrom)
Zr 0.00 1.870038 1.289000
Zr 3.239000 3.740075 9.023001
Zr 1.619500 4.675094 1.289000
Zr 1.619500 0.935019 9.023001
Zr -1.619500 4.675094 1.289000
Zr 4.858500 0.935019 9.023001
Zr 3.239000 3.740075 3.867000
Zr 1.619500 0.935019 3.867000
Zr 4.858500 0.935019 3.867000
Zr 0.00 1.870038 6.445000
Zr 1.619500 4.675094 6.445000
Zr -1.619500 4.675094 6.445000
Zr 3.239000 1.870038 1.289000
Zr 0.00 3.740075 9.023001
Zr 0.00 3.740075 3.867000
Zr 3.239000 1.870038 6.445000
/
CELL_PARAMETERS (ANGSTROM)
6.4780001640 0.00 0.00
-3.239820 5.6101127078 0.00
0.00 0.00 10.3120002747
/
K_POINTS AUTOMATIC
5 5 3 0 0 0
EOF

Can you kindly let me know why I am getting the following error:

from card_atomic_positions : error # 2
 two occurrences

I will be grateful if you can help me in solving the problem.

Thanks,
Regards,
krish
--
Dr. Krishnendu Mukherjee,

Principal Scientist,
CSIR-NML,
Jamshedpur.

___
Pw_forum mailing list
Pw_forum@pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum



--
Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222

___
Pw_forum mailing list
Pw_forum@pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum
___
Pw_forum mailing list
Pw_forum@pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum

Re: [Pw_forum] Zr supercell with ibrav=0

2018-02-02 Thread Paolo Giannozzi 
Lines with "/" should be used to close namelists, not cards. Remove the two
at the end of cards ATOMIC_ POSITIONS and CELL_PARAMETERS

P.

On Fri, Feb 2, 2018 at 8:34 AM, Krishnendu Mukherjee <
krishnendu.mukherjee...@gmail.com> wrote:

>
> Dear experts,
>
>  I am interested in calculation of elastic constants of Zr using a
> supercell of 2*2*2. I have used ibrav=0. I used the following input:
>
>
> cat > thermo_control << EOF
>  _THERMO
>   what='mur_lc_elastic_constants',
>   frozen_ions=.FALSE.
>  /
> EOF
>
> cat > zr.elastic.in << EOF
>  
> calculation = 'scf'
> restart_mode='from_scratch',
> prefix='zr',
> tstress = .true.,
>tprnfor = .true.,
> pseudo_dir = '$PSEUDO_DIR/',
> outdir='$TMP_DIR/'
>  /
>  
> ibrav= 0,
> nat= 16,
> ntyp= 1,
> ecutwfc=50.0,
>ecutrho = 430,
>occupations='smearing',
>smearing='marzari-vanderbilt',
>degauss=0.02
>starting_magnetization(1) = 0.7,
>  /
>  
> conv_thr =  1.0d-12
>   /
> ATOMIC_SPECIES
>  Zr  91.22  Zr.pz-spn-kjpaw_psl.1.0.0.UPF
> ATOMIC_POSITIONS (angstrom)
> Zr 0.00 1.870038 1.289000
> Zr 3.239000 3.740075 9.023001
> Zr 1.619500 4.675094 1.289000
> Zr 1.619500 0.935019 9.023001
> Zr -1.619500 4.675094 1.289000
> Zr 4.858500 0.935019 9.023001
> Zr 3.239000 3.740075 3.867000
> Zr 1.619500 0.935019 3.867000
> Zr 4.858500 0.935019 3.867000
> Zr 0.00 1.870038 6.445000
> Zr 1.619500 4.675094 6.445000
> Zr -1.619500 4.675094 6.445000
> Zr 3.239000 1.870038 1.289000
> Zr 0.00 3.740075 9.023001
> Zr 0.00 3.740075 3.867000
> Zr 3.239000 1.870038 6.445000
> /
> CELL_PARAMETERS (ANGSTROM)
> 6.4780001640 0.00 0.00
> -3.239820 5.6101127078 0.00
> 0.00 0.00 10.3120002747
> /
> K_POINTS AUTOMATIC
> 5 5 3 0 0 0
> EOF
>
> Can you kindly let me know why I am getting the following error:
>
> from card_atomic_positions : error # 2
>  two occurrences
>
> I will be grateful if you can help me in solving the problem.
>
> Thanks,
> Regards,
> krish
> --
> Dr. Krishnendu Mukherjee,
>
> Principal Scientist,
> CSIR-NML,
> Jamshedpur.
>
> ___
> Pw_forum mailing list
> Pw_forum@pwscf.org
> http://pwscf.org/mailman/listinfo/pw_forum
>



-- 
Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222
___
Pw_forum mailing list
Pw_forum@pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum

[Pw_forum] Zr supercell with ibrav=4

2018-02-02 Thread Krishnendu Mukherjee 
Dear experts,

 I am interested in calculation of elastic constants of Zr using a
supercell of 2*2*2. I created this supercell in VESTA, using Space group
No. 194, P 63/m m c. For the unit cell structure Parameters I used:

0.33 0.67 0.25
and
0.67 0.33 0.75

I have input the atomic positions into the following input:


calculation = 'scf'
restart_mode='from_scratch',
prefix='zr',
tstress = .true.,
   tprnfor = .true.,
pseudo_dir = '/home/krishna/QE/qe-6.2/pseudo/',
outdir='/home/krishna/QE/qe-6.2/tempdir/'
 /
 
ibrav=  4,
celldm(1) =12.241645,
celldm(3) = 1.59185,
nat= 16,
ntyp= 1,
ecutwfc=50.0,
   ecutrho = 430,
   occupations='smearing',
   smearing='marzari-vanderbilt',
   degauss=0.02
   starting_magnetization(1) = 0.7,
 /
 
conv_thr =  1.0d-12
 /
ATOMIC_SPECIES
 Zr  91.22  Zr.pz-spn-kjpaw_psl.1.0.0.UPF
ATOMIC_POSITIONS (angstrom)
Zr0.001.8700381.289000
Zr3.2390003.7400759.023001
Zr1.6195004.6750941.289000
Zr1.6195000.9350199.023001
Zr   -1.6195004.6750941.289000
Zr4.8585000.9350199.023001
Zr3.2390003.7400753.867000
Zr1.6195000.9350193.867000
Zr4.8585000.9350193.867000
Zr0.001.8700386.445000
Zr1.6195004.6750946.445000
Zr   -1.6195004.6750946.445000
Zr3.2390001.8700381.289000
Zr0.003.7400759.023001
Zr0.003.7400753.867000
Zr3.2390001.8700386.445000
K_POINTS AUTOMATIC
5 5 3 0 0 0

However, in out.1_0, in notice that

Space group nymber  164

Is it an error, because I generated the supercell using space group number
194?

 If it is an error can you please let me know, how to modify the input?

However, when I ran the program with an unit cell of two atoms the space
group number was rightly identified as 194.

Thanks,
Best regards,
Krish

-- 
Dr. Krishnendu Mukherjee,

Principal Scientist,
CSIR-NML,
Jamshedpur.
___
Pw_forum mailing list
Pw_forum@pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum

[Pw_forum] Zr supercell with ibrav=0

2018-02-02 Thread Krishnendu Mukherjee 
Dear experts,

 I am interested in calculation of elastic constants of Zr using a
supercell of 2*2*2. I have used ibrav=0. I used the following input:


cat > thermo_control << EOF
 _THERMO
  what='mur_lc_elastic_constants',
  frozen_ions=.FALSE.
 /
EOF

cat > zr.elastic.in << EOF
 
calculation = 'scf'
restart_mode='from_scratch',
prefix='zr',
tstress = .true.,
   tprnfor = .true.,
pseudo_dir = '$PSEUDO_DIR/',
outdir='$TMP_DIR/'
 /
 
ibrav= 0,
nat= 16,
ntyp= 1,
ecutwfc=50.0,
   ecutrho = 430,
   occupations='smearing',
   smearing='marzari-vanderbilt',
   degauss=0.02
   starting_magnetization(1) = 0.7,
 /
 
conv_thr =  1.0d-12
  /
ATOMIC_SPECIES
 Zr  91.22  Zr.pz-spn-kjpaw_psl.1.0.0.UPF
ATOMIC_POSITIONS (angstrom)
Zr 0.00 1.870038 1.289000
Zr 3.239000 3.740075 9.023001
Zr 1.619500 4.675094 1.289000
Zr 1.619500 0.935019 9.023001
Zr -1.619500 4.675094 1.289000
Zr 4.858500 0.935019 9.023001
Zr 3.239000 3.740075 3.867000
Zr 1.619500 0.935019 3.867000
Zr 4.858500 0.935019 3.867000
Zr 0.00 1.870038 6.445000
Zr 1.619500 4.675094 6.445000
Zr -1.619500 4.675094 6.445000
Zr 3.239000 1.870038 1.289000
Zr 0.00 3.740075 9.023001
Zr 0.00 3.740075 3.867000
Zr 3.239000 1.870038 6.445000
/
CELL_PARAMETERS (ANGSTROM)
6.4780001640 0.00 0.00
-3.239820 5.6101127078 0.00
0.00 0.00 10.3120002747
/
K_POINTS AUTOMATIC
5 5 3 0 0 0
EOF

Can you kindly let me know why I am getting the following error:

from card_atomic_positions : error # 2
 two occurrences

I will be grateful if you can help me in solving the problem.

Thanks,
Regards,
krish
-- 
Dr. Krishnendu Mukherjee,

Principal Scientist,
CSIR-NML,
Jamshedpur.
___
Pw_forum mailing list
Pw_forum@pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum