[Pw_forum] Phonon DOS per polarization

[Lorenzo Paulatto]

Dear Bo,
as long as you can properly characterize the band, it is not hard to do:
you can use matdyn.x to compute the phonon in a dense grid of q-points, you
can generate it with pw.x or with the kpoint.x utility. Then load the grid
in matlab or octave or similar and integrate it properly. Since some time
ago, the matdyn code produce a *.gp code which is very practical for this
kind of analysis.

The problem is deciding which is band X, as soon as they start to cross
deciding which is which is not trivial. There is an option in matdyn to
assign the phonon bands order using eigenvectors continuity. However, this
method works well for high-symmetry lines, but may be not so robust when
doing a 3D grid of points. Yet, it is worth trying.

Provided all these difficulties, in many case and as long as you are
interested in a phonon band that is well separated from  the others there
may be no problem at all. Finally, you can think of a specific criteria to
discriminate the bands in a specific material, but implementing it is up to
you.

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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[Pw_forum] cpmd2upf sodium pseudopotentials

[Paolo Giannozzi]

On Oct 25, 2012, at 18:36 , Ananya Mondal wrote:

> I am not sure of the local reference state used in this pseudos.

it looks like it is L=0:

> |LOC=S  LMAX=P |

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

[Pw_forum] cartesian (angstrom) to alat units

[Ari P Seitsonen]

Hello,

   In order to clarify: There are several ways to specify the coordinates 
to PWSCF/QE:

  - In ?ngstr?m
  - In Bohr
  - In units of lattice constant, 'celldm(1)' in Bohr or 'a' in ?ngstr?m
  - In units of lattice vectors

   This you can choose on the line containing 'ATOMIC_POSITIONS'. Like 
noted above, one can use 'celldm(1:6)', alternatively 'a', 'b' and 'c' 
(plus 'cosab', 'cosac', 'cosbc') if you want to use ?ngstr?ms instead. 
Please have a look in the documentation, in particular 'INPUT_PW.*', below 
the section 'ibrav'. One more to specify the cell vectors is 'ibrav = 0' 
and the section 'CELL_PARAMETERS'.

   Hopefully this helps.

 Greetings,

apsi

-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-
   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


On Thu, 25 Oct 2012, Gisela Bocan wrote:

> Hi,
>  If I am not mistaken, every coordinate should be in celldm(1) units. 
> celldm(1) should be in bohr, so, if you have a coordinate X in Ang you should 
> write X_bohr/celldm(1) (where X_bohr
> is X converted to bohr).
> 
> Hope it helps!
> Bye!
> Gisela.
> 
> On Thu, Oct 25, 2012 at 4:09 PM, Bodiford, Nelli K  mavs.uta.edu> wrote:
>   Celldm should be in Bohr, that's what I have been using and it works. 
> Hope it helps!
> 
> On Oct 25, 2012, at 1:54 PM, David Furman wrote:
>
>   Dear Espresso fans,
> ?
> I would like to make a series of calculations in different lattice parameter 
> values.
> If I understand correctly, the atomic positions should be in units of the 
> lattice parameter "a" (default) in order for them to stay the same for every 
> lattice parameter.
> So, I assume each Cartesian coordinate in Ang should be a fraction of lattice 
> parameter: X/a
> But, does the lattice parameter should be in bohr (like in celldm(1)) or in 
> Ang as well ?
> ?
> Thank you
> ?
> ?
> ?
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://pwscf.org/mailman/listinfo/pw_forum
> 
> 
> 
> ___
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> Pw_forum at pwscf.org
> http://pwscf.org/mailman/listinfo/pw_forum
> 
> 
> 
>

[Pw_forum] CIF to PWSCF

[Yue-Wen Fang]

one way is to write a script to convert them!
i usually use castep in Materials Studio to convert the CIF files.

Best!


2012/10/24 Ben Palmer 

> Hi,
>
> I'm new to pwscf and I'm trying to find the relaxed co-ordinates for an
> Iron crystal.  I've been trying to set up the initial crystal from a cif
> file.  Is there a way to convert from cif to the pwscf format?
>
> Thanks
>
> Ben
>
>
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://pwscf.org/mailman/listinfo/pw_forum
>



-- 

Yue-Wen Fang
East China Normal Univ, China
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[Pw_forum] cartesian (angstrom) to alat units

[David Furman]

Dear Espresso fans,

 

I would like to make a series of calculations in different lattice parameter
values. 

If I understand correctly, the atomic positions should be in units of the
lattice parameter "a" (default) in order for them to stay the same for every
lattice parameter.

So, I assume each Cartesian coordinate in Ang should be a fraction of
lattice parameter: X/a

But, does the lattice parameter should be in bohr (like in celldm(1)) or in
Ang as well ?

 

Thank you

 

 

 

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[Pw_forum] Questions about the DFPT review paper

[Caloma Trumica]

Can someone help answer my questions. Thank you so much!

On Wed, Oct 24, 2012 at 7:38 PM, Caloma Trumica  wrote:

> Dear all,
>
> I do not understand why the two highlighted places in the attached DFPT
> review paper are correct.
>
> I repeat my questions here:
>
> 1. Why the contributions from valence bands cancel each other?
>
> 2. Why the left side of Eq.25 has a null eigenvalue?
>
> Thank you!
>
> Andy
>
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[Pw_forum] cartesian (angstrom) to alat units

[Bodiford, Nelli K]

Celldm should be in Bohr, that's what I have been using and it works. Hope it 
helps!


On Oct 25, 2012, at 1:54 PM, David Furman wrote:

Dear Espresso fans,

I would like to make a series of calculations in different lattice parameter 
values.
If I understand correctly, the atomic positions should be in units of the 
lattice parameter "a" (default) in order for them to stay the same for every 
lattice parameter.
So, I assume each Cartesian coordinate in Ang should be a fraction of lattice 
parameter: X/a
But, does the lattice parameter should be in bohr (like in celldm(1)) or in Ang 
as well ?

Thank you



___
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http://pwscf.org/mailman/listinfo/pw_forum

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[Pw_forum] CIF to PWSCF

[Carlo Nervi]

Another way is to use Moldraw, written by a collegue of mine. It can be 
downloaded for free from:

http://www.moldraw.unito.it/

Moldraw can read cif file and convert, for example, in CRYSTAL format.
Remember to "Make a cell" before to export. From this format you should 
be able with a text editor and a minimum of efforts to write a Quantum 
Espresso compatible input file.

HTH,
Carlo

Il 25/10/2012 15.02, Yue-Wen Fang ha scritto:
> one way is to write a script to convert them!
> i usually use castep in Materials Studio to convert the CIF files.
>
> Best!
>
>
> 2012/10/24 Ben Palmer  >
>
> Hi,
>
> I'm new to pwscf and I'm trying to find the relaxed co-ordinates for an
> Iron crystal.  I've been trying to set up the initial crystal from a cif
> file.  Is there a way to convert from cif to the pwscf format?
>
> Thanks
>
> Ben
>
>
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org 
> http://pwscf.org/mailman/listinfo/pw_forum
>
>
>
>
> --
> 
> Yue-Wen Fang
> East China Normal Univ, China
>
>
>
>
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://pwscf.org/mailman/listinfo/pw_forum
>


-- 

Prof. Carlo Nervi carlo.nervi at unito.it  Tel:+39 0116707507/8
Fax: +39 0116707855  -  Dipartimento di Chimica, via
P. Giuria 7, 10125 Torino, Italy.http://lem.ch.unito.it/

[Pw_forum] cartesian (angstrom) to alat units

[Gisela Bocan]

Hi,
 If I am not mistaken, every coordinate should be in celldm(1) units.
celldm(1) should be in bohr, so, if you have a coordinate X in Ang you
should write X_bohr/celldm(1) (where X_bohr is X converted to bohr).

Hope it helps!
Bye!
Gisela.

On Thu, Oct 25, 2012 at 4:09 PM, Bodiford, Nelli K <
nelli.bodiford at mavs.uta.edu> wrote:

>  Celldm should be in Bohr, that's what I have been using and it works.
> Hope it helps!
>
>
>  On Oct 25, 2012, at 1:54 PM, David Furman wrote:
>
>   Dear Espresso fans,
>  ** **
>  I would like to make a series of calculations in different lattice
> parameter values.
>  If I understand correctly, the atomic positions should be in units of the
> lattice parameter "a" (default) in order for them to stay the same for
> every lattice parameter.
>  
>  So, I assume each Cartesian coordinate in Ang should be a fraction of
> lattice parameter: X/a
>  But, does the lattice parameter should be in bohr (like in celldm(1)) or
> in Ang as well ?
>  ** **
>  Thank you
>  * *
>  * *
>  ** **
>  ___
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://pwscf.org/mailman/listinfo/pw_forum
>
>
>
> ___
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> Pw_forum at pwscf.org
> http://pwscf.org/mailman/listinfo/pw_forum
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[Pw_forum] HYBRID XC not allowed in non-scf calculations

[Layla Martin-Samos]

Dear Simon, one can think to do an interpolation calculating psi_k+q' and
V(q'), but pf, Let'S first stabilize exx.f90!

cheers

Layla

2012/10/25 Simon Binnie 

> I've always wondered about this. Surely if you've converged your initial
> scf calculation with respect to q and k-point sampling this change of grid
> doesn't matter, for your new q' points you just end up setting your V(q')
> to be the same as the nearest original V(q) ?
>
> Obviously I'm not volunteering to code this up :)
>
> Simon
>
> On Thu, 25 Oct 2012 15:01:22 +0200, Layla Martin-Samos
>  wrote:
>
> > Dear Eduardo, it is also related to kpoint samplig and q vectors. If one
> > changes k sampling between the scf and the nonscf you can not have the
> > same
> > v(q) (the same fock). I order to avoid confusion nscf has been disable in
> > all the cases.
> >
> > cheers
> >
> > Layla
> >
>
> --
> Simon Binnie | Post Doc, Condensed Matter Sector
> Scuola Internazionale di Studi Avanzati (SISSA)
> Via Bonomea 256 | 34100 Trieste | sbinnie at sissa.it
> ___
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[Pw_forum] HYBRID XC not allowed in non-scf calculations

[Simon Binnie]

I've always wondered about this. Surely if you've converged your initial  
scf calculation with respect to q and k-point sampling this change of grid  
doesn't matter, for your new q' points you just end up setting your V(q')  
to be the same as the nearest original V(q) ?

Obviously I'm not volunteering to code this up :)

Simon

On Thu, 25 Oct 2012 15:01:22 +0200, Layla Martin-Samos  
 wrote:

> Dear Eduardo, it is also related to kpoint samplig and q vectors. If one
> changes k sampling between the scf and the nonscf you can not have the  
> same
> v(q) (the same fock). I order to avoid confusion nscf has been disable in
> all the cases.
>
> cheers
>
> Layla
>

-- 
Simon Binnie | Post Doc, Condensed Matter Sector
Scuola Internazionale di Studi Avanzati (SISSA)
Via Bonomea 256 | 34100 Trieste | sbinnie at sissa.it

[Pw_forum] HYBRID XC not allowed in non-scf calculations

[Layla Martin-Samos]

Dear Eduardo, it is also related to kpoint samplig and q vectors. If one
changes k sampling between the scf and the nonscf you can not have the same
v(q) (the same fock). I order to avoid confusion nscf has been disable in
all the cases.

cheers

Layla

2012/10/25 Eduardo Ariel Menendez Proupin 

> Hi,
> Why ?
>  Error in routine setup (1):
>  HYBRID XC not allowed in non-scf calculations
>
> I guess that to compute the exchange potential one needs to use the SCF
> wavefunctions, and not only the charge density, and for this the
> input/output of the wfc must be restructured.  Is it implemented in trunk
> version. Is there a more fundamental reason for not doing it?
>
> --
>
>
> Eduardo Menendez Proupin
> Departamento de Qu?mica Fisica Aplicada
> Facultad de Ciencias
> Universidad Aut?noma de Madrid
> 28049 Madrid, Spain
> Phone: +34 91 497 6706
>
> ___
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> Pw_forum at pwscf.org
> http://pwscf.org/mailman/listinfo/pw_forum
>
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[Pw_forum] HYBRID XC not allowed in non-scf calculations

[Eduardo Ariel Menendez Proupin]

Hi,
Why ?
 Error in routine setup (1):
 HYBRID XC not allowed in non-scf calculations

I guess that to compute the exchange potential one needs to use the SCF
wavefunctions, and not only the charge density, and for this the
input/output of the wfc must be restructured.  Is it implemented in trunk
version. Is there a more fundamental reason for not doing it?

-- 


Eduardo Menendez Proupin
Departamento de Qu?mica Fisica Aplicada
Facultad de Ciencias
Universidad Aut?noma de Madrid
28049 Madrid, Spain
Phone: +34 91 497 6706
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[Pw_forum] cpmd2upf sodium pseudopotentials

[Ananya Mondal]

Dear pwscf users,
I am trying to convert semi core norm conserving TM pseudopotentials
for Na atoms using cpmd2upf.x converter. I am however not sure of what
I should do. In particular, I am not sure
of the local reference state used in this pseudos.
For the Na atom, I attached the cpmd pseudopotential and  here are the
instructions I gave for conversion:
./cpmd2upf.x
Input file > Na_MT_PBE_SEMI.psp
Radial grid r(i) has  650 points
Assuming log radial grid: r(i)=exp[(i-1)*amesh]*r(1), with:
amesh = log (r(mesh)/r(1))/(mesh-1) =   0.017349

|Pseudopotential Report|

|  Atomic Symbol   :   NA  |
|  Atomic Number   :  11   |
|  Number of core states   :   1   |
|  Number of valence states:   2   |
|  Exchange-Correlation Functional :   |
| Slater exchange :  0.6667|
| LDA correlation : Ceperley-Alder |
| Exchange GC : Perdew-Burke-Ernzerhof |
| Correlation GC  : Perdew-Burke-Ernzerhof |
|  Scalar-relativistic calculation |
|  Electron Configuration :   N   L  Occupation|
| 1   S2.  |
| 2   S2.  |
| 2   P6.  |
|  Full Potential Total Energy = -179.798823   |
|  Trouiller-Martins normconserving PP |
| nlrc   energy|
| 2S1. -2.36868|
| 2P1. -1.33583|
| 3D1. -1.33583|
|  Number of Mesh Points :   650   |
|  Pseudoatom Total Energy =  -47.408078   |
|  Warning: semi-core PP to be used with 80 Ry cut-off |
|LOC=S  LMAX=P |

max L to use ( <= 2 ) > 2
local L ( <= 2 ), Rc for local pot (au) > 1
1.889725989
Assuming DFT: SLA-PW-PBX-PBC . Please check this is what you want
Wavefunction # 1: label (e.g. 4s), occupancy > 2s 2.0
Wavefunction # 2: label (e.g. 4s), occupancy > 2p 6.0
Wavefunction # 3: label (e.g. 4s), occupancy > 3d 0.0
Pseudopotential successfully converted
Output PP file in UPF format :  Na_MT_PBE_SEMI.psp.UPF
Pseudopotential successfully written
Please review the content of the PP_INFO fields
*** Please TEST BEFORE USING !!! ***

I have used "local L" > 1, is it correct?
Of course, I should test these converted pseudopotentials, but I would
like to be aware of potential problems before.

It is highly appreciated that if someone can send the
Troullier-Martins norm-conserving pseudopotentials  for sodium and
pottasium in UPF format.

I would be very thankfull for any help,

Best regards,
Ananya

[Pw_forum] Phonon DOS per polarization

[Bo Qiu]

Dear developers and users,

I learned that QHA can be used to compute partial phonon DOS, but it seems
from the output it only decomposes total DOS into per atom and
per Cartesian direction contributions. I wonder if there is an option to
decompose into per polarization contributions as LA1, LA2, TA, LO1, TO1,
TO2,  etc. Thanks a lot!

Bo
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[Pw_forum] calculate equation of state in Quantum Espresso

[Layla Martin-Samos]

Yes you have to calculate the total energy for different lattice
parameters. 1) and 2) yes, E-V is a parabola where the min is the
equilibrium lattice parameters is always better to have points on both
sides. 3) only relax as if you relax the cell you will always fall into the
min.

cheers

Layla

2012/10/24 David Furman 

> Dear all,
>
> ** **
>
> I want to calculate equation of state (E-V curve) with Quantum Espresso.**
> **
>
> What is the procedure to do so ? 
>
> ** **
>
> I think to calculate the total energy of different lattice parameters and
> then fit to analytic equation of state.
>
> ** **
>
> 1. Do I additionally to compressing (setting smaller and smaller values
> for lattice parameter) need to calculate energy for lattice parameters
> larger than equilibrium ? 
>
> ** **
>
> 2. If yes, then what sense does expanding the unit cell mean regarding to
> experiment ? 
>
>  Or is it done just to improve the statistics of the fit ?
>
> ** **
>
> 3. Do I have to do relax or vc-relax runs to optimize atomic positions at
> each lattice parameter ?
>
> ** **
>
> Thanks for you kind help,
>
> ** **
>
> ** **
>
> David
>
> ** **
>
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[Pw_forum] CIF to PWSCF

[Paolo Giannozzi]

On Oct 24, 2012, at 17:27 , Ben Palmer wrote:

> Is there a way to convert from cif to the pwscf format?

an automatic way? I am not aware of any converter

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

[Pw_forum] Pseudopotentials for Praseodymium

[Paolo Giannozzi]

On Oct 25, 2012, at 5:28 , W2AGZ wrote:

> 59pr.13.hgh
>
this can be converted to UPF using the latest cpmd2upf converter
(you need the potential in CPMD format, attached). I got this:
www.fisica.uniud.it/~giannozz/public/Pr-q13.UPF
May or may not work: I have used some of these HGH
(Hartwigsen. Goedecker Hutter) PPs with success, but most of
them either crash the atomic code or yield funny results for the
atom. They are also very hard: don't even think using less than
300Ry for Pr.
> Pr_HSCV_LDA-1.0.xml
>
> Pr_HSCV_PBE-1.0.xml
>
these should also be convertible to UPF using Francois Gygi'
converter qso2upf: http://eslab.ucdavis.edu/software/index.htm

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