Re: [Pw_forum] Charge of a supercell with a vacancy

[Mostafa Youssef]

Dear David,

In experiments , neutral O2 gas leaves the TiO2 crystal causing the creation of 
oxygen vacancies behind.  However, these vacancies can have any charge state.  
Neutral in which the two electrons (reminiscent of O2- ion) set around the 
vacancy forming polarons, 2+ in which the two electrons leaves the vacant site 
and go somewhere else, or 1+ which is intermediate between the past two cases.

Have a look at the following paper for theoretical analysis of the oxygen 
vacancy in TiO2:
J. Phys. Chem. C 2010, 114, 21694–21704


For an experimental point view, have a look at figure 2.4 (and the associated 
discussion) in the following thesis:

https://scholar.google.com.eg/citations?view_op=view_citation&hl=en&user=1Ga4WncJ&sortby=pubdate&citation_for_view=1Ga4WncJ:u-x6o8ySG0sC



Regards,
Mostafa
MIT
___
Pw_forum mailing list
Pw_forum@pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum

[Pw_forum] vc-relax for B-N-C cannot be truely converged

[Lei Cao]

Dear All,

I have been trying to optimize the structure of single layer hexagonal BNC.
The vc-relax run finished smoothly and gave me the optimized positions of
each atom and the lattice parameters.

However, if I use these optimized values for scf calculation, it gave me
large force between atom and large stress. If I use these values for
another vc-relax run, then it will take quite a few bfgs steps to get the
optimized atomic positions and lattice parameters. Surprisingly, they are
different from the values I got from the last vc-relax run.

Could you please help me with this? My code is pasted below.

Thanks,
Lei

--

 &control

calculation = 'vc-relax'

restart_mode='from_scratch',

prefix='BNC',

tstress = .true.

tprnfor = .true.

pseudo_dir = '/home/QE/pseudo/',

outdir='./temp_dir/'

 /

 &system

ibrav=  4, celldm(1)= 9.53616076609, celldm(3) = 3.99905580615, nat= 8,
ntyp= 3,

ecutwfc = 120.0

occupations='smearing', smearing = 'mv', degauss = 0.002

 /

 &electrons

diagonalization='david'

mixing_mode = 'plain'

mixing_beta = 0.7

conv_thr =  1.d-13,

 /

 &IONS

 /

 &CELL

cell_dynamics = 'bfgs' ,

press = 0.00,

wmass =  0.0070,

press_conv_thr = 0.1,

cell_dofree = '2Dxy'

 /

ATOMIC_SPECIES

 B   10.811 B.pbe-mt_fhi.UPF

 N   14.00674   N.pbe-mt_fhi.UPF

 C   12.0107   C.pbe-mt_fhi.UPF

ATOMIC_POSITIONS crystal

B0.002466254   0.004932509  -0.0

N0.170582689   0.341165379  -0.0

N0.496083977  -0.007832045  -0.0

B0.664200413   0.328400824   0.0

C0.013913144   0.504233187   0.0

C0.176346623   0.829100147  -0.0

C0.490320044   0.504233187   0.0

C0.652753523   0.829100147   0.0

K_POINTS automatic

 16 16 1 0 0 0
___
Pw_forum mailing list
Pw_forum@pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum

[Pw_forum] Charge of a supercell with a vacancy

[David Foster]

Dear Users

In an Oxygen-Vacancy of a supercell of TiO2, how should I set supercell charge? 
For one O-vacancy is it +2 or neutral?

In experimental works, oxygen separated and goes to the infinity with minus 
charge or it is in neutral radical form?

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

[Pw_forum] Different Raman configurations

[jiaxu yan]

Dear QE users,

Anyone knows how to modify the Raman configuration defined in the
dynmat.f90 code?

For example, I want to perform some polarized back-scattering Raman
configurations, i.e. Z(xy)Z', X(yy)X'.

According to PRB 54, 7830 (1996),  the dynmat.f90 code write the raman
intenisty as

(45.d0*alpha**2 + 7.0d0*beta2)*amu_ry

with

alpha = (raman(1,1,nu) + raman(2,2,nu) + raman(3,3,nu))/3.d0

Beta2 = ( (raman(1,1,nu) - raman(2,2,nu))**2 + &
 (raman(1,1,nu) - raman(3,3,nu))**2 + &
 (raman(2,2,nu) - raman(3,3,nu))**2 + 6.d0 * &
  (raman(1,2,nu)**2 + raman(1,3,nu)**2 + raman(2,3,nu)**2) )/2.d0

It is non-polarized Raman intensity. So, how to modify alpha and beta2?

Best regards,

Jiaxu Yan

Division of Physics and Applied Physics
School of Physical and Mathematical Sciences
Nanyang Technological University
21 Nanyang Link
Singapore 637371
___
Pw_forum mailing list
Pw_forum@pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum

Re: [Pw_forum] Errors with structure optimization

[Oanh Nguyen]

Thank you for your help. I will set cell_parameter and run again.
I have a question, if the total force can not go to zero ( or not smaller
than threshold values that I set at namelist &control). So what can I
change this one to have the best result in structure optimization?
Best.

2016-10-26 19:44 GMT+07:00 stefano de gironcoli :

> I think this happens because the cell shrinks very much and the effective
> cutoff grows above beyond a certain fraction (set with the cell_factor) of
> the input cutoff.
> restarting after setting a larger cell_factor should work.
> restarting from scratch from the latest volume should also work.
>
> stefano
>
>
> On 26/10/2016 10:38, Oanh Nguyen wrote:
>
> Dear users!
> I am optimising "vc_relax" for PdxTaSe2. I have a problem when I am
> running.
> Not enough space allocated for radial FFT: try restarting with a larger
> cell_factor.
> Running with "relax" is ok
>
> Here is my inputfile.
> I already use lattice constant from experimental result.
>
> How to the way to fix it?
>
>
> ___
> Pw_forum mailing 
> listPw_forum@pwscf.orghttp://pwscf.org/mailman/listinfo/pw_forum
>
>
>
> ___
> 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] Errors with structure optimization

[stefano de gironcoli]

I think this happens because the cell shrinks very much and the 
effective cutoff grows above beyond a certain fraction (set with the 
cell_factor) of the input cutoff.

restarting after setting a larger cell_factor should work.
restarting from scratch from the latest volume should also work.

stefano


On 26/10/2016 10:38, Oanh Nguyen wrote:

Dear users!
I am optimising "vc_relax" for PdxTaSe2. I have a problem when I am 
running.
Not enough space allocated for radial FFT: try restarting with a 
larger cell_factor.

Running with "relax" is ok

Here is my inputfile.
I already use lattice constant from experimental result.

How to the way to fix it?


___
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] qe-6.0 test suite

[Paolo Giannozzi]

You shouldn't execute "run-pw.sh". You should type "make" in the
"test-suite/" directory, then choose what you want to "make".

On Wed, Oct 26, 2016 at 12:37 AM, Divya Bohra - TNW 
wrote:

>
>
> After configuring qe-6.0, the script run-pw.sh keeps waiting for input
> from the QE website:www.quantum-espresso.org/wp-content/uploads/upf_files/
> which does not arrive [...] Can someone please help?
>
>
>
> Thanks in advance,
>
>
>
> Divya Bohra
>
> PhD student
>
> Materials for Energy Conversion and Storage
>
> TU Delft, The Netherlands
>
> ___
> 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

Re: [Pw_forum] oxygen gas cif file

[Winfred Mulwa]

Thank you so much Giovanni
Kind regards

On Wed, Oct 26, 2016 at 12:36 PM, Giovanni Cantele <
giovanni.cant...@spin.cnr.it> wrote:

> Unless I miss something, CIF stands for Crystallographic Information File
>  and is intended for represent crystal structures. The O2 molecule is not a
> crystal but can be represented,
> within a plane wave code, with the supercell approach, where as fictitious
> periodic crystal of non-interacting units is set up. See, for example,
> http://qe-forge.org/pipermail/pw_forum/2008-December/085479.html
>
> Giovanni
>
>
> On 26 Oct 2016, at 12:27, Winfred Mulwa  wrote:
>
> Dear all,
> I want to calculate the chemical potential of O2 . Somebody please help me
> with the cif file of oxygen gas. Thank you so much.
> Kind regards
> Mulwa Winfred.
> D Phil Student, Computational Material Science Group,
> University of the Free State - QwaQwa,
> South Africa.
> ___
> Pw_forum mailing list
> Pw_forum@pwscf.org
> http://pwscf.org/mailman/listinfo/pw_forum
>
>
> --
>
> Giovanni Cantele, PhD
> CNR-SPIN
> c/o Dipartimento di Fisica
> Universita' di Napoli "Federico II"
> Complesso Universitario M. S. Angelo - Ed. 6
> Via Cintia, I-80126, Napoli, Italy
> e-mail: giovanni.cant...@spin.cnr.it
> Phone: +39 081 676910
> Skype contact: giocan74
>
> ResearcherID: http://www.researcherid.com/rid/A-1951-2009
> Web page: http://people.na.infn.it/~cantele
>
>
> ___
> Pw_forum mailing list
> Pw_forum@pwscf.org
> http://pwscf.org/mailman/listinfo/pw_forum
>



-- 
Mulwa Winfred.
D Phil Student, Computational Material Science Group,
University of the Free State - QwaQwa,
South Africa.
___
Pw_forum mailing list
Pw_forum@pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum

Re: [Pw_forum] oxygen gas cif file

[Giovanni Cantele]

Unless I miss something, CIF stands for Crystallographic Information File  and 
is intended for represent crystal structures. The O2 molecule is not a crystal 
but can be represented,
within a plane wave code, with the supercell approach, where as fictitious 
periodic crystal of non-interacting units is set up. See, for example,
http://qe-forge.org/pipermail/pw_forum/2008-December/085479.html 


Giovanni


> On 26 Oct 2016, at 12:27, Winfred Mulwa  wrote:
> 
> Dear all,
> I want to calculate the chemical potential of O2 . Somebody please help me 
> with the cif file of oxygen gas. Thank you so much.
> Kind regards
> Mulwa Winfred.
> D Phil Student, Computational Material Science Group,
> University of the Free State - QwaQwa,
> South Africa.
> ___
> Pw_forum mailing list
> Pw_forum@pwscf.org
> http://pwscf.org/mailman/listinfo/pw_forum

-- 

Giovanni Cantele, PhD
CNR-SPIN
c/o Dipartimento di Fisica
Universita' di Napoli "Federico II"
Complesso Universitario M. S. Angelo - Ed. 6
Via Cintia, I-80126, Napoli, Italy
e-mail: giovanni.cant...@spin.cnr.it
Phone: +39 081 676910
Skype contact: giocan74

ResearcherID: http://www.researcherid.com/rid/A-1951-2009
Web page: http://people.na.infn.it/~cantele

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

[Pw_forum] oxygen gas cif file

[Winfred Mulwa]

Dear all,
I want to calculate the chemical potential of O2 . Somebody please help me
with the cif file of oxygen gas. Thank you so much.
Kind regards
Mulwa Winfred.
D Phil Student, Computational Material Science Group,
University of the Free State - QwaQwa,
South Africa.
___
Pw_forum mailing list
Pw_forum@pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum

[Pw_forum] Errors with structure optimization

[Oanh Nguyen]

Dear users!
I am optimising "vc_relax" for PdxTaSe2. I have a problem when I am running.
Not enough space allocated for radial FFT: try restarting with a larger
cell_factor.
Running with "relax" is ok

Here is my inputfile.
I already use lattice constant from experimental result.

How to the way to fix it?


C2HF.vcrelax
Description: Binary data
___
Pw_forum mailing list
Pw_forum@pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum

Re: [Pw_forum] Ge.pz-hgh.UPF

[Paolo Giannozzi]

Ge.pz-hgh.UPF was, like all HGH pseudopotentials available on the QE site,
converted from HGH pseudopotentials in the CPMD format, available on
Mattias Krack's web site (there is a link on the QE site which however is
no longer valid). Information on pseudo-orbitals  and pseudo-charge
density, useful to start the calculation and needed to compute PDOS and the
like, was separately computed using the "atomic" code of QE and included
into UPF files with a semi-automatic procedure, whose correctness is likely
but far from guaranteed. Not all UPF files contain those pieces of
information, since many HGH PPs gave problems with the atomic code, for
unclear (to me) reasons. I don't remember why lmax in UPF equals lmax-1 in
CPMD format. In the UPF format, lmax=2 means s,p,d channels. I guess, and
you may easily verify, that lmax=3 in CPMD format means the same: three
channels, s,p,d.

Cutoff radii should be in a.u.. I don't remember what they are supposed to
mean in your case.

Paolo

On Mon, Oct 24, 2016 at 7:08 PM, Gabriel Greene 
wrote:

> Hello,
>
> After converting the pseudo on https://www.cp2k.org/static/potentials/ from
> CPMD format to UPF using cpmd2upf.x from QEv5.2.0, and then running in
> pwscf, I realised it may be the same pseudopotential as Ge.pz-hgh.UPF on
> http://www.quantum-espresso.org/pseudopotentials
> .
>
> However, now I am a bit confused because in the CPMD format it says
>
> &END
>  &POTENTIAL
>  GOEDECKER
>  3LMAX
>
>
> Which I thought would indicate that lmax is 3. However after converting to 
> UPF, it says lmax="2" in the PP_HEADER section. Assuming converting between 
> formats doesnt change the actual pseudo, then is the definition of lmax 
> different for CPMD compared to UPF?
>
>
> Also, the number of wavefunctions is 0 in the pseudo I converted from CPMD 
> (Ge_GTH_LDA_fromCP2K.UPF in attachments), and it is 3 in Ge.pz-hgh.UPF... and 
> obviously the entries in PP_PSWFC sections are completely different (missing 
> in Ge_GTH_LDA_fromCP2K.UPF...), as are the charge density PP_RHOATOM sections 
> of the files. In Ge.pz-hgh.UPF, there are orbitals generated with ld1.x, so 
> again I thought the pseudos must be generated differently after all..
>
>
> Yet they yield very similar results (total energies, bandgaps, relaxed 
> lattice constants, see attached inputs and outputs). Comparing the pwscf 
> outputs I see that the starting point for SCF was superposition of atomic 
> orbitals for Ge.pz-hgh.UPF and totally random wfcs for Ge_GTH_LDA_CP2K.UPF. 
> So I am assuming because of the similarity of the potentials, the resulting 
> self-consistent densities and potentials after iterating to convergence end 
> up to be the same, despite the different starting wfcs.
>
>
> Yet I am still unsure about how Ge.pz-hgh.UPF was generated. Looking at the 
> non-local projectors of this file, the cutoff radius of for e.g. 1S is
>
> cutoff_radius="3.893327136974858E+000"
>
> and the cutoff radius of the valence orbitals (PP_CHI), taking 4S as an 
> example
>
> cutoff_radius="1.876811407389333E+000"
>
> I would have thought the cutoff radii of core orbitals which are to be 
> pseudized should be smaller than the r_cutoff of the resulting valence pseudo 
> orbitals? What are the units are these cutoff radii?
>
>
> Please let me know if I am misinterpreting something. I would really 
> appreciate any help on this.
>
>
>
> Gabriel,
>
> Research Associate,
>
> Atomistic Simulation Centre,
>
> School of Mathematics and Physics,
>
> Queen's University Belfast
>
>
>
>
> On Fri, Oct 21, 2016 at 6:45 PM, Gabriel Greene <
> gabriel.green...@gmail.com> wrote:
>
>> Dear Ari,
>>
>> Thank you but I am not looking for a new GTH-type pseudopotential for Ge,
>> nor am I trying to generate a new Ge pseudo. I am looking for the
>> generation information of the specific Ge GTH pseudo that is hosted on the
>> QE website, with file name "Ge.pz-hgh.UPF". See first attachment.
>>
>> Thank you for the link, I used your instructions to get the 2nd attached
>> file. Seeing as lmax is different here compared to Ge.pz-hgh.UPF, I am
>> presuming these are different pseudopotentials (not just different file
>> formats).
>>
>> Specifically, I am looking for lmax, r_cut for each l-channel, and
>> generating XC functional for Ge.pz-hgh.UPF. I have lmax (2) and the XC
>> funct (PZ-LDA), so really I just need the cutoff radii that were used to
>> generate this pseudo, if available.
>>
>>
>> On another point, I find that the link to M. Kracks pseudopotentials on
>> the page http://www.quantum-espresso.org/pseudopotentials/about/  is
>> currently broken (leads to a "phonebook" page, no pseudo details anywhere).
>> Thank you again for the correct link to this page.
>>
>>
>> Thanks again,
>>
>> Gabriel
>>
>> Research Associate,
>>
>> Atomistic Simulation Centre,
>>
>> School of Mathematics and Physics,
>>
>> Queen's University Belfast
>>
>>
>>