Re: [QE-users] Zero padding FFT

[Sonu Kumar]

>
> Hi users,
>
> For a given orbital, coefficients in g-space are defined up to 4*ecutwfc,
> a sphere. To get to the reciprocal space FFT grid, a box, do we place zeros
> everywhere else (outside the sphere but inside the FFT grid)?
>

Yes, see developer manual, section 6.1. Note the sphere is inscribed inside
the FFT grid.

*SKumar |  PhD.*

>
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[QE-users] Zero padding FFT

[Andrew Xu]

Hi users,

For a given orbital, coefficients in g-space are defined up to 4*ecutwfc, a
sphere. To get to the reciprocal space FFT grid, a box, do we place zeros
everywhere else (outside the sphere but inside the FFT grid)?

If so, do you know where that is done in the code -- the closest I found is
ggen in recvec_subs.f90, but that seems to only generate the G-vectors?

Best,
Andrew
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Re: [QE-users] [External Email] (no subject)

[Hari Paudyal]

Hi Peshal,

You can play with the following four parameters; cut off (ecutwfc and hence
ecutrho),  conv_thr,  k mesh, and mixing_beta. Usually, I ignore this
warning and should not cause a problem if it is not present in the last
step of the scf calculation.

Best,
Hari Paudyal

On Thu, Nov 12, 2020 at 3:28 PM Peshal Karki  wrote:

> Hello,
> I was doing an nscf calculation after getting  a smooth output from scf
> calculation of cubic CsPbI3 structure. But I encountered an error in the
> output file of nscf calculation as below.
>
>  Error in routine c_bands (1):
>  too many bands are not converged
>
> Then I tried increasing ecutwfc value and decreasing conv_thr but it did
> not help. Then I changed the diagonalization from 'david' to 'cg'. Though
> it finished the nscf calculation and showed the Fermi energy but still many
> lines in output saying
>
>  c_bands:  2 eigenvalues not converged
>  c_bands:  3 eigenvalues not converged
>  c_bands:  3 eigenvalues not converged
>  c_bands:  2 eigenvalues not converged
>  c_bands:  2 eigenvalues not converged
>  c_bands:  2 eigenvalues not converged
>  c_bands:  2 eigenvalues not converged
>  c_bands:  2 eigenvalues not converged
>  c_bands:  4 eigenvalues not converged
>  c_bands:  2 eigenvalues not converged
>
> Please help me. What should I do ?
> I have attached the nscf input file with cg diagonalisation.
>
> Thank you.
>
> With regards
> Peshal Karki
>
>
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[QE-users] (no subject)

[Peshal Karki]

Hello,
I was doing an nscf calculation after getting  a smooth output from scf
calculation of cubic CsPbI3 structure. But I encountered an error in the
output file of nscf calculation as below.

 Error in routine c_bands (1):
 too many bands are not converged

Then I tried increasing ecutwfc value and decreasing conv_thr but it did
not help. Then I changed the diagonalization from 'david' to 'cg'. Though
it finished the nscf calculation and showed the Fermi energy but still many
lines in output saying

 c_bands:  2 eigenvalues not converged
 c_bands:  3 eigenvalues not converged
 c_bands:  3 eigenvalues not converged
 c_bands:  2 eigenvalues not converged
 c_bands:  2 eigenvalues not converged
 c_bands:  2 eigenvalues not converged
 c_bands:  2 eigenvalues not converged
 c_bands:  2 eigenvalues not converged
 c_bands:  4 eigenvalues not converged
 c_bands:  2 eigenvalues not converged

Please help me. What should I do ?
I have attached the nscf input file with cg diagonalisation.

Thank you.

With regards
Peshal Karki


nscf.in
Description: Binary data
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Re: [QE-users] Dangling bonds with CdS

[Giuseppe Mattioli]

Dear Kumar
There is some sort of misunderstanding here. If you remove one (S or  
Cd) atom, you create a (S or Cd) vacancy, which is a point defect and  
is not generally referred to as "dangling bond", even if its formation  
may involve the creation of internal dangling bonds. First of all you  
should use a supercell (I would say at least a 2x2x2 64-atom  
supercell) to investigate the properties of a vacancy, because in a  
1x1x1 simple cubic cell you would have an unphysical 25% concentration  
of vacancies. You don't need to have particular care in the simulation  
(e.g. use of different pseudopotentials), but try to compare results  
obtained by relaxing the fully symmetric system and a less symmetric  
system obtained by very small (0.01 A) and randomized displacements of  
atoms in the supercell (by hand or by using some tool such as atomsk).  
Generally the latter starting configuration ensures the possibility  
that the vacancy site relaxes its geometry along less symmetric (and  
sometimes more stable) paths.

HTH
Giuseppe


Quoting "Dr. SUNIL KUMAR" :


Thank you for your quick response.
To create a dangling bond, I need to remove one atom of Cd (or S) form
periodic CdS system. Is it correct method to create a Dangling bond?
Dr. Sunil Kumar
Ph.D (Chemical Engg. IIT Delhi)
M.Tech (Chemical Engg. IIT Delhi)
B.Tech (Chemical Engg. IET-CSJMU Kanpur)
Scientist-C and Assistant Professor
CSIR-National Metallurgical Laboratory Jamshedpur-831007
http://www.nmlindia.org/
https://scholar.google.co.in/citations?user=OchYqugJ&hl=en&oi=sra



On Thu, Nov 12, 2020 at 10:28 PM Giuseppe Mattioli <
giuseppe.matti...@ism.cnr.it> wrote:



Dear Kumar
In your attached file there is a correct and fully periodic CdS
zincblend structure. I don't see any dangling bond.

  >> I have one more question. Is it sufficient to remove one atom Cd (or
S)
>> form CdS crystal

To obtain what?

>> i need to modify/regenerate pseudo-potential file
>> to calculate properties related to Dangling bond during DFT simulation?

No, you don't

HTH
Giuseppe

Quoting "Dr. SUNIL KUMAR" :

> I have carried out some dft simulations as attached file.
> Dr. Sunil Kumar
> Ph.D (Chemical Engg. IIT Delhi)
> M.Tech (Chemical Engg. IIT Delhi)
> B.Tech (Chemical Engg. IET-CSJMU Kanpur)
> Scientist-C and Assistant Professor
> CSIR-National Metallurgical Laboratory Jamshedpur-831007
> http://www.nmlindia.org/
> https://scholar.google.co.in/citations?user=OchYqugJ&hl=en&oi=sra
>
>
>
> On Thu, Nov 12, 2020 at 10:10 PM Dr. SUNIL KUMAR 
> wrote:
>
>> Thankyou for your explanation regarding Dangling bond.
>> I have one more question. Is it sufficient to remove one atom Cd (or  S)
>> form CdS crystal or also i need to modify/regenerate pseudo-potential
file
>> to calculate properties related to Dangling bond during DFT simulation?
>> thanks
>> Dr. Sunil Kumar
>> Ph.D (Chemical Engg. IIT Delhi)
>> M.Tech (Chemical Engg. IIT Delhi)
>> B.Tech (Chemical Engg. IET-CSJMU Kanpur)
>> Scientist-C and Assistant Professor
>> CSIR-National Metallurgical Laboratory Jamshedpur-831007
>> http://www.nmlindia.org/
>> https://scholar.google.co.in/citations?user=OchYqugJ&hl=en&oi=sra
>>
>>
>>
>> On Thu, Nov 12, 2020 at 8:53 PM Giuseppe Mattioli <
>> giuseppe.matti...@ism.cnr.it> wrote:
>>
>>>
>>> Dear Tamas and Kumar
>>> only to add a few words to the (very pertinent) Tamas' reply:
>>> 1) Semiconductor surfaces can undergoes very complex reconstruction
>>> patterns (the 7x7 Si(111) reconstruction being likely the most famous
>>> case). You will not find complex reconstructions by simply cutting and
>>> relaxing the slabs, and it is best to search in experimental
>>> literature, in order not to waste time simulating unphysical systems
>>> which are never going to converge.
>>>
>>> 2) Dangling bonds can be also created inside crystals (e.g, by atomic
>>> vacancies). It is not clear what kind of dangling bond you are
>>> referring to.
>>>
>>> 3) There is an additional problem when you want to simulate some
>>> process happening on the surface (e.g., adsorptions of molecules).
>>> Various strategies can be used, including the saturation of dangling
>>> bonds on one side of the slab by "pseudohydrogen atoms" having
>>> fractional charge mimicking that of the pristine bond broken by
>>> cleavage.
>>>
>>> This said, you should "make an educated guess" [cit. John Malkovich
>>> :-)] and ask less general questions which may (or may not) generate
>>> more useful answers.
>>>
>>> HTH
>>> Giuseppe
>>>
>>> Quoting Tamas Karpati :
>>>
>>> > Dear Dr. Kumar,
>>> >
>>> > I guess dangling bonds are written about in DFT textbooks of the
>>> > physicists' style
>>> > (in quantum chemistry, ie. clusters rather than crystals, it is less
>>> > of a problem).
>>> >
>>> > The typical problem is that you cut chemical bonds when cleave the
>>> > crystal (to get a slab).
>>> > In case of bonds originally dominated by ionic (Coulomb) forces you
>>> > may still have a closed
>>> > shell syste

Re: [QE-users] npw vs npwx

[Andrew Xu]

Thank you both!
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Re: [QE-users] Incorrect identification+generations of atoms in specialpositions (space_group options used).

[José C . Conesa]

Thanks, Paolo. I will try whay you say. Still, a similar thing might 
happen with other structures... I will try to tweak the last decimal(s), 
if I see any problem.


El 12/11/2020 a las 17:50, Paolo Giannozzi escribió:
On Thu, Nov 12, 2020 at 1:34 PM José Carlos Conesa Cegarra 
mailto:jccon...@icp.csic.es>> wrote:


Last 11th of september I sent a similar question, but the answer,
provided by Paolo Giannozzi, did not clarify much. I can say that
in that occasion I was using qe-6.5. Should I use qe -6.6?


not necessarily so: the Wyckoff machinery is unchanged since two 
years, to the best of my knowledge. Instead you should have read my 
unclear answer again, or just the last sentence: /I suspect that one 
or more of the Ge positions are not exact Wyckoff positions but very 
close to them/, and verified it. There are just three Wyckoff Ge 
positions, and since atomic positions are expanded in the order they 
are provided, the problematic one seems to be the second:

  Ge   0.0   -0.49511   -0.50488
that looks almost like (0,-x,x). Almost. With 0.0 -0.49511 
-0.50489 you get 56 atoms. not 59.


Paolo
//

Regards,

José C. Conesa

El 12/11/2020 a las 11:30, Pietro Delugas escribió:


Hi

 which version of the code are you using ?

with qe-6.6 using  your parameters I got two positions

  site n. atom  positions (alat units)

 1   Zn tau(   1) = (   0.4873906   2.5406690
1.4472625  )

 2   Zn tau(   2) = (   0.3343454   0.8468897
0.4736359  )

With alat = 11.5468  a.u.

alat = 11.5468  a.u.

ibrav=-12

hope it helps

greetings  - Pietro

Sent from Mail 
for Windows 10

*From: *Michal Husak 
*Sent: *Thursday, November 12, 2020 10:34 AM
*To: *users@lists.quantum-espresso.org

*Subject: *[QE-users] Incorrect identification+generations of
atoms in specialpositions (space_group options used).

I


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https://lists.quantum-espresso.org/mailman/listinfo/users  



-- 
José C. Conesa

Research Professor
Instituto de Catálisis y Petroleoquímica, CSIC
Marie Curie, 2; Campus de Cantoblanco
28028 Madrid (Spain)
Telef. +34 915854766

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--
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


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--
José C. Conesa
Research Professor
Instituto de Catálisis y Petroleoquímica, CSIC
Marie Curie 2, Cantoblanco
28049 Madrid, Spain
Tel. (+34)915854766

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Re: [QE-users] Dangling bonds with CdS

[Dr. SUNIL KUMAR]

Thank you for your quick response.
To create a dangling bond, I need to remove one atom of Cd (or S) form
periodic CdS system. Is it correct method to create a Dangling bond?
Dr. Sunil Kumar
Ph.D (Chemical Engg. IIT Delhi)
M.Tech (Chemical Engg. IIT Delhi)
B.Tech (Chemical Engg. IET-CSJMU Kanpur)
Scientist-C and Assistant Professor
CSIR-National Metallurgical Laboratory Jamshedpur-831007
http://www.nmlindia.org/
https://scholar.google.co.in/citations?user=OchYqugJ&hl=en&oi=sra



On Thu, Nov 12, 2020 at 10:28 PM Giuseppe Mattioli <
giuseppe.matti...@ism.cnr.it> wrote:

>
> Dear Kumar
> In your attached file there is a correct and fully periodic CdS
> zincblend structure. I don't see any dangling bond.
>
>   >> I have one more question. Is it sufficient to remove one atom Cd (or
> S)
> >> form CdS crystal
>
> To obtain what?
>
> >> i need to modify/regenerate pseudo-potential file
> >> to calculate properties related to Dangling bond during DFT simulation?
>
> No, you don't
>
> HTH
> Giuseppe
>
> Quoting "Dr. SUNIL KUMAR" :
>
> > I have carried out some dft simulations as attached file.
> > Dr. Sunil Kumar
> > Ph.D (Chemical Engg. IIT Delhi)
> > M.Tech (Chemical Engg. IIT Delhi)
> > B.Tech (Chemical Engg. IET-CSJMU Kanpur)
> > Scientist-C and Assistant Professor
> > CSIR-National Metallurgical Laboratory Jamshedpur-831007
> > http://www.nmlindia.org/
> > https://scholar.google.co.in/citations?user=OchYqugJ&hl=en&oi=sra
> >
> >
> >
> > On Thu, Nov 12, 2020 at 10:10 PM Dr. SUNIL KUMAR 
> > wrote:
> >
> >> Thankyou for your explanation regarding Dangling bond.
> >> I have one more question. Is it sufficient to remove one atom Cd (or  S)
> >> form CdS crystal or also i need to modify/regenerate pseudo-potential
> file
> >> to calculate properties related to Dangling bond during DFT simulation?
> >> thanks
> >> Dr. Sunil Kumar
> >> Ph.D (Chemical Engg. IIT Delhi)
> >> M.Tech (Chemical Engg. IIT Delhi)
> >> B.Tech (Chemical Engg. IET-CSJMU Kanpur)
> >> Scientist-C and Assistant Professor
> >> CSIR-National Metallurgical Laboratory Jamshedpur-831007
> >> http://www.nmlindia.org/
> >> https://scholar.google.co.in/citations?user=OchYqugJ&hl=en&oi=sra
> >>
> >>
> >>
> >> On Thu, Nov 12, 2020 at 8:53 PM Giuseppe Mattioli <
> >> giuseppe.matti...@ism.cnr.it> wrote:
> >>
> >>>
> >>> Dear Tamas and Kumar
> >>> only to add a few words to the (very pertinent) Tamas' reply:
> >>> 1) Semiconductor surfaces can undergoes very complex reconstruction
> >>> patterns (the 7x7 Si(111) reconstruction being likely the most famous
> >>> case). You will not find complex reconstructions by simply cutting and
> >>> relaxing the slabs, and it is best to search in experimental
> >>> literature, in order not to waste time simulating unphysical systems
> >>> which are never going to converge.
> >>>
> >>> 2) Dangling bonds can be also created inside crystals (e.g, by atomic
> >>> vacancies). It is not clear what kind of dangling bond you are
> >>> referring to.
> >>>
> >>> 3) There is an additional problem when you want to simulate some
> >>> process happening on the surface (e.g., adsorptions of molecules).
> >>> Various strategies can be used, including the saturation of dangling
> >>> bonds on one side of the slab by "pseudohydrogen atoms" having
> >>> fractional charge mimicking that of the pristine bond broken by
> >>> cleavage.
> >>>
> >>> This said, you should "make an educated guess" [cit. John Malkovich
> >>> :-)] and ask less general questions which may (or may not) generate
> >>> more useful answers.
> >>>
> >>> HTH
> >>> Giuseppe
> >>>
> >>> Quoting Tamas Karpati :
> >>>
> >>> > Dear Dr. Kumar,
> >>> >
> >>> > I guess dangling bonds are written about in DFT textbooks of the
> >>> > physicists' style
> >>> > (in quantum chemistry, ie. clusters rather than crystals, it is less
> >>> > of a problem).
> >>> >
> >>> > The typical problem is that you cut chemical bonds when cleave the
> >>> > crystal (to get a slab).
> >>> > In case of bonds originally dominated by ionic (Coulomb) forces you
> >>> > may still have a closed
> >>> > shell system (ie. just paired electrons) after the cleavage. As for
> >>> > the more covalent
> >>> > bonds, radicals are generated and such high multiplicity electronic
> >>> > states (large
> >>> > magnetizations in terms of QE/PW.x inputs) reorganize to the more
> >>> > stable closed
> >>> > shell systems by changing geometry (you need to reoptimize their
> >>> > geometry) and
> >>> > simultaneously forming new bonds. This way every few surface atom
> >>> > pairs get closer
> >>> > and such bonds form, ie. bonds that were dangling after you made the
> >>> > cut are now
> >>> > in covalent bonds again (no dangling anymore).
> >>> > This you can model by reoptimizing with low (not sure but probably
> >>> > zero) magnetization.
> >>> >
> >>> > CdS has strong bonds carrying both ionic (maybe less) and covalent
> >>> nature
> >>> > (more of the latter). Depending on the cleaving plane you applied to

Re: [QE-users] Dangling bonds with CdS

[Giuseppe Mattioli]

Dear Kumar
In your attached file there is a correct and fully periodic CdS  
zincblend structure. I don't see any dangling bond.


 >> I have one more question. Is it sufficient to remove one atom Cd (or  S)

form CdS crystal


To obtain what?


i need to modify/regenerate pseudo-potential file
to calculate properties related to Dangling bond during DFT simulation?


No, you don't

HTH
Giuseppe

Quoting "Dr. SUNIL KUMAR" :


I have carried out some dft simulations as attached file.
Dr. Sunil Kumar
Ph.D (Chemical Engg. IIT Delhi)
M.Tech (Chemical Engg. IIT Delhi)
B.Tech (Chemical Engg. IET-CSJMU Kanpur)
Scientist-C and Assistant Professor
CSIR-National Metallurgical Laboratory Jamshedpur-831007
http://www.nmlindia.org/
https://scholar.google.co.in/citations?user=OchYqugJ&hl=en&oi=sra



On Thu, Nov 12, 2020 at 10:10 PM Dr. SUNIL KUMAR 
wrote:


Thankyou for your explanation regarding Dangling bond.
I have one more question. Is it sufficient to remove one atom Cd (or  S)
form CdS crystal or also i need to modify/regenerate pseudo-potential file
to calculate properties related to Dangling bond during DFT simulation?
thanks
Dr. Sunil Kumar
Ph.D (Chemical Engg. IIT Delhi)
M.Tech (Chemical Engg. IIT Delhi)
B.Tech (Chemical Engg. IET-CSJMU Kanpur)
Scientist-C and Assistant Professor
CSIR-National Metallurgical Laboratory Jamshedpur-831007
http://www.nmlindia.org/
https://scholar.google.co.in/citations?user=OchYqugJ&hl=en&oi=sra



On Thu, Nov 12, 2020 at 8:53 PM Giuseppe Mattioli <
giuseppe.matti...@ism.cnr.it> wrote:



Dear Tamas and Kumar
only to add a few words to the (very pertinent) Tamas' reply:
1) Semiconductor surfaces can undergoes very complex reconstruction
patterns (the 7x7 Si(111) reconstruction being likely the most famous
case). You will not find complex reconstructions by simply cutting and
relaxing the slabs, and it is best to search in experimental
literature, in order not to waste time simulating unphysical systems
which are never going to converge.

2) Dangling bonds can be also created inside crystals (e.g, by atomic
vacancies). It is not clear what kind of dangling bond you are
referring to.

3) There is an additional problem when you want to simulate some
process happening on the surface (e.g., adsorptions of molecules).
Various strategies can be used, including the saturation of dangling
bonds on one side of the slab by "pseudohydrogen atoms" having
fractional charge mimicking that of the pristine bond broken by
cleavage.

This said, you should "make an educated guess" [cit. John Malkovich
:-)] and ask less general questions which may (or may not) generate
more useful answers.

HTH
Giuseppe

Quoting Tamas Karpati :

> Dear Dr. Kumar,
>
> I guess dangling bonds are written about in DFT textbooks of the
> physicists' style
> (in quantum chemistry, ie. clusters rather than crystals, it is less
> of a problem).
>
> The typical problem is that you cut chemical bonds when cleave the
> crystal (to get a slab).
> In case of bonds originally dominated by ionic (Coulomb) forces you
> may still have a closed
> shell system (ie. just paired electrons) after the cleavage. As for
> the more covalent
> bonds, radicals are generated and such high multiplicity electronic
> states (large
> magnetizations in terms of QE/PW.x inputs) reorganize to the more
> stable closed
> shell systems by changing geometry (you need to reoptimize their
> geometry) and
> simultaneously forming new bonds. This way every few surface atom
> pairs get closer
> and such bonds form, ie. bonds that were dangling after you made the
> cut are now
> in covalent bonds again (no dangling anymore).
> This you can model by reoptimizing with low (not sure but probably
> zero) magnetization.
>
> CdS has strong bonds carrying both ionic (maybe less) and covalent
nature
> (more of the latter). Depending on the cleaving plane you applied to
> the crystal,
> you have a high chance to see new Cd-S bonds form. Less probable is
> that you'll
> have Cd-Cd bonds or -S-S- bridges but these are also possible if your
surface
> atoms are situated so.
>
> Another way of treating such systems is to keep the structure as you
have cut
> from the crystal and apply a high starting_magnetization in a PW/relax
job.
>
> Be careful, though, as the chemistries you describe by the above two
methods
> (reorganization vs. high magnetization) are living in two distant
Universes.
>
> I hope this helps,
>   Tamas
>
> On Thu, Nov 12, 2020 at 8:13 AM Dr. SUNIL KUMAR
>  wrote:
>>
>> Dear QE developers and Users.
>> I am struggling to carry out a DFT simulation of CdS with dangling
>> bonds using Quantum Espresso DFT packages. I am unable to
>> understand the phenomena of Dangling bond and its implementation in
>> QE DFT simulation. I would like to request to you all, kindly
>> suggest me some tutorial and sample QE scripts for CdS with
>> Dangling bonds. I will be grateful to you.
>>
>> Thanks
>> With regards
>> SUNIL
>> Dr. Sunil Kumar
>> Ph.D (Chemical Engg. 

Re: [QE-users] Incorrect identification+generations of atoms in specialpositions (space_group options used).

[Paolo Giannozzi]

On Thu, Nov 12, 2020 at 1:34 PM José Carlos Conesa Cegarra <
jccon...@icp.csic.es> wrote:

Last 11th of september I sent a similar question, but the answer, provided
> by Paolo Giannozzi, did not clarify much. I can say that in that occasion I
> was using qe-6.5. Should I use qe -6.6?
>

not necessarily so: the Wyckoff machinery is unchanged since two years, to
the best of my knowledge. Instead you should have read my unclear answer
again, or just the last sentence: *I suspect that one or more of the Ge
positions are not exact Wyckoff positions but very close to them*, and
verified it. There are just three Wyckoff Ge positions, and since atomic
positions are expanded in the order they are provided, the problematic one
seems to be the second:
  Ge   0.0   -0.49511   -0.50488
that looks almost like (0,-x,x). Almost. With 0.0 -0.49511 -0.50489 you
get 56 atoms. not 59.

Paolo

> Regards,
>
> José C. Conesa
> El 12/11/2020 a las 11:30, Pietro Delugas escribió:
>
> Hi
>
>  which version of the code are you using ?
>
>
>
> with qe-6.6 using  your parameters I got two positions
>
>
>
>   site n. atom  positions (alat units)
>
>  1   Zn  tau(   1) = (   0.4873906   2.5406690
> 1.4472625  )
>
>  2   Zn  tau(   2) = (   0.3343454   0.8468897
> 0.4736359  )
>
>
>
> With alat = 11.5468  a.u.
>
>
>
> alat = 11.5468  a.u.
>
>
>
> ibrav=-12
>
>
>
>
>
> hope it helps
>
> greetings  - Pietro
>
>
>
>
>
> Sent from Mail  for
> Windows 10
>
>
>
> *From: *Michal Husak 
> *Sent: *Thursday, November 12, 2020 10:34 AM
> *To: *users@lists.quantum-espresso.org
> *Subject: *[QE-users] Incorrect identification+generations of atoms in
> specialpositions (space_group options used).
>
>
>
> I
>
>
>
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> Quantum ESPRESSO is supported by MaX (www.max-centre.eu)
> users mailing list 
> users@lists.quantum-espresso.orghttps://lists.quantum-espresso.org/mailman/listinfo/users
>
> --
> José C. Conesa
> Research Professor
> Instituto de Catálisis y Petroleoquímica, CSIC
> Marie Curie, 2; Campus de Cantoblanco
> 28028 Madrid (Spain)
> Telef. +34 915854766
>
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-- 
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
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Re: [QE-users] Dangling bonds with CdS

[Dr. SUNIL KUMAR]

I have carried out some dft simulations as attached file.
Dr. Sunil Kumar
Ph.D (Chemical Engg. IIT Delhi)
M.Tech (Chemical Engg. IIT Delhi)
B.Tech (Chemical Engg. IET-CSJMU Kanpur)
Scientist-C and Assistant Professor
CSIR-National Metallurgical Laboratory Jamshedpur-831007
http://www.nmlindia.org/
https://scholar.google.co.in/citations?user=OchYqugJ&hl=en&oi=sra



On Thu, Nov 12, 2020 at 10:10 PM Dr. SUNIL KUMAR 
wrote:

> Thankyou for your explanation regarding Dangling bond.
> I have one more question. Is it sufficient to remove one atom Cd (or  S)
> form CdS crystal or also i need to modify/regenerate pseudo-potential file
> to calculate properties related to Dangling bond during DFT simulation?
> thanks
> Dr. Sunil Kumar
> Ph.D (Chemical Engg. IIT Delhi)
> M.Tech (Chemical Engg. IIT Delhi)
> B.Tech (Chemical Engg. IET-CSJMU Kanpur)
> Scientist-C and Assistant Professor
> CSIR-National Metallurgical Laboratory Jamshedpur-831007
> http://www.nmlindia.org/
> https://scholar.google.co.in/citations?user=OchYqugJ&hl=en&oi=sra
>
>
>
> On Thu, Nov 12, 2020 at 8:53 PM Giuseppe Mattioli <
> giuseppe.matti...@ism.cnr.it> wrote:
>
>>
>> Dear Tamas and Kumar
>> only to add a few words to the (very pertinent) Tamas' reply:
>> 1) Semiconductor surfaces can undergoes very complex reconstruction
>> patterns (the 7x7 Si(111) reconstruction being likely the most famous
>> case). You will not find complex reconstructions by simply cutting and
>> relaxing the slabs, and it is best to search in experimental
>> literature, in order not to waste time simulating unphysical systems
>> which are never going to converge.
>>
>> 2) Dangling bonds can be also created inside crystals (e.g, by atomic
>> vacancies). It is not clear what kind of dangling bond you are
>> referring to.
>>
>> 3) There is an additional problem when you want to simulate some
>> process happening on the surface (e.g., adsorptions of molecules).
>> Various strategies can be used, including the saturation of dangling
>> bonds on one side of the slab by "pseudohydrogen atoms" having
>> fractional charge mimicking that of the pristine bond broken by
>> cleavage.
>>
>> This said, you should "make an educated guess" [cit. John Malkovich
>> :-)] and ask less general questions which may (or may not) generate
>> more useful answers.
>>
>> HTH
>> Giuseppe
>>
>> Quoting Tamas Karpati :
>>
>> > Dear Dr. Kumar,
>> >
>> > I guess dangling bonds are written about in DFT textbooks of the
>> > physicists' style
>> > (in quantum chemistry, ie. clusters rather than crystals, it is less
>> > of a problem).
>> >
>> > The typical problem is that you cut chemical bonds when cleave the
>> > crystal (to get a slab).
>> > In case of bonds originally dominated by ionic (Coulomb) forces you
>> > may still have a closed
>> > shell system (ie. just paired electrons) after the cleavage. As for
>> > the more covalent
>> > bonds, radicals are generated and such high multiplicity electronic
>> > states (large
>> > magnetizations in terms of QE/PW.x inputs) reorganize to the more
>> > stable closed
>> > shell systems by changing geometry (you need to reoptimize their
>> > geometry) and
>> > simultaneously forming new bonds. This way every few surface atom
>> > pairs get closer
>> > and such bonds form, ie. bonds that were dangling after you made the
>> > cut are now
>> > in covalent bonds again (no dangling anymore).
>> > This you can model by reoptimizing with low (not sure but probably
>> > zero) magnetization.
>> >
>> > CdS has strong bonds carrying both ionic (maybe less) and covalent
>> nature
>> > (more of the latter). Depending on the cleaving plane you applied to
>> > the crystal,
>> > you have a high chance to see new Cd-S bonds form. Less probable is
>> > that you'll
>> > have Cd-Cd bonds or -S-S- bridges but these are also possible if your
>> surface
>> > atoms are situated so.
>> >
>> > Another way of treating such systems is to keep the structure as you
>> have cut
>> > from the crystal and apply a high starting_magnetization in a PW/relax
>> job.
>> >
>> > Be careful, though, as the chemistries you describe by the above two
>> methods
>> > (reorganization vs. high magnetization) are living in two distant
>> Universes.
>> >
>> > I hope this helps,
>> >   Tamas
>> >
>> > On Thu, Nov 12, 2020 at 8:13 AM Dr. SUNIL KUMAR
>> >  wrote:
>> >>
>> >> Dear QE developers and Users.
>> >> I am struggling to carry out a DFT simulation of CdS with dangling
>> >> bonds using Quantum Espresso DFT packages. I am unable to
>> >> understand the phenomena of Dangling bond and its implementation in
>> >> QE DFT simulation. I would like to request to you all, kindly
>> >> suggest me some tutorial and sample QE scripts for CdS with
>> >> Dangling bonds. I will be grateful to you.
>> >>
>> >> Thanks
>> >> With regards
>> >> SUNIL
>> >> Dr. Sunil Kumar
>> >> Ph.D (Chemical Engg. IIT Delhi)
>> >> M.Tech (Chemical Engg. IIT Delhi)
>> >> B.Tech (Chemical Engg. IET-CSJMU Kanpur)
>> >> Scientist-C and

Re: [QE-users] Dangling bonds with CdS

[Dr. SUNIL KUMAR]

Thankyou for your explanation regarding Dangling bond.
I have one more question. Is it sufficient to remove one atom Cd (or  S)
form CdS crystal or also i need to modify/regenerate pseudo-potential file
to calculate properties related to Dangling bond during DFT simulation?
thanks
Dr. Sunil Kumar
Ph.D (Chemical Engg. IIT Delhi)
M.Tech (Chemical Engg. IIT Delhi)
B.Tech (Chemical Engg. IET-CSJMU Kanpur)
Scientist-C and Assistant Professor
CSIR-National Metallurgical Laboratory Jamshedpur-831007
http://www.nmlindia.org/
https://scholar.google.co.in/citations?user=OchYqugJ&hl=en&oi=sra



On Thu, Nov 12, 2020 at 8:53 PM Giuseppe Mattioli <
giuseppe.matti...@ism.cnr.it> wrote:

>
> Dear Tamas and Kumar
> only to add a few words to the (very pertinent) Tamas' reply:
> 1) Semiconductor surfaces can undergoes very complex reconstruction
> patterns (the 7x7 Si(111) reconstruction being likely the most famous
> case). You will not find complex reconstructions by simply cutting and
> relaxing the slabs, and it is best to search in experimental
> literature, in order not to waste time simulating unphysical systems
> which are never going to converge.
>
> 2) Dangling bonds can be also created inside crystals (e.g, by atomic
> vacancies). It is not clear what kind of dangling bond you are
> referring to.
>
> 3) There is an additional problem when you want to simulate some
> process happening on the surface (e.g., adsorptions of molecules).
> Various strategies can be used, including the saturation of dangling
> bonds on one side of the slab by "pseudohydrogen atoms" having
> fractional charge mimicking that of the pristine bond broken by
> cleavage.
>
> This said, you should "make an educated guess" [cit. John Malkovich
> :-)] and ask less general questions which may (or may not) generate
> more useful answers.
>
> HTH
> Giuseppe
>
> Quoting Tamas Karpati :
>
> > Dear Dr. Kumar,
> >
> > I guess dangling bonds are written about in DFT textbooks of the
> > physicists' style
> > (in quantum chemistry, ie. clusters rather than crystals, it is less
> > of a problem).
> >
> > The typical problem is that you cut chemical bonds when cleave the
> > crystal (to get a slab).
> > In case of bonds originally dominated by ionic (Coulomb) forces you
> > may still have a closed
> > shell system (ie. just paired electrons) after the cleavage. As for
> > the more covalent
> > bonds, radicals are generated and such high multiplicity electronic
> > states (large
> > magnetizations in terms of QE/PW.x inputs) reorganize to the more
> > stable closed
> > shell systems by changing geometry (you need to reoptimize their
> > geometry) and
> > simultaneously forming new bonds. This way every few surface atom
> > pairs get closer
> > and such bonds form, ie. bonds that were dangling after you made the
> > cut are now
> > in covalent bonds again (no dangling anymore).
> > This you can model by reoptimizing with low (not sure but probably
> > zero) magnetization.
> >
> > CdS has strong bonds carrying both ionic (maybe less) and covalent nature
> > (more of the latter). Depending on the cleaving plane you applied to
> > the crystal,
> > you have a high chance to see new Cd-S bonds form. Less probable is
> > that you'll
> > have Cd-Cd bonds or -S-S- bridges but these are also possible if your
> surface
> > atoms are situated so.
> >
> > Another way of treating such systems is to keep the structure as you
> have cut
> > from the crystal and apply a high starting_magnetization in a PW/relax
> job.
> >
> > Be careful, though, as the chemistries you describe by the above two
> methods
> > (reorganization vs. high magnetization) are living in two distant
> Universes.
> >
> > I hope this helps,
> >   Tamas
> >
> > On Thu, Nov 12, 2020 at 8:13 AM Dr. SUNIL KUMAR
> >  wrote:
> >>
> >> Dear QE developers and Users.
> >> I am struggling to carry out a DFT simulation of CdS with dangling
> >> bonds using Quantum Espresso DFT packages. I am unable to
> >> understand the phenomena of Dangling bond and its implementation in
> >> QE DFT simulation. I would like to request to you all, kindly
> >> suggest me some tutorial and sample QE scripts for CdS with
> >> Dangling bonds. I will be grateful to you.
> >>
> >> Thanks
> >> With regards
> >> SUNIL
> >> Dr. Sunil Kumar
> >> Ph.D (Chemical Engg. IIT Delhi)
> >> M.Tech (Chemical Engg. IIT Delhi)
> >> B.Tech (Chemical Engg. IET-CSJMU Kanpur)
> >> Scientist-C and Assistant Professor
> >> CSIR-National Metallurgical Laboratory Jamshedpur-831007
> >> http://www.nmlindia.org/
> >> https://scholar.google.co.in/citations?user=OchYqugJ&hl=en&oi=sra
> >>
> >> ___
> >> Quantum ESPRESSO is supported by MaX (www.max-centre.eu)
> >> users mailing list users@lists.quantum-espresso.org
> >> https://lists.quantum-espresso.org/mailman/listinfo/users
> > ___
> > Quantum ESPRESSO is supported by MaX (www.max-centre.eu)
> > users mailing list u

Re: [QE-users] Dangling bonds with CdS

[Giuseppe Mattioli]

Dear Tamas and Kumar
only to add a few words to the (very pertinent) Tamas' reply:
1) Semiconductor surfaces can undergoes very complex reconstruction  
patterns (the 7x7 Si(111) reconstruction being likely the most famous  
case). You will not find complex reconstructions by simply cutting and  
relaxing the slabs, and it is best to search in experimental  
literature, in order not to waste time simulating unphysical systems  
which are never going to converge.


2) Dangling bonds can be also created inside crystals (e.g, by atomic  
vacancies). It is not clear what kind of dangling bond you are  
referring to.


3) There is an additional problem when you want to simulate some  
process happening on the surface (e.g., adsorptions of molecules).  
Various strategies can be used, including the saturation of dangling  
bonds on one side of the slab by "pseudohydrogen atoms" having  
fractional charge mimicking that of the pristine bond broken by  
cleavage.


This said, you should "make an educated guess" [cit. John Malkovich  
:-)] and ask less general questions which may (or may not) generate  
more useful answers.


HTH
Giuseppe

Quoting Tamas Karpati :


Dear Dr. Kumar,

I guess dangling bonds are written about in DFT textbooks of the
physicists' style
(in quantum chemistry, ie. clusters rather than crystals, it is less
of a problem).

The typical problem is that you cut chemical bonds when cleave the
crystal (to get a slab).
In case of bonds originally dominated by ionic (Coulomb) forces you
may still have a closed
shell system (ie. just paired electrons) after the cleavage. As for
the more covalent
bonds, radicals are generated and such high multiplicity electronic
states (large
magnetizations in terms of QE/PW.x inputs) reorganize to the more  
stable closed
shell systems by changing geometry (you need to reoptimize their  
geometry) and

simultaneously forming new bonds. This way every few surface atom
pairs get closer
and such bonds form, ie. bonds that were dangling after you made the  
cut are now

in covalent bonds again (no dangling anymore).
This you can model by reoptimizing with low (not sure but probably
zero) magnetization.

CdS has strong bonds carrying both ionic (maybe less) and covalent nature
(more of the latter). Depending on the cleaving plane you applied to
the crystal,
you have a high chance to see new Cd-S bonds form. Less probable is  
that you'll

have Cd-Cd bonds or -S-S- bridges but these are also possible if your surface
atoms are situated so.

Another way of treating such systems is to keep the structure as you have cut
from the crystal and apply a high starting_magnetization in a PW/relax job.

Be careful, though, as the chemistries you describe by the above two methods
(reorganization vs. high magnetization) are living in two distant Universes.

I hope this helps,
  Tamas

On Thu, Nov 12, 2020 at 8:13 AM Dr. SUNIL KUMAR  
 wrote:


Dear QE developers and Users.
I am struggling to carry out a DFT simulation of CdS with dangling  
bonds using Quantum Espresso DFT packages. I am unable to  
understand the phenomena of Dangling bond and its implementation in  
QE DFT simulation. I would like to request to you all, kindly  
suggest me some tutorial and sample QE scripts for CdS with  
Dangling bonds. I will be grateful to you.


Thanks
With regards
SUNIL
Dr. Sunil Kumar
Ph.D (Chemical Engg. IIT Delhi)
M.Tech (Chemical Engg. IIT Delhi)
B.Tech (Chemical Engg. IET-CSJMU Kanpur)
Scientist-C and Assistant Professor
CSIR-National Metallurgical Laboratory Jamshedpur-831007
http://www.nmlindia.org/
https://scholar.google.co.in/citations?user=OchYqugJ&hl=en&oi=sra

___
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users mailing list users@lists.quantum-espresso.org
https://lists.quantum-espresso.org/mailman/listinfo/users

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GIUSEPPE MATTIOLI
CNR - ISTITUTO DI STRUTTURA DELLA MATERIA
Via Salaria Km 29,300 - C.P. 10
I-00015 - Monterotondo Scalo (RM)
Mob (*preferred*) +39 373 7305625
Tel + 39 06 90672342 - Fax +39 06 90672316
E-mail: 

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Re: [QE-users] Dangling bonds with CdS

[Tamas Karpati]

Dear Dr. Kumar,

I guess dangling bonds are written about in DFT textbooks of the
physicists' style
(in quantum chemistry, ie. clusters rather than crystals, it is less
of a problem).

The typical problem is that you cut chemical bonds when cleave the
crystal (to get a slab).
In case of bonds originally dominated by ionic (Coulomb) forces you
may still have a closed
shell system (ie. just paired electrons) after the cleavage. As for
the more covalent
bonds, radicals are generated and such high multiplicity electronic
states (large
magnetizations in terms of QE/PW.x inputs) reorganize to the more stable closed
shell systems by changing geometry (you need to reoptimize their geometry) and
simultaneously forming new bonds. This way every few surface atom
pairs get closer
and such bonds form, ie. bonds that were dangling after you made the cut are now
in covalent bonds again (no dangling anymore).
This you can model by reoptimizing with low (not sure but probably
zero) magnetization.

CdS has strong bonds carrying both ionic (maybe less) and covalent nature
(more of the latter). Depending on the cleaving plane you applied to
the crystal,
you have a high chance to see new Cd-S bonds form. Less probable is that you'll
have Cd-Cd bonds or -S-S- bridges but these are also possible if your surface
atoms are situated so.

Another way of treating such systems is to keep the structure as you have cut
from the crystal and apply a high starting_magnetization in a PW/relax job.

Be careful, though, as the chemistries you describe by the above two methods
(reorganization vs. high magnetization) are living in two distant Universes.

I hope this helps,
  Tamas

On Thu, Nov 12, 2020 at 8:13 AM Dr. SUNIL KUMAR  wrote:
>
> Dear QE developers and Users.
> I am struggling to carry out a DFT simulation of CdS with dangling bonds 
> using Quantum Espresso DFT packages. I am unable to understand the phenomena 
> of Dangling bond and its implementation in QE DFT simulation. I would like to 
> request to you all, kindly suggest me some tutorial and sample QE scripts for 
> CdS with Dangling bonds. I will be grateful to you.
>
> Thanks
> With regards
> SUNIL
> Dr. Sunil Kumar
> Ph.D (Chemical Engg. IIT Delhi)
> M.Tech (Chemical Engg. IIT Delhi)
> B.Tech (Chemical Engg. IET-CSJMU Kanpur)
> Scientist-C and Assistant Professor
> CSIR-National Metallurgical Laboratory Jamshedpur-831007
> http://www.nmlindia.org/
> https://scholar.google.co.in/citations?user=OchYqugJ&hl=en&oi=sra
>
> ___
> Quantum ESPRESSO is supported by MaX (www.max-centre.eu)
> users mailing list users@lists.quantum-espresso.org
> https://lists.quantum-espresso.org/mailman/listinfo/users
___
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Re: [QE-users] Incorrect identification+generations of atoms in specialpositions (space_group options used).

[Michal Husak]

Dear C. Conesa

I was afraid I am faced exactly with the same 
problem you mentioned in your contribution ...

But had identified 2 problems on my side instead :
1)  I forget to use uniqueb = .true. => incorrect 
identification of special positions
2) after correcting mistake 1) I had used 
incorrect CIF with multiple inclusion of the same 
atoms  (CSD Mercury Bug/Future

related to molecules completed by symmetry operations).

If you can E-mail me directly (hus...@vscht.cz) your
CIF file, + QE inoput file with potentials in /potential sub directory
I can try to analyze your problem ( I am primary 
a crystallographer teaching symmetry operations e.t.c.) ...


Michal


nguage: es-ES

Dear all,

Last 11th of september I sent a similar 
question, but the answer, provided by Paolo 
Giannozzi, did not clarify much. I can say that 
in that occasion I was using qe-6.5. Should I use qe -6.6?


Regards,

José C. Conesa


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Re: [QE-users] Incorrect identification+generations of atoms inspecialpositions (space_group options used).

[Michal Husak]

Problem solved on my side ...
I apology for disturbing :-).
The CSD Mercury software added to the CIF file 
from some reason some symmetry generated atoms ...
It probably try to save the whole molecule (1/2 
generated by mirror operation) = create incorrect 
cif with duplicated atoms positions ...
So e.g. one O atoms was found in the file 2x (but 
with different x,y,z so manual identification was complex)...
It error was clear from total number of symmetry 
independent atoms in the CIF (correct 40 , incorrect  73) ...


I can confirm QE had correctly identified the Zn, 
S, C placed on the mirror operation symmetry and it did not

generated them 4x, but correctly 2x



It tells me atom 7 and 150 overlap, 7 should be

O -0.503 0.4513 0.3517

As for 150 I don’t know, not very easy to spot in a short time.

Pietro


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Re: [QE-users] Incorrect identification+generations of atoms in specialpositions (space_group options used).

[José Carlos Conesa Cegarra]

Dear all,

Last 11th of september I sent a similar question, but the answer, 
provided by Paolo Giannozzi, did not clarify much. I can say that in 
that occasion I was using qe-6.5. Should I use qe -6.6?


Regards,

José C. Conesa

El 12/11/2020 a las 11:30, Pietro Delugas escribió:


Hi

 which version of the code are you using ?

with qe-6.6 using  your parameters I got two positions

  site n. atom  positions (alat units)

 1   Zn  tau( 1) = (   0.4873906   2.5406690   
1.4472625  )


 2   Zn  tau( 2) = (   0.3343454   0.8468897   
0.4736359  )


With alat = 11.5468  a.u.

alat = 11.5468  a.u.

ibrav=-12

hope it helps

greetings  - Pietro

Sent from Mail  for 
Windows 10


*From: *Michal Husak 
*Sent: *Thursday, November 12, 2020 10:34 AM
*To: *users@lists.quantum-espresso.org 

*Subject: *[QE-users] Incorrect identification+generations of atoms in 
specialpositions (space_group options used).


I


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--
José C. Conesa
Research Professor
Instituto de Catálisis y Petroleoquímica, CSIC
Marie Curie, 2; Campus de Cantoblanco
28028 Madrid (Spain)
Telef. +34 915854766

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Re: [QE-users] Incorrect identification+generations of atoms inspecialpositions (space_group options used).

[Paolo Giannozzi]

On Thu, Nov 12, 2020 at 12:35 PM Pietro Delugas  wrote:

> It tells me atom 7 and 150 overlap, 7 should be
>
> O -0.503 0.4513 0.3517
>

well, no, 7 and 150 in  the list of all atoms, not of Wyckoff positions.
Atom 7 is n.4 in the list:
  O -0.1486 0.54916 0.09311
atom 150 is n. 41:
  O -0.1486 -0.04916 0.09311
in crystal coordinates.

Paolo


As for 150 I don’t know, not very easy to spot in a short time.
>
> Pietro
>
>
>
>
>
> Sent from Mail  for
> Windows 10
>
>
>
> *From: *Michal Husak 
> *Sent: *Thursday, November 12, 2020 12:19 PM
> *To: *Quantum ESPRESSO users Forum 
> *Subject: *Re: [QE-users] Incorrect identification+generations of atoms
> inspecialpositions (space_group options used).
>
>
>
> H
>
>
> ___
> Quantum ESPRESSO is supported by MaX (www.max-centre.eu)
> users mailing list users@lists.quantum-espresso.org
> https://lists.quantum-espresso.org/mailman/listinfo/users



-- 
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
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Re: [QE-users] Incorrect identification+generations of atoms inspecialpositions (space_group options used).

[Pietro Delugas]

It tells me atom 7 and 150 overlap, 7 should be 
O -0.503 0.4513 0.3517
As for 150 I don’t know, not very easy to spot in a short time. 
Pietro 


Sent from Mail for Windows 10

From: Michal Husak
Sent: Thursday, November 12, 2020 12:19 PM
To: Quantum ESPRESSO users Forum
Subject: Re: [QE-users] Incorrect identification+generations of atoms 
inspecialpositions (space_group options used).

H

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Re: [QE-users] Incorrect identification+generations of atoms in specialpositions (space_group options used).

[Michal Husak]

Hi Pietro

I use 6.4.1 (the latest one for witch Windows binary are available 
for download from QE listed WWW).


The whole non functional input follows. If you can check this, it 
will be very helpful.


Michal


&CONTROL
  calculation = 'scf'
  etot_conv_thr =   1.46d-03
  forc_conv_thr =   1.00d-04
  outdir = './out/'
  prefix = 'aiida'
  pseudo_dir = './pseudo/'
  tprnfor = .true.
  tstress = .true.
  verbosity = 'high'
/
&SYSTEM
  ecutrho =   4.80d+02
  ecutwfc =   6.00d+01
  uniqueb = .true.
  space_group = 11 ! 1 21/m 1
  A = 6.1103
  B = 20.6990
  C = 11.7877
  cosBC = 0 ! alpha
  cosAC = -0.092405345 ! beta
  cosAB = 0 ! gamma
  nat = 73
  ntyp = 6
  occupations = 'fixed'
/
&ELECTRONS
  conv_thr =   2.92d-08
  electron_maxstep = 80
  mixing_beta =   4.00d-01
/
ATOMIC_SPECIES
C  12.011 C.pbe-n-kjpaw_psl.1.0.0.UPF
H  1.00794 H.pbe-rrkjus_psl.1.0.0.UPF
N  14.0067 N.pbe-n-radius_5.UPF
O  15.9994 O.pbe-n-kjpaw_psl.0.1.UPF
S  32.066 s_pbe_v1.4.uspp.F.UPF
Zn 65.39 Zn_pbe_v1.uspp.F.UPF
ATOMIC_POSITIONS crystal_sg
Zn 0.37830 0.2500 0.24657
S 0.8360 0.2500 0.58850
S 0.87002 0.2500 -0.03294
O -0.1486 0.54916 0.09311
O -0.503 0.4513 0.3517
N 0.5387 0.2500 0.3965
N 0. 0.2500 0.1203
N 0.1723 0.32744 0.24257
N -0.2534 0.54195 0.17640
N -0.3909 0.49661 0.32605
C 0.6628 0.2500 0.4774
C 0.6876 0.2500 0.0565
C 0.0542 0.33986 0.3306
H 0.0712 0.3127 0.3936
C -0.0898 0.39033 0.3324
H -0.1703 0.3965 0.3947
C -0.1145 0.43227 0.24017
C 0.0033 0.41927 0.1484
H -0.0113 0.4456 0.0842
C 0.1430 0.36680 0.1531
H 0.2207 0.3585 0.0905
C -0.2567 0.48945 0.2472
C -0.4264 0.58903 0.2024
C -0.4780 0.56359 0.3210
C -0.6128 0.57937 0.1075
H -0.6679 0.5360 0.1105
H -0.5579 0.5867 0.0348
H -0.7292 0.6094 0.1176
C -0.3382 0.65732 0.1980
H -0.3119 0.6677 0.1211
H -0.2031 0.6605 0.2462
H -0.4437 0.6869 0.2240
C -0.3517 0.59922 0.4198
H -0.1986 0.6008 0.4076
H -0.3693 0.5769 0.4897
H -0.4077 0.6424 0.4242
C -0.7202 0.56226 0.3416
H -0.7356 0.5461 0.4168
H -0.7984 0.5346 0.2864
H -0.7794 0.6052 0.3346
O -0.1486 -0.04916 0.09311
O -0.503 0.0487 0.3517
N 0.1723 0.17256 0.24257
N -0.2534 -0.04195 0.17640
N -0.3909 0.00339 0.32605
C 0.0542 0.16014 0.3306
H 0.0712 0.1873 0.3936
C -0.0898 0.10967 0.3324
H -0.1703 0.1035 0.3947
C -0.1145 0.06773 0.24017
C 0.0033 0.08073 0.1484
H -0.0113 0.0544 0.0842
C 0.1430 0.13320 0.1531
H 0.2207 0.1415 0.0905
C -0.2567 0.01055 0.2472
C -0.4264 -0.08903 0.2024
C -0.4780 -0.06359 0.3210
C -0.6128 -0.07937 0.1075
H -0.6679 -0.0360 0.1105
H -0.5579 -0.0867 0.0348
H -0.7292 -0.1094 0.1176
C -0.3382 -0.15732 0.1980
H -0.3119 -0.1677 0.1211
H -0.2031 -0.1605 0.2462
H -0.4437 -0.1869 0.2240
C -0.3517 -0.09922 0.4198
H -0.1986 -0.1008 0.4076
H -0.3693 -0.0769 0.4897
H -0.4077 -0.1424 0.4242
C -0.7202 -0.06226 0.3416
H -0.7356 -0.0461 0.4168
H -0.7984 -0.0346 0.2864
H -0.7794 -0.1052 0.3346
K_POINTS automatic
6 2 3 0 0 0






Hi

 which version of the code are you using ?



with qe-6.6 using  your parameters I got two positions



  site n. atom  positions (alat units)

 1   Zn  tau(   1) = (   0.4873906   2.5406690   1.4472625  )

 2   Zn  tau(   2) = (   0.3343454   0.8468897   0.4736359  )



With alat = 11.5468  a.u.



alat = 11.5468  a.u.



ibrav=-12





hope it helps

greetings  - Pietro





Sent from Mail for Windows 10



From: Michal Husak
Sent: Thursday, November 12, 2020 10:34 AM
To: users@lists.quantum-espresso.org
Subject: [QE-users] Incorrect identification+generations of atoms in 
specialpositions (space_group options used).




I


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___
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users mailing list users@lists.quantum-espresso.org
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Re: [QE-users] Incorrect identification+generations of atoms in specialpositions (space_group options used).

[Pietro Delugas]

Hi 
 which version of the code are you using ? 
 
with qe-6.6 using  your parameters I got two positions 

  site n. atom  positions (alat units)
 1   Zn  tau(   1) = (   0.4873906   2.5406690   1.4472625  )
 2   Zn  tau(   2) = (   0.3343454   0.8468897   0.4736359  )

With alat = 11.5468  a.u.

alat = 11.5468  a.u.

ibrav=-12


hope it helps 
greetings  - Pietro 


Sent from Mail for Windows 10

From: Michal Husak
Sent: Thursday, November 12, 2020 10:34 AM
To: users@lists.quantum-espresso.org
Subject: [QE-users] Incorrect identification+generations of atoms in 
specialpositions (space_group options used).

I

___
Quantum ESPRESSO is supported by MaX (www.max-centre.eu)
users mailing list users@lists.quantum-espresso.org
https://lists.quantum-espresso.org/mailman/listinfo/users

[QE-users] Incorrect identification+generations of atoms in special positions (space_group options used).

[Michal Husak]

I had carefully checked this mailing list and I had found several 
topic related to the same issue - QE generates multiple atoms for 
atoms in special positions.

Not solved in any answer.
What I mean:

General position:  x,y,z crystallographic position, atom not on a 
symmetry element (e.g. for spac egropu number 11, P21/m , 4 atoms are 
generated).


Special position: eg 2e x,z, (for space group 11, 2 atoms should be generated).
Atom is on the mirror element.

I had a structure described by CIF information in following way:

_symmetry_Int_Tables_number  11
_cell_length_a   6.1103(2)
_cell_length_b   20.6990(10)
_cell_length_c   11.7877(5)
_cell_angle_alpha90.00
_cell_angle_beta 95.302(3)
_cell_angle_gamma90.00

Zn 0.37830 0.2500 0.24657

The Zn is on the mirror

This can be transferred to QE input:

space_group = 11
uniqueb = .true.
A = 6.1103
B = 20.6990
C = 11.7877
cosAB = 0
cosAC = -0.092405345
cosBC = 0

And:
ATOMIC_POSITIONS crystal_sg
Zn 2e 0.37830 0.24657

Or
Zn 0.37830 0.2500 0.24657

Both input generate error = overlapped atoms.
What is wrong ?

Michal

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