Re: [Pw_forum] How to select unit cell for optimization calculation?

[Youssef]

Dear Max,

You can use the following 14 atoms coordinates for spinel AB2O4 (fd-3m 
origin choice 2), replace "x" with oxygen parameter from 32e wykoff 
site (0.2627 for your case)


A0.125   0.125   0.125
A0.875   0.375   0.375
B0.5 0.5 0.5
B0.250.750
B0.750   0.25
B0   0.250.75
O(x) (x) (x)
O(1.25-x)(x+0.5) (1.75-x)
O(x+0.75)(x+0.25)(1.5-x)
O(x+0.25)(1.5-x) (1.75+x)
O(1.75-x)(1.25-x)(x+0.5)
O(x+0.5) (1.75-x)(1.25-x)
O(1-x)   (1-x)   (1-x)
O(1.5-x) (x+0.75)(x+0.25)


to be used with  ibarv = 2 and ATOMIC_POSITIONS alat (not crystal) , I 
didn't test it in QE, please confirm if it works!


Youssef Aharbil,
Laboratory of Physics and Chemistry of Materials
Faculty of sciences Ben msik, Casablanca
Morocco
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Re: [Pw_forum] Convergence Problem for Ni111-3 layer system

[Youssef]

Dear Massoud,


If I was you, first thing I do is to minimize the electronic 
convergence threshold to 1.0D-9 Ry, the calculated forces are simply 
wrong  (>10x scf Correction).
! conv_thr=1.0D-8 is ignored,  QE took the default value of 1.0D-6 
which isn't enough in your case.


Youssef Aharbil,
Laboratory of Physics and Chemistry of Materials
Faculty of sciences Ben msik, Casablanca
Morocco


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Re: [Pw_forum] How to select unit cell for optimization calculation?

[Youssef]

Dear Max,

I think that this rule is a myth,  for the simple reason that more 
ecutwfc=more plane waves = more energy, In addition to that , the more 
system is big the bigger is the energy (and the energy jumps vs 
ecutwfc).
I suggest you to rerun the calculations with tstress = .true.  & 
tprnfor = .true. , then you look after on the impact of ecutwfc upon 
force and stress tensor.


By plotting your data, I suggest that ecutwfc threshold is laying 
between 50 to 150 Ry.


On Fri, Jul 10, 2015 at 1:02 AM, max <aquiles...@gmail.com> wrote:

Dear Youssef and Giovanni,

Thank you very much, I have doubt about convergence energy.

I run scf  calculations for ecutwfc from 10 to 250 Ry using 
ecutrho=4*ecutwfc and I get the values bellow ecutwfc vs etotal 
(values in Ry). I read that the convergence will be achieved when the 
difference between two adjacent scf calculation is smaller than 0.1 
meV [1] or 1 mRy [2], but this is for unit cell or for atoms (divide 
the energy difference between the number of atoms in unit cell)?


Other question, is normal that the convergence value for ecutwfc be 
more than 200 Ry?
 
ecutwfc etotal

10-941.67085713
15-1005.07732548
20-1038.00240543
25-1058.8736733
30-1073.25016374
35-1082.62081233
40-1089.10688841
45-1093.8583202
50-1097.63582121
55-1100.63775846
60-1103.0243432
65-1105.15423136
70-1107.08545327
75-1108.79020201
80-1110.27166937
85-.59023819
90-1112.768963
100-1114.66472444
110-1116.05760199
120-1117.06611139
130-1117.76952606
140-1118.25442342
150-1118.58413784
160-1118.80480982
170-1118.95194442
180-1119.0489105
190-1119.11208313
200-1119.15329918
210-1119.17990393
220-1119.19703143
230-1119.20790385
240-1119.21481705
250-1119.21915626

[1] https://www.mail-archive.com/pw_forum%40pwscf.org/msg11093.html
[2] http://qe-forge.org/pipermail/pw_forum/2013-February/101122.html

On Tue, Jul 7, 2015 at 7:35 PM, Youssef <ahar...@gmail.com> wrote:

Dear Max,

You can use the following 14 atoms coordinates for spinel AB2O4 
(fd-3m origin choice 2), replace "x" with oxygen parameter from 32e 
wykoff site (0.2627 for your case)


A0.125   0.125   0.125
A0.875   0.375   0.375
B0.5 0.5 0.5
B0.250.750
B0.750   0.25
B0   0.250.75
O(x) (x) (x)
O(1.25-x)(x+0.5) (1.75-x)
O(x+0.75)(x+0.25)(1.5-x)
O(x+0.25)(1.5-x) (1.75+x)
O(1.75-x)(1.25-x)(x+0.5)
O(x+0.5) (1.75-x)(1.25-x)
O(1-x)   (1-x)   (1-x)
O(1.5-x) (x+0.75)(x+0.25)


to be used with  ibarv = 2 and ATOMIC_POSITIONS alat (not crystal) , 
I didn't test it in QE, please confirm if it works!


Youssef Aharbil,
Laboratory of Physics and Chemistry of Materials
Faculty of sciences Ben msik, Casablanca
Morocco




--
El éxito solo es para los que se arriesgan por sus objetivos.

 Máximo Ramírez Mateo
  Desarrollador de Software
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Re: [Pw_forum] How to select unit cell for optimization calculation?

[Youssef]

Dear Max,

The decision return to you, you shouldn't to choose the minimal value 
of course, but the value beyond which the criteria doesn't change 
significantly and the relative differences are accepted with respect to 
computational cost and accuracy.
You've do the same thing with energy but as you noticed the decision 
using force is more easy.


Youssef Aharbil,
Laboratory of Physics and Chemistry of Materials
Faculty of sciences Ben msik, Casablanca
Morocco


On Fri, Jul 10, 2015 at 10:15 PM, max <aquiles...@gmail.com> wrote:

Dear Youssef,

I attach a pdf with result of my last calculations (data and graph).

Ecut vs Etotal and Ecut vs Total force.

If the rules about 1mRy for energy and 1.0D10-04Ry/au per atoms are 
myths. How can I choose the correct value for convergence?


The minimun value of total force is 0.004268 Ry/au for Ecut = 75 Ry 
can I choose this value for convergence?
 
--

 Máximo Ramírez
 Physics Degree
 Universidad Autónoma de Santo Domingo
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[Pw_forum] Fwd: Final iteration often crashes after structure optimization

[Youssef]

Dear Ronald,

Strange behavior, it happens here (ggen.f90)  :

IF (ngm > ngm_g) CALL errore ('ggen', 'too many g-vectors', ngm)

I am not QE developer, but firstly I suggest to lower ecutrho to 280 Ry 
and see!!!


Youssef Aharbil,
Laboratory of Physics and Chemistry of Materials
Faculty of sciences Ben msik, Casablanca
Morocco



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[Pw_forum] Existing USPPs for Potassium

[Youssef]

Dear Eric,

May be it was generated from an earlier ps library,

Have a look on this page:

http://people.sissa.it/~dalcorso/pslibrary_help.html

Youssef Aharbil,
Laboratory of Physics and Chemistry of Materials
Faculty of sciences Ben msik, Casablanca
Morocco



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[Pw_forum] magnetic anisotropy calculation using fully-relativistic PPs

[Youssef]

Dear Yun-Peng,

Generally non-collinear calculation is hardest to converge, but I can't 
figure it out without knowing your physical system nor without a 
complete scf file.


But firstly,  you should reduce your mixing factor instead of increase 
it , start with   mixing_beta = 0.1 and compare.


Youssef Aharbil,
Laboratory of Physics and Chemistry of Materials
Faculty of sciences Ben msik, Casablanca
Morocco






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[Pw_forum] Application of LDA+U in phonon calculations.

[Youssef]

Dear Saswata,

Have checked your structure with xcrysden?
For a double perovskite, your input structure is wrong.
When using ibrav=2 you should process your dimensionless atomic 
coordinates before using them with "ATOMIC_POSITIONS crystal" or simply 
use "ATOMIC_POSITIONS alat" instead as longs as a=b=c.


Youssef Aharbil,
Laboratory of Physics and Chemistry of Materials
Faculty of sciences Ben msik, Casablanca
Morocco
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Re: [Pw_forum] Application of LDA+U in phonon calculations.

[Youssef]

Dear Saswata,

Have you checked your structure with xcrysden?
For a double perovskite, your input structure is wrong.
When using ibrav=2 you should process your dimensionless atomic 
coordinates before using them with "ATOMIC_POSITIONS crystal" or simply 
use "ATOMIC_POSITIONS alat" instead as longs as a=b=c.


Youssef Aharbil,
Laboratory of Physics and Chemistry of Materials
Faculty of sciences Ben msik, Casablanca
Morocco
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[Pw_forum] Non linear Uout=f( Uin) Self consistent Hubbard U determination

[Youssef]

Dear Quantum espresso Community,

I used to calculate the Uscf via  the method proposed by Cococcioni et 
al for several compounds and species, the method was very successful 
especially when systematically getting the linear behavior of Uin vs 
Uout (around Uscf of course), However I've noticed that nickel TMO  
represent always make an exception against this linearity, I wonder if 
the problem stem from the fact that  the studied d states are almost 
occupied (d8 for Ni)?


I have checked my inputs and everthing look find, I studied recently a 
pervoskite compound with multiple d state ions and get linear behavior 
for Mo and non linear one for Ni (see attached graph).


Thanks.

Youssef Aharbil,
Laboratory of Physics and Chemistry of Materials
Faculty of sciences Ben msik, Casablanca
Morocco
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[Pw_forum] Possible Bugs in bands.x

[Youssef]

Dear all,

I am facing a problem when using bands.x  with spin_component = 2 , in 
fact, the printed values of kx  are always zero whilst kx= kxmod when 
spin_component = 1.
In order to reproduce the problem I modified example06 in PP folder, and 
then I got the same behavior:


from modified example06 with spin down component:

 Check: negative/imaginary core charge=   -0.590.00
 high-symmetry point:  0. 0. 0.   x coordinate 0.
 high-symmetry point:  0.-0.3750 0.3750   x coordinate 0.
 high-symmetry point:  0. 0.5000-0.5000   x coordinate 0.
 high-symmetry point: -0.1250-0.1250 0.2500   x coordinate 0.
 high-symmetry point: -0.1250-0.2500 0.3750   x coordinate 0.
 high-symmetry point: -0.1250 0.6250-0.5000   x coordinate 0.
 high-symmetry point: -0.2500 0.7500-0.5000   x coordinate 0.
 high-symmetry point: -0.2500 0.6250-0.3750   x coordinate 0.
 high-symmetry point:  0. 0. 0.2500   x coordinate 0.
 high-symmetry point:  0.-0.2500 0.5000   x coordinate 0.
 high-symmetry point:  0. 0.6250-0.3750   x coordinate 0.
 high-symmetry point: -0.1250-0.1250 0.5000   x coordinate 0.
 high-symmetry point: -0.1250 0.7500-0.3750   x coordinate 0.
 high-symmetry point: -0.2500 0.2500 0.2500   x coordinate 0.
 high-symmetry point: -0.2500 0.7500-0.2500   x coordinate 0.
 high-symmetry point:  0.6250-0.6250 0.2500   x coordinate 0.
 high-symmetry point:  0.5000-0.5000 0.2500   x coordinate 0.
 high-symmetry point:  0.5000-0.6250 0.3750   x coordinate 0.
 high-symmetry point:  0. 0. 0.5000   x coordinate 0.
 high-symmetry point:  0.-0.1250 0.6250   x coordinate 0.
 high-symmetry point:  0. 0.7500-0.2500   x coordinate 0.
 high-symmetry point: -0.1250 0.8750-0.2500   x coordinate 0.
 high-symmetry point:  0.5000-0.5000 0.5000   x coordinate 0.
 high-symmetry point:  0. 0. 0.7500   x coordinate 0.
 high-symmetry point:  0. 0.8750-0.1250   x coordinate 0.
 high-symmetry point:  0. 0.-1.   x coordinate 0.


from modified example06 with spin up component:

 Check: negative/imaginary core charge=   -0.590.00
 high-symmetry point:  0. 0. 0.   x coordinate 0.
 high-symmetry point:  0.-0.3750 0.3750   x coordinate 0.5303
 high-symmetry point:  0. 0.5000-0.5000   x coordinate 0.5303
 high-symmetry point: -0.1250-0.1250 0.2500   x coordinate 0.5303
 high-symmetry point: -0.1250-0.2500 0.3750   x coordinate 0.7071
 high-symmetry point: -0.1250 0.6250-0.5000   x coordinate 0.7071
 high-symmetry point: -0.2500 0.7500-0.5000   x coordinate 0.8839
 high-symmetry point: -0.2500 0.6250-0.3750   x coordinate 1.0607
 high-symmetry point:  0. 0. 0.2500   x coordinate 1.0607
 high-symmetry point:  0.-0.2500 0.5000   x coordinate 1.4142
 high-symmetry point:  0. 0.6250-0.3750   x coordinate 1.4142
 high-symmetry point: -0.1250-0.1250 0.5000   x coordinate 1.4142
 high-symmetry point: -0.1250 0.7500-0.3750   x coordinate 1.4142
 high-symmetry point: -0.2500 0.2500 0.2500   x coordinate 2.2243
 high-symmetry point: -0.2500 0.7500-0.2500   x coordinate 2.9314
 high-symmetry point:  0.6250-0.6250 0.2500   x coordinate 4.6362
 high-symmetry point:  0.5000-0.5000 0.2500   x coordinate 4.8130
 high-symmetry point:  0.5000-0.6250 0.3750   x coordinate 4.9897
 high-symmetry point:  0. 0. 0.5000   x coordinate 5.7998
 high-symmetry point:  0.-0.1250 0.6250   x coordinate 5.9766
 high-symmetry point:  0. 0.7500-0.2500   x coordinate 5.9766
 high-symmetry point: -0.1250 0.8750-0.2500   x coordinate 6.1534
 high-symmetry point:  0.5000-0.5000 0.5000   x coordinate 6.1534
 high-symmetry point:  0. 0. 0.7500   x coordinate 6.9034
 high-symmetry point:  0. 0.8750-0.1250   x coordinate 8.1408
 high-symmetry point:  0. 0.-1.   x coordinate 9.3783



Youssef Aharbil,

Laboratory of Physics and Chemistry of Materials

Faculty of sciences Ben msik, Casablanca

Morocco


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[Pw_forum] Possible Bugs in bands.x

[Youssef]

Dear all,

I am facing a problem when using bands.x  with spin_component = 2 , in 
fact, the printed values of kx  are always zero whilst kx= kxmod when 
spin_component = 1.
In order to reproduce the problem I modified example06 in PP folder, 
then I got the same behavior:


from modified example06 with spin down component:

 Check: negative/imaginary core charge=   -0.59 0.00
 high-symmetry point:  0. 0. 0.   x coordinate 0.
 high-symmetry point:  0.-0.3750 0.3750   x coordinate 0.
 high-symmetry point:  0. 0.5000-0.5000   x coordinate 0.
 high-symmetry point: -0.1250-0.1250 0.2500   x coordinate 0.
 high-symmetry point: -0.1250-0.2500 0.3750   x coordinate 0.
 high-symmetry point: -0.1250 0.6250-0.5000   x coordinate 0.
 high-symmetry point: -0.2500 0.7500-0.5000   x coordinate 0.
 high-symmetry point: -0.2500 0.6250-0.3750   x coordinate 0.
 high-symmetry point:  0. 0. 0.2500   x coordinate 0.
 high-symmetry point:  0.-0.2500 0.5000   x coordinate 0.
 high-symmetry point:  0. 0.6250-0.3750   x coordinate 0.
 high-symmetry point: -0.1250-0.1250 0.5000   x coordinate 0.
 high-symmetry point: -0.1250 0.7500-0.3750   x coordinate 0.
 high-symmetry point: -0.2500 0.2500 0.2500   x coordinate 0.
 high-symmetry point: -0.2500 0.7500-0.2500   x coordinate 0.
 high-symmetry point:  0.6250-0.6250 0.2500   x coordinate 0.
 high-symmetry point:  0.5000-0.5000 0.2500   x coordinate 0.
 high-symmetry point:  0.5000-0.6250 0.3750   x coordinate 0.
 high-symmetry point:  0. 0. 0.5000   x coordinate 0.
 high-symmetry point:  0.-0.1250 0.6250   x coordinate 0.
 high-symmetry point:  0. 0.7500-0.2500   x coordinate 0.
 high-symmetry point: -0.1250 0.8750-0.2500   x coordinate 0.
 high-symmetry point:  0.5000-0.5000 0.5000   x coordinate 0.
 high-symmetry point:  0. 0. 0.7500   x coordinate 0.
 high-symmetry point:  0. 0.8750-0.1250   x coordinate 0.
 high-symmetry point:  0. 0.-1.   x coordinate 0.


from modified example06 with spin up component:

 Check: negative/imaginary core charge=   -0.59 0.00
 high-symmetry point:  0. 0. 0.   x coordinate 0.
 high-symmetry point:  0.-0.3750 0.3750   x coordinate 0.5303
 high-symmetry point:  0. 0.5000-0.5000   x coordinate 0.5303
 high-symmetry point: -0.1250-0.1250 0.2500   x coordinate 0.5303
 high-symmetry point: -0.1250-0.2500 0.3750   x coordinate 0.7071
 high-symmetry point: -0.1250 0.6250-0.5000   x coordinate 0.7071
 high-symmetry point: -0.2500 0.7500-0.5000   x coordinate 0.8839
 high-symmetry point: -0.2500 0.6250-0.3750   x coordinate 1.0607
 high-symmetry point:  0. 0. 0.2500   x coordinate 1.0607
 high-symmetry point:  0.-0.2500 0.5000   x coordinate 1.4142
 high-symmetry point:  0. 0.6250-0.3750   x coordinate 1.4142
 high-symmetry point: -0.1250-0.1250 0.5000   x coordinate 1.4142
 high-symmetry point: -0.1250 0.7500-0.3750   x coordinate 1.4142
 high-symmetry point: -0.2500 0.2500 0.2500   x coordinate 2.2243
 high-symmetry point: -0.2500 0.7500-0.2500   x coordinate 2.9314
 high-symmetry point:  0.6250-0.6250 0.2500   x coordinate 4.6362
 high-symmetry point:  0.5000-0.5000 0.2500   x coordinate 4.8130
 high-symmetry point:  0.5000-0.6250 0.3750   x coordinate 4.9897
 high-symmetry point:  0. 0. 0.5000   x coordinate 5.7998
 high-symmetry point:  0.-0.1250 0.6250   x coordinate 5.9766
 high-symmetry point:  0. 0.7500-0.2500   x coordinate 5.9766
 high-symmetry point: -0.1250 0.8750-0.2500   x coordinate 6.1534
 high-symmetry point:  0.5000-0.5000 0.5000   x coordinate 6.1534
 high-symmetry point:  0. 0. 0.7500   x coordinate 6.9034
 high-symmetry point:  0. 0.8750-0.1250   x coordinate 8.1408
 high-symmetry point:  0. 0.-1.   x coordinate 9.3783



Youssef Aharbil,

Laboratory of Physics and Chemistry of Materials

Faculty of sciences Ben msik, Casablanca

Morocco


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[Pw_forum] PWgui installation Problem

[Youssef]

Dear Muthu.V ,
Have tried :
sudo apt-get install tcl8.5 iwidgets4

Youssef Aharbil,
Laboratory of Physics and Chemistry of Materials
Faculty of sciences Ben msik, Casablanca
Morocco

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[Pw_forum] Compilation with intel compiler and MKL.

[Youssef]

Dear *Yeonung,

I used to compile qe-5.30 with intel parallel studio 2016, using this 
statements:


**export FC=mpiifort
export F90=mpiifort
export F77=mpiifort
export MPIF90=mpiifort
export CC=mpiicc
export CPP="icc -E"
export CFLAGS=$FCFLAGS
export AR=xiar
export BLAS_LIBS=""
export LAPACK_LIBS="-lmkl_blacs_intelmpi_lp64"
export SCALAPACK_LIBS="-lmkl_scalapack_lp64 -lmkl_blacs_intelmpi_lp64"
export FFT_LIBS="-L$MKLROOT/intel64"
./configure  --enable-parallel
*
you can save it as a bash script, an run it inside qe folder.

Of course  make sure that the intel parallel studio wrapper is in your 
path (e.g. :  source /opt/intel/bin/compilervars.sh intel64 ), this  
invoke all the needed environmental variables.


Youssef Aharbil,

Laboratory of Physics and Chemistry of Materials

Faculty of sciences Ben msik, Casablanca

Morocco



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Re: [Pw_forum] Hubbard for oxygen

[Youssef]

Dear Giuseppe,

Thank you very much for your help, I was really stuck.

I have another question about the linear response approach, in fact I
successfully got the liner behavior of alpha=f(dn) and alpha=f(dn0) on
conventional cell, with a very good value of U with respect to the
literature, now when I move to supercell (2x2x2) the linearity is
broken !!!

Any idea about this issue?

P.S: The convergence criterion's are well tested in addition to cell and
atomic positions are relaxed

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Re: [Pw_forum] Hubbard for oxygen

[Youssef]

Dear Mattioli,,

Normally we apply an infinitesimal value of U with a finite one for
alpha, do you mean that we do apply the converged value of U ( for
example 2.5 ev for W from conventional cell ) in stead, and continue
with standard procedure to determine the new U (U_out)??
  
-- 
Youssef Aharbil,
Laboratory of Physics and Chemistry of Materials
Faculty of sciences Ben msik, Casablanca
Morocco

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Re: [Pw_forum] Regarding polarisation from Berry phase

[Mostafa Youssef Mahmoud Youssef]

Dear Varadharajan ,



This paper clarifies a lot of the ambiguities associated with determining the 
spontaneous polarization. Particularly the discussion around Fig. 9.


http://arxiv.org/abs/1202.1831


Best,
Mostafa
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Re: [Pw_forum] Regarding Absolute band-edges

[Mostafa Youssef Mahmoud Youssef]

Dear Vipul,


This is an old problem in semiconductor physics. In summary you need 2 set of 
calculations. One for a surface (interface) and another one for bulk.

Key papers to review are:

http://journals.aps.org/prb/abstract/10.1103/PhysRevB.35.8154

http://journals.aps.org/prl/abstract/10.1103/PhysRevLett.61.734


There are many modern examples as well. In my opinion absolute alignment to 
vacuum is more difficult than aliment of material 1 to material 2.


Best Regards,
Mostafa
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[QE-users] magnetism in hematite (alpha-Fe2O3)

[Mostafa Youssef]

 Dear all

Hematite (alpha-Fe2O3) crystallizes in the corundum structure.  The
primitive cell is rhombohedral containing 2 formula units, whereas the
conventional cell is hexagonal containing 6 formula units. I'm trying to
model the antiferromagnetic phase of hematite with spin ordering (+--+) in
the primitive cell. Relaxation (or variable cell relaxation) works nicely
for the primitive cell and I obtain a reasonable final structure and
magnetic moments on iron ions and zero magnetic moment in oxygen ions. This
is consistent with literature. Note that all iron ions are equivalent
crystallographically and all oxygen ions are crystallographyically.
However, when I try to relax (or vc-relax) the corresponding conventional
cell, some symmetry breaking occurs and few iron ions develop magnetic
moment different than the rest. Additionally some oxygen ions develop
magnetic moment as well.  The final result is antiferromagnetic still, but
of course the structure is not consistent with prior reports and is not
consistent with primitive cell calculations.  Also the energy/Fe2O3 for the
conventional cell is higher than the primitive cell. I tried many things to
avoid this strange-looking local minimum such as:

1- Using cg instead of david algorithm.
2- Different starting magnetization
3- Different initial experimentally determined atom positions
4- Different pseudopotentials
5- Applying smearing
6- Gamma-centered vs. shifted k-points
7-Using ibrav = 4  and listing a and c, vs. using ibrav = 0 and providing
cell_parameters list

but nothing really seems to work.
Any suggestions are thoughts arevery appreciated. I provide below the input
files for both primitive and conventional cells and I'm using version
6.2.1. I also provide the final magnetization of the ions in the
conventional cell.

Best Regards,
Mostafa Youssef
AUC -  Egypt

# Input file for the primitive cell

   calculation =   'vc-relax'   ,
   verbosity = 'high' ,
   restart_mode = 'from_scratch' ,
   prefix='fe2o3' ,
   outdir='/data/mostafa/Fe2O3/fix_magnet_strucutre2/scratch/' ,
   pseudo_dir = '/home/mostafa/data/Fe2O3/PP' ,
   tstress = .true.  ,
   tprnfor= .true.  ,
   nstep = 2000 ,
   etot_conv_thr = 7.7D-6  ,
   forc_conv_thr = 4.0D-5 ,
 /
 
   ibrav = 0 ,
nat  =  10 ,
   ntyp  =  3 ,
   nbnd  = 96 ,
  ecutwfc  =  90 ,
  ecutrho  =  1080 ,
  nosym =.true.
  occupations = 'fixed',
  nspin = 2 ,
  starting_magnetization(1)=1.0,
  starting_magnetization(2)=-1.0,
  tot_magnetization = 0
 /
 
diagonalization='david',
mixing_mode = 'plain' ,
mixing_beta = 0.5,
startingwfc = 'random',
conv_thr  =  1.0d-9  ,
  /

ion_dynamics='bfgs'
/

   cell_dynamics = 'bfgs' ,
   cell_dofree = 'all',
   press_conv_thr = 0.5 , ! This is the default
 /
CELL_PARAMETERS  angstrom
 5.42000.0.
 3.087050004.454943000.
 3.087050001.616616004.15127400
ATOMIC_SPECIES
Fe1  55.845 Fe.pbe-spn-rrkjus_psl.0.2.1.UPF
Fe2  55.845 Fe.pbe-spn-rrkjus_psl.0.2.1.UPF
O15.999 O.pbe-n-rrkjus_psl.0.1.UPF
ATOMIC_POSITIONS crystal
Fe1   0.14500  0.14500  0.14500
Fe1   0.85500  0.85500  0.85500
Fe2   0.35500  0.35500  0.35500
Fe2   0.64500  0.64500  0.64500
O 0.75000  0.45800  0.04200
O 0.95800  0.25000  0.54200
O 0.45800  0.04200  0.75000
O 0.25000  0.54200  0.95800
O 0.04200  0.75000  0.45800
O 0.54200  0.95800  0.25000
K_POINTS automatic
  4 4 4  1 1 1

# Conventional cell


   calculation =   'vc-relax'   ,
   verbosity = 'high' ,
   restart_mode = 'from_scratch' ,
   prefix='fe2o3' ,
   outdir='/data/mostafa/Fe2O3/fix_magnet_conventional_str3_gamma/scratch/'
,
   pseudo_dir = '/home/mostafa/data/Fe2O3/PP' ,
   tstress = .true.  ,
   tprnfor= .true.  ,
   nstep = 2000 ,
   etot_conv_thr = 7.7D-6  ,
   forc_conv_thr = 4.0D-5 ,
 /
 
   ibrav = 0 ,
nat  =  30 ,
   ntyp  =  3 ,
   nbnd  = 176 ,
  ecutwfc  =  90 ,
  ecutrho  =  1080 ,
  !!!nosym =.true.
  occupations = 'fixed',
  nspin = 2 ,
  starting_magnetization(1)= 1.0,
  starting_magnetization(2)= -1.0,
  !!starting_magnetization(3)= 0.0,
  tot_magnetization = 0
 /
 
diagonalization='david',
mixing_mode = 'plain' ,
mixing_beta = 0.5,
startingwfc = 'random',
conv_thr  =  1.0d-9  ,
  /

ion_dynamics='bfgs'
/

   cell_dynamics = 'bfgs' ,
   cell_dofree = 'all',
   press_conv_thr = 0.5 , ! This is the default
 /
CELL_PARAMETERS  angstrom
5.0288000107 0.00 0.00
   -2.514453 4.3550685598 0.00
0.00 0.0013.7302999496

Re: [QE-users] magnetism in hematite (alpha-Fe2O3)

[Mostafa Youssef]

Dear Yasser,

Thank you for your response and suggestion. I agree that DFT+U would
improve the electronic structure of Fe-oxides, but the problem I'm facing
is more related to symmetry. But to confirm this, I did actually try a
quick DFT+U  calculation and I still have the same problem that some oxygen
ions in the conventional cell develop antiferromagnetic ordering.
 I would not be worried if all oxygen ions did this (both in the
conventional and primitive cells). But the fact that only some of the
oxygen ions (in the conventional cell only) exhibit this ordering is what
makes me concerned about the way I'm setting up the system. So still any
suggestions are welcome.


Regards,
Mostafa
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Re: [Pw_forum] Zr supercell

[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
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Re: [Pw_forum] Problems computing cholensky

[Mostafa Youssef]

Dear Laurens,


When I get this error, it is typically due to a parallelization issue.
A quick fix that worked for me is using  -ndiag 1 , so for example:

pw.x_location  -ndiag 1  output_file.

Check the manual and forums for more details.


Regards,
Mostafa Youssef
AUC, Egypt.
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[Pw_forum] car parrinello md

[Youssef Aharbil]

Dear Quantum espresso Community,

I want to use the car parrinello molecular dynamics code cp.x, but first i
want to ask some basics questions about this techniques:

1-What was the main motiviation  for the use of the car parrinello md  over
the conventional variable cell relation (bfgs and damp)?
2-Is it 100% ab inition md?
3-Is there any gain in therms of accuracy or speed vs the conventinoanl
vc-relax?
4-Can I use it on crystals?

Thanks in advance.

Youssef Aharbil,
Laboratory of Physics and Chemistry of Materials
Faculty of sciences Ben msik, Casablanca
Morocco
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[Pw_forum] Questions related to Co and Fe Pseudopotentials in pslib 1and 0.31

[Mostafa Youssef]

Dear all,

I have few questions related to the above mentioned PP's.

(1)  After generating the PAW and USPP versions of these PP (pslib1.0.0) using 
ld1 code provided with  q.e.5.1.2, I applied the test script.  The output seems 
to be fine in the case of USPP but for PAW extra few lines are printed. For 
example, in the case of LDA scalar-rel Fe, I get:

Making   Fe.pz-n-kjpaw_psl.0.2.4.test.in  ...  Done !
 3 2 3D   1( 7.00)   -0.41920   -0.41398   -0.00522  !
Making   Fe.pz-n-kjpaw_psl.1.0.0.test.in  ...  Done
Making   Fe.pz-n-rrkjus_psl.0.2.4.test.in  ...  Done
Making   Fe.pz-n-rrkjus_psl.1.0.0.test.in  ...  Done
Making   Fe.pz-spn-kjpaw_psl.1.0.0.test.in  ...  Done
Making   Fe.pz-spn-rrkjus_psl.1.0.0.test.in  ...  Done

And in the case of  Fe-rel I get:

Making   Fe.rel-pz-n-kjpaw_psl.0.2.4.test.in  ...  Done !
 3 2 1.5 3D   1( 4.00)   -0.42153   -0.41623   -0.00530  !
 3 2 2.5 3D   1( 3.00)   -0.41137   -0.40618   -0.00519  !
Making   Fe.rel-pz-n-kjpaw_psl.1.0.0.test.in  ...  Done
Making   Fe.rel-pz-n-rrkjus_psl.0.2.4.test.in  ...  Done
Making   Fe.rel-pz-n-rrkjus_psl.1.0.0.test.in  ...  Done
Making   Fe.rel-pz-spn-kjpaw_psl.1.0.0.test.in  ...  Done
Making   Fe.rel-pz-spn-rrkjus_psl.1.0.0.test.in  ...  Done

Similar output obtained for Co PAW.  Are these extra printed lines indicative 
of some error in the generation?


(2) The charge density cutoff recommended (in the UPF files) for these PP is 
about 12 *ecutwfc. This large cutoff for the charge density was also employed 
in a recent paper using Fe (pslib0.31) (http://arxiv.org/pdf/1502.01534.pdf) . 
However, when I did convergence test for the total energy on a unit cell of 
SrFeO3 , and SrCO3, and it looks like 4* ecutwfc is sufficient to achieve 
convergence. The convergence in the case of SrFeO3 (pslib0.3, USPP) can be 
found here (http://web.mit.edu/myoussef/www/Fe_16e_pslib.pdf).  The pink bound 
indicates that convergence was achieved within 25 mev/unit cell (5 meV/atom)  
at ecutwfc=85 Ry and ecutrho =4 *ecutwfc. It seems to me that the recommend 
ecutrho it too strict.  Are there other tests that one needs to perform to 
check the convergence of charge density cutoff?

(3) The recommended ecutwfc and ecutrho for this set of PP in Pslib do not 
change from PAW to USPP and do not depend on the functional. I did preliminary 
tests  and it seems so far that the values work for GGA also work for LDA 
consistent with the recommendation. I wonder if one could test convergence of 
ecutwfc and ecutrho for LDA only and apply the outcome to all other semilocal 
functionals, or are there cases where one encounters different convergence 
depending on the functional.


Thank you in advance for reading and help!
Mostafa Youssef
MIT




Fe_16e_pslib0.3.pdf
Description: Fe_16e_pslib0.3.pdf
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Re: [Pw_forum] Questions related to Co and Fe Pseudopotentials in pslib 1and 0.31

[Mostafa Youssef]

Thank you very much for your reply, Prof. Dal Corso. And of course many thanks 
for the development of the library!


Mostafa Youssef
MIT
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Re: [Pw_forum] PPs for V and Cs

[Mostafa Youssef]

Hi Carlo

Both pslib0.31 (http://theossrv1.epfl.ch/Main/Pseudopotentials)  and pslib1.0.0 
(http://qe-forge.org/gf/project/pslibrary/) have relativistic PP for those two 
elements.


Mostafa Youssef
MIT
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Re: [Pw_forum] Negative Polarization !!!

[Mostafa Youssef]

Hi Mojtaba,

Polarization is a vector, so negative or positive just indicate its direction. 
So no worries about negative polarization. But in periodic boundary conditions 
you may still need to add (subtract) multiples of the polarization quantum in 
order to get the "reasonable" value of the spontaneous polarization of the 
material.

A favorite of mine which go over some of these difficulties is this  paper:

http://journals.aps.org/prb/abstract/10.1103/PhysRevB.71.014113


Mostafa Youssef
MIT


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[Pw_forum] Finite electric field (smearing , DFT+U, and total energy)

[Mostafa Youssef]

Dear PWscf users and developers,

I have 2 questions and a comment on finite electric field calculations in PWscf 
and your help and thoughts are very appreciated.


Questions:

(1)  PWscf refuses smearing in Berry phase calculations (lelfield=.true.). 
However, smearing could help in accelerating the convergence of some in-gap 
states for semiconductors that arise because of a defect or impurity. Is there 
a fundamental reason for why smearing should not be used with Berry phase 
calculations, or is it possible to modify PWscf to accept smearing?


(2) I recall Prof. Giannozzi in this mailing list mentioned that DFT+U is not 
tested with Berry phase calculations. The code does not complain about DFT+U 
with Berry phase and I have performed preliminary tests on metal oxides and 
found out that dielectric constant predicted using DFT+U and (lelfield=.true.) 
are reasonable compared to results obtained with other codes using DFTP(+U).  I 
wonder if somebody did more tests on DFT+U with Berry phase and would like to 
share their conclusion.


Comment:

(3)  The total energies that PWscf outputs in finite electric field 
calculations are in fact electric enthalpies.  One could check that the ( 
Harris-Foulkes estimate   +  (total dipole x filed)) is the what PWscf prints 
as the total energy. I think it would be nice to designate this output as the 
electric enthalpy espeically that this will be consistent with what PWscf 
prints out for calculations under pressure. (Of course with the implicit 
warning that the enthalpy inherits the uncertainty in the polarization quantum).


Thank you,
Mostafa Youssef
MIT


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Re: [Pw_forum] Finite electric field (smearing , DFT+U, and total energy)

[Mostafa Youssef]

Thank you very much for addressing my questions, Prof. Giannozzi ! I will keep 
the mailing list updated if I succeed in reasonably getting smearing work with 
finite electric fields.


Mostafa Youssef
MIT


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Re: [Pw_forum] HSE Si Lattice Parameter

[Mostafa Youssef]

Hi Galvin,

Examining the energies and stresses you obtain from your calculations by the 
eye is not a very accurate way to obtain the lattice parameter that minimizes 
the energy and corresponds to a zero pressure. More accurate is to fit your 
results to an equation of state such as Birch-Murnaghan or Vinet.  The reason 
is that most likely the optimal lattice parameter lies in between the values 
you obtained from your scf results. As a bonus you get also other useful 
parameters form the fit like the bulk modulus.
However, make sure that all the data points you use in the fit correspond to 
hydrostatic stress by examining the stress tensor printed in output file. This 
is because all these equation of states assume hydrostatic stress in their 
derivation.


Mostafa
MIT
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Re: [Pw_forum] Ion

[Mostafa Youssef]

Hi Ashkan,

Click on the title your thread or alternatively search the forum with the 
keyword ion and you will find detailed answers to your question.

See for example:

http://www.mail-archive.com/pw_forum%40pwscf.org/msg09585.html


and also the manual entry:

http://www.quantum-espresso.org/wp-content/uploads/Doc/INPUT_PW.html#idp110032


Mostafa Youssef
MIT
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Re: [Pw_forum] spin polarization

[Mostafa Youssef]

Hi Tayebeh

I think all what you need to calculate a helix of magntic moments for Co ions 
in  SrCO3 would be:

1- Noncollinear calculations.
2- A larger supercell to accommodate the helix.
3- Fully relativistic pseudopotentials (such as those in Pslib)
4- Define different Co species each with different direction for the magnetic 
moment
5- You might also wish to use vc_relax rather than relax with cell_dofree to 
fix the volume but vary the shape of the cell. Or just vc_relax if you want to 
get a quick answer.


I think all these ingredients are available and Pwscf is ready to tackle SrCO3 !


Mostafa Youssef
MIT

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Re: [Pw_forum] control strain calculations

[Mostafa Youssef]

Hi Imène,


I guess the sopping criterion is  press_conv_thr.


http://www.quantum-espresso.org/wp-content/uploads/Doc/INPUT_PW.html#idp365664


Mostafa Youssef
MIT
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Re: [Pw_forum] Is geometry optimization same to MD?

[Mostafa Youssef]

Hi Shaofeng,


Relaxation will give you "a" structure but most likely it is not a 
representative  structure. MD will give you a set of possibly meaningful and 
representative solvation structures. If you average over these  meaningful 
structures, you can get useful information about the solvation of arsenic ion.

Arsenic is anticipated to be ionized in water, so you will need a charged 
system but Q.E. will automatically apply a neutralizing background.

Have a look at some of the early DFT MD work on solvation to get a better idea 
about what can and cannot be done.
For example:

http://www.sciencedirect.com/science/article/pii/S0009261497006180

Mostafa Y.
MIT
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Re: [Pw_forum] control strain calculations

[Mostafa Youssef]

>if you can please give me more details about how to control the number of cell 
>relaxed , because it is the same with
>different press-conv-thr . for example I want to relax only the c axis keeping 
>a and b fixes, by using cell-dofree='z' ,
>but I would give the number of c which i want to relax ? is that possible?!


Hi Imène,
I'm not very sure that I understand, but I guess if you use cell-dofree='z'
and vary press_conv_thr (to smaller values) and still get the same value of
the c-axis after vc_relax than that indicates that the results that you get
for the c-axis is not that sensitive to the stopping criterion imposed by
press_conv_thr.  If you the post the input file with more details then may be
somebody with better expertise in this can help.


Mostafa Y.
MIT

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Re: [Pw_forum] How to calculate charged system binding energy?

[Mostafa Youssef]

Dear Bahadir

First, charged slabs are problematic because their total energy does not 
converge with respect to vacuum thickness. You can test on a simple model.  
However, there is a trick to go around this by inserting a dopant far a way 
from the critical reaction zone.  For example suppose you want to study +1 
charged defect on ZrO2 surface.  Then you can insert one Y ion(typically 3+ and 
hence -1 with respect to Zr4+) .   This should generate a positive charge 
somewhere else in the slab and one hopes that this positive charge will 
localize correctly where you expect it to localize.  But one has to be cautious 
because this also generates a large dipole across the slab. One way to go 
around this by symmetrizing the slab such that dipoles cancel.


Second, even if charged slabs work, I think you are not conserving the charge 
when you calculate the binding energy. Because you mentioned you used  
tot_charge=-1 in the slab+molecule , slab only, molecule only. To me this will 
not conserve the charge when you calculate the binding energy (B.E.)

B.E. =(slab+molec.)  - (slab) - (molec)

Although I have seen papers defining binding energies that do not conserve the 
charge, I do not think this is meaningful.

Mostafa Y.
MIT
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Re: [Pw_forum] Can I obtain IR spectrum from CPMD trajectory in Quantum Espresso?

[Mostafa Youssef]

Dear Yin,

You already got great suggestions. I would like to add one more option to 
calculate IR from ab initio MD. You could do scf calculation on each 
configuration obtained via MD to calculate Maximally Localized Wannier 
Functions (MLWF). From MLWF you could calculate the dipole moment of the 
simulation cell or even for single molecules inside the cell at each time step. 
It is straightforward to obtain IR  once you have the dipole moment at each 
time step.

An example for this option can be found here:

http://journals.aps.org/prl/abstract/10.1103/PhysRevLett.98.247401

Note that the authors of this paper implemented Wannier on the fly which I 
think is not available in Q.E. But the computational cost to re-track the 
trajectory and calculate MLWF should not be too expensive if one already 
affords the MD run.


Mostafa Youssef
MIT


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Re: [Pw_forum] tot_charge flag with DFT+U calculations

[Mostafa Youssef]

Dear J. Park,

In principle there is no problem at all and there have been publications 
addressing charged defects based on Q.E. calculations employing DFT+U.  See for 
example:
http://pubs.acs.org/doi/abs/10.1021/jp1041316

The only practical detail worth mentioning in my opinion is that if you use 
fixed occupations then you are forced to specify the total magnetization of the 
super cell instead relying on self-constant determination of the magnetic 
moment.  One way to go around this is to use small smearing and then 
self-consistent determination of the total magnetic moment is possible (of 
course starting from some initial guess).

Mostafa Youssef
MIT
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Re: [Pw_forum] DFT+U calculatoopns

[Mostafa Youssef]

Hi Adnan,


The effect of DFT+U on the phonon dispersion of materials with soft-modes such 
as TiO2 is large. Not only quantitatively but also qualitatively.  See for 
example:

http://www.sciencedirect.com/science/article/pii/S1567173910004682


and figure 8 in:

http://iopscience.iop.org/0953-8984/26/12/122203/


If your main goal is to study phonons of TiO2 , I would recommend LDA or 
PBEsol.  But if you insist on using DFT+U , then you can use PHONOPY + PWscf 
code of Q.E equipped with a *large* supercell of TiO2.  This should allow you 
to calculate phonon dispersion in frozen phonon approximation with Parlinski et 
al interpolation.  Please follow the instructions on PHONOPY website.


Mostafa YOussef
MIT
P.S. Somehow I read the title of your thread as DFT+U cartoons !
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Re: [Pw_forum] DFT+U calculations

[Mostafa Youssef]

Dear Muhammad ,

This is really tricky. Using DFT+U for 0K energies followed by DFT for phonons 
is a bit inconsistent.  I would rather be consistent and understand the 
limitations of the theory rather than trying to mix inconsistent parts together.

You could ignore the vibrational contribution as suggested by Jia Chen , 
although I think at high temperature this contribution might be significant. 
Alternatively you could resort to the extremely expensive hybrid functionals  
to do both 0K energies and phonons (within frozen phonon approximation). 
Another sound alternative is just to use DFT+U for 0K energies and phonons with 
the clear understanding that therer might be some error associated with the 
phonons part.  In fact, although literature clearly shows that DFT+U predicts 
qualitatively problematic phonon dispersion for soft-mode materials such as 
TiO2 , there has not been a systematic investigation of the performance of 
DFT+U in predicting vibrational free energy *differences* between a perfect 
crystal (TiO2) and a defective one (TiO2-x) for this class of materials.  I 
would be very interested if somebody can point out to a paper that addressed 
this.


Mostafa Youssef
MIT
<http://www.mail-archive.com/search?l=pw_forum@pwscf.org=from:%22Muhammad+Adnan%22>
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Re: [Pw_forum] DFT+U calculations

[Mostafa Youssef]

Dear Adnan,

Please check the two papers I cited  in my earlier message.  In  the 2014 J. 
Phys. Condens. Matt. paper , it was shown that U on Ti in SrTiO3  removes the 
the Gamma point instability and enhances the M-point instability.  In the other 
paper there is more discussion of the effect of U on TiO2 phonons.



Mostafa Youssef
MIT
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[Pw_forum] Serial vs. parallel runs of berry.in test case

[Mostafa Youssef]

Dear all,

I tried to run the standard tests of PWscf  both in series and in parallel. In 
series all is fine.  In parallel, I found the case of berry.in to be 
problematic as I got an error:

 Error in routine addusdens_r (1):
 WRONG CHARGE expected  44.00, found  44.404701: ions may be overlapping or 
increase ecutrho

And the code stops at the first scf step. When I double the energy and charge 
density cutoffs , it works  well in parallel. This behavior is reproduced in 
versions 5.1.1, 5.1.2, and 5.2.0.

Any thoughts on the possible reasons are appreciated.


Thank you,
Mostafa Youssef
MIT
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Re: [Pw_forum] Serial vs. parallel runs of berry.in test case

[Mostafa Youssef]

Thank you, Prof. Giannozzi.  I tested one more time and found out that by 
removing tqr=.true. it works on 8 processors even with an FFT grid of 36x36x36. 
 With tqr=.true. , the FFT grid has to be multiples of 8.



Best Regards,
Mostafa Youssef
MIT

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Re: [Pw_forum] Serial vs. parallel runs of berry.in test case

[Mostafa Youssef]

Thank you very much for fixing this, Prof. Giannozzi !


Best Regards,
Mostafa Youssef
MIT
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Re: [Pw_forum] nscf+lelfield -----> Wrong k-string? Error

[Mostafa Youssef]

Dear Mojtaba,

I have not encountered this error before, so I cannot comment on it.

But I think it is a little bit strange to apply the electric field in the nscf 
calculation only.  If you would like to calculate the polarization in the 
presence of the electric field , you need 2 scf calculations. The first at zero 
field but still with lelfield=.true., the second starts from the wave functions 
generated from the first but has the magnitude of the field you would like to 
apply.  Please see example 10 in PW/examples.



Mostafa Youssef
MIT
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Re: [Pw_forum] Question on pseudopotential

[Mostafa Youssef]

Hi Sridhar,

Of course you can do this mix. Please have a look at:

http://www.quantum-espresso.org/faq/pseudopotentials/#2.3


M. Y.
MIT
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Re: [Pw_forum] Failed in tests and examples

[Mostafa Youssef]

Hi Fei Mao,

Please post the error message in the file  b3lyp-h2o.out. Apparently the test 
stopped when it encountered error message here.


M. Y.

MIT
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Re: [Pw_forum] Choice of Pseudopotential

[Mostafa Youssef]

Hi Elham,

Testing Pseudopotentials and choosing optimal ones is a daunting task that 
needs some serious work. In addition to the valuable advice you quoted from 
Prof. de Gironcoli, I'd add that converging total energy will lead you to a 
very safe e_cut and rho_cut but probably one can afford a little less accuracy 
than the very safe one. The way to test is to focus on the quantity you care 
about and try to check its convergence.


See for example this descent work on testing PP's and finding optimal cutoffs 
based on phonon frequency convergence and equation of state error with respect 
to all electron calculations (among other things):

http://materialscloud.org/sssp/

A similar example is GBRV library for which the criteria for convergence (as 
stated in the authors paper) is energy difference rather than absolute total 
energy:

http://www.physics.rutgers.edu/gbrv/


I hope this helps.
M. Y.
MIT
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Re: [Pw_forum] Failed in tests and examples

[Mostafa Youssef]

Dear Fei

As the message indicates there is a problem in reading the norm conserving 
pseudopotential file. I think this may also be the reason why example01 did not 
work because it uses NC PP for Si.

Try the attached version of the H and O PP used in the H2O test. The attached 
worked for me. Or may be download a Si NCPP from Q.E website and try again 
example 1 (of course after modifying the name of the PP in the input file). Or 
even try example with Ultrasoft PP to see if it works at all with your compiled 
version of Q.E.


Also diff the attached with the ones you have to see what is the cause of the 
problem.


Mostafa
MIT


H.blyp-vbc.UPF
Description: H.blyp-vbc.UPF


O.blyp-mt.UPF
Description: O.blyp-mt.UPF
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[Pw_forum] Force calculation time in relaxation under electric field

[Mostafa Youssef]

Dear all,


I performed ionic relaxation for 3x3x3 unit cells of a semiconducting oxide 
under electric field (lelfield =.true.) using ultrasoft PP and 1x1x3 MP K-point 
grid where 3 is in the direction of the electric field. These are GGA+U 
calculations. I noticed in the time report that force calculations time is 
becoming even more than the electrons time as shown below:

 init_run :  8.32s CPU  8.91s WALL (   1 calls)
 electrons:  42723.25s CPU  44995.21s WALL (   5 calls)
 update_pot   :  2.62s CPU  3.19s WALL (   4 calls)
 forces   :  66735.95s CPU  66943.64s WALL (   5 calls)

This is first time in which I find PWscf use more time in force calculations 
than in electrons. For the same system and without electric field , forces time 
would be about 0.2 of electrons time.  Is this a normal behavior and is there a 
recommended possibility to reduce force calculation time?

I attempted using Norm Conserving PP's but unfortunately I could not get the 
code pass the 1 ionic step because of the S matrix not being positive definite.

I appreciate your thoughts on this.

Regards,
Mostafa Youssef
MIT

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Re: [Pw_forum] Force calculation time in relaxation under electric field

[Mostafa Youssef]

Thank you for replying, Prof. Giannozzi.  I'm using version 5.2.0, the system 
has 135 atoms  of which 108 has U correction.   I'm running it on 32 processors 
with 1 pool,  a serial algorithm for Linear algebra to avoid "error in Cholesky 
decomposition",  and 1 task group.

I'm a bit surprised because the time report of the same system without electric 
field and with a denser Kpoint grid (2x2x2) looks like:

 init_run : 38.32s CPU 39.48s WALL (   1 calls)
 electrons:   9042.53s CPU   9168.56s WALL (   8 calls)
 update_pot   :  4.99s CPU  6.13s WALL (   7 calls)
 forces   :873.59s CPU949.08s WALL (   8 calls)
 stress   :   3211.03s CPU   3260.70s WALL (   8 calls)

Here the forces is just a tiny fraction of the electrons time.


Regards,
Mostafa
MIT


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Re: [Pw_forum] Force calculation time in relaxation under electric field

[Mostafa Youssef]

The last time report I quoted is with Hubbard U and this in fact what I 
typically find in PWscf relaxation calculation.

I will send you the two output files offline. Thank you very much for your help!


Regards,
Mostafa
MIT
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Re: [Pw_forum] Temperature effect on band gap

[Mostafa Youssef]

Dear Reza,


In addition to what Lorenzo suggested in relation to the accuracy of DFT in 
describing the band gap,  there is a possibility that point defects can play a 
role in reducing the gap as the temperature increases.  You might need to 
inspect the literature more to see how the observed reduction in the band gap 
was explained for the material of interest.



Regards,
Mostafa
MIT

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Re: [Pw_forum] Finding the most stable structure

[Mostafa Youssef]

Dear Reza,

Exploring the potential energy surface of glassy systems is not a trivial 
problem not to mention impurities in glassy systems. Depending on how deep you 
want to explore this,  you may want to explore PLUMED package which is 
compatible with PWscf.

http://www.plumed-code.org/

For something quick, I would run an MD at very high temperature , take 100 
snapshots from the run , and relax them at zero temperature.

Regards,
Mostafa
MIT
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[Pw_forum] Total potential under Berry phase electric field

[Mostafa Youssef]

Dear all,

I plotted the total potential (bare + Hartee + xc) for MgO under finite 
electric field applied via Berry Phase approach. This is basically example 09 
in  CPV/examples and I run the same calculation also using PWscf.  Attached is 
the result. In particular the macroscopic average of the total potential is 
zero.  Is the total scalar potential really flat under electric field applied 
via Berry phase or is there something wrong with what the code prints as the 
total potential?

I'm still trying to understand how the electric field is applied in this case , 
in particular how the non-periodicity of the scalar potential is avoided.

Any thoughts or references are highly appreciated.

Mostafa Youssef
MIT


MgO_poential.pdf
Description: MgO_poential.pdf
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Re: [Pw_forum] Total potential under Berry phase electric field

[Mostafa Youssef]

This question is resolved.  I understand a little better now that in small 
field regime one solves for polarized Bloch states and as such the charge 
density is indeed periodic.


Mostafa
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Re: [Pw_forum] DFT+U with static homogeneous finite electric field or Uniaxial tensile strain

[Mostafa Youssef]

Dear Yusuf,


I'm not a developer but from my limited experience,  I can tell that 
cell_dofree tag (the key to apply uniaxial strain) works well with DFT+U  (With 
NC and USPP, I'm not sure about PAW).  Finite electric field with DFT+U (NC and 
USPP) seems to work well too based on few tests I did on computing the 
dielectric constant for oxides with DFT+U.


Examples 08, 10 and VCSexample give you the basic elements for what you asked. 
But you need to combine and compose something out of these examples to meet 
your needs.


Mostafa
MIT


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Re: [Pw_forum] total energy for charged defects in semiconductors

[Mostafa Youssef]

Dear  Manhong,

As far I know the incosistency of treating charged defects within PAW formalism 
discussed in  PHYSICAL REVIEW B 89, 045116 (2014) has not been resolved in any 
pseudopotential code. I  wish I can devote more time  to study this paper more 
carefully.

Regarding the second paper,  PHYSICAL REVIEW B 91, 024107 (2015), it suggests 
that the arbitrariness  in the reference of the electrostatic potential has a 
sizable effect on the pressure (stress) calculated by DFT codes for charged 
systems.  Figure 1 tells the whole story.  The authors suggested a method to 
correct for that given the bulk modulus (eleastic constants) and the 
deformation potential. of the host semiconductor.  However, the paper is of 
concern if you plan to do variable cell relaxation.  Most of the charged 
defects papers focus on fixed volume calculations claiming that this is a good 
way to represent dilute limit of defects.

In summary, if you plan to do fixed volume calculations, the second paper 
should not be of concern  (roughly speaking).  Resolving the inconsistency of 
the first paper is to be implemented. To avoid it one might use all electron 
code.


M. Y.
MIT
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Re: [Pw_forum] Band gap hybrid functionals

[Mostafa Youssef]

Dear Phil and all,


Note that for a functional with exact exchange, the difference between 
ionization potential and electron affinity (I-A) is not the same as the 
Kohn-Sham single particle states  gap.  The consensus, as far as I know, is 
that I-A is more physical and relevant to comparison with experimental band 
gaps.  Calculating I-A  requires 3 scf calculations (neutral cell, +electorn, 
-electron).  The cases of +/- e require high smearing similar to that of metals 
(or you could use the tetrahedron method but I doubt it is implemented for 
hybrids). Also +/-  calculations require large cells and correction for a 
charged cell (Makov-Payne for example).  See section III-A in this paper for 
elaboration on computational details:

PHYSICAL REVIEW B 78, 235104 ?2008?

For PBE, LDA, ...  I-A is the same as  Kohn-Sham gap.

For elaboration on the theoretical aspects and why I-A is not the same as K-S 
band gap for the exact exchange, consult the work of A. J. Cohen and 
collaborators .

Mostafa
MIT
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Re: [Pw_forum] optimized Vanderbilt pseudos

[Mostafa Youssef]

Dear Stephan,

The ONCV are norm conserving  so 4*ecutwfc should be fine.



Mostafa Youssef
MIT
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Re: [Pw_forum] DOS Without 'Relax' ?

[Mostafa Youssef]

Dear Victor,


I think there is nothing fundamentally wrong with calculating DOS from 
snapshots obtained from finite T MD. I  also have seen this once in the 
literature from the work of Prof. A. Selloni group on TiO2/water interfaces 
somewhere around 2010.

 One could argue that even the single particle Kohn Sham DOS obtained for a 
relaxed structure are meaningless  but a lot of the researchers in 
computational materials pragmatically accept it as an insightful tool. My 
opinion is one can compute, think, and interpret but keep in mind that DFT is a 
ground state theory.

Mostafa
MIT


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Re: [Pw_forum] non-cubic dielectric tensor in a cubic crystal.

[Mostafa Youssef]

Hi Eduardo,


I also get a non-cubic dielectric tensor for cubic semiconductors when I allow 
the computation of the nonanalytic terms by specifying a q-vector and q is not 
equal 0.  But I do not fully understand what is going on here.  I think (but 
not very sure) if you do not specify q then you actually calculate the 
nonanalytic terms for q->0 and then you recover the correct cubic tensor with 
zone center phonons contribution.

On the other hand calculating epsilon_0 by applying electric field and relaxing 
the ions yields a reasonable cubic dielectric tensor.


I hope somebody can help in clarifying this.

Mostafa Youssef
MIT
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[Pw_forum] Error in routine punch_band_2d (1): Problems with k points

[Youssef Aharbil]

Dear all,

I am studying a double perovskite band structure under a trigonal crystal
system (ibrav = 5), the Brillouin zone sampling has been performed using
this path:

K_POINTS tpiba_b
11
gG 25
L  25
B1 1
B  25
Z  25
gG 25
X  1
Q 25
F 25
P1 25
Z  1
L  25
P 1

all calculations run well, till the stage of the extraction of bands using
bands.x, I got this error while plot_2D = .true.

 %%
 Error in routine punch_band_2d (1):
 Problems with k points
 %%

 stopping ...

The problem disappear when plot_2D = .false..

This error has been already posted in a previous thread, Prof Paolo
suggested to check these conditions (from bands.f90) :

!  This routine opens a file for each band and writes on output
!  kx, ky, energy,
!  kx, ky, energy
!  .., .., ..
!  where kx and ky are proportional to the length
!  of the vectors k_1 and k_2 specified in the input of the 2d plot.
!
!  The k points are supposed to be in the form
!  xk(i,j) = xk_0 + dkx *(i-1) + dky * (j-1)  1

Re: [Pw_forum] Oxidation state for dopants in TiO2

[Mostafa Youssef]

Dear Giacomo,

If the supercell is charge neutral which is the default, then one aims at 
simulating a neutral substitutional defect with respect to Ti. In this case V 
in 4+ oxidation state which corresponds in the naive fully ionic picture to V 
losing 4 of its valence electrons to oxygen and retaining the last one as you 
said.  The question arises whether this  electron is localized on the V site 
and it is really in 4+ oxidation state. The other alternative is that the 
electron delocalizes and the supercell contains V in 5+ oxidation state and an 
extra "free" electron. In my opinion the best  way to analyze this problem is 
to  start from the most positive oxidation state and systematically reduce it. 
In the case of V you can do 6 separate relaxation simulations starting from 
tot_charge=+1 which corresponds to V on 5+ oxidation state, all the way to 
tot_charge=-4 which corresponds to V in 0 oxidation state. After these 6 
simulations are done you can track the changes in the charge density and spin 
density when you go from the oxidation state q to the oxidation state q-1. In 
my experience V in oxides such as TiO2 can take oxidation states from 5+ to 2+. 
 If you compare 1+ and 2+ you will notice that the extra electron you add to 2+ 
to achieve 1+ never localizes on V and as such 2+ is likely the lowest 
oxidation state for V in these oxides.


If you do not want to do this lengthy analysis and you just want to check 
whether you have 4+ or not , check the spin density. V4+ will likely have a net 
magnetic moment close to 1 Bohr Mag.


Also there are many cases in literature where achieving certain oxidation state 
never happens because of electron (hole) delocalization. For example, if you 
try to model neutral hydrogen interstitial in ZnO or ZrO2, you will get 
interstitial proton and a free delocalized electron. See for example:
http://journals.aps.org/prl/abstract/10.1103/PhysRevLett.85.1012


A final word of caution, analyzing the oxidation states of transition metal 
dopants and their changes by adding or removing electrons requires very dense 
and accurate grids for representing the charge (and spin) density. The reason 
is that the change of the localized charge (if any) on the transition metal 
defect while going from formal oxidation state q to q-1 is usually very low (in 
my experience in the order of 0.1 e). This observation was discussed in this 
article: http://www.nature.com/nature/journal/v453/n7196/full/nature07009.html

(It is also fun and instructive to follow the debate that this paper raised in 
literature!)

Best Regards,
Mostafa Youssef
MIT
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Re: [Pw_forum] Spin-Polarized NEB

[Mostafa Youssef]

Dear Giuseppe,


The ethylene rotation example you mentioned is very interesting.  I wonder if 
there is a reference you recommend that carefully analyzed this case with DFT 
or other quantum chemical approaches.


Best Regards,
Mostafa
MIT



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[Pw_forum] Ultrasoft or Norm conserinvg PP for Ce

[Mostafa Youssef]

Dear all,


I wonder if there is a reasonably performing Ce PP,  US or NC , with 12 valence 
electrons and  non-linear core correction.


Thank you,
Mostafa
MIT
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Re: [Pw_forum] Ultrasoft or Norm conserinvg PP for Ce

[Mostafa Youssef]

Dear Mehmet,

Thank you for the link to the PAW dataset and your advice regarding the 
convergence of DFT+U.  As much as I'm willing to test this dataset ,  my 
current investigations require Ultrasoft or Norm conserving PP because of the 
limited implementation of PAW calculations in Q.E. package.


Best Regards,
Mostafa
MIT

From: Mehmet Topsakal [mtops...@umn.edu]
Sent: Thursday, March 10, 2016 3:58 PM
To: PWSCF Forum; Mostafa Youssef
Subject: Re: [Pw_forum] Ultrasoft or Norm conserinvg PP for Ce

Dear Mostafa,

Please find our PAW potentials for rare-earth elements here :
http://www.vlab.msi.umn.edu/resources/repaw/index.shtml
and our paper
http://www.sciencedirect.com/science/article/pii/S0927025614005059

I've tested these for various different systems. I always compare QE and VASP 
results.
I have not noticed any discrepancy between my potentials and VASP.

You should be careful with the occupations. Usually it is necessary to enter 
occupations
by hand using starting_ns_eigenvalue(m,ispin,I)  
http://www.quantum-espresso.org/wp-content/uploads/Doc/INPUT_PW.html#idm6307200.
Otherwise calculations do not converge !!!

Bests



On Tue, Mar 8, 2016 at 1:39 AM, Mostafa Youssef 
<myous...@mit.edu<mailto:myous...@mit.edu>> wrote:
Dear all,


I wonder if there is a reasonably performing Ce PP,  US or NC , with 12 valence 
electrons and  non-linear core correction.


Thank you,
Mostafa
MIT

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--
Mehmet Topsakal
Chemical Engineering and Materials Science,
University of Minnesota, Research Associate,
http://www.researchgate.net/profile/Mehmet_Topsakal
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Re: [Pw_forum] vc-relax problem

[Mostafa Youssef]

Dear David,


In principle, starting from a 2D material and applying vc_relax should end up 
with the 3D version of the material. That is in the graphene case you should 
end up with graphite upon complete convergence.  I doubt that this simulation 
is your intention here.

If you would like , instead, to study biaxial strain effect on doped graphene, 
then simple manual changes of the a and b of the supercell and relax  
calculation should do the job.



Best Regards,
Mostafa
MIT
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[Pw_forum] negative occupations in DFT+U for nonmagnetic semiconductor

[Mostafa Youssef]

Dear all,

I'm relaxing the structure of rutile TiO2 using ultrasoft pseudopotentials for 
Ti and O and PBEsol + U with U=5 eV on Ti.  For that purpose I use occupations 
= 'fixed'.  But I found that one of the Ti ions has negative occupations. To me 
this looks a bit strange since I'm not using any smearing.  The same result can 
be obtained by another set of PP. Improving the cutoffs or the k-point sampling 
does not resolve the problem. Any thoughts about the reason and possible 
remedies are appreciated.  I copy below the occupation matrices for the two Ti 
ions in the cell and the input file.


Thank you,
Mostafa Youssef
MIT

The matrices are:

atom1   Tr[ns(na)] =   2.70769
eigenvalues:
  0.142  0.177  0.182  0.417  0.436
eigenvectors:
  0.675  0.000  0.000  0.325  0.000
  0.000  0.000  0.500  0.000  0.500
  0.000  0.000  0.500  0.000  0.500
  0.000  1.000  0.000  0.000  0.000
  0.325  0.000  0.000  0.675  0.000
occupations:
  0.231  0.000  0.000  0.000 -0.129
  0.000  0.309 -0.127  0.000  0.000
  0.000 -0.127  0.309  0.000  0.000
  0.000  0.000  0.000  0.177  0.000
 -0.129  0.000  0.000  0.000  0.328
atom2   Tr[ns(na)] =   2.70768
eigenvalues:
  0.142  0.177  0.182  0.417  0.436
eigenvectors:
  0.675  0.000  0.000  0.325  0.000
  0.000  0.000  0.500  0.000  0.500
  0.000  0.000  0.500  0.000  0.500
  0.000  1.000  0.000  0.000  0.000
  0.325  0.000  0.000  0.675  0.000
occupations:
  0.231  0.000  0.000  0.000  0.129
  0.000  0.309  0.127  0.000  0.000
  0.000  0.127  0.309  0.000  0.000
  0.000  0.000  0.000  0.177  0.000
  0.129  0.000  0.000  0.000  0.328
N of occupied +U levels =5.415371

The input file:

   calculation =   'vc-relax'   ,
   verbosity = 'high' ,
   restart_mode = 'from_scratch' ,
   outdir='./' ,
   pseudo_dir = './' ,
   tstress = .true.  ,
   tprnfor= .true.  ,
   nstep = 2000 ,
   etot_conv_thr = 1.0D-7  ,
   forc_conv_thr = 4.0D-5 ,
 /
 
   ibrav = 0 ,
nat  =  6 ,
   ntyp  =  2 ,
   nbnd  = 48 ,
  ecutwfc  =  45 ,
  ecutrho  =  360 ,
  nosym =.true.
  occupations = 'fixed',
  lda_plus_u = .true.,
  Hubbard_U(1) = 5.0 ,
  Hubbard_U(2) = 0.0 ,
 /
 
diagonalization='david',
mixing_mode = 'plain' ,
mixing_beta = 0.7,
startingwfc = 'random',
conv_thr  =  1.0d-8  ,
  /

ion_dynamics='bfgs'
/

   cell_dynamics = 'bfgs' ,
   cell_dofree = 'shape',
   press_conv_thr = 0.5 ,
 /
CELL_PARAMETERS  angstrom
4.63202526698411180.0.
0.4.63202526698411180.
0.0.2.960893414442
ATOMIC_SPECIES
  Ti   47.867   ti_pbesol_v1.4.uspp.F.UPF
  O15.9994  o_pbesol_v1.2.uspp.F.UPF
ATOMIC_POSITIONS crystal
Ti   0.  0.  0.
Ti   0.5000  0.5000  0.5000
O0.3048741584772117  0.3048741584772117  0.
O0.6951258415227883  0.6951258415227883  0.
O0.8048741584772117  0.1951258415227883  0.5000
O0.1951258415227883  0.8048741584772117  0.5000
K_POINTS automatic
  4 4 6  1 1 1

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Re: [Pw_forum] negative occupations in DFT+U for nonmagnetic semiconductor

[Mostafa Youssef]

Thank you for the clarification, Prof. de Gironcoli.  I think I misinterpreted 
the meaning of the matrix elements.

Best Regards,
Mostafa
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Re: [Pw_forum] Full k-points in Brillouin Zone (turning-off all symmetries)

[Mostafa Youssef]

Thank you for clarification, Ryky!


Best Regards,
Mostafa
MIT
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[Pw_forum] space_group, crystal_sg, and Wyckoff position still implemented in QE?

[Youssef Aharbil]

Dear han.
Because "nat" means simply the number of lines to be input not the number
of atoms generated via all of wyckoff sites.

Youssef Aharbil.
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Re: [Pw_forum] Band gap value through charged supercell calculation

[Mostafa Youssef]

Dear Perevalov,


The K-S gap in left panel of Fig.2  in the paper is not what you get directly 
from the occupations of the neutral cell. What is shown in the figure is 
calculated using equation 13  which uses eigenvalues from the neutral cell and 
occupations from charged cell. This way there will a dependence on carrier 
concentration.
I believe what you plotted  and found to be independent of "cell size" is K-S 
gap using both eignevalues and occupations of the neutral cell.


You mentioned;  "I understand that dependence on the supercell size is due to 
compensating charge background". In fact even if you correct for the 
compensating background , you will still observe dependence on the charge 
density for I-A  and K-S calculated with equation 13.  In the dilute limit of 
charged carriers you should converge to K-S gap of the neutral cell in the case 
of functionals that do not have exact exchange (LDA, GGA, BYLP, ...).  For 
hybrid functionals that contains exact exchange (PBE0, HSE, ...) there will be 
a difference  between I-A and K-S (neutral) even in the dilute limit.  This is 
also discussed in the paper you cited right before Fig. 2.

It is common, at least in semiconductor defects  studies , to regard I-A as 
"the" band gap of the material.  Some may agree , others do not.


For  monoclinic ZrO2,  the first order M-P correction was reported here:

http://journals.aps.org/prb/abstract/10.1103/PhysRevB.75.104112

Of course based on the lattice parameters and supercells that the authors 
reported.


In computing the K-S gap of a neutral cell I would use the tetrahedron method  
or fixed occupations (i.e no smearing) and a dense K-point mesh

 Regards,
Mostafa  Youssef
MIT




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Re: [Pw_forum] Band gap value through charged supercell calculation

[Mostafa Youssef]

Dear Evan and Layla,
E(N+x)  where x is a real number can be calculated using tot_charge:

http://www.quantum-espresso.org/wp-content/uploads/Doc/INPUT_PW.html#idm6396048


The ionization potential is not well-defined in bulk as Layla described but the 
difference I-A is well-defined for bulk.

I-A= E(N+1)+E(N)-2E(N)


Regards,
Mostafa
MIT
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Re: [Pw_forum] Question about electron (pseudo-)charge density calculations in QE

[Mostafa Youssef]

Dear Reza,


If hydrogen can transform to Silicon than Quantum Espresso is an all Nucleon 
code that simulates Fusion :-)

Check your Pseudo !


Regards,
Mostafa
MIT
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Re: [Pw_forum] Band gap value through charged supercell calculation

[Mostafa Youssef]

Correction:


I-A= E(N+1)+E(N-1)-2E(N)



Mostafa
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Re: [Pw_forum] Band gap value through charged supercell calculation

[Mostafa Youssef]

Dear Evan,


I would consult literature for that matter.  It is very difficult and 
counterproductive to discuss this in an online forum.


Mostafa
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Re: [Pw_forum] Band Offsets too large

[Mostafa Youssef]

Dear Dae Kwang Jun,

You also need 2 bulk calculations for AlAs and GaAs to get their band edges 
with respect to to their bulk electrostatic potentials. Then you can use the 
interface potential to align the band edges of the two semiconductors.  It 
looks like you missed this step.



Mostafa
MIT


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Re: [Pw_forum] Band Offsets too large

[Mostafa Youssef]

Dear Dae Kwang Jun


In addition for each bulk calculation one needs to calculate the bulk average 
electrostatic potential.  Then for each compound you refer its EVBM to the 
electrostatic potential calculated in  its bulk (not yet the interface).  Only 
then you can use the interface electrostatic potential according too:

EVBM_offset =  EVBM_AlAs   -  EVBM_GaAs +  del_V_interface_AlAS/GaAS

where EVBM_AlAs is referred to bulk V_AlAs and EVBM_GaAs is referred to bulk 
V_GaAs.


Regards,
Mostafa
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Re: [Pw_forum] Band Offsets too large

[Mostafa Youssef]

Dear  Dae Kwang Jun

Equation (1) that you wrote is the correct one.

And you are right  bulk V_AlAs and bulk V_GaAs are obtained in a similar way as 
in the interface but you need bulk cells.  Their values can be anything , 
positive or negative it does not matter and  in fact they are arbitrary.


Regards,
Mostafa

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[Pw_forum] epsilon calculation in the case of a soft mode

[Mostafa Youssef]

Dear all,


I'm studying an oxide with an optical mode frequency that is imaginary before 
applying a.s.r. and becomes real once a.s.r is applied. In the same input file 
for dynmat.x I requested computing epsilon. But it seems that epsilon is 
calculated based on frequencies (w2) before applying a.s.r.

Is there a way to enforce epsilon calculations based on frequencies after a.s.r 
application ?


I'm using Q.E.5.2.0 but I believe recent versions do not have updates in this 
part of the code.



Thank you,
Mostafa Youssef
MIT
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Re: [Pw_forum] Macroscopic Polarization

[Mostafa Youssef]

Dear Subhodip,

Check example04 provided with pw.x. You can find it  in:

/Espresso_folder/PW/examples/example04



>From README:
example04:
This example shows how to calculate the polarization via Berry
Phase in PBTiO3 (contributed by the Vanderbilt Group in Rutgers
University).

I would also recommend this paper:
https://arxiv.org/abs/1202.1831



Mostafa
MIT
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Re: [Pw_forum] rectangular surface of Al2O3

[Mostafa Youssef]

Dear Andrey,


I'm not particularly familiar with Al2O3 surfaces, but in general cutting 
rectangular surfaces can be accomplished in many cases by cutting the same 
surface from primitive cell instead of the conventional well.

For example (111) is not rectangular in tetragonal Hf2O based on the 
conventional cell. Starting from the primitive cell, this surface  becomes 
(101) and the cut becomes rectangular.

I believe the primitive cell of Al2O3 is Rhombohedral.



Hope this helps.


Regards,
Mostafa
MIT
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Re: [Pw_forum] Upper estimation of lattice parameter by LDA pseudopotential -regarding

[Mostafa Youssef]

Dear  Suresh,


I think the reason is the Ti pseudopotential.  This one has 4 valence electrons 
and freezes the rest.  This leads to larger ionic sizes and overestimation of 
the lattice constant.  Allowing more Ti valence electrons, means further 
relaxation for the outer electronic shell and better adoption to the crystal 
environment.  Try  a Ti PP that has 12 electrons.  Pslib from which you 
obtained this one, has also ultrasoft pseudos with 12 electrons.



Regards,
Mostafa
MIT
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[Pw_forum] Doubt in ibrav = 7

[Youssef Aharbil]

Dear QE Users,

I have encountered lot of problems with ibrav = 7, when plotting the
structure with xcrysden it seems that the atoms aren't at the right
positions, using "crystal" for ATOMIC_POSITIONS give incorrect atoms
coordinates while visualization, I corrected that issue using "bohr" in
stead off "crystal"  (of course by doing conversion), but it seems that one
atom is missing (Second La atom with coordinate 0.5 0 0.25 ) even if it
exist well in the input file.
Please tell me if that's just a bug on xcrysden or something is wrong with
my data.
Please help because the calculation not converged after 100 iteration.
My input file

 
 calculation = 'scf' ,
  outdir = './' ,
  pseudo_dir = './' ,
  prefix = 'La2CrMoO6' ,
 disk_io = 'low' ,
 /
 
   ibrav = 7,
   celldm(1) = 10.4576559546,
   celldm(3) = 1.5084687551,
 nat = 10,
ntyp = 4,
 ecutwfc = 88 ,
 occupations = 'smearing' ,
 degauss = 0.005 ,
smearing = 'methfessel-paxton' ,
   nspin = 2 ,
   starting_magnetization(2) = 0.7,
   starting_magnetization(3) = -0.7,
exxdiv_treatment = 'gygi-baldereschi' ,
  lda_plus_u = .true. ,
 lda_plus_u_kind = 1 ,
Hubbard_U(2) = 4,
Hubbard_U(3) = 3,
   Hubbard_J0(2) = 0.89,
   Hubbard_J0(3) = 0.89,
 /
 
conv_thr = 1.0e-8 ,
 mixing_beta = 0.7 ,
 /
ATOMIC_SPECIES
   La  138.91000  La.pbe-hgh.UPF
   Cr   51.99610  Cr.pbe-mt_fhi.UPF
   Mo   95.94000  Mo.pbe-mt_fhi.UPF
O   15.99940  O.pbe-mt_fhi.UPF
ATOMIC_POSITIONS bohr
   La  0.05.2288279773.943761815
   La  5.2288279770.03.943761815
   Cr  0.00.00.0
   Mo  0.00.07.887523630
O  0.00.04.038412098
O  0.00.0   11.736635161
O  1.7161013423.6559965220.0
O  8.7415546126.8016594330.0
O  6.8016594331.7161013420.0
O  3.6559965228.7415546120.0
K_POINTS automatic
  3 3 3   1 1 1


using QE 5.0.2 and xcrysden 1.5.53

Youssef Aharbil
PhD Student
Laboratory of Chemistry of material
Morocco
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[Pw_forum] Detecting Magnetic ion

[Youssef Aharbil]

Dear Quantum espresso community,

I am dealing with the investigation of magnetic properties of ternary
compound,  as you know you must tell the code the start_magnetization per
element to take in account to break the symmetry, hence one  must study
case by case by iterating +1,0,-1 initial guess. the number of
possibilities is very huge.
Is there any hint or trick to accelerate that iterative process?

Youssef Aharbil
PhD Student
Faculty of sciences ben msik
Morocco
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[Pw_forum] Accelerating multiple calculations with same phase

[Youssef Aharbil]

Dear Quantum espresso users and developers,

I am working on several phases, investigating for each phase I need to

1-Determine lattice constant and atomic positions with non magnetic state
2-Determine magnetic ground states (by testing all of magnetic states
possibilities for each ions)
3-Determine lattice constant and atomic positions with  magnetic states
4-Construct several super-cells and invert ion position.

As you can see, I must do lot of calculation for each phase by modifying
it slightly.

My question is what's the best procedure to do that safely and/or  quickly,
I mean whether:

-Do it safely and delete wfc and xml data for every new calculation (I am
calculation on the same folder for each precedent step)
-Do it more quickly and keep old wfc and xml data.


Another question related with same topic: how relax subroutine success
improving convergence steps just after running the first cycle? can I
capitalize something for my case?

P.S. :
Thanks in advance.
Youssef Aharbil
PhD
Laboratory of Physics and Chemistry of Material
Morocco
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[Pw_forum] manypw.x

[Youssef Aharbil]

Dear Quantum espresso,

What's the utility of the new program manypw.x?, I got a look in manypw.f90
but didn't find lot of explanation.

Youssef Aharbil
PhD
Laboratory of Physics and Chemistry of Material
Morocco
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Re: [Pw_forum] Accelerating multiple calculations with same phase

[Youssef Aharbil]

This is a kind reminder.
Can some one answer me please.

-- Forwarded message --
From: Youssef Aharbil <ahar...@gmail.com>
Date: 2014-11-15 20:44 GMT+00:00
Subject: Accelerating multiple calculations with same phase
To: ‫Pw_forum@pwscf.org‬


Dear Quantum espresso users and developers,

I am working on several phases, investigating for each phase I need to

1-Determine lattice constant and atomic positions with non magnetic state
2-Determine magnetic ground states (by testing all of magnetic states
possibilities for each ions)
3-Determine lattice constant and atomic positions with  magnetic states
4-Construct several super-cells and invert ion position.

As you can see, I must do lot of calculation for each phase by modifying
it slightly.

My question is what's the best procedure to do that safely and/or  quickly,
I mean whether:

-Do it safely and delete wfc and xml data for every new calculation (I am
calculation on the same folder for each precedent step)
-Do it more quickly and keep old wfc and xml data.


Another question related with same topic: how relax subroutine success
improving convergence steps just after running the first cycle? can I
capitalize something for my case?

P.S. :
Thanks in advance.
Youssef Aharbil
PhD
Laboratory of Physics and Chemistry of Material
Morocco




-- 
والله ولي التوفيق
يوسف أحربيل
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[Pw_forum] Negative starting charge for Zr USPP

[Mostafa Youssef]

Dear all,

When I use an USPP for Zr that contains nonlinear core corrections to study 
ZrO2, I always get negative starting charge. For example, I see the following 3 
lines:

Check: negative/imaginary core charge=   -0.040.00
Check: negative starting charge=   -0.238895
 negative rho (up, down):  2.389E-01 0.000E+00

I tried to increase the energy cutoff to 85 Ry and charge density cutoff to 850 
Ry but this has no effect at all.

However, if I use an USPP for Zr that does not have nonlinear core corrections, 
this negative charge does not show up in the output file.

In the FAQ, it says that one should worry if this negative charge is 0.001x no. 
of electrons, in the case of Zr it is about 0.002 x no. of electrons.

Any suggestions on how to avoid this negative charge while retaining nonlinear 
core corrections.

Thank you
Mostafa Youssef
Postdoctoral Associate
MIT
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[Pw_forum] lelfield=.true. with USPP , PAW and non-orthorhombic cells

[Mostafa Youssef]

Dear all,

I wonder whether applying finite homogeneous electric field in PWscf  supports:

(1) USPP

(2) PAW PP

(3) Non-orthorhombic cells

Thank you,
Mostafa Youssef
MIT
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[Pw_forum] lelfield=.true. with USPP , PAW and non-orthorhombic cells

[Mostafa Youssef]

>From the header of the file, bp_c_phase.f90, I can see that only USPP and NCPP 
> are supported when applying a homogeneous electric field in PWscf.  But I 
>still could not resolve whether non-orthorhombic cells are supported. Any 
>hints are appreciated.

Thank you,
Mostafa Youssef
MIT
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Re: [Pw_forum] Negative starting charge for Zr USPP

[Mostafa Youssef]

As an update for the issue of negative charge for Zr USPP; I tested few other 
PP's which include nonlinear core corrections. Out of many of these PP's, I 
found the one provided in the PSLIB to be free from the problem of negative 
charge.


Mostafa Youssef
MIT
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Re: [Pw_forum] lelfield=.true. with USPP , PAW and non-orthorhombic cells

[Mostafa Youssef]

Thank you Prof. Giannozzi.  I tested running PWscf to calculate the ground 
state of monoclinic ZrO2 under finite homogeneous electric field using PAW PP.  
I could not find error messages in the output file to warn against using PAW 
PP. After the first electronic step, I can see the Berry phase calculations 
running smoothly.

I'm using the latest version of Q.E. , v.5.1.1. and below is the input file I 
used.  (The PAW PP are from the PSLIB.)

Thank you for your help!
Mostafa Youssef
MIT


   calculation =   'scf'   ,
   verbosity = 'high' ,
   restart_mode = 'from_scratch' ,
   prefix='ZrO2field' ,
   lelfield=.true.,
   nberrycyc=5
   outdir='/home/mostafa/scratch' ,
   pseudo_dir = '/home/mostafa/Pseudo' ,
   tstress = .true.  ,
   tprnfor= .true.  ,
  ! nstep = 200
   etot_conv_thr = 1.0D-5  ,
   forc_conv_thr = 1.0D-4 ,
 /
 
   ibrav = 0 ,
nat  =  12 ,
   ntyp  =  2 ,
   nbnd  = 57 ,
  ecutwfc  =  30.0 ,
  ecutrho  =  240.0 ,
  occupations = 'fixed',
 /
 
diagonalization='david',
mixing_mode = 'plain' ,
mixing_beta = 0.7,
conv_thr  =  1.0d-8  ,
startingwfc='file',
efield_cart(1)=0.d0,efield_cart(2)=0.d0,efield_cart(3)=0.001d0
 /

CELL_PARAMETERS (angstrom)
   5.189965747  -0.07006  -0.002141956
  -0.07049   5.238515103   0.01854
  -0.905139810   0.03114   5.303173936
ATOMIC_SPECIES
   Zr   91.224Zr.pbe-spn-kjpaw_psl.0.2.3.upf
   O15.9994   O.pbe-n-kjpaw_psl.0.1.upf
ATOMIC_POSITIONS (crystal)
Zr  -0.000557560   0.94241  -0.000195601
Zr  -0.000582096   0.412544098   0.499834659
Zr   0.448111392   0.912556904   0.579763060
Zr   0.448101200   0.500091161   0.079794722
O0.272545775   0.199845543   0.313995079
O0.174768376   0.699867447   0.765505431
O0.788062644   0.131237361   0.640894726
O0.659267458   0.631148068   0.438855221
O0.174850646   0.713107769   0.265525640
O0.788180411   0.281699370   0.140856377
O0.272465073   0.213166721   0.813976952
O0.659131481   0.781858917   0.938902935
K_POINTS automatic
  4 4 12   1 1 1

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Re: [Pw_forum] lelfield=.true. with USPP , PAW and non-orthorhombic cells

[Mostafa Youssef]

Thank you Prof. Giannozzi.  I tested running PWscf to calculate the ground
state of monoclinic ZrO2 under finite homogeneous electric field using PAW PP.
I could not find error messages in the output file to warn against using PAW
PP. After the first electronic step, I can see the Berry phase calculations
running smoothly.

I'm using the latest version of Q.E. , v.5.1.1. and below is the input file I
used.  (The PAW PP are from the PSLIB.)

Thank you for your help!
Mostafa Youssef
MIT


   calculation =   'scf'   ,
   verbosity = 'high' ,
   restart_mode = 'from_scratch' ,
   prefix='ZrO2field' ,
   lelfield=.true.,
   nberrycyc=5
   outdir='/home/mostafa/scratch' ,
   pseudo_dir = '/home/mostafa/Pseudo' ,
   tstress = .true.  ,
   tprnfor= .true.  ,
  ! nstep = 200
   etot_conv_thr = 1.0D-5  ,
   forc_conv_thr = 1.0D-4 ,
/

   ibrav = 0 ,
nat  =  12 ,
   ntyp  =  2 ,
   nbnd  = 57 ,
  ecutwfc  =  30.0 ,
  ecutrho  =  240.0 ,
  occupations = 'fixed',
/

diagonalization='david',
mixing_mode = 'plain' ,
mixing_beta = 0.7,
conv_thr  =  1.0d-8  ,
startingwfc='file',
efield_cart(1)=0.d0,efield_cart(2)=0.d0,efield_cart(3)=0.001d0
/

CELL_PARAMETERS (angstrom)
   5.189965747  -0.07006  -0.002141956
  -0.07049   5.238515103   0.01854
  -0.905139810   0.03114   5.303173936
ATOMIC_SPECIES
   Zr   91.224Zr.pbe-spn-kjpaw_psl.0.2.3.upf
   O15.9994   O.pbe-n-kjpaw_psl.0.1.upf
ATOMIC_POSITIONS (crystal)
Zr  -0.000557560   0.94241  -0.000195601
Zr  -0.000582096   0.412544098   0.499834659
Zr   0.448111392   0.912556904   0.579763060
Zr   0.448101200   0.500091161   0.079794722
O0.272545775   0.199845543   0.313995079
O0.174768376   0.699867447   0.765505431
O0.788062644   0.131237361   0.640894726
O0.659267458   0.631148068   0.438855221
O0.174850646   0.713107769   0.265525640
O0.788180411   0.281699370   0.140856377
O0.272465073   0.213166721   0.813976952
O0.659131481   0.781858917   0.938902935
K_POINTS automatic
  4 4 12   1 1 1


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Re: [Pw_forum] Magnetic moment values

[Youssef Aharbil]

Dear All,

This is a kind reminder about my question, especially I am waiting a
response from the developers of the 5.1 version, what's the main difference
the between printed magnetic moment from pw.x and the polarization
recollted by projwfc.x?

2015-01-01 21:47 GMT+00:00 Youssef Aharbil <ahar...@gmail.com>:

> Dear Quantum espresso users,
>
> Latest version of QE print the magnetic moment per SCF cycle, I think it's
> good think.
>
> but when comparing the values of magnetic moments printed by the last SCF
> cycle from pw.x and the polarization form projwfc.x , I realized that's :
>
> 1-The values different seriously between one another
> 2-The sum of the magnetics moments from projwfc.x agree with the total
> magnetization moment.
> 3-The sum of the magnetics moments from pw.x don't agree with the total
> magnetization moment.
>
> Can someone explain me Why?
>
> Below the outputs
>
> Projwfc.x
>
> Lowdin Charges:
>
>  Atom #   1: total charge =  13.3560, s =  2.3377, p =  7.0615, d =
> 3.9568,
>  spin up  =   6.6471, s =  1.1698,
>  spin up  =   6.6471, p =  3.5293, pz=  1.1764, px=
> 1.1764, py=  1.1764,
>  spin up  =   6.6471, d =  1.9480, dz2=  0.4120, dxz=
> 0.3747, dyz=  0.3747, dx2-y2=  0.4120, dxy=  0.3747,
>  spin down=   6.7089, s =  1.1679,
>  spin down=   6.7089, p =  3.5322, pz=  1.1774, px=
> 1.1774, py=  1.1774,
>  spin down=   6.7089, d =  2.0087, dz2=  0.3995, dxz=
> 0.4032, dyz=  0.4032, dx2-y2=  0.3995, dxy=  0.4032,
>  polarization =  -0.0617, s =  0.0018, p = -0.0029, d =
> -0.0607,
>  Atom #   2: total charge =   8.6873, s =  0., p =  1.0208, d =
> 7.,
>  spin up  =   5.6434, s =  0.1712,
>  spin up  =   5.6434, p =  0.5111, pz=  0.1704, px=
> 0.1704, py=  0.1704,
>  spin up  =   5.6434, d =  4.9611, dz2=  0.9929, dxz=
> 0.9918, dyz=  0.9918, dx2-y2=  0.9929, dxy=  0.9918,
>  spin down=   3.0439, s =  0.1621,
>  spin down=   3.0439, p =  0.5097, pz=  0.1699, px=
> 0.1699, py=  0.1699,
>  spin down=   3.0439, d =  2.3722, dz2=  0.1424, dxz=
> 0.6958, dyz=  0.6958, dx2-y2=  0.1424, dxy=  0.6958,
>  polarization =   2.5995, s =  0.0091, p =  0.0014, d =
> 2.5890,
>  Atom #   3: total charge =   8.3142, s =  1.9641, p =  6.3501, d =
> 0.,
>  spin up  =   4.1549, s =  0.9809,
>  spin up  =   4.1549, p =  3.1740, pz=  1.0580, px=
> 1.0580, py=  1.0580,
>  spin up  =   4.1549, d =  0., dz2=  0., dxz=
> 0., dyz=  0., dx2-y2=  0., dxy=  0.,
>  spin down=   4.1593, s =  0.9832,
>  spin down=   4.1593, p =  3.1761, pz=  1.0587, px=
> 1.0587, py=  1.0587,
>  spin down=   4.1593, d =  0., dz2=  0., dxz=
> 0., dyz=  0., dx2-y2=  0., dxy=  0.,
>  polarization =  -0.0044, s = -0.0023, p = -0.0021, d =
> 0.,
>  Atom #   4: total charge =   8.5059, s =  2.0182, p =  6.4877, d =
> 0.,
>  spin up  =   4.2496, s =  1.0078,
>  spin up  =   4.2496, p =  3.2418, pz=  1.0806, px=
> 1.0806, py=  1.0806,
>  spin up  =   4.2496, d =  0., dz2=  0., dxz=
> 0., dyz=  0., dx2-y2=  0., dxy=  0.,
>  spin down=   4.2563, s =  1.0104,
>  spin down=   4.2563, p =  3.2459, pz=  1.0820, px=
> 1.0820, py=  1.0820,
>  spin down=   4.2563, d =  0., dz2=  0., dxz=
> 0., dyz=  0., dx2-y2=  0., dxy=  0.,
>  polarization =  -0.0067, s = -0.0026, p = -0.0041, d =
> 0.,
>  Atom #   5: total charge =   6.6051, s =  1.6515, p =  4.9537, d =
> 0.,
>  spin up  =   3.3426, s =  0.8307,
>  spin up  =   3.3426, p =  2.5118, pz=  0.8518, px=
> 0.8082, py=  0.8518,
>  spin up  =   3.3426, d =  0., dz2=  0., dxz=
> 0., dyz=  0., dx2-y2=  0., dxy=  0.,
>  spin down=   3.2625, s =  0.8207,
>  spin down=   3.2625, p =  2.4418, pz=  0.8326, px=
> 0.7766, py=  0.8326,
>  spin down=   3.2625, d =  0., dz2=  0., dxz=
> 0., dyz=  0., dx2-y2=  0., dxy=  0.,
>  polarization =   0.0800, s =  0.0100, p =  0.0700, d =
> 0.,
>  Atom #   6: total charge =   6.6051, s =  1.6515, p =  4.9537, d =
> 0.0

[Pw_forum] Question regarding Hubbard U

[Youssef Aharbil]

Dear Quantum espresso community and Dear Dr Matteo,

I have a question about how to deal with compound with mixed elemnts > 3
(eg : with 3d open or clos shell , 2p sell ...), how can we compute U?

Should I perturb all the elements even for those without  d or f  shell
likewise the case of oxygen (eg: Al in presence of Fe in my case) , if not
, should I take them in consideration on r.x input (position input file)

Thank you in advance.




Youssef Aharbil
PhD
Laboratory of Physics and Chemistry of Material
Morocco
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[Pw_forum] Cesium Pseudo-potential with spin-orbit coupling effect

[Mostafa Youssef]

Hi Yuping,



PSLIB has relativistic PP for Cs and Rb.



http://theossrv1.epfl.ch/Main/Pseudopotentials



Mostafa Youssef

MIT
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[Pw_forum] Another question regarding

[Youssef Aharbil]

Dear QE community and Dear Dr Matteo,

I have succedded to calculte the U parameters for some compounds including
double perovskite.

I've found for Ba2MgWO6 :

U for W=2.65 ev and U for O =14ev

Now I've apply this values to get the energy band gap and I found it 5ev
while the experimental one is 3.5ev, I think it's a strange result about
the overestimating the band gap while it's known that DFT underestimate it.

I Think that the root cause of that issue is the Hubbard of U of oxygen
which is double counted because O is only bonded to W with 50% ratio. I've
apply U for O = 7 and i get best result (Eg=3.2ev).

What do think about my logic


-- 

والله ولي التوفيق
يوسف أحربيل
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[Pw_forum] Hubbard for oxygen

[Youssef Aharbil]

Dear Quantum espresso community,

It's well known that adapting the Hubbard model in DFT give a better
insight for the electronic structure on correlated materials, here the
systems with d and f shell localisation are corrected by applying a U
potential, but I don't understand why do we apply U also for oxygen,
unfortunately I can't find any reference (may be my research wasn't so
deep) giving more explanation.

Finally I would like to discuss the effect of hybridisation on U,
especially with mixed compounds where the oxygen electrons are shared on
between both Hubbard and non Hubbard atoms, from my experience on double
pervoskite the calculated value of U on Hubbard atoms including oxygen
using the linear response approach by cococcioni et al  overestimate the
band gap .

>From my point of view I think that the value of U must be proportional to
the number of electron only shared between Hubbard atoms and the oxygen.

Thanks in advance.

Youssef Aharbil
Faculty of sciencs ben msik.
Morocco
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