[QE-users] How to calculate the electron-phonon coupling as a function of phonon frequency?

[Zhibin Gao]

Dear all,

I am a new user of pwscf and finished the example 03 about the
electron-phonon coupling
of metal aluminum (version 6.3). But I was trapped by a small question. How
to calculate
the electron-phonon coupling as a function of phonon frequency? I did not
find it in the
output files. Could someone give me a suggestion? Thanks for your kind help!

Best wishes,
Zhibin
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Re: [QE-users] Question regarding mixing of PBE and PBESOL PP

[Paolo Giannozzi]

On Sat, May 4, 2019 at 6:27 AM Yeon, Jejoon  wrote:

For Ca, PBE is only available option from QE PP webpage, there is no PBESOL
> for Ca yet.
>

it can be easily generated from the PSLibrary. I have one on my computer
that you can find here:

http://www.fisica.uniud.it/~giannozz/Public/Ca.pbesol-spn-kjpaw_psl.1.0.0.UPF.xz
(uncompress with "xz -d")

Paolo
-- 
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] Three-dimensional plot of a band structure

[Lorenzo Paulatto]

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 ?


Dear Arena,
there are two problems here:
1. compute the bands in a list of k-points that form a 2D surface
2. plot these points

1. Can be done by hand, by generating the list of k-points with mathlab 
or similar software, or it can be done marginally easier by using the 
"tpiba_c" option in the KPOINTS card. Check the INPUT_PW.html manual 
that you can find in PW/Doc or online.
Of course, this list of k-points must be computed with pw.x as a non 
self-consistent BANDS calculation, starting from a well converged total 
energy calculation.


2. You can extract the list of points and energies using bands.x, be 
sure to use the plot_2d=.true. option to get a file suitable for the 
kind of plot you need. Then you should be able to plot it with gnuplot

  plot "file.dat" using 1:2:3 with image
or any other plotting software

hth


--
Lorenzo Paulatto - Paris
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Re: [QE-users] Question regarding mixing of PBE and PBESOL PP

[Holzwarth, Natalie]

We are slowly updating our ATOMPAW webpage http://pwpaw.wfu.edu to include
LDA and PBESOL PAW datasets that are more reliable when used with Quantum
Espresso.I just added Ca and could add more as needed.   Of course,
although similar datasets have been used in the past,   the new ones always
need to be tested.

N. A. W. Holzwarth   email:
nata...@wfu.edu
Department of Physics  web:
http://www.wfu.edu/~natalie
Wake Forest University phone:
1-336-758-5510
Winston-Salem, NC 27109 USA office: Rm. 300 Olin
Physical Lab


On Sat, May 4, 2019 at 12:27 AM Yeon, Jejoon  wrote:

> 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.
>
>
> &CONTROL
>   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
> /
>
> &SYSTEM
>   ibrav=0,
>   nat=20,
>   ntyp=4,
>   ecutwfc=80,
>   ecutrho=800,
>   occupations='smearing',
>   smearing='methfessel-paxton',
>   degauss=0.005000,
>   input_dft='PBESOL'
> /
>
> &ELECTRONS
>   diagonalization='cg',
>   conv_thr=1d-07,
>   mixing_mode='plain',
>   mixing_beta=0.100,
> /
>
> &IONS
>   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
>
>
>
> ___
> 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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users mailing list us

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

[Yeon, Jejoon]

Thank you so much for answers and link for PPs!!


From: users  on behalf of Holzwarth, 
Natalie 
Sent: Saturday, May 4, 2019 3:00:31 PM
To: Quantum Espresso users Forum
Subject: Re: [QE-users] Question regarding mixing of PBE and PBESOL PP

We are slowly updating our ATOMPAW webpage http://pwpaw.wfu.edu to include LDA 
and PBESOL PAW datasets that are more reliable when used with Quantum Espresso. 
   I just added Ca and could add more as needed.   Of course, although 
similar datasets have been used in the past,   the new ones always need to be 
tested.

N. A. W. Holzwarth   email: 
nata...@wfu.edu
Department of Physics  web: 
http://www.wfu.edu/~natalie
Wake Forest University phone: 1-336-758-5510
Winston-Salem, NC 27109 USA office: Rm. 300 Olin Physical 
Lab


On Sat, May 4, 2019 at 12:27 AM Yeon, Jejoon 
mailto:jy...@udel.edu>> wrote:

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.


&CONTROL
  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
/

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

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

&IONS
  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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(www.max-centre.eu/quantum-espresso)
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Re: [QE-users] Three-dimensional plot of a band structure

[Reza Shojaei]

Dear Arena,

If you have already have the outputs you can easily plot band structure
using "gnuplot".

Reza

On Sat, May 4, 2019 at 12:48 PM Lorenzo Paulatto  wrote:

> > 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 ?
>
> Dear Arena,
> there are two problems here:
> 1. compute the bands in a list of k-points that form a 2D surface
> 2. plot these points
>
> 1. Can be done by hand, by generating the list of k-points with mathlab
> or similar software, or it can be done marginally easier by using the
> "tpiba_c" option in the KPOINTS card. Check the INPUT_PW.html manual
> that you can find in PW/Doc or online.
> Of course, this list of k-points must be computed with pw.x as a non
> self-consistent BANDS calculation, starting from a well converged total
> energy calculation.
>
> 2. You can extract the list of points and energies using bands.x, be
> sure to use the plot_2d=.true. option to get a file suitable for the
> kind of plot you need. Then you should be able to plot it with gnuplot
>plot "file.dat" using 1:2:3 with image
> or any other plotting software
>
> hth
>
>
> --
> 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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