[Pw_forum] Bad energetic of Li adsorbed graphene by DFT-D2 using QE

[Saif Ullah]

Dear QE users,

I'm trying to reproduce the Li adsorbed graphene with DFT-D2 using QE. The
adsorption energy is very much underestimated (-0.66 eV/Li) as compared to
the values found in the literature. My SIESTA vdW-DF/DZP value is -1.11
eV/Li, pretty much in agreement with the literature. I have used different
cutoff values with different pseudopotentials. I don't know where is the
problem. Following is one of my inputs. Need your suggestions, please.
Thanks

&CONTROL
   calculation='vc-relax',
  outdir='.',
  prefix='calc',
  pseudo_dir='.',
  verbosity='high',
 tstress=.true.
tprnfor=.true.
etot_conv_thr=1.0D-4
forc_conv_thr=1.D-3
wf_collect=.true.
nstep=1000
/

&SYSTEM
  ibrav=0,
  nat=51,
  ntyp=2,
  ecutwfc=40,
  ecutrho=320,
   input_dft='PBE',
  occupations='smearing',
  smearing='mp',
  degauss=0.01d0,
 vdw_corr='Grimme-D2',
!  nspin=2,
!  starting_magnetization(1)=0.7
!  starting_magnetization(2)=0.6
/

&ELECTRONS
   diagonalization='cg',
  conv_thr=1d-08,
  mixing_mode='local-TF',
  mixing_beta=0.500d0,
 electron_maxstep=2000
/
&IONS
ion_dynamics='bfgs'
/
&CELL
   cell_dynamics = 'bfgs' ,
  cell_dofree='2Dxy'
/
ATOMIC_SPECIES
C 12.010700d0 C.pbe-van_ak.UPF
Li  6.941000d0 Li.pbe-n-van.UPF
CELL_PARAMETERS (angstrom)
  12.353060724   0.000889035  -0.20145
  -6.175669462  10.698563666   0.20131
  -0.49454   0.28549  20.0

ATOMIC_POSITIONS (angstrom)
C   -0.123777599   0.044352021   0.750813339
C2.347139643   0.044536664   0.710530839
C4.816959818   0.046608474   0.671588196
C7.288030852   0.047974520   0.631371477
C9.759254756   0.046949526   0.590970165
C   -1.361324273   2.182837743   0.784592128
C1.111661447   2.176898866   0.738849472
C3.584693057   2.183131578   0.703985603
C6.053702309   2.186196980   0.671658550
C8.522771292   2.186413475   0.631364175
C   -2.598243992   4.325485482   0.824910219
C   -0.131078480   4.322022349   0.764237921
C2.354133011   4.322141066   0.723759919
C4.821870209   4.325914119   0.703967494
C7.288439627   4.327051393   0.671562970
C   -3.831089225   6.466525503   0.871657296
C   -1.366959478   6.470638409   0.819586551
C1.111648295   6.474564682   0.764205441
C3.590771165   6.470877940   0.738791095
C6.055337825   6.467163164   0.710460311
C   -5.064123742   8.605360424   0.914570582
C   -2.595447017   8.606844025   0.871611006
C   -0.124940436   8.609595937   0.824824937
C2.349153535   8.609719150   0.784488796
C4.820054590   8.607291549   0.750697179
C   -0.125510159   1.469181337   0.757732918
C2.348583973   1.469399905   0.717413261
C4.819499832   1.472058312   0.683659878
C7.288388407   1.473415839   0.646082581
C9.757057163   1.472349661   0.603098319
C   -1.367183927   3.608059861   0.792700719
C1.111411672   3.604765482   0.737260404
C3.590550668   3.608523771   0.711920217
C6.055141240   3.612373570   0.683651546
C8.521773207   3.612481509   0.643390074
C   -2.598108408   5.752895502   0.838312859
C   -0.130966528   5.757101185   0.12574
C2.354245670   5.757343547   0.737229826
C4.822007602   5.753541812   0.717366687
C7.288591341   5.752608946   0.684948021
C   -3.829804361   7.892507839   0.886438561
C   -1.360854441   7.895696352   0.838263118
C1.112121068   7.902104754   0.792620096
C3.585162055   7.896134775   0.757637017
C6.054187493   7.893269674   0.725270353
C1.111459010  -0.667769729   0.725378109
C3.582681447  -0.666400412   0.685002360
C6.052708940  -0.664305301   0.643406933
C8.523624623  -0.664119335   0.603107212
C   10.993446884  -0.665855193   0.564139854
Li   1.142006551   5.022080560   2.622103194
K_POINTS automatic
 6 6 1 0 0 0
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[Pw_forum] Bad energetic of Li adsorbed graphene by DFT-D2 using QE

[Saif Ullah]

Dear QE users,

I'm trying to reproduce the Li adsorbed graphene with DFT-D2 using QE. The
adsorption energy is very much underestimated (-0.66 eV/Li) as compared to
the values found in the literature. My SIESTA vdW-DF/DZP value is -1.11
eV/Li, pretty much in agreement with the literature. I have used different
cutoff values with different pseudopotentials. I don't know where is the
problem. Following is one of my inputs. Need your suggestions, please.
Thanks

&CONTROL
   calculation='vc-relax',
  outdir='.',
  prefix='calc',
  pseudo_dir='.',
  verbosity='high',
 tstress=.true.
tprnfor=.true.
etot_conv_thr=1.0D-4
forc_conv_thr=1.D-3
wf_collect=.true.
nstep=1000
/

&SYSTEM
  ibrav=0,
  nat=51,
  ntyp=2,
  ecutwfc=40,
  ecutrho=320,
   input_dft='PBE',
  occupations='smearing',
  smearing='mp',
  degauss=0.01d0,
 vdw_corr='Grimme-D2',
!  nspin=2,
!  starting_magnetization(1)=0.7
!  starting_magnetization(2)=0.6
/

&ELECTRONS
   diagonalization='cg',
  conv_thr=1d-08,
  mixing_mode='local-TF',
  mixing_beta=0.500d0,
 electron_maxstep=2000
/
&IONS
ion_dynamics='bfgs'
/
&CELL
   cell_dynamics = 'bfgs' ,
  cell_dofree='2Dxy'
/
ATOMIC_SPECIES
C 12.010700d0 C.pbe-van_ak.UPF
Li  6.941000d0 Li.pbe-n-van.UPF
CELL_PARAMETERS (angstrom)
  12.353060724   0.000889035  -0.20145
  -6.175669462  10.698563666   0.20131
  -0.49454   0.28549  20.0

ATOMIC_POSITIONS (angstrom)
C   -0.123777599   0.044352021   0.750813339
C2.347139643   0.044536664   0.710530839
C4.816959818   0.046608474   0.671588196
C7.288030852   0.047974520   0.631371477
C9.759254756   0.046949526   0.590970165
C   -1.361324273   2.182837743   0.784592128
C1.111661447   2.176898866   0.738849472
C3.584693057   2.183131578   0.703985603
C6.053702309   2.186196980   0.671658550
C8.522771292   2.186413475   0.631364175
C   -2.598243992   4.325485482   0.824910219
C   -0.131078480   4.322022349   0.764237921
C2.354133011   4.322141066   0.723759919
C4.821870209   4.325914119   0.703967494
C7.288439627   4.327051393   0.671562970
C   -3.831089225   6.466525503   0.871657296
C   -1.366959478   6.470638409   0.819586551
C1.111648295   6.474564682   0.764205441
C3.590771165   6.470877940   0.738791095
C6.055337825   6.467163164   0.710460311
C   -5.064123742   8.605360424   0.914570582
C   -2.595447017   8.606844025   0.871611006
C   -0.124940436   8.609595937   0.824824937
C2.349153535   8.609719150   0.784488796
C4.820054590   8.607291549   0.750697179
C   -0.125510159   1.469181337   0.757732918
C2.348583973   1.469399905   0.717413261
C4.819499832   1.472058312   0.683659878
C7.288388407   1.473415839   0.646082581
C9.757057163   1.472349661   0.603098319
C   -1.367183927   3.608059861   0.792700719
C1.111411672   3.604765482   0.737260404
C3.590550668   3.608523771   0.711920217
C6.055141240   3.612373570   0.683651546
C8.521773207   3.612481509   0.643390074
C   -2.598108408   5.752895502   0.838312859
C   -0.130966528   5.757101185   0.12574
C2.354245670   5.757343547   0.737229826
C4.822007602   5.753541812   0.717366687
C7.288591341   5.752608946   0.684948021
C   -3.829804361   7.892507839   0.886438561
C   -1.360854441   7.895696352   0.838263118
C1.112121068   7.902104754   0.792620096
C3.585162055   7.896134775   0.757637017
C6.054187493   7.893269674   0.725270353
C1.111459010  -0.667769729   0.725378109
C3.582681447  -0.666400412   0.685002360
C6.052708940  -0.664305301   0.643406933
C8.523624623  -0.664119335   0.603107212
C   10.993446884  -0.665855193   0.564139854
Li   1.142006551   5.022080560   2.622103194
K_POINTS automatic
 6 6 1 0 0 0
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[Pw_forum] How to choose ecutwfc value?

[Saif Ullah]

Dear qe users,

I'm a qe beginner, therefore, came up with a simple question. If i have to
study the interaction of Li/Na with graphene, so in this case how will i
choose the ecutwfc value? Should i do a convergence test w.r.t ecutwfc for
pure graphene or I must check the convergence of Li adsorbed graphene and
Na adsorbed graphene separately? For my pristine graphene, I found the 40Ry
value to be enough to converge graphene but when I studied the Li
interaction, my calculated adsorption value was very much underestimated
from my SIESTA/Gaussian/VASP values. Finally, I checked the convergence of
ecutwfc of Li/Na adsorbed graphene and found that 110Ry value is better for
both the Na and Li. This being said that an enormous increase in
computational time. I have seen a paper in which the authors used 30Ry and
reported the accurate results. My question is, the 110Ry is ok for Li/Na
graphene systems or I have done a mistake? Thanks in advance

Saif
Department of physics, ufjf, Brazil


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Re: [Pw_forum] Selection of K point for band structure calculation

[Saif Ullah]

Dear Madhurya,

1) You just need to go through the high symmetry points. The link may be
useful:  http://web.mit.edu/xcrysden_v1.5.60/www/XCRYSDEN/doc/kpath.html)

2) Fermi energy is important. You can use grep Fermi filename-scf.out, The
other values are for the energy range and how it will be divided. you can
choose e.g 0.1 10 etc.

Regards
Saif
Department of physics, UFJF, Brazil

On Sat, Oct 21, 2017 at 8:59 AM, Madhurya Chandel 
wrote:

> Respected QE Users
>
> 1)I have a doubt that how to choose the number of K point for band
> structure calculation using Xcysden K path selection?
> 2) while doing the band structure calculation how to chose Fermi energy
> (=  eV), deltaE and reference energy? Do these values affect the band
> structure plot?
>
> Thanking you
>
> With regards
>
> *Madhurya Chandel*
>
> *Research Scholar *
>
> *Department of Chemistry *
>
> *BITS PILANI, GOA campus*
>
> *+91-7507546773 <+91%2075075%2046773>*
>
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[Pw_forum] Which PPs should be used for vdW-df calculation?

[Saif Ullah]

Dear QE users,

I have studied that now VDW-DF (non-local) is implemented in QE. To use
this, you just need to change the input_dft accordingly. I also read that
you need revPBE for vdW-df calculations. I was not able to find the revPBE
PPs. My question is, can we use PBE PPs if we are interested in VDW-DF? I
hope not as the VDW-DF is a non-local. Where can we find the revPBE pps?
Any alternatives?

Thanks in Advance

Saif

Department of Physics, UFJF, Brazil
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Re: [Pw_forum] Selection of K point for band structure calculation

[Saif Ullah]

How to decide that? For inverse spinel (CuFe2O4) with FCC structure (56
atoms), what is the minimum number of K point (approx) required?

There is no such thing like minimum or maximum. You need to look at your
bands. If it is smooth, then the number is fine. To be on a safer side, I
would recommend 50 along each of the high symmetry points. If your cell is
too small, then you need to increase and vice versa.

Regards
Saif
Department of Physics, UFJF, Brazil

On Mon, Oct 23, 2017 at 2:55 PM, Madhurya Chandel 
wrote:

> Thank you for your kind reply.
>
> The number of points is free, but you have to take it large enough that
> the bands look smooth and not jagged.
>
> How to decide that? For inverse spinel (CuFe2O4) with FCC structure (56
> atoms), what is the minimium number of K point (approx) required?
>
> Also, the continuity analysis done by bands.x
> what is the continuity analysis?
>
>
>  You just need to go through the high symmetry points. The link may be
> useful:  http://web.mit.edu/xcrysden_v1.5.60/www/XCRYSDEN/doc/kpath.html)
> Thank you for your help but I already referred this
>
> With regards
> Madhurya
>
>
> On Mon, Oct 23, 2017 at 6:09 PM, Lorenzo Paulatto 
> wrote:
>
>> On 21/10/17 12:59, Madhurya Chandel wrote:
>>
>> Respected QE Users
>>
>> 1)I have a doubt that how to choose the number of K point for band
>> structure calculation using Xcysden K path selection?
>>
>>
>> Hello,
>>
>> I also recommend trying the seekpath online tool
>> 
>> , it is a bit
>> easier than xcrysden to use for this task, as it also suggests a possible
>> choice of path. The number of points is free, but you have to take it large
>> enough that the bands look smooth and not jagged. Also the continuity
>> analysis done by bands.x may not work if too few points are present. Note
>> that if you use the tpiba_b or crystal_b format for the points, you only
>> need to specify the path high-symmetry turning points, and the number of
>> k-points in between (check the manual)
>>
>> 2) while doing the band structure calculation how to chose Fermi energy
>> (=  eV), deltaE and reference energy? Do these values affect the band
>> structure plot?
>>
>>
>> They do not, it is just a rigid shift. It is customary to shift the bands
>> so that the Fermi energy is at zero. Of course, if your material is an
>> insulator there is not Fermi energy, if you have empty bands you can take
>> it in the middle of the gap (average of highest occupied and lowest
>> unoccupied energy levels). All these values are printed at the end of any
>> SCF and NSCF (not BANDS) calculation, check the output file.
>>
>> hope this helps
>>
>>
>> Thanking you
>>
>> With regards
>>
>> *Madhurya Chandel*
>>
>> *Research Scholar *
>>
>> *Department of Chemistry *
>>
>> *BITS PILANI, GOA campus *
>>
>> *+91-7507546773 <+91%2075075%2046773>*
>>
>>
>> ___
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>>
>> --
>> Lorenzo Paulatto - Paris
>>
>>
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>
>
>
> --
>
> *Madhurya Chandel*
>
> *Research Scholar *
>
> *Department of Chemistry *
>
> *BITS PILANI, GOA campus*
>
> *+91-7507546773 <+91%2075075%2046773>*
>
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[Pw_forum] How to use vdW-df in QE?

[Saif Ullah]

Dear QE users,

I'm interested in using vdW-df in QE. My simple question is: Can we use PBE
PPs by just changing the input_dft parameter from pbe to vdW-DF etc, just
like we do in VASP? Or we need to generate a vdW-DF PPs the way we generate
for use in SIESTA? Or we need to use revPBE pps?

Can someone provide an input example or a link to generate pps in qe?

Thank you very much.

Regards
Saif

Department of Physics, UFJF, Brazil
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Re: [Pw_forum] How to use vdW-df in QE?

[Saif Ullah]

Dear Paolo/Karim,

Thank you very much for your prompt response. Actually, you missed the
first part of my question. Can we use PBE pps by just changing the
input_dft? Of course, the generate_vdw_kernel_table should be present. We
use VDW-DF-SIESTA and M06 etc in Gaussian and sometimes we also use VASP.
Our generated vdW-DF-SIESTA pps give the same results as that of Gaussian
and VASP. SOmedays ago, I posted a problem regarding the bad energetics of
graphene+Li. One of the QE developers asks me to calculate different
systems with the different level of theories. The binding energy for
Li+graphene is found to be overestimated using QE, while for Na the results
were pretty much comparable. I also calculated vdW-DF (optb88-vdW) using
PBE pps in QE and luckily the binding energy was the same as calculated by
optpbe-vdW using VASP. I'm interested to use different pps and different
level of theories using QE and compare with the other codes. Therefore, I
came up with this question. Learning PPs generation needs lots of time as I
already spent much time in learning for SIESTA.

Dear Karim,

Thank you very much. That's why I came up with this question as by using
optb88-vdW with PBE pps gave me the same results of Na binding on graphene
as of optpbe-vdW using VASP.

Let's see what experts say.

Thanks

Saif
Department of Physics, UFJF, Brazil

On Tue, Oct 24, 2017 at 12:06 PM, Karim Elgammal  wrote:

> Hi Saif;
> to the extend of my limited experience; yes, you can use by changing the
> input_dft and ofcourse generating the vdW kernel using 
> generate_vdW_kernel_table.x
> before you start your calculation..
>
> input_dft: will override the functional definition in your input PPs...
>
> note: wait also for opinions from experts here, I am just sharing my
> experience.
>
> Karim Elgammal
> KTH
> Sweden
>
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Re: [Pw_forum] Van der Waals interactions

[Saif Ullah]

As per my limited knowledge, only one option can be used. vdW-df is
non-local, so it does not need C6 etc.

On Fri, Oct 27, 2017 at 6:10 PM, Eleftheria Gkogkosi 
wrote:

> Hello,
>
> Is it acceptable to set input_dft='vdw-DF' and then also use
> vdw_corr='DFT-D' in order to adjust london_c6(1) parameters?
>
> Or does one have to choose between a) non local functions (e.g. vdw-DF)
> and b) london correction to the, say, PBE functionals?
>
> --
> Eleftheria Gkogkosi
>
> Applied Mathematics & Physics Dept.
> National Technical University of Athens
> http://users.ntua.gr/elefthe
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[Pw_forum] revPBE + vdW-df-c09x

[Saif Ullah]

Dear QE users,

Can we use vdW-DF-c09x with revPBE pps or we need to build vdW-DF-c09x pp?
Previously, I was told that no one generate PPs with vdW-df and in the
funct.f90, I haven't found even a closer functional.

Thanks

Regards
Saif

Department of physics, UFJF, Brazil
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Re: [Pw_forum] Calculations stopped without printing any error

[Saif Ullah]

Dear all,

I have solved the problem.

Thanks
Saif
Department of Physics, UFJF, Brazil

On Fri, Nov 3, 2017 at 8:46 PM, Saif Ullah  wrote:

> Dear QE users,
>
> I'm trying to reproduce the Li adsorption on a benzene ring reported in
> this paper (Chemical Physics Letters 573 (2013) 15–18) using vdW-DF. The
> calculations stopped without printing any error in the output file. The
> input and output files are attached in addition to the error file
> (DFT.exxx).
>
> Please help in this regard.
>
> Thank you very much.
>
> Regards
> Saif
>
> Department of Physics, UFJF, Brazil
>
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[Pw_forum] Calculations stopped without printing any error

[Saif Ullah]

Dear QE users,

I'm trying to reproduce the Li adsorption on a benzene ring reported in
this paper (Chemical Physics Letters 573 (2013) 15–18) using vdW-DF. The
calculations stopped without printing any error in the output file. The
input and output files are attached in addition to the error file
(DFT.exxx).

Please help in this regard.

Thank you very much.

Regards
Saif

Department of Physics, UFJF, Brazil


DFT.e
Description: Binary data


relax.in.in
Description: Binary data


relax.ou
Description: Binary data
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Re: [Pw_forum] how to calculate binding energy of NaBiO3

[Saif Ullah]

Dear,

Ebin = Etot - ENi - EBi - 3EO

Or depends on how you write.

For stability, you need to calculate phonons.

Regards
Saif
Dept. Physics, UFJF, Brazil

On 14 Nov 2017 6:51 am, "Sudha Priyanka"  wrote:

> Can anyone suggest how to calculate binding energy of my crystal NaBiO3 by
> using Quantum Espresso?
>
> I have successfully completed the SCF of NaBiO3 using GGA-PBE. I have
> checked the SCF file and found the energy value : -333.03842 Ry/unit cell.
>
> I have performed total energy calculation of isolated atoms Na, Bi and O
> and found energy value as -192.232097 Ry, -141.20403847 Ry, -126.84166 Ry
> respectively.
>
> Now, please guide me how to calculate the binding energy of NaBiO3.
>
> Also I would like to know what should be the binding energy value for a
> crystal to be stable? It should be positive or negative value?
>
> Please suggests formula to calculate binding energy for this perovskite
> and suggest me some link or any related papers.
>
> Your help will be appreciated
>
> Thanks in advance
>
> Sudha Priyanka
>
>
>
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Re: [Pw_forum] how to calculate binding energy of NaBiO3

[Saif Ullah]

I'm not aware of the system under study, but if it is a new material, then
one should calculate phonons to check the stability.

If the system is already synthesized and you are studying the effect of
doping/adsorption, then binding/formation/cohesive/adsorption energy(ies)
is(are) enough.

Also, keep in mind that the value (-/+) depends on the order of the
equation.

Regards
Saif
Dept. Physics, UFJF, Brazil

On Tue, Nov 14, 2017 at 8:26 AM, Rajesh  wrote:

> Dear Saif Ullah,
> The negative value of binding energy is not enough to predict stability?
> Why do we need phonon calculations for that?
>
> On Tue, Nov 14, 2017 at 2:37 PM, Saif Ullah  wrote:
>
>> Dear,
>>
>> Ebin = Etot - ENi - EBi - 3EO
>>
>> Or depends on how you write.
>>
>> For stability, you need to calculate phonons.
>>
>> Regards
>> Saif
>> Dept. Physics, UFJF, Brazil
>>
>> On 14 Nov 2017 6:51 am, "Sudha Priyanka" 
>> wrote:
>>
>>> Can anyone suggest how to calculate binding energy of my crystal NaBiO3 by
>>> using Quantum Espresso?
>>>
>>> I have successfully completed the SCF of NaBiO3 using GGA-PBE. I have
>>> checked the SCF file and found the energy value : -333.03842 Ry/unit cell.
>>>
>>> I have performed total energy calculation of isolated atoms Na, Bi and O
>>> and found energy value as -192.232097 Ry, -141.20403847 Ry, -126.84166 Ry
>>> respectively.
>>>
>>> Now, please guide me how to calculate the binding energy of NaBiO3.
>>>
>>> Also I would like to know what should be the binding energy value for a
>>> crystal to be stable? It should be positive or negative value?
>>>
>>> Please suggests formula to calculate binding energy for this perovskite
>>> and suggest me some link or any related papers.
>>>
>>> Your help will be appreciated
>>>
>>> Thanks in advance
>>>
>>> Sudha Priyanka
>>>
>>>
>>>
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>>
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Re: [Pw_forum] how to calculate binding energy of NaBiO3

[Saif Ullah]

Dear Rajesh,
Yes, you are right.
The order does matter.
Eb= Et-Ex
Eb= Ex-Et
In the first case, negative is preferable while in the second case, a
positive value is...

Regards
Saif

On 14 Nov 2017 1:03 pm, "Rajesh"  wrote:

I think order doesn't matter. It's a simple concept. If energy of
individual atoms is more than the compound, the compound is more stable and
vice-versa.

On Nov 14, 2017 19:01, "Saif Ullah"  wrote:

> I'm not aware of the system under study, but if it is a new material, then
> one should calculate phonons to check the stability.
>
> If the system is already synthesized and you are studying the effect of
> doping/adsorption, then binding/formation/cohesive/adsorption energy(ies)
> is(are) enough.
>
> Also, keep in mind that the value (-/+) depends on the order of the
> equation.
>
> Regards
> Saif
> Dept. Physics, UFJF, Brazil
>
> On Tue, Nov 14, 2017 at 8:26 AM, Rajesh 
> wrote:
>
>> Dear Saif Ullah,
>> The negative value of binding energy is not enough to predict stability?
>> Why do we need phonon calculations for that?
>>
>> On Tue, Nov 14, 2017 at 2:37 PM, Saif Ullah 
>> wrote:
>>
>>> Dear,
>>>
>>> Ebin = Etot - ENi - EBi - 3EO
>>>
>>> Or depends on how you write.
>>>
>>> For stability, you need to calculate phonons.
>>>
>>> Regards
>>> Saif
>>> Dept. Physics, UFJF, Brazil
>>>
>>> On 14 Nov 2017 6:51 am, "Sudha Priyanka" 
>>> wrote:
>>>
>>>> Can anyone suggest how to calculate binding energy of my crystal NaBiO3
>>>> by using Quantum Espresso?
>>>>
>>>> I have successfully completed the SCF of NaBiO3 using GGA-PBE. I have
>>>> checked the SCF file and found the energy value : -333.03842 Ry/unit cell.
>>>>
>>>> I have performed total energy calculation of isolated atoms Na, Bi and
>>>> O and found energy value as -192.232097 Ry, -141.20403847 Ry, -126.84166 Ry
>>>> respectively.
>>>>
>>>> Now, please guide me how to calculate the binding energy of NaBiO3.
>>>>
>>>> Also I would like to know what should be the binding energy value for a
>>>> crystal to be stable? It should be positive or negative value?
>>>>
>>>> Please suggests formula to calculate binding energy for this perovskite
>>>> and suggest me some link or any related papers.
>>>>
>>>> Your help will be appreciated
>>>>
>>>> Thanks in advance
>>>>
>>>> Sudha Priyanka
>>>>
>>>>
>>>>
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>>>> Pw_forum mailing list
>>>> Pw_forum@pwscf.org
>>>> http://pwscf.org/mailman/listinfo/pw_forum
>>>>
>>>
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Re: [Pw_forum] Lattice constant from hgh pp

[Saif Ullah]

One quick question. Did you already optimize the structure using relax
or vc-relax?

Regards
Saif
Department of physics, UFJF, Brazil

On Wed, Nov 22, 2017 at 10:58 AM, Dhara Raval 
wrote:

> Dear all,
>
>  my name is  Dhara i'm M.Phil student from gujarat university
> ,India and working with qe-6.1. I already optimized ecut and K-point for my
> system ErCu. The lattice constant that i get 4.595 a.u. which is very low
> compare to experimental value  6.481760 a.u. why that happaning 
>
>
> my input script as under,
>
>
>  &control
> calculation = 'scf'
> prefix='ErCu'
> pseudo_dir = '$PSEUDO_DIR/'
> outdir= '$TMP_DIR/'
>
>  /
>  &system
> ibrav= 1
> celldm(1)= $e
> nat= 2
> ntyp= 2
> ecutwfc = 370
> occupations= 'smearing'
> smearing= 'Gauss'
> degauss= 0.02
>
>  /
>  &electrons
>
> mixing_beta = 0.7
>  /
> ATOMIC_SPECIES
> Er 167.259  Er.pz-sp-hgh.UPF
> Cu 63.55Cu.pz-hgh.UPF
>
> ATOMIC_POSITIONS {crystal}
> Er 0.00 0.00 0.00
> Cu 0.50 0.50 0.50
>
> K_POINTS {automatic}
> 12 12 12 1 1 1
>
>
>
> please kindly reply me as soon as possible
>
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Re: [Pw_forum] Error in running pdos calculations

[Saif Ullah]

Dear Mohammad,

Would you like share your inputs...

The following link may be helpful.

http://www.democritos.it/pipermail/pw_forum/2009-August/013787.html

Regards
Saif
Department of Physics, UFJF, Brazil

On Wed, Nov 29, 2017 at 3:48 AM, Ubaid Mohd  wrote:

> Dear QE users:
>
> A davcio error came up when I was doing Lowdin analysis using projwfc.x. I
> first carried out a scf calculation followed by nscf with a extended k-mesh
> and everything went smoothly. But when it comes to pdos calculation, the
> program crashed and kept saying the following error message:
>
>  Calling projwave 
>
>  
> %%
>
>  
> %%
>  from davcio : error #10
>  error while reading from file
>  
> %%
>
> There was no problem when I was running
> example08 (the pdos example come with the PWscf package), so probably there
> are some problems caused by my own system.
>
> Regards
>
> *Mohammad Ubaid*
> *PhD Research Scholar*
> *Department of Physics*
> *Jamia Millia Islamia University*
> *New Delhi - 110025*
>
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Re: [Pw_forum] Pseudopotential for indium

[Saif Ullah]

Dear Boulet,

I think I found where the error is. You are using the atomic number of In
instead of its atomic mass.

Regards
Saif
Department of physics, UFJF, Brazil



On Wed, Dec 6, 2017 at 6:45 PM, Pascal Boulet 
wrote:

> Thanks Lorenzo for the suggestion. I have tried with Ecut=120 Ry and
> Ecutrho=1200 Ry. I get a slightly better result (but c is still very bad):
> 3.2168 x 3.2168 x 5.3095
>
> as compared with:
> exp.: 3.2449 x 3.2449 x 4.9420 angström
> previous calc.: 3.2715 x 3.2715 x 5.4541 angström
>
>
> Best,
>
> Pascal Boulet
> —
> *Professor in computational chemistry - DEPARTEMENT OF CHEMISTRY*
> Aix-Marseille University - ST JEROME - Avenue Escadrille Normandie Niemen
> - F-13013 Marseille - FRANCE
> Tél: +33(0)4 13 55 18 10 <+33%204%2013%2055%2018%2010> - Fax : +33(0)4 13
> 55 18 50 <+33%204%2013%2055%2018%2050>
> Site : http://madirel.univ-amu.fr/pages_web_BOULET_PASCAL/infos - Email :
> pascal.bou...@univ-amu.fr
>
>
>
>
> Le 6 déc. 2017 à 18:54, Lorenzo Paulatto  a écrit :
>
> Hello,
> can you try with a much higher cutoff (100 Ry or more) and see if the
> lattice parameter improves? I've noticed that sometimes pslibrary pseudos
> are much a harder than they look, especially when converging stress
>
> Cheers
>
> --
> Lorenzo Paulatto
> Written on a virtual keyboard with real fingers
>
> On Dec 6, 2017 18:32, "Pascal Boulet"  wrote:
>
> Dear all,
>
> We are working on some In-containing semiconductors M(1-x)In(x)L. M is
> supposed to be a smaller atom than In. We are facing the problem that when
> we vary x from 0 to 1 the cell parameters is decreasing instead of
> increasing. Although this may happen, it should not be the case here since
> ‘pure’ ML has a smaller cell parameter than ‘pure’ InL.
>
> We have run some calculations on crystal indium using the PSL library
> pseudo potentials (both PAW and USPP). one of the calculated cell
> parameters are miles away from the experimental ones:
> exp.: 3.2449 x 3.2449 x 4.9420 angström
> calc.: 3.2715 x 3.2715 x 5.4541 angström
>
> Does anyone have tested the In pseudo potentials of the PSL library or
> faced this problem with indium?
>
> Thank you for your help and time.
>
> Best regards
>
> PS1. here are some information from the input file:
>
>  calculation= 'vc-relax’,
>   etot_conv_thr  = 1d-7,
>   forc_conv_thr  = 5d-5,
>   ibrav  = 0,
>nat= 2,
>   ntyp   = 1,
>   ecutwfc= 45.d0,
>   ecutrho= 450.d0,
>   nbnd = 18
> &ELECTRONS
>   conv_thr   = 1d-8,
> &CELL
>   press_conv_thr = 0.01d0,
>   cell_factor= 1.5,
> ATOMIC_SPECIES
> In 49.0 In.pbe-dn-kjpaw_psl.1.0.0.UPF
> K_POINTS automatic
> 8 8 4 1 1 1
> CELL_PARAMETERS angstroms
> 3.2449 0. 0.
> 0. 3.2449 0.
> 0. 0. 4.9420
> ATOMIC_POSITIONS crystal
> In   0.0.0.
> In   0.50000.50000.5000
>
> PS2. And some from the output:
>
> bfgs converged in  18 scf cycles and  15 bfgs steps
>  (criteria: energy <  1.0E-07 Ry, force <  5.0E-05Ry/Bohr, cell <
>  1.0E-02kbar)
> CELL_PARAMETERS (angstrom)
>3.271466870   0.0   0.0
>0.0   3.271466870   0.0
>0.0   0.0   5.454067219
> !total energy  =-821.46750731 Ry
> total   stress  (Ry/bohr**3)   (kbar) P=0.30
>
> Pascal Boulet
> —
> *Professor in computational chemistry - DEPARTEMENT OF CHEMISTRY*
> Aix-Marseille University - ST JEROME - Avenue Escadrille Normandie Niemen
> - F-13013 Marseille - FRANCE
> Tél: +33(0)4 13 55 18 10 <04%2013%2055%2018%2010> - Fax : +33(0)4 13 55
> 18 50 <04%2013%2055%2018%2050>
> Site : http://madirel.univ-amu.fr/pages_web_BOULET_PASCAL/infos - Email :
> pascal.bou...@univ-amu.fr
>
>
>
>
>
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Re: [Pw_forum] Pseudopotential for indium

[Saif Ullah]

Yes, I think 114.818d0 should be used instead of 49.0. I'm pretty much sure
that this may be the reason (or one of the reasons). Once, I used the
atomic mass of B for Be and I faced this kind of weird situation.

Anyway, I'm running the same geometry with 8x8x6 kpoints.

Thanks

On Wed, Dec 6, 2017 at 8:03 PM, Paolo Giannozzi 
wrote:

> You mean: the value 49.0 here?
> ATOMIC_SPECIES
> In 49.0 In.pbe-dn-kjpaw_psl.1.0.0.UPF
> Iit is used only by molecular dynamics, not by structural optimization.
>
> I don't remember In to be an especially nasty element, at least for simple
> III-V compounds like InAs. I would examine the effect of a denser k-point
> grid, and of spin-orbit
>
> Paolo
>
>
> On Wed, Dec 6, 2017 at 10:46 PM, Saif Ullah  wrote:
>
>> Dear Boulet,
>>
>> I think I found where the error is. You are using the atomic number of In
>> instead of its atomic mass.
>>
>> Regards
>> Saif
>> Department of physics, UFJF, Brazil
>>
>>
>>
>> On Wed, Dec 6, 2017 at 6:45 PM, Pascal Boulet 
>> wrote:
>>
>>> Thanks Lorenzo for the suggestion. I have tried with Ecut=120 Ry and
>>> Ecutrho=1200 Ry. I get a slightly better result (but c is still very bad):
>>> 3.2168 x 3.2168 x 5.3095
>>>
>>> as compared with:
>>> exp.: 3.2449 x 3.2449 x 4.9420 angström
>>> previous calc.: 3.2715 x 3.2715 x 5.4541 angström
>>>
>>>
>>> Best,
>>>
>>> Pascal Boulet
>>> —
>>> *Professor in computational chemistry - DEPARTEMENT OF CHEMISTRY*
>>> Aix-Marseille University - ST JEROME - Avenue Escadrille Normandie
>>> Niemen - F-13013 Marseille - FRANCE
>>> Tél: +33(0)4 13 55 18 10 <+33%204%2013%2055%2018%2010> - Fax : +33(0)4
>>> 13 55 18 50 <+33%204%2013%2055%2018%2050>
>>> Site : http://madirel.univ-amu.fr/pages_web_BOULET_PASCAL/infos -
>>> Email : pascal.bou...@univ-amu.fr
>>>
>>>
>>>
>>>
>>> Le 6 déc. 2017 à 18:54, Lorenzo Paulatto  a écrit :
>>>
>>> Hello,
>>> can you try with a much higher cutoff (100 Ry or more) and see if the
>>> lattice parameter improves? I've noticed that sometimes pslibrary pseudos
>>> are much a harder than they look, especially when converging stress
>>>
>>> Cheers
>>>
>>> --
>>> Lorenzo Paulatto
>>> Written on a virtual keyboard with real fingers
>>>
>>> On Dec 6, 2017 18:32, "Pascal Boulet"  wrote:
>>>
>>> Dear all,
>>>
>>> We are working on some In-containing semiconductors M(1-x)In(x)L. M is
>>> supposed to be a smaller atom than In. We are facing the problem that when
>>> we vary x from 0 to 1 the cell parameters is decreasing instead of
>>> increasing. Although this may happen, it should not be the case here since
>>> ‘pure’ ML has a smaller cell parameter than ‘pure’ InL.
>>>
>>> We have run some calculations on crystal indium using the PSL library
>>> pseudo potentials (both PAW and USPP). one of the calculated cell
>>> parameters are miles away from the experimental ones:
>>> exp.: 3.2449 x 3.2449 x 4.9420 angström
>>> calc.: 3.2715 x 3.2715 x 5.4541 angström
>>>
>>> Does anyone have tested the In pseudo potentials of the PSL library or
>>> faced this problem with indium?
>>>
>>> Thank you for your help and time.
>>>
>>> Best regards
>>>
>>> PS1. here are some information from the input file:
>>>
>>>  calculation= 'vc-relax’,
>>>   etot_conv_thr  = 1d-7,
>>>   forc_conv_thr  = 5d-5,
>>>   ibrav  = 0,
>>>nat= 2,
>>>   ntyp   = 1,
>>>   ecutwfc= 45.d0,
>>>   ecutrho= 450.d0,
>>>   nbnd = 18
>>> &ELECTRONS
>>>   conv_thr   = 1d-8,
>>> &CELL
>>>   press_conv_thr = 0.01d0,
>>>   cell_factor= 1.5,
>>> ATOMIC_SPECIES
>>> In 49.0 In.pbe-dn-kjpaw_psl.1.0.0.UPF
>>> K_POINTS automatic
>>> 8 8 4 1 1 1
>>> CELL_PARAMETERS angstroms
>>> 3.2449 0. 0.
>>> 0. 3.2449 0.
>>> 0. 0. 4.9420
>>> ATOMIC_POSITIONS crystal
>>> In   0.0.0.
>>> In   0.50000.50000.5000
>>>
>>> PS2. And some from the output:
>>>
>>> bfgs converged in  18 scf cycles and  15 

Re: [Pw_forum] Pseudopotential for indium

[Saif Ullah]

Yes,
using pseudopotentials from the SSSP,

I got 3.170301541 x 3.170301541 x 5.302690101 using 8x8x6 kpoints.

Did you notice that c/a ratio is nearly constant?



On Thu, Dec 7, 2017 at 11:23 AM, Pascal Boulet 
wrote:

> Dear Nicola,
>
> You are right I also noticed that the ‘pseudo' state energies match very
> well the AE ones.
>
> Regarding the alloys Vegard’s law should hold according to experimental
> data. We are indeed using supercells.
>
> I am currently running tests on pure indium. As mentioned by Paolo, the
> mass is irrelevant in the results for static calculations (as expected!). I
> have preliminary results with relativistic+SO calculation that are a bit
> better:
> 3.0786 x 3.0786 x 5.0095
>
> Recall:
> exp.: 3.2449 x 3.2449 x 4.9420
> previous calc.: 3.2168 x 3.2168 x 5.3095
>
> This is obtained with Ecut=50 Ry Ecutrho=500 Ry, 8x8x8 kpts=40 kpts
> With these parameters c improves substantially (1.4% off) but a and c
> worsen a bit (5% off).
>
> I am running a test with more kpts first. In a second step I will increase
> Ecut and Ecutrho and will report to the forum.
>
> Pascal
>
>
>
>
>
>
>
> Pascal Boulet
> —
> *Professor in computational chemistry - DEPARTEMENT OF CHEMISTRY*
> Aix-Marseille University - ST JEROME - Avenue Escadrille Normandie Niemen
> - F-13013 Marseille - FRANCE
> Tél: +33(0)4 13 55 18 10 <+33%204%2013%2055%2018%2010> - Fax : +33(0)4 13
> 55 18 50 <+33%204%2013%2055%2018%2050>
> Site : http://madirel.univ-amu.fr/pages_web_BOULET_PASCAL/infos - Email :
> pascal.bou...@univ-amu.fr
>
>
>
>
> Le 6 déc. 2017 à 23:24, Nicola Marzari  a écrit :
>
>
> Dear Pascal,
>
>
> the comparison with all-electron calculations looks good to me - see
> here for tests and for the other pseudos:
> http://materialscloud.org/sssp/results/In_conv_patt.png
>
> Comparing with expts is more delicate -  c/a with PBE is
> quite a bit off e.g. in ferroelectric perovskites.
>
> Re the alloy, how are you constructing the intermediate concentrations?
> Supercells? (Vegard law should hold)
>
> nicola
>
> On 06/12/2017 23:03, Paolo Giannozzi wrote:
>
> You mean: the value 49.0 here?
> ATOMIC_SPECIES
> In 49.0 In.pbe-dn-kjpaw_psl.1.0.0.UPF
> Iit is used only by molecular dynamics, not by structural optimization.
>
> I don't remember In to be an especially nasty element, at least for
> simple III-V compounds like InAs. I would examine the effect of a denser
> k-point grid, and of spin-orbit
>
> Paolo
>
>
> On Wed, Dec 6, 2017 at 10:46 PM, Saif Ullah  <mailto:kiterunn...@gmail.com>> wrote:
>
>Dear Boulet,
>
>I think I found where the error is. You are using the atomic number
>of In instead of its atomic mass.
>
>Regards
>Saif
>Department of physics, UFJF, Brazil
>
>
>
>On Wed, Dec 6, 2017 at 6:45 PM, Pascal Boulet
>mailto:pascal.bou...@univ-amu.fr>> wrote:
>
>Thanks Lorenzo for the suggestion. I have tried with Ecut=120 Ry
>and Ecutrho=1200 Ry. I get a slightly better result (but c is
>still very bad):
>3.2168 x 3.2168 x 5.3095
>
>as compared with:
>exp.: 3.2449 x 3.2449 x 4.9420 angström
>previous calc.: 3.2715 x 3.2715 x 5.4541 angström
>
>
>Best,
>
>Pascal Boulet
>—
>/Professor in computational chemistry - DEPARTEMENT OF CHEMISTRY/
>Aix-Marseille University - ST JEROME - Avenue Escadrille
>Normandie Niemen - F-13013 Marseille - FRANCE
>Tél: +33(0)4 13 55 18 10 <+33%204%2013%2055%2018%2010>
>  - Fax
>: +33(0)4 13 55 18 50 <+33%204%2013%2055%2018%2050>
> 
>Site : http://madirel.univ-amu.fr/pages_web_BOULET_PASCAL/infos
><http://madirel.univ-amu.fr/pages_web_BOULET_PASCAL/infos> -
>Email : pascal.bou...@univ-amu.fr <mailto:pascal.bou...@univ-amu.fr
> >
>
>
>
>
>Le 6 déc. 2017 à 18:54, Lorenzo Paulatto <mailto:paul...@gmail.com>> a écrit :
>
>Hello,
>can you try with a much higher cutoff (100 Ry or more) and see
>if the lattice parameter improves? I've noticed that sometimes
>pslibrary pseudos are much a harder than they look, especially
>when converging stress
>
>Cheers
>
>--
>Lorenzo Paulatto
>Written on a virtual keyboard with real fingers
>
>On Dec 6, 2017 18:32, "Pascal Boulet"
>mailto:pascal.bou...@univ-amu.fr>>
>wrote:
>
>Dear all,
>
>We are working on some In-containing semicondu

Re: [Pw_forum] error- dE0s is positive which should never happen

[Saif Ullah]

It is a well-known error.

The following links may be helpful.
http://qe-forge.org/pipermail/pw_forum/2014-September/105225.html
https://www.mail-archive.com/pw_forum@pwscf.org/msg29759.html

Regards
Saif


On Tue, Dec 19, 2017 at 7:38 AM, B S Bhushan  wrote:

> Dear experts...
>
> I have received this following error when I was trying to optimize a doped
> graphene sheet.
>
> 
> %%
>  Error in routine bfgs (1):
>  dE0s is positive which should never happen
>  %%%
> %%%
>
> Please suggest me how to avoid this error.
>
> Thank you very much for your precious time and knowledge.
>
> Sincerely,
> B S Bhushan,
> Ph.D Scholar,
> ABV-IIITM Gwalior, India.
>
>
>
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Re: [Pw_forum] error- dE0s is positive which should never happen

[Saif Ullah]

Dear Bhushan,

It means that you have already achieved (nearly achieved) the convergence
as can be concluded from the following sentence by prof. Paolo
(This kind of errors invariably happens when you are very close

to the minimum and you have some numerical noise on forces. It
is useless in my opinion to insist: your system is sufficiently
relaxed


Paolo)

I'm surely not a QE expert but when I have this kind of problem, I usually
change (a bit) the positions of few atoms and do a relax calculation
following by an scf-calc.

Regards
Saif

Saif Ullah
Departamento de Física
Instituto de Ciências Exatas - ICE
Universidade Federal de Juiz de Fora - UFJF
Juiz de Fora - MG - Brazil - CEP 36036-330
sul...@fisica.ufjf.br
Cell# +55 32 9110-7851
https://www.researchgate.net/profile/Saif_Ullah41

On Tue, Dec 19, 2017 at 11:43 AM, B S Bhushan  wrote:

> Dear Dr. Saif,
>
> I have through this link before posting the error. However, I could not
> find a solution to my problem there.
>
>
> On Tue, Dec 19, 2017 at 6:07 PM, Saif Ullah  wrote:
>
>> It is a well-known error.
>>
>> The following links may be helpful.
>> http://qe-forge.org/pipermail/pw_forum/2014-September/105225.html
>> https://www.mail-archive.com/pw_forum@pwscf.org/msg29759.html
>>
>> Regards
>> Saif
>>
>>
>> On Tue, Dec 19, 2017 at 7:38 AM, B S Bhushan 
>> wrote:
>>
>>> Dear experts...
>>>
>>> I have received this following error when I was trying to optimize a
>>> doped graphene sheet.
>>>
>>> 
>>> %%
>>>  Error in routine bfgs (1):
>>>  dE0s is positive which should never happen
>>>  %%%
>>> %%%
>>>
>>> Please suggest me how to avoid this error.
>>>
>>> Thank you very much for your precious time and knowledge.
>>>
>>> Sincerely,
>>> B S Bhushan,
>>> Ph.D Scholar,
>>> ABV-IIITM Gwalior, India.
>>>
>>>
>>>
>>> ___
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>>>
>>
>>
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>
>
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Re: [Pw_forum] Phonon calculation of Silicene: ph.x

[Saif Ullah]

In addition, looking to the celldm, don't you think that a 15x10x1 mesh or
so can be a reasonable choice?

On 12 Jan 2018 4:51 am, "NEELESH GUPTA"  wrote:

> Dear Jagdish,
>  Yes sir you are right. Please consider it as a typo
> error.
>
> On Thu, Jan 11, 2018 at 10:08 PM, Jagdish verma 
> wrote:
>
>> Dear Neelesh,
>>
>> I don't know about the error. But in scf input , I think you should have
>> 36 36 1 0 0 0 k grid because silicene  has 2D structure. It will decrease k
>> points in scf.out. Please correct me if I said anything wrong.
>>
>> On Thu, Jan 11, 2018 at 5:50 PM, NEELESH GUPTA 
>> wrote:
>>
>>> Dear All ,
>>>
>>> I'm trying to perform a phonon calculation of silicne using using ph.x
>>> on QE v 6.0.
>>>
>>> I running this simulation using parallelzation
>>> mpirun -np 32 -hostfile machine ph.x -ndiag4  -nk 2  ph.out
>>>
>>>
>>>
>>> Error generated...
>>>
>>>  %%%
>>> %%%
>>>  Error in routine set_kplusq (23976):
>>>  too many k points
>>>  %%%
>>> %%%
>>>
>>>  stopping ...
>>>
>>> :
>>>
>>> ##I have done the scf calculation is done with k-points
>>>   36  36  36  0 0 0
>>>
>>> ##  Detailed paramters
>>>   ibrav=4,
>>>   celldm(1)=7.3321373633d0, celldm(3)=12.8865979381d0,
>>>   nat=2,
>>>   ntyp=1,
>>>
>>>
>>> ## the ph code is
>>> Ph
>>>  &inputph
>>> prefix='calc'
>>> outdir='Xe',
>>> fildyn='calc.dyn',
>>> tr2_ph=1.0d-16,
>>> alpha_mix=0.7,
>>> verbosity='high',
>>> ldisp=.true.,
>>> epsil= .false.
>>> trans=.true,
>>> nq1=4,nq2=4,nq3=1,
>>>
>>>
>>>
>>> I have tried with -nimage in mpi run  but it stops and in crash files it 
>>> shows error of too many k-points.
>>>
>>>
>>> *Thanks in advance!*
>>>
>>>
>>>
>>>
>>> Warm regards
>>> Neelesh Gupta
>>> Research Scholar,ECE
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
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>>
>>
>>
>> --
>> With best regards,
>> Jagdish Verma,
>>
>>
>>
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>
>
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Re: [Pw_forum] how to fix cellside

[Saif Ullah]

Or you can take a look at

cell_dofree tag

Regards

Saif Ullah
Departamento de Física
Instituto de Ciências Exatas - ICE
Universidade Federal de Juiz de Fora - UFJF
Juiz de Fora - MG - Brazil - CEP 36036-330
sul...@fisica.ufjf.br
Cell# +55 32 9110-7851
https://www.researchgate.net/profile/Saif_Ullah41

On Tue, Jan 16, 2018 at 5:13 AM, Maxim Arsentev  wrote:

>  Dear Quantum-Espresso users and developers,
>
> I need to fix cell side during geometry optimization in espresso. How it
> can be done?
>
> Best wishes,
> Maxim Arsent'ev, Ph.D. (Chemistry)
> Laboratory of research of nanostructures
> Institute of Silicate Chemistry of RAS
>
>
>
>
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Re: [Pw_forum] dependence of bandstructure to the basis set

[Saif Ullah]

Would you like to share your band structure plots?

We haven't found such differences using different codes (siesta, gaussian,
qe, vasp). It is difficult to say anything without looking at the bands,
but i guess you are working with borophene.

Regards

Saif Ullah
Departamento de Física
Instituto de Ciências Exatas - ICE
Universidade Federal de Juiz de Fora - UFJF
Juiz de Fora - MG - Brazil - CEP 36036-330
sul...@fisica.ufjf.br
Cell# +55 32 9110-7851
https://www.researchgate.net/profile/Saif_Ullah41

On Wed, Jan 24, 2018 at 2:08 PM, Zara Nosh  wrote:

> ​​Dear experts,
> I have calculated the bandstructure of a 2d periodic system using PWscf
> and siesta. the overall pictures of bandstructure are same however there
> are some differences between them.
>
> The bandstructure calculated by vasp ( with planwave basis) is also
> similar to PWscf bandstructure. And it shows that the difference is due to
> the atomic like basis set of siesta.
>
> Now my question is that which bandstructures are more reliable? I guess
> that as the structure is periodic the planewave should give a better
> simulation; is it right?
>
> Best regards,
> Zahra
>
>
>
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Re: [Pw_forum] How to sum pdos from the different pdos file

[Saif Ullah]

The following link might be helpful.

http://larrucea.eu/sum_states-py-2/

Regards
Saif

Saif Ullah
Departamento de Física
Instituto de Ciências Exatas - ICE
Universidade Federal de Juiz de Fora - UFJF
Juiz de Fora - MG - Brazil - CEP 36036-330
sul...@fisica.ufjf.br
Cell# +55 32 9110-7851
https://www.researchgate.net/profile/Saif_Ullah41

On Wed, Feb 14, 2018 at 1:28 PM, Madhurya Chandel 
wrote:

> Dear users
>
> I have calculated the pdos of two elements and got s, p, and d orbital
> pdos value.
>  Now I want to sum the s orbital for one element and same for other.
> How to proceed for that?
>
>
> With regards
>
> *Madhurya Chandel*
>
> *Research Scholar *
>
> *Department of Chemistry *
>
> *BITS PILANI, GOA campus*
>
> *+91-7507546773 <+91%2075075%2046773>*
>
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Re: [Pw_forum] Plotting phonon dispersion

[Saif Ullah]

Dear Eleni,

Did you use ibrav=0? If so, then you need to use   q_in_band_form=.false.
q_in_cryst_coord=.true.

You can get the path using Xcrysden

Best,

Saif Ullah
Departamento de Física
Instituto de Ciências Exatas - ICE
Universidade Federal de Juiz de Fora - UFJF
Juiz de Fora - MG - Brazil - CEP 36036-330
sul...@fisica.ufjf.br
Cell# +55 32 9110-7851
https://www.researchgate.net/profile/Saif_Ullah41

On Mon, Feb 19, 2018 at 10:29 AM,  wrote:

>
> Thank you Vahid Askarpour.
>
> I have two questions:
>
> a) Is there a problem if I don't specify amass?
>
> b) I have already done this procedure using the following files:
>
> ph.x:
>
> &inputph
>prefix   = 'Si',
>epsil= .false.,
>fildyn   = 'diam.dyn',
>ldisp= .true.
>fildvscf = 'dvscf'
>nq1=6,
>nq2=6,
>nq3=1,
>tr2_ph   =  1.0d-12,
>recover = .true.
>   /
>
> This run ok
>
> q2r.in:
>
>   &input
>fildyn='diam.dyn',
>flfrc='Si.rc'
>   /
>
> This run ok
>
> matdyn.in:
>
>   &input
>  flfrc='Si.rc',
>  flfrq='Si.freq',
>  q_in_band_form=.true.
>   /
>   4
>   gG 50
>X 50
>M 50
>gG 8
>
> And I got the following error:
>
>
> 
> %%
>   Error in routine find_bz_type (1):
>   Wrong ibrav
>
> 
> %%
>
> Is it possible that this is because I messed up the names of the
> files, or do I need to include explicitly the coordinates of the high
> symmetry points?
>
>
> Regards
>
> Eleni
>
>
>
>
> Quoting Vahid Askarpour :
>
> > Once you get all the .dyn files from the ph.x run, use the following
> > input to q2r.x to get the force constants:
> >
> >  &input
> >fildyn=’Si.dyn', zasr='simple', flfrc=’Si.ifc2’
> > /
> >
> > Then use the following input to matdyn.x:
> >
> > &input
> > asr='simple',  amass(1)= 28.0855
> > flfrc=’Si.ifc2', flfrq=’Si.freq', q_in_band_form=.true.
> > /
> > 6  ! number of high-symmetry points
> > 0.0 0.0 0.0 200
> > 0.0 0.0 1.0 200
> > etc.
> >
> > The coordinates of the high symmetry points should be in cartesian
> > coordinates. 200 points will be calculated for each segment. The
> > phonon dispersion is in the .gp output file.
> >
> > Cheers,
> >
> > Vahid
> >
> > Vahid Askarpour
> > Department of Physics and Atmospheric Science
> > Dalhousie University,
> > Halifax, NS, Canada
> >
> >> On Feb 19, 2018, at 4:54 AM, elch...@auth.gr wrote:
> >>
> >> Hello all,
> >>
> >> I am using ph.x to get the phonon frequencies and dynamical matrices
> >> for an epw.x calculation, however, I would like to plot my phonon
> >> dispersions from the ph.x calculation for far, as for example is shown
> >> in
> >>
> >> http://epw.org.uk/Documentation/B-dopedDiamond
> >>
> >> I am lost as to how I can do that. My ph.x file is as follows,
> >>
> >> &inputph
> >>   prefix   = 'Si',
> >>   epsil= .false.,
> >>   fildyn   = 'diam.dyn',
> >>   ldisp= .true.
> >>   fildvscf = 'dvscf'
> >>   nq1=6,
> >>   nq2=6,
> >>   nq3=1,
> >>   tr2_ph   =  1.0d-12,
> >>   recover = .true.
> >>  /
> >>
> >> Do I need to use q2r.x and matdyn.x to the files for plotting?
> >>
> >>
> >> Thank you
> >>
> >>
> >>
> >> --
> >> Dr. Eleni Chatzikyriakou
> >> Computational Physics lab
> >> Aristotle University of Thessaloniki
> >> elch...@auth.gr - tel:+30 2310 998109
> >>
> >> ___
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> >
> >
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>
>
> --
> Dr. Eleni Chatzikyriakou
> Computational Physics lab
> Aristotle University of Thessaloniki
> elch...@auth.gr - tel:+30 2310 998109
>
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