[QE-users] Query regarding restarting the relax calculation with updated parameters

[Dr. K. C. Bhamu]

Dear Experts,
I want to restart a job with updated parameters (degauss, Hubbard
parameter, convergence thresholds).
I had gone through the mailing list and I found one response for the k-mesh
change [1]. There, it is suggested to restart the job with charge density
not with the wavefunction.

I have a few queries for restarting the job without deleting the output
directory:

1. Can I change more than one parameter at a time (like degauss, U, and
convergence thresholds) in the restart?
2. as suggested in the thread [1], how can I avoid using wavefunction for
the k-mesh update?

[1].
https://lists.quantum-espresso.org/pipermail/users/2018-September/041299.html

Thanks in advance for your help.

Regards
Bhamu
University of Ulsan
South Korea
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Re: [QE-users] Ph.x with grimme D3

[Dr. K. C. Bhamu]

If you check the output file or error file, you will see a message that
grimme-D3 correction is not implemented in ph.x.

I use grimme-D2 correction.


Regards
Bhamu

On Tue, Feb 22, 2022, 5:38 PM Lorenzo Mariano <
antonio-lorenzo.mari...@grenoble-inp.fr> wrote:

> Dear QE users,
>
> I am running phonons calculations using QE 6.4. When I use PBE+D3,
> everything converges without any warning or error message even if
> phq_readin.f90 is supposed to complain because of the use of grimme-D3
> correction. Am I computing phonons with PBE-D3 or not?
>
> Best regards,
>
> L. Mariano,
> Simap laboratory
> Grenoble (France)
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Re: [QE-users] ICOHP lobster and bond strength

[Dr. K. C. Bhamu]

I have covered ICOHP and ICOOP in my recent work (1) for a hydrocarbon
molecule.

I also got the same value. I have verified it using C2H6, C2H4 and C2H2. So
it may be a qualitative information.

(1). https://www.sciencedirect.com/science/article/abs/pii/S0360319922001008



Regards
Bhamu


On Sat, Feb 5, 2022, 4:13 AM Максим Арсентьев  wrote:

> Dear QE users,
>
> I'm trying to calculate the bond strength in diamond using quantum
> espresso and lobster code. I got 9.0 eV for integrated ICOHP for C-C bond
> in agreement with the results from other papers like this one
> https://www.sciencedirect.com/science/article/abs/pii/S0008622319302945 .
> Is it possible to exactly calculate the bond strength by ICOHP, or ICOHP
> is only a qualitative assessment. Because 9.0 eV is too high maybe (it
> should be 3.65eV).
>
> --
> Best wishes,
> Maxim Arsent'ev, Ph.D. (Chemistry)
> Laboratory of research of nanostructures
> Institute of Silicate Chemistry of RAS
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Re: [QE-users] convergence issue in DFT_U+V calculation

[Dr. K. C. Bhamu]

Thanks dear Dr. Timrov,
I will run a new job with tight convergence criteria in QE input file.
Here are my output files:
https://we.tl/t-wzfGtXEWiu

Regards
Bhamu

On Wed, Dec 1, 2021 at 3:29 PM Iurii TIMROV via users <
users@lists.quantum-espresso.org> wrote:

> Dear Bhamu,
>
>
> > conv_thr =   1.00d-06
>
>
> In addition to Matteo's comments I would suggest to converge better the
> ground state. Indeed, something strange is happening at the 4th iteration -
> a detailed inspection of the output files is needed, but please check what
> Matteo wrote.
>
>
> HTH
>
>
> Iurii
>
>
> --
> Dr. Iurii TIMROV
> Senior Research Scientist
> Theory and Simulation of Materials (THEOS)
> Swiss Federal Institute of Technology Lausanne (EPFL)
> CH-1015 Lausanne, Switzerland
> +41 21 69 34 881
> http://people.epfl.ch/265334
> --
> *From:* users  on behalf of
> Matteo Cococcioni 
> *Sent:* Wednesday, December 1, 2021 9:47:06 AM
> *To:* Quantum ESPRESSO users Forum
> *Subject:* Re: [QE-users] convergence issue in DFT_U+V calculation
>
> the fourth iteration does not look too good to me as the U for Fe2 is
> suddenly going from 4.31 to 0.7.
> Fe3O4 is a difficult system of its own. are you sure that all the Fe1 are
> of the same kind (3+)? The system is for sure
> a mixed valence one but I don't remember how this matches its magnetic
> structure. Are you relaxing the structure in between?
> Maybe because of the structure changes hp is not recognizing the neighbors
> it had before for each Fe.
>
> Regards,
>
> Matteo
>
> Il giorno mer 1 dic 2021 alle ore 06:07 Dr. K. C. Bhamu <
> kcbham...@gmail.com> ha scritto:
>
>> Dear Iurii,
>> This is from the calculation without nbnd in QE input file (QE input and
>> HP input are supplied at the end of this email).
>> I am trying to get a converged value of U+V. Up to four steps, all the
>> calculations seem to be fine (other than the converged value of U+V). But
>> in the 5th step, I see that my calculations are not converging.
>>
>> I am getting this message:
>>   atom #  5   q point #   3   iter # 180
>>   chi:   1 -83.8242814567   residue:  103.6191835332
>>   chi:   2 -83.8242814548   residue:  103.6191835384
>>   chi:   3 **   residue:  381.0626501229
>>   chi:   4 **   residue:  326.7198566114
>>   chi:   5 317.5473216386   residue:  329.6382092529
>>   chi:   6 **   residue:  580.5784405595
>>   chi:   7   9.0496504843   residue:1.9763844786
>>   chi:   8  -6.2884312048   residue:   21.8495062869
>>   chi:   9   9.0496505082   residue:1.9763845088
>>   chi:  10  -6.2884312084   residue:   21.8495062832
>>   chi:  11  10.2338160751   residue:7.3557134894
>>   chi:  12  -5.1687829951   residue:   22.9825921172
>>   chi:  13   6.7503553298   residue:7.1360232476
>>   chi:  14  -3.9982889995   residue:   27.0388948104
>>   Average number of iter. to solve lin. system:   23.6
>>   Total CPU time : 63284.6 s
>> ###
>>   atom #  5   q point #   3   iter # 274
>>   chi:   1 **   residue:  **
>>   chi:   2 **   residue:  **
>>   chi:   3 **   residue:  **
>>   chi:   4 **   residue:  **
>>   chi:   5 **   residue:  **
>>   chi:   6 **   residue:  **
>>   chi:   7 **   residue:   78.8265104616
>>   chi:   8 190.5140692168   residue:  **
>>   chi:   9 **   residue:   78.8264974402
>>   chi:  10 190.5140679621   residue:  **
>>   chi:  11 **   residue:  **
>>   chi:  12 544.1915326984   residue:  **
>>   chi:  13 **   residue:  **
>>   chi:  14 **   residue:  **
>>
>> U+V value from four completed calculations is given below:
>>
>>
>> site n.  type  label  spin  new_type  new_label  Hubbard U (eV)
>>   11Fe1 1  1 Fe15.1791
>>   52Fe2-1  2 Fe25.0962
>>   73O   0  3 O  7.1203
>>
>> site n.  type  label  spin  new_type  new_label  Hubbard U (eV)
>>   11Fe1 1  1 Fe15.6013
>>   52Fe2-1  2 Fe24.3164
>>   73O   0  3 O 

Re: [QE-users] convergence issue in DFT_U+V calculation

[Dr. K. C. Bhamu]

Dear Dr. Matteo,

Thank you very much for the quick response.

Yes, I am doing vc-relax in between each step.  Doing vc-relax without
adopting geometry information from the previous run. I am only supplying
the HP file containing U+V obtained from the previous run for the vc-relax
for the next step.

Fe1 (octahedral coordination) atom has a mixed charge state (Fe3+ and Fe2+).
The magnetic moment of Fe1( Fe3+) cancels out with Fe2 (tetrahedral
coordination; all Fe3+) and the resultant magnetic moment comes from Fe1
(2+) atoms.
According to Ref. [1]
<https://www.sciencedirect.com/science/article/abs/pii/S0039602812000544>,
I set all Fe1 as up and all Fe2 as down spins.

Do you think my input still has some issues?

---
I am providing some additional information here.

Additional information:

Ref. [1]
<https://www.sciencedirect.com/science/article/abs/pii/S0039602812000544>
Just below Fig. 3 it is mentioned that "For Fe3O4 having ferrimagnetic
property, the spin of the octahedral and tetrahedral Fe was set as up and
down, respectively."


Relevant para from Ref. [2]
<https://link.springer.com/article/10.1134%2FS1027451010030079> is as below:
Fe2+ cations in the face-centered cubic lattice formed by oxygen anions
occupy octahedral sites, while Fe3+ cations are distributed between
octahedral and tetrahedral sites. The trivalent Fe3+ ion is in the state
with a spin S = 5/2 and zero orbital moments. The bivalent Fe2+ ion has a
spin of 2, and its contribution comes to ~4μB unless one considers a
certain possible contribution from the orbital moment [2]. The measured
value of the magnetic moment for magnetite is 4.1μB. The magnetic moments
of Fe3+ ions are antiparallel to each other, and the observed moment is
determined by Fe2+ ions only (Fig. 1).


Thanks and regards
Bhamu



On Wed, Dec 1, 2021 at 2:17 PM Matteo Cococcioni 
wrote:

> the fourth iteration does not look too good to me as the U for Fe2 is
> suddenly going from 4.31 to 0.7.
> Fe3O4 is a difficult system of its own. are you sure that all the Fe1 are
> of the same kind (3+)? The system is for sure
> a mixed valence one but I don't remember how this matches its magnetic
> structure. Are you relaxing the structure in between?
> Maybe because of the structure changes hp is not recognizing the neighbors
> it had before for each Fe.
>
> Regards,
>
> Matteo
>
> Il giorno mer 1 dic 2021 alle ore 06:07 Dr. K. C. Bhamu <
> kcbham...@gmail.com> ha scritto:
>
>> Dear Iurii,
>> This is from the calculation without nbnd in QE input file (QE input and
>> HP input are supplied at the end of this email).
>> I am trying to get a converged value of U+V. Up to four steps, all the
>> calculations seem to be fine (other than the converged value of U+V). But
>> in the 5th step, I see that my calculations are not converging.
>>
>> I am getting this message:
>>   atom #  5   q point #   3   iter # 180
>>   chi:   1 -83.8242814567   residue:  103.6191835332
>>   chi:   2 -83.8242814548   residue:  103.6191835384
>>   chi:   3 **   residue:  381.0626501229
>>   chi:   4 **   residue:  326.7198566114
>>   chi:   5 317.5473216386   residue:  329.6382092529
>>   chi:   6 **   residue:  580.5784405595
>>   chi:   7   9.0496504843   residue:1.9763844786
>>   chi:   8  -6.2884312048   residue:   21.8495062869
>>   chi:   9   9.0496505082   residue:1.9763845088
>>   chi:  10  -6.2884312084   residue:   21.8495062832
>>   chi:  11  10.2338160751   residue:7.3557134894
>>   chi:  12  -5.1687829951   residue:   22.9825921172
>>   chi:  13   6.7503553298   residue:7.1360232476
>>   chi:  14  -3.9982889995   residue:   27.0388948104
>>   Average number of iter. to solve lin. system:   23.6
>>   Total CPU time : 63284.6 s
>> ###
>>   atom #  5   q point #   3   iter # 274
>>   chi:   1 **   residue:  **
>>   chi:   2 **   residue:  **
>>   chi:   3 **   residue:  **
>>   chi:   4 **   residue:  **
>>   chi:   5 **   residue:  **
>>   chi:   6 **   residue:  **
>>   chi:   7 **   residue:   78.8265104616
>>   chi:   8 190.5140692168   residue:  **
>>   chi:   9 **   residue:   78.8264974402
>>   chi:  10 190.5140679621   residue:  **
>>   chi:  11 **   residue:  **
>>   chi:  12 544.1915326984   residue:  **
>>   chi:  13 ** 

[QE-users] convergence issue in DFT_U+V calculation

[Dr. K. C. Bhamu]

Dear Iurii,
This is from the calculation without nbnd in QE input file (QE input and HP
input are supplied at the end of this email).
I am trying to get a converged value of U+V. Up to four steps, all the
calculations seem to be fine (other than the converged value of U+V). But
in the 5th step, I see that my calculations are not converging.

I am getting this message:
  atom #  5   q point #   3   iter # 180
  chi:   1 -83.8242814567   residue:  103.6191835332
  chi:   2 -83.8242814548   residue:  103.6191835384
  chi:   3 **   residue:  381.0626501229
  chi:   4 **   residue:  326.7198566114
  chi:   5 317.5473216386   residue:  329.6382092529
  chi:   6 **   residue:  580.5784405595
  chi:   7   9.0496504843   residue:1.9763844786
  chi:   8  -6.2884312048   residue:   21.8495062869
  chi:   9   9.0496505082   residue:1.9763845088
  chi:  10  -6.2884312084   residue:   21.8495062832
  chi:  11  10.2338160751   residue:7.3557134894
  chi:  12  -5.1687829951   residue:   22.9825921172
  chi:  13   6.7503553298   residue:7.1360232476
  chi:  14  -3.9982889995   residue:   27.0388948104
  Average number of iter. to solve lin. system:   23.6
  Total CPU time : 63284.6 s
###
  atom #  5   q point #   3   iter # 274
  chi:   1 **   residue:  **
  chi:   2 **   residue:  **
  chi:   3 **   residue:  **
  chi:   4 **   residue:  **
  chi:   5 **   residue:  **
  chi:   6 **   residue:  **
  chi:   7 **   residue:   78.8265104616
  chi:   8 190.5140692168   residue:  **
  chi:   9 **   residue:   78.8264974402
  chi:  10 190.5140679621   residue:  **
  chi:  11 **   residue:  **
  chi:  12 544.1915326984   residue:  **
  chi:  13 **   residue:  **
  chi:  14 **   residue:  **

U+V value from four completed calculations is given below:


site n.  type  label  spin  new_type  new_label  Hubbard U (eV)
  11Fe1 1  1 Fe15.1791
  52Fe2-1  2 Fe25.0962
  73O   0  3 O  7.1203

site n.  type  label  spin  new_type  new_label  Hubbard U (eV)
  11Fe1 1  1 Fe15.6013
  52Fe2-1  2 Fe24.3164
  73O   0  3 O  7.5401

site n.  type  label  spin  new_type  new_label  Hubbard U (eV)
  11Fe1 1  1 Fe15.6013
  52Fe2-1  2 Fe24.3164
  73O   0  3 O  7.5401

site n.  type  label  spin  new_type  new_label  Hubbard U (eV)
  11Fe1 1  1 Fe14.4843
  52Fe2-1  2 Fe20.7259
  73O   0  3 O  7.3480


I do not think changing "conv_thr_chi" will help here as the number is
still oscillating in integer values.

What suggestions do you have for this situation?


HP input file:

 
   prefix = 'pwscf',
niter_max=300
   outdir = './temp/',
   nq1 = 2, nq2 = 2, nq3 = 2,
   conv_thr_chi = 1.0d-5,
find_atpert = 1
docc_thr=1.d-3
!disable_type_analysis=.true.,
/

QE input file:

  calculation = 'vc-relax'
  restart_mode='from_scratch',
  etot_conv_thr =   1.40d-04
  forc_conv_thr =   1.00d-04
  outdir = './temp/'
  prefix = 'pwscf'
  pseudo_dir = '~/PPs/jana_2/'
  tprnfor = .true.
  tstress = .true.
  verbosity = 'high'
/

  degauss =   0.022
  ecutrho =   320
  ecutwfc =   40
  occupations = 'smearing' ,smearing = 'mp'
  ibrav = 0
  nat = 14
  nosym = .false.
  ntyp = 3
nspin=2
  starting_magnetization(1) =   0.8
  starting_magnetization(2) =   -0.8
  starting_magnetization(3) =   0.0

  lda_plus_u = .true.,
  lda_plus_u_kind = 2,
  U_projection_type = 'ortho-atomic',
  !Hubbard_V(1,1,1) = 1.d-8
  !Hubbard_V(5,5,1) = 1.d-8
  !Hubbard_V(7,7,1) = 1.d-8
Hubbard_parameters = 'file'


/

  conv_thr =   1.00d-06
  electron_maxstep = 400
  mixing_beta =   1.50d-01
/

ion_dynamics = 'bfgs'
 /

/

ATOMIC_SPECIES
Fe1 55.845 Fe.pbe-nd-rrkjus.UPF
Fe2 55.845 Fe.pbe-nd-rrkjus.UPF
O  15.9994 O.pbe-rrkjus.UPF
ATOMIC_POSITIONS (crystal)
Fe1   0.00   -0.00   -0.00
Fe1   0.500.000.00
Fe1   0.9998920.500216   -0.00
Fe1   0.650.560.500115
Fe2   0.37499937210.37499933490.3750019210
Fe2   0.62500062250.6250006532

[QE-users] Convergence issue in HP code with nbnd

[Dr. K. C. Bhamu]

Dear Iurii,

As per our previous conversation,  I am running my Fe3O4 case with nbnd and
without nbnd. It seems that calculations without nbnd is running file
(second self-consistent calculations has finished based on U+V from 1st
SCF) but with nbnd, I see HP calculations are not converging for 2nd
q-point of 5th atom.

I am perturbing three atoms in my Fe3O4 system as below:
 List of  3 atoms which will be perturbed (one at a time):

1  Fe155.8450   tau( 1) = (  0.0  0.0 -0.0  )
5  Fe255.8450   tau( 5) = (  0.75736  0.43726  0.30920  )
7  O  15.9994   tau( 7) = (  0.49572  0.28620  0.20238  )

I am getting below message:

atom #  5   q point #   2   iter # 300
"NOT MENTIONING SOME LINES HERE TO KEEP THE EMAIL SHORT"

  Average number of iter. to solve lin. system:   10.6
  Total CPU time : 60285.4 s
  Convergence has not been reached after 300 iterations!
  The best overall accuracy which was reached :
  diff =0.114935  iter = 273


Here is my HP input file:

 
   prefix = 'pwscf',
niter_max=300
   outdir = './temp/',
   nq1 = 2, nq2 = 2, nq3 = 2,
   conv_thr_chi = 1.0d-5,
find_atpert = 1
docc_thr=1.d-3
!disable_type_analysis=.true.,
/

I understand that I may need to reduce the mixing factor of alpha_mix(i).
But could you please elaborate some more, how how can I take/understand
this i-th iteration?
 Because in the description, it is mentioned that alpa_mix is applied in
some for the i-th iteration.

Is it okay, if I simply use alpha_mix(1)=0.2 (or some smalled value) ? Or
do I need to take care of something else?

Thanks and Regards

K C Bhamu
Postdoctoral Fellow
University of Ulsan
ROK
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[QE-users] Possibly too few bands at point 2 message in DFT+U+V calculation

[Dr. K. C. Bhamu]

Dear Dr. Timrov,

I have set verbosity = high in QE input file without specifying nbnd.
In the HP output file, I am getting below two messages:

   - Possibly too few bands at point2

If this is really related to QE input file then why I do not see any such
message in QE output file?
Should we set nbnd in QE input file or we can ignore it?

   - Number of k-points >= 100: set verbosity='high' to print the bands.

I do not find q verbosity tag in "hp.x input description" file instead I
found iverbosity.  Anyway, it should not affect the final U+V value as we
do not see any effect of verbosity on band structure calculation. RIght? or
I should set iverbosity=2 in HP input file?

Thank you for guiding me.

Regards

K C Bhamu
Postdoctoral Fellow
School of Chemical Engineering
University of Ulsan
South Korea
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Re: [QE-users] Query for skip_type and equiv_type for DFT+U+V

[Dr. K. C. Bhamu]

Thank you so much Dr. Timrov

Regards
Bhamu

On Wed, Nov 24, 2021 at 8:11 PM Iurii TIMROV via users <
users@lists.quantum-espresso.org> wrote:

> Ok, so you have this:
>
>
> atom1   Tr[ns(na)]=   6.2349321 -> Fe1
> atom2   Tr[ns(na)]=   6.2349321 -> Fe1
> atom3   Tr[ns(na)]=   6.2349321 -> Fe1
> atom4   Tr[ns(na)]=   6.2348428 -> Fe1
> atom5   Tr[ns(na)]=   6.1942515 -> Fe2
> atom6   Tr[ns(na)]=   6.1942515 -> Fe2
>
>
> Just use find_atpert=1 and docc_thr=1.d-4. This will perturb one Fe1 atom
> and one Fe2 atom, because they have different occupations. If you want to
> have the same U for both Fe1 and Fe2 then set  docc_thr=5.d-2: in this
> case the code will perturb only Fe1 atom.
>
>
> HTH
>
>
> Iurii
>
>
> --
> Dr. Iurii TIMROV
> Senior Research Scientist
> Theory and Simulation of Materials (THEOS)
> Swiss Federal Institute of Technology Lausanne (EPFL)
> CH-1015 Lausanne, Switzerland
> +41 21 69 34 881
> http://people.epfl.ch/265334
> --
> *From:* users  on behalf of Dr.
> K. C. Bhamu 
> *Sent:* Wednesday, November 24, 2021 3:31:30 PM
> *To:* Quantum ESPRESSO users Forum
> *Subject:* Re: [QE-users] Query for skip_type and equiv_type for DFT+U+V
>
> Thanks  Iurii,
> I find that "find_atpert" is by default set at 1.
> With the setting mention in my previous mail, I got the below error:
>  Error in routine hp_find_inequiv_sites (1):
>  skip_type must not be setup from the input when find_atpert=1.
> For magnetite structure (Fe3O4), Fe has two states: Fe2+ and Fe3+.
>
>  Here is the Tr[ns(na)] and input file
> atom1   Tr[ns(na)]=   6.2349321
> atom1   Mag[ns(na)]=   3.5251042
> atom2   Tr[ns(na)]=   6.2349321
> atom2   Mag[ns(na)]=   3.5251042
> atom3   Tr[ns(na)]=   6.2349321
> atom3   Mag[ns(na)]=   3.5251042
> atom4   Tr[ns(na)]=   6.2348428
> atom4   Mag[ns(na)]=   3.5251547
> atom5   Tr[ns(na)]=   6.1942515
> atom5   Mag[ns(na)]=  -3.5314272
> atom6   Tr[ns(na)]=   6.1942515
> atom6   Mag[ns(na)]=  -3.5314272
> atom7   Tr[ns(na)]=   5.0802986
> atom7   Mag[ns(na)]=   0.0754368
> atom8   Tr[ns(na)]=   5.0802986
> atom8   Mag[ns(na)]=   0.0754368
> atom9   Tr[ns(na)]=   5.0802986
> atom9   Mag[ns(na)]=   0.0754368
> atom   10   Tr[ns(na)]=   5.0802986
> atom   10   Mag[ns(na)]=   0.0754368
> atom   11   Tr[ns(na)]=   5.0802986
> atom   11   Mag[ns(na)]=   0.0754368
> atom   12   Tr[ns(na)]=   5.0802986
> atom   12   Mag[ns(na)]=   0.0754368
> atom   13   Tr[ns(na)]=   5.0802792
> atom   13   Mag[ns(na)]=   0.0754401
> atom   14   Tr[ns(na)]=   5.0802792
> atom   14   Mag[ns(na)]=   0.0754401
>
> Input file:
>
> 
>   calculation = 'vc-relax'
>   restart_mode='from_scratch',
>   etot_conv_thr =   0.0001
>   forc_conv_thr =   0.001
>   outdir = './temp/'
>   prefix = 'pwscf'
>   pseudo_dir = '~/PP/'
>   tprnfor = .true.
>   tstress = .true.
>   verbosity = 'high'
> /
> 
>   degauss =   0.022
>   ecutrho =   320
>   ecutwfc =   40
>   occupations = 'smearing' ,smearing = 'mp'
>   ibrav = 0
>   nat = 14
>   nosym = .false.
>   ntyp = 3
> nspin=2
>   starting_magnetization(1) =   0.8
>   starting_magnetization(2) =   -0.8
>   starting_magnetization(3) =   0.0
>
>   lda_plus_u = .true.,
>   lda_plus_u_kind = 2,
>   U_projection_type = 'ortho-atomic',
>   Hubbard_V(1,1,1) = 1.d-8
>   Hubbard_V(5,5,1) = 1.d-8
>   Hubbard_V(7,7,1) = 1.d-8
> !Hubbard_parameters = 'file'
>
>
> /
> 
>   conv_thr =   1.00d-06
>   electron_maxstep = 400
>   mixing_beta =   1.50d-01
> /
> 
> ion_dynamics = 'bfgs'
>  /
> 
> /
>
> ATOMIC_SPECIES
> Fe1 55.845 Fe.pbe-nd-rrkjus.UPF
> Fe2 55.845 Fe.pbe-nd-rrkjus.UPF
> O  15.9994 O.pbe-rrkjus.UPF
> ATOMIC_POSITIONS (crystal)
> Fe1   0.00   -0.00   -0.00
> Fe1   0.500.000.00
> Fe1   0.9998920.500216   -0.00
> Fe1   0.650.560.500115
> Fe2   0.37499937210.37499933490.3750019210
> Fe2   0.62500062250.62500065320.6249981020
> O 0.24548684150.24548683990.2454949640
> O 0.75451318450.75451310980.7545050345
> O 0.76353135460.24548683990.2454949640
> O 0.23646867130.75451310980.7545050345
> O 0.24548683070.76353137460.2454949640

Re: [QE-users] Query for skip_type and equiv_type for DFT+U+V

[Dr. K. C. Bhamu]

Thanks  Iurii,
I find that "find_atpert" is by default set at 1.
With the setting mention in my previous mail, I got the below error:
 Error in routine hp_find_inequiv_sites (1):
 skip_type must not be setup from the input when find_atpert=1.
For magnetite structure (Fe3O4), Fe has two states: Fe2+ and Fe3+.

 Here is the Tr[ns(na)] and input file
atom1   Tr[ns(na)]=   6.2349321
atom1   Mag[ns(na)]=   3.5251042
atom2   Tr[ns(na)]=   6.2349321
atom2   Mag[ns(na)]=   3.5251042
atom3   Tr[ns(na)]=   6.2349321
atom3   Mag[ns(na)]=   3.5251042
atom4   Tr[ns(na)]=   6.2348428
atom4   Mag[ns(na)]=   3.5251547
atom5   Tr[ns(na)]=   6.1942515
atom5   Mag[ns(na)]=  -3.5314272
atom6   Tr[ns(na)]=   6.1942515
atom6   Mag[ns(na)]=  -3.5314272
atom7   Tr[ns(na)]=   5.0802986
atom7   Mag[ns(na)]=   0.0754368
atom8   Tr[ns(na)]=   5.0802986
atom8   Mag[ns(na)]=   0.0754368
atom9   Tr[ns(na)]=   5.0802986
atom9   Mag[ns(na)]=   0.0754368
atom   10   Tr[ns(na)]=   5.0802986
atom   10   Mag[ns(na)]=   0.0754368
atom   11   Tr[ns(na)]=   5.0802986
atom   11   Mag[ns(na)]=   0.0754368
atom   12   Tr[ns(na)]=   5.0802986
atom   12   Mag[ns(na)]=   0.0754368
atom   13   Tr[ns(na)]=   5.0802792
atom   13   Mag[ns(na)]=   0.0754401
atom   14   Tr[ns(na)]=   5.0802792
atom   14   Mag[ns(na)]=   0.0754401

Input file:


  calculation = 'vc-relax'
  restart_mode='from_scratch',
  etot_conv_thr =   0.0001
  forc_conv_thr =   0.001
  outdir = './temp/'
  prefix = 'pwscf'
  pseudo_dir = '~/PP/'
  tprnfor = .true.
  tstress = .true.
  verbosity = 'high'
/

  degauss =   0.022
  ecutrho =   320
  ecutwfc =   40
  occupations = 'smearing' ,smearing = 'mp'
  ibrav = 0
  nat = 14
  nosym = .false.
  ntyp = 3
nspin=2
  starting_magnetization(1) =   0.8
  starting_magnetization(2) =   -0.8
  starting_magnetization(3) =   0.0

  lda_plus_u = .true.,
  lda_plus_u_kind = 2,
  U_projection_type = 'ortho-atomic',
  Hubbard_V(1,1,1) = 1.d-8
  Hubbard_V(5,5,1) = 1.d-8
  Hubbard_V(7,7,1) = 1.d-8
!Hubbard_parameters = 'file'


/

  conv_thr =   1.00d-06
  electron_maxstep = 400
  mixing_beta =   1.50d-01
/

ion_dynamics = 'bfgs'
 /

/

ATOMIC_SPECIES
Fe1 55.845 Fe.pbe-nd-rrkjus.UPF
Fe2 55.845 Fe.pbe-nd-rrkjus.UPF
O  15.9994 O.pbe-rrkjus.UPF
ATOMIC_POSITIONS (crystal)
Fe1   0.00   -0.00   -0.00
Fe1   0.500.000.00
Fe1   0.9998920.500216   -0.00
Fe1   0.650.560.500115
Fe2   0.37499937210.37499933490.3750019210
Fe2   0.62500062250.62500065320.6249981020
O 0.24548684150.24548683990.2454949640
O 0.75451318450.75451310980.7545050345
O 0.76353135460.24548683990.2454949640
O 0.23646867130.75451310980.7545050345
O 0.24548683070.76353137460.2454949640
O 0.75451325230.23646862170.7545050345
O 0.24549085930.24549082220.7635274591
O 0.75450906290.75450917410.2364725394

CELL_PARAMETERS (angstrom)
   5.944682649   0.0   0.0
   2.972341325   5.148246192   0.0
   2.972341325   1.716082064   4.853885701

K_POINTS automatic
7 7 7 0 0 0

Regards
Bhamu



>
> > As all Fe will have the same Hubbard parameter (as reported in the
> literature for the same system)...
>
>
> In the literature people often use empirical U, so that's why they use a
> single value of U for all Fe atoms. With the HP code you can do things
> better, i.e. to find out if there are non-equivalent Fe atoms that require
> their own first-principles U.
>
>
> HTH
>
>
> Iurii
>
>
> P.S.: "Dr." is used with the last name not with the first name, so in my
> case this will be "Dear Dr. Timrov". But if you want to address me using my
> first name then just write "Dear Iurii". Sorry, I don't want to bother
> you with this, but just to makes things clear 
>
>
> --
> Dr. Iurii TIMROV
> Senior Research Scientist
> Theory and Simulation of Materials (THEOS)
> Swiss Federal Institute of Technology Lausanne (EPFL)
> CH-1015 Lausanne, Switzerland
> +41 21 69 34 881
> http://people.epfl.ch/265334
> --
> *From:* users  on behalf of Dr.
> K. C. Bhamu 
> *Sent:* Wednesday, November 24, 2021 1:00:13 PM
> *To:* Quantum Espresso users Forum
> *Subject:* [QE-users] Query for skip_type and equiv_type for DFT+U+V
>
> Dear Dr. Iurii (),
>
> The ATOMIC_POSITIONS cart of my structure (ferrimagnetic system with ntyp
> = 3 ) is
>
> ATOMIC_POSITIONS (crys

[QE-users] Query for skip_type and equiv_type for DFT+U+V

[Dr. K. C. Bhamu]

Dear Dr. Iurii (),

The ATOMIC_POSITIONS cart of my structure (ferrimagnetic system with ntyp =
3 ) is

ATOMIC_POSITIONS (crystal)
Fe1   0.00   -0.00   -0.00 (four
times)
Fe2   0.37499937210.37499933490.3750019210 (two
times)
O 0.24548684150.24548683990.2454949640 (eight
times)

Previously, based on ATOMIC_SPECIES cart, I defined my Hubbard tag as below

  Hubbard_V(1,1,1) = 1.d-8
  Hubbard_V(2,2,1) = 1.d-8
  Hubbard_V(3,3,1) = 1.d-8

In the hp output file, I saw that only one  Fe1 atom was perturbed.

Then I defined below Hubbard tags according to ATOMIC_POSITIONS cart as

  Hubbard_V(1,1,1) = 1.d-8
  Hubbard_V(5,5,1) = 1.d-8
  Hubbard_V(7,7,1) = 1.d-8

which perturbed four atoms

1  Fe155.8450   tau( 1) = (  0.0  0.0  0.0  )
4  Fe155.8450   tau( 4) = (  1.75000  1.01036  0.40825  )
5  Fe255.8450   tau( 5) = (  0.75000  0.43301  0.30619  )
7  O  15.9994   tau( 7) = (  0.49098  0.28347  0.20045  )

As all Fe will have the same Hubbard parameter (as reported in the
literature for the same system), I would like to skip the perturbation for
atom Fe1(4) and Fe2(5).

Is it okay if I do so?

To skip the perturbation for Fe1(4) and Fe2(5), I have updated below tags
in my hp input file:

skip_type(1)=.true.
skip_type(2)=.true.
equiv_type(1)=1
equiv_type(2)=1
disable_type_analysis=.true.,

Could you please correct me if this modification is correct or not?

Sorry for the list of questions. But I am sure, my these queries will be
helpful for others too.

Thanks and regards

K C Bhamu

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

Re: [QE-users] Need some comments on my U+V values obtained using self-consistently

[Dr. K. C. Bhamu]

Thank you so much Dr. Lurii.
It helped me a lot.

Regards
Bhamu

On Wed, Nov 24, 2021 at 4:11 PM Iurii TIMROV via users <
users@lists.quantum-espresso.org> wrote:

> Dear Bhamu,
>
>
> Just for reference, the protocol/workflow for a self-consistent
> calculation of Hubbard parameters is shown in Fig. 1 of Phys. Rev. B103,
> 045141 (2021).
>
>
> > I performed only relaxed calculations in each step without updating the
> ionic positions for the next step.
>
>
> calculation = 'relax' means that you optimize atomic positions while the
> lattice parameters are not changed. In our protocol in Fig. 1 by
> "structural optimization" we mean actually vc-relax, i.e. we optimize both
> the atomic positions AND lattice parameters.
>
>
> > Do you think, I have followed a correct approach to get
> the converged U+V value?
>
>
> It seems yes accept for the fact that you did 'relax' instead of
> 'vc-relax'.
>
>
> > Do you think, the value I obtained for U+V is a converged value?
>
>
> It depends what accuracy for Hubbard parameters you need. In your case you
> have 5.0651-5.0513=0.0138, which means that your U values are converged
> with the accuracy of ~0.01 eV which is more than enough for the majority of
> applications. But I recommend to perform 'vc-relax' between HP
> calculations.
>
> HTH
>
>
> Iurii
>
>
> --
> Dr. Iurii TIMROV
> Senior Research Scientist
> Theory and Simulation of Materials (THEOS)
> Swiss Federal Institute of Technology Lausanne (EPFL)
> CH-1015 Lausanne, Switzerland
> +41 21 69 34 881
> http://people.epfl.ch/265334
> --
> *From:* users  on behalf of Dr.
> K. C. Bhamu 
> *Sent:* Wednesday, November 24, 2021 10:06:49 AM
> *To:* Quantum ESPRESSO users Forum
> *Subject:* Re: [QE-users] Need some comments on my U+V values obtained
> using self-consistently
>
> Hii Niharika,
> I did not do vc-relax in between all steps except.
> I performed only relaxed calculations in each step without updating the
> ionic positions for the next step.
>
> Here is my script, I used for the automation:
>
> DIR1=dir1
> DIR2=dir2
> DIR3=dir3
> srun /home/kcbhamu/soft/qe67_kg/bin/pw.x   < FO.scf.in > FO.scf.out
> srun /home/kcbhamu/soft/qe67_kg/bin/hp.x   < FO.hp.in > FO.hp.out
>
>
> mkdir $DIR1
> mv *Hubbard_parameters.dat $DIR1
> mv parameters.out $DIR1
> cp $DIR1/parameters.out parameters.in
> mv *out $DIR1
> rm -rf temp/
>
> sed -i 's/Hubbard_V/!Hubbard_V/g' FO.scf.in
> sed -i 's/!Hubbard_parameters/Hubbard_parameters/g' FO.scf.in
>
> srun /home/kcbhamu/soft/qe67_kg/bin/pw.x   < FO.scf.in > FO.scf.out
> srun /home/kcbhamu/soft/qe67_kg/bin/hp.x   < FO.hp.in > FO.hp.out
>
> mkdir $DIR2
> mv *Hubbard_parameters.dat $DIR2
> mv parameters.out $DIR2
> cp $DIR2/parameters.out parameters.in
> mv *out $DIR2
> rm -rf temp/
>
> srun /home/kcbhamu/soft/qe67_kg/bin/pw.x   < FO.scf.in > FO.scf.out
> srun /home/kcbhamu/soft/qe67_kg/bin/hp.x   < FO.hp.in > FO.hp.out
>
> mkdir $DIR3
> cp *Hubbard_parameters.dat $DIR3
> cp parameters.out $DIR3
> cp $DIR3/parameters.out parameters.in
> cp *out $DIR3
> rm -rf temp/
>
> Regards
> Bhamu
>
>
> On Wed, Nov 24, 2021 at 2:23 PM Niharika Joshi via users <
> users@lists.quantum-espresso.org> wrote:
>
>> Dear Bhamu sir,
>> I have never done convergence for U+V.
>> However I have done convergence of U and I did it in the similar fashion
>> as you have described.
>> Only one check...when you said that you did a fresh calculation with
>> Hubbard_parameters='file' ,
>> you meant you again performed vc-relax and then an scf, right?
>>
>> Best regards,
>> Niharika
>>
>> --
>> *From: *kcbham...@gmail.com
>> *To: *users@lists.quantum-espresso.org
>> *Sent: *Wednesday, November 24, 2021 1:02:31 PM
>> *Subject: *[QE-users] Need some comments on my U+V values obtained
>> usingself-consistently
>>
>> Dear Dr.  Lurii,
>> I could manage the HP code to obtain U+V value for my system.
>> Could you please comment on my approach and value obtained as mentioned
>> below?
>>
>>
>> 1. vc-relax with PBE (with all converged parameters of the input file,
>> like ecut, k-points...).
>> 2.(i): Using optimized geometry of step-1
>>
>> calculation = 'relax' ;  nspin=2
>>   starting_magnetization(1) =   0.8;   starting_magnetization(2) =   -0.8
>> ;   starting_magnetization(3) =   0.0
>>   lda_plus_u = .true., ;   lda_plus_u_kind = 2, ;   U_projection_type =
>> 'ortho-atomic'

Re: [QE-users] Need some comments on my U+V values obtained using self-consistently

[Dr. K. C. Bhamu]

Hii Niharika,
I did not do vc-relax in between all steps except.
I performed only relaxed calculations in each step without updating the
ionic positions for the next step.

Here is my script, I used for the automation:

DIR1=dir1
DIR2=dir2
DIR3=dir3
srun /home/kcbhamu/soft/qe67_kg/bin/pw.x   < FO.scf.in > FO.scf.out
srun /home/kcbhamu/soft/qe67_kg/bin/hp.x   < FO.hp.in > FO.hp.out


mkdir $DIR1
mv *Hubbard_parameters.dat $DIR1
mv parameters.out $DIR1
cp $DIR1/parameters.out parameters.in
mv *out $DIR1
rm -rf temp/

sed -i 's/Hubbard_V/!Hubbard_V/g' FO.scf.in
sed -i 's/!Hubbard_parameters/Hubbard_parameters/g' FO.scf.in

srun /home/kcbhamu/soft/qe67_kg/bin/pw.x   < FO.scf.in > FO.scf.out
srun /home/kcbhamu/soft/qe67_kg/bin/hp.x   < FO.hp.in > FO.hp.out

mkdir $DIR2
mv *Hubbard_parameters.dat $DIR2
mv parameters.out $DIR2
cp $DIR2/parameters.out parameters.in
mv *out $DIR2
rm -rf temp/

srun /home/kcbhamu/soft/qe67_kg/bin/pw.x   < FO.scf.in > FO.scf.out
srun /home/kcbhamu/soft/qe67_kg/bin/hp.x   < FO.hp.in > FO.hp.out

mkdir $DIR3
cp *Hubbard_parameters.dat $DIR3
cp parameters.out $DIR3
cp $DIR3/parameters.out parameters.in
cp *out $DIR3
rm -rf temp/

Regards
Bhamu


On Wed, Nov 24, 2021 at 2:23 PM Niharika Joshi via users <
users@lists.quantum-espresso.org> wrote:

> Dear Bhamu sir,
> I have never done convergence for U+V.
> However I have done convergence of U and I did it in the similar fashion
> as you have described.
> Only one check...when you said that you did a fresh calculation with
> Hubbard_parameters='file' ,
> you meant you again performed vc-relax and then an scf, right?
>
> Best regards,
> Niharika
>
> --
> *From: *kcbham...@gmail.com
> *To: *users@lists.quantum-espresso.org
> *Sent: *Wednesday, November 24, 2021 1:02:31 PM
> *Subject: *[QE-users] Need some comments on my U+V values obtained
> usingself-consistently
>
> Dear Dr.  Lurii,
> I could manage the HP code to obtain U+V value for my system.
> Could you please comment on my approach and value obtained as mentioned
> below?
>
>
> 1. vc-relax with PBE (with all converged parameters of the input file,
> like ecut, k-points...).
> 2.(i): Using optimized geometry of step-1
>
> calculation = 'relax' ;  nspin=2
>   starting_magnetization(1) =   0.8;   starting_magnetization(2) =   -0.8
> ;   starting_magnetization(3) =   0.0
>   lda_plus_u = .true., ;   lda_plus_u_kind = 2, ;   U_projection_type =
> 'ortho-atomic',
>   Hubbard_V(1,1,1) = 1.d-8;   Hubbard_V(2,2,1) = 1.d-8 ;
> Hubbard_V(3,3,1) = 1.d-8
> !   Hubbard_parameters = 'file'
>
> *head pwscf.Hubbard_parameters.dat*
> site n.  type  label  spin  new_type  new_label  Hubbard U (eV)
>  11Fe1 1  1 Fe14.6800
>  21Fe1 1  1 Fe14.6800
>  31Fe1 1  1 Fe14.6800
>  41Fe1 1  1 Fe14.6795
>
> *grep '11' parameters.out*
> dir1/parameters.out: 11   4.6800
>
> 2.(ii) In a fresh directory with parameters.in of previous step.
> kept all the parameters as such except
>  !  Hubbard_V(1,1,1) = 1.d-8;   !   Hubbard_V(2,2,1) = 1.d-8 ;   !
> Hubbard_V(3,3,1) = 1.d-8
> Hubbard_parameters = 'file'
>
> *head pwscf.Hubbard_parameters.dat*
> site n.  type  label  spin  new_type  new_label  Hubbard U (eV)
>  11Fe1 1  1 Fe15.0513
>  21Fe1 1  1 Fe15.0513
>  31Fe1 1  1 Fe15.0513
>  41Fe1 1  1 Fe15.0514
> *grep '11' parameters.out*
> parameters.out: 11   5.0513
>
> 2.(iii) In a fresh directory with parameters.in of previous step.
> kept all the parameters as such except
>  !   Hubbard_V(1,1,1) = 1.d-8;   !   Hubbard_V(2,2,1) = 1.d-8 ;   !
>  Hubbard_V(3,3,1) = 1.d-8
> Hubbard_parameters = 'file'
> *head pwscf.Hubbard_parameters.dat*
> site n.  type  label  spin  new_type  new_label  Hubbard U (eV)
>  11Fe1 1  1 Fe15.0651
>  21Fe1 1  1 Fe15.0651
>  31Fe1 1  1 Fe15.0651
>  41Fe1 1  1 Fe15.0651
>
> *grep '11' parameters.out*
> parameters.out: 11   5.0651
>
>
>
>1. Do you think, I have followed a correct approach to get
>the converged U+V value?
>2. Do you think, the value I obtained for U+V is a converged value?
>
>
> I am looking forward to hearing from you.
>
> Regards
> Bhamu
>
>
>
>
>
> ___
> Quantum ESPRESSO is supported by MaX (www.max-centre.eu)
> users mailing list users@lists.quantum-espresso.org
> https://lists.quantum-espresso.org/mailman/listinfo/users
>
>
> ___
> Quantum ESPRESSO is 

[QE-users] Need some comments on my U+V values obtained using self-consistently

[Dr. K. C. Bhamu]

Dear Dr.  Lurii,
I could manage the HP code to obtain U+V value for my system.
Could you please comment on my approach and value obtained as mentioned
below?


1. vc-relax with PBE (with all converged parameters of the input file, like
ecut, k-points...).
2.(i): Using optimized geometry of step-1

calculation = 'relax' ;  nspin=2
  starting_magnetization(1) =   0.8;   starting_magnetization(2) =   -0.8
;   starting_magnetization(3) =   0.0
  lda_plus_u = .true., ;   lda_plus_u_kind = 2, ;   U_projection_type =
'ortho-atomic',
  Hubbard_V(1,1,1) = 1.d-8;   Hubbard_V(2,2,1) = 1.d-8 ;   Hubbard_V(3,3,1)
= 1.d-8
!   Hubbard_parameters = 'file'

*head pwscf.Hubbard_parameters.dat*
site n.  type  label  spin  new_type  new_label  Hubbard U (eV)
 11Fe1 1  1 Fe14.6800
 21Fe1 1  1 Fe14.6800
 31Fe1 1  1 Fe14.6800
 41Fe1 1  1 Fe14.6795

*grep '11' parameters.out*
dir1/parameters.out: 11   4.6800

2.(ii) In a fresh directory with parameters.in of previous step.
kept all the parameters as such except
 !  Hubbard_V(1,1,1) = 1.d-8;   !   Hubbard_V(2,2,1) = 1.d-8 ;   !
Hubbard_V(3,3,1) = 1.d-8
Hubbard_parameters = 'file'

*head pwscf.Hubbard_parameters.dat*
site n.  type  label  spin  new_type  new_label  Hubbard U (eV)
 11Fe1 1  1 Fe15.0513
 21Fe1 1  1 Fe15.0513
 31Fe1 1  1 Fe15.0513
 41Fe1 1  1 Fe15.0514
*grep '11' parameters.out*
parameters.out: 11   5.0513

2.(iii) In a fresh directory with parameters.in of previous step.
kept all the parameters as such except
 !   Hubbard_V(1,1,1) = 1.d-8;   !   Hubbard_V(2,2,1) = 1.d-8 ;   !
 Hubbard_V(3,3,1) = 1.d-8
Hubbard_parameters = 'file'
*head pwscf.Hubbard_parameters.dat*
site n.  type  label  spin  new_type  new_label  Hubbard U (eV)
 11Fe1 1  1 Fe15.0651
 21Fe1 1  1 Fe15.0651
 31Fe1 1  1 Fe15.0651
 41Fe1 1  1 Fe15.0651

*grep '11' parameters.out*
parameters.out: 11   5.0651



   1. Do you think, I have followed a correct approach to get
   the converged U+V value?
   2. Do you think, the value I obtained for U+V is a converged value?


I am looking forward to hearing from you.

Regards
Bhamu
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[QE-users] error while creating HP directory

[Dr. K. C. Bhamu]

Dear QE Users,
Have any of you faced this problem while running HP code?
I am running QE_6.7 version which is compiled with mpiifort
of compilers_and_libraries_2020.2.254.

tas % from create_directory : error # 1
 unable to create directory ./tmp/HP/

How can I resolve this?


Regards

K C Bhamu

Postdoctoral Fellow
School of Chemical Engineering
University of Ulsan
South Korea
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Re: [QE-users] FFT grid error with DFT+U+V

[Dr. K. C. Bhamu]

With ibrav=0 I dont see any error so far.
Earlier, I used ibrav=1 and celldm(1)= xyz.

Regards
Bhamu

On Tue, Nov 16, 2021 at 10:23 AM Dr. K. C. Bhamu 
wrote:

> Dear QE Users,
> I am trying to run DFT+U+V using hp.x for magnetite (Fe3O4) structure
> using QE_6.7 which is compiled using "MPIF90=mpiifort F90=mpiifort
> F77=mpiifort CC=mpiicc --disable-openmp --enable-parallel
> --with-scalapack=intel".
>
> My hp.x command is:
> srun $home/qe67/bin/hp.x   < FO.hp.in > FO.hp.out.  I am using 20 cores
> for this job.
>
> For the hp.x run, I am getting the below error (listed in between ==
> ...===):
> =
>  Error in routine scale_sym_ops (6):
>  incompatible FFT grid
>
>  
> %%
>  stopping ...
>  Message from routine scale_sym_ops:
>  found fractional translation not compatible with FFT grid
> =
>
> FFT grid information from the *out files is as below:
>
> FO.hp.out: Dense  grid:   352839 G-vectors FFT dimensions: (  90,
>  90,  90)
> FO.hp.out: Smooth grid:67715 G-vectors FFT dimensions: (  54,
>  54,  54)
> FO.hp.out: G cutoff = 1922.9437  (  17645 G-vectors) FFT grid: (
> 90, 90, 90)
> FO.hp.out: incompatible FFT grid
> FO.hp.out: found fractional translation not compatible with FFT grid
> FO.hp.out: incompatible FFT grid
>
> FO.scf.out: Dense  grid:   352839 G-vectors FFT dimensions: (  90,
>  90,  90)
> FO.scf.out: Smooth grid:67715 G-vectors FFT dimensions: (  54,
>  54,  54)
>
> Could you tell me how can I remove this error?
>
> Please let me know if I need to provide some additional information. The
> QE input file is provided in my previous email.
> My hp.in file is:
>  
>prefix = 'pwscf',
>outdir = './tmp/',
>nq1 = 2, nq2 = 2, nq3 = 2,
>conv_thr_chi = 1.0d-8,
>iverbosity = 2
> /
>
>
> Regards
> Bhamu
>
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Re: [QE-users] Need some suggestion regarding the band gap issue of Fe3O4

[Dr. K. C. Bhamu]

Dear Dr. Lurii,
Thank you for your important suggestions.
I have started HP code and got some errors which I have posted in a
separate email.
I am looking into more details and will get back to you with some updates.

Regards
Bhamu


On Mon, Nov 15, 2021 at 9:55 PM Iurii TIMROV via users <
users@lists.quantum-espresso.org> wrote:

> Dear K C Bhamu,
>
>
> > Do you think my input file (see below) has any issues? I have defined
> all tetra-Fe sites dn-spin and all octahedra Fe sites up-spin.
>
>
> I recommend to check with the QE input generator:
> https://www.materialscloud.org/work/tools/qeinputgenerator
>
>
> > What other things I should take care of to reproduce the band gap (0.14
> eV to 0.3 eV)?
>
>
> I never studied this system but I can give general comments:
>
> - you can try to determine Hubbard parameters using the HP code of QE
>
> - you can try to use "ortho-atomic" Hubbard projectors instead of "atomic"
> (U_projection_type): https://www.mdpi.com/2076-3417/11/5/2395
>
> - maybe try DFT+U+V?
> https://journals.aps.org/prmaterials/abstract/10.1103/PhysRevMaterials.5.104402
> (see Fig. 6) Tutorial: https://www.youtube.com/watch?v=WSABAqPWNH0=5s
>
>
> > In the research paper [3]
> <https://iopscience.iop.org/article/10.1088/1468-6996/15/4/044202>, the
> authors used VASP and the valence configuration for the Fe atom was taken
> as 3d64s1. I could not find any PP from the list I mention below which has
> this configuration. Does this may be an issue? If anyone has PP of Fe
> with 3d64s1 configuration, please provide me.
>
>
> Check SSSP: https://www.materialscloud.org/discover/sssp/table/efficiency
>
>
> HTH
>
>
> Iurii
>
>
> --
> Dr. Iurii TIMROV
> Senior Research Scientist
> Theory and Simulation of Materials (THEOS)
> Swiss Federal Institute of Technology Lausanne (EPFL)
> CH-1015 Lausanne, Switzerland
> +41 21 69 34 881
> http://people.epfl.ch/265334
> --
> *From:* users  on behalf of Dr.
> K. C. Bhamu 
> *Sent:* Monday, November 15, 2021 11:47:16 AM
> *To:* Quantum Espresso users Forum
> *Subject:* [QE-users] Need some suggestion regarding the band gap issue
> of Fe3O4
>
> Dear QE Users,
>
> This email may be large for you all as I am trying to put all the
> information so that I do not miss any information in your response.
> I sincerely apologize for this long email.
>
>
> I am dealing with ferrimagnetic Fe3O4 (with QE6.6) and trying to
> reproduce its band gap. In the literature, its experimental band gap was
> reported to be in the range of 0.14-0.3eV, Table SI-1 [1]
> <https://aip.scitation.org/doi/10.1063/1.5138941> for the up-spin state.
> For Fe3O4 nanoparticles, the band gap is reported ~2eV.
>
> I have tried with all available PPs (mentioned below in different sets)
> and U values from 1eV to 7eV. At lower U (=1-2eV), I am getting this
> system a direct band-gap half-metal (a gap is opened in the spin-up
> channel) and with increasing the U value, the direct band-gap (=~1eV)
> nature changes to the indirect (=~2eV) band gap. At U=7eV with the rrkjus
> PPs, it showed a metallic character.
>
> I have also carried out the band structure, by keeping the lattice
> parameters fixed at experimental values and only relaxing ionic position,
> with varying U-values. But still, the nature of the bang-gap is similar
> to what I just mentioned above(band gap varies from ~1eV to ~2eV with
> U=1eV to 7eV, respectively).
>
> The lattice parameters, magnetic moments, and the charge on Fe_tet and
> Fe_oct sites I am getting reasonably in accordance with the Table SI-1
> <https://aip.scitation.org/doi/10.1063/1.5138941>.
>
> A sample of my input file is also shown below (the only PPs are different
> with respective cutoffs).
>
> Information collected from other research papers:
> 1.  See [2]
> <https://www.sciencedirect.com/science/article/abs/pii/S0039602812000544>
> (In section 3.1. Bulk Fe3O4: 0.33 eV band gap with VASP with U=3.8eV ).
> 2.  See [3]
> <https://iopscience.iop.org/article/10.1088/1468-6996/15/4/044202>   (Page-4,
> bottom left para: 2.1 eV using VASP with U=4 eV).   This paper only shows
> the direct band-gap of 2.1eV.
> Based on my already finished calculations and the details that I have
> covered above, I have a few queries:
>
>1. Do you think my input file (see below) has any issues? I have
>defined all tetra-Fe sites dn-spin and all octahedra Fe sites up-spin.
>2. What other things I should take care of to reproduce the band gap
>(0.14 eV to 0.3 eV)?
>3. In the research paper [3]
><https://iopscience.iop.org/article/10.1088/1468-6996/15/4

[QE-users] FFT grid error with DFT+U+V

[Dr. K. C. Bhamu]

Dear QE Users,
I am trying to run DFT+U+V using hp.x for magnetite (Fe3O4) structure using
QE_6.7 which is compiled using "MPIF90=mpiifort F90=mpiifort F77=mpiifort
CC=mpiicc --disable-openmp --enable-parallel --with-scalapack=intel".

My hp.x command is:
srun $home/qe67/bin/hp.x   < FO.hp.in > FO.hp.out.  I am using 20 cores for
this job.

For the hp.x run, I am getting the below error (listed in between ==
...===):
=
 Error in routine scale_sym_ops (6):
 incompatible FFT grid
 %%
 stopping ...
 Message from routine scale_sym_ops:
 found fractional translation not compatible with FFT grid
=

FFT grid information from the *out files is as below:

FO.hp.out: Dense  grid:   352839 G-vectors FFT dimensions: (  90,
 90,  90)
FO.hp.out: Smooth grid:67715 G-vectors FFT dimensions: (  54,
 54,  54)
FO.hp.out: G cutoff = 1922.9437  (  17645 G-vectors) FFT grid: (
90, 90, 90)
FO.hp.out: incompatible FFT grid
FO.hp.out: found fractional translation not compatible with FFT grid
FO.hp.out: incompatible FFT grid

FO.scf.out: Dense  grid:   352839 G-vectors FFT dimensions: (  90,
 90,  90)
FO.scf.out: Smooth grid:67715 G-vectors FFT dimensions: (  54,
 54,  54)

Could you tell me how can I remove this error?

Please let me know if I need to provide some additional information. The QE
input file is provided in my previous email.
My hp.in file is:
 
   prefix = 'pwscf',
   outdir = './tmp/',
   nq1 = 2, nq2 = 2, nq3 = 2,
   conv_thr_chi = 1.0d-8,
   iverbosity = 2
/


Regards
Bhamu
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[QE-users] Need some suggestion regarding the band gap issue of Fe3O4

[Dr. K. C. Bhamu]

Dear QE Users,

This email may be large for you all as I am trying to put all the
information so that I do not miss any information in your response.
I sincerely apologize for this long email.


I am dealing with ferrimagnetic Fe3O4 (with QE6.6) and trying to reproduce
its band gap. In the literature, its experimental band gap was reported to
be in the range of 0.14-0.3eV, Table SI-1 [1]
 for the up-spin state.
For Fe3O4 nanoparticles, the band gap is reported ~2eV.

I have tried with all available PPs (mentioned below in different sets) and
U values from 1eV to 7eV. At lower U (=1-2eV), I am getting this system a
direct band-gap half-metal (a gap is opened in the spin-up channel) and
with increasing the U value, the direct band-gap (=~1eV) nature changes to
the indirect (=~2eV) band gap. At U=7eV with the rrkjus PPs, it showed a
metallic character.

I have also carried out the band structure, by keeping the lattice
parameters fixed at experimental values and only relaxing ionic position,
with varying U-values. But still, the nature of the bang-gap is similar to
what I just mentioned above(band gap varies from ~1eV to ~2eV with U=1eV to
7eV, respectively).

The lattice parameters, magnetic moments, and the charge on Fe_tet and
Fe_oct sites I am getting reasonably in accordance with the Table SI-1
.

A sample of my input file is also shown below (the only PPs are different
with respective cutoffs).

Information collected from other research papers:
1.  See [2]

(In section 3.1. Bulk Fe3O4: 0.33 eV band gap with VASP with U=3.8eV ).
2.  See [3]
   (Page-4,
bottom left para: 2.1 eV using VASP with U=4 eV).   This paper only shows
the direct band-gap of 2.1eV.
Based on my already finished calculations and the details that I have
covered above, I have a few queries:

   1. Do you think my input file (see below) has any issues? I have defined
   all tetra-Fe sites dn-spin and all octahedra Fe sites up-spin.
   2. What other things I should take care of to reproduce the band gap
   (0.14 eV to 0.3 eV)?
   3. In the research paper [3]
   , the
   authors used VASP and the valence configuration for the Fe atom was taken
   as 3d64s1. I could not find any PP from the list I mention below which has
   this configuration. Does this may be an issue? If anyone has PP of Fe
   with 3d64s1 configuration, please provide me.
   4. As mentioned in the research paper [4]
   , the authors
   have mentioned that "Our results show that, upon releasing the symmetry
   constraint on the density but not on the geometry, charge
   disproportionation (Fe2+/Fe3+) is observed, resulting in a band gap of
   around 0.2 eV at the Fermi level."  How can I release symmetry constrain
   on the density? I used nonsym=True also but the calculation was not
   converging in this case.

Supporting information for this email:


*Combinations of my PPs:*

Set-1 (ecutwfc/ecutrho = 40/320Ry)
Fe.pbe-nd-rrkjus.UPF
O.pbe-rrkjus.UPF

Set-2  (ecutwfc/ecutrho = 45/450Ry)
Fe.pbe-sp-van_mit.UPF
O.pbe-rrkjus.UPF

*Set-3  (ecutwfc/ecutrho = 65/785Ry)  >> similar to yours*

*Fe.pbe-spn-rrkjus_psl.1.0.0.UPFO.pbe-n-rrkjus_psl.1.0.0.UPF*

set-4  (ecutwfc/ecutrho = 64/782Ry)
Fe.pbe-spn-kjpaw_psl.0.2.1.UPF
O.pbe-n-kjpaw_psl.0.1.UPF

*QE input file:*


  calculation = 'scf'
  etot_conv_thr =   1.00d-04
  forc_conv_thr =   1.00d-03
!  disk_io= 'none'
  outdir = './tmp/'
  prefix = 'pwscf'
  pseudo_dir = '~/PPs/'
!  tprnfor = .true.
 ! tstress = .true.
!  verbosity = 'high'
/

  degauss =   0.01
  ecutrho =   785
  ecutwfc =   65
  ibrav = 0
  nat = 56
  nosym = .false.!! I have tried with .True. also but my calculations
were not converging.
  ntyp = 3
  occupations = 'smearing' ,smearing = 'mp'
 starting_magnetization(1) =  1
 starting_magnetization(2) =  -1
  nspin = 2
  lda_plus_u=.true.
  Hubbard_U(1)=X   (tried 1eV to 7eV)
  Hubbard_U(2)=X   (tried 1eV to 7eV)


/

  conv_thr =   1.0d-6
  electron_maxstep = 200
  mixing_beta =   3.00d-01
/

ion_dynamics = 'bfgs'
 /

/

ATOMIC_SPECIES
Fe1 55.845 Fe.pbe-spn-rrkjus_psl.1.0.0.UPF
Fe2 55.845 Fe.pbe-spn-rrkjus_psl.1.0.0.UPF
O  15.9994 O.pbe-n-rrkjus_psl.1.0.0.UPF
ATOMIC_POSITIONS crystal
Fe1   0.625000   0.625000   0.625000
Fe1   0.625000   0.375000   0.375000
Fe1   0.375000   0.625000   0.375000
Fe1   0.375000   0.375000   0.625000
Fe1   0.625000   0.875000   0.875000
Fe1   0.875000   0.625000   0.875000
Fe1   0.875000 

[QE-users] Reference for BFGS ion dynamics

[Dr. K. C. Bhamu]

Dear QE Users,
I am looking for an original Ref. for BFGS ion dynamics to cite in my
manuscript.

I am mentioning here a few but not sure to use them or not.

1. Refs. [6-9] from this paper:
https://aip.scitation.org/doi/10.1063/1.4905665
2.
https://www.wiley.com/en-sg/Practical+Methods+of+Optimization%2C+2nd+Edition-p-9780471494638


Regards
K C Bhamu
University of Ulsan
ROK
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Re: [QE-users] Forces are oscillating for P

[Dr. K. C. Bhamu]

A gentle reminder.

Regards
Bhamu

On Tue, Aug 3, 2021, 8:12 PM Dr. K. C. Bhamu  wrote:

> Dear QE Users,
> I am trying to run phosphorus  with QE_6.4 but the forces are
> oscillating between two values as shown below:
> scf.in.out: Total force = 0.008737 Total SCF correction =
> 0.02
> scf.in.out: Total force = 0.014135 Total SCF correction =
> 0.02
> scf.in.out: Total force = 0.008737 Total SCF correction =
> 0.02
> scf.in.out: Total force = 0.014135 Total SCF correction =
> 0.02
>
> Could you please advise me on how can I handle this?
> Below is my input file.
>
> 
>   calculation = 'vc-relax'
>etot_conv_thr = 0.0001
>forc_conv_thr = 0.001
>   outdir = './tmp'
>   prefix = 'pwscf'
>   pseudo_dir = './PPs'
>   tprnfor = .true.
>   tstress = .true.
> /
> 
>   degauss =   1.4699723600d-02
>   ecutrho =   4.50d+02
>   ecutwfc =   4.50d+01
>   ibrav = 0
>   nat = 24
>   nosym = .false.
>   ntyp = 1
>   occupations = 'smearing'
>   smearing = 'cold'
>
> /
> 
>   conv_thr =   1.00d-010
>   electron_maxstep = 100
>   mixing_beta =   3.00d-01
> /
> 
> ion_dynamics = 'bfgs'
>  /
> 
> /
> ATOMIC_SPECIES
>   P 30.973800d0 P.pbe-n-rrkjus_psl.1.0.0.UPF
> ATOMIC_POSITIONS crystal
> P0.072058   0.002225   0.186819
> P0.927942   0.997775   0.813181
> P0.850467   0.952993   0.312077
> P0.149533   0.047007   0.687923
> P0.006843   0.134953   0.309157
> P0.993157   0.865047   0.690843
> P0.221928   0.011505   0.366927
> P0.778072   0.988495   0.633073
> P0.763585   0.368292   0.057523
> P0.236415   0.631708   0.942477
> P0.592584   0.186137   0.034895
> P0.407416   0.813863   0.965105
> P0.513831   0.305591   0.165930
> P0.486169   0.694409   0.834070
> P0.396884   0.320114   0.985814
> P0.603116   0.679886   0.014186
> P0.296883   0.682883   0.463448
> P0.703117   0.317117   0.536552
> P0.947588   0.627152   0.367824
> P0.052412   0.372848   0.632176
> P0.201284   0.515294   0.359954
> P0.798716   0.484706   0.640046
> P0.236519   0.676026   0.277493
> P0.763481   0.323974   0.722507
> K_POINTS automatic
> 6 3 3 0 0 0
> CELL_PARAMETERS angstrom
>   6.024789   0.00   0.00
>  -2.0978219998  11.6760139950   0.00
>  -1.8239009989  -1.2036659990  11.818676
>
>
> Regards
> Bhamu
>
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[QE-users] Forces are oscillating for P

[Dr. K. C. Bhamu]

Dear QE Users,
I am trying to run phosphorus  with QE_6.4 but the forces are
oscillating between two values as shown below:
scf.in.out: Total force = 0.008737 Total SCF correction =
0.02
scf.in.out: Total force = 0.014135 Total SCF correction =
0.02
scf.in.out: Total force = 0.008737 Total SCF correction =
0.02
scf.in.out: Total force = 0.014135 Total SCF correction =
0.02

Could you please advise me on how can I handle this?
Below is my input file.


  calculation = 'vc-relax'
   etot_conv_thr = 0.0001
   forc_conv_thr = 0.001
  outdir = './tmp'
  prefix = 'pwscf'
  pseudo_dir = './PPs'
  tprnfor = .true.
  tstress = .true.
/

  degauss =   1.4699723600d-02
  ecutrho =   4.50d+02
  ecutwfc =   4.50d+01
  ibrav = 0
  nat = 24
  nosym = .false.
  ntyp = 1
  occupations = 'smearing'
  smearing = 'cold'

/

  conv_thr =   1.00d-010
  electron_maxstep = 100
  mixing_beta =   3.00d-01
/

ion_dynamics = 'bfgs'
 /

/
ATOMIC_SPECIES
  P 30.973800d0 P.pbe-n-rrkjus_psl.1.0.0.UPF
ATOMIC_POSITIONS crystal
P0.072058   0.002225   0.186819
P0.927942   0.997775   0.813181
P0.850467   0.952993   0.312077
P0.149533   0.047007   0.687923
P0.006843   0.134953   0.309157
P0.993157   0.865047   0.690843
P0.221928   0.011505   0.366927
P0.778072   0.988495   0.633073
P0.763585   0.368292   0.057523
P0.236415   0.631708   0.942477
P0.592584   0.186137   0.034895
P0.407416   0.813863   0.965105
P0.513831   0.305591   0.165930
P0.486169   0.694409   0.834070
P0.396884   0.320114   0.985814
P0.603116   0.679886   0.014186
P0.296883   0.682883   0.463448
P0.703117   0.317117   0.536552
P0.947588   0.627152   0.367824
P0.052412   0.372848   0.632176
P0.201284   0.515294   0.359954
P0.798716   0.484706   0.640046
P0.236519   0.676026   0.277493
P0.763481   0.323974   0.722507
K_POINTS automatic
6 3 3 0 0 0
CELL_PARAMETERS angstrom
  6.024789   0.00   0.00
 -2.0978219998  11.6760139950   0.00
 -1.8239009989  -1.2036659990  11.818676


Regards
Bhamu
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[QE-users] A quick question about vc-relax for 2dxz

[Dr. K. C. Bhamu]

Dear QE Users,
We want to do a vc-relax for our structure which is having vacuum along
y-direction.
By default option in QE is to do a vc-relax with cell_dofree='2Dxy'.
To change it to 2Dxz, I have modified and compiled the pw.x with below
setting

CASE ('2Dxy')
  iforceh  = 0
  iforceh(1,1) = 1
  iforceh(3,3) = 1
  iforceh(1,3) = 1
  iforceh(3,1) = 1

Am I doing it right? Or do I need to change some other parameters too?

Thank you very much
Regards
Bhamu
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Re: [QE-users] Top surface layer seems to be isolated from the rest of the system

[Dr. K. C. Bhamu]

Dear QE Users,
Could you please suggest any possible solution?

Regards
Bhamu

On Tue, Jun 22, 2021 at 1:44 PM Dr. K. C. Bhamu  wrote:

> Dear QE Users,
>
> I am trying to relax the (100) surface of WO3 (SG pm-3m: 221).
> The relaxation for bulk and the surface has conversed smoothly.
> The problem  I am facing for the surface is that the top layer (5 layer
> system keeping the bottom 3 layers fixed)  is dissociating from the
> surface. The bond length between vertical W-O is getting elongated to 2.21
> Ang from 1.91 Ang and the top surface layer seems to be isolated from the
> rest of the system.
>
> When I use 6 layer system keeping bottom 3 layers fixed, then the top two
> layers seem to be isolated from the rest of the system and the top two
> isolated layers also separated from each other.
> The input and output files can be accessed from here:
> https://we.tl/t-AlHUBg1DwE.
>
> I am wondering whether the high symmetric atomic positions of WO3 are
> culprits?
>
> Any suggestions will be appreciated.
>
> Regards
>
> K C Bhamu
>
> University of Ulsan,
> Republic of Korea
>
>
>
>
>
>
>
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[QE-users] Top surface layer seems to be isolated from the rest of the system

[Dr. K. C. Bhamu]

Dear QE Users,

I am trying to relax the (100) surface of WO3 (SG pm-3m: 221).
The relaxation for bulk and the surface has conversed smoothly.
The problem  I am facing for the surface is that the top layer (5 layer
system keeping the bottom 3 layers fixed)  is dissociating from the
surface. The bond length between vertical W-O is getting elongated to 2.21
Ang from 1.91 Ang and the top surface layer seems to be isolated from the
rest of the system.

When I use 6 layer system keeping bottom 3 layers fixed, then the top two
layers seem to be isolated from the rest of the system and the top two
isolated layers also separated from each other.
The input and output files can be accessed from here:
https://we.tl/t-AlHUBg1DwE <(https://we.tl/t-AlHUBg1DwE>.

I am wondering whether the high symmetric atomic positions of WO3 are
culprits?

Any suggestions will be appreciated.

Regards

K C Bhamu

University of Ulsan,
Republic of Korea
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Re: [QE-users] Error in neb.x calculation on Cedar cluster

[Dr. K. C. Bhamu]

Could you please check with

srun neb.x -inp RR8.in > RR8.out

Replace -i with -inp


Thank you
Bhamu

On Mon, Apr 5, 2021, 07:29 Rutika Savaliya 
wrote:

> Hello
> My name is Rutika, user srutika. I run quantum espresso calculation on the
> Cedar cluster. The Job script is located /scratch/srutika. While neb.x
> calculation is running into the same issue after starting. It started after
> recent changes on computecanada. My run.sh file and error appearing is as
> below:
>
> #!/bin/sh
> #SBATCH --nodes=6
> #SBATCH --ntasks-per-node=48
> #SBATCH --time=08-00:00
> #MPI tasks
> #SBATCH --mem=0
> #SBATCH --account=def-jkopysci
>
> module load quantumespresso/6.5
>
> srun neb.x -i RR8.in > RR8.out
>
>
> My error is as below:
>
> [cdr2189:54345] *** An error occurred in MPI_Type_free
> [cdr2189:54345] *** reported by process [500170752,196]
> [cdr2189:54345] *** on communicator MPI_COMM_WORLD
> [cdr2189:54345] *** MPI_ERR_TYPE: invalid datatype
> [cdr2189:54345] *** MPI_ERRORS_ARE_FATAL (processes in this communicator
> will now abort,
> [cdr2189:54345] ***and potentially your MPI job)
> In: PMI_Abort(3, N/A)
> slurmstepd: error: *** STEP 65543632.0 ON cdr2092 CANCELLED AT
> 2021-04-04T13:58:54 ***
> srun: Job step aborted: Waiting up to 32 seconds for job step to finish.
> srun: error: cdr2106: tasks 96-143: Killed
> srun: launch/slurm: _step_signal: Terminating StepId=65543632.0
> srun: error: cdr2096: tasks 48-95: Killed
> srun: error: cdr2159: tasks 144-191: Killed
> srun: error: cdr2189: tasks 192-195,197-239: Killed
> srun: error: cdr2092: tasks 0-47: Killed
> srun: error: cdr2190: tasks 240-287: Killed
> srun: error: cdr2189: task 196: Exited with exit code 3
>
>
> I have also attached the slurm file for reference.
>
> Hope to find the solution for this issue.
>
> Thank You.
> Rutika
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[QE-users] shell script for vib. entropy calculation for molecules

[Dr. K. C. Bhamu]

Dear Dr. Lorenzo
The file size is big (134MB) and it is failing to download because of my
poor internet connection. I need to find a good network.

If you do not mind, I would like to ask you to have a look at my small
shell script that can calculate the vibrational entropy using dynmat.out
file.

NOTE: It requires only a dynmat.out file and degree of freedom for the
molecule.

I used the Eqn of "S" provided HERE

to write this script.

#!/bin/bash
#Constants=
DOF=5 #Trans. + Rot. DOF for the molecule, Here I use 5 (3+2) for H2, for
3D Molec. I would take it 6
THz2Hz='1e+12' #Freq in s^(-1)
KJPerMol=96 #KJ/mol
KCalPerMol=23 #Kcal/mol
Kb='8.6173303E-5' #boltzmann's constant in eV/K
T=450 #Temperature in K
Pconst='4.135667696e-15' #planck's constant in eV.S
K_to_eV='0.8617328149741'
#=== How many Frequencies
Total_freq=$(grep freq dynmat.out | cut -f 2 -d = | cut -f 1 -d [ | wc -l)
# How many vibrational Frequencies
Vibrational_Freq=$(echo "$Total_freq" "$DOF" | awk '{print $1-$2}')

# Summing all vib. Freq., converting into Hz  and storing as a variable
FreqHz=$(grep freq dynmat.out | cut -f 2 -d = | cut -f 1 -d [ | tail -n
$Vibrational_Freq | awk '{print $1}' | awk -F',' '{sum+=$1;}END{print
sum;}' | awk '{print $1*(1e+12)}')

#===Calculation of vibrational entropy using formula of entropy from [1] in
eV/K  and storing as a variable
Freq_in_eV_per_K=$(echo "$Kb" "$T" "$Pconst" "$FreqHz" | awk '{print
-$1*(log(1-exp(-(($3*$4)/($1*$2) + ($3/$2)*($4/(exp(($3*$4)/($1*$2))-1)
)}')

#=== Converting eV/K to eV and storing as a variable
eV_per_K_to_eV=$(echo "$Freq_in_eV_per_K" "$K_to_eV" | awk '{print $1*$2}')
#converting eV to KCal/mol
echo "$eV_per_K_to_eV" "$KCalPerMol" | awk '{print $1*$2}'

#converting eV to KJ/mol
echo "$eV_per_K_to_eV" "$KJPerMol" | awk '{print $1*$2}'
#END
I look forward to hearing from you or anyone from the  QE  list whether it
is correct or not.
Regards
Bhamu

On Wed, Mar 24, 2021 at 2:46 PM Lorenzo Paulatto  wrote:

>
> Let me try D3Q code.
>
>
> If you can compile your own version of QE, you may want to use a recent
> snapshot of espresso+d3q, as I have added a few features recently.
> https://mycore.core-cloud.net/index.php/s/1RxbPmcxvHunFVF
> 
> cheer
>
> --
> Lorenzo Paulatto - Paris
>
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Re: [QE-users] 0.0000 in QHA outputs

[Dr. K. C. Bhamu]

Dear Lorenzo,
Thank you for the information.
I don't have good experience with thermo_pw.

Let me try D3Q code.

Thank you
Bhamu

On Wed, Mar 24, 2021, 17:52 Lorenzo Paulatto  wrote:

>
> Dear KC,
> the QHA package has not been maintained in a while, but there are otehr
> QHA packages that can easily interface with QE. One, written by me, is
> included in the D3Q code <https://anharmonic.github.io/thermal2/#d3_qhax-1
> <https://link.getmailspring.com/link/487f4982-0a00-40f9-a327-876653d92...@getmailspring.com/0?redirect=https%3A%2F%2Fanharmonic.github.io%2Fthermal2%2F%23d3_qhax-1=dXNlcnNAbGlzdHMucXVhbnR1bS1lc3ByZXNzby5vcmc%3D>>,
> I think there is another one in the thermo_pw <
> https://dalcorso.github.io/thermo_pw/
> <https://link.getmailspring.com/link/487f4982-0a00-40f9-a327-876653d92...@getmailspring.com/1?redirect=https%3A%2F%2Fdalcorso.github.io%2Fthermo_pw%2F=dXNlcnNAbGlzdHMucXVhbnR1bS1lc3ByZXNzby5vcmc%3D>>
> codes.
>
> hth
>
>
> --
> Lorenzo Paulatto - Paris
> On Mar 24 2021, at 5:10 am, Dr. K. C. Bhamu  wrote:
>
> Dear Quantum Espresso/QHA Users
> I am trying to calculate the entropy of a molecule (49atoms, C and H) in
> the gas phase using QHA provided with QE6.6.
> I could run the examples supplied with the QHA code.
> But when I run it for H2 molecule, I always get 0. in the
> case(H2).QHA.out file.
> Similar information (0.000) is written in other files also.
>
> What could be wrong?
> I have edited the Edit_Me file properly.
> Few header rows from H2.QHA.out file is mentioned below while the entire
> directory can be downloaded from here
> <https://link.getmailspring.com/link/487f4982-0a00-40f9-a327-876653d92...@getmailspring.com/2?redirect=https%3A%2F%2Fwe.tl%2Ft-EfBU7ZFvWE=dXNlcnNAbGlzdHMucXVhbnR1bS1lc3ByZXNzby5vcmc%3D>
> .
>
> # Zero vibration energy:  0.00  (Ry/cell)
> # Phonon DOS norm  :  0.00  ! 3N for check purpose, N
> number of atoms in the unit cell
> # T in K, F_vib in Ry/cell, C_v in R (the universal gas constant by 3N
> modes), S in k_B
> #
> #   T E_internalF_vibration  Specific heat (C_v)
> Entropy
>
> 
> 5.00  0.00  0.00   0.00
>0.00  *>> I used step 0.75 too*
>10.00  0.00  0.00   0.00
>0.00
>15.00  0.00  0.00   0.00
>0.00
>20.00  0.00  0.00   0.00
>0.00
>
> Any help would be appreciated.
>
> Regards
>
> KC Bhamu(Ph.D.)
> University of Ulsan
> South Korea
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>
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[QE-users] 0.0000 in QHA outputs

[Dr. K. C. Bhamu]

Dear Quantum Espresso/QHA Users
I am trying to calculate the entropy of a molecule (49atoms, C and H) in
the gas phase using QHA provided with QE6.6.
I could run the examples supplied with the QHA code.
But when I run it for H2 molecule, I always get 0. in the
case(H2).QHA.out file.
Similar information (0.000) is written in other files also.

What could be wrong?
I have edited the Edit_Me file properly.
Few header rows from H2.QHA.out file is mentioned below while the entire
directory can be downloaded from here .

# Zero vibration energy:  0.00  (Ry/cell)
# Phonon DOS norm  :  0.00  ! 3N for check purpose, N
number of atoms in the unit cell
# T in K, F_vib in Ry/cell, C_v in R (the universal gas constant by 3N
modes), S in k_B
#
#   T E_internalF_vibration  Specific heat (C_v)
Entropy

5.00  0.00  0.00   0.00
 0.00  *>> I used step 0.75 too*
   10.00  0.00  0.00   0.00
 0.00
   15.00  0.00  0.00   0.00
 0.00
   20.00  0.00  0.00   0.00
 0.00

Any help would be appreciated.

Regards

KC Bhamu(Ph.D.)
University of Ulsan
South Korea
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[QE-users] convergence issue with OH adsorbed beta-Ni(OH)2 10(-1)0 slab

[Dr. K. C. Bhamu]

Dear QE Users

I am trying to converge a beta-Ni(OH)2  structure with five layered  3x2x1
supercell for 10(-1)0 surface (you can find the input and output files for
bulk, clean surface and OH adsorbed surface from here [1] along with PPs)
with QE version 6.6.

For the clean surface (without any adsorption) convergence is
smoothly achieved (used gaussian smearing) but for the H2O or OH adsorbed
case  the forces are oscillating and the structure is not converging.

I have tried with gaussian, mv and mp smearing and also used local-TF as a
mixing mode.
It would be a great help if someone can guide me how to converge the
structure.

[1]. https://we.tl/t-27mNW4yeKg

   1. scf_without_any_adsorption.(in)out the converged output file without
   any adsorbed molecule and
   2. scf_with_adsorption.(in)/out is the one which is not converging with
   OH molecule.
   3. pristine.in is the input file for bulk system

Any help would be appreciated.

Thank you very much

K C Bhamu
Postdoctoral Fellow
University of Ulsan
ROK
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Re: [QE-users] [De/hydrogenation] How can I get thermodynamic and activation parameters at some particular T and P using QE or other QE based codes

[Dr. K. C. Bhamu]

Dear Dr. Michal Krompiec
Thank you very much for the quick response.

Additionally I need to mimic the experimental synthesis conditions for
which I need to add the pressure effect.

How can it be done with QE?

Thank you
Bhamu



On Mon, Jan 18, 2021 at 4:03 PM Michal Krompiec 
wrote:

> Dear K C Bhamu,
> To get the enthalpy and entropy at T>0 (and the zero-point energy which
> you haven't included yet) you need to perform a phonon calculation.
> Best regards,
> Michal Krompiec
>
> On Mon, 18 Jan 2021 at 10:16, Dr. K. C. Bhamu  wrote:
>
>> Dear QE Users,
>> [I am using QE_6.4 and 6.6!!]
>> I am looking for a QE based good reference and some advice for my work:
>> dehydrogenation of a molecule (let's say it is C6H12).
>>
>> I am trying to calculate dehydrogenation enthalpy of this molecule.
>>
>> I have obtained my dehydrogenation reaction energy diagram for each step
>> but that is at 0K and 0P.
>> ΔG = ΔH - T* ΔS
>> In QE we have T=0, so ΔG = ΔH.
>>
>> Now I want to calculate the thermodynamic and activation parameters at
>> standard (~25 °C, and 0.1MPa) and experimental conditions (~150 °C, and
>> 7MPa) {Please seeTable 1,2 of [1] what I mean for it} with and without the
>> solvent.
>>
>> How can I get these thermodynamic and activation parameters at some
>> particular temperature and pressure?
>>
>> If I am wrong,  then I need to use environ code [2] to include the
>> solvent effect in my study. Right?
>> [1].
>> https://www.sciencedirect.com/science/article/pii/S0360319915005753#appsec1
>> [2]. https://github.com/environ-developers/Environ/releases
>>
>> If I missed something to explain my problem, I am sorry and I will share
>> it if you suggest the missing information.
>>
>> Any help will be appreciated.
>>
>> Thank you very much
>>
>> Regards
>> K C Bhamu
>> University of Ulsan
>> ROK
>>
>>
>>
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>> users mailing list users@lists.quantum-espresso.org
>> https://lists.quantum-espresso.org/mailman/listinfo/users
>
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[QE-users] [De/hydrogenation] How can I get thermodynamic and activation parameters at some particular T and P using QE or other QE based codes

[Dr. K. C. Bhamu]

Dear QE Users,
[I am using QE_6.4 and 6.6!!]
I am looking for a QE based good reference and some advice for my work:
dehydrogenation of a molecule (let's say it is C6H12).

I am trying to calculate dehydrogenation enthalpy of this molecule.

I have obtained my dehydrogenation reaction energy diagram for each step
but that is at 0K and 0P.
ΔG = ΔH - T* ΔS
In QE we have T=0, so ΔG = ΔH.

Now I want to calculate the thermodynamic and activation parameters at
standard (~25 °C, and 0.1MPa) and experimental conditions (~150 °C, and
7MPa) {Please seeTable 1,2 of [1] what I mean for it} with and without the
solvent.

How can I get these thermodynamic and activation parameters at some
particular temperature and pressure?

If I am wrong,  then I need to use environ code [2] to include the solvent
effect in my study. Right?
[1].
https://www.sciencedirect.com/science/article/pii/S0360319915005753#appsec1
[2]. https://github.com/environ-developers/Environ/releases

If I missed something to explain my problem, I am sorry and I will share it
if you suggest the missing information.

Any help will be appreciated.

Thank you very much

Regards
K C Bhamu
University of Ulsan
ROK
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Re: [QE-users] convergence problem for a molecule

[Dr. K. C. Bhamu]

Dear Dr. Giuseppe
You suggestion worked for me.
 "occupations='smearing', smearing='gaussian', degauss=0.01,"
The structure even converged when I excluded the vdw_corr tag.

Thank you very much
Bhamu



On Tue, Jan 5, 2021 at 11:48 PM Giuseppe Mattioli <
giuseppe.matti...@ism.cnr.it> wrote:

>
> Dear K C Bhamu
> When you simulate molecules having a large amount of rotational
> degrees of freedom, I recommend to use first a tight-binding or
> empirical tool to explore configurations, to avoid high-energy
> structures. The following one is excellent, very easy to use and very
> fast to run.
>
> https://xtb-docs.readthedocs.io/en/latest/contents.html
>
> This said, your starting configuration was trapped in an unfortunate
> structure where two sp2 C atoms (numbers 33 and 35) were twisted
> instead of being planar. You probably removed two H atoms from sp3
> atoms without relaxing them. The following structure, simply optimized
> with a force-field, should not give problems (but I have not run the
> calculation...).
>
> 45
>  Energy:  52.7144978
> H  8.48608   10.45663   13.88529
> C 10.12285   10.35161   10.80715
> H  9.750819.36965   10.43974
> C 11.49997   10.08512   11.39597
> H 12.307569.85722   10.70499
> C 11.75878   10.11652   12.72470
> C 10.64679   10.32692   13.74405
> H 10.743179.58583   14.56637
> H 10.73789   11.33550   14.19281
> C  9.24848   10.13193   13.14479
> H  9.072919.05796   12.91129
> C  9.14194   10.92818   11.85742
> H  8.10293   10.88215   11.46867
> H  9.38712   11.98966   12.08748
> C  8.94637   11.522018.84268
> C 10.25893   11.302879.59702
> H  9.13189   12.174917.96386
> H  8.19218   12.022979.48301
> H  8.54193   10.551558.48460
> H 10.65844   12.286369.92936
> H 10.98302   10.862138.87653
> C 13.174409.88279   13.22285
> H 13.118889.04537   13.95078
> H 13.837079.54798   12.39520
> C 15.69736   11.92481   15.44478
> H 16.74498   11.70891   15.74860
> H 15.07047   11.97162   16.36387
> C 15.58617   13.25420   14.70482
> H 16.14427   13.14997   13.74597
> C 14.09237   13.52300   14.41126
> H 14.03472   14.35009   13.67327
> H 13.54419   13.83190   15.32752
> C 13.36446   12.32498   13.84523
> C 13.87547   11.06693   13.87464
> C 15.21374   10.78810   14.53332
> H 15.142949.87981   15.16991
> H 15.94984   10.58575   13.72543
> C 16.23591   15.73576   14.79615
> C 16.23058   14.39236   15.52642
> H 16.75074   16.49369   15.42343
> H 15.20340   16.09456   14.60831
> H 16.77780   15.64679   13.83071
> H 15.70219   14.50766   16.49821
> H 17.28870   14.12285   15.73764
> H 12.40535   12.52093   13.38556
>
> Finally,
>
> >   occupations='smearing',
> >   smearing='mv',
> >   degauss=0.005d0,
>
> This is just a fine way for me to calculate a bunch of unoccupied
> molecular orbitals, but there is no need to use 'mv', which is for
> metals and less stable than 'gaussian', suitable for an "insulator"
> such as your molecule. I would use instead
>
>  occupations='smearing', smearing='gaussian', degauss=0.01,
>
> HTH
> Giuseppe
>
>
> Quoting "Dr. K. C. Bhamu" :
>
> > Dear QE Users
> > I wish you all a very happy new year 2021!
> >
> > I am running a molecule  with QE_6.6  but facing a convergence problem.
> > I tried with and without 'local-TF' and both the options are not working.
> >
> > Could someone please have a look and suggest to me any solution?
> >
> >
> > 
> >  calculation = 'relax'
> > restart_mode = 'from_scratch'
> >   outdir = './tmp'
> >   pseudo_dir = '/home/kcbhamu/PPs'
> >   prefix = 'pwscf'
> > ! disk_io = 'none'
> >verbosity = 'default'
> >etot_conv_thr = 0.0001
> >forc_conv_thr = 0.001
> > 

Re: [QE-users] convergence problem for a molecule

[Dr. K. C. Bhamu]

Dear Dr. Giuseppe

Thank you very much for the detailed information.

Yes, I removed 4 H-atoms (two hydrogen molecules) not  2 (-1H2).
I am trying for liberation of different H-atoms and with this particular
configurations the structure didn't converge.

I will check it out with your suggestions.

Thank you very much
Bhamu

On Wed, Jan 6, 2021, 03:18 Giuseppe Mattioli 
wrote:

>
> Dear K C Bhamu
> When you simulate molecules having a large amount of rotational
> degrees of freedom, I recommend to use first a tight-binding or
> empirical tool to explore configurations, to avoid high-energy
> structures. The following one is excellent, very easy to use and very
> fast to run.
>
> https://xtb-docs.readthedocs.io/en/latest/contents.html
>
> This said, your starting configuration was trapped in an unfortunate
> structure where two sp2 C atoms (numbers 33 and 35) were twisted
> instead of being planar. You probably removed two H atoms from sp3
> atoms without relaxing them. The following structure, simply optimized
> with a force-field, should not give problems (but I have not run the
> calculation...).
>
> 45
>  Energy:  52.7144978
> H  8.48608   10.45663   13.88529
> C 10.12285   10.35161   10.80715
> H  9.750819.36965   10.43974
> C 11.49997   10.08512   11.39597
> H 12.307569.85722   10.70499
> C 11.75878   10.11652   12.72470
> C 10.64679   10.32692   13.74405
> H 10.743179.58583   14.56637
> H 10.73789   11.33550   14.19281
> C  9.24848   10.13193   13.14479
> H  9.072919.05796   12.91129
> C  9.14194   10.92818   11.85742
> H  8.10293   10.88215   11.46867
> H  9.38712   11.98966   12.08748
> C  8.94637   11.522018.84268
> C 10.25893   11.302879.59702
> H  9.13189   12.174917.96386
> H  8.19218   12.022979.48301
> H  8.54193   10.551558.48460
> H 10.65844   12.286369.92936
> H 10.98302   10.862138.87653
> C 13.174409.88279   13.22285
> H 13.118889.04537   13.95078
> H 13.837079.54798   12.39520
> C 15.69736   11.92481   15.44478
> H 16.74498   11.70891   15.74860
> H 15.07047   11.97162   16.36387
> C 15.58617   13.25420   14.70482
> H 16.14427   13.14997   13.74597
> C 14.09237   13.52300   14.41126
> H 14.03472   14.35009   13.67327
> H 13.54419   13.83190   15.32752
> C 13.36446   12.32498   13.84523
> C 13.87547   11.06693   13.87464
> C 15.21374   10.78810   14.53332
> H 15.142949.87981   15.16991
> H 15.94984   10.58575   13.72543
> C 16.23591   15.73576   14.79615
> C 16.23058   14.39236   15.52642
> H 16.75074   16.49369   15.42343
> H 15.20340   16.09456   14.60831
> H 16.77780   15.64679   13.83071
> H 15.70219   14.50766   16.49821
> H 17.28870   14.12285   15.73764
> H 12.40535   12.52093   13.38556
>
> Finally,
>
> >   occupations='smearing',
> >   smearing='mv',
> >   degauss=0.005d0,
>
> This is just a fine way for me to calculate a bunch of unoccupied
> molecular orbitals, but there is no need to use 'mv', which is for
> metals and less stable than 'gaussian', suitable for an "insulator"
> such as your molecule. I would use instead
>
>  occupations='smearing', smearing='gaussian', degauss=0.01,
>
> HTH
> Giuseppe
>
>
> Quoting "Dr. K. C. Bhamu" :
>
> > Dear QE Users
> > I wish you all a very happy new year 2021!
> >
> > I am running a molecule  with QE_6.6  but facing a convergence problem.
> > I tried with and without 'local-TF' and both the options are not working.
> >
> > Could someone please have a look and suggest to me any solution?
> >
> >
> > 
> >  calculation = 'relax'
> > restart_mode = 'from_scratch'
> >   outdir = './tmp'
> >   pseudo_dir = '/home/kcbhamu/PPs'
> >   prefix = 'pwscf'
> > ! disk_io = 'none'
> >verbosity = 'default'
> >etot_conv_thr = 0.0001
&

[QE-users] convergence problem for a molecule

[Dr. K. C. Bhamu]

Dear QE Users
I wish you all a very happy new year 2021!

I am running a molecule  with QE_6.6  but facing a convergence problem.
I tried with and without 'local-TF' and both the options are not working.

Could someone please have a look and suggest to me any solution?



 calculation = 'relax'
restart_mode = 'from_scratch'
  outdir = './tmp'
  pseudo_dir = '/home/kcbhamu/PPs'
  prefix = 'pwscf'
! disk_io = 'none'
   verbosity = 'default'
   etot_conv_thr = 0.0001
   forc_conv_thr = 0.001
   nstep = 400
 tstress = .true.
 tprnfor = .true.
 /


  ibrav=1,
  celldm(1)=47.2431531141d0,
  nat=45,
  ntyp=2,
  ecutwfc=65,
  ecutrho=650,
  occupations='smearing',
  smearing='mv',
  degauss=0.005d0,
 vdw_corr = 'DFT-D3'
 assume_isolated='mt'
/


electron_maxstep=999
  conv_thr=1d-06,
  mixing_beta=0.2,
mixing_mode='local-TF'

 /

ion_dynamics = 'bfgs'
 /

ATOMIC_SPECIES
C   12.010700  C.pbe-n-rrkjus_psl.1.0.0.UPF
H1.007900  H.pbe-rrkjus_psl.1.0.0.UPF


ATOMIC_POSITIONS {crystal}
   H   0.3386670148d0   0.4101931225d0   0.5567254731d0
   C   0.4036222773d0   0.4149138472d0   0.4333448459d0
   H   0.3896346255d0   0.3765041141d0   0.4161167921d0
   C   0.4581434036d0   0.4058061800d0   0.4574431361d0
   H   0.4912475090d0   0.4017946150d0   0.4290030859d0
   C   0.469124d0   0.4031817060d0   0.5099401207d0
   C   0.4253264110d0   0.4071145213d0   0.5513729998d0
   H   0.4327529164d0   0.3774401630d0   0.5831675023d0
   H   0.4276381009d0   0.4464313224d0   0.5714430496d0
   C   0.3695729050d0   0.3993621172d0   0.5273547231d0
   H   0.3636345597d0   0.3567170026d0   0.5178739313d0
   C   0.3632663685d0   0.4323236400d0   0.4762330101d0
   H   0.3222111650d0   0.4290965819d0   0.4608472936d0
   H   0.3700270318d0   0.4749720278d0   0.4855397879d0
   C   0.3550607872d0   0.4623307485d0   0.3556503474d0
   C   0.4072533598d0   0.4549686753d0   0.3866434814d0
   H   0.3606425820d0   0.4892876373d0   0.3214193048d0
   H   0.3233410756d0   0.4794322728d0   0.3807732671d0
   H   0.3403880199d0   0.4238800875d0   0.3400782741d0
   H   0.4209431037d0   0.4937648655d0   0.4025522295d0
   H   0.4387880407d0   0.4413449118d0   0.3590270889d0
   C   0.5253811195d0   0.3963553146d0   0.5303629030d0
   H   0.5275121376d0   0.3597814346d0   0.5550954410d0
   H   0.5527498198d0   0.3902494747d0   0.4963382387d0
   C   0.6241002137d0   0.4781543529d0   0.6196978697d0
   H   0.6647510385d0   0.4689076884d0   0.6339462788d0
   H   0.5991190333d0   0.4830564471d0   0.6558173241d0
   C   0.6245138950d0   0.5312336801d0   0.5887880064d0
   H   0.6519223460d0   0.5264394769d0   0.5543229817d0
   C   0.5684449407d0   0.5426728657d0   0.566474d0
   H   0.5687315910d0   0.5794127480d0   0.5422455469d0
   H   0.5411292134d0   0.5502889434d0   0.6003493599d0
   C   0.5467291274d0   0.4961698023d0   0.5329872592d0
   H   0.5063039439d0   0.5054115901d0   0.5182523433d0
   C   0.5462494021d0   0.4434602904d0   0.5642948220d0
   C   0.6023141698d0   0.4317080266d0   0.5862549648d0
   H   0.6016470576d0   0.3946830496d0   0.6101287345d0
   H   0.6295099445d0   0.4241153738d0   0.5522682608d0
   C   0.6550325759d0   0.6297412310d0   0.5941577656d0
   C   0.6461033707d0   0.5769127641d0   0.6236837684d0
   H   0.6727321964d0   0.6599556430d0   0.6206848621d0
   H   0.6175101186d0   0.6464185973d0   0.5785534114d0
   H   0.6823409744d0   0.6243625417d0   0.5600843513d0
   H   0.6183422352d0   0.5832463756d0   0.6574159578d0
   H   0.6841825362d0   0.5638719462d0   0.6416905666d0

K_POINTS (gamma)



Thank you very much
K C Bhamu
University of Ulsan
ROK
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[QE-users] necessity of U for OER

[Dr. K. C. Bhamu]

Dear Expert QE users

I need your input whether it is a good idea to apply U or not to my OER
calculations of ZnO slab.
I am not intended to produce the band gap.

Your opinion will help me a lot.

I am doing the calculations with Hubbard "U" but I am not able to apply
dipole corrections correctly.
I am wondering how this "U" will change the final OER results.


Thank you very much

KC Bhamu
University of Ulsan
ROK
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Re: [QE-users] Vanderbilt Pseudopotential generation issue

[Dr. K. C. Bhamu]

Dear Dr. Andrii
I do not find   vdb2upf.x and uspp2upf.x  in upftools dir.
$QE/upftools]$ ls
how_to_fix_upf.md  README


Regards
Bhamu

On Mon, Dec 14, 2020 at 11:14 PM Andrii Shyichuk via users <
users@lists.quantum-espresso.org> wrote:

> Dear Dr Bhamu,
>
> You should have a upftools folder in your QE directory.
> There must be vdb2upf.x and uspp2upf.x in there, one of them should do.
>
> Best regards.
> Andrii Shyichuk, University of Wrocław
>
> W dniu 2020-12-14 15:12, Dr. K. C. Bhamu napisał:
>
> Dear QE users
> I wanted to use the Vanderbilt Pseudopotential for my Ni based slab as
> these are already used [1].
> I have downloaded [2] the tar file and followed the instructions to
> generate the PPs for Ni.
> I got the unformatted PP (binary format) for Ni in Pot dir.
> Now I need to use the reform.f program (from utility dir) to make them in
> a usable format.
> On top of this file, I see, I should define F77 but in the whole file, I
> could not find where to define the F77.
>
> Could someone please help me with this? How can I convert this binary
> format of the Ni PP to uspp?
>
> [1]. https://journals.aps.org/prb/pdf/10.1103/PhysRevB.101.195401
> <https://journals.aps.org/prb/pdf/10.1103/PhysRevB.101.195401>
> [2]. http://www.physics.rutgers.edu/~dhv/uspp/#DOWNLOAD
>
> I use ifort2020 and I usually use below for the QE compilation.
>
>  FOPTS= -O -FR -mp1 -w -prec_div -pc80 -pad -ip -DINTEL_VML -traceback
> -assume buffered_io -I$(MKLROOT)/include
>
>
>
> Thank you very much
> K.C. Bhamu
> University of Ulsan
> ROK
>
>
>
>
>
> ___
> Quantum ESPRESSO is supported by MaX (www.max-centre.eu)
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>
>
>
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[QE-users] qe6.6 is not writing wavefunctions in tmp dir

[Dr. K. C. Bhamu]

Dear QE Users

I am using PAW PPs from the QE webpage with QE-6.6. The code is compiled
with MKL-ifort-2020.

I noticed that it is not writing wavefunction in the tmp directory and
stuck after printing the Energy (grep ! *out). Then I need to delete the
job.

What could be the problem?



Thank you very much

K.C. Bhamu
University of Ulsan
ROK
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[QE-users] Vanderbilt Pseudopotential generation issue

[Dr. K. C. Bhamu]

Dear QE users
I wanted to use the Vanderbilt Pseudopotential for my Ni based slab as
these are already used [1].
I have downloaded [2] the tar file and followed the instructions to
generate the PPs for Ni.
I got the unformatted PP (binary format) for Ni in Pot dir.
Now I need to use the reform.f program (from utility dir) to make them in a
usable format.
On top of this file, I see, I should define F77 but in the whole file, I
could not find where to define the F77.

Could someone please help me with this? How can I convert this binary
format of the Ni PP to uspp?

[1]. https://journals.aps.org/prb/pdf/10.1103/PhysRevB.101.195401

[2]. http://www.physics.rutgers.edu/~dhv/uspp/#DOWNLOAD

I use ifort2020 and I usually use below for the QE compilation.

 FOPTS= -O -FR -mp1 -w -prec_div -pc80 -pad -ip -DINTEL_VML -traceback
-assume buffered_io -I$(MKLROOT)/include



Thank you very much
K.C. Bhamu
University of Ulsan
ROK
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Re: [QE-users] Error in routine diropn (34): can't open a connected unit

[Dr. K. C. Bhamu]

Dear Dr. Lurii
My phonon band structure was not converged in 100 cycles.
I am getting below message in last few iterations:
 Pert. #  1: Fermi energy shift (Ry) =-3.1160E+75-9.3536E+49

  iter #  96 total cpu time : 40259.0 secs   av.it.: 280.8
  thresh= 1.000E-02 alpha_mix =  0.300 |ddv_scf|^2 =  2.136+147

What could be the possible issue?
Below are my ph.in and scf.in files:



recover=.true.,
tr2_ph = 1.0d-12
prefix ='pwscf'
alpha_mix =0.3
ldisp = .true.,
trans=.true.,
nq1=1
nq2=4
nq3=4
outdir ='./tmp'
fildyn = 'slab.dyn'
/


scf.in


 calculation = 'scf'
  outdir = './tmp'
  pseudo_dir = '.'
  prefix = 'pwscf'
   verbosity = 'default'
   etot_conv_thr = 0.1
   forc_conv_thr = 0.0001
   nstep = 400
 tstress = .true.
 tprnfor = .true.

/


   ibrav = 0
celldm(1)=42.3160703759d0,
 nat = 15
ntyp = 3
 ecutwfc = 85
 ecutrho = 680
starting_magnetization(1)= 1,
occupations='smearing', smearing='mv', degauss=0.005,
nspin=2,
lda_plus_u=.true.  Hubbard_U(1)=5.5

 /
 
electron_maxstep = 700
conv_thr = 1.0D-8
 /

ion_dynamics = 'bfgs'
 /

/
ATOMIC_SPECIES
Ni 58.6934 ni_pbe_v1.4.uspp.F.UPF
H  1.00794 H.pbe-rrkjus_psl.1.0.0.UPF
O  15.9994 O.pbe-n-kjpaw_psl.0.1.UPF

ATOMIC_POSITIONS {crystal}
Ni0.40862711800.250.0562779067
Ni0.53102979780.750.1575988843
Ni0.65559178060.250.2252620504
H 0.35567189120.750.7569475855
H 0.49059898500.250.7519547270
H 0.68131263580.750.8495914755
H 0.30511779570.250.2908234852
H 0.42870251600.750.4856771252
H 0.56637853490.250.5842143961
O 0.39915823060.750.7744084930
O 0.52456039480.250.8820391483
O 0.68678591210.751.0544632655
O 0.32173069690.250.0997462181
O 0.44572564380.750.2821321300
O 0.57518806680.250.3748931091

CELL_PARAMETERS {alat}
  1.d0  0.d0  0.d0
  0.d0  0.142952837309d0  0.d0
  0.d0  0.d0  0.209983610730d0

K_POINTS automatic
1 4 4   0 0 0


Thank you very much.

Bhamu



On Tue, Dec 1, 2020 at 7:15 PM Timrov Iurii  wrote:

> Dear Bhamu,
>
>
> Actually it is not a warning, it just tells you which Hubbard manifold in
> DFT+U is used (you can have 'atomic' and 'ortho-atomic' orbitals for the
> Hubbard manifold, and the Phonon+U code supports only 'atomic'). So yes you
> can continue the calculation, and in the publication you should specify
> that the atomic orbitals were used (without the Lowdin orthogonalization).
> You can have a look at this paper for more details:
>
> https://arxiv.org/abs/2010.13485
>
>
> Greetings,
>
> Iurii
>
>
> --
> Dr. Iurii TIMROV
> Postdoctoral Researcher
> STI - IMX - THEOS and NCCR - MARVEL
> Swiss Federal Institute of Technology Lausanne (EPFL)
> CH-1015 Lausanne, Switzerland
> +41 21 69 34 881
> http://people.epfl.ch/265334
> --
> *From:* users  on behalf of Dr.
> K. C. Bhamu 
> *Sent:* Tuesday, December 1, 2020 2:37:16 PM
> *To:* Quantum ESPRESSO users Forum
> *Subject:* Re: [QE-users] Error in routine diropn (34): can't open a
> connected unit
>
> Dear Dr. Lurii,
> Thank you for the suggestion.
> Now the phonon calculation has started.
>
> I am getting a new warning now:
>
> Atomic wfc used for the projector on the Hubbard manifold are NOT
> orthogonalized
>
>  Calculating the dnsbare matrix...
>
>  Calculating the dnsorth_cart matrix...
>
> Can I ignore this warning?
>
> Thank you very much
> Bhamu
>
>
>
> On Tue, Dec 1, 2020 at 6:09 PM Timrov Iurii  wrote:
>
>> Actually you need to remove this: fildvscf='dvscf'
>>
>> Also I would remove this: electron_phonon= " "
>>
>>
>> Iurii
>>
>>
>> --
>> Dr. Iurii TIMROV
>> Postdoctoral Researcher
>> STI - IMX - THEOS and NCCR - MARVEL
>> Swiss Federal Institute of Technology Lausanne (EPFL)
>> CH-1015 Lausanne, Switzerland
>> +41 21 69 34 881
>> http://people.epfl.ch/265334
>> -

Re: [QE-users] Error in routine diropn (34): can't open a connected unit

[Dr. K. C. Bhamu]

Dear Dr. Lurii,
Thank you for the good comment and providing the reference paper. I will
read it.

With the same phonon input file, I have computed phonon band structure for
various compounds and I never faced any such warning, Error in routine
diropn (34):.
Could you please make any comment on this? The present structure is a slab
while my previous structures were 3D structures.



Thank you
Bhamu



On Tue, Dec 1, 2020 at 7:15 PM Timrov Iurii  wrote:

> Dear Bhamu,
>
>
> Actually it is not a warning, it just tells you which Hubbard manifold in
> DFT+U is used (you can have 'atomic' and 'ortho-atomic' orbitals for the
> Hubbard manifold, and the Phonon+U code supports only 'atomic'). So yes you
> can continue the calculation, and in the publication you should specify
> that the atomic orbitals were used (without the Lowdin orthogonalization).
> You can have a look at this paper for more details:
>
> https://arxiv.org/abs/2010.13485
>
>
> Greetings,
>
> Iurii
>
>
> --
> Dr. Iurii TIMROV
> Postdoctoral Researcher
> STI - IMX - THEOS and NCCR - MARVEL
> Swiss Federal Institute of Technology Lausanne (EPFL)
> CH-1015 Lausanne, Switzerland
> +41 21 69 34 881
> http://people.epfl.ch/265334
> --
> *From:* users  on behalf of Dr.
> K. C. Bhamu 
> *Sent:* Tuesday, December 1, 2020 2:37:16 PM
> *To:* Quantum ESPRESSO users Forum
> *Subject:* Re: [QE-users] Error in routine diropn (34): can't open a
> connected unit
>
> Dear Dr. Lurii,
> Thank you for the suggestion.
> Now the phonon calculation has started.
>
> I am getting a new warning now:
>
> Atomic wfc used for the projector on the Hubbard manifold are NOT
> orthogonalized
>
>  Calculating the dnsbare matrix...
>
>  Calculating the dnsorth_cart matrix...
>
> Can I ignore this warning?
>
> Thank you very much
> Bhamu
>
>
>
> On Tue, Dec 1, 2020 at 6:09 PM Timrov Iurii  wrote:
>
>> Actually you need to remove this: fildvscf='dvscf'
>>
>> Also I would remove this: electron_phonon= " "
>>
>>
>> Iurii
>>
>>
>> --
>> Dr. Iurii TIMROV
>> Postdoctoral Researcher
>> STI - IMX - THEOS and NCCR - MARVEL
>> Swiss Federal Institute of Technology Lausanne (EPFL)
>> CH-1015 Lausanne, Switzerland
>> +41 21 69 34 881
>> http://people.epfl.ch/265334
>> --
>> *From:* users  on behalf of
>> Timrov Iurii 
>> *Sent:* Tuesday, December 1, 2020 1:27:51 PM
>> *To:* Quantum Espresso users Forum
>> *Subject:* Re: [QE-users] Error in routine diropn (34): can't open a
>> connected unit
>>
>>
>> Can you share your PW and PH input and output files using Google Drive?
>> Did you check whether the PW calculation finished successfully?
>>
>>
>> If the PW calculation finished successfully, then you can try to remove
>> recover=.true. in the PH input and try again.
>>
>>
>> Greetings,
>>
>> Iurii
>> --
>> *From:* users  on behalf of
>> Dr. K. C. Bhamu 
>> *Sent:* Tuesday, December 1, 2020 12:04:50 PM
>> *To:* Quantum Espresso users Forum
>> *Subject:* [QE-users] Error in routine diropn (34): can't open a
>> connected unit
>>
>> Dear Users
>> I am trying to calculate the phonon band structure of Ni(OH)2 slab on a
>> well converged scf.
>>
>> I am using QE version 6.6 (also tried 6.5 and 6.4.1). QE is compiled with
>> the mkl-2020.2.254 parallel library.
>> I am getting below error:
>>
>>  Error in routine diropn (34):
>>  can't open a connected unit
>>
>>  
>> %%
>>
>>  stopping ...
>>
>> I have checked the mailing list but it could not help me.
>> For the bulk system, it is running well.
>>
>> Below are my qe.in and ph.in files:
>>
>> 
>>  calculation = 'scf'
>>   outdir = './tmp'
>>   pseudo_dir = './'
>>   prefix = 'pwscf'
>>verbosity = 'default'
>>etot_conv_thr = 0.1
>>forc_conv_thr = 0.0001
>>nstep = 400
>>  tstress = .true.
>>  tprnfor = .true.
>>
>> /
>>
>> 
>>ibrav = 0
>> celldm(1)=42.3160703759d0,
>>  nat = 15
>> ntyp = 3
>>  ecutw

Re: [QE-users] Error in routine diropn (34): can't open a connected unit

[Dr. K. C. Bhamu]

Dear Dr. Lurii,
Thank you for the suggestion.
Now the phonon calculation has started.

I am getting a new warning now:

Atomic wfc used for the projector on the Hubbard manifold are NOT
orthogonalized

 Calculating the dnsbare matrix...

 Calculating the dnsorth_cart matrix...

Can I ignore this warning?

Thank you very much
Bhamu



On Tue, Dec 1, 2020 at 6:09 PM Timrov Iurii  wrote:

> Actually you need to remove this: fildvscf='dvscf'
>
> Also I would remove this: electron_phonon= " "
>
>
> Iurii
>
>
> --
> Dr. Iurii TIMROV
> Postdoctoral Researcher
> STI - IMX - THEOS and NCCR - MARVEL
> Swiss Federal Institute of Technology Lausanne (EPFL)
> CH-1015 Lausanne, Switzerland
> +41 21 69 34 881
> http://people.epfl.ch/265334
> --
> *From:* users  on behalf of
> Timrov Iurii 
> *Sent:* Tuesday, December 1, 2020 1:27:51 PM
> *To:* Quantum Espresso users Forum
> *Subject:* Re: [QE-users] Error in routine diropn (34): can't open a
> connected unit
>
>
> Can you share your PW and PH input and output files using Google Drive?
> Did you check whether the PW calculation finished successfully?
>
>
> If the PW calculation finished successfully, then you can try to remove
> recover=.true. in the PH input and try again.
>
>
> Greetings,
>
> Iurii
> --
> *From:* users  on behalf of Dr.
> K. C. Bhamu 
> *Sent:* Tuesday, December 1, 2020 12:04:50 PM
> *To:* Quantum Espresso users Forum
> *Subject:* [QE-users] Error in routine diropn (34): can't open a
> connected unit
>
> Dear Users
> I am trying to calculate the phonon band structure of Ni(OH)2 slab on a
> well converged scf.
>
> I am using QE version 6.6 (also tried 6.5 and 6.4.1). QE is compiled with
> the mkl-2020.2.254 parallel library.
> I am getting below error:
>
>  Error in routine diropn (34):
>  can't open a connected unit
>
>  
> %%
>
>  stopping ...
>
> I have checked the mailing list but it could not help me.
> For the bulk system, it is running well.
>
> Below are my qe.in and ph.in files:
>
> 
>  calculation = 'scf'
>   outdir = './tmp'
>   pseudo_dir = './'
>   prefix = 'pwscf'
>verbosity = 'default'
>etot_conv_thr = 0.1
>forc_conv_thr = 0.0001
>nstep = 400
>  tstress = .true.
>  tprnfor = .true.
>
> /
>
> 
>ibrav = 0
> celldm(1)=42.3160703759d0,
>  nat = 15
> ntyp = 3
>  ecutwfc = 85
>  ecutrho = 680
> starting_magnetization(1)= 1,
> occupations='smearing', smearing='mv', degauss=0.005,
> nspin=2,
> lda_plus_u=.true.  Hubbard_U(1)=5.5
>
>  /
>  
> electron_maxstep = 700
> conv_thr = 1.0D-8
>  /
> 
> ion_dynamics = 'bfgs'
>  /
> 
> /
> ATOMIC_SPECIES
> Ni 58.6934 ni_pbe_v1.4.uspp.F.UPF
> H  1.00794 H.pbe-rrkjus_psl.1.0.0.UPF
> O  15.9994 O.pbe-n-kjpaw_psl.0.1.UPF
>
> ATOMIC_POSITIONS {crystal}
> Ni0.40862711800.250.0562779067
> Ni0.53102979780.750.1575988843
> Ni0.65559178060.250.2252620504
> H 0.35567189120.750.7569475855
> H 0.49059898500.250.7519547270
> H 0.68131263580.750.8495914755
> H 0.30511779570.250.2908234852
> H 0.42870251600.750.4856771252
> H 0.56637853490.250.5842143961
> O 0.39915823060.750.7744084930
> O 0.52456039480.250.8820391483
> O 0.68678591210.751.0544632655
> O 0.32173069690.250.0997462181
> O 0.44572564380.750.2821321300
> O 0.57518806680.250.3748931091
>
> CELL_PARAMETERS {alat}
>   1.d0  0.d0  0.d0
>   0.d0  0.142952837309d0  0.d0
>   0.d0  0.d0  0.209983610730d0
>
> K_POINTS automatic
> 1 4 4   0 0 0
>
>
> ph.in
>
> 
> recover=.true.,
> tr2_ph = 1.0d-12
&

[QE-users] Error in routine diropn (34): can't open a connected unit

[Dr. K. C. Bhamu]

Dear Users
I am trying to calculate the phonon band structure of Ni(OH)2 slab on a
well converged scf.

I am using QE version 6.6 (also tried 6.5 and 6.4.1). QE is compiled with
the mkl-2020.2.254 parallel library.
I am getting below error:

 Error in routine diropn (34):
 can't open a connected unit
 %%

 stopping ...

I have checked the mailing list but it could not help me.
For the bulk system, it is running well.

Below are my qe.in and ph.in files:


 calculation = 'scf'
  outdir = './tmp'
  pseudo_dir = './'
  prefix = 'pwscf'
   verbosity = 'default'
   etot_conv_thr = 0.1
   forc_conv_thr = 0.0001
   nstep = 400
 tstress = .true.
 tprnfor = .true.

/


   ibrav = 0
celldm(1)=42.3160703759d0,
 nat = 15
ntyp = 3
 ecutwfc = 85
 ecutrho = 680
starting_magnetization(1)= 1,
occupations='smearing', smearing='mv', degauss=0.005,
nspin=2,
lda_plus_u=.true.  Hubbard_U(1)=5.5

 /
 
electron_maxstep = 700
conv_thr = 1.0D-8
 /

ion_dynamics = 'bfgs'
 /

/
ATOMIC_SPECIES
Ni 58.6934 ni_pbe_v1.4.uspp.F.UPF
H  1.00794 H.pbe-rrkjus_psl.1.0.0.UPF
O  15.9994 O.pbe-n-kjpaw_psl.0.1.UPF

ATOMIC_POSITIONS {crystal}
Ni0.40862711800.250.0562779067
Ni0.53102979780.750.1575988843
Ni0.65559178060.250.2252620504
H 0.35567189120.750.7569475855
H 0.49059898500.250.7519547270
H 0.68131263580.750.8495914755
H 0.30511779570.250.2908234852
H 0.42870251600.750.4856771252
H 0.56637853490.250.5842143961
O 0.39915823060.750.7744084930
O 0.52456039480.250.8820391483
O 0.68678591210.751.0544632655
O 0.32173069690.250.0997462181
O 0.44572564380.750.2821321300
O 0.57518806680.250.3748931091

CELL_PARAMETERS {alat}
  1.d0  0.d0  0.d0
  0.d0  0.142952837309d0  0.d0
  0.d0  0.d0  0.209983610730d0

K_POINTS automatic
1 4 4   0 0 0


ph.in


recover=.true.,
tr2_ph = 1.0d-12
prefix ='pwscf'
alpha_mix =0.3
ldisp = .true.,
trans=.true.,
fildvscf='dvscf'
electron_phonon= " "
nq1=1
nq2=4
nq3=4
outdir ='./tmp'
fildyn = 'slab.dyn'
/


Any suggestion will be appreciated.

Thank you very much.


K.C. Bhamu
Postdoctoral Fellow
University of Ulsan
ROK
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Re: [QE-users] How to plot phonon band structure with LO-TO splitting

[Dr. K. C. Bhamu]

Thank you very much Dear Lorenzo.
I will do it.

Regards
Bhamu


On Mon, Nov 4, 2019 at 2:15 PM Lorenzo Paulatto  wrote:

> you can just edit by hand the dyn1 file and remove the dielectric
> constants and effective charges, then rerun q2r
>
> regards
>
> On 11/4/19 9:29 AM, Dr. K. C. Bhamu wrote:
> > Dear Lorenzo,
> >
> > My motive is to plot phonon band structure with and without LO-TO
> > splitting in a single plot and I would run (may be  wrong but giving it
> > a try)two separate gamma calculation one with epsil=.false. and other
> > with .true.for this.
> >
> > If you have any previous experiencethen you can save my computational
> time.
> >
> > regards
> > Bhamu
> >
> >
> > On Mon, Nov 4, 2019 at 1:46 PM Lorenzo Paulatto  > <mailto:paul...@gmail.com>> wrote:
> >
> > > Could someone please guide me how to plot phonon band structure
> with the
> > > LO-TO splitting?
> >
> > LO-TO splitting is automatically included if you do the phonon
> > calculation for an insulator (i.e. no smearing in pw.x)
> >
> > kind regards
> >
> > --
> > Lorenzo Paulatto - Paris
> > ___
> > Quantum ESPRESSO is supported by MaX
> > (www.max-centre.eu/quantum-espresso
> > <http://www.max-centre.eu/quantum-espresso>)
> > users mailing list users@lists.quantum-espresso.org
> > <mailto:users@lists.quantum-espresso.org>
> > https://lists.quantum-espresso.org/mailman/listinfo/users
> >
> >
> > ___
> > Quantum ESPRESSO is supported by MaX (www.max-centre.eu/quantum-espresso
> )
> > users mailing list users@lists.quantum-espresso.org
> > https://lists.quantum-espresso.org/mailman/listinfo/users
> >
>
> --
> Lorenzo Paulatto - Paris
> ___
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Re: [QE-users] How to plot phonon band structure with LO-TO splitting

[Dr. K. C. Bhamu]

Dear Lorenzo,

My motive  is to plot phonon band structure with and without LO-TO
splitting in a single plot and I would run (may be  wrong but giving it a
try)  two separate gamma calculation one with epsil=.false. and other with .
true. for this.

If you have any previous experience then you can save my computational time.

regards
Bhamu


On Mon, Nov 4, 2019 at 1:46 PM Lorenzo Paulatto  wrote:

> > Could someone please guide me how to plot phonon band structure with the
> > LO-TO splitting?
>
> LO-TO splitting is automatically included if you do the phonon
> calculation for an insulator (i.e. no smearing in pw.x)
>
> kind regards
>
> --
> Lorenzo Paulatto - Paris
> ___
> Quantum ESPRESSO is supported by MaX (www.max-centre.eu/quantum-espresso)
> users mailing list users@lists.quantum-espresso.org
> https://lists.quantum-espresso.org/mailman/listinfo/users
>
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[QE-users] How to plot phonon band structure with LO-TO splitting

[Dr. K. C. Bhamu]

Dear QE users,

I have attempted to see the LO-TO splitting in polar material (AlAS: SG216).

My LO-TO splitting values are in the tune with what I have seen in various
tutorials.

# mode   [cm-1][THz]  IR
1   0.00 0. 0.
2   0.00 0. 0.
3   0.00 0. 0.
4*352.99   10.5824*5.3390
5*352.99   10.5824*5.3390
6*392.54   11.7681*5.3390

Without LO-TO splitting, the phonon band structure is here:
https://we.tl/t-eU2SfLYlMu  (from MP) where we can see that LO-TO at Gamma
point are degenerate. When we account for the non-analytic corrections, the
LO-TO branch at Gamma point should split (by ~1THz as above).

Could someone please guide me how to plot phonon band structure with the
LO-TO splitting?

I can plot the regular phonon band structure with q2r.x > matdyn.x but
could not find a way to plot with the above corrections.



Regards

K.C. Bhamu
CSIR-NCL, Pune
India
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Re: [QE-users] dexx is negative with QE_6.4.1

[Dr. K. C. Bhamu]

I could manage it by playing with ecutwfc and ecutfock.

Regards
Bhamu


On Mon, Aug 19, 2019 at 1:32 PM Dr. K. C. Bhamu  wrote:

> Dear Experts,
> I am running GAUPBE calculations for a FCC binary scalar relativistic case
> with latest version of QE with mkl-2015 on a cluster with pseudo-dojo PPs
> and SG15 ONCV.
> K_POINTS {automatic}
>  X X X 0 0 0(X=12, 15).
> taking converged value of ecutwfc (4meV). Beyond this criteria I am facing
> memory issue.
>
> I am getting the dexx is negative error:
> Error in routine electrons (1):
>  dexx is negative!  Check that exxdiv_treatment is appropriate for the
> system, or ecutfock may be too low
>
> I would like to mention two case where I encounter this error:
>  1.
> k_POINTS
> 12 12 12 0 0 0
> nqx=1,2,3,6 finished well but error was occurred with nqx=4.
> 2.
> k_POINTS
> 15 15 15 0 0 0
> nqx=1,5 finished well but error was occurred with nqx=3.
>
> I have looked over all the available threads on this forum and trying to
> overcome this error.
>
> To dig into the available options I would like to ask about input
> variables of gaupbe.
>
> 1. exxdiv_treatment:  as per pw.x input descriptions it should be none but
> the error says "exxdiv_treatment" ?
> Can we use other approach to be used for treating the Coulomb potential
> divergencies? I am afraid of using option other than none as the other
> options are suggested for supercells.
>
> 2. By default  ecutvcut is 0.0.
> Can we vary this ecutvcut with gaupbe? if yes then what is the approximate
> range?
>
>
> regards
> Bhamu
>
>
>
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[QE-users] dexx is negative with QE_6.4.1

[Dr. K. C. Bhamu]

Dear Experts,
I am running GAUPBE calculations for a FCC binary scalar relativistic case
with latest version of QE with mkl-2015 on a cluster with pseudo-dojo PPs
and SG15 ONCV.
K_POINTS {automatic}
 X X X 0 0 0(X=12, 15).
taking converged value of ecutwfc (4meV). Beyond this criteria I am facing
memory issue.

I am getting the dexx is negative error:
Error in routine electrons (1):
 dexx is negative!  Check that exxdiv_treatment is appropriate for the
system, or ecutfock may be too low

I would like to mention two case where I encounter this error:
 1.
k_POINTS
12 12 12 0 0 0
nqx=1,2,3,6 finished well but error was occurred with nqx=4.
2.
k_POINTS
15 15 15 0 0 0
nqx=1,5 finished well but error was occurred with nqx=3.

I have looked over all the available threads on this forum and trying to
overcome this error.

To dig into the available options I would like to ask about input variables
of gaupbe.

1. exxdiv_treatment:  as per pw.x input descriptions it should be none but
the error says "exxdiv_treatment" ?
Can we use other approach to be used for treating the Coulomb potential
divergencies? I am afraid of using option other than none as the other
options are suggested for supercells.

2. By default  ecutvcut is 0.0.
Can we vary this ecutvcut with gaupbe? if yes then what is the approximate
range?


regards
Bhamu
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Re: [QE-users] Error in routine write_rhog (1): error opening file ./tmp/pwscf.save/charge-density

[Dr. K. C. Bhamu]

Thanks Lorenzo,

Its working now with the same job file but in scratch instead of home.

Happy Computing !!



On Wed, Aug 7, 2019 at 4:18 PM Lorenzo Paulatto  wrote:

>
> Could someone please suggest me how to solve this trouble?
>>
>
> The staff who compiled the code should be able to help
>
> Regards
>
>>
>> Regards
>> Bhamu
>>
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>
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[QE-users] Error in routine write_rhog (1): error opening file ./tmp/pwscf.save/charge-density

[Dr. K. C. Bhamu]

Dear Users and QE Developers,
I am running relax/scf/vc-relax calculation  using  pw.x 6.4.1 on the
cluster "NERSC " with parallel_studio_xe_2018* with
68 cores on a single node. The QE_6.4.1 is installed by the technical staff
of the cluster.
The error what I am getting is already reported in the mailing list [1] but
still I could not solve as I do not have any access of
 Modules/qeh5_module.f90.
[1]
https://www.mail-archive.com/users@lists.quantum-espresso.org/msg35505.html

The input file information is

  calculation='relax',
  outdir='./',
  prefix='pwscf',
!restart_mode='from_scratch'
  pseudo_dir='../',
  verbosity='low',
!disk_io='none'
max_seconds=3500
etot_conv_thr=0.01
forc_conv_thr=0.1
nstep=400
tstress=.true.
tprnfor=.true.
/


  ibrav=6,
  celldm(1)=6.0361820843d0, celldm(3)=2.5214998388d0,
  nat=6,
  ntyp=3,
  ecutwfc=115,
!  ecutrho=120,
!  input_dft='lda',
  occupations='smearing',
  smearing='mv',
  degauss=0.005d0,

/


  conv_thr=1d-010,
  mixing_beta=0.7d0,
mixing_mode='local-TF',

/

/

/

## SYSTEM INFORMATION###

K_POINTS {automatic}
  7 7 3 0 0 0
Could someone please suggest me how to solve this trouble?

Regards
Bhamu
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Re: [QE-users] how to do parallelization for a gamma centered calculation

[Dr. K. C. Bhamu]

Dear Expert Users and the Developers of QE,
Could you please have a look for this thread?

regards
Bhamu


On Wed, Jul 31, 2019 at 6:08 PM Dr. K. C. Bhamu  wrote:

> Dear QE users and developers,
>
> Greetings!!
>
> I am looking for a help to do the effective parallelization for a gamma
> centered calculation with qe-6.4.1 with intel mkl 2015 with external fftw3
> or internal fftw3 on a cluster having 32 processors on each node.
>
> The system is a binary  case with 128 atoms (1664.00 electrons) as first
> case and in another case we are having 250 atoms (3250.00 electrons).
> Job on 32 processor for the scf file with 128 atoms is running well but
> for the other file (250 atoms, other parameters are same) we are getting
> the error after first iteration as  appended at the bottom of the email .
> If we use two nodes for the second case then the CPU time is too much (~
> five times to the first case).
> Could someone please help me to run the jobs with effective
> parallelization for gamma k-point calculations with 1/2/3/4.. nodes (32
> proc for each node)?
>
>
> The other useful information that may be required by you to diagnosis the
> problem is:
>  Parallel version (MPI), running on32 processors
>
>  MPI processes distributed on 1 nodes
>  R & G space division:  proc/nbgrp/npool/nimage =  32
>  Waiting for input...
>  Reading input from standard input
>
>  Current dimensions of program PWSCF are:
>  Max number of different atomic species (ntypx) = 10
>  Max number of k-points (npk) =  4
>  Max angular momentum in pseudopotentials (lmaxx) =  3
>
>  gamma-point specific algorithms are used
>
>  Subspace diagonalization in iterative solution of the eigenvalue
> problem:
>  one sub-group per band group will be used
>  scalapack distributed-memory algorithm (size of sub-group:  4*  4
> procs)
>
>  Parallelization info
>  
>  sticks:   dense  smooth PW G-vecs:dense   smooth  PW
>  Min 936 936233   107112   107112   13388
>  Max 937 937236   107120   107120   13396
>  Sum   29953   29953   7495  3427749  3427749  428575
>  total cpu time spent up to now is  143.9 secs
>
> and
>
>  number of k points= 1
>cart. coord. in units 2pi/alat
> k(1) = (   0.000   0.000   0.000), wk =   2.000
>
>  Dense  grid:  1713875 G-vectors FFT dimensions: ( 216, 225, 216)
>
>  Estimated max dynamical RAM per process >   1.01 GB
>
>  Estimated total dynamical RAM >  64.62 GB
>
>  Initial potential from superposition of free atoms
>
>  starting charge 3249.86289, renormalised to 3250.0
>  Starting wfcs are 2125 randomized atomic wfcs
>
> == Below is the error for the case with 250 atoms run over 32
> procs=
>
>
>  Self-consistent Calculation
>
>  iteration #  1 ecut=80.00 Ry beta= 0.70
>  Davidson diagonalization with overlap
>
>
> ===
> =   BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
> =   PID 154663 RUNNING AT node:1
> =   EXIT CODE: 9
> =   CLEANING UP REMAINING PROCESSES
> =   YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
>
> ===
> APPLICATION TERMINATED WITH THE EXIT STRING: Killed (signal 9)
>
>
>
> On the other cluster (68 procs per node) I do not observe any error.
>
> Please let me know if I need to provide some additional information.
>
> Looking forward to hearing from the experts.
>
> Regards
>
> K.C. Bhamu, Ph.D.
> Postdoctoral Fellow
> CSIR-NCL, Pune
> India
>
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[QE-users] how to do parallelization for a gamma centered calculation

[Dr. K. C. Bhamu]

Dear QE users and developers,

Greetings!!

I am looking for a help to do the effective parallelization for a gamma
centered calculation with qe-6.4.1 with intel mkl 2015 with external fftw3
or internal fftw3 on a cluster having 32 processors on each node.

The system is a binary  case with 128 atoms (1664.00 electrons) as first
case and in another case we are having 250 atoms (3250.00 electrons).
Job on 32 processor for the scf file with 128 atoms is running well but for
the other file (250 atoms, other parameters are same) we are getting the
error after first iteration as  appended at the bottom of the email .
If we use two nodes for the second case then the CPU time is too much (~
five times to the first case).
Could someone please help me to run the jobs with effective parallelization
for gamma k-point calculations with 1/2/3/4.. nodes (32 proc for each node)?


The other useful information that may be required by you to diagnosis the
problem is:
 Parallel version (MPI), running on32 processors

 MPI processes distributed on 1 nodes
 R & G space division:  proc/nbgrp/npool/nimage =  32
 Waiting for input...
 Reading input from standard input

 Current dimensions of program PWSCF are:
 Max number of different atomic species (ntypx) = 10
 Max number of k-points (npk) =  4
 Max angular momentum in pseudopotentials (lmaxx) =  3

 gamma-point specific algorithms are used

 Subspace diagonalization in iterative solution of the eigenvalue
problem:
 one sub-group per band group will be used
 scalapack distributed-memory algorithm (size of sub-group:  4*  4
procs)

 Parallelization info
 
 sticks:   dense  smooth PW G-vecs:dense   smooth  PW
 Min 936 936233   107112   107112   13388
 Max 937 937236   107120   107120   13396
 Sum   29953   29953   7495  3427749  3427749  428575
 total cpu time spent up to now is  143.9 secs

and

 number of k points= 1
   cart. coord. in units 2pi/alat
k(1) = (   0.000   0.000   0.000), wk =   2.000

 Dense  grid:  1713875 G-vectors FFT dimensions: ( 216, 225, 216)

 Estimated max dynamical RAM per process >   1.01 GB

 Estimated total dynamical RAM >  64.62 GB

 Initial potential from superposition of free atoms

 starting charge 3249.86289, renormalised to 3250.0
 Starting wfcs are 2125 randomized atomic wfcs

== Below is the error for the case with 250 atoms run over 32
procs=


 Self-consistent Calculation

 iteration #  1 ecut=80.00 Ry beta= 0.70
 Davidson diagonalization with overlap

===
=   BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
=   PID 154663 RUNNING AT node:1
=   EXIT CODE: 9
=   CLEANING UP REMAINING PROCESSES
=   YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
===
APPLICATION TERMINATED WITH THE EXIT STRING: Killed (signal 9)



On the other cluster (68 procs per node) I do not observe any error.

Please let me know if I need to provide some additional information.

Looking forward to hearing from the experts.

Regards

K.C. Bhamu, Ph.D.
Postdoctoral Fellow
CSIR-NCL, Pune
India
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Re: [QE-users] Problems with DFT + U Calculations: Fatal error in PMPI_Bcast

[Dr. K. C. Bhamu]

Dear Prof. Paolo,

I am also having same error on same cluster which Mr. A. Kar using with
QE_6.3 and "composer_xe_2015".
I am invoking the command "mpirun -np 32 $QE/pw.x -npool 2 *in ...
*out  for vc-relax.
For me it happen in the last scf, after a message "End final coordinates".
It went okay till scf cycle 53.
It happens in some cases only.

Below seems strand for me: (grep scf *out)

A final scf calculation at the relaxed structure.
 estimated scf accuracy<   0.35117344 Ry
 estimated scf accuracy<  32.50696577 Ry
 estimated scf accuracy<   0.15737732 Ry
 estimated scf accuracy<   0.08941433 Ry
 estimated scf accuracy<   0.04130004 Ry
 estimated scf accuracy<   0.03367160 Ry
 estimated scf accuracy<   0.01518230 Ry
 estimated scf accuracy<   0.01241863 Ry
 estimated scf accuracy<   0.00237884 Ry
 estimated scf accuracy<   0.02059544 Ry
 estimated scf accuracy<   0.01326459 Ry
 estimated scf accuracy<   0.02823102 Ry
 estimated scf accuracy<   0.14757734 Ry
 estimated scf accuracy<   0.05952341 Ry
 estimated scf accuracy<   0.05929330 Ry
 estimated scf accuracy<   0.00738492 Ry
 estimated scf accuracy<   0.00555608 Ry
 estimated scf accuracy<   0.00535798 Ry
 estimated scf accuracy<   0.00688829 Ry
 estimated scf accuracy<   0.00169491 Ry
 estimated scf accuracy<   0.00067948 Ry
 estimated scf accuracy<   0.06297539 Ry
 estimated scf accuracy<   0.05981938 Ry
 estimated scf accuracy<   0.05814955 Ry
 estimated scf accuracy<   0.06202781 Ry
 estimated scf accuracy<   0.06178400 Ry
 estimated scf accuracy<   0.05837077 Ry
 estimated scf accuracy<   0.07705482 Ry
 estimated scf accuracy<   0.03734422 Ry
 estimated scf accuracy<   0.01355381 Ry
 estimated scf accuracy<   0.02777065 Ry
 estimated scf accuracy<   0.02632385 Ry
 estimated scf accuracy<   0.02607268 Ry
 estimated scf accuracy<   0.01001318 Ry
 estimated scf accuracy<   0.00563499 Ry
 estimated scf accuracy<   0.5798 Ry
 estimated scf accuracy<   0.00066655 Ry
 estimated scf accuracy<   0.0103 Ry
 estimated scf accuracy<   0.0082 Ry
 estimated scf accuracy<   0.0002 Ry
 estimated scf accuracy<   0.0001 Ry
 estimated scf accuracy<  6.0E-11 Ry
 estimated scf accuracy<   0.7832 Ry
 estimated scf accuracy<   0.7830 Ry
 estimated scf accuracy<   0.7712 Ry
 estimated scf accuracy<   0.7558 Ry
 estimated scf accuracy<   0.7271 Ry
 estimated scf accuracy<   0.6239 Ry
 estimated scf accuracy<   0.4313 Ry
 estimated scf accuracy<   0.2601 Ry


I still have double on my PPs. If this is due to something else, please let
me know what additional information I can supply to reproduce the error
message.

Kind regards
Bhamu

CSIR-NCL, Pune
India

On Mon, Oct 22, 2018 at 11:19 AM Paolo Giannozzi 
wrote:

> QE version?
>
> On Sat, Oct 20, 2018 at 9:01 AM arini kar  wrote:
>
>> Dear Quantum Espresso users,
>>
>> I have been trying to relax a 2x2x1 supercell of hematite doped with Ge
>> and an oxygen vacancy. However, after a few electronic iterations, I
>> received the following error:
>>
>> Fatal error in PMPI_Bcast: Other MPI error, error stack:
>> PMPI_Bcast(2112): MPI_Bcast(buf=0x11806c00, count=7500,
>> MPI_DOUBLE_PRECISION, root=0, comm=0x8405) failed
>> MPIR_Bcast_impl(1670)...:
>> I_MPIR_Bcast_intra(1887): Failure during collective
>> MPIR_Bcast_intra(1524)..: Failure during collective
>> Fatal error in PMPI_Bcast: Other MPI error, error stack:
>> PMPI_Bcast(2112): MPI_Bcast(buf=0x56fced0, count=7500,
>> MPI_DOUBLE_PRECISION, root=0, comm=0x8405) failed
>> MPIR_Bcast_impl(1670)...:
>> I_MPIR_Bcast_intra(1887): Failure during collective
>> MPIR_Bcast_intra(1524)..: Failure during collective
>> Fatal error in PMPI_Bcast: Other MPI error, error stack:
>> PMPI_Bcast(2112): MPI_Bcast(buf=0x1080d330, count=7500,
>> MPI_DOUBLE_PRECISION, root=0, comm=0x8405) failed
>> MPIR_Bcast_impl(1670)...:
>> I_MPIR_Bcast_intra(1887): Failure during collective
>> MPIR_Bcast_intra(1524)..: Failure during collective
>> Fatal error in PMPI_Bcast: Other MPI error, error stack:
>> PMPI_Bcast(2112): MPI_Bcast(buf=0x10c025c0, count=7500,
>> MPI_DOUBLE_PRECISION, root=0, comm=0x8405) failed
>> MPIR_Bcast_impl(1670)...:
>> I_MPIR_Bcast_intra(1887): Failure during collective
>> MPIR_Bcast_intra(1524)..: Failure during collective
>> Fatal error in PMPI_Bcast: Other MPI error, error stack:

[QE-users] PP of I from PSlib

[Dr. K. C. Bhamu]

Hii List,

I tried to get PP of "I" from PSlibrary  and I could not get UPF format
instead I am getting "I.pbe-n-rrkjus_psl.1.0.0.UPF.xml".
Could someone please suggest me how may I have PP of "I" from 1.0.0 version
in UPF format ?
Also, SSSP library do not have uspp for "I".

regards
Bhamu


K. C. Bhamu
CSIR-NCL, Pune
India
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Re: [QE-users] Pseudopotentials

[Dr. K. C. Bhamu]

As you said that you did  copy paste. So there might be some format issue.
I suggest you to directly save the PP into your machine instead of copy and
paste and transfer it wherever you want to put.
.
Some time copy and paste may change the formate of PP file.

regards
Bhamu


On Wed, Sep 5, 2018 at 9:09 PM, Hari Paudyal 
wrote:

> Hi Dr. Zacharies,
>
> I just tested the potential in case of graphene, it worked fine for me. I
> used the recommended eutoffs from the potential and qe-6.3 version. I
> wonder, if you have something problem downloading the potential correctly,
> otherwise it should go fine, I guess.
>
> Cheers,
> Hari Paudyal
> SUNY Binghamton, USA
>
> On Wed, Sep 5, 2018 at 10:44 AM, Zacharias Fthenakis <
> zfthena...@mail.usf.edu> wrote:
>
>> Is there any problem with pseudopotentials released recently (4 Sept.
>> 2018)? I used copy and paste to get a copy of C.pbe-n-kjpaw_psl.1.0.0.UPF
>> from https://www.quantum-espresso.org/pseudopotentials/ps-library/c in
>> my account, but when I tried to run the code, it didn't work. I get the
>> error message "Error in routine read_ncpp (5):  pseudo file is empty or
>> wrong". Moreover, on top of the webpage there is the following message
>> "This XML file does not appear to have any style information associated
>> with it. The document tree is shown below." The corresponding
>> pseudopotential for Cobalt, (Co.pbe-spn-kjpaw_psl.0.3.1.UPF) created in
>> May 4, 2018 seems to work fine and the message for the XML file did not
>> appear. Does anyone know what is going on?
>>
>>
>>
>> --
>> ---
>> Dr Zacharias G. Fthenakis
>> Research Associate
>> Physics Department
>> University of South Florida
>> 4202 E Fowler Ave. ISA5119
>> Tampa, FL, 33620, USA
>> ---
>>
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>
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[QE-users] Expert users view required on FFT_LIBS and IFLAGS with QE-6.2.1

[Dr. K. C. Bhamu]

Dear Developer and Users,

I am trying to install the recent version of QE on a cluster with
Intel ScaLAPACK and ifort, icc.


I found on QE page the performance can be boosted if a right combination
of  ScaLAPACK and fftw is used.


My query is for FFT_LIBS and IFLAGS:

Which combination of flags for "FFT_LIBS and IFLAGS" gives
better performance:
1. internal (I assume that it will be used at default if we do not specify
anything about fftw)
2. MKL
3. External (downloaded from fftw website)
4. Can be mixed FFT_LIBS and IFLAGS from both MKL and external?


Looking forward to hearing from experts!


Kind regards
Bhamu
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[QE-users] magnetic moment issue for a half-metal

[Dr. K. C. Bhamu]

Dear QE Users,

I am running a AFM case, QE.in is undermentioned, aiming to get the atomic
magnetic moment for Cr. In literature, it is reported ~1.5 mue_b for each
Cr.

I tried with many configurations for starting magnetization and for each
configuration I am getting total (MMT)  and well atomic magnetic (MMI)
moment zero.

I am only getting the magnetic moment in the vicinity of reported value if
I take ecutwfc 20 and ecutrho 200 which is below and in tune with
literature.

I took
  nspin=2,
  starting_magnetization(3)=1,
  starting_magnetization(4)=-1,

 Magnetic moment per site:
 atom:1charge:2.1886magn:   -0.0429constr:0.
 atom:2charge:   10.6671magn:0.0204constr:0.
 atom:3charge:   12.3448magn:   -1.7550constr:0.
 atom:4charge:   12.3094magn:1.8137constr:0.


for rest, all configurations, the MMT (total) or MMI (atom dependent) is
always zero.


other configurations, that I used.

  nspin=2,
  starting_magnetization(3)=2,
  starting_magnetization(4)=-2,
or
  nspin=2,
 starting_magnetization(3)=1,
or
  nspin=2,
  starting_magnetization=05d,

*for a range of ecutwfc and ecutrho*

Could you please correct me if I am doing any mistake somewhere? I am using
rrkjus PPs.

# QE.in ==


  calculation='scf',
  outdir='.',
  prefix='pwscf',
  pseudo_dir='.',
  verbosity='low',
/


  ibrav=2,
  celldm(1)=11.0560959151d0,
  nat=4,
  ntyp=3,
  ecutwfc=$k,
  ecutrho=$p,
  input_dft='pbe',
  occupations='smearing',
  smearing='mv',
  degauss=0.005d0,
/


  conv_thr=1d-08,
  mixing_beta=0.7d0,
/

ATOMIC_SPECIES
  Cr 51.996100d0 Cr.UPF
  Si 28.085500d0 Si.UPF
  Zn 65.409000d0 Zn.UPF

ATOMIC_POSITIONS {crystal}
  Si   0.00d0   0.00d0   0.00d0
  Zn   0.75d0   0.75d0   0.75d0
  Cr   0.25d0   0.25d0   0.25d0
  Cr   0.50d0   0.50d0   0.50d0

K_POINTS {automatic}
  12 12 12 0 0 0
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[QE-users] final scf stuck in first iteration and relaxed hexagonal cell parameters changes abnormally

[Dr. K. C. Bhamu]

Dear Users,

I have three queries as mentioned below:

Query-1

I am relaxing (vc-relax and vc-relax with cell_dofree=xyz) the hybrid
perovskite structure. In both, the case the vc-relax goes well and prints
final relaxed ordinates (End final coordinates
).
As in the newest QE version, 6.2.1, the pw.x run a final scf at the
vc-relaxed structure.

In my case, the final scf starts but it always stuck at the first iteration:



iteration #  1 ecut=50.00 Ry beta= 0.70
 Davidson diagonalization with overlap



Could you please help me to figure out the issue why it stuck and what
should I do so that the final scf ends without any error.



Query-2


My structure is hexagonal with the initial cell dimensions;

  celldm(1)=16.1636080003d0, celldm(3)=1.3049995364d0,

or

 a= 8.56909772473  b= 8.57159817464  c= 11.2622477409Vol.=
716.067118376, c/a= 1.31428629976;  alpha= 90.0   beta= 90.0   gamma=
120.045402959


after vc-relax I am getting the final cell parameters as below:


a= 8.71101209853  b= 8.85373809923  c= 11.4881609903Vol.=
750.696449907,   c/a= 1.31880898113'   alpha= 86.512834873   beta=
92.9705116854   gamma= 121.889941369

you see here that the a and b are slightly different while in the hexagonal
system they should be same. Also the alpha, beta and gamma are also not at
90, 90 and 120 as supposed to remain at this value in the hexagonal system.


To overcome this issue, I have done another vc-relax with "cell_dofree=xyz"
to keep fix the lattice angles) I am getting the final cell parameters as
below:


AA a= 8.87533777693  b= 8.52082228214  c= 11.6157398387Vol.=
753.329940336,c/a= 1.30876594566 ;  alpha= 90.0   beta= 90.0   gamma=
120.954649993

Again we see the variation in the cell parameters. However, the variation
is small in comparison to pure vc-relax and alpha and beta are now at fix
value.


Could you please tell me why I am getting this variation in the cell
parameters?



Quer-3


If possible, please also cover my previous post which is here:

https://www.mail-archive.com/users@lists.quantum-espresso.org/msg33935.html



with kind regards


K.C. Bhamu
CSIR-NCL, Pune, India
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Re: [QE-users] query about system dependent etot_conv_thr, forc_conv_thr and conv_thr

[Dr. K. C. Bhamu]

Hii,
Just to add some data to my previous post:

The difference in scf energy (in Ry) for my system having 36 atoms is:

ecut vs energy

30 -1.42256
40 -0.0765211
45 -0.00623776
50 -0.00420366
60 -0.00482638
65 -0.00095532

So if I divide energy wrt 45ecut by  36 (number of atoms), it comes out:
-0.0001732 Ry or -0.002356487 eV/atom
For 50 and 60 ecut this difference becomes ~0.00017 Ry or ~0.0016 eV/atom.

For the ecut (the difference between ecut 60 and 65) the  difference is:
-0.26 Ry/atom or 0.00036eV/atom.


What value of ecut is the perfect choice for my case: 45 or 50 or 60?

I just doing vc relaxation with free xyz.



Kind regards

Bhamu





On Sat, May 5, 2018 at 11:12 PM, Dr. K. C. Bhamu <kcbham...@gmail.com>
wrote:

> Dear QE Users,
>
> For simple compounds (binary or ternary), I know the said parameters may
> be fixed tight  (etot_conv_thr, 1e-5,  and forc_conv_thr, 1e-5 and
> conv_thr. 1d-07 or 1d-08 or 1d-09). But for complex systems, if we set them
> high then it would cost much wall time.
>
> To avoid this, Is there any thumb rule to decide the above parameters to
> be kept fix for complex bulk structures (having a combination of organic
> and inorganic elements), i.e. as the number of atoms increases in the
> system the above parameters can be lowered?
> As far as I know, these parameters have much importance if we see per
> atom. So, if we increase the number of atoms the parameters can be lowered
> (Ex. for hybrid perovskites with 36 atoms in a unit cell, etot_conv_thr,
> 1e-3,  and forc_conv_thr, 1e-3 and conv_thr. 1d-06 ), is it?
>
>
> Any comment will be helpful to improve my understanding or in correcting
> me if I am wrong, also will save computational cost.
>
>
> Thanks and regards,
>
>
> Dr. K. C. Bhamu
> National Postdoctoral Fellow,
> Physical and Materials Chemistry Division
> CSIR-NCL, Pune
> Mob. No.  +91-9975238952
>
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[QE-users] query about system dependent etot_conv_thr, forc_conv_thr and conv_thr

[Dr. K. C. Bhamu]

Dear QE Users,

For simple compounds (binary or ternary), I know the said parameters may be
fixed tight  (etot_conv_thr, 1e-5,  and forc_conv_thr, 1e-5 and conv_thr.
1d-07 or 1d-08 or 1d-09). But for complex systems, if we set them high then
it would cost much wall time.

To avoid this, Is there any thumb rule to decide the above parameters to be
kept fix for complex bulk structures (having a combination of organic and
inorganic elements), i.e. as the number of atoms increases in the system
the above parameters can be lowered?
As far as I know, these parameters have much importance if we see per atom.
So, if we increase the number of atoms the parameters can be lowered (Ex.
for hybrid perovskites with 36 atoms in a unit cell, etot_conv_thr, 1e-3,
and forc_conv_thr, 1e-3 and conv_thr. 1d-06 ), is it?


Any comment will be helpful to improve my understanding or in correcting me
if I am wrong, also will save computational cost.


Thanks and regards,


Dr. K. C. Bhamu
National Postdoctoral Fellow,
Physical and Materials Chemistry Division
CSIR-NCL, Pune
Mob. No.  +91-9975238952
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[QE-users] dE0s is positive

[Dr. K. C. Bhamu]

Dear QW Users,

The vc-relax for my system was stopped after default nstep.

I re-submitted it with restart mode and I got a warning message  that is
already described here:


http://qe-forge.org/pipermail/pw_forum/2014-September/105225.html

According to reply from Paolo, it is a numerical noise on forces and my
structure has relaxed.

Could you please tell me how to collect relaxed parameters from the
vc-relax.out file?
I do not see any message indicating "Final coordinates" as we see in a well
conversed-relax calculation.


Kind regards


K. C. Bhamu
National Postdoctoral Fellow,
CSIR-NCL, Pune
Mob. No.  +91-9975238952
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Re: [QE-users] query regarding card in case of half metal

[Dr. K. C. Bhamu]

Dear Users,

Could you please have a look at it?

regards
Bhamu


On Thu, Apr 12, 2018 at 11:44 AM, Dr. K. C. Bhamu <kcbham...@gmail.com>
wrote:

>
>
> Dear List,
>
> I am running a case on the recent version of QE which shows metal
> character with GGA while with HSE06 it is showing band gap ~0.3eV
>
> So how I should treat below options/metal or semiconductor?  I am running
> job with uspp taken from GBRV with PBE.
>
>
> occupations='smearing',
>   smearing='mv',
>   degauss=0.005d0
>
>
> What would be conv_thr in such case.
>
>
>
> Regards
>
> K C Bhamu
> CSIR-NCL, Pune
> India
>
>
>
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[QE-users] query regarding card in case of half metal

[Dr. K. C. Bhamu]

Thanks, *Paolo* for kind response!



Dear List,

I am running a case on the recent version of QE which shows metal character
with GGA while with HSE06 it is showing band gap ~0.3eV

So how I should treat below options/metal or semiconductor?  I am running
job with uspp taken from GBRV with PBE.


occupations='smearing',
  smearing='mv',
  degauss=0.005d0


What would be conv_thr in such case.



Regards

K C Bhamu
CSIR-NCL, Pune
India
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Re: [Pw_forum] Error optmizing doped graphene

[Dr. K. C. Bhamu]

Dear Bushan,

Please check your wall time.

Regards
Bhamu


Dr. K. C. Bhamu
National Postdoctoral Fellow,
Physical and Materials Chemistry Division
Mob. No.  +91-9975238952
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[Pw_forum] Thank you Paolo

[Dr. K. C. Bhamu]

Dear Dr. Paolo
thank you very much,

now my problem "ev.x" has been solved.

Kind regards
Bhamu
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[Pw_forum] regarding ev.x program

[Dr. K. C. Bhamu]

Dear QE users,

This is in continuation of my previous email

https://www.mail-archive.com/pw_forum@pwscf.org/msg30052.html
here I received two solutions.

I forgot to check the form. I supposed to get alert in my email. So sorry
for writing aging after 10 days.

*As suggested by Amer: '*hex' and 'noncubic' are the same for ev.xyou have
this error because you write 'noncubic' like this "non cubic".
>>>No, I wrote it ad noncubic. However, hex is working fine but are you
sure it is same as noncubic??

*Next: *By Paolo,
https://www.mail-archive.com/pw_forum@pwscf.org/msg30052.html

>>>I replaced ev.f90 with that of you provided but the issue is still same.
Should I recompile the program?

I should mention that my QE is already latest one 6.0.

regards


Dr. K. C. Bhamu
(UGC-Dr. D. S. Kothari Postdoc Fellow)
Department of Physics
Goa University, Goa-403 206
India
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[Pw_forum] ev.x issue on recent QE release

[Dr. K. C. Bhamu]

Dear QE Community members,

I am facing an issue in ev.x command, see below;

laptop/new:~/Espresso_test/PbO$ *ev.x*
 Lattice parameter or Volume are in (au, Ang) > *au*
 Enter type of bravais lattice (fcc, bcc, sc, noncubic) > *noncubic*
 *ev: unexpected lattice non   *
* >>> how to overcome this problem?*
laptop/new:~/Espresso_test/PbO$

I found a link to solve it but it contains very short description.  please
help me.

http://www.qe-forge.org/gf/project/q-e/tracker/?action=Track
erItemEdit_item_id=162

One of my colleague have different option. In his version he has "hex"
option instead of nocubic.

Waiting for our kind response

Kind regards

K. C. Bhamu
Department of Physics
Goa University, Goa-403 206
India
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