[QE-users] Question regarding mixing of PBE and PBESOL PP

[Yeon, Jejoon]

Hello


I ran several DFTs few times before, but I only have limited amount of 
knowledge and experience in DFTs.


I have Pyrope (Mg3Al2Si3O12) and Grossular (Ca3Al2Si3O12) unit cell, and wish 
to preform relax and vc-relax. After I get the relaxed atomic structure and 
cell size, I wish to make an energy curve of Pyrope / Grossular structure 
w.r.t. compression and expansion of volume, using expanded / compressed unit 
cells. Purpose of this DFT is to get the database for the parametrization of 
empirical force field, especially for mechanical properties like stress-strain 
curve and elastic constants.


Now, I have PBE-PAW(kjpaw) and PBESOL-PAW(kjpaw) PPs for all atom types. I have 
no problem about Pyrope, I can run it with PBESOL. But Grossular is an issue. 
For Ca, PBE is only available option from QE PP webpage, there is no PBESOL for 
Ca yet. Accordingly, if I want to calculate energies of Grossular structure, I 
have three options as far as I know:

1) input_dft = 'PBE', while mix the PBE (Ca) and PBESOL (Al, Si, O)

2) inout_dft = 'PBESOL', while mix the PBE (Ca) and PBESOL (Al, Si, O)

3) just use PBE PPs for all 4 atom types.



At this point, I'm not sure what would be the good choice for my purpose. I 
wish to use PBESOL because it is known to have better prediction for solid 
properties. But I'm not sure if I can mix them with PBE, and if I mix, which 
input_dft option should I need to choose.


I ran test relaxations for 3 cases, and I found that the final atom coordinates 
of all 3 cases are very similar, they are mostly the same up to second decimal 
point numbers. Their final optimized energies are different, but as far as I 
know I can't compare them, isn't it? I'm not sure on which criteria should I 
need compare and select the best one from those three options.


Or, if anyone had a similar experience, I welcome any advises or suggestions.


Just in case, following is my example in file.



  prefix="03_Relax_Grossular_80_800_PBESOL",
  calculation='relax',
  
outdir="/scratch/jj/20190501_QEDFT_Grossular_EoS/03_Relax_Grossular_80_800_PBESOL/tmp",
  pseudo_dir="/home/QE_pseudo/",
  restart_mode= 'from_scratch',
  nstep = 1000
/


  ibrav=0,
  nat=20,
  ntyp=4,
  ecutwfc=80,
  ecutrho=800,
  occupations='smearing',
  smearing='methfessel-paxton',
  degauss=0.005000,
  input_dft='PBESOL'
/


  diagonalization='cg',
  conv_thr=1d-07,
  mixing_mode='plain',
  mixing_beta=0.100,
/


  ion_dynamics = 'bfgs',
/

ATOMIC_SPECIES
  Ca 40.078000 Ca.pbe-spn-kjpaw_psl.1.0.0.UPF
  Al 26.981539 Al.pbesol-n-kjpaw_psl.1.0.0.UPF
  Si 28.085500 Si.pbesol-n-kjpaw_psl.1.0.0.UPF
  O 15.999400 O.pbesol-n-kjpaw_psl.1.0.0.UPF

ATOMIC_POSITIONS {angstrom}
Ca1.4807500.002.961500
Ca2.9615001.4807500.00
Ca0.002.9615001.480750
Al0.000.000.00
Al2.9615002.9615002.961500
Si0.002.9615004.442250
Si4.4422500.002.961500
Si2.9615004.4422500.00
O 0.4501485.3934841.791116
O 1.7911160.4501485.393484
O 5.3934841.7911160.450148
O 3.4910162.5113524.752616
O 2.5113524.7526163.491016
O 4.7526163.4910162.511352
O 5.4728520.5295164.131885
O 4.1318855.4728520.529516
O 0.5295164.1318855.472852
O 2.4319843.4116481.170385
O 3.4116481.1703852.431984
O 1.1703852.4319843.411648

K_POINTS {automatic}
  4 4 4 0 0 0

CELL_PARAMETERS {angstrom}
   5.92300   0.0   0.0
   0.0   5.92300   0.0
   0.0   0.0   5.92300


Thank you


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Re: [QE-users] From bands input error #1

[Michael Adventure Hopkins]

Thank you Paolo, I think that fits the bill for the issue. I am planning on
using WanT for Wannierization of the bands that are generated in QE. Is
there a proper way that you know of for disentangling the "bands.x"
nomenclature between the programs without breaking either?
In the meantime I will look into using "bands.x" of WanT.
Again thank you for your time.

Michael Hopkins
Portland State University

On Fri, May 3, 2019 at 12:26 AM Paolo Giannozzi 
wrote:

> Due to lack of imagination, there is a "bands.x" code in WanT and a
> "bands.x" code in QE (and of course, they are completely different). You
> are running the WanT version.  Is this what you want?
>
> Paolo
>
>
> On Thu, May 2, 2019 at 1:33 AM Michael Adventure Hopkins <
> hopm...@gmail.com> wrote:
>
>> Receiving the error:
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> *==
>> ==  = *** WanT
>> *** Wannier Transport Code=  =
>> (www.wannier-transport.org )
>> =  =  Ultra Soft Pseudopotential Implem.=
>> ==
>> ==
>> Program   v. 2.5.0  starts ...  Date  1May2019 at 16: 2:15
>> Serial run.  BUILT :Wed 05 Dec 2018 01:23:57 PM PST
>> HOST :x86_64-unknown-linux-gnu   ARCH :x86_64
>> CC :ccCPP :cppF90 :gfortran
>> F77 :gfortran DFLAGS :-D__GFORTRAN -D__STD_F95
>> -D__FFTW3  BLAS LIBS :
>> -L/vol/apps/hpc/src/q-e-qe-6.3/want/extlibs/blas/lib -lblasLAPACK LIBS
>> :-L/vol/apps/hpc/src/q-e-qe-6.3/want/extlibs/lapack/lib -llapack
>> FFT LIBS :-lfftw3  MASS LIBS :
>>  
>> %%
>> from bands_input : error # 1 Unable to read namelist
>> INPUT 
>> %%
>> stopping ...*
>>
>> On the forums I see that this is generally due to an old call to
>> , but I have checked that I am using  in my input file. Is
>> there another reason for this error?
>>
>> Thank you ~Mike H.
>> ___
>> 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
>
>
>
> --
> Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,
> Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
> Phone +39-0432-558216, fax +39-0432-558222
>
> ___
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[QE-users] Three-dimensional plot of a band structure

[Arena Konta]

Hi all,

Any advice how to create 3D plot of a band structure in QE? It means, for 
example, axis x == kx,  y = ky and z = E ?

Thank you in advance


-- 
with regards
 
Arena Konta
The Institute of Thermophysics in Novosibirsk Scientific Center

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Re: [QE-users] bands namelist error

[Fabrizio Cossu]

Oohps, that was a trivial mistake.
Thank you, Paolo, for pointing it out! It worked fine as it should be.

Fabrizio

On Fri, 3 May 2019 at 16:23, Paolo Giannozzi  wrote:

> "lsym" is a logical variable, so lsym=.true., not  lsym='true'
>
> Paolo
>
> On Fri, May 3, 2019 at 8:03 AM Fabrizio Cossu 
> wrote:
>
>>Dear QE Users,
>> I'm calculating the band structure of NbP, and I successfully run up to
>> the 'nscf'. However, with bands.x I get the following error message (see
>> also attachment):
>>
>> ***
>> [...]
>>  MPI processes distributed on 3 nodes
>>  R & G space division:  proc/nbgrp/npool/nimage =  84
>>
>>
>>  
>> %%
>>  Error in routine bands (64):
>>  reading bands namelist
>>
>>  
>> %%
>>
>>  stopping ...
>> [...]
>> ***
>> I searched in the past discussions, but I have none of the errors pointed
>> out therein.
>> What's the cause of the present error?
>>
>> Here are the commands I used to call the executables and relative input
>> files:
>> ***
>> module load QuantumESPRESSO/6.4-nsc1-intel-2018b-eb
>>
>>  mpprun -n 84 pw.x -nk 4 -inp scf.in > scf.out 2>&1
>>  mpprun -n 84 pw.x -nk 4 -inp nscf.in > nscf.out 2>&1
>>  mpprun -n 84 pw.x -nk 4 -inp em-prop.in > em-prop.out 2>&1
>>  mpprun -n 84 bands.x -nk 1 -inp bands.in > bands.out 2>&1
>> ***
>>
>>
>>Thank you in advance for any help.
>>
>>Kind regards,
>>Fabrizio
>>
>> --
>>
>> *Fabrizio Cossupostdoctoral fellow at APCTP (Asia Pacific Center for
>> Theoretical Physics)*,
>> Hogil Kim Memorial Building #501
>> POSTECH, 67 Cheongam-Ro, Nam-Gu,
>> Pohang-si, Gyeongsangbuk-do,
>> 790-784 (37673), Republic of Korea
>>
>>|
>>   .. .. .. |  ..   ===
>>   ,| || |  |  ||   http://www.apctp.org/?JrgId=16
>>   `^ |' `' `' |'   ===
>>  ||
>>
>> ___
>> 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
>
>
>
> --
> Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,
> Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
> Phone +39-0432-558216, fax +39-0432-558222
>
> ___
> Quantum Espresso is supported by MaX (www.max-centre.eu/quantum-espresso)
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> https://lists.quantum-espresso.org/mailman/listinfo/users
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[QE-users] restarting issues

[Mauricio Rincón Bonilla]

Dear all

I have run some relaxation jobs, setting up a 'max_seconds' time of 5 min
to end the jobs orderly. However, when I restart my simulations, they
doesn't go past the following point for the entire run:

 Checking if some PAW data can be deallocated...

Why is it stuck there? Does it mean that 6 minutes were not enough?

Cheers,
Mauricio


-- 
Mauricio Rincon Bonilla
Postdoc Fellow
*BCAM - *Basque Center for Applied Mathematics
Alameda de Mazarredo, 14
E-48009 Bilbao, Basque Country - Spain
Tel. +34 946 567 842
mrin...@bcamath.org | www.bcamath.org/mrincon

*(**matematika mugaz bestalde)*
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[QE-users] problem when run ph.x with assume_isolated='2D'

[jinlong.ma]

Dear all,


I want to calculated the phonon dispersion of 2D materials by adding 
[assume_isolated = '2D'] in scf.in. However the code stops at the second 
q-point in ph.x process. I have tried to calculate without  [assume_isolated = 
'2D'], the code works very well. Can you help to find where is my mistake? 
thanks!


The input files are:
--
scf.in:


 
calculation = 'scf'   
prefix  = 'InSe'
pseudo_dir  = '../pp'
outdir  = './'   
wf_collect  = .true.
 /
 
ibrav   = 4
celldm(1)   = 7.660990171749583
celldm(3)   = 4.933478001288765
nat = 4
ntyp= 2
ecutwfc = 48
occupations = 'smearing'
smearing= 'gaussian'
degauss = 0.02
assume_isolated = '2D'! for 2D system
 /
 
diagonalization = 'david'
mixing_beta = 0.7
conv_thr= 1.0d-10
 /
ATOMIC_SPECIES
 In 114.818 In.pbe-mt_fhi.UPF
 Se  78.963 Se.pbe-mt_fhi.UPF
ATOMIC_POSITIONS {crystal}
 In  0.7   0.3   0.069938180   
 In  0.7   0.3  -0.069938180   
 Se  0.3   0.7  -0.133696094   
 Se  0.3   0.7   0.133696094   
K_POINTS {automatic}
 16 16 1  0 0 0

--
ph.in:


phonon of InSe

  prefix   = 'InSe'
  fildyn   = 'InSe.dyn'
  epsil= .false.   
  ldisp= .true.
  fildvscf = 'dvscf'   
  nq1 = 16
  nq2 = 16
  nq3 = 1
  tr2_ph   =  1.0d-16
 /

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Re: [QE-users] From bands input error #1

[Paolo Giannozzi]

Due to lack of imagination, there is a "bands.x" code in WanT and a
"bands.x" code in QE (and of course, they are completely different). You
are running the WanT version.  Is this what you want?

Paolo


On Thu, May 2, 2019 at 1:33 AM Michael Adventure Hopkins 
wrote:

> Receiving the error:
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
> *==
> ==  = *** WanT
> *** Wannier Transport Code=  =
> (www.wannier-transport.org )
> =  =  Ultra Soft Pseudopotential Implem.=
> ==
> ==
> Program   v. 2.5.0  starts ...  Date  1May2019 at 16: 2:15
> Serial run.  BUILT :Wed 05 Dec 2018 01:23:57 PM PST
> HOST :x86_64-unknown-linux-gnu   ARCH :x86_64
> CC :ccCPP :cppF90 :gfortran
> F77 :gfortran DFLAGS :-D__GFORTRAN -D__STD_F95
> -D__FFTW3  BLAS LIBS :
> -L/vol/apps/hpc/src/q-e-qe-6.3/want/extlibs/blas/lib -lblasLAPACK LIBS
> :-L/vol/apps/hpc/src/q-e-qe-6.3/want/extlibs/lapack/lib -llapack
> FFT LIBS :-lfftw3  MASS LIBS :
>  
> %%
> from bands_input : error # 1 Unable to read namelist
> INPUT 
> %%
> stopping ...*
>
> On the forums I see that this is generally due to an old call to ,
> but I have checked that I am using  in my input file. Is there
> another reason for this error?
>
> Thank you ~Mike H.
> ___
> Quantum Espresso is supported by MaX (www.max-centre.eu/quantum-espresso)
> users mailing list users@lists.quantum-espresso.org
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-- 
Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222
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Re: [QE-users] 2D band surface plot

[Giovanni Cantele]

you should provide the input file of the nscf calculation to figure out if 
something strange is happening
Giovanni

> On 30 Apr 2019, at 08:50, elch...@auth.gr wrote:
> 
> 
> Quoting Oleksandr Motornyi :
> 
>> Hello Eleni
>> 
>> Could you please provide an input as well as the strange outputs? It is hard 
>> to give any advice or example without knowing what are you dealing with 
>> exactly.
>> 
>> Regards,
>> 
>> Oleksandr
>> 
>> Oleksandr Motornyi
>> PhD
>> 
>> Laboratoire des Solides Irradies
>> Ecole Polytechnique (Palaiseau, France)
>> 
>> On 29/04/19 18:12, elch...@auth.gr wrote:
>>> Hello everyone,
>>> 
>>> Do you have an example with a grid used for 2D surface plot in bands.x? I 
>>> am getting some really strange output.
>>> 
>>> Regards,
>>> 
>>> Eleni
>>> 
>>> 
>> 
>> ___
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>> users mailing list users@lists.quantum-espresso.org
>> https://lists.quantum-espresso.org/mailman/listinfo/users
> 
> 
> 
> -- 
> Dr. Eleni Chatzikyriakou
> Computational Physics lab
> Aristotle University of Thessaloniki
> elch...@auth.gr - tel:+30 2310 998109
> ___
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-- 

Giovanni Cantele, PhD

CNR-SPIN
c/o Dipartimento di Fisica
Universita' di Napoli "Federico II"
Complesso Universitario M. S. Angelo - Ed. 6
Via Cintia, I-80126, Napoli, Italy

e-mail: giovanni.cant...@spin.cnr.it
gcant...@gmail.com
Phone: +39 081 676910
Skype contact: giocan74
Web page: https://sites.google.com/view/giovanni-cantele

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Re: [QE-users] bands namelist error

[Paolo Giannozzi]

"lsym" is a logical variable, so lsym=.true., not  lsym='true'

Paolo

On Fri, May 3, 2019 at 8:03 AM Fabrizio Cossu 
wrote:

>Dear QE Users,
> I'm calculating the band structure of NbP, and I successfully run up to
> the 'nscf'. However, with bands.x I get the following error message (see
> also attachment):
>
> ***
> [...]
>  MPI processes distributed on 3 nodes
>  R & G space division:  proc/nbgrp/npool/nimage =  84
>
>
>  
> %%
>  Error in routine bands (64):
>  reading bands namelist
>
>  
> %%
>
>  stopping ...
> [...]
> ***
> I searched in the past discussions, but I have none of the errors pointed
> out therein.
> What's the cause of the present error?
>
> Here are the commands I used to call the executables and relative input
> files:
> ***
> module load QuantumESPRESSO/6.4-nsc1-intel-2018b-eb
>
>  mpprun -n 84 pw.x -nk 4 -inp scf.in > scf.out 2>&1
>  mpprun -n 84 pw.x -nk 4 -inp nscf.in > nscf.out 2>&1
>  mpprun -n 84 pw.x -nk 4 -inp em-prop.in > em-prop.out 2>&1
>  mpprun -n 84 bands.x -nk 1 -inp bands.in > bands.out 2>&1
> ***
>
>
>Thank you in advance for any help.
>
>Kind regards,
>Fabrizio
>
> --
>
> *Fabrizio Cossupostdoctoral fellow at APCTP (Asia Pacific Center for
> Theoretical Physics)*,
> Hogil Kim Memorial Building #501
> POSTECH, 67 Cheongam-Ro, Nam-Gu,
> Pohang-si, Gyeongsangbuk-do,
> 790-784 (37673), Republic of Korea
>
>|
>   .. .. .. |  ..   ===
>   ,| || |  |  ||   http://www.apctp.org/?JrgId=16
>   `^ |' `' `' |'   ===
>  ||
>
> ___
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-- 
Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222
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Re: [QE-users] 2D band surface plot

[elchatz]

Dear Oleksandr Motornyi,

If you mean for the energy, I am around the fermi level, but not  
exactly there.


If you mean for ky, it is the result exactly as I got it from the .dat file.

Regards,

Eleni




Quoting Oleksandr Motornyi :

What does look strange to me is scale on your plot. SCF in/out files  
would actually be more helpful here as so far we have little idea  
about your system.


Oleksandr


On 30/04/19 08:50, elch...@auth.gr wrote:


Quoting Oleksandr Motornyi :


Hello Eleni

Could you please provide an input as well as the strange outputs?  
It is hard to give any advice or example without knowing what are  
you dealing with exactly.


Regards,

Oleksandr

Oleksandr Motornyi
PhD

Laboratoire des Solides Irradies
Ecole Polytechnique (Palaiseau, France)

On 29/04/19 18:12, elch...@auth.gr wrote:

Hello everyone,

Do you have an example with a grid used for 2D surface plot in  
bands.x? I am getting some really strange output.


Regards,

Eleni




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--
Oleksandr Motornyi
PhD candidate

Laboratoire de Solides Irradies
Ecole Polytechnique (Palaiseau, France)




--
Dr. Eleni Chatzikyriakou
Computational Physics lab
Aristotle University of Thessaloniki
elch...@auth.gr - tel:+30 2310 998109

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[QE-users] bands namelist error

[Fabrizio Cossu]

   Dear QE Users,
I'm calculating the band structure of NbP, and I successfully run up to the
'nscf'. However, with bands.x I get the following error message (see also
attachment):

***
[...]
 MPI processes distributed on 3 nodes
 R & G space division:  proc/nbgrp/npool/nimage =  84

 %%
 Error in routine bands (64):
 reading bands namelist
 %%

 stopping ...
[...]
***
I searched in the past discussions, but I have none of the errors pointed
out therein.
What's the cause of the present error?

Here are the commands I used to call the executables and relative input
files:
***
module load QuantumESPRESSO/6.4-nsc1-intel-2018b-eb

 mpprun -n 84 pw.x -nk 4 -inp scf.in > scf.out 2>&1
 mpprun -n 84 pw.x -nk 4 -inp nscf.in > nscf.out 2>&1
 mpprun -n 84 pw.x -nk 4 -inp em-prop.in > em-prop.out 2>&1
 mpprun -n 84 bands.x -nk 1 -inp bands.in > bands.out 2>&1
***


   Thank you in advance for any help.

   Kind regards,
   Fabrizio

-- 

*Fabrizio Cossupostdoctoral fellow at APCTP (Asia Pacific Center for
Theoretical Physics)*,
Hogil Kim Memorial Building #501
POSTECH, 67 Cheongam-Ro, Nam-Gu,
Pohang-si, Gyeongsangbuk-do,
790-784 (37673), Republic of Korea

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