[QE-users] Convergence issue

[Mayuri Bora]

Dear QE users,

I am experiencing an issue while incorporating SOC in the system. I have
tried with relax, using different pseudopotentials (PAW, USPP, ONCV),
varying convergence threshold, increasing electron maxstep, varying
K-points etc in the input file. But still the convergence is not achieved
even after increasing the electron maxstep. I will be thankful for the
help.
The input file is as follows:
&CONTROL
  calculation='scf',
  outdir='/home/pritamd_tezu/mayuri/uspp',
  prefix='bilayer',
  pseudo_dir='/home/pritamd_tezu/mayuri/uspp',
  etot_conv_thr= 2.200d-08,
  forc_conv_thr= 1.00d-04,
  verbosity='high',
  tstress=.true.,
  tprnfor=.true.,
/
&SYSTEM
  ibrav=0,
  nat=22,
  ntyp=3,
  ecutwfc=80.0d0,
  ecutrho=900.0d0,
  input_dft='PBE',
  vdw_corr='DFT-D',
  lspinorb= .true.,
  noncolin= .true.,
  starting_magnetization(1)= 0.1,
  starting_magnetization(2)= 0.1,
  starting_magnetization(3)= 0.35714285714,
  ts_vdw_econv_thr= 1.00d-06,
  occupations='smearing',
  smearing='gaussian',
  degauss=0.0073498618000d0,
/
&ELECTRONS
  diagonalization= 'david',
  diago_thr_init=1.d-09,
  conv_thr=4.4000d-12,
  electron_maxstep=900,
  mixing_beta=0.700d0,
/
ATOMIC_SPECIES
  Br 79.904000d0 Br.rel-pbe-n-rrkjus_psl.1.0.0.UPF
  C  13.010700d0 C.rel-pbe-n-rrkjus_psl.1.0.0.UPF
  Cr 51.996100d0 Cr.rel-pbe-spn-rrkjus_psl.1.0.0.UPF

ATOMIC_POSITIONS {crystal}
C0.2370338590   0.0466579790   0.5819172260
C0.4750810860   0.0942675400   0.5821171400
C0.9512726660   0.1895037740   0.5817571880
C0.1894166470   0.2371217310   0.5817013980
C0.6656258110   0.3323957920   0.5821242930
C0.9036366340   0.3800025580   0.5819604400
C0.3798963730   0.4752872590   0.5818429590
C0.6179666520   0.5228227970   0.5820887090
C0.0941461250   0.6180914640   0.5820779200
C0.3322389720   0.6657285090   0.5819960240
C0.8084381220   0.7609310750   0.5821903940
C0.0464906100   0.8085246090   0.5820961590
C0.5227361320   0.9037968520   0.5820508600
C0.7607774140   0.9513681530   0.5819959040
Br   0.5214065310   0.1659515950   0.5063270930
Br   0.1714701210   0.5149154070   0.5061650870
Br   0.8211319450   0.8163818720   0.5062854290
Br   0.8191159960   0.169990   0.4423690140
Br   0.5236960050   0.5189570190   0.4423690140
Br   0.1714060010   0.8143770100   0.4423690140
Cr   0.8380730150   0.50   0.4741629960
Cr   0.5047389860   0.840290   0.4741629960

K_POINTS {automatic}
3 3 1 0 0 0
CELL_PARAMETERS {angstrom}
  6.3488101959   0.00   0.00
 -3.1744050980   5.4982309135   0.00
  0.00   0.00  45.2111015320

The output is-
iteration #897 ecut=80.00 Ry beta= 0.70
 Davidson diagonalization with overlap
 c_bands:  2 eigenvalues not converged
 c_bands:  2 eigenvalues not converged
 c_bands:  2 eigenvalues not converged
 c_bands:  1 eigenvalues not converged
 c_bands:  1 eigenvalues not converged
 c_bands:  2 eigenvalues not converged
 ethr =  4.97E-09,  avg # of iterations = 17.9

 negative rho (up, down):  4.580E-01 6.033E-01

 total cpu time spent up to now is29196.4 secs

 total energy  =-703.53181584 Ry
 Harris-Foulkes estimate   =-703.14239084 Ry
 estimated scf accuracy<   4.25990051 Ry

 total magnetization   = 0.44 0.63 0.59 Bohr mag/cell
 absolute magnetization=   244.14 Bohr mag/cell

 iteration #898 ecut=80.00 Ry beta= 0.70
 Davidson diagonalization with overlap
 ethr =  4.97E-09,  avg # of iterations = 14.0

 negative rho (up, down):  5.032E-01 5.390E-01

 total cpu time spent up to now is29240.1 secs

 total energy  =-703.06735008 Ry
 Harris-Foulkes estimate   =-703.82964135 Ry
 estimated scf accuracy<   6.87305235 Ry

 total magnetization   = 0.47 0.58 0.74 Bohr mag/cell
 absolute magnetization=   243.34 Bohr mag/cell

 iteration #899 ecut=80.00 Ry beta= 0.70
 Davidson diagonalization with overlap
 ethr =  4.97E-09,  avg # of iterations = 10.9

 negative rho (up, down):  4.948E-01 6.983E-01

 total cpu time spent up to now is29280.7 secs

 total energy  =-702.85218585 Ry
 Harris-Foulkes estimate   =-703.21192343 Ry
 estimated scf accuracy<   4.49406597 Ry

 total magnetization   = 0.29 0.73 0.98 Bohr mag/cell
 absolute magnetization=   243.35 Bohr mag/cell

 iteration #900 ecut= 

Re: [QE-users] Convergence issue

[Jibiao Li]

Hi Mayuri,


Please try to more extra bands by using nbnd, it usually helps convergence.


Jibiao Li


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Re: [QE-users] ph.x Raman calculations

[Paolo Giannozzi]

On Mon, Mar 29, 2021 at 6:54 PM Jessica Johnson 
wrote:

I understood that anharmonicity is taken into account with the inclusion of
> second and third order energy derivatives.
>

anharmonicity "may" be taken into account with the inclusion  of second and
third order energy derivatives, but in order to reach such goal, additional
calculations - and not simple ones - are needed

Paolo
-- 
Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,
Univ. Udine, via delle Scienze 206, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222
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[QE-users] I have failed to reproduce phonon dispersion of graphene

[Evgenii]

Dear Quantum Espresso experts,  I am having trouble calculating the phonon bands of graphene. First, I took the cif-file of the already relaxed graphite cell from the Materials Project site https://next-gen.materialsproject.org/ and made graphene cell from it by hand.Then I relaxed the cell obtained with vc-relax and 12x12x1 k-point set.I used the same parameters to perform a scf calculation: &CONTROLcalculation='scf'title='graphene'prefix='graphene'verbosity='high'restart_mode='from_scratch'nstep=1000iprint=1tstress=.true.tprnfor=.true.disk_io='default'pseudo_dir = '/home/mxm2/Desktop/Graphene',outdir='/home/mxm2/Desktop/Graphene/temp'/&SYSTEMibrav = 0,celldm(1)=1.889726,nat = 2,ntyp = 1,ecutwfc = 60.0 ,ecutrho = 480.0 ,/&ELECTRONSelectron_maxstep = 1000,conv_thr = 1.0d-12 ,mixing_mode = 'plain' ,mixing_beta = 0.7d0 ,/ATOMIC_SPECIESC 12.011 C.pz-rrkjus.UPFATOMIC_POSITIONS (crystal)C        0.0   0.0   0.000861580C        0.33000   0.67000   0.000838420CELL_PARAMETERS (alat)   2.438515837  -0.0   0.0  -1.219257919   2.111816662   0.0  -0.0  -0.0  19.995916314 K_POINTS automatic12 12 1 0 0 0 Then, I run ph.in calculation: &inputphrecover=.true.tr2_ph=1.0d-14,  prefix='graphene',ldisp=.true. nq1=12, nq2=12, nq3=1,  amass(1)=12.011,   outdir='/home/mxm2/Desktop/Graphene/temp', fildyn='graphene.dyn',    / My q2r: &inputfildyn='graphene.dyn',zasr='simple',flfrc='graphene.12x12x1.fc'/ Matdyn input: &inputasr='simple',amass(1)=12.011,flfrc='graphene.12x12x1.fc', flfrq='graphene.disp.freq' q_in_band_form=.true.,/4 ! number of q-points0.000 0.000 0.000 10 ! gamma point0.500 0.000 0.000 10 ! M0.333 0.333 0.000 10 ! K0.000 0.000 0.000  1 ! gamma point Plotband: graphene.disp.freq0 1600graphene.disp.freq.datgraphene.disp.freq.ps0100 0 Why the phonon dispersion does not match the pictures from the papers and for calculations with e.g. 18x18x1 k-point and nq-point sets the output file of graphene.dyn1 look like: Dielectric Tensor:         166.332153320312          0.        166.332275390625          0.          0.          0.          1.116060253916      Effective Charges E-U: Z_{alpha}{s,beta}      atom #    1  -7471.575740195811         -0.002632206306          0.         -0.002632205375-7471.579664016142            0.          0.          0.         -0.003734609171          Also, what is the best way to set the lattice parameters, via Ibrav or CELL_PARAMETERS?Any help is appreciated. Best regards,Evgeniy Sysoev.___
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Re: [QE-users] I have failed to reproduce phonon dispersion of graphene

[Vahid Askarpour]

The coordinates of the high-symmetry points in matdyn.in should be in cartesian 
not crystal because you are specifying q_in_band_form=.true.

Cheers,
Vahid

Vahid Askarpour
Department of physics and atmospheric science
Dalhousie University
Halifax, NS
CANADA

On Mar 30, 2021, at 11:19 AM, Evgenii 
mailto:eisyso...@stud.eltech.ru>> wrote:

CAUTION: The Sender of this email is not from within Dalhousie.
Dear Quantum Espresso experts,

I am having trouble calculating the phonon bands of graphene.

First, I took the cif-file of the already relaxed graphite cell from the 
Materials Project site https://next-gen.materialsproject.org/ and made graphene 
cell from it by hand.
Then I relaxed the cell obtained with vc-relax and 12x12x1 k-point set.
I used the same parameters to perform a scf calculation:

&CONTROL
calculation='scf'
title='graphene'
prefix='graphene'
verbosity='high'
restart_mode='from_scratch'
nstep=1000
iprint=1
tstress=.true.
tprnfor=.true.
disk_io='default'
pseudo_dir = '/home/mxm2/Desktop/Graphene',
outdir='/home/mxm2/Desktop/Graphene/temp'
/
&SYSTEM
ibrav = 0,
celldm(1)=1.889726,
nat = 2,
ntyp = 1,
ecutwfc = 60.0 ,
ecutrho = 480.0 ,
/
&ELECTRONS
electron_maxstep = 1000,
conv_thr = 1.0d-12 ,
mixing_mode = 'plain' ,
mixing_beta = 0.7d0 ,
/
ATOMIC_SPECIES
C 12.011 C.pz-rrkjus.UPF
ATOMIC_POSITIONS (crystal)
C0.0   0.0   0.000861580
C0.33000   0.67000   0.000838420
CELL_PARAMETERS (alat)
   2.438515837  -0.0   0.0
  -1.219257919   2.111816662   0.0
  -0.0  -0.0  19.995916314

K_POINTS automatic
12 12 1 0 0 0

Then, I run ph.in calculation:

&inputph
recover=.true.
tr2_ph=1.0d-14,
prefix='graphene',
ldisp=.true.
nq1=12,
nq2=12,
nq3=1,
amass(1)=12.011,
outdir='/home/mxm2/Desktop/Graphene/temp',
fildyn='graphene.dyn',
/

My q2r:

&input
fildyn='graphene.dyn',
zasr='simple',
flfrc='graphene.12x12x1.fc'
/

Matdyn input:

&input
asr='simple',
amass(1)=12.011,
flfrc='graphene.12x12x1.fc',
flfrq='graphene.disp.freq'
q_in_band_form=.true.,
/
4 ! number of q-points
0.000 0.000 0.000 10 ! gamma point
0.500 0.000 0.000 10 ! M
0.333 0.333 0.000 10 ! K
0.000 0.000 0.000  1 ! gamma point

Plotband:

graphene.disp.freq
0 1600
graphene.disp.freq.dat
graphene.disp.freq.ps
0
100 0

Why the phonon dispersion does not match the pictures from the papers and for 
calculations with e.g. 18x18x1 k-point and nq-point sets the output file of 
graphene.dyn1 look like:

Dielectric Tensor:

166.332153320312  0.
166.332275390625  0.
  0.  0.  1.116060253916

 Effective Charges E-U: Z_{alpha}{s,beta}

 atom #1
  -7471.575740195811 -0.002632206306  0.
 -0.002632205375-7471.5796640161420.
  0.  0. -0.003734609171

Also, what is the best way to set the lattice parameters, via Ibrav or 
CELL_PARAMETERS?
Any help is appreciated.

Best regards,
Evgeniy Sysoev.
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Re: [QE-users] I have failed to reproduce phonon dispersion of graphene

[Evgenii]

Dear Vahid, If we use the default values of the q_in_band_form variables, then how do we find intermediate points between the points of high symmetry, as for example on this site https://www.afs.enea.it/buonocor/graphane-with-phonon.html ? Are intermediate points always needed, we noticed that in some examples they are missing. Thanks for the help. Evgeniy Sysoev 30.03.2021, 17:28, "Vahid Askarpour" :
The coordinates of the high-symmetry points in matdyn.in should be in cartesian not crystal because you are specifying q_in_band_form=.true.


Cheers,
Vahid


Vahid Askarpour
Department of physics and atmospheric science
Dalhousie University
Halifax, NS
CANADA


On Mar 30, 2021, at 11:19 AM, Evgenii  wrote:







CAUTION: The Sender of this email is not from within Dalhousie.







Dear Quantum Espresso experts, 
 
I am having trouble calculating the phonon bands of graphene.
 
First, I took the cif-file of the already relaxed graphite cell from the Materials Project site
https://next-gen.materialsproject.org/ and made graphene cell from it by hand.
Then I relaxed the cell obtained with vc-relax and 12x12x1 k-point set.
I used the same parameters to perform a scf calculation:
 
&CONTROL
calculation='scf'
title='graphene'
prefix='graphene'
verbosity='high'
restart_mode='from_scratch'
nstep=1000
iprint=1
tstress=.true.
tprnfor=.true.
disk_io='default'
pseudo_dir = '/home/mxm2/Desktop/Graphene',
outdir='/home/mxm2/Desktop/Graphene/temp'
/
&SYSTEM
ibrav = 0,
celldm(1)=1.889726,
nat = 2,
ntyp = 1,
ecutwfc = 60.0 ,
ecutrho = 480.0 ,
/
&ELECTRONS
electron_maxstep = 1000,
conv_thr = 1.0d-12 ,
mixing_mode = 'plain' ,
mixing_beta = 0.7d0 ,
/
ATOMIC_SPECIES
C 12.011 C.pz-rrkjus.UPF
ATOMIC_POSITIONS (crystal)
C        0.0   0.0   0.000861580
C        0.33000   0.67000   0.000838420
CELL_PARAMETERS (alat)
   2.438515837  -0.0   0.0
  -1.219257919   2.111816662   0.0
  -0.0  -0.0  19.995916314
 
K_POINTS automatic
12 12 1 0 0 0
 
Then, I run ph.in calculation:
 
&inputph
recover=.true.
tr2_ph=1.0d-14,  
prefix='graphene',
ldisp=.true. 
nq1=12, 
nq2=12, 
nq3=1,  
amass(1)=12.011,   
outdir='/home/mxm2/Desktop/Graphene/temp', 
fildyn='graphene.dyn',    
/
 
My q2r:
 
&input
fildyn='graphene.dyn',
zasr='simple',
flfrc='graphene.12x12x1.fc'
/
 
Matdyn input:
 
&input
asr='simple',
amass(1)=12.011,
flfrc='graphene.12x12x1.fc', 
flfrq='graphene.disp.freq' 
q_in_band_form=.true.,
/
4 ! number of q-points
0.000 0.000 0.000 10 ! gamma point
0.500 0.000 0.000 10 ! M
0.333 0.333 0.000 10 ! K
0.000 0.000 0.000  1 ! gamma point
 
Plotband:
 
graphene.disp.freq
0 1600
graphene.disp.freq.dat
graphene.disp.freq.ps
0
100 0
 
Why the phonon dispersion does not match the pictures from the papers and for calculations with e.g. 18x18x1 k-point and nq-point sets the output file of graphene.dyn1 look like:
 
Dielectric Tensor:
 
        166.332153320312          0.
        166.332275390625          0.
          0.          0.          1.116060253916
 
     Effective Charges E-U: Z_{alpha}{s,beta}
 
     atom #    1
  -7471.575740195811         -0.002632206306          0.
         -0.002632205375-7471.579664016142            0.
          0.          0.         -0.003734609171
          

Also, what is the best way to set the lattice parameters, via Ibrav or CELL_PARAMETERS?

Any help is appreciated.
 
Best regards,
Evgeniy Sysoev.




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Re: [QE-users] I have failed to reproduce phonon dispersion of graphene

[Paolo Giannozzi]

On Tue, Mar 30, 2021 at 4:20 PM Evgenii  wrote:


>  Dielectric Tensor:
>
> 166.332153320312  0.
> 166.332275390625  0.
>   0.  0.  1.116060253916
>

This is the expected behavior for a zero-gap crystal: the dielectric
constant diverges.


>
> Also, what is the best way to set the lattice parameters, via Ibrav or
> CELL_PARAMETERS?
>

they are equivalent[*], as long as you provide correct data; but, if you
specify the lattice parameters and atomic positions with the proper
symmetry you are less likely to run into trouble with symmetry in poorly
defined crystal structures.

Paolo

[*] but  allow me to declare that the setting celldm(1)=1.889726 to convert
from A to a.u. is abominable
-- 
Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,
Univ. Udine, via delle Scienze 206, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222
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Re: [QE-users] I have failed to reproduce phonon dispersion of graphene

[Vahid Askarpour]

Dear Evgeniy,

I use the following  for my graphene dispersion. Please note that the actual 
coordinates depend on the PSP.

4
0.0 0.0 0.0 150 ! G
0.000  -0.577588 0.0 150 ! M
-0.3334706  -0.577588 0.0 150 ! K
0.0 0.0 0.0 1

So the matdyn.x code will automatically set 150 points between the first 2 
high-symmetry points and so on.

Cheers,
Vahid

On Mar 30, 2021, at 11:58 AM, Evgenii 
mailto:eisyso...@stud.eltech.ru>> wrote:

CAUTION: The Sender of this email is not from within Dalhousie.
Dear Vahid,

If we use the default values of the q_in_band_form variables, then how do we 
find intermediate points between the points of high symmetry, as for example on 
this site https://www.afs.enea.it/buonocor/graphane-with-phonon.html ? Are 
intermediate points always needed, we noticed that in some examples they are 
missing.

Thanks for the help.

Evgeniy Sysoev



30.03.2021, 17:28, "Vahid Askarpour" mailto:vh261...@dal.ca>>:
The coordinates of the high-symmetry points in matdyn.in should be in cartesian 
not crystal because you are specifying q_in_band_form=.true.

Cheers,
Vahid

Vahid Askarpour
Department of physics and atmospheric science
Dalhousie University
Halifax, NS
CANADA

On Mar 30, 2021, at 11:19 AM, Evgenii 
mailto:eisyso...@stud.eltech.ru>> wrote:

CAUTION: The Sender of this email is not from within Dalhousie.
Dear Quantum Espresso experts,

I am having trouble calculating the phonon bands of graphene.

First, I took the cif-file of the already relaxed graphite cell from the 
Materials Project site https://next-gen.materialsproject.org/ and made graphene 
cell from it by hand.
Then I relaxed the cell obtained with vc-relax and 12x12x1 k-point set.
I used the same parameters to perform a scf calculation:

&CONTROL
calculation='scf'
title='graphene'
prefix='graphene'
verbosity='high'
restart_mode='from_scratch'
nstep=1000
iprint=1
tstress=.true.
tprnfor=.true.
disk_io='default'
pseudo_dir = '/home/mxm2/Desktop/Graphene',
outdir='/home/mxm2/Desktop/Graphene/temp'
/
&SYSTEM
ibrav = 0,
celldm(1)=1.889726,
nat = 2,
ntyp = 1,
ecutwfc = 60.0 ,
ecutrho = 480.0 ,
/
&ELECTRONS
electron_maxstep = 1000,
conv_thr = 1.0d-12 ,
mixing_mode = 'plain' ,
mixing_beta = 0.7d0 ,
/
ATOMIC_SPECIES
C 12.011 C.pz-rrkjus.UPF
ATOMIC_POSITIONS (crystal)
C0.0   0.0   0.000861580
C0.33000   0.67000   0.000838420
CELL_PARAMETERS (alat)
   2.438515837  -0.0   0.0
  -1.219257919   2.111816662   0.0
  -0.0  -0.0  19.995916314

K_POINTS automatic
12 12 1 0 0 0

Then, I run ph.in calculation:

&inputph
recover=.true.
tr2_ph=1.0d-14,
prefix='graphene',
ldisp=.true.
nq1=12,
nq2=12,
nq3=1,
amass(1)=12.011,
outdir='/home/mxm2/Desktop/Graphene/temp',
fildyn='graphene.dyn',
/

My q2r:

&input
fildyn='graphene.dyn',
zasr='simple',
flfrc='graphene.12x12x1.fc'
/

Matdyn input:

&input
asr='simple',
amass(1)=12.011,
flfrc='graphene.12x12x1.fc',
flfrq='graphene.disp.freq'
q_in_band_form=.true.,
/
4 ! number of q-points
0.000 0.000 0.000 10 ! gamma point
0.500 0.000 0.000 10 ! M
0.333 0.333 0.000 10 ! K
0.000 0.000 0.000  1 ! gamma point

Plotband:

graphene.disp.freq
0 1600
graphene.disp.freq.dat
graphene.disp.freq.ps
0
100 0

Why the phonon dispersion does not match the pictures from the papers and for 
calculations with e.g. 18x18x1 k-point and nq-point sets the output file of 
graphene.dyn1 look like:

Dielectric Tensor:

166.332153320312  0.
166.332275390625  0.
  0.  0.  1.116060253916

 Effective Charges E-U: Z_{alpha}{s,beta}

 atom #1
  -7471.575740195811 -0.002632206306  0.
 -0.002632205375-7471.5796640161420.
  0.  0. -0.003734609171

Also, what is the best way to set the lattice parameters, via Ibrav or 
CELL_PARAMETERS?
Any help is appreciated.

Best regards,
Evgeniy Sysoev.
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,

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Re: [QE-users] I have failed to reproduce phonon dispersion of graphene

[Lorenzo Paulatto]

You have specified the q-points in crystal fractionary units, hence you have to 
specify q_in_cryst_coord=.true.
This can be safely used in conjunction with q_in_band_form, which is a 
completely unrelated option.

Also:
You way of specifying the cell parameters is discouraged and may cause problems 
with symmetry detection, but it should work.

Using a k-points grid that includes the K point can be a source of troubles, I 
would recommend using 16x16x1 or even 32x32x1 for better results.

hth
--
Lorenzo Paulatto - Paris
On Mar 30 2021, at 4:19 pm, Evgenii  wrote:
> Dear Quantum Espresso experts,
>
> I am having trouble calculating the phonon bands of graphene.
>
> First, I took the cif-file of the already relaxed graphite cell from the 
> Materials Project site https://next-gen.materialsproject.org/ and made 
> graphene cell from it by hand.
> Then I relaxed the cell obtained with vc-relax and 12x12x1 k-point set.
> I used the same parameters to perform a scf calculation:
>
> &CONTROL
> calculation='scf'
> title='graphene'
> prefix='graphene'
> verbosity='high'
> restart_mode='from_scratch'
> nstep=1000
> iprint=1
> tstress=.true.
> tprnfor=.true.
> disk_io='default'
> pseudo_dir = '/home/mxm2/Desktop/Graphene',
> outdir='/home/mxm2/Desktop/Graphene/temp'
> /
> &SYSTEM
> ibrav = 0,
> celldm(1)=1.889726,
> nat = 2,
> ntyp = 1,
> ecutwfc = 60.0 ,
> ecutrho = 480.0 ,
> /
> &ELECTRONS
> electron_maxstep = 1000,
> conv_thr = 1.0d-12 ,
> mixing_mode = 'plain' ,
> mixing_beta = 0.7d0 ,
> /
> ATOMIC_SPECIES
> C 12.011 C.pz-rrkjus.UPF
> ATOMIC_POSITIONS (crystal)
> C 0.0 0.0 0.000861580
> C 0.33000 0.67000 0.000838420
> CELL_PARAMETERS (alat)
> 2.438515837 -0.0 0.0
> -1.219257919 2.111816662 0.0
> -0.0 -0.0 19.995916314
>
> K_POINTS automatic
> 12 12 1 0 0 0
>
> Then, I run ph.in calculation:
>
> &inputph
> recover=.true.
> tr2_ph=1.0d-14,
> prefix='graphene',
> ldisp=.true.
> nq1=12,
> nq2=12,
> nq3=1,
> amass(1)=12.011,
> outdir='/home/mxm2/Desktop/Graphene/temp',
> fildyn='graphene.dyn',
> /
>
> My q2r:
>
> &input
> fildyn='graphene.dyn',
> zasr='simple',
> flfrc='graphene.12x12x1.fc'
> /
>
> Matdyn input:
>
> &input
> asr='simple',
> amass(1)=12.011,
> flfrc='graphene.12x12x1.fc',
> flfrq='graphene.disp.freq'
> q_in_band_form=.true.,
> /
> 4 ! number of q-points
> 0.000 0.000 0.000 10 ! gamma point
> 0.500 0.000 0.000 10 ! M
> 0.333 0.333 0.000 10 ! K
> 0.000 0.000 0.000 1 ! gamma point
>
> Plotband:
>
> graphene.disp.freq
> 0 1600
> graphene.disp.freq.dat
> graphene.disp.freq.ps
> 0
> 100 0
>
> Why the phonon dispersion does not match the pictures from the papers and for 
> calculations with e.g. 18x18x1 k-point and nq-point sets the output file of 
> graphene.dyn1 look like:
>
> Dielectric Tensor:
>
>  166.332153320312 0.
> 166.332275390625 0.
> 0. 0. 1.116060253916
>
> Effective Charges E-U: Z_{alpha}{s,beta}
>
> atom # 1
> -7471.575740195811 -0.002632206306 0.
> -0.002632205375-7471.579664016142 0.
> 0. 0. -0.003734609171
>
> Also, what is the best way to set the lattice parameters, via Ibrav or 
> CELL_PARAMETERS?
>
> Any help is appreciated.
>
> Best regards,
> Evgeniy Sysoev.
>
>
> ___
> 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

___
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Re: [QE-users] ph.x Raman calculations

[Kazume NISHIDATE]

Hi, Jessica

> 2021/03/30 1:53、Jessica Johnson のメール:
> 
> I have a very general question about Raman calculations (I will include that 
> I am using QE version 6.4.1 per the posting guidelines in case that helps my 
> answer my question). 


The derivatives of the potential give the T^2 and T^3 dependencies for
the Raman spectrum. To evaluate the quantities there may be two
strategies.

1) Calculate the dynamics at the specified temperature using the
Car–Parrinello MD or the BO-MD and evaluate the specified Raman mode.
The temperature dependencies of the mode, such as the shift and the
width, are the direct results of the anharmonic effects.

2) Evaluate the potential by slightly displacing the atoms following
the Raman mode. The polynomial fit to the obtained potential curvature
will give the third and forth derivatives and you may be able to
evaluate the anharmonicities.


I found the following ref. and hope it gives you a helpful hint.

"Lattice dynamics of anharmonic solids from first principles"
O. Hellman, I. A. Abrikosov, and S. I. Simak
Phys. Rev. B 84, 180301(R) – Published 14 November 2011


best regards
kazume NISHIDATE
敬具　西館数芽

nisid...@iwate-u.ac.jp
kazume.nishid...@gmail.com










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Re: [QE-users] ph.x Raman calculations

[Lorenzo Paulatto]

Hello you can take into account anharmonicity with the d3q code which is 
included in QE, but also has its own homepage at https://anharmonic.github.io/ 
where you may find more documentation and examples. In particular, I recently 
added an example on how to compute the vibrational spectral weight measured by 
Raman, i.e. like in fig.3 of PhysRevLett.125.145301. It is in the MgO example.

There is currently no automatic way to include both Raman cross section and 
anharmonic phonon line shape in the same calculation, but this can be easily 
done by hand.
hth
--
Lorenzo Paulatto - Paris
On Mar 29 2021, at 6:53 pm, Jessica Johnson  wrote:
>
> Hello QE world,
>
>
> I have a very general question about Raman calculations (I will include that 
> I am using QE version 6.4.1 per the posting guidelines in case that helps my 
> answer my question).
>
> Background: I am calculating Raman shifts in strained 2D MoS2 polymorphs.
>
> It was mentioned to me to by a non-QE user (but a computational chemist) that 
> adding a correction for anharmonicity is sometimes done for Raman 
> calculations, at least in other software packages. Having read "QUANTUM 
> ESPRESSO: a modular and open-source software project for quantum simulations 
> of materials", I understood that anharmonicity is taken into account with the 
> inclusion of second and third order energy derivatives. Am I understanding 
> this correctly? If I am, I would conclude that the suggestion made to me 
> (referenced above) would be moot.
>
> If I am misunderstanding, are there post-processing procedures I should 
> include?
>
> (This is my first time posting. I believe I have adhered sufficiently to the 
> posting guidelines, but apologies in advance if I missed something.)
>
> thank you,
> Jessica Johnson
> Graduate Research Assistant
> Materials Science and Engineering Department
> Rutgers University, New Brunswick
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> users mailing list users@lists.quantum-espresso.org
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Re: [QE-users] I have failed to reproduce phonon dispersion of graphene

[Lorenzo Paulatto]

> Using a k-points grid that includes the K point can be a source of troubles, 
> I would recommend using 16x16x1 or even 32x32x1 for better results.
p.s. and treat it as a metal, adding some smearing, to avoid the absurd 
dielectric constant

--
Lorenzo Paulatto - Paris
On Mar 30 2021, at 5:00 pm, Lorenzo Paulatto  wrote:
> You have specified the q-points in crystal fractionary units, hence you have 
> to specify q_in_cryst_coord=.true.
> This can be safely used in conjunction with q_in_band_form, which is a 
> completely unrelated option.
>
> Also:
> You way of specifying the cell parameters is discouraged and may cause 
> problems with symmetry detection, but it should work.
>
>
> > Using a k-points grid that includes the K point can be a source of 
> > troubles, I would recommend using 16x16x1 or even 32x32x1 for better 
> > results.
> hth
> --
> Lorenzo Paulatto - Paris
>
> On Mar 30 2021, at 4:19 pm, Evgenii  wrote:
> > Dear Quantum Espresso experts,
> >
> > I am having trouble calculating the phonon bands of graphene.
> >
> > First, I took the cif-file of the already relaxed graphite cell from the 
> > Materials Project site https://next-gen.materialsproject.org/ and made 
> > graphene cell from it by hand.
> > Then I relaxed the cell obtained with vc-relax and 12x12x1 k-point set.
> > I used the same parameters to perform a scf calculation:
> >
> > &CONTROL
> > calculation='scf'
> > title='graphene'
> > prefix='graphene'
> > verbosity='high'
> > restart_mode='from_scratch'
> > nstep=1000
> > iprint=1
> > tstress=.true.
> > tprnfor=.true.
> > disk_io='default'
> > pseudo_dir = '/home/mxm2/Desktop/Graphene',
> > outdir='/home/mxm2/Desktop/Graphene/temp'
> > /
> > &SYSTEM
> > ibrav = 0,
> > celldm(1)=1.889726,
> > nat = 2,
> > ntyp = 1,
> > ecutwfc = 60.0 ,
> > ecutrho = 480.0 ,
> > /
> > &ELECTRONS
> > electron_maxstep = 1000,
> > conv_thr = 1.0d-12 ,
> > mixing_mode = 'plain' ,
> > mixing_beta = 0.7d0 ,
> > /
> > ATOMIC_SPECIES
> > C 12.011 C.pz-rrkjus.UPF
> > ATOMIC_POSITIONS (crystal)
> > C 0.0 0.0 0.000861580
> > C 0.33000 0.67000 0.000838420
> > CELL_PARAMETERS (alat)
> > 2.438515837 -0.0 0.0
> > -1.219257919 2.111816662 0.0
> > -0.0 -0.0 19.995916314
> >
> > K_POINTS automatic
> > 12 12 1 0 0 0
> >
> > Then, I run ph.in calculation:
> >
> > &inputph
> > recover=.true.
> > tr2_ph=1.0d-14,
> > prefix='graphene',
> > ldisp=.true.
> > nq1=12,
> > nq2=12,
> > nq3=1,
> > amass(1)=12.011,
> > outdir='/home/mxm2/Desktop/Graphene/temp',
> > fildyn='graphene.dyn',
> > /
> >
> > My q2r:
> >
> > &input
> > fildyn='graphene.dyn',
> > zasr='simple',
> > flfrc='graphene.12x12x1.fc'
> > /
> >
> > Matdyn input:
> >
> > &input
> > asr='simple',
> > amass(1)=12.011,
> > flfrc='graphene.12x12x1.fc',
> > flfrq='graphene.disp.freq'
> > q_in_band_form=.true.,
> > /
> > 4 ! number of q-points
> > 0.000 0.000 0.000 10 ! gamma point
> > 0.500 0.000 0.000 10 ! M
> > 0.333 0.333 0.000 10 ! K
> > 0.000 0.000 0.000 1 ! gamma point
> >
> > Plotband:
> >
> > graphene.disp.freq
> > 0 1600
> > graphene.disp.freq.dat
> > graphene.disp.freq.ps
> > 0
> > 100 0
> >
> > Why the phonon dispersion does not match the pictures from the papers and 
> > for calculations with e.g. 18x18x1 k-point and nq-point sets the output 
> > file of graphene.dyn1 look like:
> >
> > Dielectric Tensor:
> >
> >  166.332153320312 0.
> > 166.332275390625 0.
> > 0. 0. 1.116060253916
> >
> > Effective Charges E-U: Z_{alpha}{s,beta}
> >
> > atom # 1
> > -7471.575740195811 -0.002632206306 0.
> > -0.002632205375-7471.579664016142 0.
> > 0. 0. -0.003734609171
> >
> > Also, what is the best way to set the lattice parameters, via Ibrav or 
> > CELL_PARAMETERS?
> >
> > Any help is appreciated.
> >
> > Best regards,
> > Evgeniy Sysoev.
> >
> >
> > ___
> > 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
>

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Re: [QE-users] ph.x Raman calculations

[Kazume NISHIDATE]

> 2021/03/31 1:00、Lorenzo Paulatto のメール:
> 
> Hello you can take into account anharmonicity with the d3q code which is 
> included in QE, 


This may be the most sophisticated way to account for the
anharmonicity from first principle. I'm impress by the ingeniousness.
Thank you for your notice.

btw-
The methods described in my previous message are heavily relying upon
a brute force manner. The only advantage of the method should be the
automatic inclusion of higher order terms beyond the third-order, but
of course its resolution, especially when it was obtained by MD, would
be very low.




best regards
kazume NISHIDATE
敬具　西館数芽

nisid...@iwate-u.ac.jp
kazume.nishid...@gmail.com










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Re: [QE-users] ph.x Raman calculations

[Terry Frankcombe]

While we are talking about interesting ways to include anharmonic
effects, it's worth taking a look at SSCHA: http://sscha.eu/

Not necessarily computationally inexpensive.


On Wed, 2021-03-31 at 07:20 +0900, Kazume NISHIDATE wrote:
> > 2021/03/31 1:00、Lorenzo Paulatto のメール:
> > 
> > Hello you can take into account anharmonicity with the d3q code which is 
> > included in QE, 
> 
> 
> This may be the most sophisticated way to account for the
> anharmonicity from first principle. I'm impress by the ingeniousness.
> Thank you for your notice.
> 
> btw-
> The methods described in my previous message are heavily relying upon
> a brute force manner. The only advantage of the method should be the
> automatic inclusion of higher order terms beyond the third-order, but
> of course its resolution, especially when it was obtained by MD, would
> be very low.
> 
> 
> 
> 
> best regards
> kazume NISHIDATE
> 敬具　西館数芽
> 
> nisid...@iwate-u.ac.jp
> kazume.nishid...@gmail.com
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> ___
> 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


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