Re: [QE-users] wfck2r.x

[Duy Le]

I doubt that you will be able to get anything meaningful
with , as difference in the random phases of the two
wavefunctions is not possible to be eliminated. How about ||^2?

Duy Le
(UCF)

On Mon, Nov 2, 2020 at 10:47 AM Thomas Brumme 
wrote:

> OK, at least the different sizes were probably a problem on my side - I
> was using the dev version of wfck2r with the rest in an older version.
> Using only the dev version I have the binary file being approximately 2.7
> times bigger which can be explained - I guess - with the missing second
> component. But I'm still not sure whether I can simply integrate
>  and expect something useful if both wave functions are from
> different calculations...
>
>
> --
> Dr. rer. nat. Thomas Brumme
> Theoretical chemistry
> TU Dresden - BAR / II49
> Helmholtzstr. 18
> 01069 Dresden
>
> Tel:  +49 (0)351 463 40844
>
> email: thomas.bru...@tu-dresden.de
>
> --
> *Von:* users  im Auftrag von
> Thomas Brumme 
> *Gesendet:* Montag, 2. November 2020 15:21
> *An:* users@lists.quantum-espresso.org
> *Betreff:* [QE-users] wfck2r.x
>
>
> Dear all,
>
>
> I want to calculate wave function overlaps in order to extract some
> parameters for a collaborator.
>
> Since I want the overlap in a heterostructure of 2 monolayers for the wave
> functions of the single layers (i.e., I need 3 calculations), the easiest
> solution would be to look at the changes in the projection on the atomic
> states using projwfc. Yet, this local basis is not complete and I would
> like to know how "much" is missing.
>
>
> I found the wfck2r.f90 code. Yet, I think there are several problems with
> using this and maybe someone can comment. I think I once read that one
> cannot easily compare the wave functions between different calculation
> because of an arbitrary phase shift. Is this correct? Because if I can't
> do this, then I don't even need to consider using the code. If I can do
> it, then am I right, that the wfck2r code does not include the SOC case
> for output in octave format? Because in line 248, only pol=1 is used...
> Another problem I noticed is a huge difference in sizes of the octave
> output and the binary output. The octave output was in my test case about
> 68 MB while the binary file was 6 GB.
>
>
> Kind regards
>
>
> Thomas
>
> --
> Dr. rer. nat. Thomas Brumme
> Theoretical chemistry
> TU Dresden - BAR / II49
> Helmholtzstr. 18
> 01069 Dresden
>
> Tel:  +49 (0)351 463 40844
>
> email: thomas.bru...@tu-dresden.de
>
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Re: [QE-users] second scf calculation in relax calculation not converging

[Duy Le]

This is somehow the real-life version of huge force applied on an object
https://www.youtube.com/watch?v=pP88-4AIb1c
After first step, your system is in a weird configuration that the chosen
algorithm can't solve.

Duy Le
(UCF)

On Fri, Jul 10, 2020 at 2:38 PM Coralie Khabbaz 
wrote:

> Also, when I performed the first relaxation, the first scf step converged
> so then I stopped it, took the new atomic positions I got and redid a
> relaxation calculation. Again, my first step converged but the second
> didn't. I don't understand why the first step converges even with the new
> positions but it didn't converge the first time (at the second step).
>
> On Fri, 10 Jul 2020 at 14:17, Coralie Khabbaz 
> wrote:
>
>> I don't see why I need to change my structure entirely, as I already
>> performed relaxation calculations and they worked. All my scf calculations
>> also worked. Is there something else you can think of? Thank you!
>>
>> On Fri, 10 Jul 2020 at 14:09, Duy Le  wrote:
>>
>>> Unit should be Ry/au. Try to remake your structure with reasonable bond
>>> length and angle so force can be reduced to as small as possible (less than
>>> 1Ry/au)
>>>
>>> Duy Le
>>> (UCF)
>>>
>>> On Fri, Jul 10, 2020 at 2:02 PM Coralie Khabbaz <
>>> khabbaz.cora...@gmail.com> wrote:
>>>
>>>> My force is around -18900 Ry. Do you think it's reasonable? Thank you!
>>>>
>>>> On Fri, 10 Jul 2020 at 14:00, Duy Le  wrote:
>>>>
>>>>> Meaning not too large. Large forces would lead to bad relaxation to
>>>>> unrealistic structure that cause convergence problems
>>>>>
>>>>> Duy Le
>>>>> (UCF)
>>>>>
>>>>> On Fri, Jul 10, 2020 at 1:13 PM Coralie Khabbaz <
>>>>> khabbaz.cora...@gmail.com> wrote:
>>>>>
>>>>>> Hello Duy Le,
>>>>>>
>>>>>> Thank you so much for your answer. What do you mean by reasonable
>>>>>> forces? I have performed several scf calculations before and I get energy
>>>>>> values that are consistent.
>>>>>>
>>>>>> On Fri, 10 Jul 2020 at 13:08, Duy Le  wrote:
>>>>>>
>>>>>>> It could be because of non-realistic structure as a result of
>>>>>>> relaxation. Please check the force in previously converged scf to see if
>>>>>>> they are reasonable. If not you may need to remake the starting 
>>>>>>> structure
>>>>>>> so it has reasonable forces.
>>>>>>>
>>>>>>> Duy Le
>>>>>>> (UCF)
>>>>>>>
>>>>>>> On Fri, Jul 10, 2020 at 12:53 PM Coralie Khabbaz <
>>>>>>> khabbaz.cora...@gmail.com> wrote:
>>>>>>>
>>>>>>>> Also, when I perform scf calculation (and not relaxation), my
>>>>>>>> energy value converges!!
>>>>>>>>
>>>>>>>> On Fri, 10 Jul 2020 at 12:30, Coralie Khabbaz <
>>>>>>>> khabbaz.cora...@gmail.com> wrote:
>>>>>>>>
>>>>>>>>> Hello,
>>>>>>>>>
>>>>>>>>> I am performing a relaxation calculation on my Tungsten nitride
>>>>>>>>> (WN) slab with a methane molecule adsorbed on its surface. My first 
>>>>>>>>> scf
>>>>>>>>> calculations always converges, but all the other scf calculations keep
>>>>>>>>> oscillating a little bit, like this:
>>>>>>>>>
>>>>>>>>> iteration #107 ecut=50.39 Ry beta=0.10
>>>>>>>>>  Davidson diagonalization with overlap
>>>>>>>>>  ethr =  1.00E-02,  avg # of iterations =  3.2
>>>>>>>>>
>>>>>>>>>  negative rho (up, down):  1.877E+02 1.832E+02
>>>>>>>>>
>>>>>>>>>  total cpu time spent up to now is 6820.6 secs
>>>>>>>>>
>>>>>>>>>  total energy  =  -22310.34633946 Ry
>>>>>>>>>  Harris-Foulkes estimate   =  -22286.51427887 Ry
>>>>>>>>>  estimated scf accuracy<   36291.44935321 Ry
>>>>>>>>>
>>>>>>>>>  

Re: [QE-users] second scf calculation in relax calculation not converging

[Duy Le]

Meaning not too large. Large forces would lead to bad relaxation to
unrealistic structure that cause convergence problems

Duy Le
(UCF)

On Fri, Jul 10, 2020 at 1:13 PM Coralie Khabbaz 
wrote:

> Hello Duy Le,
>
> Thank you so much for your answer. What do you mean by reasonable forces?
> I have performed several scf calculations before and I get energy values
> that are consistent.
>
> On Fri, 10 Jul 2020 at 13:08, Duy Le  wrote:
>
>> It could be because of non-realistic structure as a result of relaxation.
>> Please check the force in previously converged scf to see if they are
>> reasonable. If not you may need to remake the starting structure so it has
>> reasonable forces.
>>
>> Duy Le
>> (UCF)
>>
>> On Fri, Jul 10, 2020 at 12:53 PM Coralie Khabbaz <
>> khabbaz.cora...@gmail.com> wrote:
>>
>>> Also, when I perform scf calculation (and not relaxation), my energy
>>> value converges!!
>>>
>>> On Fri, 10 Jul 2020 at 12:30, Coralie Khabbaz 
>>> wrote:
>>>
>>>> Hello,
>>>>
>>>> I am performing a relaxation calculation on my Tungsten nitride (WN)
>>>> slab with a methane molecule adsorbed on its surface. My first scf
>>>> calculations always converges, but all the other scf calculations keep
>>>> oscillating a little bit, like this:
>>>>
>>>> iteration #107 ecut=50.39 Ry beta=0.10
>>>>  Davidson diagonalization with overlap
>>>>  ethr =  1.00E-02,  avg # of iterations =  3.2
>>>>
>>>>  negative rho (up, down):  1.877E+02 1.832E+02
>>>>
>>>>  total cpu time spent up to now is 6820.6 secs
>>>>
>>>>  total energy  =  -22310.34633946 Ry
>>>>  Harris-Foulkes estimate   =  -22286.51427887 Ry
>>>>  estimated scf accuracy<   36291.44935321 Ry
>>>>
>>>>  total magnetization   = 0.88 Bohr mag/cell
>>>>  absolute magnetization=13.09 Bohr mag/cell
>>>>
>>>>  iteration #108 ecut=50.39 Ry beta=0.10
>>>>  Davidson diagonalization with overlap
>>>>  ethr =  1.00E-02,  avg # of iterations =  2.0
>>>>
>>>>  negative rho (up, down):  1.828E+02 1.844E+02
>>>>
>>>>  total cpu time spent up to now is 6849.8 secs
>>>>
>>>>  total energy  =  -22482.46538384 Ry
>>>>  Harris-Foulkes estimate   =  -22312.40216721 Ry
>>>>  estimated scf accuracy<   36350.61037433 Ry
>>>>
>>>>  total magnetization   = 0.84 Bohr mag/cell
>>>>  absolute magnetization=11.93 Bohr mag/cell
>>>>
>>>>  iteration #109 ecut=50.39 Ry beta=0.10
>>>>  Davidson diagonalization with overlap
>>>>  ethr =  1.00E-02,  avg # of iterations =  3.0
>>>>
>>>>  negative rho (up, down):  1.848E+02 1.794E+02
>>>>
>>>>  total cpu time spent up to now is 6888.4 secs
>>>>
>>>>  total energy  =  -22531.89474337 Ry
>>>>  Harris-Foulkes estimate   =  -22546.66368909 Ry
>>>>  estimated scf accuracy<   34615.41965371 Ry
>>>>
>>>>  total magnetization   = 0.49 Bohr mag/cell
>>>>  absolute magnetization= 8.33 Bohr mag/cell
>>>>
>>>>  iteration #110 ecut=50.39 Ry beta=0.10
>>>>  Davidson diagonalization with overlap
>>>>  ethr =  1.00E-02,  avg # of iterations =  3.5
>>>>
>>>>  negative rho (up, down):  1.882E+02 1.776E+02
>>>>
>>>>  total cpu time spent up to now is 6947.2 secs
>>>>
>>>>  total energy  =  -22697.64012878 Ry
>>>>  Harris-Foulkes estimate   =  -22561.26019900 Ry
>>>>  estimated scf accuracy<   35110.57986884 Ry
>>>>
>>>>  total magnetization   = 1.02 Bohr mag/cell
>>>>  absolute magnetization= 8.80 Bohr mag/cell
>>>>
>>>>  iteration #111 ecut=50.39 Ry beta=0.10
>>>>  Davidson diagonalization with overlap
>>>>  ethr =  1.00E-02,  avg # of iterations =  3.0
>>>>
>>>>  negative rho (up, down):  1.953E+02 1.846E+02
>>>>
>>>>  total cpu time spent up to now is 6984.5 

Re: [QE-users] second scf calculation in relax calculation not converging

[Duy Le]

It could be because of non-realistic structure as a result of relaxation.
Please check the force in previously converged scf to see if they are
reasonable. If not you may need to remake the starting structure so it has
reasonable forces.

Duy Le
(UCF)

On Fri, Jul 10, 2020 at 12:53 PM Coralie Khabbaz 
wrote:

> Also, when I perform scf calculation (and not relaxation), my energy value
> converges!!
>
> On Fri, 10 Jul 2020 at 12:30, Coralie Khabbaz 
> wrote:
>
>> Hello,
>>
>> I am performing a relaxation calculation on my Tungsten nitride (WN) slab
>> with a methane molecule adsorbed on its surface. My first scf calculations
>> always converges, but all the other scf calculations keep oscillating a
>> little bit, like this:
>>
>> iteration #107 ecut=50.39 Ry beta=0.10
>>  Davidson diagonalization with overlap
>>  ethr =  1.00E-02,  avg # of iterations =  3.2
>>
>>  negative rho (up, down):  1.877E+02 1.832E+02
>>
>>  total cpu time spent up to now is 6820.6 secs
>>
>>  total energy  =  -22310.34633946 Ry
>>  Harris-Foulkes estimate   =  -22286.51427887 Ry
>>  estimated scf accuracy<   36291.44935321 Ry
>>
>>  total magnetization   = 0.88 Bohr mag/cell
>>  absolute magnetization=13.09 Bohr mag/cell
>>
>>  iteration #108 ecut=50.39 Ry beta=0.10
>>  Davidson diagonalization with overlap
>>  ethr =  1.00E-02,  avg # of iterations =  2.0
>>
>>  negative rho (up, down):  1.828E+02 1.844E+02
>>
>>  total cpu time spent up to now is 6849.8 secs
>>
>>  total energy  =  -22482.46538384 Ry
>>  Harris-Foulkes estimate   =  -22312.40216721 Ry
>>  estimated scf accuracy<   36350.61037433 Ry
>>
>>  total magnetization   = 0.84 Bohr mag/cell
>>  absolute magnetization=11.93 Bohr mag/cell
>>
>>  iteration #109 ecut=50.39 Ry beta=0.10
>>  Davidson diagonalization with overlap
>>  ethr =  1.00E-02,  avg # of iterations =  3.0
>>
>>  negative rho (up, down):  1.848E+02 1.794E+02
>>
>>  total cpu time spent up to now is 6888.4 secs
>>
>>  total energy  =  -22531.89474337 Ry
>>  Harris-Foulkes estimate   =  -22546.66368909 Ry
>>  estimated scf accuracy<   34615.41965371 Ry
>>
>>  total magnetization   = 0.49 Bohr mag/cell
>>  absolute magnetization= 8.33 Bohr mag/cell
>>
>>  iteration #110 ecut=50.39 Ry beta=0.10
>>  Davidson diagonalization with overlap
>>  ethr =  1.00E-02,  avg # of iterations =  3.5
>>
>>  negative rho (up, down):  1.882E+02 1.776E+02
>>
>>  total cpu time spent up to now is 6947.2 secs
>>
>>  total energy  =  -22697.64012878 Ry
>>  Harris-Foulkes estimate   =  -22561.26019900 Ry
>>  estimated scf accuracy<   35110.57986884 Ry
>>
>>  total magnetization   = 1.02 Bohr mag/cell
>>  absolute magnetization= 8.80 Bohr mag/cell
>>
>>  iteration #111 ecut=50.39 Ry beta=0.10
>>  Davidson diagonalization with overlap
>>  ethr =  1.00E-02,  avg # of iterations =  3.0
>>
>>  negative rho (up, down):  1.953E+02 1.846E+02
>>
>>  total cpu time spent up to now is 6984.5 secs
>>
>>  total energy  =  -22595.85493501 Ry
>>  Harris-Foulkes estimate   =  -22716.54469069 Ry
>>  estimated scf accuracy<   35636.87841917 Ry
>>
>>  total magnetization   = 1.33 Bohr mag/cell
>>  absolute magnetization=11.84 Bohr mag/cell
>>
>>  iteration #112 ecut=50.39 Ry beta=0.10
>>  Davidson diagonalization with overlap
>>  ethr =  1.00E-02,  avg # of iterations =  3.0
>>
>>  negative rho (up, down):  2.248E+02 1.996E+02
>>
>>  total cpu time spent up to now is 7023.3 secs
>>
>>  total energy  =  -22958.24642440 Ry
>>  Harris-Foulkes estimate   =  -22626.00971729 Ry
>>  estimated scf accuracy<   38324.66640261 Ry
>>
>>  total magnetization   = 1.31 Bohr mag/cell
>>  absolute magnetization=10.12 Bohr mag/cell
>>
>>  iteration #113 ecut=50.39 Ry beta=0.10
>>  Davidson diagonalization with overlap
>>  ethr =  1.00E-02,  avg # of iterations =  3.0
>>
>>  negative rh

Re: [QE-users] Relax calculations stops after few iterations

[Duy Le]

perhaps you have a wrong or very bad starting structure.

Duy Le
University of Central Florida

On Sat, Jun 6, 2020 at 5:47 AM Poonam Kaushik 
wrote:

> Hello All,
> I want to do a relax calculation for FeS. The forces  that I calculated is
> Total force =11.363189 Total SCF correction = 0.000116
>  entering subroutine stress ...
> total   stress  (Ry/bohr**3)   (kbar) P=82027.53
>0.53727930   0.   0.  79036.50  0.00  0.00
>0.   0.53727930   0.  0.00  79036.50  0.00
>0.   0.   0.59827705  0.00  0.00  88009.58
>
> When I am performing the relax calculations, it stops after few iterations
> and not proceeding further. Here is my input file relax.in
> 
> calculation  = "relax",
> restart_mode = "from_scratch",
> wf_collect   = .true.
> tstress  = .true.
> tprnfor  = .true.
> pseudo_dir = '/home/poonam/fes3/pseudo',
> outdir='ami'
> /
> 
> ibrav = 0,
> nat= 24, ntyp= 3,
> ecutwfc = 55.0,
> occupations='smearing', degauss=0.01
> nspin = 2,
> starting_magnetization(1)= 0.5
> starting_magnetization(2)=-0.5,
> lda_plus_u = .true.,
> !U_projection_type = 'ortho-atomic'
> Hubbard_U(1) = 7.1,
> Hubbard_U(2) = 7.1
> /
> 
>   conv_thr =   4.80d-09
>   electron_maxstep = 80
>   mixing_beta =   4.00d-01
> /
> 
> /
> 
> /
> CELL_PARAMETERS angstrom
>  5.9487492159093023   -0.   -0.
> -2.97437460795465115.15176794171171260.
> -0.0.   11.7211034581915818
> ATOMIC_SPECIES
>  Fe1 55.847 Fe.pz-nd-rrkjus.UPF
>  Fe2 55.847 Fe.pz-nd-rrkjus.UPF
>  S   32.066 S.pz-n-rrkjus_psl.0.1.UPF
> ATOMIC_POSITIONS crystal
> Fe1  0.3954866316692124  0.0721204949184797  0.1217724210678790
> Fe1  0.9278795160815250  0.3233661487507409  0.1217724210678790
> Fe1  0.6766338512492591  0.6045133683307876  0.1217724210678790
> Fe2  0.3954866316692124  0.0721204949184797  0.3782275859321179
> Fe2  0.9278795160815250  0.3233661487507409  0.3782275859321179
> Fe2  0.6766338512492591  0.6045133683307876  0.3782275859321179
> Fe1  0.0721204949184797  0.3954866316692124  0.6217724140678820
> Fe1  0.3233661487507409  0.9278795160815250  0.6217724140678820
> Fe1  0.6045133683307876  0.6766338512492591  0.6217724140678820
> Fe2  0.0721204949184797  0.3954866316692124  0.8782275859321180
> Fe2  0.3233661487507409  0.9278795160815250  0.8782275859321180
> Fe2  0.6045133683307876  0.6766338512492591  0.8782275859321180
> S   -0. -0.  0.
> S   -0. -0.  0.5000
> S0.33342996  0.66687029  0.0251416953082458
> S0.33342996  0.66687029  0.4748582936917498
> S0.66687029  0.33342996  0.9748582936917498
> S0.66687029  0.33342996  0.5251417063082502
> S0.6643064194527374  0.477489745914  0.2500
> S0.522750254107  0.6643586704781460  0.2500
> S0.3356412995218515  0.3356935805472627  0.2500
> S0.477489745914  0.6643064194527374  0.7500
> S0.6643586704781460  0.522750254107  0.7500
> K_POINTS (automatic)
> 4 4 4 0 0 0
> I am not able to understand, after a few iterations, why it is not
> proceeding further. I tried with a different ecut, K points, and changing
> the diagonalization, but nothing is working.
>  Please have a look, any suggestions would be greatly appreciable.
>
> warm regards,
> Poonam Sharma
>
>
>
>
>
>
>
> -
> Poonam Sharma
> Research Scholar
> Department of Physics
> Indian Institute of Technology Bombay
> Mumbai - 400076
> India.
>
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[QE-users] Wave function on dense grid

[Duy Le]

Dear Developers (and all),

I want to have wave function and charge density on the same real-space grid
(preferably on dfftp). I tried 2 ways:
call invfft ('Rho', psic, dfftp)
Or
call invfft ('Wave', psic, dffts)
call fft_interpolate (dffts, psic, dfftp, psic )

Both give identical results. I wonder if they are both correct ways to do
this. Or did I miss something

Another question: there are couple different way to get Fourier Coefficient
(davcio, read_collected_wfc, get_buffer). I test them all and they seem to
work well. I wonder if you could tell me the advantage/disadvantage of each
subroutine?

Thank you very much.
Duy Le
University of Central Florida
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Re: [QE-users] Inconsistent total energy between different version

[Duy Le]

Thank Kevin,

That would explain it. It was my bad that I did not see the note.

Best,

Duy Le
UCF

On Thu, Apr 19, 2018 at 1:38 PM, Kevin May <k...@mit.edu> wrote:

> Hi,
>
> In the release notes for 6.2 it says:
>
> * Some constants in the definition of PBE functionals were truncated to
> 6 significant digits. While not a bug, this could lead to tiny differences
> with respect to previous results and other XC implementations (r13592)
>
>
> I would guess this explains it.
>
> Best
>
> Kevin May
> PhD Candidate
> Department of Mechanical Engineering
> MIT
>
>
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[QE-users] Inconsistent total energy between different version

[Duy Le]

Dear all,

I wonder if any of you experience this behavior. Basically, the total
energy is the same for all version til 6.1.0.
6.2.0 and SVN versions produce a slight difference in total energy. The
input can be found at the end of the message
Or you see all input and output for this test at

https://gitlab.com/zoowe/q-e/tree/master/ERROR

Version Energy [Ry]
5.0 -328.17737884
5.4.0   -328.17737884
6.0 -328.17737884
6.1.0   -328.17737884
6.2.0   -328.17776289
20180418-328.17776289

Duy Le
University of Central Florida


---
cat input.inp


! .control.settings.
calculation   = 'scf',
restart_mode  = 'from_scratch',
prefix= 'pwscf',
pseudo_dir= './',

! .control.io.
verbosity = 'high',
disk_io   = 'none',
wf_collect= .true.,
outdir= './tmp/',

! .control.ion_relax.
etot_conv_thr = 0.1,
forc_conv_thr = 0.001,
nstep = 100,
tprnfor   = .true.,
tstress   = .true.,
/


! .system.structure.
a = 1.0,
ibrav = 0,
nat   = 2,
ntyp  = 1,

! .system.ecut.
ecutwfc   = 50,
ecutrho   = 200,

! .system.occupations.
occupations   = 'smearing',
degauss   = 0.007,
smearing  = 'gaussian',
/


! .electrons.
diagonalization   = 'david',
mixing_mode   = 'plain',
electron_maxstep  = 100,
mixing_beta   = 0.7,
conv_thr  = 1e-07,
/

ATOMIC_SPECIES
   Ge  72.6300 Ge.pbe-n-kjpaw_psl.1.0.0.UPF

ATOMIC_POSITIONS  crystal
 Ge 0.00 0.00 0.00   1   1
 1
 Ge 0.25 0.25 0.25   1   1
 1
CELL_PARAMETERS
0.00 2.83 2.83
2.83 0.00 2.83
2.83 2.83 0.00

K_POINTS automatic
   3 3 3 0 0 0
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Re: [Pw_forum] HELP !!! How to know the DOS out file right or wrong ?!

[Duy Le]

Please be more specific. What is the number did you get?
I am not assuming you have 8 valence electrons. Check your scf or nscf
output to see number of electrons.

DL

On Mon, Oct 2, 2017 at 12:53 PM, Nga Do <dong...@gmail.com> wrote:

> Dear Duy Le,
>
> I would like to check the values of the DOS file right or not, so I
> calculate the total valence electron.
> I do a Integral from the Fermi level to minus infinite. Total valence
> electrons in ZnO are 8.
> But the obtained result is not equal 8. It is always larger than 8.
> please give me some advices for this.
>
> Best regards,
> Nga
>
>
> On Mon, Oct 2, 2017 at 9:16 PM, Duy Le <ttdu...@gmail.com> wrote:
>
>> I don't see any problem with the plot.
>> That was the effect of broadening. Check keywords: nguass and degauss
>>
>> On Mon, Oct 2, 2017 at 2:51 AM, Nga Do <dong...@gmail.com> wrote:
>>
>>> Dear Manu,
>>>
>>> I am using GGA in the scheme of Perdew-Burke-Ernzerhof and ultrasoft
>>> pseudopotential with the value for cut-off energy 40 Ry for all my
>>> calculations.
>>>
>>> Dear Duy,
>>>
>>> Here is the plot. Please take a look.
>>>
>>> Best regards,
>>> Nga
>>>
>>>
>>>
>>> On Mon, Oct 2, 2017 at 2:47 AM, Duy Le <ttdu...@gmail.com> wrote:
>>>
>>>> Please post a plot, instead of data file.
>>>> Thanks
>>>>
>>>> Duy Le
>>>> University of Central Florida
>>>>
>>>> On Sun, Oct 1, 2017 at 1:09 AM, Nga Do <dong...@gmail.com> wrote:
>>>>
>>>>> ​
>>>>> Dear QE users,
>>>>>
>>>>> I am a new QE user and trying to calculate the electron concentration
>>>>> of pure ZnO and some different kind of defects in same system from DOS
>>>>> file. But the problem is I am not sure that the DOS file that I calculated
>>>>> is right.
>>>>> Please give me some advices and suggestions !!!
>>>>>
>>>>> These are my following steps to calculate DOS ( the attached files
>>>>> below)
>>>>> 1) scf calculation
>>>>> 2) none scf calculation
>>>>> 3) calculate DOS. When I plot the DOS I did shift the Fermi level
>>>>> (9.5021 eV) (I take it from scf.out file ) to zero ( "F_zno_1.dos" file. )
>>>>> .
>>>>>
>>>>> Mesh of k-points in scf calculation is 4x4x3. Firstly, I keep the same
>>>>> mesh of k-points for the n-scf calculation.
>>>>> I set "occupations = 'fixed'" to find the gap first, and then set
>>>>> "occupations = 'tetrahedra' to the DOS step.
>>>>> But when I checked the DOS file, I found that there were still states
>>>>> between highest occupied ( 8.8056 eV) and lowest unoccupied level  (9.6268
>>>>> eV).
>>>>> I plot the DOS and can see where is the gap, but why there are states
>>>>> in the gap ?!
>>>>> I timed double the mesh of k-points for n-scf calculation 8x8x6 and
>>>>> the results did not change much. I think the gap from the Fermi level to
>>>>> the bottom of Conduction band should not have any states in it.
>>>>> Please check my calculations and give me some advices about this
>>>>> issue!?
>>>>> Here is the link to attached files, please take a look:
>>>>> https://drive.google.com/open?id=0BwnHIyCcZ3jbb0c4eDBXZldOc1E
>>>>>
>>>>> Best regards,
>>>>> Nga​
>>>>>
>>>>> --
>>>>> Nga Do
>>>>> Ho Chi Minh City Institute of Physics
>>>>> Third floor, Building 1, Mac Dinh Chi street, Ben Nghe Ward, District
>>>>> 1, Ho Chi Minh City, Vietnam
>>>>> website: www.vast.ac.vn
>>>>> Mobile: +84 938 672 414 <+84%2093%20867%2024%2014>
>>>>>
>>>>>
>>>>>
>>>>> ___
>>>>> Pw_forum mailing list
>>>>> Pw_forum@pwscf.org
>>>>> http://pwscf.org/mailman/listinfo/pw_forum
>>>>>
>>>>
>>>>
>>>> ___
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>>>> http://pwscf.org/mailman/listinfo/pw_forum
>>>>
>>>
>>>
>>>
>>> --
>>> Nga Do
>>> Ho Chi Minh City Institute of Physics
>>> Third floor, Building 1, Mac Dinh Chi street, Ben Nghe Ward, District 1,
>>> Ho Chi Minh City, Vietnam
>>> website: www.vast.ac.vn
>>> Mobile: +84 938 672 414 <+84%2093%20867%2024%2014>
>>>
>>>
>>>
>>> ___
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>>> Pw_forum@pwscf.org
>>> http://pwscf.org/mailman/listinfo/pw_forum
>>>
>>
>>
>> ___
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>>
>
>
>
> --
> Nga Do
> Ho Chi Minh City Institute of Physics
> Third floor, Building 1, Mac Dinh Chi street, Ben Nghe Ward, District 1,
> Ho Chi Minh City, Vietnam
> website: www.vast.ac.vn
> Mobile: +84 938 672 414 <+84%2093%20867%2024%2014>
>
>
>
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Re: [Pw_forum] HELP !!! How to know the DOS out file right or wrong ?!

[Duy Le]

I don't see any problem with the plot.
That was the effect of broadening. Check keywords: nguass and degauss

On Mon, Oct 2, 2017 at 2:51 AM, Nga Do <dong...@gmail.com> wrote:

> Dear Manu,
>
> I am using GGA in the scheme of Perdew-Burke-Ernzerhof and ultrasoft
> pseudopotential with the value for cut-off energy 40 Ry for all my
> calculations.
>
> Dear Duy,
>
> Here is the plot. Please take a look.
>
> Best regards,
> Nga
>
>
>
> On Mon, Oct 2, 2017 at 2:47 AM, Duy Le <ttdu...@gmail.com> wrote:
>
>> Please post a plot, instead of data file.
>> Thanks
>>
>> Duy Le
>> University of Central Florida
>>
>> On Sun, Oct 1, 2017 at 1:09 AM, Nga Do <dong...@gmail.com> wrote:
>>
>>> ​
>>> Dear QE users,
>>>
>>> I am a new QE user and trying to calculate the electron concentration of
>>> pure ZnO and some different kind of defects in same system from DOS file.
>>> But the problem is I am not sure that the DOS file that I calculated is
>>> right.
>>> Please give me some advices and suggestions !!!
>>>
>>> These are my following steps to calculate DOS ( the attached files below)
>>> 1) scf calculation
>>> 2) none scf calculation
>>> 3) calculate DOS. When I plot the DOS I did shift the Fermi level
>>> (9.5021 eV) (I take it from scf.out file ) to zero ( "F_zno_1.dos" file. )
>>> .
>>>
>>> Mesh of k-points in scf calculation is 4x4x3. Firstly, I keep the same
>>> mesh of k-points for the n-scf calculation.
>>> I set "occupations = 'fixed'" to find the gap first, and then set
>>> "occupations = 'tetrahedra' to the DOS step.
>>> But when I checked the DOS file, I found that there were still states
>>> between highest occupied ( 8.8056 eV) and lowest unoccupied level  (9.6268
>>> eV).
>>> I plot the DOS and can see where is the gap, but why there are states in
>>> the gap ?!
>>> I timed double the mesh of k-points for n-scf calculation 8x8x6 and the
>>> results did not change much. I think the gap from the Fermi level to the
>>> bottom of Conduction band should not have any states in it.
>>> Please check my calculations and give me some advices about this issue!?
>>> Here is the link to attached files, please take a look:
>>> https://drive.google.com/open?id=0BwnHIyCcZ3jbb0c4eDBXZldOc1E
>>>
>>> Best regards,
>>> Nga​
>>>
>>> --
>>> Nga Do
>>> Ho Chi Minh City Institute of Physics
>>> Third floor, Building 1, Mac Dinh Chi street, Ben Nghe Ward, District 1,
>>> Ho Chi Minh City, Vietnam
>>> website: www.vast.ac.vn
>>> Mobile: +84 938 672 414 <+84%2093%20867%2024%2014>
>>>
>>>
>>>
>>> ___
>>> Pw_forum mailing list
>>> Pw_forum@pwscf.org
>>> http://pwscf.org/mailman/listinfo/pw_forum
>>>
>>
>>
>> ___
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>> http://pwscf.org/mailman/listinfo/pw_forum
>>
>
>
>
> --
> Nga Do
> Ho Chi Minh City Institute of Physics
> Third floor, Building 1, Mac Dinh Chi street, Ben Nghe Ward, District 1,
> Ho Chi Minh City, Vietnam
> website: www.vast.ac.vn
> Mobile: +84 938 672 414 <+84%2093%20867%2024%2014>
>
>
>
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> Pw_forum@pwscf.org
> http://pwscf.org/mailman/listinfo/pw_forum
>
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Re: [Pw_forum] How can vc-relax nanosheet that will fall apart or would be bulk?

[Duy Le]

You should try to do a normal relaxation to see if your structure is
stable. Then use the relaxed one to start vc-relax.

Duy Le
University of Central Florida

On Sat, Sep 30, 2017 at 11:34 AM, khadije alvani <khadijealv...@gmail.com>
wrote:

> Dear Q-E users,
> I try to  get vc-relax with setting ( using q-e 6.1):
>
> 
>  calculation = 'vc-relax' ,
> restart_mode = 'from_scratch' ,
> etot_conv_thr = 1.0E-5  ,
>forc_conv_thr = 1.0D-4 ,
>outdir=
> pseudo_dir =
> tprnfor   = .true.
> tstress = .true.
>  /
>  
> ibrav = 4,
>celldm(1)=7.3509958804,
>celldm(3)=3.8560411311,
>  nbnd =16,
>  nat =2,
> ntyp = 2,
>  ecutwfc = 185 ,
>  ecutrho = 740,
>  /
>  
>   conv_thr = 1.D-8 ,
>   electron_maxstep = 5000
>   mixing_beta = 0.7,
> /
> 
>   ion_dynamics= 'bfgs',
>   upscale  = 100.d0,
>
>
> /
>  
>cell_dynamics = 'bfgs' ,
>cell_factor = 2
>   /
> ATOMIC_SPECIES
> Zn65.380Zn.pbe-d-hgh.UPF
> S32.065S.pbe-hgh.UPF
> ATOMIC_POSITIONS (angstrom)
> Zn0.02.2487.5
> S1.94682510771.1247.5
> K_POINTS {automatic}
> 8 8 1   0 0 0
>
> but when I set  'Z=7.5 ‘ and ' cell _dofree=2Dxy ‘,  the structure of the
> nano sheet fell apart and when I relax in 3 directions , Z direction is
> decreased and would be bulk structure, so the nano sheet structure will
> lose.
> Of course it has already been done with gasp,win2k,.. .
>
> I will sincerely appreciate any comment that can help me proceed with my
> calculations.
> thank you.
> with regards
> khadije alvani
> student of university of IRAN.
> tel:  +98  916 813 4896 <+98%20916%20813%204896>
>
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Re: [Pw_forum] HELP !!! How to know the DOS out file right or wrong ?!

[Duy Le]

Please post a plot, instead of data file.
Thanks

Duy Le
University of Central Florida

On Sun, Oct 1, 2017 at 1:09 AM, Nga Do <dong...@gmail.com> wrote:

> ​
> Dear QE users,
>
> I am a new QE user and trying to calculate the electron concentration of
> pure ZnO and some different kind of defects in same system from DOS file.
> But the problem is I am not sure that the DOS file that I calculated is
> right.
> Please give me some advices and suggestions !!!
>
> These are my following steps to calculate DOS ( the attached files below)
> 1) scf calculation
> 2) none scf calculation
> 3) calculate DOS. When I plot the DOS I did shift the Fermi level (9.5021
> eV) (I take it from scf.out file ) to zero ( "F_zno_1.dos" file. ) .
>
> Mesh of k-points in scf calculation is 4x4x3. Firstly, I keep the same
> mesh of k-points for the n-scf calculation.
> I set "occupations = 'fixed'" to find the gap first, and then set
> "occupations = 'tetrahedra' to the DOS step.
> But when I checked the DOS file, I found that there were still states
> between highest occupied ( 8.8056 eV) and lowest unoccupied level  (9.6268
> eV).
> I plot the DOS and can see where is the gap, but why there are states in
> the gap ?!
> I timed double the mesh of k-points for n-scf calculation 8x8x6 and the
> results did not change much. I think the gap from the Fermi level to the
> bottom of Conduction band should not have any states in it.
> Please check my calculations and give me some advices about this issue!?
> Here is the link to attached files, please take a look:
> https://drive.google.com/open?id=0BwnHIyCcZ3jbb0c4eDBXZldOc1E
>
> Best regards,
> Nga​
>
> --
> Nga Do
> Ho Chi Minh City Institute of Physics
> Third floor, Building 1, Mac Dinh Chi street, Ben Nghe Ward, District 1,
> Ho Chi Minh City, Vietnam
> website: www.vast.ac.vn
> Mobile: +84 938 672 414 <+84%2093%20867%2024%2014>
>
>
>
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>
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Re: [Pw_forum] Calculation of transition dipole moment

[Duy Le]

Or you can get wave function for each bands, then write a code to calculate
the dipoles.
pw2casino option should give you humanly readable wave function.

On Wed, Feb 15, 2017 at 10:31 AM, dario rocca  wrote:

> Dear Huy Pham,
> I don't know if this is the easiest way but you could use the turboTDDFT
> code
> https://arxiv.org/pdf/1402.0486.pdf
> If you use the davidson diagonalization and the option no_hxc=.true. you
> will obtain as output some oscillator strengths which are
> proportional to the transition dipole moments between Kohn-Sham valence
> and conduction states. You will need to verify the units.
> If no_hxc=.false. you obtain a similar quantity at the TDDFT level. In
> this case conduction (and valence) bands are mixed together by Hartree-xc
> effects in
> the TDDFT kernel.
> Best,
> Dario
>
> On Wed, Feb 15, 2017 at 1:19 AM, Huy Pham  wrote:
>
>> Dear QE users,
>>
>> I want to calculate the transition dipole moment between conduction and
>> valence bands for an isolated molecule using QE. I searched the forum but
>> didn't find much information.
>> Can anyone give me some suggestions?
>>
>> Thanks,
>> Huy
>>
>> --
>> Huy Pham, PhD
>> Postdoctoral Researcher
>> Department of Chemistry and Biochemistry
>> University of California, San Diego
>> 9500 Gilman Drive
>> Urey Hall 4205
>> La Jolla, CA 92093
>> E-mail:
>> pchuy1...@gmail.com
>>
>>
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>
>
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Re: [Pw_forum] problem in post-processing: charge density minus superposition of atomic densities

[Duy Le]

It should give zero or very close to zero, unless your calculation is not
accurate or your grid is not dense enough.

Duy Le
University of Central Florida.
On Nov 2, 2016 11:17 AM, "Uri Argaman" <argam...@post.bgu.ac.il> wrote:

> Dear QE experts
> I do a PP calculation to get the charge density minus superposition of
> atomic densities with the following input:
>  
> prefix  = 'ti'
> outdir = '/home/uriargaman/tmp8086/TMP_PLOTDELTARHO/'
> filplot = 'ti_delta_charge'
> plot_num= 9
>  /
>  
> nfile = 1
> filepp(1) = 'ti_delta_charge'
> weight(1) = 1.0
> iflag = 3
> output_format = 5
> fileout = 'ti.delta_rho.xsf'
> e1(1) =1.0, e1(2)=0.0, e1(3) = 0.0,
> e2(1) =0.0, e2(2)=1.0, e2(3) = 0.0,
> e3(1) =0.0, e3(2)=0.0, e3(3) = 1.0,
> nx=50, ny=50, nz=50
> The most negative value is: -0.008 and the most positive value is: 0.05.
> In addition, the positive values do not balanced with the negative values
> (the integral over all space is positive). Why this integral do not vanish?
> Thank you very much
> Uri Argaman
> Ben-Gurion University
> Israel
>
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Re: [Pw_forum] nscf calculation

[Duy Le]

Hi Wang,
You should ask that "somebody" to see what he is trying to do. These steps
look unconventional, not doable to me. I doubt that he get something
meaningful out of them.

Duy Le
University of Central Florida
On Nov 3, 2016 2:21 AM, "Q.J.Wang" <wang...@126.com> wrote:

> Dear Paolo,
>
> I found somebody to calculate differential charge of materials using nscf
> and scf, the calculation steps are described as belowing:
>
> 1.  Doing a non-self-consistent calculation using *pw.x*
>  (setting electron_maxstep=0), and obtaining the total charge data using
> *pp.x* (e.g. filplot='nscf_charge.dat', plot_num=0);
>
> 2.  Doing another self-consistent calculation using *pw.x*,
> and obtaining the total charge data using*pp.x* (e.g. filplot='scf_
> charge.dat', plot_num=0);
>
> At last, the differential charge is gotten by a post-processing utility,
> however, I can't perform the nscf without scf at first.
>
>
> --
>
> Best regards
>
>
>
> Q.J. Wang
>
> XiangTan University
>
>
>
>
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[Pw_forum] DOS

[Duy Le]

You need increase k-point sampling you can and reduce smearing.

Duy Le
Postdoctoral Associate
Department of Physics
University of Central Florida.
Website: http://www.physics.ucf.edu/~dle


On Wed, Dec 18, 2013 at 3:26 PM, ehsan targholi  wrote:
> hi
> Dear all
> i want to calculate DOS for graphene , but my result not  compatible with
> reference . the range of -1.5 to 1.5 is important for me . for this range
> the result of reference is lower than of my calculated DOS . the reference
> DOS in zero value of energy is zero but my calculated DOS not zero,please
> help me to solve this problem.
> the image of reference DOS & my cal. DOS is attached.
>
>
> best regard
> ehsan targholi
> graduate student of chemistry department of iust
>
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[Pw_forum] Forces are not zero (for atoms in non-primitive cell)

[Duy Le]

Thank Lorenzo,

I did assure those settings. I can get identical energy. However, the
x-y forces are not going to zero.

Duy

Duy Le
Postdoctoral Associate
Department of Physics
University of Central Florida.
Website: http://www.physics.ucf.edu/~dle


On Wed, Nov 20, 2013 at 12:16 PM, Lorenzo Paulatto
 wrote:
> On 11/20/2013 05:54 PM, Duy Le wrote:
>> Dear all,
>>
>> I wonder if anyone knows how to vanish the forces acting on atoms in a
>> non-primitive cell. I saw that if I have 1x1x5 cell of Cu(111) (or any
>> other systems), the x-y components of forces are zero but when I make
>> 2x2x5 or other supercell, these forces becomes non-zero. Of course,
>> these values are quite small. I used lot of significant digits for
>> coordinates and cell parameters but they do not help.
>
> To get exactly the same result for the bigger cell you must assure that
> the FFT grid scales proportionally and the K points grid scales inversely.
>
> I.e. lest say that the unit cell has nr1=10, nr2=10,nr3=10 (either
> specified by hand or automatically selected, it does not matter) and a
> 10x10x10 grid of k-points. If you build a 2x2x2 supercell you will have
> to check that nr1=20, nr2=20, nr3=20 and in case enforce it manually.
> You will also have to use 5x5x5 k-points, keeping in mind that if the
> grid was shifted it may be impossible to have exact equivalence.
>
> good work
>
>
> --
> Dr. Lorenzo Paulatto
> IdR @ IMPMC -- CNRS & Universit? Paris 6
> +33 (0)1 44 275 084 / skype: paulatz
> http://www-int.impmc.upmc.fr/~paulatto/
> 23-24/4?16 Bo?te courrier 115, 4 place Jussieu 75252 Paris C?dex 05
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[Pw_forum] Forces are not zero (for atoms in non-primitive cell)

[Duy Le]

Dear all,

I wonder if anyone knows how to vanish the forces acting on atoms in a
non-primitive cell. I saw that if I have 1x1x5 cell of Cu(111) (or any
other systems), the x-y components of forces are zero but when I make
2x2x5 or other supercell, these forces becomes non-zero. Of course,
these values are quite small. I used lot of significant digits for
coordinates and cell parameters but they do not help.

Many thanks.

Duy Le
Postdoctoral Associate
Department of Physics
University of Central Florida.
Website: http://www.physics.ucf.edu/~dle

[Pw_forum] plotting of the wfn with phases

[Duy Le]

You can use lsign in pp.x


Duy Le
Postdoctoral Associate
Department of Physics
University of Central Florida.
Website: http://www.physics.ucf.edu/~dle


On Fri, Jun 28, 2013 at 6:28 AM, Davide Tiana  wrote:
> Dear all,
> I would like to compare the crystalline orbitals of periodic calc made
> with pw.x with molecular made with gamess on a single molecule.
> using pw.x is it possible have the full information of the wfn (so
> including the phases) at the gamma point?
>
> Cheers,
> Davide
>
>
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[Pw_forum] Intermediate restart

[Duy Le]

Hi,
You should take a closer look at outdir and prefix. You need
appropriate values for these parameters.

Duy Le
Postdoctoral Associate
Department of Physics
University of Central Florida.
Website: http://www.physics.ucf.edu/~dle


On Tue, Jun 25, 2013 at 12:20 PM, Simone Marocchi  
wrote:
> Dear All,
> I have just one silly question about the functioning of the 
> pwscf
> software.
>
> 1) Can I put the final wavefunctions of my calculation in a different
> directory respect to the one of the input ? e.g. if I use wf_collect and
> I reach the convergence for my calculation saving my data in
> my_system.save , is it possible to start an other calculation
> restarting my previous data and saving the output in my_system_2.save, or 
> maybe
> I have to cp the *.save dir and then restarting from that one, writing
> the new path in the  prefix parameter of the input file ?
>
> Thanks for your help
>
> Sincerely,
> Simone Marocchi,
> PhD student,
> University of Modena and Reggio-Emilia
>
>
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[Pw_forum] Mn doped ZnS in high spin configuration

[Duy Le]

Well, if the "high spin" is not the ground state of your system, it is
very hard to achieve.
Try tot_magnetization or constrained_magnetization to enforce the high
spin state.

BTW, starting_magnetization can not be larger than 1.
------------
Duy Le
Postdoctoral Associate
Department of Physics
University of Central Florida.
Website: http://www.physics.ucf.edu/~dle


On Fri, Jun 21, 2013 at 11:26 AM, Bruno Camino  
wrote:
> Dear all,
>
> I am trying to calculate the properties of Mn doped ZnS in its high spin
> configuration . Using the Following PP
>
>
> Zn 65.38 Zn.pbe-van.UPF
>
> S 32.065 S.pbe-van_bm.UPF
>
> Mn 54.938049 Mn.pbe-sp-van_mit.UPF
>
>
> The system converges to the high spin solution (5 unpaired electrons). When
> trying to use the norm conserving pseudo potentials
>
>
> Zn 65.38 Zn.pz-spd-hgh.UPF
>
> S 32.065 S.pz-hgh.UPF
>
> Mn 54.938049 Mn.pz-sp-hgh.UPF
>
>
> The options we are using are
>
>
> 
>
> ibrav =12,
>
> A= 10.95828616
>
> B= 5.47914308
>
> C= 5.47914308
>
> cosAB =0.,
>
> cosAC =0.,
>
> cosBC =0.,
>
> nat = 16,
>
> ntyp = 3,
>
> ecutwfc = 150.0,
>
> force_symmorphic= .true.,
>
> occupations='smearing', smearing='gauss', degauss=0.005,
>
> nspin = 2
>
> starting_magnetization(3)=5.00
>
> /
>
>
> 
>
> diago_full_acc=.true.,
>
> conv_thr = 1.0d-5
>
> mixing_beta= 0.55
>
>
>
> I can only achieve the low spin solution or a non magnetic system.
>
> Can someone tell me how to achieve the high spin solution?
>
> Thank you in advance
>
>
> Bruno Camino
>
> Universit? degli Studi di Torino
>
>
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://pwscf.org/mailman/listinfo/pw_forum

[Pw_forum] Reg: starting_magnetization

[Duy Le]

They are "starting" values. You can set whatever you want as long as
you get right results. However, for faster convergence, you should use
 educated guesses.

------------
Duy Le
Postdoctoral Associate
Department of Physics
University of Central Florida.
Website: http://www.physics.ucf.edu/~dle


On Sat, Jun 22, 2013 at 1:47 AM, Peram sreenivasa reddy
 wrote:
> Dear Forum,
>   I have a doubt regarding the 'starting_magnetization'. I
> have X2YZ type magnetic system . My script is shown below..
>
> 
> ibrav = 2,
> celldm(1) = 12.925725762,
> nat = 4,
> ntyp = 3,
> occupations = 'smearing',
> nspin = 2,
> starting_magnetization(1)=0.7,
> starting_magnetization(2)=0.7,
> smearing = 'methfessel-paxton',
> ecutwfc = 45,
> degauss = 0.02,
> ecutrho =450.0,
> la2F = .true.,
>
> I have three different type of atoms. For each atom am i have to give the
> 'starting_magnetization' option like as shown below
>
> starting_magnetization(1)=0.7,
> starting_magnetization(2)=0.7,
> starting_magnetization(3)=0.7,
>
> Please suggest me...
>
> Thank you in advance...
>
>
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://pwscf.org/mailman/listinfo/pw_forum

[Pw_forum] imaginary phonon frequency for different degauss

[Duy Le]

Without info. about smearing method, it is hard to tell. Some methods
may give you incorrect forces, resulting in incorrect phonon.
degauss and k-point mesh should be well tested TOGETHER.

Check out the following:
http://caribeictp.uis.edu.co/lectures/R.Gebauer/Gebauer_Course2_KpointsMetals.pdf


Duy Le
Postdoctoral Associate
Department of Physics
University of Central Florida.
Website: http://www.physics.ucf.edu/~dle


On Sat, Jun 22, 2013 at 9:05 AM, Miao Gao  wrote:
> Dear all?
>
> I am calculating phonon with QE-5.0.1.
> A 20x20x10 k-mesh is used in scf calculation. Phonon wave vectors are
> sampled
> on 10x10x5 mesh. But when I set degauss=0.03Ry in scf run, a imaginary
> frequency
> was found for the first branch with omega= -105.6 cm^-1 at wave vector (0.2,
> 0.346410162, 0.0).
> But if degauss=0.05Ry in scf run, this imaginary frequency disappear and
> become 132.1 cm^-1.
> Meanwhile, the frequencies of all other branches change slightly for these
> two degauss values.
> So my question is which results should I trust, degauss=0.03 Ry or 0.05Ry?
>
> Btw: both lattice parameters and the inner coordinates of atoms are well
> relaxed for
> different degauss values.
>
> I am greatly indebted to you for your help. Thanks again!
>
> Best
> Miao Gao
>
> ---
> Ph.D. student of Department of Physics,
> Renmin University of China.
> ---
>
>
>
>
>
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://pwscf.org/mailman/listinfo/pw_forum

[Pw_forum] A strange problem in phonon calculation

[Duy Le]

Did you perform the test for q-mesh? I would do 2x2x1, 3x3x1 and
higher (if it is not that expensive) to see the evolution of
phonon-dispersion. Usually, 4x4x1 q-mesh is enough for converged
dispersion.



Duy Le
Postdoctoral Associate
Department of Physics
University of Central Florida.
Website: http://www.physics.ucf.edu/~dle


On Wed, Jun 19, 2013 at 4:45 PM, Paolo Giannozzi
 wrote:
> You can make a calculation at a q point that has imaginary
> frequencies, verify if you get the same result or if it is
> an artifact of Fourier interpolation
>
> P.
>
> On Tue, 2013-06-18 at 09:38 +0800, Wei-Bing Zhang wrote:
>> Dear all
>>
>>
>> Recently, I am trying to calculate the phonon dispersion of 2D
>> materials. I used 4x4x1 q-points in phonon calculation whereas a
>> 16x16x1 k-points for self-consistent electronic calculation. The
>> direct calculations indicate that all phonons frequencies are above
>> zero on the grid of q-vectors including the Gamma point. However, when
>> I transformed the dynamical matrices from G- to R-space and calculated
>> phonon dispersions using ?matdyn.x?, some negative frequencies appear
>> in acoustic mode ZA near Gamma point.  Since I am really a new user
>> for phonon calculation, I am not sure what happened. The input and
>> output file are enclosed. Could you tell me what?s wrong with my
>> calculations? Any suggestions will be appreciated.
>>
>>
>>
>> Thanks and best regards
>>
>>
>>
>> Wei-Bing Zhang
>>
>>
>>
>>
>> --
>> Dr. Wei-Bing Zhang
>>
>> School of Physics and Electronic Sciences
>> Changsha University of Science and Technology,
>> Changsha, People?s Republic of China
>> Phone : +86 186 73108538
>> E-mail: zwb256 at hotmail.com, weibingzhangavh at gmail.com
>> --
>> ___
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://pwscf.org/mailman/listinfo/pw_forum
>
> --
> Paolo Giannozzi, Dept. Chemistry,
> Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
> Phone +39-0432-558216, fax +39-0432-558222
>
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://pwscf.org/mailman/listinfo/pw_forum

[Pw_forum] Parallelization

[Duy Le]

Just want to be clear, I am not Paolo !!!

If you need more memory, you should not increase number of cores to a
huge number. Instead, you can ask for more nodes but use less number
of cores per node.

For instant, you can ask for 16 nodes and use 6 cores per node. Check
you environment, but it is highly that you need to use something like
size = 192
aprun -n 96 -N 6 pw.x ...

If you regret to waste 1/2 node, check OPENMP for options.



Duy Le
Postdoctoral Associate
Department of Physics
University of Central Florida.
Website: http://www.physics.ucf.edu/~dle


On Tue, Jun 11, 2013 at 3:57 PM, vijaya subramanian
 wrote:
> Hi Paolo
> I am running an scf calculation on gold slabs. I have somewhat limited
> resources on a supercomputer
> and would like to optimize my runs.  (Cray XT5 with 9,408 compute nodes
> interconnected with the SeaStar router through HyperTransport. The SeaStars
> are all interconnected in a 3-D torus topology. It is a massively parallel
> processing (MPP) machine. Each compute node has two six-core 2.6 GHz AMD
> Opterons for a total of 112,896 cores. All nodes have 16 Gbytes of DDR2
> memory: 1.33 Gbytes of memory per core.)
> A 54 gold atom slab scf calculation worked best with 120
> processors/npool=2/ndiag=49/ntg6.
> 240 processors and I get very good speed.  64 processors and I get an out of
> memory issue.
> When I use a larger unit cell I run into problems.
> I have attached two files with different configurations of gold atoms in a
> slab calculation with larger unit cells.
> The unit cells are different, one has six layers of gold atoms (unit cell -
> 16.12x48.36x60.8 in Bohr) and the other 2 layers of gold atoms (unit
> cell-54.x43.x54.).
> For some reason I  cannot get the 160 atom problem to work. (>2000 still
> doesn't work). For the 6 layer 162 atom problem(nproc=720 works).   If I use
> fewer number of processors I get an out of memory
> problem.
> Do you have any suggestions for what the problem may be?
>
> I have given partial output for the two calcs below:
> 160 atoms-1200 processors-the run failed before the diagonalization began.
>  Parallelization info
>  
>  sticks:   dense  smooth PW G-vecs:dense   smooth
>  Min 105  31  824383 3975
>  Max 106  32  924398 4042
>  Sum   75823   22755   5881 17559633  2885465  37
>
>
>  bravais-lattice index =0
>  lattice parameter (alat)  =  54.5658  a.u.
>  unit-cell volume  =  129972.7994 (a.u.)^3
>  number of atoms/cell  =  160
>  number of atomic types=1
>  number of electrons   =  1760.00
>  number of Kohn-Sham states= 2112
>  kinetic-energy cutoff =  30.  Ry
>  charge density cutoff = 400.  Ry
>  convergence threshold =  1.0E-06
>  mixing beta   =   0.7000
>  number of iterations used =8  plain mixing
>  Exchange-correlation  =  SLA  PW   PBX  PBC ( 1 4 3 4 0)
>  EXX-fraction  =0.00
> 
>  Dense  grid: 17559633 G-vectors FFT dimensions: ( 360, 288, 360)
>
>  Smooth grid:  2885465 G-vectors FFT dimensions: ( 192, 160, 192)
>
>  Largest allocated arrays est. size (Mb) dimensions
> Kohn-Sham Wavefunctions32.87 Mb (   1020, 2112)
> NL pseudopotentials42.33 Mb (510, 5440)
> Each V/rho on FFT grid  1.58 Mb ( 103680)
> Each G-vector array 0.19 Mb (  24385)
> G-vector shells 0.09 Mb (  11350)
>  Largest temporary arrays est. size (Mb) dimensions
> Auxiliary wavefunctions   131.48 Mb (   1020, 8448)
> Each subspace H/S matrix3.36 Mb ( 469, 469)
> Each <psi_i|beta_j> matrix350.63 Mb (   5440,   2, 2112)
> Arrays for rho mixing  12.66 Mb ( 103680,   8)
>
>  Initial potential from superposition of free atoms
>  Check: negative starting charge=   -0.028620
>
>  starting charge 1759.98221, renormalised to 1760.0
>
>  negative rho (up, down):  0.286E-01 0.000E+00
>  Starting wfc are 2880 randomized atomic wfcs
> Application 5992317 exit signals: Killed
>
> 162 atom run:
>  Parallelization info
>  
>  sticks:   dense  smooth PW G-vecs:dense   smooth  PW
>  Min  34  10  2 8950 1450 178
>  Max  35  11  3

[Pw_forum] Fermi Energy of Cu

[Duy Le]

Hi,

The absolute value of energy level is meaning less, depending on how the
zero level is defined. You should, thus, calculate and compare work
functions or any other quantities that are the differences between energy
levels.


Best,
D.


Duy Le
Postdoctoral Associate
Department of Physics
University of Central Florida.
Website: http://www.physics.ucf.edu/~dle


On Tue, May 14, 2013 at 2:49 PM, Jennifer Wohlwend wrote:

> I'm running a simple example using Cu and the Fermi energy listed is about
> double that in the literature; mine: 13-15 eV (depending on pp). I've tried
> the suggestions concerning increasing nbnd and cutoff energy as well as
> reducing the mixing coefficient and using all of the different pps on the
> site. I'm using espresso-4.0.3 (in order to run epw.x) but have also
> checked w/ 5.0.1 and get the same issue. My input is below:
>  
> calculation='scf',
> prefix='Cu',
> pseudo_dir = 'pp/',
> outdir='./',
> tprnfor = .true.,
> tstress = .true.,
>  /
>  
> ibrav = 2 ,
> celldm(1) = $lp,
> nat=  1 ,
> ntyp = 1 ,
> ecutwfc = 80.0,
> ecutrho = 800.0,
> occupations = 'smearing',
> smearing = 'cold',
> nbnd = 22,
> degauss = 0.005
>  /
>  
> mixing_beta = 0.1
> conv_thr =  1.0d-8
>  /
> ATOMIC_SPECIES
>   Cu 63.55  Cu.pbe-d-rrkjus.UPF
> ATOMIC_POSITIONS crystal
> Cu0.0   0.0   0.0
> K_POINTS AUTOMATIC
> 16 16 16 0 0 0
>
> Is there something I'm missing here or is the Fermi energy output not what
> I think it is...I apologize in advance if this is something obvious that
> I've overlooked.
> Thank you,
> J. Wohlwend
>
> Universal Tech. Corp.
>
>
> ___
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> Pw_forum at pwscf.org
> http://pwscf.org/mailman/listinfo/pw_forum
>
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[Pw_forum] davcio : error# 10

[Duy Le]

Hi,

 %%
>  from davcio : error #10
>  error while reading from file
>
>  
> %%
>

This is a famous one. I guess most of QE users face this error at least
once. Most of the time, it relates to missing/unlocated/incorrect
wavefunctions. Make sure the following:

1. you have wavefunction written
2. your pp input points to the right path
3. Unless you use wf_collect = .True. when generating wave function, you
MUST use the same number of cores for pp.

Best,
------------
Duy Le
Postdoctoral Associate
Department of Physics
University of Central Florida.
Website: http://www.physics.ucf.edu/~dle
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[Pw_forum] Relax Calculation in ZnO

[Duy Le]

Hi Angga,

1. tetrahedra is not a suitable method for force/relaxation...
calculations.
There is no fundamental problem of using smearing for
semi-conductor/insulator. The only problem is it takes a little bit more
time to converge.

2. No. Unless you need some quantities or files that were not calculated or
generated during relaxation.
 
Duy Le
Postdoctoral Associate
Department of Physics
University of Central Florida.
Website: http://www.physics.ucf.edu/~dle


On Thu, Jan 10, 2013 at 3:12 AM, Angga Fauzi wrote:

> Dear all QE users,
>
> I am trying to run relax calculation for my ZnO system. There are
> something I want to ask.
>
>1. In running relax calculation, what occupations should I use? I am
>trying to use occupations = 'tetrahedra', but it doesn't work. I am afraid
>if I use occupations = 'smearing', my result calculation doesn't valid
>since ZnO is a semiconductor, not a metal.
>2. After my relax calculation is done, should I run a scf calculation
>again with atomic positions I get from relax calculation?
>
> My input file is below.
>
>  
>title = 'ZnO' ,
>  calculation = 'relax',
>   outdir = '$TMP_DIR' ,
>   pseudo_dir = '$PSEUDO_DIR' ,
>   prefix = 'ZnO',
>   wf_collect = .true.
>  tprnfor = .true.
>forc_conv_thr = 1.0d-3
>  /
>  
>ibrav = 4,
>celldm(1) = 12.998 ,
>celldm(3) = 1.625 ,
>  nat = 32,
> ntyp = 2,
>  ecutwfc = 30.0,
>  occupations = 'smearing',
> smearing = 'mv',
>  degauss = 0.02,
>nspin = 2,
>starting_magnetization(1) = 0.0,
>  /
>  
>  mixing_beta = 0.62
> conv_thr = 1.0d-3
>  /
>  
> ion_dynamics = 'bfgs',
>ion_positions = 'default',
>  phase_space = 'full',
>pot_extrapolation = 'atomic',
>wfc_extrapolation = 'none',
> remove_rigid_rot = .false.
>  /
> ATOMIC_SPECIES
>Zn   65.38000  Zn.pbe-van.UPF
> O   15.99900  O.pbe-van_ak.UPF
> ATOMIC_POSITIONS crystal
>Zn  0.166000.333000.0
> O  0.166000.333000.18960
>Zn  0.333000.166000.25000
> O  0.333000.166000.43960
>Zn  0.666000.333000.0
> O  0.666000.333000.18960
>Zn  0.833000.166000.25000
> O  0.833000.166000.43960
>Zn  0.166000.833000.0
> O  0.166000.833000.18960
>Zn  0.333000.666000.25000
> O  0.333000.666000.43960
>Zn  0.666000.833000.0
> O  0.666000.833000.18960
>Zn  0.833000.666000.25000
> O  0.833000.666000.43960
>Zn  0.166000.333000.5
> O  0.166000.333000.68960
>Zn  0.333000.166000.75000
> O  0.333000.166000.93960
>Zn  0.666000.333000.5
> O  0.666000.333000.68960
>Zn  0.833000.166000.75000
> O  0.833000.166000.93960
>Zn  0.166000.833000.5
> O  0.166000.833000.68960
>Zn  0.333000.666000.75000
> O  0.333000.666000.93960
>Zn  0.666000.833000.5
> O  0.666000.833000.68960
>Zn  0.833000.666000.75000
> O  0.833000.666000.93960
> K_POINTS automatic
>   12 12 8   0 0 0
>
> Thank you very much for your attention.
>
> Regards,
> Angga
>
> Angga Dito Fauzi
> Undergraduate Student
> Department of Physics, Faculty of Mathematics and Natural Sciences
> Universitas Indonesia, Depok 16424, Indonesia
> Phone: +628124139348
> Email: angga_dito_fauzi at yahoo.com
>
> ___
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> Pw_forum at pwscf.org
> http://pwscf.org/mailman/listinfo/pw_forum
>
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[Pw_forum] changing total energy due to changing ibrav

[Duy Le]

Should you compare total energy per atom or total energy per unit volume?
Of course, you have to use well-converged cutoff and k-point sampling.

Duy Le
Postdoctoral Associate
Department of Physics
University of Central Florida.
Website: http://www.physics.ucf.edu/~dle


On Wed, Jan 16, 2013 at 3:25 AM, Lorenzo Paulatto <
lorenzo.paulatto at impmc.upmc.fr> wrote:

> On 16 January 2013 02:33, Tram Bui  wrote:
>
>> Dear QE Users,
>>I ran the calculation for a simple 1x1x1 unit cell SiC (zinc blend
>> structure) . The calculated total energy for when ibrav=2 (two atoms per
>> cell) is different from when ibrav=0 (8 atoms per cell). Would you give me
>> some information on why the total energy changes?
>>
>
>
> Dear Tram,
> maybe you did not use 2 sets of k-points that map perfectly from one
> system to the other.
>
> bests
>
> --
> Dr. Lorenzo Paulatto
> IdR @ IMPMC -- CNRS & Universit? Paris 6
> phone: +33 (0)1 44275 084 / skype: paulatz
> www:   http://www-int.impmc.upmc.fr/~paulatto/
> mail:  23-24/4?16 Bo?te courrier 115, 4 place Jussieu 75252 Paris C?dex 05
>
> ___
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> http://pwscf.org/mailman/listinfo/pw_forum
>
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[Pw_forum] Gamm-point tricks

[Duy Le]

Someone has asked exactly the same question not long ago. Google it for
more details.
Basically, you can not use Gamma only calculation.

Duy Le
Postdoctoral Associate
Department of Physics
University of Central Florida.
Website: http://www.physics.ucf.edu/~dle


On Sun, Jul 22, 2012 at 8:14 AM, henry odhiambo  wrote:

>  Gamma-point tricks
>
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[Pw_forum] Input error?

[Duy Le]

On Wed, Jul 18, 2012 at 5:05 PM, Pedro Augusto F. P. Moreira <
pmoreira at ifi.unicamp.br> wrote:

>   Dear all,
>
>   I am trying  to pw.x, but the following error happens:
>
>
> %%
>   task # 0
>   from diropn : error #10
>   error opening /home/pedro/Documentos/espresso-5.0/exec/h2o.wfc1
>
> %%
>
>   I imagine that the pw.x should open the wcf1 file.


It does not need to open any file since you start your calculation from
scratch

Am I rigth? Can
> anyone say why this error is happening? I managed to run the same
> simulation, but with an isolated molecule. My input follows below.
>
>
Delete outdir or change prefix will help.
----
Duy Le
Postdoctoral Associate
Department of Physics
University of Central Florida.
Website: http://www.physics.ucf.edu/~dle


>   Thanks,
>
>   Pedro
>
> --
> Pedro Moreira
>
> IFGW - Unicamp - Brazil
>
> #
> 
> calculation='relax',
> restart_mode='from_scratch',
> pseudo_dir='/home/pedro/Documentos/espresso-5.0/pseudo',
> outdir='/home/pedro/Documentos/espresso-5.0/exec',
> prefix='h2o',
> tprnfor = .true.,
> nstep = 1,
> /
> 
> ibrav = 0,
> nat = 1080, ntyp = 2,
> ecutwfc = 70.0, ecutrho = 850.0,
> /
> 
> electron_maxstep = 500,
> /
> 
> /
> ATOMIC_SPECIES
> H 1.00790 H.blyp-van_ak.UPF
> O 15.9994 O.blyp-van_ak.UPF
> CELL_PARAMETERS angstrom
> 22.15 0.000 0.000
> 0.000 23.02 0.000
> 0.000 0.000 21.55
> K_POINTS crystal
> 1
> 0. 0. 0. 1.00e+00
> ATOMIC_POSITIONS angstrom
>
> 1080 atoms
> ##
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[Pw_forum] I can't find the error :-(

[Duy Le]

It is usually easier for pwscfers to help you if you post error messages as
well.

BTW, what are the question marks (?) in cosAB... standing for?

-D


Duy Le
Postdoctoral Associate
Department of Physics
University of Central Florida.
Website: http://www.physics.ucf.edu/~dle


On Thu, Jul 5, 2012 at 3:17 PM, Davide Tiana  wrote:

> Dear all,
> sorry if I bother you with a silly pw input. I can't figure out why
> this input is wrong. Comparing with similar ones everything seems to
> be fine.
> (I don't know if it is another clue but it can be open with no problem
> with PWgui).
> Thanks in advanced for any helps you can give me.
>
> where is the error in this input file?
>
> 
>  calculation='relax',
>  title='zigzag',
>  wf_collect=.true.,
>  outdir='./',
>  prefix='zigzag',
>  etot_conv_thr=5.0d-4,
>  forc_conv_thr=1.0d-3,
>   /
>   
> ibrav=14,
> A=7.0008,
> B=9.7164,
> C=16.693,
> cosBC=?0.073568915,
> cosAC=?0.163584241,
> cosAB=?0.046461386,
> nat=53,
> ntyp=6,
> tot_charge=0.0,
> ecutwfc=45.0,
> ecutrho=450.0,
> nosym=.false.,
> nosym_evc=.false.,
> london=.true.,
> london_s6=0.75,
> london_rcut=200,
> occupations='smearing',
> smearing='marzari-vanderbilt'
> degauss=0.04
>   /
>   
> electron_maxstep=80,
> conv_thr=1.0d-6,
> mixing_mode='plain',
> mixing_beta=0.7,
> mixing_ndim=8,
> mixing_fixed_ns=0,
> diagonalization='david',
>   /
>   
> ion_dynamics='bfgs',
> ion_positions='default',
> phase_space='full',
> pot_extrapolation='atomic',
> wfc_extrapolation='none',
> remove_rigid_rot=.false.,
> upscale=100.d0,
> bfgs_ndim=1,
> trust_radius_max=0.8D0,
> trust_radius_min=1.D-3,
> trust_radius_ini=0.5D0,
> w_1=0.01D0
> w_2=0.5D0
>   /
>   ATOMIC_SPECIES
> H  1.007   H.pw91-rrkjus.UPF
> C  12.011  C.pw91-n-rrkjus.UPF
> N  14.007  N.pw91-n-rrkjus.UPF
> O  15.999  O.pw91-n-rrkjus.UPF
> S  32.066  S.pw91-n-rrkjus.UPF
> Zn 65.409  Zn.pw91-dn-rrkjus.UPF
> ATOMIC_POSITIONS (crystal)
> Zn 0.578420  0.797930  0.245020
> S  0.892900  0.754800  0.321720
> S  0.532400  0.630140  0.359300
> C  0.775600  0.651200  0.377600
> C  0.893100  0.574400  0.441400
> C  0.802500  0.499300  0.494300
> C  1.092900  0.573600  0.448400
> H  0.658484  0.497791  0.491135
> H  1.162620  0.626518  0.411599
> S  0.232700  0.793820  0.174940
> S  0.513200  0.591440  0.145020
> C  0.286200  0.648800  0.123000
> C  0.138700  0.573400  0.060200
> C  0.053700  0.395600 -0.051300
> C  0.191700  0.466400  0.008600
> H  0.093523  0.320982 -0.088598
> H  0.329520  0.440313  0.014493
> O  0.543300  0.972400  0.325600
> C  0.401000  0.972900  0.360600
> C  0.495200  1.200600  0.427500
> C  0.202400  1.072700  0.453100
> N  0.365000  1.076500  0.411100
> H  0.312744  0.887449  0.347623
> H  0.632077  1.173674  0.441456
> H  0.461004  1.259340  0.474237
> H  0.481812  1.253835  0.378051
> H  0.200577  1.162451  0.486274
> H  0.079775  1.057289  0.412588
> H  0.213205  0.995558  0.489830
> O  0.687700  0.922400  0.166600
> C  0.597200  1.022500  0.140400
> C  0.540300  1.212500  0.055600
> C  0.818000  1.065600  0.046900
> N  0.647900  1.095500  0.082600
> H  0.481877  1.044650  0.166216
> H  0.630783  1.296591  0.061083
> H  0.437698  1.228952  0.089877
> H  0.478294  1.192415 -0.002688
> H  0.918244  1.143828  0.062698
> H  0.781594  1.053830 -0.013740
> H  0.871518  0.978618  0.067224
> O  1.235300  0.156000  0.202600
> C  1.085900  0.157600  0.233400
> C  1.063400  0.403000  0.231000
> C  0.820300  0.263900  0.285800
> N  0.993400  0.269100  0.249500
> H  1.037676  0.064331  0.245752
> H  0.950768  0.458791  0.212031
> H  1.143621  0.451642  0.281051
> H  1.11  0.391320  0.187189
> H  0.711560  0.301097  0.248624
> H  0.785186  0.165940  0.294816
> H  0.844111  0.320974  0.339219
> K_POINTS {automatic}
> 4 3 7 0 0 0
>
>
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[Pw_forum] Problems about magnetic properties

[Duy Le]

This is a well-known situation.
If
you have modified  set_hubbard_l.f90 and tabd.f90 to add new elements
and if
you have checked carefully pseudopotential files
but it still gives you the same error,

you should check if you have recompiled the code yet. (hope that you did)


Duy Le
Postdoctoral Associate
Department of Physics
University of Central Florida.
Website: http://www.physics.ucf.edu/~dle


On Fri, Jun 29, 2012 at 9:45 AM, shayan hemmatiyan <
shayan.hematiyan at gmail.com> wrote:

> Howdy,
>
> Did you copy pseudopotential for all of your elements into pseudo path or
> write them into your input?
>
> Best,
> Shayan
>
> On Jun 29, 2012 8:38 AM, "zafar rasheed"  wrote:
> >
> > Dear Pwscf Users
> >
> > I want to calculate magnetic properties of ZnTe and ZnSe. But  this
> error occurs.
> >
> > 
> >  from set_hubbard_l : error # 1
> >  pseudopotential not yet inserted
> > +
> >
> > error occur. I know that I have to do some changing in
> /PW/set_hubbard_l.f90 and tabed.f90
> > by putting
> >
> > ===
> > ! ... other elements
> >  !
> >  CASE( 'H' )
> > !
> > hubbard_l =  0
> > !
> >  CASE( 'C', 'N', 'O', 'S', 'Se', 'Te' )= here i think that I m
> doing some thing wrong but what?
> > !
> > hubbard_l =  1
> > !
> > CASE DEFAULT
> > !
> > hubbard_l = -1
> > !
> >
> >   WRITE( stdout, '(/,"psd = ",A,/)' ) psd
> > !
> >
> =
> >
> > but  same error occurs.
> >
> > Last time I have do this perform some calculation but now i forget this
> change and I do not write it any where. Would any body help me to correct
> this file.
> >
> > Muhammad Zafar
> > PhD Scholar
> > Department of Physics
> > The Islamia University of Bahawalpur,Pakistan
> >
> > ___
> > Pw_forum mailing list
> > Pw_forum at pwscf.org
> > http://www.democritos.it/mailman/listinfo/pw_forum
> >
>
>
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>
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[Pw_forum] Charge Density of Each State

[Duy Le]

You should check out how many bands you have in your calculations. It looks
like to me that you don't have that many bands.
6 C + 1 Li -> 25 electrons
----
Duy Le
Postdoctoral Associate
Department of Physics
University of Central Florida.
Website: http://www.physics.ucf.edu/~dle


On Wed, Jun 27, 2012 at 6:19 PM, Gulcin Kucukdalyan
wrote:

> Below is my input and output file:
>
> INpiut:
>
>  # self-consistent calculation
> cat > gli.scf.in << EOF
>  
> calculation = 'scf'
> restart_mode='from_scratch',
> prefix='gli',
> pseudo_dir = '$PSEUDO_DIR/',
> outdir='$TMP_DIR/'
>  /
>  
> ibrav=  4, celldm(1) =8.0777, celldm(3)=0.83305, nat=  7, ntyp= 2,
> ecutwfc =60.0,
> ecutrho = 500.0
>  occupations='smearing', smearing='methfessel-paxton', degauss=0.02
>  /
>  
> mixing_mode = 'plain'
> mixing_beta = 0.7
> conv_thr =  1.0d-7
>  /
> ATOMIC_SPECIES
>  C   12.0107  C.pz-rrkjus.UPF
>  Li  6.9142   Li.pz-n-vbc.UPF
> ATOMIC_POSITIONS
> C   -0.000169177  -0.000292351   0.0
> C0.333413183  -0.000292351   0.0
> C0.500204479   0.288597992   0.0
> C0.333413183   0.577488334   0.0
> C   -0.000169177   0.577488334   0.0
> C   -0.166960373   0.288597992   0.0
> Li   0.166621953   0.288597992   0.416524683
> K_POINTS AUTOMATIC
> 5 5 6 0 0 0
> EOF
> $ECHO "  running the scf calculation for Gr-Li...\c"
> $PW_COMMAND < gli.scf.in > gli.scf.out
> check_failure $?
> $ECHO " done"
>
> # post-processing for charge density
> cat > gli.pp.in << EOF
>
>prefix  = 'gli'
>outdir = '$TMP_DIR/'
>filplot = 'gli.pp'
>plot_num= 7
>kpoint = 36
>kband = 32
>spin_component = 0
>
> /
>
>  
> nfile = 1
> filepp(1) = 'gli.pp'
> weight(1) = 1.0
> iflag = 3
> output_format = 5
> fileout = 'gli.xsf'
> /
>
>
> Output:
>
>   Plotting k_point =  36  band = 32
>
>
>  
> %%
>
>
>  
> %%
>  from local_dos : error # 1
>  wrong band specified
>
>  
> %%
>
>  stopping ...
>
>
>  
> %%
>  from local_dos : error # 1
>  wrong band specified
>
>  
> %%
>
>  stopping ...
>
>
>  
> %%
>  from local_dos : error # 1
>  wrong band specified
>
>  
> %%
>
>  stopping ...
>  from local_dos : error # 1
>  wrong band specified
>
>  
> %%
>
>  stopping ...
>
>
>  
> %%
>  from local_dos : error # 1
>  wrong band specified
>
>  
> %%
>
>  stopping ...
>
>
>  
> %%
>  from local_dos : error # 1
>  wrong band specified
>
>  
> %%
>
>  stopping ...
>
> Thank you
>
>
>
>  On Wed, Jun 27, 2012 at 5:31 PM, Lorenzo Paulatto <
> lorenzo.paulatto at impmc.upmc.fr> wrote:
>
>>  On Wed, Jun 27, 2012 at 11:03 PM, Gulcin Tetiker > > wrote:
>>
>>> Thanks for the response. I used those numbers also but the code gave
>>> error. I guess they symbolize different things. For example, if we only
>>> wanna calculate the charge density in gamma point kpoint should be 1. Also,
>>> for kband someone use "band near fermi level". I was just wondering where
>>> can i get all these information
>>>
>>
>> I do not understand what you mean by "band near fermi level".
>>
>> kband is an interger positive number, it must be smaller or equal to the
>> number of bands.
>>
>> If you ar

[Pw_forum] Charge density of each state

[Duy Le]

Yes. It should be an integer number corresponding to a band (Kohn-Sham
state) in which you are interested.

Duy Le
Postdoctoral Associate
Department of Physics
University of Central Florida.
Website: http://www.physics.ucf.edu/~dle


On Wed, Jun 27, 2012 at 1:41 PM, Gulcin Tetiker wrote:

> Hi Duy,
>
> Thank you for your response. It helped me a lot. I prepared the input file
> but getting error in the code. I believe the kband value is not correct. I
> am writing
> kband= band near fermi level. I think i should write it with numbers. What
> is the appropriate value for the kband? Thanks
>
> Sent from my iPhone
>
> On Jun 25, 2012, at 3:21 PM, Duy Le  wrote:
>
> > Hi Gulcin,
> >
> > For each Kohn-Sham state? Have you ever read the input description of
> PP.x?
> > http://www.quantum-espresso.org/wp-content/uploads/Doc/INPUT_PP.html
> > You just need to use appropriate plot_num and corresponding options.
> >
> > -D
> > 
> > Duy Le
> > Postdoctoral Associate
> > Department of Physics
> > University of Central Florida.
> > Website: http://www.physics.ucf.edu/~dle
> >
> >
> > On Mon, Jun 25, 2012 at 3:12 PM, Gulcin Tetiker 
> wrote:
> >> Hi All,
> >>
> >> I need to calculate the charge density of each state ,not the total
> charge,and make a 2 and 3D plot of it.
> >>
> >> I could not figure out how to do so. Can someone please help me with
> this?
> >>
> >> Thanks,
> >>
> >> Gulcin
> >>
> >>
> >> ___
> >> Pw_forum mailing list
> >> Pw_forum at pwscf.org
> >> http://www.democritos.it/mailman/listinfo/pw_forum
> > ___
> > Pw_forum mailing list
> > Pw_forum at pwscf.org
> > http://www.democritos.it/mailman/listinfo/pw_forum
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[Pw_forum] Charge density of each state

[Duy Le]

Hi Gulcin,

For each Kohn-Sham state? Have you ever read the input description of PP.x?
http://www.quantum-espresso.org/wp-content/uploads/Doc/INPUT_PP.html
You just need to use appropriate plot_num and corresponding options.

-D

Duy Le
Postdoctoral Associate
Department of Physics
University of Central Florida.
Website: http://www.physics.ucf.edu/~dle


On Mon, Jun 25, 2012 at 3:12 PM, Gulcin Tetiker  
wrote:
> Hi All,
>
> I need to calculate the charge density of each state ,not the total 
> charge,and make a 2 and 3D plot of it.
>
> I could not figure out how to do so. Can someone please help me with this?
>
> Thanks,
>
> Gulcin
>
>
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum

[Pw_forum] PAW potential for C

[Duy Le]

On Wed, Nov 9, 2011 at 5:55 PM, chengyu yang wrote:

> explain my other two questions, like: if the choice of potential and k
> point change the final binding energy of two systems.  Thank you.
>   Best regards.
>
>
The best way to answer these two questions is to test them. The tests are
very simple and easy to perform:

1. Use different potential to calculate the quantity in question.

2. Use different k-point set to calculate the quantity in question.

------
Duy Le
PhD Candidate
Department of Physics
University of Central Florida.

"Men don't need hand to do things"
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[Pw_forum] modifying sumpdos.f90

[Duy Le]

On Wed, Sep 14, 2011 at 6:48 AM, maaly  wrote:
> Dear all,
> I?need to modify sumpdos.f90 to sum??one of the pdos(up) and pdos(dwn)
> columns for selected atoms instead of summing ldos(up) and ldos(dwn)
> and i'm not that familiar with fortran,

Fortran is not the only option. And you don't have to modify
sumpdos.f90 and you should not mess it up if you are not familiar with
Fortran
>so it will be very?great if any one
> can tell me how.
You can use any plotting softwares to do the job. Even Microsoft Excel
can help you :)

----------
Duy Le
PhD Candidate
Department of Physics
University of Central Florida.

"Men don't need hand to do things"


>
>
>
>
>
> Best regards,
>
> Maaly Ghariballah
> Graduate student
> Alneelain university,sudan
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> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>

[Pw_forum] cannot allocate memory error

[Duy Le]

On Sat, Sep 3, 2011 at 11:23 AM, Elie Moujaes
 wrote:
> Dear all,
> I am having a problem when I am running a scf calculation for a 72-atom
> supercell of Carbon grain boundaries. The calculations start and then after
> a few minutes stop with the following error:
> Operating system error: Cannot allocate memory
> operating system error: cannot allocate memory
> out of memory
> Can anyone tell me what is going on? I am not sure if it is really a memory
> problem or something else?
Yes. It said that. Your system is quite large for running on a
personal desktop. Check output to see how much memory you need for
this system.
------
Duy Le
PhD Candidate
Department of Physics
University of Central Florida.

"Men don't need hand to do things"

[Pw_forum] Lattice constants with vdW-DF/vdW-DF2

[Duy Le]

It is well-known that vdW-DF and vdW-DF2 overestimate lattice
parameters of solids
See this work: Phys. Rev. B 83, 195131 (2011)
--
Duy Le
PhD Candidate
Department of Physics
University of Central Florida.

"Men don't need hand to do things"



On Thu, Sep 1, 2011 at 3:27 PM, Ari P Seitsonen  
wrote:
>
> Dear Colleagues,
>
> ?I want to calculate molecules adsorbing on metallic surfaces, and since the
> adsorption energy of them is know to be small, I would like to apply the
> vdW-DF/vdW-DF2 for the calculations. When I calculate the lattice constant
> with those functionals, I seem to get very large lattice constants, 5-10 %
> larger than the experimental one. An example for bulk, fcc gold is attached.
> I perform the calculation looping over different values for the lattice
> constant; the result seems to be independent of the cut-off energies (in
> this case I have large values for 'ecutwfc'/'ecutrho' because this was the
> last run for the convergence tests).
>
> ?Thus my question, does any one see something wrong in my input? Since the
> exchage part of the exchange and correlation is treated with a GGA
> functional (independently whether I use vdW-DF2 and PW86 or vdW-DF and
> revPBE) and correlation with LDA, plus an attractive(?) long-range
> contribution, I would expect lattice constants much closer to the
> experiments.
>
> ? ?Greetings from Wroclaw,
>
> ? ? ? apsi
>
> PS Apologies if the topic of my mail is an FAQ/discussed already!
>
> -=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-
> ?Ari P Seitsonen / Ari.P.Seitsonen at iki.fi / http://www.iki.fi/~apsi/
> ?Physikalisch-Chemisches Institut der Universitaet Zuerich
> ?Tel: +41 44 63 54 497 ?/ ?Mobile: +41 79 71 90 935
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>
>

[Pw_forum] large error in RuO2 lattice parameter

[Duy Le]

On Thu, Aug 4, 2011 at 12:36 AM, mohnish pandey  
wrote:
> Dear QE users,
> 2.7438
> I want to study RuO2 surfaces. I did calculation of ruthenium metal and
> found the lattice constant right(experimental = 2.70 and 1.584, I got 2.7438
> and 1.582) But after doing calculation of bulk ruthenium oxide I am getting
> very different lattice parameter as compared to the experimental value.
> Experimental value is 4.494 and 3.107 and I am getting the value of 4.6421
> and 3.1888.
> Can anybody please tell from where the discrepancy is coming?
It comes from the difference between theory and experiment.
If you check literature of similar calculation (S. Hong et al, surf.
sci. 2010), you will see that your numbers are really good.

------
Duy Le
PhD Candidate
Department of Physics
University of Central Florida.

"Men don't need hand to do things"
> Thanks a lot in advance
>
> input file
>
> 
> ??? calculation = 'vc-relax',
> ??? restart_mode='restart',
> ??? nstep=100
> ??? outdir='/home/mohnish/Desktop/Ruo2-bulk',
> ??? pseudo_dir='/home/mohnish/Desktop/Ruo2-bulk',
> ??? prefix='Ruo2',
> ??? tstress = .true.,
> ??? tprnfor = .true.,
> ? /
> ? 
> ??? ibrav=? 6, a = 4.6379, c = 3.1844,nat=? 6, ntyp= 2,
> ??? ecutwfc =
> 40,ecutrho=400,occupations='smearing',degauss=0.01,smearing='gaussian'
> ? /
> ? 
> ?? diagonalization='david'
> ?? mixing_mode = 'plain'
> ?? mixing_beta = 0.7
> ?? conv_thr = 1.0d-8
> ?? startingpot = 'file'
> ?? startingwfc = 'file'
> ?/
> 
> ?ion_dynamics='bfgs'
> /
> 
> ?cell_dynamics = 'bfgs'
> /
> ATOMIC_SPECIES
> ? Ru 101.07 Ru.pbe-n-van.UPF
> ? O? 15.099 O.pbe-rrkjus.UPF
> ?ATOMIC_POSITIONS (crystal)
> Ru? 0.? 0.? 0.
> Ru? 0.5000? 0.5000? 0.5000
> O?? 0.3060? 0.3060? 0.
> O?? 0.6940? 0.6940? 0.
> O?? 0.1940? 0.8060? 0.5000
> O?? 0.8060? 0.1940? 0.5000
> ?K_POINTS (automatic)
> ?10 10 12 0 0 0
>
>
> Section of output file,
>
> bfgs converged in?? 8 scf cycles and?? 4 bfgs steps
>  (criteria: energy < 0.10E-03, force < 0.10E-02, cell < 0.50E+00)
>
>  End of BFGS Geometry Optimization
>
>  Final enthalpy =??? -227.8256404205 Ry
> Begin final coordinates
>  new unit-cell volume =??? 463.72196 a.u.^3 (??? 68.71650 Ang^3 )
>
> CELL_PARAMETERS (alat=? 8.76436083)
> ?? 1.000910330?? 0.0?? 0.0
> ?? 0.0?? 1.000910330?? 0.0
> ?? 0.0?? 0.0?? 0.687553615
>
> ATOMIC_POSITIONS (crystal)
> Ru?? 0.0?? 0.0?? 0.0
> Ru?? 0.5?? 0.5?? 0.5
> O??? 0.306258404?? 0.306258404?? 0.0
> O??? 0.693741596?? 0.693741596?? 0.0
> O??? 0.193741596?? 0.806258404?? 0.5
> O??? 0.806258404?? 0.193741596?? 0.5
> End final coordinates
>
> --
> Regards,
> MOHNISH,
> -
> Mohnish Pandey
> Senior Project Associate,
> Department of Chemical Engineering,
> IIT KANPUR, UP, INDIA
> -
>
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> http://www.democritos.it/mailman/listinfo/pw_forum
>
>

[Pw_forum] Change of occupation number and cut3d

[Duy Le]

2011/7/30 Samuel Ponc? :
> I did try to add the variable tot_charge = +0.00046875 because I have 64 k
> points and 4 valences band ( 4-(63*4+3.97)/64)

Not sure what you were calculating. tot_charge is additional charge
you add to your system.
For example, if you have a system with 8 electron, and if you define
tot_charge = +1, you will have 8-1=7 electron in the system.

> However if I add the variable 'occupations = "fixed"' then I get the
> following WARNING:
>  WARNING: integrated charge= 8., expected= 7.99953125
>
> I off course get the exact same total energy as with tot_charge = 0 (this is
> not the expected behaviour).
>
> I did try without the variable 'occupation' (by the way what is the default
> value for occupation?) and also get the exact same total energy.

This does not depend on occupation. Read manual about occupation for
more details.
If you do a simple math: 7.99953125+0.00046875 you will see a "magic" number.


> I also do not understand why I don't have an occupation of 2.0 for all my
> valence states?
>
> ?k = 0. 0. 0. (? 1243 PWs)?? bands (ev):
>
> ??? -7.9264? 13.7887? 13.7887? 13.7887
>
>  occupation numbers
>  0.0312?? 0.0312?? 0.0312?? 0.0312
you should post your input for further advice.
--
Duy Le
PhD Candidate
Department of Physics
University of Central Florida.

"Men don't need hand to do things"


>
>
> 2011/7/30 GAO Zhe 
>>
>> Dear Ponce:
>> I am sorry that I may not catch the right meaning of your first question.
>> If you mean how to make extra or less charge for a model, you can use
>> "total_charge" in  namelist.
>> If you wanna get information of wavefunction, you'd better read
>> Doc/INPUT_PP. For the charge density at specified k-point and band, you can
>> calculate |psi|^2 through pp.x. Moreover, if you want to obtain the charge
>> density for all k-points on specified bands, you can summary them by pp.x,
>> too. P.S.: the original code of pp.x can just allow 7 filepp, but you can
>> change the variable, nfilemax, in PP/chdens.f90, then make pp.x.
>> Good Luck.
>> --
>> GAO Zhe
>> CMC Lab, MSE, SNU, Seoul, S.Korea
>>
>> At 2011-07-29 17:27:27,"Samuel?Ponc?"? wrote:
>>
>> Dear Quantum espresso user/developers,
>>
>> I have two questions:
>>
>> 1) Is it possible in pwscf to change "by hand" the occupation number ( and
>> impose a charge compensation accordingly) and if so how to do it?
>> I would like to do so because the sum over the different mode of the
>> partial derivative of the phonon frequency with respect of the occupation
>> number gives the zero point motion renormalization using Brooks theorem. I
>> would like to do this by finite difference (hence doing by hand some
>> calculation at different occupation number).
>>
>> ?2) Is it possible to extract informations in text format form the
>> wavefunctions? What is the right post processing tool to do so? Like having
>> the value of the wavefunction for a defined k points and band index?
>>
>> Thanks you!
>>
>> Samuel Ponc?.
>> (phD student, Universit? Catholique de Louvain, Belgium).
>>
>>
>>
>> ___
>> Pw_forum mailing list
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>> http://www.democritos.it/mailman/listinfo/pw_forum
>>
>
>
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>
>

[Pw_forum] vdw2

[Duy Le]

One thing you should do is to read at least 2 papers:
vdW-DF: PRL 92, 246401 (2004)
vdW-DF2: Phys. Rev. B 82, 081101 (2010)
They will tell you what are the differences between vdW-DF and vdW-DF2.

In short, they differ in the exchange part, gradient coefficient etc...
--
Duy Le
PhD Candidate
Department of Physics
University of Central Florida.

"Men don't need hand to do things"



On Sat, Jul 30, 2011 at 11:06 AM, DONG Rui  wrote:
> Hi, all
>
> Thanks for last reply.
> Now I am wondering, what is the difference between vdw1 and vdw2?
> In the short name definition, vdw-df=".+vdw", I guess, it is vdw1
> because in the output is shows,
> ? Exchange-correlation? = SLA+PW+RPB+VDW ( 1 4 4 0 1)
> But, when I define the input_dft=" SLA+PW+RPB+VDW2", output says "conflict",
>
> Now, Can anyone tell me the difference?
> Are the 1 and 2 from the two references consequently?
>
> Thank you!
>
> Rui
>
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>

[Pw_forum] init_london Error

[Duy Le]

I don't remember. You can always calculate it easily:
the ratio between C6 (or R0) of Cacbon in mm_dispersion.f90 and in
dft-d3 code will give you an idea how to convert them.
--
Duy Le
PhD Candidate
Department of Physics
University of Central Florida.

"Men don't need hand to do things"



On Tue, Jun 21, 2011 at 3:19 PM, Vikas Varshney  wrote:
> Dear Duy, All,
> I have converted the R0 from the dftd3.f code to QE code (from Angs to Bohr
> with 1.1 further scaling factor). However, I dont know what is the scaling
> factor that is used for C6 in mm_dispersion.f90. Any insight will be highly
> appreciated.
>
> Best Regards,
>
> Vikas Varshney,
> Computational Materials Scientist,
> Wright-Patterson Air Force Base, Dayton-OH (USA).
>
> On Tue, Jun 21, 2011 at 11:27 AM, Vikas Varshney  wrote:
>>
>> Dear Duy,
>> Thank you very much for the input. I will look into that today itself.
>>
>> Best Regards,
>> Vikas
>>
>> On Tue, Jun 21, 2011 at 10:51 AM, Duy Le  wrote:
>>>
>>> Dear Vikas,
>>> One simplest thing you can do is to read the DFT-D2 part of DFT-D3
>>> code provided by Grimme's group (http://toc.uni-muenster.de/DFTD3/)
>>> You will be able to find all necessary coefficients for all atoms with
>>> Z<=86. Then you have to add them to mm_dispersion.f90. Recompile QE,
>>> then you are good to go.
>>> --
>>> Duy Le
>>> PhD Candidate
>>> Department of Physics
>>> University of Central Florida.
>>>
>>> "Men don't need hand to do things"
>>>
>>>
>>>
>>> On Tue, Jun 21, 2011 at 10:40 AM, Vikas Varshney 
>>> wrote:
>>> > Dear All,
>>> >
>>> > I am trying to relax my WS2 unit cell structure using vc-relax (using
>>> > PBE
>>> > pps) and I want to include disperson corrections to it. So, I tried
>>> > using
>>> > the london flag = .true. However, on starting my job I got an error
>>> >
>>> >
>>> > ?%%
>>> >  from? init_london? : error # 1
>>> >  atom W?? not found
>>> >
>>> > ?%%
>>> >
>>> > After going through mm_dispersion.f90, I found that the vdw_radius and
>>> > c_6
>>> > parameters are given for first 54 atoms only (which corresponds to
>>> > first 5
>>> > periods of periodic table). Tungsten (W), with atomic number of 74 is
>>> > in 6th
>>> > period.
>>> >
>>> > I emailed Prof. Stefan Grimme (author of the references that are
>>> > mentioned
>>> > in mm_dispersion.f90) if anything was further pursued. He replied
>>> > mentioning
>>> > that they have approached this problem further and referred me to his
>>> > website,
>>> >
>>> > http://toc.uni-muenster.de/DFTD3/
>>> >
>>> > and told me that this has already been implemented into major QM codes.
>>> >
>>> > Mentioning that, I have few questions.
>>> > 1. I wanted to ask if QE has incorporated the additions DFT-D,
>>> > recently.
>>> > 2. Are there any other ways to incorporate dispersion interactions in
>>> > calculations in DFT.
>>> >
>>> > Currently, I am running my simulations on 4.2 version of the code that
>>> > I
>>> > downloaded few months ago. I would high appreciate your insights in how
>>> > should I go about solving this problem regarding dispersion
>>> > interactions in
>>> > Tungsten.
>>> >
>>> > Looking forward for a positive reply.
>>> >
>>> > Best Regards,
>>> >
>>> > Vikas Varshney,
>>> > Computational Materials Scientist,
>>> > Wright-Patterson Air Force Base, Dayton-OH (USA).
>>> >
>>> > ___
>>> > Pw_forum mailing list
>>> > Pw_forum at pwscf.org
>>> > http://www.democritos.it/mailman/listinfo/pw_forum
>>> >
>>> >
>>> ___
>>> Pw_forum mailing list
>>> Pw_forum at pwscf.org
>>> http://www.democritos.it/mailman/listinfo/pw_forum
>>
>
>
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> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>

[Pw_forum] init_london Error

[Duy Le]

Dear Vikas,
One simplest thing you can do is to read the DFT-D2 part of DFT-D3
code provided by Grimme's group (http://toc.uni-muenster.de/DFTD3/)
You will be able to find all necessary coefficients for all atoms with
Z<=86. Then you have to add them to mm_dispersion.f90. Recompile QE,
then you are good to go.
--
Duy Le
PhD Candidate
Department of Physics
University of Central Florida.

"Men don't need hand to do things"



On Tue, Jun 21, 2011 at 10:40 AM, Vikas Varshney  wrote:
> Dear All,
>
> I am trying to relax my WS2 unit cell structure using vc-relax (using PBE
> pps) and I want to include disperson corrections to it. So, I tried using
> the london flag = .true. However, on starting my job I got an error
>
> ?%%
>  from? init_london? : error # 1
>  atom W?? not found
> ?%%
>
> After going through mm_dispersion.f90, I found that the vdw_radius and c_6
> parameters are given for first 54 atoms only (which corresponds to first 5
> periods of periodic table). Tungsten (W), with atomic number of 74 is in 6th
> period.
>
> I emailed Prof. Stefan Grimme (author of the references that are mentioned
> in mm_dispersion.f90) if anything was further pursued. He replied mentioning
> that they have approached this problem further and referred me to his
> website,
>
> http://toc.uni-muenster.de/DFTD3/
>
> and told me that this has already been implemented into major QM codes.
>
> Mentioning that, I have few questions.
> 1. I wanted to ask if QE has incorporated the additions DFT-D, recently.
> 2. Are there any other ways to incorporate dispersion interactions in
> calculations in DFT.
>
> Currently, I am running my simulations on 4.2 version of the code that I
> downloaded few months ago. I would high appreciate your insights in how
> should I go about solving this problem regarding dispersion interactions in
> Tungsten.
>
> Looking forward for a positive reply.
>
> Best Regards,
>
> Vikas Varshney,
> Computational Materials Scientist,
> Wright-Patterson Air Force Base, Dayton-OH (USA).
>
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>

[Pw_forum] Problems about vibration mode and minimization

[Duy Le]

2011/6/3 yhho :
> Dear all,
>
> The vibration mode I got by QE has?6?figures
> which are looks like?rotation?mode in the first 3 figures.(the force
> directions are the same)
> Is that really rotation mode?
>
> Besides, when I do minimization calaulation?by QE.
> It took very long time (ex. a week) and didn't converge finally.
> I try to decrease the ecut, but the error appeared soon.
>
>  from read_rho_xml : error # 1
>  dimensions do not match
> Why can't I lower the ecut ?
Of course you can but not together with restart_mode ='restart'
> or how can I lower the cpu time ?
you can also consider to change  ion_dynamics if your calculation
experiences too many iterations.
----------
Duy Le
PhD Student
Department of Physics
University of Central Florida.

"Men don't need hand to do things"
> Thanks a lot.
>
> (my input file)
> # self-consistent calculation
> ?
> ??? calculation ='relax',
> ??? restart_mode ='restart',
> ??? prefix ='2FCT_TS',
> ??? pseudo_dir = '/usr1/yhho/espresso-4.0.3-ifort/pseudo/',
> ??? outdir ='/usr1/yhho/yhho/QE-tmp/2FCT_prod/',
> ?/
> ?
> ??? ibrav =0,
> ??? celldm(1) = 1.0D0,
> ??? nat =41,
> ??? ntyp =6,
> ??? ecutwfc = 30,
> ??? ecutrho = 300.0,
> ??? occupations ='smearing',
> ??? degauss =0.02,
> /
> ?
> ??? conv_thr = 1.0e-08,
> ??? mixing_beta = 0.7,
> /
> 
> ??? ion_dynamics='damp',
> ??? pot_extrapolation='second_order',
> ??? wfc_extrapolation='second_order',
> /
> ATOMIC_SPECIES
> C? 12.01? C.pbe-van_ak.UPF
> N? 14.01? N.pbe-van_ak.UPF
> Fe 55.85? Fe.pbe-sp-van_ak.UPF
> Cl 35.45? Cl.pbe-n-van.UPF
> O? 16.00? O.pbe-van_ak.UPF
> H? 1.008? H.pbe-van_ak.UPF
> ATOMIC_POSITIONS { crystal }
> Fe?? 10.000 10.000 10.000
> Cl?? 8.389 11.825 9.605
> C?? 13.257 12.763 9.815
> C?? 11.995 12.384 9.518
> C?? 13.060 10.605 10.234
> C?? 11.351 10.629 14.078
> C?? 11.100 9.818 13.021
> C?? 10.076 11.716 12.643
> C?? 8.988 7.451 10.515
> C?? 10.423 7.199 10.339
> C?? 10.981 5.793 10.501
> C?? 12.470 5.757 10.140
> C?? 13.056 4.360 10.194
> N?? 13.911 11.621 10.246
> N?? 11.903 11.038 9.769
> N?? 10.672 11.811 13.823
> N?? 10.317 10.518 12.138
> O?? 8.223 6.511 10.800
> O?? 8.550 8.620 10.334
> O?? 11.162 8.153 10.117
> O?? 14.302 4.222 10.066
> O?? 12.303 3.404 10.415
> O?? 6.840 10.443 11.915
> O?? 9.784 9.627 7.802
> H?? 14.871 11.571 10.522
> H?? 11.212 13.016 9.154
> H?? 13.274 9.605 10.548
> H?? 10.638 12.605 14.430
> H?? 11.449 8.814 12.898
> H?? 9.495 12.483 12.176
> H?? 10.915 5.557? 11.543
> H?? 10.478 5.181 9.781
> H?? 12.972 6.318 10.900
> H?? 12.534 6.065 9.117
> H?? 7.440 11.192 11.915
> H?? 7.346 9.627 11.915
> H?? 10.384 10.376 7.802
> H?? 10.290 8.811 7.802
> H?? 13.738 13.715 9.725
> H?? 11.898 10.456 14.981
> H?? 14.754? 4.843 10.642
>
> CONSTRAINTS
> ? 36 1.0E-6
> ? distance? 3? 14? 1.38479
> ? distance? 14? 5? 1.32537
> ? distance? 5? 15? 1.31999
> ? distance? 15? 4? 1.37229
> ? distance? 4?? 3? 1.35074
> ? distance? 6? 16? 1.38679
> ? distance? 16? 8? 1.32538
> ? distance? 8? 17? 1.32224
> ? distance? 17? 7? 1.37241
> ? distance? 7?? 6? 1.35572
> ? distance? 9? 19? 1.26141
> ? distance? 9? 18? 1.24501
> ? distance? 9? 10? 1.46755
> ? distance? 10 11? 1.52133
> ? distance? 11 12? 1.53256
> ? distance? 12 13? 1.51589
> ? distance? 13 21? 1.26014
> ? distance? 13 22? 1.23685
> ? distance? 10 20? 1.22700
> ? distance? 23 36? 0.96015
> ? distance? 23 35? 0.95969
> ? distance? 24 37? 0.95969
> ? distance? 24 38? 0.96015
> ? distance? 1? 39? 1.07040
> ? distance? 14 25? 1.00014
> ? distance? 4? 26? 1.07005
> ? distance? 5? 27? 1.06976
> ? distance? 6? 40? 1.09684
> ? distance? 16 28? 1.2
> ? distance? 7? 29? 1.07002
> ? distance? 8? 30? 1.06955
> ? distance? 11 31? 1.07043
> ? distance? 11 32? 1.07049
> ? distance? 12 33? 1.06973
> ? distance? 12 34? 1.07028
> ? distance? 21 41? 0.96006
>
> K_POINTS {automatic}
> 10 10 10 0 0 0
>
> CELL_PARAMETERS {cubic}
> 40.000 0. 0.
> 0. 40.000 0.
> 0. 0. 40.000
>
> --
> Yu-Han Ho
> Research Assistant
> Institute of Atomic and Molecular Sciences(IAMS), lab503
> No. 1, Roosevelt Rd., Sec. 4, Taipei, 10617, Taiwan
> Tel: 886-2-2362-0212
>
>
>
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>
>

[Pw_forum] pw.x stuck

[Duy Le]

Have you ever done vc-relax with a much smaller system? Say 1-3 atoms.
--
Duy Le
PhD Student
Department of Physics
University of Central Florida.

"Men don't need hand to do things"



On Thu, Jun 2, 2011 at 4:12 PM, Yongsheng Zhang  wrote:
> Firstly, this system was running throughout using previous PWSCF version, 
> v4.2.1.
>
> Further tests with v4.3 using different CPUs, pw.x is stuck at different 
> places.
>
> (1) 1CUP: after one static iteration, it leaves error message,
> ? ? WARNING: integrated charge= ? ? 0., expected= ? ?64.
>
> ?%%
> ? ? from electrons : error # ? ? ? ? 1
> ? ? charge is wrong: smearing is needed
> ?%%
>
> (2) 4 CPUs: the system did relaxed. But when it run the "final scf", it is 
> stuck at,
> ? ?A final scf calculation at the relaxed structure.
>
> ? ? The G-vectors are recalculated.
>
> (3) 8 CPUs: after one static iteration, it is stuck at,
>
> ? ? ? ?k( ? ?1) = ( ? 0.1249057 ? 0.1249057 ? 0.1531359), wk = ? 0.250
> ? ? ? ?k( ? ?2) = ( ? 0.1249057 ? 0.3747172 ? 0.1531359), wk = ? 0.500
> ? ? ? ?k( ? ?3) = ( ? 0.3747172 ? 0.3747172 ? 0.1531359), wk = ? 0.250
> ? ? ? ?k( ? ?4) = ( ?-0.1249057 ? 0.1249057 ?-0.1531359), wk = ? 0.250
> ? ? ? ?k( ? ?5) = ( ?-0.1249057 ? 0.3747172 ?-0.1531359), wk = ? 0.500
> ? ? ? ?k( ? ?6) = ( ?-0.3747172 ? 0.3747172 ?-0.1531359), wk = ? 0.250
>
> I am kind of pretty sure that there is something wrong in the compiling the 
> code. Then, I did my best to change the make.sys file and recompile the code. 
> The best results I can get so far is: pw.x do relax the system, but when it 
> is trying to run "A final scf calculation at the relaxed structure", it stops 
> at,
> ? ? G cutoff = 2508.9230 ?( 852531 G-vectors) ? ? FFT grid: (108,108,180)
> ? ? G cutoff = 1003.5692 ?( 215507 G-vectors) ?smooth grid: ( 64, 64,108)
>
> ? ? Largest allocated arrays ? ? est. size (Mb) ? ? dimensions
> ? ? ? ?Kohn-Sham Wavefunctions ? ? ? ? 1.65 Mb ? ? ( ? 3377, ?32)
> ? ? ? ?NL pseudopotentials ? ? ? ? ? ? 5.77 Mb ? ? ( ? 3377, 112)
> ? ? ? ?Each V/rho on FFT grid ? ? ? ? ?4.09 Mb ? ? ( 268272)
> ? ? ? ?Each G-vector array ? ? ? ? ? ? 0.81 Mb ? ? ( 106570)
> ? ? ? ?G-vector shells ? ? ? ? ? ? ? ? 0.36 Mb ? ? ( ?47252)
> ? ? Largest temporary arrays ? ? est. size (Mb) ? ? dimensions
> ? ? ? ?Auxiliary wavefunctions ? ? ? ? 6.60 Mb ? ? ( ? 3377, 128)
> ? ? ? ?Each subspace H/S matrix ? ? ? ?0.25 Mb ? ? ( ? ?128, 128)
> ? ? ? ?Each <psi_i|beta_j> matrix ? ? ?0.05 Mb ? ? ( ? ?112, ?32)
> ? ? ? ?Arrays for rho mixing ? ? ? ? ?32.75 Mb ? ? ( 268272, ? 8)
>
>
> And give the following error message:
> forrtl: severe (41): insufficient virtual memory
> Image ? ? ? ? ? ? ?PC ? ? ? ? ? ? ? ?Routine ? ? ? ? ? ?Line ? ? ? ?Source
> pw.x ? ? ? ? ? ? ? 01124F0D ?Unknown ? ? ? ? ? ? ? Unknown ?Unknown
> pw.x ? ? ? ? ? ? ? 01123A15 ?Unknown ? ? ? ? ? ? ? Unknown ?Unknown
> pw.x ? ? ? ? ? ? ? 010C2C39 ?Unknown ? ? ? ? ? ? ? Unknown ?Unknown
> pw.x ? ? ? ? ? ? ? 0105885D ?Unknown ? ? ? ? ? ? ? Unknown ?Unknown
> pw.x ? ? ? ? ? ? ? 0109736E ?Unknown ? ? ? ? ? ? ? Unknown ?Unknown
> pw.x ? ? ? ? ? ? ? 0053EEBF ?allocate_nlpot_ ? ? ? ? ? ?68 
> ?allocate_nlpot.f90
> pw.x ? ? ? ? ? ? ? 00454D76 ?init_run_ ? ? ? ? ? ? ? ? ?60 
> ?init_run.f90
> pw.x ? ? ? ? ? ? ? 004716B7 ?move_ions_ ? ? ? ? ? ? ? ?290 
> ?move_ions.f90
> pw.x ? ? ? ? ? ? ? 0044AA55 ?MAIN__ ? ? ? ? ? ? ? ? ? ?173 ?pwscf.f90
> pw.x ? ? ? ? ? ? ? 0044A60C ?Unknown ? ? ? ? ? ? ? Unknown ?Unknown
> libc.so.6 ? ? ? ? ?2AE8FFD68974 ?Unknown ? ? ? ? ? ? ? Unknown ?Unknown
> pw.x ? ? ? ? ? ? ? 0044A519 ?Unknown ? ? ? ? ? ? ? Unknown ?Unknown
>
>
> I am wondering that why the "insufficient virtual memory" happens at the last 
> step. If there is no sufficient virtual memory, the code should not even run 
> at the first iteration. While, I collect the relaxed structure and re-run 
> pw.x, it works without any problem.
>
> Thanks
> Yongsheng
>
>
> --- On Thu, 6/2/11, Paolo Giannozzi  wrote:
>
>> From: Paolo Giannozzi 
>> Subject: Re: [Pw_forum] pw.x stuck
>> To: "PWSCF Forum" 
>> Date: Thursday, June 2, 2011, 1:45 AM
>>
>> On Jun 1, 2011, at 19:05 , Jack London wrote:
>>
>> > Yes, I have tried many times
>>
>> many times in the same conditions is better than nothing,
>> but you should try in different conditions as well.
>>
>> P.
>

[Pw_forum] Using mixture of pseudo potential

[Duy Le]

On Tue, May 31, 2011 at 1:11 PM, Vi Vo  wrote:
> Hi Pine,
>
> Thank you.? Yes, I know that I have to do different tests for ecutrho and
> ecutwfc, but my questions are different. I would like to know what is the
> default setting for ecutrho the code would assume. I restate my question as
> follows:
>
> If I forgot to specify the ecutrho, what default value of? ecutrho would the
> code assume for US PP?? (I guess it still uses the default
> ecutrho=4*ecutwfc).
>
> On the other hand, assuming I set the ecutrho=9*ecutwfc, does then the same
> value of ecutrho=8*ecutwfc also apply to NC PP, or does the value of
> ecutrho=4*ecutwfc will be used for NC PP.

If there is nothing changed, according to the QE manual, the default
factor of 4 does not depend on the type of potential.
Also, there is only one ecutrho in a single calculation, and it is
written in the output (most of parameters can be found in the output).


>
> Thank you,
>
------
Duy Le
PhD Student
Department of Physics
University of Central Florida.

"Men don't need hand to do things"

> Vi
>
>
> 
> From: lucking-pine 
> To: PWSCF Forum 
> Sent: Mon, May 30, 2011 9:35:59 PM
> Subject: Re: [Pw_forum] Using mixture of pseudo potential
>
> Hi,
> In my way,I usually test ecutrho = X*ecutwfc using scf?or relax.I look the
> result of total energy or enthalpy.
> Such as:
> 1.ecutwfc=47 ecutrho=400, total energy= -290.983
> 2.ecutwfc=47 ecutrho=380, total energy= -290.993
> So,I thought '2' is better than '1'.
>
> Bests,
> Pine.
> 2011/5/31 Vi Vo 
>>
>> Dear All,
>>
>> In my calculation, I used a mixture of pseudo potentials, ie.
>> norm-conserving pp (NC pp)? for one element and ultrasoft pp (US pp) for
>> another.? If I don't specify ecutrho in the input, what will be the default
>> value for ecutrho for the ultrasoft pp.? I know that for NC pp, ecutrho =
>> 4*ecutwfc, but I do not know if the same value is used for US pp.? On the
>> other hand, if I specify ecutrho = 8*ecutwfc, then does the same value apply
>> to the NC pp.
>>
>> Thank you very much,
>>
>> Vi
>> University of Houston
>>
>>
>>
>> ___
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://www.democritos.it/mailman/listinfo/pw_forum
>>
>
>
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>
>

[Pw_forum] FFT grid and cutoff energy.

[Duy Le]

On Tue, May 31, 2011 at 9:02 PM, Hongsheng Zhao  
wrote:
> Hi all,
>
> I've learned that, for all of the PW based DFT codes, such as,
> VASP/PWscf/Abinit/CASTEP, the
> FFT grid is generated based on the cutoff energy.

Not really true. There is no direct relationship between FFT grid and
cutoff energy (I supposed that by cutoff energy you meant Kinetic
energy cutoff for the planewave expansion)
FFT mesh is calculated based on the cutoff for charge density. In any
code, the coder usually set a default relationship between cutoff for
PW expansion and cutoff for charge density. For example, in QE, the
later is 4 time larger.

> So if we have tested the
> convergence total energy vs cutoff energy, then the
> FFT grid used for our calcultions should also be OK based on the selected
> cutoff energy.? In other words, it is unnecessary to do a
>
> Independent FFT grid convergence test. Am I right?
>
It depends. If that default value is good enough, you don't have to do
an additional test. The default value is good enough for PAW
potential, but too small for US or NC potential.
BTW, I understood that by saying "Independent FFT grid convergence
test" you really meant "Independent *cutoff energy for the charge
density* convergence test"

--
Duy Le
PhD Student
Department of Physics
University of Central Florida.

"Men don't need hand to do things"
> Regards.
> --
>
> Hongsheng Zhao 
> School of Physics and Electrical Information Science,
> Ningxia University, Yinchuan 750021, China
>
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>

[Pw_forum] very high pressure in scf

[Duy Le]

1. How does the pressure come out in the 2nd input? Coordinates of
atoms in the first and 2nd inputs are different, hope you can see
that.

2. What are these lattice parameter of the system calculated with
ABINIT and QE? They are using different potential so the lattice
parameters are not be the same. A few % of changing in lattice
parameter (in comparison to equilibrium lattice parameter) can lead to
a huge change in the pressure.
--
Duy Le
PhD Student
Department of Physics
University of Central Florida.

"Men don't need hand to do things"



On Fri, May 27, 2011 at 6:24 AM, Paolo Giannozzi  
wrote:
> On Fri, 2011-05-27 at 15:50 +0530, Sanjeev Gupta wrote:
>
>> Herewith, I am putting my input file, here again i am getting pressure
>> too large as compare in ABINIT.
>> Kindly suggest me, why i am getting large pressure.
>
> do you get the same results with the same psedupotentials?
> You should. If you don't, you should first understand why
>
> P.
> --
> Paolo Giannozzi, IOM-Democritos and University of Udine, Italy
>
>
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[Pw_forum] very high pressure in scf

[Duy Le]

On Thu, May 26, 2011 at 10:13 AM, Sanjeev Gupta
 wrote:
> ??? tstress = .true.
> ??? ecutwfc = 20,
> ??? ecutrho=200,
Did you check these cutoff values?

----------
Duy Le
PhD Student
Department of Physics
University of Central Florida.

"Men don't need hand to do things"

[Pw_forum] Running parallel in some example of 2 cup is wrong?

[Duy Le]

2011/5/26 lucking-pine :
> My computer is 2 cpu and 8 core of Dell. In some examples are crash. Such
> as:co.out of example 03 show that 'from d_&_i:error;some nodes have no k
> points'.
> And the environment_varibles of examples I set :
>
> PARA_PREFIX="mpiexec -n 8"
> PARA_POSTFIX="-npool 2"
>
> And how odd is when I set :
>
> PARA_PREFIX="mpiexec -n 4"
> PARA_POSTFIX="-npool 1"
>
You need understand the parallelism of QE before using it.
http://www.quantum-espresso.org/user_guide/node15.html

For example, it is obvious that if you have only one k-point, you can
not distribute it to 2 different pools.
--
Duy Le
PhD Student
Department of Physics
University of Central Florida.

"Men don't need hand to do things"


> the example 03 can be work.
>
> The?similar case occur also in some of?other examples.
>
> ?Please tell what problem isthanks.
> ps:my compiler is:icc11.1.075,ifort11.1.075,mpich2,pwscf 4.2.1
> system is red hat enterprise linux 5
>
> Best
> Pine.
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>

[Pw_forum] Minor problem in tests and cptests scripts for QE 4.3

[Duy Le]

On Wed, May 25, 2011 at 11:59 AM, Paolo Giannozzi
 wrote:
>
> On May 25, 2011, at 17:56 , Duy Le wrote:
>
>> But it is weird. QE does not take TMP_DIR or PSEUDO_DIR
>
> it uses ESPRESSO_PSEUDO and ESPRESSO_TMPDIR, if
> defined and not overridden by input variables
>
Right. I meant Cristian's claim (of using two new ENV. variables) and
your answer (about weird machine) are not compatible.
------
Duy Le
PhD Student
Department of Physics
University of Central Florida.

"Men don't need hand to do things"
> P.
> ---
> Paolo Giannozzi, Dept of Chemistry,
> Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
> Phone +39-0432-558216, fax +39-0432-558222
>
>
>
>
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[Pw_forum] Minor problem in tests and cptests scripts for QE 4.3

[Duy Le]

On Wed, May 25, 2011 at 11:51 AM, Paolo Giannozzi
 wrote:
>
> On May 25, 2011, at 11:37 , Cristian Degli Esposti Boschi wrote:
>
>> Am I missing something or is it a minor problem with the scripts?
>
> or maybe your are using some weird machine that does not
> honor "getenv". One such machine I known is IBM BG.
>
But it is weird. QE does not take TMP_DIR or PSEUDO_DIR
----------
Duy Le
PhD Student
Department of Physics
University of Central Florida.

"Men don't need hand to do things"
> PS: post from the same e-mail you used to register or else
> your messages will not go through
>
>
> P.
> ---
> Paolo Giannozzi, Dept of Chemistry,
> Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
> Phone +39-0432-558216, fax +39-0432-558222
>
>
>
>
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>

[Pw_forum] box size in example03

[Duy Le]

On Tue, May 24, 2011 at 4:03 PM, Amin Torabi  wrote:
> Hi all,
> ../examples/example03/README says that "The molecule is put in a cubic box
> of side 12 bohr"
> My questions are:
>
> how did you chose it to be 12? I tried different numbers and noticed that
> the total energy depends on this value.

Indeed. 
Energy_of_system=Energy_of_molecule+Interaction_energy_with_neighboring_molecules.
Different box sizes yield different Interaction energies.

> Is it not a calculation on an isolated molecule? cause for an isolated
> molecule, it should not be important what the size of the box is.

No, it is not. It is a calculation of bunch of molecules. By changing
box size, you change the interaction between those molecules.
Eventually, those interactions are almost negligible, you'll get
isolated molecules.

>

----------
Duy Le
PhD Student
Department of Physics
University of Central Florida.

"Men don't need hand to do things"

[Pw_forum] Error message from scf calculation

[Duy Le]

Sorry, I answer wrong question. Please ignore my previous email.
For your calculation, it is hard to tell because we don't know the
reference for the calculated total energy. On top of that, it should
not be POSITIVE. You should optimize the lattice parameter for Cs and
then calculate its cohesive energy. You can compare the cohesive
energy with experimental or other theoretical data.
--
Duy Le
PhD Student
Department of Physics
University of Central Florida.

"Men don't need hand to do things"



On Fri, May 20, 2011 at 5:02 PM, Duy Le  wrote:
> I believe that you have asked us about the calculation for an
> isolated atom sometimes ago. It was about C. You should have done the
> same approach.
> ----------
> Duy Le
> PhD Student
> Department of Physics
> University of Central Florida.
>
> "Men don't need hand to do things"
>
>
>
> On Fri, May 20, 2011 at 4:40 PM, Tram Bui  wrote:
>> I'm so sorry I forgot the file:) here it is. And I have added the variables
>> of : occupations='smearing', and degauss=0.01. And the calculation ran fine.
>> It gave me a total energy value for Cs of 0.01301261 Ry. does it seem
>> trustable?
>>
>> Thank you very much,
>> Tram
>>
>> On Fri, May 20, 2011 at 12:06 AM, Paolo Giannozzi 
>> wrote:
>>>
>>> On May 20, 2011, at 24:34 , Tram Bui wrote:
>>>
>>> > "charge is wrong: smearing is needed". Would you please
>>> > give me some information on how to solve this error?
>>>
>>> use smearing
>>>
>>> > I have enclosed the input file here
>>>
>>> >
>>>
>>> really?
>>>
>>> P.
>>> ---
>>> Paolo Giannozzi, Dept of Chemistry,
>>> Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
>>> Phone +39-0432-558216, fax +39-0432-558222
>>>
>>>
>>>
>>>
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>>
>>
>>
>> --
>> Tram Bui
>>
>> M.S. Materials Science & Engineering
>> trambui at u.boisestate.edu
>>
>>
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>>
>>
>

[Pw_forum] Error message from scf calculation

[Duy Le]

I believe that you have asked us about the calculation for an
isolated atom sometimes ago. It was about C. You should have done the
same approach.
--
Duy Le
PhD Student
Department of Physics
University of Central Florida.

"Men don't need hand to do things"



On Fri, May 20, 2011 at 4:40 PM, Tram Bui  wrote:
> I'm so sorry I forgot the file:) here it is. And I have added the variables
> of : occupations='smearing', and degauss=0.01. And the calculation ran fine.
> It gave me a total energy value for Cs of 0.01301261 Ry. does it seem
> trustable?
>
> Thank you very much,
> Tram
>
> On Fri, May 20, 2011 at 12:06 AM, Paolo Giannozzi 
> wrote:
>>
>> On May 20, 2011, at 24:34 , Tram Bui wrote:
>>
>> > "charge is wrong: smearing is needed". Would you please
>> > give me some information on how to solve this error?
>>
>> use smearing
>>
>> > I have enclosed the input file here
>>
>> >
>>
>> really?
>>
>> P.
>> ---
>> Paolo Giannozzi, Dept of Chemistry,
>> Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
>> Phone +39-0432-558216, fax +39-0432-558222
>>
>>
>>
>>
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>> http://www.democritos.it/mailman/listinfo/pw_forum
>
>
>
> --
> Tram Bui
>
> M.S. Materials Science & Engineering
> trambui at u.boisestate.edu
>
>
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>

[Pw_forum] Negative phonon frequency

[Duy Le]

Did you optimize WELL the structure of SrFeO?
--
Duy Le
PhD Student
Department of Physics
University of Central Florida.

"Men don't need hand to do things"



On Wed, May 11, 2011 at 5:48 AM, mayank gupta  wrote:
> Hi Dear User's
>
>
> I am trying to calculate the phonon frequency of SrFeO compund, but I
> got negative frequancies at gamma also at other Q points, while I have
> chossen very high cutoff (ecut=100Ry and ecut_rho=1000), while
> experimentally the structure is stable at room temperature even up to
> very low temperature. what could be the possible reason for such
> negative frequecies.
>
> --
> Mayank
>
> BHABHA ATOMIC RESEARCH CENTER
> MUMBAI
> Office: ?022-25595606
> Home: 9920397437/9869834437
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[Pw_forum] grid of spacing k-vectors

[Duy Le]

If you can not find the equivalent mesh for a specific spacing, you
just need to list all special k-points with their weight.

And yes, you can always generate anything you want. A small, simple
code will help you to do the job.
--
Duy Le
PhD Student
Department of Physics
University of Central Florida.

"Men don't need hand to do things"



On Thu, May 5, 2011 at 10:14 AM, Eric Germaneau  
wrote:
> Dear all,
>
> I'm wondering whether it's possible to generate k-vectors for the Brillouin
> sampling using
> a grid of spacing instead of a number of vectors.
> Thank you,
>
> ? ? ? ? ? ? ? ? ? ? ? ?ric.
>
> --
> Be the change you wish to see in the world
> ? Mahatma Gandhi ?
>
> Dr. ?ric Germaneau
>
> College of Physical Sciences
> Graduate University of Chinese Academy of Sciences
> Yuquan Road 19A
> Beijing 100049
> China
>
> Please, if possible, don't send me MS Word or PowerPoint attachments
> Why? See: http://www.gnu.org/philosophy/no-word-attachments.html
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>

[Pw_forum] vdW functional not implemented for spin polarized runs

[Duy Le]

On Fri, Apr 29, 2011 at 3:49 AM, Stefano de Gironcoli  
wrote:
> Dear all,
>
> ? ? I inquired Timo Thonhauser (now Wake Forest ?University), the main
> character behind the vdW-DF functional implementation in Quantum
> ESPRESSO, ?about the issue of the spin-polarized version of vdW-DF.
>
> I'm reporting his opinion below:
>
> "In general, at the moment there exists NO true extension of vdW-DF for
> spin-polarized cases. Several groups have expressed interest in working
> on it, but nothing has been published yet. Note that just evaluating
> vdW-DF for the two spin densities separately, while simple to implement,
> is an approximation which is difficult to justify: there is no
> quantitative measure of the error being made, other than hand waving
> arguments that it has to be small. Also, we did not implement that
> simple fix, because we were afraid that people would use it as a
> black-box for spin-polarized calculations, not knowing that there is no
> spin-polarized vdW-DF"
>
> hope this helps to clarify the situation.
>
> stefano

Thank you Stefano and Thonhauser Timo for the clarification.

--
Duy Le
PhD Student
Department of Physics
University of Central Florida.

"Men don't need hand to do things"

>
>
>
> On 04/27/2011 04:45 PM, Duy Le wrote:
>> --
>> Duy Le
>> PhD Student
>> Department of Physics
>> University of Central Florida.
>>
>> "Men don't need hand to do things"
>>
>>
>>
>> On Wed, Apr 27, 2011 at 3:29 AM, Stefano de Gironcoli 
>> ?wrote:
>>> the vdW energy depends on the local polarizability of the electron gas ..
>>> does it depend on the spin density ? I would say so.
>> I would depend as we expected, however, from the formalism of vdW-DF,
>> spin is not taken into account. So, I think in the limit of vdW-DF,
>> the spin-dependence is ignored.
>>
>>> Is it taken into account in the current definition of vdw-DF ? I would say
>>> no...
>>> how is it implemented in GPAW ? just blindly or with some argument ?
>> I am not sure. Did not have a chance to look at it and there is no
>> found document about this.
>>
>>> stefano
>>>
>>> On 04/27/2011 06:35 AM, WANG Wei wrote:
>>>
>>> Thank you for your advice, Deu. Yes, the non-local energy is independent the
>>> spin density.
>>>
>>>
>>> On 27 April 2011 12:34, Duy Le ?wrote:
>>>
>>> --
>>> Duy Le
>>> PhD Student
>>> Department of Physics
>>> University of Central Florida.
>>>
>>> "Men don't need hand to do things"
>>>
>>>
>>>
>>> On Tue, Apr 26, 2011 at 1:00 PM, Stefano de Gironcoli
>>> wrote:
>>>
>>> Dear ?WANG Wei
>>> ? ?the vdw-DF functional form is not defined for spin polarized system...
>>>
>>> Or it does mean that non-local energy is not spin-dependent but
>>> charge-density-dependent only.
>>>
>>> ? ?if you define, implement and test it, you could even get a nice
>>> publication out of it. thank you.
>>>
>>> The spin-polarized vdW-DF has been implemented in GPAW.
>>>
>>> stefano
>>>
>>>
>>>
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>>>
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>>>
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[Pw_forum] vdW functional not implemented for spin polarized runs

[Duy Le]

--
Duy Le
PhD Student
Department of Physics
University of Central Florida.

"Men don't need hand to do things"



On Wed, Apr 27, 2011 at 3:29 AM, Stefano de Gironcoli  
wrote:
> the vdW energy depends on the local polarizability of the electron gas ..
> does it depend on the spin density ? I would say so.

I would depend as we expected, however, from the formalism of vdW-DF,
spin is not taken into account. So, I think in the limit of vdW-DF,
the spin-dependence is ignored.

> Is it taken into account in the current definition of vdw-DF ? I would say
> no...
> how is it implemented in GPAW ? just blindly or with some argument ?

I am not sure. Did not have a chance to look at it and there is no
found document about this.

> stefano
>
> On 04/27/2011 06:35 AM, WANG Wei wrote:
>
> Thank you for your advice, Deu. Yes, the non-local energy is independent the
> spin density.
>
>
> On 27 April 2011 12:34, Duy Le  wrote:
>
> --
> Duy Le
> PhD Student
> Department of Physics
> University of Central Florida.
>
> "Men don't need hand to do things"
>
>
>
> On Tue, Apr 26, 2011 at 1:00 PM, Stefano de Gironcoli 
> wrote:
>
> Dear  WANG Wei
>   the vdw-DF functional form is not defined for spin polarized system...
>
> Or it does mean that non-local energy is not spin-dependent but
> charge-density-dependent only.
>
>   if you define, implement and test it, you could even get a nice
> publication out of it. thank you.
>
> The spin-polarized vdW-DF has been implemented in GPAW.
>
> stefano
>
>
>
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>
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>

[Pw_forum] vdW functional not implemented for spin polarized runs

[Duy Le]

--
Duy Le
PhD Student
Department of Physics
University of Central Florida.

"Men don't need hand to do things"



On Tue, Apr 26, 2011 at 1:00 PM, Stefano de Gironcoli  
wrote:
> Dear ?WANG Wei
> ? the vdw-DF functional form is not defined for spin polarized system...
Or it does mean that non-local energy is not spin-dependent but
charge-density-dependent only.
> ? if you define, implement and test it, you could even get a nice
> publication out of it. thank you.
The spin-polarized vdW-DF has been implemented in GPAW.
> stefano
>
>
> Quoting WANG Wei :
>
>> Dear everyone,
>>
>> I want to investigate the vdW systems with spin polarized calculations.
>> However, I found that the vdW functional is not implemented for spin
>> polarized calculations yet. It would be better if it will be supported in
>> the near future. Thank you.
>>
>> Sincerely yours,
>> WANG
>>
>>
>> +-+
>>
>> Kawazoe's Lab
>> Institute for Materials Research (IMR),
>> Tohoku University2-1-1 Katahira, Aoba-ku, Sendai,
>> Japan
>> +-+
>>
>
>
>
> 
> ? SISSA Webmail https://webmail.sissa.it/
> ? Powered by Horde http://www.horde.org/
>
>
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[Pw_forum] TDDFT approach for periodic system

[Duy Le]

If you do a little homework (such as googling keyword TD-DFPT), you'll
find this link
http://qe-forge.org/projects/tddfpt/
I have not read it carefully but I guess it contains some useful information.
--
Duy Le
PhD Student
Department of Physics
University of Central Florida.

"Men don't need hand to do things"



On Tue, Apr 19, 2011 at 3:26 PM, Johari, Priya Sudhir
 wrote:
> TD-DFPT

[Pw_forum] Fortan compiler cannot create executables

[Duy Le]

So you simply don't have a fortran compiler installed properly. Need to get
one first before compiling QE
--
Duy Le
PhD Student
Department of Physics
University of Central Florida.

"Men don't need hand to do things"


On Sun, Apr 17, 2011 at 10:13 PM, Elie Moujaes
wrote:

>  I am really thankful for your help. I renamed it and now it displayed :
> checking for g95.g95 but it stopped with another error:
>
> Configure: WARNING: In the future, Auticonfig will not detect cross-tools
> whose name does not start with the host triplet. If you think this
> configuration is useful to you, please write to autoconf at gnu.org. Checking
> for Fortran compiler default output filename...Configure: error: Fortran
> compiler cannot create executables
>
>
> Elie
>
> --
> From: ttduyle at gmail.com
> Date: Sun, 17 Apr 2011 21:23:36 -0400
>
> To: pw_forum at pwscf.org
> Subject: Re: [Pw_forum] Fortan compiler cannot create executables
>
> Rename or make an sanple link i686-pc-linux-gnu-g95  to g95 and try. QE
> looks for g95 file, you don't have it.
> --
> Duy Le
> PhD Student
> Department of Physics
> University of Central Florida.
>
> "Men don't need hand to do things"
>
>
> On Sun, Apr 17, 2011 at 9:16 PM, Elie Moujaes  hotmail.co.uk>wrote:
>
>  Dear Duy Le,
>
> Thanks for your reply. The executable is "i686-pc-linux-gnu-g95" and is in
> the bin folder in g95-install. Adding this to the path i.e :
> /exp/home/caiapo/emoujaes/espresso/espresso-4.3/g95-install/bin produces the
> same error  : checking for g95...no
>
> Elie
>
> > Date: Sun, 17 Apr 2011 20:55:58 -0400
> > From: ttduyle at gmail.com
>
> > To: pw_forum at pwscf.org
> > Subject: Re: [Pw_forum] Fortan compiler cannot create executables
> >
> > You just need to identify CORRECTLY the PATH of g95 excutable, not the
> > source code PATH
> >
> > On Sunday, April 17, 2011, Elie Moujaes 
> wrote:
> > >
> > >
> > >
> > >
> > >
> > > Dear Masoud,
> > >
> > > I have tried setenv but it did not really work. Initially, my PATH was:
> /usr/local/bin:/usr/bin:/bin:/usr/bin/X11:/ysr/games now I used setenv and
> the new path is:
> > >
> > >
> /usr/local/bin:/usr/bin:/bin:/usr/bin/X11:/usr/games:/exp/home/caiapo/emoujaes/espresso/espresso-4.3/g95-install
> > >
> > > but when I ./configure again, I still get checking for g95..noso I
> am not sure what is still going wrong
> > >
> > > ELie
> > >
> > > Date: Sun, 17 Apr 2011 09:26:17 +0430
> > > From: masoudnahali at gmail.com
> > > To: pw_forum at pwscf.org
> > > Subject: Re: [Pw_forum] Fortan compiler cannot create executables
> > >
> > >Dear Elie
> > >
> > >   Using csh/tcsh you should try "setenv" instead of "export".
> > >
> > >
> > >
> > >
> > > Elie on Sun, 17 Apr 2011 00:31:35 wrote:
> > >
> > > Unfortunately, my CSH shell does not support the EXPORT command.
> > > Best Wishes
> > >
> > >
> > >  Masoud
> > > --
> > > Masoud Nahali, Ph. D Student
> > > Sharif University of Technology
> > >
> > >
> > > ___
> > > Pw_forum mailing list
> > > Pw_forum at pwscf.org
> > > http://www.democritos.it/mailman/listinfo/pw_forum
> > >
> >
> > --
> > --
> > Duy Le
> > PhD Student
> > Department of Physics
> > University of Central Florida.
> >
> > "Men don't need hand to do things"
> > ___
> > Pw_forum mailing list
> > Pw_forum at pwscf.org
> > http://www.democritos.it/mailman/listinfo/pw_forum
>
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>
>
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[Pw_forum] Fortan compiler cannot create executables

[Duy Le]

Rename or make an sanple link i686-pc-linux-gnu-g95  to g95 and try. QE
looks for g95 file, you don't have it.
--
Duy Le
PhD Student
Department of Physics
University of Central Florida.

"Men don't need hand to do things"


On Sun, Apr 17, 2011 at 9:16 PM, Elie Moujaes wrote:

>  Dear Duy Le,
>
> Thanks for your reply. The executable is "i686-pc-linux-gnu-g95" and is in
> the bin folder in g95-install. Adding this to the path i.e :
> /exp/home/caiapo/emoujaes/espresso/espresso-4.3/g95-install/bin produces the
> same error  : checking for g95...no
>
> Elie
>
> > Date: Sun, 17 Apr 2011 20:55:58 -0400
> > From: ttduyle at gmail.com
>
> > To: pw_forum at pwscf.org
> > Subject: Re: [Pw_forum] Fortan compiler cannot create executables
> >
> > You just need to identify CORRECTLY the PATH of g95 excutable, not the
> > source code PATH
> >
> > On Sunday, April 17, 2011, Elie Moujaes 
> wrote:
> > >
> > >
> > >
> > >
> > >
> > > Dear Masoud,
> > >
> > > I have tried setenv but it did not really work. Initially, my PATH was:
> /usr/local/bin:/usr/bin:/bin:/usr/bin/X11:/ysr/games now I used setenv and
> the new path is:
> > >
> > >
> /usr/local/bin:/usr/bin:/bin:/usr/bin/X11:/usr/games:/exp/home/caiapo/emoujaes/espresso/espresso-4.3/g95-install
> > >
> > > but when I ./configure again, I still get checking for g95..noso I
> am not sure what is still going wrong
> > >
> > > ELie
> > >
> > > Date: Sun, 17 Apr 2011 09:26:17 +0430
> > > From: masoudnahali at gmail.com
> > > To: pw_forum at pwscf.org
> > > Subject: Re: [Pw_forum] Fortan compiler cannot create executables
> > >
> > >Dear Elie
> > >
> > >   Using csh/tcsh you should try "setenv" instead of "export".
> > >
> > >
> > >
> > >
> > > Elie on Sun, 17 Apr 2011 00:31:35 wrote:
> > >
> > > Unfortunately, my CSH shell does not support the EXPORT command.
> > > Best Wishes
> > >
> > >
> > >  Masoud
> > > --
> > > Masoud Nahali, Ph. D Student
> > > Sharif University of Technology
> > >
> > >
> > > ___
> > > Pw_forum mailing list
> > > Pw_forum at pwscf.org
> > > http://www.democritos.it/mailman/listinfo/pw_forum
> > >
> >
> > --
> > --
> > Duy Le
> > PhD Student
> > Department of Physics
> > University of Central Florida.
> >
> > "Men don't need hand to do things"
> > ___
> > Pw_forum mailing list
> > Pw_forum at pwscf.org
> > http://www.democritos.it/mailman/listinfo/pw_forum
>
> ___
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>
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[Pw_forum] Fortan compiler cannot create executables

[Duy Le]

You just need to identify CORRECTLY the PATH of g95 excutable, not the
source code PATH

On Sunday, April 17, 2011, Elie Moujaes  wrote:
>
>
>
>
>
> Dear Masoud,
>
> I have tried setenv but it did not really work. Initially, my PATH was: 
> /usr/local/bin:/usr/bin:/bin:/usr/bin/X11:/ysr/games now I used setenv and 
> the new path is:
>
> /usr/local/bin:/usr/bin:/bin:/usr/bin/X11:/usr/games:/exp/home/caiapo/emoujaes/espresso/espresso-4.3/g95-install
>
> but when I ./configure again, I still get checking for g95..noso I am not 
> sure what is still going wrong
>
> ELie
>
> Date: Sun, 17 Apr 2011 09:26:17 +0430
> From: masoudnahali at gmail.com
> To: pw_forum at pwscf.org
> Subject: Re: [Pw_forum] Fortan compiler cannot create executables
>
> ?? Dear Elie
>
> ? Using csh/tcsh you should try "setenv" instead of "export".
>
>
>
>
> Elie on Sun, 17 Apr 2011 00:31:35 wrote:
>
> Unfortunately, my CSH shell does not support the EXPORT command.
>  Best Wishes
>
>
> ?Masoud
> --
> Masoud Nahali, Ph. D Student
> Sharif University of Technology
>
>
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
> 
>

-- 
--
Duy Le
PhD Student
Department of Physics
University of Central Florida.

"Men don't need hand to do things"

[Pw_forum] total energy

[Duy Le]

Maybe I am too picky. You should NOT start a new email when replying any
message in the forum. Followers can not understand what you are trying to
say. Just hit reply and do NOT delete relevant body message. Thank you.
--
Duy Le
PhD Student
Department of Physics
University of Central Florida.

"Men don't need hand to do things"


On Fri, Apr 15, 2011 at 5:46 AM, Shyam Khambholja wrote:

> no, neither using qha nor md,
> but using mean field potential approach or quasi harmonic debye model.
>
>
>
> --
> Mr. Shyam G Khambholja,
> Research student,
> Depratment of Physics,
> Sardar Patel University, Gujarat
>
>
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>
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[Pw_forum] Regarding accuracy in total energy

[Duy Le]

On Tue, Apr 12, 2011 at 2:52 AM, Stefano de Gironcoli  
wrote:
> change the format statements in electrons (label? 9060 and the like) and
> converge energy accordingly.
Is this true? This solution will give you number of digits but how
about the accuracy as Shyam asked? Due to the numerical error, I don't
think we can get that accuracy.
BTW, you need also to set all convergence categories to 1.0D-10 at least.
> however ... why do you need more than 10 digits ?
Perhaps to calculate Lamb Shift :)
>

----------
Duy Le
PhD Student
Department of Physics
University of Central Florida.

"Men don't need hand to do things"
>
> On 04/12/2011 08:43 AM, Shyam Khambholja wrote:
>
> Dear all,
>
> I want to calculate total energy of compounds with accuarcy upto tenth digit
> after decimal point. what should I need to edit ?
>
> with thanks,
>
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>

[Pw_forum] Calculation of DOS at the Fermi energy

[Duy Le]

Did you call pp.x or dos.x?
--
Duy Le
PhD Student
Department of Physics
University of Central Florida.

"Men don't need hand to do things"


On Sat, Apr 9, 2011 at 11:05 AM, r s  wrote:

> Dear all,
> i want to calculate density of state at fermi energy,
> therefore i use pp.x code with following input file:
>
> 
> prefix= 'ccb'
> outdir= 'root/espresso-4.3/ccb/results',
> plot_num= 3,
> filplot= 'dos'
> /
>
> but after running, get following text:
> %%%
> from local_dos : error # 1
> guassian broadening needed
> %%%
>
> why the guassian broadening?!
> i use smearing= 'mp' in my calculations and don't want to use gaussian
> broadening.
> please guide me,
> thanks,
>
> Regards,
> --
> Romeda Azeen,
> Bhavnagar University Bhavnagar 364002 Gujarat India
>
>
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[Pw_forum] Generating ultra soft pseudopotential

[Duy Le]

Some available PP of Cs can be found at
http://charter.cnf.cornell.edu/psplist.php?element=Cs
If you can not find what you need there, you can follow the
instruction (videos and slides) July 25
http://media.quantum-espresso.org/santa_barbara_2009_07/index.php
--
Duy Le
PhD Student
Department of Physics
University of Central Florida.

"Men don't need hand to do things"



On Tue, Apr 5, 2011 at 5:42 PM, Tram Bui  wrote:
> Dear Folks,
>  I'm trying to build an input file for generating the Cs
> pseudopotential. when I run the ld1.x on my input file. I got an error
> message saying that i'm using the wrong core. would you help me with extra
> information of where I can find the help for how to choose the right core
> for some atoms such as in my case it is Cs.
>
> Thank you very much,
> Tram Bui
>
> M.S. Materials Science & Engineering
> trambui at u.boisestate.edu
>
>
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>
>

[Pw_forum] Shift of Energy

[Duy Le]

On Mon, Apr 4, 2011 at 10:32 AM, pari shok  wrote:
> Dear All,
> Thank you very much for your help.
> Please let me ask my final question w.r.t DOS shift of energy of SiC
> supercell.
> The total energy of the 8-atom cell of SiC is: -76.276 Ry, while that of
> 72-atom SiC is -694 Ry. Neglecting almost -7 Ry, the total energy is scaling
> accordingly.
If you are doing correctly, the results must be identical. So make
sure to check the structures, and the convergence of total energy vs.
cutoff energy and k-point sampling.
> However, I still see the shift of energy in DOS diagram of two slabs (the
> max and min of bandgap shifts, although the gap is almost 2.1 eV for both
> 4H-SiC slabs). I was wondering whether this shift of energy is inevitable or
> it is as the result of my input file.
Slab? I though you are performing bulk calculation. Anyway, the shift
of energies' levels is normal. You should set the reference as center
of the gap (set it to be zero) then compare the DOS or band
structures.
By the way, if your bigger slab experiences the reconstruction, the
two slabs (8 atoms and 72 atoms) won't be identical => you should not
get the same results in this case. But 7Ry seems to be huge.
> I kept k points (w.r.t. crystal), and cut off energy the same for both
> structures. Should I scale the cut off energy as well. If positive, is there
Okie, but you should scale the k-point sampling accordingly because
the BZ of 72 atoms cell is smaller. But this won't harm the results if
total energy is already converged vs. k-point sampling.
> any relation between scaling the cell and cut off energy.
No. Cut off energy depends on only pseudo potential.
> As you know, I need to find a reference for my further calculations.
> I really really appreciate your help.
> Yours
> P Shok
>

--
Duy Le
PhD Student
Department of Physics
University of Central Florida.

"Men don't need hand to do things"
> Dear  All,
>  let me clarify a little point.
>  The potential (hence the eigenvalues) of  any calculation in
> periodic boundary conditions, not just a plane-wave one , is defined up
>
> to  an additive constant... In a finite system a reeference can be fixed
> by requiring that the potential goes to zero at infinite distance but in
> a periodic system this cannot be defined as there is nothing like a
>
> point at infinite distance ...
> In most codes (and in pw.x) this arbitrary constant is fixed by
> setting the average electrostatic potential to zero. If the supercell is
> properly constructed, with the properly scaled dimensions, the same
>
> cutoff, equivalent k-points etc.. the two calculations should be
> equivalent and the eigenvalues should be exactly mapped, the average
> potential should be the same, the total energy should be an exact
> multiple of the one of the original cell.
>
>
> If this does not happen one is NOT doing the supercell calculation properly.
>
> So if when doing a supercell you do not get the scaled result check your
> system definition.
>
> stefano
>
>
> On 04/04/2011 11:46 AM, Giuseppe Mattioli wrote:
>
>> Dear all
>> I suspect that a a little misunderstanding has been going on here...
>> I try to reformulate the question: in the case of a 8-atoms cell the
>> valence
>> band maximum (VBM) has been found around 10 eV and the conduction band
>
>> minimum (CBM) around 12 eV with a 2 eV band gap. So there is a shift in
>> the
>> position of VBM and CBM when calculated in a 72-atoms supercell, but the
>> band
>> gap value is the same. Then, the answer to P Shok could be: plane wave
>
>> pseudopotential calculations do not ensure an universal alignment of
>> eigenvalues. You should use some "internal" reference, like the 1s
>> eigenvalue
>> of an He atom, in your cell; or trust that the two VBM values are aligned
>> "de
>
>> facto".
>> HTH
>>
>> Giuseppe
>>
>> On Monday 04 April 2011 09:39:18 Gabriele Sclauzero wrote:
>>> Yes,
>>>
>>> I perfectly agree with Eyvaz! Moreover the experimental bandgap is
>
>>> underestimated within LDA or GGA, and for 4H-SiC you would get about
>>> 2.2-2.3 eV with LDA.
>>>
>>> How do you measure the bandgap? Beware that in the fundamental cell
>>> the
>
>>> bandgap is not a direct one, but it might become such when you use a
>>> supercell (because of the refolding of the Brillouin zones).
>>>
>>>
>>> HTH
>
>>>
>>> GS
>>>
>>> Il giorno 03/apr/2011, alle ore 10.59, Eyvaz Isaev ha scritto:
>>>> Hi,
>>>>
>>>&

[Pw_forum] Type of pseudo potential using input_dft

[Duy Le]

Dear all,
It is a naive question.
As I understand, if we specify input_dft=PBESol, PBE, revpbe... the
code will override value from provided potentials.
So, could any one please explain for me what type of pseudo potential
(ultrasolf, normconserving, or paw) used if we use input_dft?

Thank you.

--
Duy Le
PhD Student
Department of Physics
University of Central Florida.

"Men don't need hand to do things"

[Pw_forum] XYZ for K-Points set

[Duy Le]

You can use xcrysden to find their coordinates. Or you can also use
condensed matter text book.
--
Duy Le
PhD Student
Department of Physics
University of Central Florida.

"Men don't need hand to do things"



On Tue, Mar 22, 2011 at 11:16 AM, Mehrnoosh Hazrati
 wrote:
> Hi dear QE users,
>
> please tell me where can i find the X,Y,Z for K-Points set? : G,F,Q,Z,G? (
> for the band structure calculations of an orthorhombic super cell .?)
>
> I wonder if you could help me.
> I thank you in advance.
>
> Regards
>
> Mehrnoosh
>
>
> --
> Mehrnoosh Kh. Hazrati, Master Student of Computational Physical Chemistry,
> KNTU, Tehran.
> Phone : +989123436300
> Mail : mehrnooshhazrati at gmail.com
>
>
>
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>
>

[Pw_forum] smearing

[Duy Le]

On Tue, Mar 15, 2011 at 1:46 PM, Iurii TIMROV
 wrote:
>> Mind, that 'tetrahedra' has to be used for DOS or SCF only, forces and
>> stresses are
>> not reliable it this case (they are not variational).
>
> Could you recommend some paper where this statement was
> mentioned/discussed/proved? Thanks!
>
Should be in the original paper about this method, by Bl?chl et al 1994
----------
Duy Le
PhD Student
Department of Physics
University of Central Florida.

"Men don't need hand to do things"

[Pw_forum] number of bands and degenerate states in supercell

[Duy Le]

The logic is simple:
#bands = #electrons/2+#unoccupied_bands
If you increase the size of unit cell, #atoms increase as well, so do #electrons
However, you will have something called band folding because the BZ shrinks.
--
Duy Le
PhD Student
Department of Physics
University of Central Florida.

"Men don't need hand to do things"



On Fri, Mar 11, 2011 at 1:37 PM, pari shok  wrote:
> Hello,
> I have a question and I appreciate your help in advance.
> I am making a supercell by repeating a unit cell of SiC. Then, instead of 8
> atom in a hexagonal structure, there are 72 atoms in a supercell.
> My question is about the number of bands.
> Theoretically, the number of bands would be just the same for the unit cell
> (32 in this case) and even if you increase them in the input file, they
> should just have degeneracy and overlap. However, they are not.
> I was wondering how I can interpret the bands.
> Yours
> P Shok
> UMD
>
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>
>

[Pw_forum] graphene's band gap

[Duy Le]

On Thu, Mar 10, 2011 at 9:52 AM, Eric Germaneau  
wrote:
> Dear Mehmet and Hui Wang,
>
> That's what I did.
> From my calculations the occupied and unoccupied bands touch only at K
> point.
> I was just confused because the scf calculation does not output a zero gap.
> I mean the line "highest occupied, lowest unoccupied level" shows two
> different values and I expected them to be equal.
This was just explained by Mehmet. Check it again
> So, it seems I did not too bad in fact.
> But how to experimentally get a zero gap then?
> Thanks,
>
> ??? Eric.
>

------
Duy Le
PhD Student
Department of Physics
University of Central Florida.

"Men don't need hand to do things"
> On 03/09/2011 07:02 AM, Mehmet Topsakal wrote:
>
> Dear?Eric,
> In addition,?if you select 18x18x1 kpoints, your mesh should include both K
> and M points.
> But for a band-structure calculation, you should arrange a kpoints list
> along special directions, such as from GAMMA-to-M-to-K-to-GAMMA, and do a
> nscf calculation
>
>
> On Wed, Mar 9, 2011 at 11:28 AM, xirainbow  wrote:
>>
>> Dear?Eric:
>> The occupied and unoccupied bands touch each other only at M point(or K
>> point, I forget it).
>> You must include this point in you k-mesh.
>> Furthermore, if you include spin-orbital coupling, the band gap will be
>> opened at this point.
>>
>> On Thu, Mar 10, 2011 at 1:30 AM, Eric Germaneau 
>> wrote:
>>>
>>> Dear all,
>>>
>>> I'm trying to compute graphene's band gap but get stuck.
>>> From my understanding a scf calculation should provide the same energy
>>> for the highest occupied and lowest occupied level which means a zero gap.
>>> I played with the number a kpoints a finally got a band gap of 0.57 which
>>> is not null.
>>> The scf convergence looks good.
>>> I'm not (yet) an expert in DFT calculation so may did something wrong or
>>> misunderstood something here.
>>> So, I wonder if someone has already successfully performed such
>>> calculation.
>>> I have attached my input file.
>>> Thanks in advance,
>>>
>>> ??? Eric.
>>>
>>> --
>>> Be the change you wish to see in the world
>>> ? Mahatma Gandhi ?
>>>
>>> Dr. ?ric Germaneau
>>>
>>> College of Physical Sciences
>>> Graduate University of Chinese Academy of Sciences
>>> Yuquan Road 19A
>>> Beijing 100049
>>> China
>>>
>>> Please consider the environment before printing this email.
>>> Consid?rez svp l'environnement avant d'imprimer cet email.
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>>>
>>
>>
>>
>> --
>> 
>> Hui Wang
>> School of physics, Fudan University, Shanghai, China
>>
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>>
>
>
>
> --
>
> Mehmet Topsakal? (Ph.D. Student)
> UNAM-Institute of Materials Science and Nanotechnology.
> Bilkent University. 06800 Bilkent, Ankara/Turkey
> Tel: 0090 312 290 3527 ; Fax: 0090 312 266 4365
> http://www.researcherid.com/rid/A-5015-2010
>
>
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>
> --
> Be the change you wish to see in the world
> ? Mahatma Gandhi ?
>
> Dr. ?ric Germaneau
>
> College of Physical Sciences
> Graduate University of Chinese Academy of Sciences
> Yuquan Road 19A
> Beijing 100049
> China
>
> Please consider the environment before printing this email.
> Consid?rez svp l'environnement avant d'imprimer cet email.
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>

[Pw_forum] calculation wouldn't run using espresso-4.2.1 but did run with espresso-4.1.3

[Duy Le]

for isolated C, you need to do spin polarized calculation with the
usage of occupation card. See example 11 for details.
--
Duy Le
PhD Student
Department of Physics
University of Central Florida.

"Men don't need hand to do things"



On Mon, Mar 7, 2011 at 7:05 PM, Tram Bui  wrote:
> Dear Emine,
> ? Thank you for your respond. And to answer your chain of questions :),
> this is what I have got
> -?? First my installation was successful. I have done tons of calculation
> for single silicon as well as silicon carbide system and everything works
> fine, except when it comes to this single carbon atom calculation.
> -?? Second, the erroe message was: "the convergence was not achieved after
> 100 interations" (so you can see that the i took really long for this
> calculation but no result was given in the end)
> -??? Third, we tried the calculation with my thesis advisor computer,it
> didn't work and gave out the same problem.
> -??? Forth, I have tried to do the calculation using older version of QE,
> and it worked!!, but again, isn't the newer version supposed to work better
> than the older one? not mention about the fact that it should give more
> accurate results.
> ??? So now both my advisor and I couldn't figure out why it is not working
> with properly in espresso-4.2.1. and I really appreciate any help from
> everyone!
>
> Thank you,
> Tram
>
> On Mon, Mar 7, 2011 at 4:44 PM, Emine Kucukbenli  wrote:
>>
>> Dear Tram Bui,
>> Doesnt it bug you that such a simple calculation which almost 'tests' the
>> pw.x doesnt work in your installation but seems to work for everyone else?
>> :)
>>
>> ok, sorry lets get serious: was your installation successful? what is the
>> error message? how does it stop? can you reproduce the same problem in
>> another machine/compiler etc?
>> what have you done to locate the problem?
>> yadda yadda.. the usual questions which i think you should have asked
>> ?yourself before posting.. :)
>>
>> emine kucukbenli, phd student, sissa, italy
>>
>>
>> Quoting Tram Bui :
>>
>>> Hi Everyone,
>>> ? ? I have post a question regarding the single atom calculation for
>>> carbon
>>> simple cubic system last month. I was using the ultra-soft
>>> pseudopotential
>>> of C as :C.pbe-van_ak.UPF. And the calculation ran fine using
>>> espresso-4.1.3
>>> (oder version), but not for espresso-4.2.1 (latest version). So would you
>>> let me know what might have been my problem? was it my input file or the
>>> new
>>> version of quantum espresso? I also attached my input file here for more
>>> info.
>>>
>>> Regard,
>>> Tram Bui
>>>
>>> M.S. Materials Science & Engineering
>>> trambui at u.boisestate.edu
>>>
>>
>>
>>
>> 
>> ?SISSA Webmail https://webmail.sissa.it/
>> ?Powered by Horde http://www.horde.org/
>>
>>
>
>
>
> --
> Tram Bui
>
> M.S. Materials Science & Engineering
> trambui at u.boisestate.edu
>
>
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>

[Pw_forum] НА: Re: problem in MPI running of QE (16 processors)

[Duy Le]

You should make sure that the mpiexec is used correctly. Try one of
these sameple in this link.
http://hamilton.nuigalway.ie/teaching/AOS/NINE/mpi-first-examples.html
--
Duy Le
PhD Student
Department of Physics
University of Central Florida.

"Men don't need hand to do things"



On Mon, Mar 7, 2011 at 11:24 AM, Alexander G. Kvashnin
 wrote:
> Dear all
>
> I tried to use full paths, but it didn't give positive results. It wrote an
> error message
> application called MPI_Abort(MPI_COMM_WORLD, 0) - process 0
>
> On 7 March 2011 10:30, Alexander Kvashnin  wrote:
>>
>> Thanks, I tried to use "<" instead of "-in" it also didn't work.
>> OK,I will try to use full paths for input and output, and answer about
>> result.
>>
>> -  ? -
>> ??: Omololu Akin-Ojo 
>> ??: 7 ? 2011 ?. 9:56
>> : PWSCF Forum 
>> : Re: [Pw_forum] ??: Re: problem in MPI running of QE (16 processors)
>>
>> Try to see if specifying the full paths help.
>> E.g., try something like:
>>
>> mpiexec /home/MyDir/bin/pw.x -in ?/scratch/MyDir/graph.inp >
>> /scratch/MyDir/graph.out
>>
>> (where /home/MyDir/bin is the full path to your pw.x and
>> /scratch/MyDir/graph.inp is the full path to your output )
>>
>> ( I see you use "-in" instead of "<" to indicate the input. I don't
>> know too much but _perhaps_ you could also _try_ using "<" instead of
>> "-in") .
>>
>> o.
>>
>> On Mon, Mar 7, 2011 at 7:31 AM, Alexander Kvashnin 
>> wrote:
>> > Yes, I wrote
>> >
>> > #PBS -l nodes=16:ppn=4
>> >
>> > And in userguide of MIPT-60 wrote,that mpiexec must choose number of
>> > processors automatically, that's why I didn't write anything else
>> >
>> >
>> > 
>> > : Huiqun Zhou 
>> > : 7 ?? 2011 ??. 7:52
>> > : PWSCF Forum 
>> > : Re: [Pw_forum] problem in MPI running of QE (16 processors)
>> >
>> > How did you apply number of node, procs per node in your job
>> > script?
>> >
>> > #PBS -l nodes=?:ppn=?
>> >
>> > zhou huiqun
>> > @earth sciences, nanjing university, china
>> >
>> >
>> > - Original Message -
>> > From: Alexander G. Kvashnin
>> > To: PWSCF Forum
>> > Sent: Saturday, March 05, 2011 2:53 AM
>> > Subject: Re: [Pw_forum] problem in MPI running of QE (16 processors)
>> > I create PBS task on supercomputer MIPT-60 where I write
>> >
>> > mpiexec ../../espresso-4.2.1/bin/pw.x -in graph.inp > output.opt
>> > all other
>>
>> [??? ??  ? ? ?]
>
>
> --
> Sincerely yours
> Alexander G. Kvashnin
> 
> Student
> Moscow Institute of Physics and Technology ? ? ? ? ?http://mipt.ru/
> 141700, Institutsky lane 9, Dolgoprudny, Moscow Region, Russia
>
> Junior research scientist
> Technological Institute for Superhard
> and Novel Carbon Materials
> http://www.ntcstm.troitsk.ru/
> 142190, Central'naya St. 7a, Troitsk, Moscow Region, Russia
> 
>
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>

[Pw_forum] problem in MPI running of QE (16 processors)

[Duy Le]

You can use:
mpiexec --help
or
man mpiexec
to see how to have correct command
--
Duy Le
PhD Student
Department of Physics
University of Central Florida.

"Men don't need hand to do things"



On Fri, Mar 4, 2011 at 1:53 PM, Alexander G. Kvashnin
 wrote:
> I create PBS task on supercomputer MIPT-60 where I write
>
> mpiexec ../../espresso-4.2.1/bin/pw.x -in graph.inp > output.opt
> all other types of this line such as
> mpiexec -np 16 ../../espresso-4.2.1/bin/pw.x -in graph.inp > output.opt
>
> doesn't work.
> Maybe this number of processor too small for parallel calculation to QE?
>
>
> On 4 March 2011 21:37, Eyvaz Isaev  wrote:
>>
>> Dear? Alexander,
>>
>> How do you run a job? You should launch a command like (some parameters
>> are omitted)
>> mpirun -np 16 -maxtime 30 ./pw.x < scf.in >scf.out
>>
>> The easiest way to be added to the forum list? is subscribing? to this
>> forum. Please visit
>> http://www.pwscf.org/contacts.php
>>
>> Please also provide your affiliation.
>>
>> Best regards,
>> ?Eyvaz.
>> ---
>> Prof. Eyvaz Isaev,
>> Department of Physics, Chemistry, and Biology (IFM), Linkoping University,
>> Sweden
>> Theoretical Physics Department, Moscow State Institute of Steel & Alloys,
>> Russia,
>> isaev at ifm.liu.se, eyvaz_isaev at yahoo.com
>>
>> 
>> From: Alexander G. Kvashnin 
>> To: pw_forum at pwscf.org
>> Sent: Fri, March 4, 2011 9:07:46 PM
>> Subject: [Pw_forum] problem in MPI running of QE (16 processors)
>>
>> Hello,
>>
>> I have some problem when I ran parallel version of QE (16 procs), I saw
>> next line in output file
>>
>> Parallel version (MPI), running on 1 processors
>> And it works using only 1 processor, but there is MPI version.
>> Help me please in my problem
>> Thank you!
>> --
>> Sincerely yours
>> Alexander G. Kvashnin
>>
>>
>> ___
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://www.democritos.it/mailman/listinfo/pw_forum
>>
>
>
>
> --
> Sincerely yours
> Alexander G. Kvashnin
>
> ___
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> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>

[Pw_forum] Lattice constant for copper

[Duy Le]

Did you check your k-point sampling?
--
Duy Le
PhD Student
Department of Physics
University of Central Florida.

"Men don't need hand to do things"



On Wed, Mar 2, 2011 at 5:58 PM, Krukau,  Aliaksandr  
wrote:
> ? Dear QE users,
> ? ?I apologize if my question seems stupid to you. I am a complete QE newbie
> and could not find any answer in the tutorials.
> ? ?I am trying to find equilibrium lattice constant for copper with PBE
> and ultrasoft pseudopotentials. I ran scf calculations for face-centered cubic
> unit cell for a number of lattice constants:
> Lattice constant 6.65 a.u. ! ? ?total energy ? ? ? ? ? ? ?=
> -121.62734203 Ry
> Lattice constant 6.66 a.u. ! ? ?total energy ? ? ? ? ? ? ?=
> -121.62735421 Ry
> Lattice constant 6.67 a.u. ! ? ?total energy ? ? ? ? ? ? ?=
> -121.62734651 Ry
> Lattice constant 6.65 a.u. ! ? ?total energy ? ? ? ? ? ? ?=
> -121.62731956 Ry
> ? ?The minimum total energy is for the lattice constant 6.66 a.u.
> But this value drastically differs from the published PBE value of 6.86 a.u.
> (Phys. Rev. B, vol. 77, 05414 (2008), Table II). It also differs from
> the experimental value of 6.83 a.u. I attach the input file that I used
> for lattice constant 6.66 a.u. below the signature.
> ? ?Why is equilibrium lattice constant so low?
> Best regards,
> Alex Krukau,
> Indiana University
>
> --
> 
> ? ?calculation='scf'
> ? ?pseudo_dir = '~/espresso-4.2.1/pseudo/ADDITIONAL',
> /
> 
> ? ?ibrav = 2,
> ? ?celldm(1) = 6.66,
> ? ?nat= 1,
> ? ?ntyp= 1,
> ? ?ecutwfc = 120.0,
> ? ?ecutrho = 1000.0
> ? ?occupations='smearing', smearing='marzari-vanderbilt', degauss=0.01
> /
> 
> ? ?conv_thr=0.001
> /
> ATOMIC_SPECIES
> Cu ?63.546 Cu.pbe-n-van_ak.UPF
> ATOMIC_POSITIONS
> Cu 0.0 0.0 0.0 ? ?1 ? 1 ? 1
> K_POINTS automatic
> 12 12 1 0 0 0
>
>
>
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> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>

[Pw_forum] about perovskite and AuCu3

[Duy Le]

It should be cubic perovskite. So
Primitive vectors  are:
a 0 0
0 a 0
0 0 a
and coordinates of atoms are:
0. 0. 0. (Au)
0.5 0.5 0. (Cu)
0.0 0.5 0.5 (Cu)
0.5 0.0 0.5 (Cu)
--
Duy Le
PhD Student
Department of Physics
University of Central Florida.

"Men don't need hand to do things"


On Wed, Feb 23, 2011 at 5:35 AM, kangbugy at lycos.co.kr
wrote:

>  Hi.
> I study QE as graduate student in Korea.
> But I have many problems.
> One of them is about AuCu3 structure.
> This basic structure is perovskite, but there is not a atom at body center.
>
> i.e., it is fcc structure.
> Because I thought fcc structure, I used that 'ibrav = 2'.
> Also,
> atomic position is
>  Au 0.00 0.00 0.00
>  Cu 0.50 0.50 0.00
> But scf.out's result appeared that 'atomic position #1 and #2 are overlap'.
> I don't understand that.
>
> Another question is scf data of perovskite.
> What can I input the data about perovskite?
>
>  
>ibrav = 1,
>A = 3.717 ,
>B = 3.717 ,
>C = 3.717 ,
>cosAB = 90 ,
>cosAC = 90 ,
>cosBC = 90 ,
>  nat = 5,
> ntyp = 3,
>  ecutwfc = 30,
>  /
>  
>  /
> ATOMIC_SPECIES
>  Mg 24.305 Mg.pz-n-vbc.UPF
>C 16.01 C.pz-rrkjus.UPF
>  Ni 58.71  Ni.pz-nd-rrkjus.UPF
>
> ATOMIC_POSITIONS
>  Mg 0.00 0.00 0.00
>C 0.50 0.50 0.50
>  Ni 0.00 0.50 0.50
>  Ni 0.50 0.50 0.00
>  Ni 0.50 0.00 0.50
>
> K_POINTS automatic
>  10 10 10 0 0 0
>
> Help me please.
>
> ___
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> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>
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[Pw_forum] A question on atomic magnetic moments

[Duy Le]

You should be able to fix magneticmoment of system at the desired
value (say 6, 6.5, 7) to see which one give you the lowest energy.
--
Duy Le
PhD Student
Department of Physics
University of Central Florida.

"Men don't need hand to do things"



On Sun, Feb 13, 2011 at 1:16 AM, Giovani Faccin
 wrote:
> Dear Paolo,
>
> Thanks for the reply.
>
> Just to make sure that the simulation cell size is not an issue (so that the
> system is really finite), I've tested different possibilities, including
> some quite big cells. Still, after a certain size the value of the
> magnetization is converging to 6.82 instead of the expected 6.
>
> So something else is causing this. Unfortunately I've got no clue as to what
> could it be.
>
> Should it be of any help, this is my input file:
>
>
> ?
>  calculation = 'scf' ,
> ??? restart_mode = 'from_scratch' ,
> ? wf_collect = .true. ,
> ? outdir = './output' ,
> ? pseudo_dir = '../pseudo/' ,
> ? prefix = 'fe' ,
> ?? etot_conv_thr = 1.0D-9 ,
> ?? forc_conv_thr = 1.0D-6 ,
>  tstress = .true. ,
>  tprnfor = .true. ,
> ?/
> ?
> ?? ibrav = 1,
> ?? celldm(1) = 43,
>  nat = 2,
> ??? ntyp = 1,
>  ecutwfc = 100 ,
>  ecutrho = 300 ,
>  occupations = 'smearing' ,
>  degauss = 0.02 ,
> ??? smearing = 'methfessel-paxton' ,
> ?? nspin = 2 ,
> ?? starting_magnetization(1) = 1.0,
> ?/
> ?
> ??? conv_thr = 1.0e-9 ,
>  mixing_beta = 0.7 ,
>  diagonalization = 'david' ,
> ?/
> ATOMIC_SPECIES
> ?? Fe?? 58.69000? Fe.pbe-nd-rrkjus.UPF
> ATOMIC_POSITIONS angstrom
> ?? Fe? 0.0??? 0.0??? 0.0
> ?? Fe? 2.047510?? 0.0??? 0.0
> K_POINTS automatic
> ? 1 1 1?? 1 1 1
>
> Any suggestions are highly welcome.
>
> Giovani
>
>
> 2011/2/12 Paolo Giannozzi 
>>
>> On Feb 11, 2011, at 17:09 , Giovani Faccin wrote:
>>
>> > My question: shouldn't those numbers be integers?
>>
>> only in finite systems, if you neglect spin-orbit.
>>
>> P.
>> ---
>> Paolo Giannozzi, Dept of Chemistry,
>> Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
>> Phone +39-0432-558216, fax +39-0432-558222
>>
>>
>>
>>
>> ___
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>> http://www.democritos.it/mailman/listinfo/pw_forum
>
>
>
> --
> Giovani
>
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>
>

[Pw_forum] Energy calculation for single carbon atom

[Duy Le]

for isolated atom, you need to perform spin-polarized DFT, and also
you need to fix occupation number by using Hund's rule(use occupations
card).
--
Duy Le
PhD Student
Department of Physics
University of Central Florida.

"Men don't need hand to do things"



On Wed, Feb 9, 2011 at 2:56 PM, Changru Ma  wrote:
> Hi Tram,
>
> Please have a look at the User's Guide first:
>
> http://www.quantum-espresso.org/user_guide/node50.html#SECTION0001110240
>
> Best wishes,
> Changru
>
>> Hi Everyone,
>> ? ? ?I'm trying to run the total energy calculation for a simple cubic of
>> carbon, in which i'm using the lattice constant of 40 Bohrs (a.u) and the
>> E
>> cut off of 30 Ryd. ?this should be a very simple calculation. when I used
>> K-points of 10x10x10, the calculation worked fine. However, I then wanna
>> try
>> with the K point of {gamma} and it kept giving me the error of " 1
>> eigensvalue is not converged". So my question is would you look at the
>> input
>> file and the (not-finished) out put file and let me know what might have
>> been my mistakes?
>>
>> Thank you and have a great week,
>>
>>
>>
>> --
>> Tram Bui
>>
>> M.S. Materials Science & Engineering
>> trambui at u.boisestate.edu
>> ___
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://www.democritos.it/mailman/listinfo/pw_forum
>>
>
>
> --
> Changru Ma, PhD Student
> SISSA and Theory at Elettra Group
> email: crma at sissa.it
>
>
> 
> ?SISSA Webmail https://webmail.sissa.it/
> ?Powered by SquirrelMail http://www.squirrelmail.org/
>
> ___
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>

[Pw_forum] a question about MnSe

[Duy Le]

On Mon, Jan 24, 2011 at 2:19 AM, Paolo Giannozzi  
wrote:
>
> On Jan 24, 2011, at 6:42 , mohnish pandey wrote:
>
>> ? ? ? ? ? ? ? ? ? ? ? ? ?I have searched in other literatures also,
>> but did not find anything with PBE functional or in general
>> plane wave DFT. Most of the work is in DFT+U..
>
> this should tell you something...
Right. The DFT+U paper will tell you exactly why they used DFT+U but
the regular DFT and also what are the expected results of using
regular DFT

----------
Duy Le
PhD Student
Department of Physics
University of Central Florida.

"Men don't need hand to do things"

> ---
> Paolo Giannozzi, Dept of Chemistry,
> Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
> Phone +39-0432-558216, fax +39-0432-558222
>
>
>
>
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>

[Pw_forum] a question about MnSe

[Duy Le]

Hi,
These numbers mean nothing to me. What I meant was whether these
numbers are close to what you expected or close to any available
experimental or theoretical data. The spin polarized calculation is
little bit tricky, the system may stuck in any local minimum.


--
Duy Le
PhD Student
Department of Physics
University of Central Florida.

"Men don't need hand to do things"



On Fri, Jan 21, 2011 at 8:15 AM, mohnish pandey  
wrote:
> Dear Duy,
> ?? ? ? ? ? ? ? I have done Lowdin analysis for MnSe wurtzite and rocksalt
> structure. The results for total polarization are:
> Wurtzite :
> Mn1 ?~ 1.82
> Mn2 ~ -1.80
> Sn ?~ ?0.0
> Spilling parameter = 0.31
> Rocksalt:
> Mn1 ~ ?0.40
> Mn2 ~ -0.40
> Sn ?~ ? 0.0
> Spilling parameter = 0.48
>
> On Fri, Jan 21, 2011 at 6:01 PM, Duy Le  wrote:
>>
>> What are the magnetic moment of Mn you got? Are they expected values?
>> --
>> Duy Le
>> PhD Student
>> Department of Physics
>> University of Central Florida.
>>
>> "Men don't need hand to do things"
>>
>>
>>
>> On Fri, Jan 21, 2011 at 6:54 AM, mohnish pandey 
>> wrote:
>> > Dear Prof. Prasenjit!
>> > ?? ? ? ? ? ? ? ? ? ? ? ? ? ? ? I have tried many initial magnetizations
>> > but
>> > final results are more or less same. I am not able to figure out the
>> > problem
>> >
>> > On Fri, Jan 21, 2011 at 1:44 PM, Prasenjit Ghosh
>> > 
>> > wrote:
>> >>
>> >> Dear Mohnish,
>> >>
>> >> One thing you may try to do is to change the value of starting
>> >> magnetization and redo the calculation.
>> >> Sometimes in case of magnetic systems (at least those which are
>> >> ferromagnetic), the code gets stuck into some local minima. Starting
>> >> from a different point might help you to reach the correct ground
>> >> state.
>> >>
>> >> Prasenjit
>> >>
>> >> On 21 January 2011 13:00, mohnish pandey 
>> >> wrote:
>> >> > Dear Lorenzo !
>> >> > ?? ? ? ? ? ? ? ? ? ? ? ?Can you give me a direction for my question
>> >> > about
>> >> > MnSe. I am really struck in it...
>> >> >
>> >> > On Fri, Jan 21, 2011 at 12:40 PM, Lorenzo Paulatto
>> >> >  wrote:
>> >> >>
>> >> >> In data 20 gennaio 2011 alle ore 19:37:16, jia chen
>> >> >>  ha scritto:
>> >> >> > I also have a question about vc-relax. How do you know if your
>> >> >> > cutoff
>> >> >> > is
>> >> >> > large enough to overcome Pulay stress, or you can do something
>> >> >> > else
>> >> >> > to
>> >> >> > get
>> >> >> > rid of it in you calculations. Thanks.
>> >> >>
>> >> >> The vc-relax algorithm keeps number of plane waves constant (i.e. it
>> >> >> changes ecutwfc as ~ V^3/2) in order to avoid Pulay stress.
>> >> >>
>> >> >> best regards
>> >> >>
>> >> >>
>> >> >> --
>> >> >> Lorenzo Paulatto
>> >> >> post-doc @ IMPMC/UPMC - Universit? Paris 6
>> >> >> phone: +33 (0)1 44 27 74 89
>> >> >> www: ? http://www-int.impmc.upmc.fr/~paulatto/
>> >> >>
>> >> >> previously (take note of the change!):
>> >> >> phd student @ SISSA ?& ?DEMOCRITOS (Trieste)
>> >> >> phone: +39 040 3787 511
>> >> >> www: ? http://people.sissa.it/~paulatto/
>> >> >> ___
>> >> >> Pw_forum mailing list
>> >> >> Pw_forum at pwscf.org
>> >> >> http://www.democritos.it/mailman/listinfo/pw_forum
>> >> >
>> >> >
>> >> >
>> >> > --
>> >> > Regards,
>> >> > MOHNISH,
>> >> > -
>> >> > Mohnish Pandey
>> >> > Y6927262,5th Year dual degree student,
>> >> > Department of Chemical Engineering,
>> >> > IIT KANPUR, UP, INDIA
>> >> > -
>> >> >
>> >> > __

[Pw_forum] a question about MnSe

[Duy Le]

What are the magnetic moment of Mn you got? Are they expected values?
--
Duy Le
PhD Student
Department of Physics
University of Central Florida.

"Men don't need hand to do things"



On Fri, Jan 21, 2011 at 6:54 AM, mohnish pandey  
wrote:
> Dear Prof. Prasenjit!
> ?? ? ? ? ? ? ? ? ? ? ? ? ? ? ? I have tried many initial magnetizations but
> final results are more or less same. I am not able to figure out the
> problem
>
> On Fri, Jan 21, 2011 at 1:44 PM, Prasenjit Ghosh 
> wrote:
>>
>> Dear Mohnish,
>>
>> One thing you may try to do is to change the value of starting
>> magnetization and redo the calculation.
>> Sometimes in case of magnetic systems (at least those which are
>> ferromagnetic), the code gets stuck into some local minima. Starting
>> from a different point might help you to reach the correct ground
>> state.
>>
>> Prasenjit
>>
>> On 21 January 2011 13:00, mohnish pandey  wrote:
>> > Dear Lorenzo !
>> > ?? ? ? ? ? ? ? ? ? ? ? ?Can you give me a direction for my question
>> > about
>> > MnSe. I am really struck in it...
>> >
>> > On Fri, Jan 21, 2011 at 12:40 PM, Lorenzo Paulatto
>> >  wrote:
>> >>
>> >> In data 20 gennaio 2011 alle ore 19:37:16, jia chen
>> >>  ha scritto:
>> >> > I also have a question about vc-relax. How do you know if your cutoff
>> >> > is
>> >> > large enough to overcome Pulay stress, or you can do something else
>> >> > to
>> >> > get
>> >> > rid of it in you calculations. Thanks.
>> >>
>> >> The vc-relax algorithm keeps number of plane waves constant (i.e. it
>> >> changes ecutwfc as ~ V^3/2) in order to avoid Pulay stress.
>> >>
>> >> best regards
>> >>
>> >>
>> >> --
>> >> Lorenzo Paulatto
>> >> post-doc @ IMPMC/UPMC - Universit? Paris 6
>> >> phone: +33 (0)1 44 27 74 89
>> >> www: ? http://www-int.impmc.upmc.fr/~paulatto/
>> >>
>> >> previously (take note of the change!):
>> >> phd student @ SISSA ?& ?DEMOCRITOS (Trieste)
>> >> phone: +39 040 3787 511
>> >> www: ? http://people.sissa.it/~paulatto/
>> >> ___
>> >> Pw_forum mailing list
>> >> Pw_forum at pwscf.org
>> >> http://www.democritos.it/mailman/listinfo/pw_forum
>> >
>> >
>> >
>> > --
>> > Regards,
>> > MOHNISH,
>> > -
>> > Mohnish Pandey
>> > Y6927262,5th Year dual degree student,
>> > Department of Chemical Engineering,
>> > IIT KANPUR, UP, INDIA
>> > -
>> >
>> > ___
>> > Pw_forum mailing list
>> > Pw_forum at pwscf.org
>> > http://www.democritos.it/mailman/listinfo/pw_forum
>> >
>> >
>>
>>
>>
>> --
>> PRASENJIT GHOSH,
>> Assistant Professor,
>> IISER Pune,
>> First floor, Central Tower, Sai Trinity Building
>> Garware Circle, Sutarwadi, Pashan
>> Pune, Maharashtra 411021, India
>>
>> Phone: +91 (20) 2590 8203
>> Fax: +91 (20) 2589 9790
>> ___
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://www.democritos.it/mailman/listinfo/pw_forum
>
>
>
> --
> Regards,
> MOHNISH,
> -
> Mohnish Pandey
> Y6927262,5th Year dual degree student,
> Department of Chemical Engineering,
> IIT KANPUR, UP, INDIA
> -
>
> ___
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>
>

[Pw_forum] a question about MnSe

[Duy Le]

Did you check the k-mesh? Are 6 6 6 and 6 6 4 good for converged energy?
--
Duy Le
PhD Student
Department of Physics
University of Central Florida.

"Men don't need hand to do things"



On Wed, Jan 19, 2011 at 11:57 AM, mohnish pandey  
wrote:
> Dear QE users,
> ?? ? ? ? ? ? ? ? ? ? ? ? ? I am trying to do bulk calculations for MnSe in
> rocksalt and wurtzite structure. Its has AFM ground state in rocksalt
> structure but after checking convergence I am finding "rocksalt" structure
> to be energetically higher than wurtzite structure. I am pasting my segments
> of input and output files. Can anybody please help me in figuring out the
> problem.
> INPUT FOR ROCKSALT
> 
> ?? ?calculation = 'vc-relax'
> ?? ?restart_mode='restart',
> ?? ?wf_collect = .true.
> ?? ?prefix='mnse',
> ?? ?pseudo_dir = '/home/mohnish/mnse-rocksalt-bulk',
> ?? ?outdir='/home/mohnish/mnse-rocksalt-bulk',
> ?? ?tprnfor = .true.,
> ?? ?tstress=.true.
> ?/
> ?
> ?? ?ibrav= ?0, celldm(1)= 10.3026, nat= ?4, ntyp= 3,
> ?? ?ecutwfc = 40.0, ecutrho = 320.0,
> ?? ?occupations='smearing', smearing='gauss', degauss=0.01,
> ?? ?nspin=2,
> ?? ?starting_magnetization(1)= 0.0,
> ?? ?starting_magnetization(2)= 0.5,
> ?? ?starting_magnetization(3)=-0.5,
> ?/
> ?
> ?? diagonalization='david'
> ?? mixing_mode = 'plain'
> ?? mixing_beta = 0.4
> ?? conv_thr = 1.0d-8
> ?? startingpot = 'file'
> ?? startingwfc = 'file'
> ?/
> 
> ??ion_dynamics='bfgs'
> ??trust_radius_max = 0.40
> ??trust_radius_ini = 0.20
> /
> 
> ??cell_dynamics='bfgs',
> /
> ATOMIC_SPECIES
> ??Se ?78.960 Se.pbe-van.UPF
> ??Mn1 54.938 Mn.pbe-sp-van_mit.UPF
> ??Mn2 54.938 Mn.pbe-sp-van_mit.UPF
> CELL_PARAMETERS
> 0.50 0.50 1.00
> 0.50 1.00 0.50
> 1.00 0.50 0.50
> ATOMIC_POSITIONS {crystal}
> ?Se ?0.25 0.25 0.25
> ?Se ?0.75 0.75 0.75
> ?Mn1 0.0 ?0.0 ?0.0
> ?Mn2 0.5 ?0.5 ?0.5
> K_POINTS {automatic}
> 6 6 6 0 0 0
> OUTPUT?FOR ROCKSALT
> ?bfgs converged in ? 8 scf cycles and ? 4 bfgs steps
> ?? ? (criteria: energy < 0.10E-03, force < 0.10E-02, cell < 0.50E+00)
> ?? ? End of BFGS Geometry Optimization
> ?? ? Final enthalpy = ? ?-464.4688263706 Ry
> Begin final coordinates
> ?? ? new unit-cell volume = ? ?533.55466 a.u.^3 ( ? ?79.06464 Ang^3 )
> CELL_PARAMETERS (alat= 10.3026)
> ?? 0.494008772 ? 0.494008772 ? 0.990589056
> ?? 0.494008772 ? 0.990589056 ? 0.494008772
> ?? 0.990589056 ? 0.494008772 ? 0.494008772
> ATOMIC_POSITIONS (crystal)
> Se ? ? ? 0.24854 ? 0.24854 ? 0.24854
> Se ? ? ? 0.75146 ? 0.75146 ? 0.75146
> Mn1 ? ? ?0.0 ? 0.0 ? 0.0
> Mn2 ? ? ?0.5 ? 0.5 ? 0.5
> End final coordinates
> INPUT FOR WURTZITE
> 
> ?? ?calculation = 'vc-relax',
> ?? ?restart_mode='restart',
> ?? ?verbosity = 'high'
> ?? ?wf_collect = .true.
> ?? ?outdir='/home/mohnish/mnse-wurtzite-bulk',
> ?? ?pseudo_dir='/home/mohnish/mnse-wurtzite-bulk'
> ?? ?prefix='mnse',
> ?? ?tstress = .true.,
> ?? ?tprnfor = .true.,
> /
> ?
> ?? ?ibrav= ?4, a = 4.178, c = 6.783,nat= 4, ntyp= 3,
> ?? ?ecutwfc =
> 40,ecutrho=320,occupations='smearing',degauss=0.01,smearing='gaussian',
> ?? ?nspin =2,starting_magnetization(1)=0.5,starting_magnetization(2)= -0.5,
> /
> ?
> ?? diagonalization='david'
> ?? mixing_mode = 'plain'
> ?? mixing_beta = 0.4
> ?? conv_thr = 1.0d-8
> ?? startingpot = 'file'
> ?? startingwfc = 'file'
> ?/
> 
> ??ion_dynamics='bfgs'
> ??trust_radius_max = 0.40
> ??trust_radius_ini = 0.20
> /
> 
> ??cell_dynamics='bfgs',
> /
> ATOMIC_SPECIES
> ??Mn1 54.938 Mn.pbe-sp-van_mit.UPF
> ??Mn2 54.938 Mn.pbe-sp-van_mit.UPF
> ??Se ?78.960 Se.pbe-van.UPF
> ATOMIC_POSITIONS (crystal)
> ??Mn1 ?0.0 ?0. ?0.0
> ??Mn2 ?0.3 ?0.6667 ?0.5
> ??Se ? 0.0 ?0. ?0.34500
> ??Se ? 0.3 ?0.6667 ?0.84500
> ?K_POINTS (automatic)
> ?6 6 4 0 0 0
> OUTPUT FOR WURTZITE
> ?End of BFGS Geometry Optimization
> ?? ? Final enthalpy = ? ?-464.4799667612 Ry
> Begin final coordinates
> ?? ? new unit-cell volume = ? ?681.36082 a.u.^3 ( ? 100.96726 Ang^3 )
> CELL_PARAMETERS (alat= ?7.89527578)
> ?? 1.001414763 ? 0.0 ? 0.0
> ??-0.500707382 ? 0.867250625 ? 0.0
> ?? 0.0 ? 0.0 ? 1.594103933
> ATOMIC_POSITIONS (crystal)
> Mn1 ? ? ?0.0 ? 0.0 ?-0.014999731
> Mn2 ? ? ?0.3 ? 0.7 ? 0.485592670
> Se ? ? ? 0.0 ? 0.0 ? 0.359333481
> Se ? ? ? 0.3 ? 0.7 ? 0.860073579
> End final coordinates
>
>
>
>
> --
> Regards,
> MOHNISH,
> -
> Mohnish Pandey
> Y6927262,5th Year dual degree student,
> Department of Chemical Engineering,
> IIT KANPUR, UP, INDIA
> -
>
> ___
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> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>

[Pw_forum] installation problem in Quantum espresso

[Duy Le]

Look weird, you have no fortran compiler. Check the $PATH to see if it
is correct.
--
Duy Le
PhD Student
Department of Physics
University of Central Florida.

"Men don't need hand to do things"



On Wed, Jan 5, 2011 at 9:42 AM, Paolo Giannozzi  
wrote:
>
> On Jan 5, 2011, at 15:01 , kanchan sonkar wrote:
>
>> checking for Fortran 77 compiler default output file name...
>> configure: error: Fortran 77 compiler cannot create executables
>
> as clear as it can be: you do not have a working fortran 77
> compiler
>
> P.
> ---
> Paolo Giannozzi, Dept of Chemistry,
> Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
> Phone +39-0432-558216, fax +39-0432-558222
>
>
>
>
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>

[Pw_forum] Bulk Modulus Calculation

[Duy Le]

it seems that you don't know how bulk modulus is actually calculated.
It is -V(d^2E/dV^2). So you need to vary the volume, calculate total
energy then fit the data to equation of states (I think ev.f90 do this
job, I am not so sure. But in any case, you can always fit these data
to equation of states by any other programs or codes). Once you have
equation of states, calculate -V(d^2E/dV^2) at the minimum >>> this is
bulk modulus.

I suggest that you should have look a http://www.pwscf.org/wiki/index.php/QESB09
and follow the Lab tutorial on Monday 20, July 2009.
The week1_day1_exersice1 is about optimizing lattice parameter,
equation of states (that includes bulk modulus)

----------
Duy Le
PhD Student
Department of Physics
University of Central Florida.

"Men don't need hand to do things"



On Tue, Jan 4, 2011 at 5:06 PM, Tram Bui  wrote:
> Hi All,
>  Hope everyone had great holidays, I had a question before regarding the
> Bulk Modulus calculation (ev.f90) But I'm having hard time understand? the
> file and don't know how to use the ev.f to help me calculate the bulk
> modulus if I have an input file is like below and the structure is zinc
> blend (b-SiC). Would you help me if you get a chance? here is my file and
> you can run it in xcyrsden to see the structure.
>
> 
> ?? calculation='scf'
> ?? restart_mode='from_scratch',
> ?? prefix='Silicon',
> ?? tprnfor=.true.
> ?? pseudo_dir='/home/trambui/QE/espresso-4.2.1/pseudo',
> ?? outdir='./tmp7/',
> /
> 
> ?? ibrav=2, celldm(1)=8.33, nat=2, ntyp=2,
> ?? ecutwfc= 30,
> /
> 
> ?? diagonalization= 'david',
> ?? mixing_mode= 'plain',
> ?? mixing_beta= 0.5,
> ?? conv_thr= 1.0d-7,
> /
> ATOMIC_SPECIES
> Si 28.086 Si.pbe-n-van.UPF
> ?C 12.011 C.pbe-van_ak.UPF
> ATOMIC_POSITIONS
> Si 0.00 0.00 0.00
> ?C 0.25 0.25 0.25
> K_POINTS automatic
> 10 10 10 0 0 0
>
> I really appreciate your helps!
>
> Tram Bui
>
> B.S. Materials Science & Engineering
> trambui at u.boisestate.edu
>
>
> ___
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> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>

[Pw_forum] atomic positions

[Duy Le]

I believe that you can find detailed description here
http://www.quantum-espresso.org/input-syntax/INPUT_PW.html
--
Duy Le
PhD Student
Department of Physics
University of Central Florida.

"Men don't need hand to do things"



On Sat, Jan 1, 2011 at 4:26 AM, Abolore Musari  wrote:
> Dear QE User,
> I need help concerning the atomic positions to compute the band structure of
> materials am working on. Pls take Sio2 in the examples file as an example.
> pls i need u to explain in details how the atomic positions of the elements
> of sio2 are gotten so that I can apply the same method to get mine. Pls? I
> really need a detailed explanation
> Thanks and happy new year to all
>
> Abolore Abdulganiy
> Dept of physics
> University of ibadan, Nigeria
>
> ___
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> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>

[Pw_forum] Bulk Modulus calculation

[Duy Le]

ev.f90 and ev.x should be in [WHEREEVER IT IS]espressso-X/pwtools/
ev.x can be also found in [WHEREEVER IT IS]espressso-X/bin

If you can not find executable file of ev.x, you should make it with:
$ cd  [WHEREEVER IT IS]espressso-X/
$ make tools
--
Duy Le
PhD Student
Department of Physics
University of Central Florida.

"Men don't need hand to do things"



On Wed, Dec 29, 2010 at 6:16 PM, Tram Bui  wrote:
> Dear All,
> ??? Hope everyone is having a great Holiday. would you please help me out
> with this, I'm looking for the "ev.f" that help to calculate the bulk
> modulus of a material. But I couldn't find it any where, please let me know
> where and how I can find that and use it to calculate for the bulk modulus,
> B.
>
> Thank you so much,
>
> Tram Bui
>
> B.S. Materials Science & Engineering
> trambui at u.boisestate.edu
>
>
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>

[Pw_forum] Details on "third order derivatives not implemented with GGA" error

[Duy Le]

FYI.
There is NO truncation on the mailing list, we got all what you sent.
You gmail did it. Click Show Quote Text for full email.

--
Duy Le
PhD Student
Department of Physics
University of Central Florida.

"Men don't need hand to do things"


On Tue, Nov 9, 2010 at 9:02 PM, Brad Malone  wrote:

> No idea why it is being truncated, so this time I'll start the email after
> the error message
> ---
> From the forums:
>
> http://www.democritos.it/pipermail/pw_forum/2008-September/010123.html
> http://www.democritos.it/pipermail/pw_forum/2010-February.txt
>
> I understand that the third derivatives were never implemented and
> that only the LDA part was calculated, for the Perdew Zunger
> parameterization. Is this third derivative the third derivative that
> is mentioned in the routine PH/raman_mat.f90 (i.e, the third
> derivative of the energy with respect to the atomic displacements and
> with respect to two electric fields, as described in Lazzeri and
> Mauri, PRL 90,036401)?
>
> I am interested in getting a feel for what would be needed to
> implement the third derivatives with GGA into the code, as well as
> what sort of errors one might expect when using the third-order term
> as currently coded with LDA pseudopotentials (comments in the forums
> have hinted that the errors are likely small).  The shift in the Raman
> spectra for cd-Si is pretty minor when using a GGA pseudo compared to
> that of an LDA calculation, but I wanted to be able to quantify the
> error better for other systems where comparing the GGA raman spectra
> to one calculated within LDA was not possible (e.g., when the system
> doesn't exhibit a gap in LDA).
>
> Thanks for the help!
>
> Best,
> Brad
> UC Berkeley
>
>
> On Tue, Nov 9, 2010 at 5:59 PM, Brad Malone  wrote:
>
>> It appears that my last email was severely truncated on the mailing list
>> (even though it looks fine in my outbox). Below is what is should have been:
>> ---
>> Hi, I am seeking more information on the error
>>
>> > from phq_setup : error # 1
>> > third order derivatives not implemented with GGA
>>
>> From the forums:
>>
>> http://www.democritos.it/pipermail/pw_forum/2008-September/010123.html
>> http://www.democritos.it/pipermail/pw_forum/2010-February.txt
>>
>> I understand that the third derivatives were never implemented and
>> that only the LDA part was calculated, for the Perdew Zunger
>> parameterization. Is this third derivative the third derivative that
>> is mentioned in the routine PH/raman_mat.f90 (i.e, the third
>> derivative of the energy with respect to the atomic displacements and
>> with respect to two electric fields, as described in Lazzeri and
>> Mauri, PRL 90,036401)?
>>
>> I am interested in getting a feel for what would be needed to
>> implement the third derivatives with GGA into the code, as well as
>> what sort of errors one might expect when using the third-order term
>> as currently coded with LDA pseudopotentials (comments in the forums
>> have hinted that the errors are likely small).  The shift in the Raman
>> spectra for cd-Si is pretty minor when using a GGA pseudo compared to
>> that of an LDA calculation, but I wanted to be able to quantify the
>> error better for other systems where comparing the GGA raman spectra
>> to one calculated within LDA was not possible (e.g., when the system
>> doesn't exhibit a gap in LDA).
>>
>> Thanks for the help!
>>
>> Best,
>> Brad
>> UC Berkeley
>>
>> On Tue, Nov 9, 2010 at 5:00 PM, Brad Malone wrote:
>>
>>> Hi, I am seeking more information on the error
>>>
>>> > from phq_setup : error # 1
>>> > third order derivatives not implemented with GGA
>>>
>>> From the forums:
>>>
>>> http://www.democritos.it/pipermail/pw_forum/2008-September/010123.html
>>> http://www.democritos.it/pipermail/pw_forum/2010-February.txt
>>>
>>> I understand that the third derivatives were never implemented and
>>> that only the LDA part was calculated, for the Perdew Zunger
>>> parameterization. Is this third derivative the third derivative that
>>> is mentioned in the routine PH/raman_mat.f90 (i.e, the third
>>> derivative of the energy with respect to the atomic displacements and
>>> with respect to two electric fields, as described in Lazzeri and
>>> Mauri, PRL 90,036401)?
>>>
>>> I am interested in getting a feel for what would be needed to
>>> implement the third derivatives with GGA into the

[Pw_forum] GDIS

[Duy Le]

GDIS is a visualization software.

Koa, you need to learn which formats GDIS supports.
--
Duy Le
PhD Student
Department of Physics
University of Central Florida.

"Men don't need hand to do things"


On Sun, Oct 31, 2010 at 4:50 PM, Stefano de Gironcoli wrote:

> Dear B. Koa
>   what is GDIS and what is TOOLS ?
> Stefano de Gironcoli - SISSA and DEMOCRITOS
>
> B. Koa wrote:
> > Dear QE Users
> >
> > I can not visualize input and output files of QE by GDIS which has been
> > introduced in the TOOLS. Is there any trick ? or is it only useful to
> > visualize some specific properties ?  Many Thanks
> >
> > 
> >
> > ___
> > Pw_forum mailing list
> > Pw_forum at pwscf.org
> > http://www.democritos.it/mailman/listinfo/pw_forum
> >
>
> ___
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> http://www.democritos.it/mailman/listinfo/pw_forum
>
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[Pw_forum] Brillouin Zone for my supercell

[Duy Le]

I doubt that QE has. Try Xcrysden.
--
Duy Le
PhD Student
Department of Physics
University of Central Florida.

"Men don't need hand to do things"


On Thu, Oct 28, 2010 at 1:22 PM, Elie Moujaes wrote:

>  Dear All,
>
> I am working with a supercell of 60 Carbon atoms. I am trying to do scf and
> band structure calculations. Is there anything in QE that is used to draw
> the Brillouin zone for my supercell as I need to find the coordinates of the
> points that are intercepts with the walls of the Brillouin zone or maybe
> find coordinates of high symmetry points in the BZ? How can I get such
> information?
>
> Regards
>
> Elie Moujaes
> University of Nottingham
> BG7 2RD
>
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>
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[Pw_forum] Nscf calculation problem

[Duy Le]

More cores may help :)
--
Duy Le
PhD Student
Department of Physics
University of Central Florida.

"Men don't need hand to do things"


On Wed, Oct 20, 2010 at 6:51 AM, Paolo Giannozzi wrote:

> wumindt2 wrote:
>
> > Is there any way to accelerate the nscf calculation?
>
> reduce the number of states (nbnd) to the minimum
>
> P.
> --
> Paolo Giannozzi, Democritos and University of Udine, Italy
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[Pw_forum] k_point for sheet in bands calculation

[Duy Le]

On Sat, Oct 16, 2010 at 8:30 AM, Farzad Molani  wrote:

> Hello,
> I'm goimg to study electronic stucture of nano sheet and I have a question
> about the
> K-point. I think for sheet we need sampling from gamma to K.
> Is it true?
>

Any direction you want. Depends on the structure of your nano sheet.

 So in bands calculation for k-point I should choice { crystal }. Am I
> right?
> I couldn't undrestand about points of { crystal } in k-point from gamma to
> K.
> what are these points depends on?
>

Go to pwsfc website. In the Tutorial section you will see a link about
Summer school at Santa Barbara  (2009). Download the exercise of week 1, day
1. Details and example of a band structure calculation can be found in this
exercise.

----------
Duy Le
PhD Student
Department of Physics
University of Central Florida.

"Men don't need hand to do things"



> Farzad Molani,
> Ph.D Student,
> Department of Theoretical Physical Chemistry,
> K. N. Toosi University of Technology,
> Tehran, Iran.
> Tel.: 009891 4442 3308
> Tel.: 009821 2306 4280
> Fax: 009821 2285 3650
> Web: http://www.chem.kntu.ac.ir/~sjalili:/
>
>
> ___
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>
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[Pw_forum] Again: unable( impossible ) to generation PP with semicore states and NLCC ?

[Duy Le]

Why do you need a +0.5 pp? Can you make pp with semicore for regular Cu?
--
Duy Le
PhD Student
Department of Physics
University of Central Florida.

"Men don't need hand to do things"



On Sat, Oct 16, 2010 at 9:17 AM, sonu kumar <1009ukumar at gmail.com> wrote:
> Dear All QE users and developers,
>
> I am very sorry for this mail again.
> I am unable ?generation of PP for Cu with TM (also with rrkj scheme)
> pseudization scheme , when i ?include semicore states 3s and 3p and NLCC,
> after making
> many-many tries ( variations in ?rc's, logder, V_loc, matching rad for aug
> func etc)
> The most comman problem is "negative rho " problem.
> I also want to use PAW , but unfortunately even unable to generate USPP.
> This is leading ?me to think (not 100% sure through ?very limited
> experience) that atomic code is unable to generate pp with both NLCC
> and?semicore states and also loosing ?my faith in atomic?code. So i need
> help from PP expert or any one willing to help.
>
> Please see below ?for input file
> ?
> ?? ? title='Cu'
> ?? ? zed=29,
> ?? ? eminld=-10.0,
> ?? ? emaxld=3.0,
> ?? ? rlderiv=2.5,
> ?? ? nld=3,
> ?? ? iswitch=3,
> ?? ? config="[Ne] 3s2 3p6 3d10.0 4s0.3 4p0.2"
> ?? ? dft='LDA'
> ?? ? rel=1,
> ??/
> ??
> ?? ?pseudotype=3,
> ?? ?nlcc=.true.,
> ?? ? ?new_core_ps = .true.
> ?? ? ?rcore=0.6000
> ?? ?lloc=-1,
> ?? ? ?rcloc=2.,
> ?? ?file_pseudopw='Cu_1.UPF'
> ?? ?zval=19,
> ?? ?lpaw=.false.
> ?? ? ?lnc2paw=.false.
> ?? ? ?which_augfun ='PSQ',
> ?? ? ?rmatch_augfun= 2.,
> ?? ?author='sk',
> ?? ?tm =.true.
> ?? ?!rho0=0.01,
>
> !nX n l ? occ ? nrg ? rmin ? rcut
> ??/
> ?8
> ?3S ?1 0 ?2.00 ? ?0.00 ? ?0.650 ? ?3. ?1
> ?3P ?2 1 ?6.00 ? ?0.00 ? ?0.650 ? ?3. ?1
> ?3D ?3 2 ?10.0 ? ?0.00 ? ?0.650 ? ?2. ? 1
> ?3D ?3 2 ?0.00 ? ?0.10 ? ?0.650 ? ?2. ? 1
> ?4S ?1 0 ?0.30 ? ?0.00 ? ?2.000 ? ?3.2000 ?1
> ?4S ?1 0 ?0.00 ? ?1.95 ? ?2.000 ? ?3.2000 ?1
> ?4P ?2 1 ?0.20 ? ?0.00 ? ?2.600 ? ?3.6000 ?1
> ?4P ?2 1 ?0.00 ? ?0.05 ? ?2.600 ? ?3.6000 ?1
>
> ?---input
> file?end---
>
>
>
> With Kind Regards,
> Sonu
>
> IITD
> ___
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> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>

[Pw_forum] Pw_forum Digest, Vol 40, Issue 20

[Duy Le]

On Thu, Oct 14, 2010 at 3:14 PM, Tram Bui  wrote:
> Hi,

Welcome!

> ? My name is Tram Bui and i'm new to the forum so i'm not quite sure how the
> Q work,

You can email any question to the mailing list. Make sure to use a
clear subject and sign in the end of your email.
If you reply from a PW-forum digest, please remove all irrelevant
content so that other member can follow easily.

>but today I want to try the forum with my very first question is
> that: If i want to calculate the total energy based on lattice parameters of
> SiC, how do you determine (or find) the ecutoff (kinetic energy cutoff of
> wave function) value for a material structure such as SiC?

You need to test this value. The total energy of a system will
converge as increasing energy cutoff.

>
> Thank you,
> Tram
>


> --
> Tram Bui
>
> B.S. Materials Science & Engineering
> trambui at u.boisestate.edu

------
Duy Le
PhD Student
Department of Physics
University of Central Florida.

"Men don't need hand to do things"

[Pw_forum] no. of nbnd

[Duy Le]

As the PW.html said, just count number of electrons then divide it by
2, then add 20% of that number.
--
Duy Le
PhD Student
Department of Physics
University of Central Florida.

"Men don't need hand to do things"



On Sat, Sep 18, 2010 at 12:33 PM, vicky singh  
wrote:
> Hi
> I am studying a supercell for Ni with 64 atoms. while specifying nbnd how
> much i select i am not sure. if i go by document PW.html it says that for
> metal it should be nelec/2 + 20 %. then should i take nbnd = 400. also it
> says minimum 4 more i.e. should i take nbnd = 330. Thanks in advance.
>
> with regards
>
> vicky singh
> research student
> Bangalore, India
>
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[Pw_forum] cu/semiconducting system

[Duy Le]

what's wrong? why don't you use non-zero gaussian spreading?
The purpose of using smearing is to avoid a step function at Fermi
level. If the system is metallic, gaussian spreading must be non-zero.
If it is not metallic, a non-zero gaussion spreading won't harm your
calculation.
--
Duy Le
PhD Student
Department of Physics
University of Central Florida.

"Men don't need hand to do things"



On Fri, Aug 27, 2010 at 3:29 PM, chengyu yang  
wrote:
> Dear all,
> ? If I have a copper/carbon nanotube system, and the nanotube is
> semiconducting, what value should the degauss be ?Is it still a metallic
> system? I used the degauss as 0,but it was wrong. I'm a little confused.
> ?thank you.
>
> 
>  calculation = 'scf' ,
> ??? restart_mode = 'from_scratch' ,
> ?? prefix = '22' ,
> ?/
> ?
> ?? ibrav = 6,celldm(1) = 21.764541128,celldm(3)=0.
> 213765379
>  nat = 10,ntyp = 2,ecutwfc = 75 ,
>  occupations='smearing', smearing='gaussian', degauss=0
> ?/
> 
> ??? conv_thr = 1.0d-8 ,
>  mixing_beta = 0.7 ,
> ?/
> ATOMIC_SPECIES
> ??? C?? 12.01100? C.pz-vbc.UPF
> ??? Cu? 63.55 Cu.pz-d-rrkjus.UPF
>
> ATOMIC_POSITIONS angstrom
> ? C??? 1.402181??? -0.00??? -1.233916
> ? C??? 0.682146 1.225067??? -1.233916
> ? C?? -0.00 1.402181??? -0.00
> ? C?? -1.225067 0.682146??? -0.00
> ? C?? -1.402181??? -0.00??? -1.233916
> ? C?? -0.682146??? -1.225067??? -1.233916
> ? C?? -0.00??? -1.402181??? -0.00
> ? C??? 1.225067??? -0.682146??? -0.00
> ? Cu?? 0??? 2.804362? 0
> ? Cu? -1.402181 2.428648737?? 0
>
>
> K_POINTS automatic
> ??? 1 1 5 0 0 0
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