[QE-users] discontinuities in phonon band and 2D phonon bandstructure

[EDUARDO ARIEL MENENDEZ PROUPIN]

Rijan,
You may find discontinuities in the phonon dispersion when approaching the 
Gamma point from different directions in non-cubic systems. I would be 
surprised if your system has cubic symmetry. The discontinuities and the LO-TO 
splitting are due to the non-analytic term as Lorenzo has already explained.

I just want to add that the non-analytic term appears because, for low 
wavevector, the phonon dispersion law crosses, in fact avoids crossing, with 
the dispersion law of light. The excitations that propagate in a crystal for a 
wavevector near Gamma are polaritons (phonons coupled with light or excitons 
coupled with light).
The dispersion law of polaritons does not have discontinuities. The phonon 
dispersion law computed by Quantum ESPRESSO for small wavevector is valid for 
as long as the wavevector q is much larger than the wavector of light with the 
same frequency as the phonon, i.e. q>>n\omega/c, n being the index of 
refraction.

A basic theory of polaritons in cubic crystals is found in solid-state physics 
books like the great one from Grosso and Pastori-Parravicini, and also the 
classic from Ashcroft if I remember well. The theory of 
phonon-polaritons in anisotropic crystals is well explained in this article by 
Ruppin and Englman and references therein

1970 Rep. Prog. Phys. 33 149
(http://iopscience.iop.org/0034-4885/33/1/304)

Hope it helps,

Eduardo A. Menéndez Proupin
Departamento de Física Aplicada I
Universidad de Sevilla
Teléfono: +34 9554 20231
https://personal.us.es/emenendez/
https://personal.us.es/emenendez/docencia/






Message: 4
Date: Mon, 17 Jun 2024 11:22:37 +0200
From: Lorenzo Paulatto 
To: 
Subject: Re: [QE-users] discontinuities in phonon band and 2D phonon
bandstructure
Message-ID: <1794c32e-54ae-49b5-9590-e7890a70c...@cnrs.fr>
Content-Type: text/plain; charset="utf-8"; Format="flowed"

Hello,

that is the non-analytical contribution to the LO-TO split. You have to
keep in mind that Gamma is actually infinity, and you can go to infinity
in many different ways. The theory is in X. Gonze, J.-C. Charlier, D.C.
Allan, and M.P. Teter Phys. Rev. B 50, 13035 (1994)


kind regards


On 13/06/2024 21:57, Karkee, Rijan via users wrote:
> Dear QE users,
>
> I am seeing discontinuity in phonon bandstructure at Gamma. Is there a
> way to get rid of this or is this trying to tell something?
>
> Also, like for electronic band calculation in pw.x? (using crystal_c
> or tpiba_c) is there a way to have 2D plot of phonon dispersion?
>
> Thanks for your suggestions.
>
>
> Best
> Rijan
>
> LANL
>

**
___
The Quantum ESPRESSO community stands by the Ukrainian
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Re: [QE-users] Thermodynamics with DFT+U

[EDUARDO ARIEL MENENDEZ PROUPIN]

Iurii , Thanks again. I am trying with determine_num_pert_only = .true.
Running  pw.x I got the error
“Too many atoms. The dimensions of Hubbard_V must be increased”
en el archivo.

Browsing in the source files I see that I can solve it increasing the parameter 
natx in the file
/home/software/qe-6.8/Modules/parameters.f90
  INTEGER, PARAMETER :: natx = 50
Is that all I need? I have requested that to the cluster admin, as was unable 
to use the compilers, so I shall wait.



>> The atom indexes are relative to the atoms in the unit cell and include the
>> neighbor atoms in the eight surrounding unit cells.

>Actually, the pw.x code generates a virtual 3x3x3 supercell with your real unit
>cell inside of it. So in total there are 27 unit cells.


I should have written 26 instead of eight. I was thinking in 2D, Kirk would 
have beaten me like he did with Khan. 

Best regards
Eduardo


Dear Eduardo,

> The atom indexes are relative to the atoms in the unit cell and include the
> neighbor atoms in the eight surrounding unit cells.

Actually, the pw.x code generates a virtual 3x3x3 supercell with your real unit
cell inside of it. So in total there are 27 unit cells.

> For defect calculations, I need to use a supercell with a different shape.
> How can I transfer the parameters to the supercell? I think this just needs a
> small code to generate
the parameter file for the supercell. I can do  it if this is not available. Is
it?

Yes, unfortunately the I and J couple indices will change if you change the
shape of the original real cell. The algorithm can be found in
PW/src/intersite_V.f90.

You can run the HP code by setting determine_num_pert_only = .true. For
DFT+U+V, it will only determine the indices of couples without running heavy
linear-response calculations. So then you can use this new file with the new
indices and add there the U and V values that you previously computed using a
smaller cell.


Eduardo A. Menéndez Proupin
Departamento de Física Aplicada I
Universidad de Sevilla
Teléfono: +34 9554 20231
https://personal.us.es/emenendez/
https://personal.us.es/emenendez/docencia/
___
The Quantum ESPRESSO community stands by the Ukrainian
people and expresses its concerns about the devastating
effects that the Russian military offensive has on their
country and on the free and peaceful scientific, cultural,
and economic cooperation amongst peoples
___
Quantum ESPRESSO is supported by MaX (www.max-centre.eu)
users mailing list users@lists.quantum-espresso.org
https://lists.quantum-espresso.org/mailman/listinfo/users

Re: [QE-users] Thermodynamics with DFT+U

[EDUARDO ARIEL MENENDEZ PROUPIN]

 properties (e.g. voltages) are worsened.
  *   If you use ACBN0 to compute U, you might get 2-3 eV, and applying this 
correction to O-2p might improve the results. So you see that it matters which 
value of U to apply to O-2 states and how it was computed. If one tunes U by 
hand, then of course you can get whatever you want. E.g. people apply empirical 
U to O-2p states in ZnO to get the right band gap. But this touches on another 
topic: DFT+U for band gaps. U generally improves the band gaps if the 
correction is applied to the edge states. Have a look at this paper: 
https://www.mdpi.com/2076-3417/11/5/2395
  *   In some works, even U from linear-response theory is applied to O-2p to 
get better band gaps.
  *   Applying U to O-2p localizes these states more. Is it good or bad? It 
depends on the system. E.g. in systems with strong covalency, this is not good 
as you will kill the hybridization between TM-3d and O-2p states. E.g. in the 
case of BaTiO3 applying U to O-2p does exactly that and one gets the cubic 
phase instead of the rhombohedral one, in contradiction to experiments. While 
not applying U to O-2p is ok, because the inter-site hybridization is there and 
the DFT+U+V approach preserves the rhombohedral symmetry: 
https://arxiv.org/abs/2309.04348


  *   A related question is whether the forces and energies are consistent with 
variable U and V. That is, Let us move the Fe impurity atom inside a crystal, 
and recompute the U and V for each position.  Force is the gradient of energy 
obtained in the Hellman-Feynman way, I guess with constant U,V.

  *   Pressure is the negative of the derivative of the energy with respect to 
volume, which implies a variation of U and V. I guess the stress is computed 
with constant U, V. I think that self-consistency could be implemented, but 
first we must be sure that comparing energies with variable, self-consistent 
parameters is correct.

Another excellent question. In Quantum ESPRESSO, U is constant and its 
derivative dU/dR is set to zero when computing Hubbard forces (and same for 
Hubbard stresses): 
https://journals.aps.org/prb/abstract/10.1103/PhysRevB.102.235159
In order to circumvent this problem, we perform the calculation of U in a 
self-consistent fashion, by performing cyclic calculations (recalculation of U 
and structural optimization with DFT+U), thus pushing the system to the energy 
extremum: https://journals.aps.org/prb/abstract/10.1103/PhysRevB.103.045141

HTH

Greetings,
Iurii

--
Dr. Iurii TIMROV
Tenure-track scientist
Laboratory for Materials Simulations (LMS)
Paul Scherrer Institut (PSI)
CH-5232 Villigen, Switzerland
+41 56 310 62 14
https://www.psi.ch/en/lms/people/iurii-timrov

From: users  on behalf of EDUARDO 
ARIEL MENENDEZ PROUPIN 
Sent: Wednesday, December 6, 2023 10:24
To: users@lists.quantum-espresso.org 
Subject: Re: [QE-users] Thermodynamics with DFT+U

Hello!
I have read this thread, which is from three years ago, and I would like to 
know if there is any update, consensus, or a study about this issue.

The topic of the thread was how to compare the energies of two systems when 
there is at least one element subject to Hubbard correction, in the case that 
the  Hubbard parameters are computed self-consistently via the HP code, and 
have different values in the two systems compared.  Should we choose one 
average value, or use the computed value for each system?  The two systems may 
be either:

  1.  Two phases of a material
  2.  Two antiferromagnetic configurations
  3.  Crystal with a transition metal impurity vs clean crystal and impurity in 
bulk metal.

I may have a case of type (b), with certain energy order when using the 
self-consistent U values for each AFM configuration, and the opposite order 
when the same U is used for both configurations. The same U was computed for 
one configuration, I am waiting for the queue to finish calculations with the 
other U, but this is published (Naveas et al, 
https://doi.org/10.1016/j.isci.2023.106033).

Concerning the advantage of self consistency, let me rise the example LiCoO2 
that comes with the HP code. The example produces U for Co and also for O, as 
well as V(Co-O). U(O-2p)=8.0439 eV. Is this parameter useful? As the example is 
not converged w.r.t. to k-points and cutoffs the number may change, but U(O-2p) 
is still there. I read PRB101, 064305 (2020) by Floris et al, and it seems that 
U(O-2p) is discarded. I am curious why, but I couldn't find a discussion. Maybe 
there is another article. My point here is that using self consistent 
parameters for some elements and shells, and discarding others is just a 
partial self-consistency.

A related question is whether the forces and energies are consistent with 
variable U and V. That is, Let us move the Fe impurity atom inside a crystal, 
and recompute the U and V for each position.  Force is the gradient of energy 
obtained

Re: [QE-users] Thermodynamics with DFT+U

[EDUARDO ARIEL MENENDEZ PROUPIN]

Hello!
I have read this thread, which is from three years ago, and I would like to 
know if there is any update, consensus, or a study about this issue.

The topic of the thread was how to compare the energies of two systems when 
there is at least one element subject to Hubbard correction, in the case that 
the  Hubbard parameters are computed self-consistently via the HP code, and 
have different values in the two systems compared.  Should we choose one 
average value, or use the computed value for each system?  The two systems may 
be either:

  1.  Two phases of a material
  2.  Two antiferromagnetic configurations
  3.  Crystal with a transition metal impurity vs clean crystal and impurity in 
bulk metal.

I may have a case of type (b), with certain energy order when using the 
self-consistent U values for each AFM configuration, and the opposite order 
when the same U is used for both configurations. The same U was computed for 
one configuration, I am waiting for the queue to finish calculations with the 
other U, but this is published (Naveas et al, 
https://doi.org/10.1016/j.isci.2023.106033).

Concerning the advantage of self consistency, let me rise the example LiCoO2 
that comes with the HP code. The example produces U for Co and also for O, as 
well as V(Co-O). U(O-2p)=8.0439 eV. Is this parameter useful? As the example is 
not converged w.r.t. to k-points and cutoffs the number may change, but U(O-2p) 
is still there. I read PRB101, 064305 (2020) by Floris et al, and it seems that 
U(O-2p) is discarded. I am curious why, but I couldn't find a discussion. Maybe 
there is another article. My point here is that using self consistent 
parameters for some elements and shells, and discarding others is just a 
partial self-consistency.

A related question is whether the forces and energies are consistent with 
variable U and V. That is, Let us move the Fe impurity atom inside a crystal, 
and recompute the U and V for each position.  Force is the gradient of energy 
obtained in the Hellman-Feynman way, I guess with constant U,V.
Pressure is the negative of the derivative of the energy with respect to 
volume, which implies a variation of U and V. I guess the stress is computed 
with constant U, V. I think that self-consistency could be implemented, but 
first we must be sure that comparing energies with variable, self-consistent 
parameters is correct.

Best regards,

Eduardo A. Menéndez Proupin
Departamento de Física Aplicada I
Universidad de Sevilla
Teléfono: +34 9554 20231
https://personal.us.es/emenendez/
https://personal.us.es/emenendez/docencia/
___
The Quantum ESPRESSO community stands by the Ukrainian
people and expresses its concerns about the devastating
effects that the Russian military offensive has on their
country and on the free and peaceful scientific, cultural,
and economic cooperation amongst peoples
___
Quantum ESPRESSO is supported by MaX (www.max-centre.eu)
users mailing list users@lists.quantum-espresso.org
https://lists.quantum-espresso.org/mailman/listinfo/users

[Pw_forum] problems with pressure calculation

[Eduardo Ariel Menendez Proupin]

Dear Paolo,
Thanks for your advice. The wild pressure oscillations dissapear using a
smaller value of con_thr.

>it looks like a nonlinear interaction between symmetry and insufficient
>convergence of self-consistency. If you reduce the convergence >threshold
>to conv_thr=1.0e-8 or so (default is 10e-6) the jumps disappear; same if
>you use all symmetries, whether their fractional translation is
>commensurate or not with the FFT grid (option use_all_frac). I guess
>that the discrepancy wrt previous versions has a similar origin.

>The default value for the convergence threshold is good if you are
>interested in energies, reasonable if you are interested in forces,
>not so good for stress and pressure

Best regards
-- 
Eduardo Menendez Proupin
Departamento de Fisica, Facultad de Ciencias, Universidad de Chile
URL: http://fisica.ciencias.uchile.cl/~emenendez
*"Lograremos el anhelado desarrollo cuando sea la ciudadan?a, y no los
cient?ficos, la que pida m?s ciencia para Chile." J. Babul*
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[Pw_forum] problems with pressure calculation

[Eduardo Ariel Menendez Proupin]

Dear colleagues,

I have found strange differences in results for the calculation of pressure
using pwscf in versions 4.3 and 5.0.N (N=1,2).  We are calculating wurtzite
CdSe, using the following UPF files.

PAW calculation
   Cd  112.4  Cd.pbe-dn-kjpaw_psl.0.2.UPF
   Se   78.96000  Se.pbe-n-kjpaw_psl.0.2.UPF


Ultrasoft PP calculation
   Cd  112.4  Cd.pbe-dn-rrkjus_psl.0.2.UPF
   Se   78.96000  Se.pbe-n-rrkjus_psl.0.2.UPF



For the PAW calculations, the convergence of pressure with the density
cutoff (euctrho) shows jumps  (see the attached  figure paw-press.eps) and
no convergence in the case of version 5.0.N, while there is convergence
with version 4.3. For both versions the total energies are the same.
The jumps are associated with differences in the number of symmetry
operations detected. The message

 " (note:  6 additional sym.ops. were found but ignored
   their fractional translations are incommensurate with FFT grid)"
is associated with higher pressures (33 kbar). Lower pressures ~ 26 kbar)
are found when the FFT grid is commensurate and all 12 sym. ops. are used.
In the calculations with version 4.3 the pressures are somewhat lower, but
apparently convergent. Also, there are less symmetry operations detected or
used than for version 5.0.N.

In the ultrasoft calculations, (see figure uspp-press), both versions 4.3
and 5.0.N produce convergent pressures vs ecutrho, but the pressures differ
almost by 10 kbar. (The total energies are almost equal, as expected).

Thanks for any comment.

-- 
Eduardo Menendez Proupin
Departamento de Fisica, Facultad de Ciencias, Universidad de Chile
URL: http://fisica.ciencias.uchile.cl/~emenendez
*"Lograremos el anhelado desarrollo cuando sea la ciudadan?a, y no los
cient?ficos, la que pida m?s ciencia para Chile." J. Babul*
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[Pw_forum] is it orthorhombic or triclinic?

[Eduardo Ariel Menendez Proupin]

I cannot answer about Materials Studio (few people can afford it). I think
it is not just a matter of lattice parameters.
The unit cell may be orthorhombic, but the basis may not be invariant for
the symmetry operations of orthorhombic space groups.



l giorno 06/mar/2013, alle ore 09.50, Krishna chaitanya ha scritto:

Dear users

I am trying to get optimized geometry of  (201) plane of Bi2O3 with three
layers. When I cleaved the tetragonal geometry of Bi2O3 crystal through
(201) plane, Material Studio software is showing it as triclinic geometry
with lattice constants a=13.8295, b=15.4760, c=34.1069 (of which
20angstroms is vacuum), alpha=beta=gamma=90 degrees. But according to
crystallographic systems, these constants should belong to orthorhombic
rather than triclinic.


A triclinic cell with all angles equal to 90? will result in an
orthorhombic cell.
You can describe it with ibrav=8, celldm(1)=a, celldm(2)=b/a, celldm(3)=c/a.

Then how Material studio is showing it as triclinic?



-- 
Eduardo Menendez Proupin
Departamento de Fisica, Facultad de Ciencias, Universidad de Chile
URL: http://fisica.ciencias.uchile.cl/~emenendez
*
*
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[Pw_forum] Can QE5.01 do RAMAN with GGA?

[Eduardo Ariel Menendez Proupin]

Is there evidence that GGA is better than LDA for  phonons and Raman ?

Eduardo Menendez
University of Chile
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[Pw_forum] Frequency Dependent Dielectric Function (Layla Martin-Samos)

[Eduardo Ariel Menendez Proupin]

Hi,
Probably you will want to apply a shift to obtain a correct bandgap. If you
want to do it with the option shit=..., first read
PRB 48, 11789 (1993).
epsilon.x has implemented what is called "naive scissors correction".
The correction is easy to implement, and I have a working one for version
4.3. Sooner or later it will get to the distribution, (if I am not wrong).

Use LDA, as in the PRB article,  and I think also semilocal GGA functionals
are fine. Do not use a hybrid functional.

-- 


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

-- Mensaje reenviado --
From: Layla Martin-Samos 
To: Iwan Darmadi , PWSCF Forum <
pw_forum at pwscf.org>
Cc:
Date: Thu, 29 Nov 2012 09:31:24 +0100
Subject: Re: [Pw_forum] Frequency Dependent Dielectric Function
Dear Iwan, take a look at epsilon.x inside PP directory. Be careful,
epsilon.x only implements RPA (Random Phase Approximation) dielectric
function with no local fields effects and without the nonlocal part of the
pseudopotential.

cheers

Layla

2012/11/29 Iwan Darmadi 
Dear All,

I am Iwan Darmadi, undergraduate physics student, Universitas Indonesia.
Currently I am running TM doped ZnO simulation using Quantum Espresso.

At the moment, I plan to calculate dielectric function (frequency
dependent) of my model. I have read the manual and other sources
but I hardly find how to calculate them.

My question is, does QE have feature to calculate frequency dependent
dielectric function ?
If yes, could anyone tell me the main steps to calculate them ?
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[Pw_forum] Putting a strain on a BCC

[Eduardo Ariel Menendez Proupin]

Dear Ben,
If you want to do many calculations with different values and shapes of the
strain tensor, the following shell script may be helpful. This is for
hexagonal crystals, you can adapt it for  BCC or for any crystal structure.

http://www.gnm.cl/wiki/index.php/Ejemplos/Script4

-- Mensaje reenviado --
From: Ben Palmer 
To: pw_forum at pwscf.org
Cc:
Date: Tue, 27 Nov 2012 17:31:49 +
Subject: [Pw_forum] Putting a strain on a BCC
Hi everyone,

I have a BCC and I'd like to put a strain on it, but I want a different
strain in each direction.  Can I specify for example celldm(1)=1.02
celldm(2)=1 celldm(3)=1, or must all three lengths be equal?  Would I need
to use another ibrav?  Sorry if there is a simple answer to this.

Thanks

Ben Palmer
PhD Student @ University of Birmingham


-- 


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

On leave from: Departamento de Fisica, Facultad de Ciencias, Universidad de
Chile URL: http://fisica.ciencias.uchile.cl/~emenendez
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[Pw_forum] Weird jump in phonon dispersion at Gamma point

[Eduardo Ariel Menendez Proupin]

Dear Yao,
The jumps probably are right. They appear in non-cubic systems. For very
very small wavevectors, when w_TO ~ cq (c the speed of light and q the
wavavector) , the phonon are coupled with photons and form the excitation
known as phonon-polariton (PP). When the PP equations are solved the jumps
dissapear. Quantum ESPRESSO only computes the phonons, and the LO-TO
splitting is what happens for wavevectors just larger than the region of
coupling. This topics is briefly explained in some Solid State Physics
books, and fully explained in this article
R. Loudon, Advances in Physics, 2001, Vol. 50, No. 7, 813-864

There is also  a short entry in Wikipedia
http://en.wikipedia.org/wiki/Polariton

Best regards,
Eduardo

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

On leave from: Departamento de Fisica, Facultad de Ciencias, Universidad de
Chile URL: http://fisica.ciencias.uchile.cl/~emenendez





- Mensaje reenviado --
From: Yao Yao 
To: 
Cc:
Date: Fri, 9 Nov 2012 11:14:39 +1100
Subject: [Pw_forum] Weird jump in phonon dispersion at Gamma point
Dear All,

I calculated a orthorhombic cell with alternating AlSb/InAs mono {110} atom
layers with QE 4.3.2. I noticed that my phonon dispersion results were with
steps at Gamma point for some optical branches. Looks you will get different
frequency at Gamma when you approach Gamma from different direction
(X->Gamma,
Y->Gamma and Z->Gamma). One picture showing this is uploaded to
http://www.picvalley.net/v.php?p=u/2753/176658145760478725413524194617CoVRtxOq5iqZ20Wa3iK.PNG

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

[Eduardo Ariel Menendez Proupin]

Hi Layla and everybody,

Let us forget the nscf calculation for the moment, as my scf calculation
was probably not fine.
I have a strongly anisotropic unit cell, and large enough not to dare to
attempt to build a quasi-cubi one, that would have about 360 atoms. For
anysotropic cell,  INPUT_PW instructs to use

  exxdiv_treatment = 'vcut_ws',
for this to work one must use
  x_gamma_extrapolation = .false.,   (b.t.w., it is
not mentioned at INPUT_PW.txt )
then I have to set the value
  ecutvcut = X ,  ! which is 0.7 Ry in the Si
example.
 so, what is the method followed by using vcut_ws ,  and how to set
ecutvcut ? Are low or high values of ecutwfc more or less accurate or more
or less expensive? Is it the method given by Sorouri, Folkes and Hine in
JCP124, 064105 (2006)?

Thanks
-- 


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

On leave from: Departamento de Fisica, Facultad de Ciencias, Universidad de
Chile URL: http://fisica.ciencias.uchile.cl/~emenendez
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[Pw_forum] CIF to PWSCF

[Eduardo Ariel Menendez Proupin]

Hi Ben
One problem is that the QE input files contains not only the structure, but
parameters for the quantum calculation. So, we have to edit the file, using
copy and paste when possible. The main problem is that the CIF files
contains olny the atomic coordinates that are non-equivalent by the
symmetry of tha space group of the crystal.
I use gdis (comes in Ubuntu distributions) to convert to other less
crystallographic format, like that of SIESTA. This automates the generation
of the symmetry equivalent positions that are not in the CIF. You can also
generate the coordinates using The  inconvenient is that it generates the
conventional cell, rather than the primitive cell. Then I use vim or gedit
to manully set the input file.

Linux distributions are plenty of programs for chemistry and physics. I
have seen that the babel code can read the CIF format and convert to many
more.

There is also a serious intenet option using the bilbao crystallographic
server. This tool is recognized by crystallographers in the International
Tables for Crsytallgraphy, so it is a trustable tool.
http://www.cryst.ehu.es/
There, you can use the programs TRANSTRU or STRCONVERT. What you need is to
convert the structure to the group P1, or  just 1, and this gives all the
information need to the QE input file. Then, use vim, gedit, or your
favorite editor.

This is not confortable at the begining, but at the end it is easy, and you
may consider it as one intiation ritual (one more, right).

For the case of iron, the stable crystal structure is so simple (BCC) that
you can write it with the only knowledge of the lattice constants, you do
not need the CIF. It is explained in the initial chapters of many (probably
all) solid state physics and materials science books. I suggest you read
that, otherwise you better quit using QE.
Best regards
Eduardo


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
> 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
>>
>> Be

--
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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] About the Ibrav parameter of body centered cubic structure ci16 or I43d structure

[Eduardo Ariel Menendez Proupin]

Hi,
You may use ibrav=0, 3, or 14.
For 3 or 14,  you need to find the atomic coordinates referred to the
primitive vectors.
For ibrav=0, you can express the coordinates and the vectors in cartesian
components.

Once you understand well the structure, this site is useful to do the
transformations of  the cells.
http://www.cryst.ehu.es/

-- Mensaje reenviado --
From: Wei Zhou 
To: PWSCF Forum 
Cc:
Date: Wed, 3 Oct 2012 20:32:11 +0800
Subject: Re: [Pw_forum] About the Ibrav parameter of body centered cubic
structure ci16 or I43d structure
sorry, the Bravais is just cubic, the space group is I43d, the lattice
parameters are as following
  4.5991000   0.000   0.000
  0.000   4.5991000   0.000
 -0.000  -0.000   4.5991000
atom positions
 0.71903002   0.28096998   0.78096998
 1.21903003   0.78096997   1.28096999
-0.21903002  -0.28096998   1.28096999
 0.28096999   0.21903002   1.78096999
-0.71903002   0.78096998  -0.28096999
-0.21903002   1.28096999   0.21903002
 1.21903003   0.21903002  -0.78096998
 1.71903003   0.71903003  -0.28096999
 0.53096998   0.96903002   1.03096999
 1.03096997   1.46903001   1.53096999
-0.03096998   0.03096998   1.53096997
 0.46903002   0.53096999   2.03096999
 1.03096997  -0.46903002  -0.03096998
 1.53096997   0.03096999   0.46903002
 0.46903002   1.46903003  -0.53096998
 0.96903004   1.96903001  -0.03096998

-- 


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

On leave from: Departamento de Fisica, Facultad de Ciencias, Universidad de
Chile URL: http://fisica.ciencias.uchile.cl/~emenendez

"*Padece, espera y trabaja para gentes que nunca conocer? y que a su vez
padecer?n, esperar?n y trabajar?n para otros, que tampoco ser?n felices,
pues el hombre ans?a siempre una felicidad situada m?s all? de la porci?n
que le es otorgada. Pero la grandeza del hombre est? precisamente en querer
mejorar lo que es. En imponerse Tareas. En el Reino de los Cielos no hay
grandeza que conquistar, puesto que all? todo es jerarqu?a establecida,
inc?gnita despejada, existir sin t?rmino, imposibilidad de sacrificio,
reposo y deleite. Por ello, agobiado de penas y de Tareas, hermoso dentro
de su miseria, capaz de amar en medio de las plagas, el hombre puede hallar
su grandeza, su m?xima medida en el Reino de este Mundo*".
Alejo Carpentier, El reino de este mundo, (1949).

"...man never knows for who he suffers and waits. He suffers and waits and
works for peoples he will never meet, and who at the same time will suffer
and wait and work for others who will also not be happy, as man always
desires a happiness that is beyond the lot that he is given. But the
greatness of man is precisely in wanting to improve what he is. In
assigning himself Tasks. In the Kingdom of Heaven there is no greatness to
conquer, for everything there is an established hierarchy, the unknown is
unobscured, existence is without end, sacrifice, rest, and delight are
impossibilities. Therefore, overwhelmed with hardships and Tasks, beautiful
within his misery, capable of loving in the middle of calamity, man can
only find his greatness, his full self-realization, in the Kingdom of this
World." - Alejo Carpentier
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[Pw_forum] ecutwfc convergence

[Eduardo Ariel Menendez Proupin]

Dear Yusuf
The cutoff depends on the pseudopotential that you use, not just on the
atom. Different pseudopotentials for the same atoms have different cutoff.
Also, some properties requiere higher cutoffs than others. For example,
forces and relative energies need lower cutoff than total energy and
stress. Using higher values does not harm, just take longer time and more
computer resources.  Some programs include recommended cutoffs in the
pseudopotential, but the user is still responsible of testing it.

If you want a starting parameter for graphene, use
C.pz-vbc.UPF with ecutwfc = 60.0 ,
or
C.pbe-rrkjus.UPF with ecutwfc = 30.0 and ecutrho = 180.0

the above work reasonably well to relax the structures with fixed
cell, and to get the bands and DOS. I fou want to calculate elastic
properties or LDA+U or PBE+U, or calculate conductance, etc, etc,
these cutoffs may be too low. Yo need to do tests increasing the
values until you see no change in the property that you want to
calculate.

If you plan to adsorb other atoms (e.g. oxygen) on the graphene, then
determine cutoffs that are valid for the full system and do all the
calculations with the same parameters.


Dear Manasaje

The system is graphene with 32 carbon atoms. The cutoff is not
specified in the pseudo and I need it before proceeding to other SCF
and nscf calculations and believe, cutoff is a property of an atom in
question. So can I still go ahead with the atoms in the unit cell.
Thank you for your quick response
Yusuf



 From: Eduardo Ariel Menendez Proupin http://www.democritos.it/mailman/listinfo/pw_forum>>
To: pw_forum at pwscf.org <http://www.democritos.it/mailman/listinfo/pw_forum>
Sent: Wednesday, September 26, 2012 7:18 PM
Subject: Re: [Pw_forum] ecutwfc convergence


Dear Yusufm

ecutwfc and ecutrho depend only on the hardest of the pseudopotentials
used for the atoms in the molecule or the crystal. If your molecule is
C32 and have no other elements, you can make tests with a C2 (which
does not exists, I guess), and the cutoffs for C32.

Anyway, if your are going to calculate something that it is not the
total energy or the DOS, let's say, the phonons, or the Raman
spectrum, it is reasonable that you test the effect of the cutoff
first on C2 and then on C32.
-- Mensaje reenviado --
From: Yusuf Zuntu <yz...@yahoo.com
<http://www.democritos.it/mailman/listinfo/pw_forum>>
To: PWSCF Forum http://www.democritos.it/mailman/listinfo/pw_forum>>
Cc:
Date: Wed, 26 Sep 2012 03:15:32 -0700 (PDT)
Subject: [Pw_forum] ecutwfc convergence

Hi,
I need clarification on kinetic energy cutoff. I have a system
comprising 32 carbon atoms. Am I to consider total 32 carbon atoms in
convergence w.r.t kinetic energy cutoff scf calculation or the two
carbon atoms in the unit cell.
Thank you for anticipated reply.
Yusuf

-- 


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

On leave from: Departamento de Fisica, Facultad de Ciencias, Universidad de
Chile URL: http://fisica.ciencias.uchile.cl/~emenendez

"*Padece, espera y trabaja para gentes que nunca conocer? y que a su vez
padecer?n, esperar?n y trabajar?n para otros, que tampoco ser?n felices,
pues el hombre ans?a siempre una felicidad situada m?s all? de la porci?n
que le es otorgada. Pero la grandeza del hombre est? precisamente en querer
mejorar lo que es. En imponerse Tareas. En el Reino de los Cielos no hay
grandeza que conquistar, puesto que all? todo es jerarqu?a establecida,
inc?gnita despejada, existir sin t?rmino, imposibilidad de sacrificio,
reposo y deleite. Por ello, agobiado de penas y de Tareas, hermoso dentro
de su miseria, capaz de amar en medio de las plagas, el hombre puede hallar
su grandeza, su m?xima medida en el Reino de este Mundo*".
Alejo Carpentier, El reino de este mundo, (1949).

"...man never knows for who he suffers and waits. He suffers and waits and
works for peoples he will never meet, and who at the same time will suffer
and wait and work for others who will also not be happy, as man always
desires a happiness that is beyond the lot that he is given. But the
greatness of man is precisely in wanting to improve what he is. In
assigning himself Tasks. In the Kingdom of Heaven there is no greatness to
conquer, for everything there is an established hierarchy, the unknown is
unobscured, existence is without end, sacrifice, rest, and delight are
impossibilities. Therefore, overwhelmed with hardships and Tasks, beautiful
within his misery, capable of loving in the middle of calamity, man can
only find his greatness, his full self-realization, in the Kingdom of this
World." - Alejo Carpentier
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[Pw_forum] ecutwfc convergence

[Eduardo Ariel Menendez Proupin]

Dear Yusufm

ecutwfc and ecutrho depend only on the hardest of the pseudopotentials used
for the atoms in the molecule or the crystal. If your molecule is C32 and
have no other elements, you can make tests with a C2 (which does not
exists, I guess), and the cutoffs for C32.

Anyway, if your are going to calculate something that it is not the total
energy or the DOS, let's say, the phonons, or the Raman spectrum, it is
reasonable that you test the effect of the cutoff first on C2 and then on
C32.

-- Mensaje reenviado --
From: Yusuf Zuntu 
To: PWSCF Forum 
Cc:
Date: Wed, 26 Sep 2012 03:15:32 -0700 (PDT)
Subject: [Pw_forum] ecutwfc convergence
Hi,
I need clarification on kinetic energy cutoff. I have a system comprising
32 carbon atoms. Am I to consider total 32 carbon atoms in  convergence
w.r.t kinetic energy cutoff scf calculation or the two carbon atoms in the
unit cell.
Thank you for anticipated reply.
Yusuf
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[Pw_forum] Error while parsing atomic positions

[Eduardo Ariel Menendez Proupin]

As S. Baroni noticed with better aye than me, "O" is different from "0",
but also you have set too many atoms positions are equivalent due to
translational symmetry.
Positions (0,0,0), (1,0,0), (0,1,0), etc are the same.
Also, with ibrav=2, you need to set only the positions of ONE Ga and ONE As
in the primitive unit cell, and also nat=2.

ATOMIC_POSITIONS {crystal}
Ga 0.O  0.0  1.0
Ga 1.0  0.0  0.0
Ga 0.5  0.0  0.5
As 0.75 0.25 0.75
As 0.25 0.25 0.25
Ga 0.5  0.5  1.0
Ga 1.0  0.5  0.5
As 0.25 0.75 0.75
As 0.75 0.75 0.25
Ga 0.0  1.0  0.0

-- Mensaje reenviado --
From: Kajal Jindal 
To: PWSCF Forum 
Cc:
Date: Tue, 25 Sep 2012 16:07:03 +0530
Subject: [Pw_forum] Error while parsing atomic positions
Hi,

I am trying to do the scf calculation on unit cell GaAs. But i am
continously observing an error "Error while parsing atomic positions" while
running it. I have checked the program several times but still not able to
troubleshoot. I am attaching my input and output file result along.

*input file*


calculation='scf'
restart_mode='from_scratch'
prefix='GaAs'
wf_collect=.true.,
pseudo_dir = '/root/pseudo',
outdir='/root/poonamGaAs/temp',

 /
 
ibrav=2, nat=10, ntyp= 2,celldm(1) = 10.20,
ecutwfc = 25.0,ecutrho=300, occupations ='fixed',

 /
 
mixing_beta = 0.1
mixing_mode = 'plain'
conv_thr =  1.0e-5
diagonalization = 'david'
 /

ATOMIC_SPECIES
Ga  69.72  Ga.pbe-n-van.UPF
As  74.92  As.pbe-n-van.UPF
ATOMIC_POSITIONS {crystal}
Ga 0.O  0.0  1.0
Ga 1.0  0.0  0.0
Ga 0.5  0.0  0.5
As 0.75 0.25 0.75
As 0.25 0.25 0.25
Ga 0.5  0.5  1.0
Ga 1.0  0.5  0.5
As 0.25 0.75 0.75
As 0.75 0.75 0.25
Ga 0.0  1.0  0.0


K_POINTS {automatic}
4 4 2 0 0 0

-- 


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

On leave from: Departamento de Fisica, Facultad de Ciencias, Universidad de
Chile URL: http://fisica.ciencias.uchile.cl/~emenendez

"*Padece, espera y trabaja para gentes que nunca conocer? y que a su vez
padecer?n, esperar?n y trabajar?n para otros, que tampoco ser?n felices,
pues el hombre ans?a siempre una felicidad situada m?s all? de la porci?n
que le es otorgada. Pero la grandeza del hombre est? precisamente en querer
mejorar lo que es. En imponerse Tareas. En el Reino de los Cielos no hay
grandeza que conquistar, puesto que all? todo es jerarqu?a establecida,
inc?gnita despejada, existir sin t?rmino, imposibilidad de sacrificio,
reposo y deleite. Por ello, agobiado de penas y de Tareas, hermoso dentro
de su miseria, capaz de amar en medio de las plagas, el hombre puede hallar
su grandeza, su m?xima medida en el Reino de este Mundo*".
Alejo Carpentier, El reino de este mundo, (1949).

"...man never knows for who he suffers and waits. He suffers and waits and
works for peoples he will never meet, and who at the same time will suffer
and wait and work for others who will also not be happy, as man always
desires a happiness that is beyond the lot that he is given. But the
greatness of man is precisely in wanting to improve what he is. In
assigning himself Tasks. In the Kingdom of Heaven there is no greatness to
conquer, for everything there is an established hierarchy, the unknown is
unobscured, existence is without end, sacrifice, rest, and delight are
impossibilities. Therefore, overwhelmed with hardships and Tasks, beautiful
within his misery, capable of loving in the middle of calamity, man can
only find his greatness, his full self-realization, in the Kingdom of this
World." - Alejo Carpentier
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[Pw_forum] differences in vdW_kernel_table

[Eduardo Ariel Menendez Proupin]

Hi,
I generated the file vdW_kernel_table with version 5.0.1 and it is
different
from the filecoming with the 4.3.2. Should they be different ?
The first numbers that are different are 1.91402358203250E+07 vs
1.87278875106385E+07

-- 


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

On leave from: Departamento de Fisica, Facultad de Ciencias, Universidad de
Chile URL: http://fisica.ciencias.uchile.cl/~emenendez

"*Padece, espera y trabaja para gentes que nunca conocer? y que a su vez
padecer?n, esperar?n y trabajar?n para otros, que tampoco ser?n felices,
pues el hombre ans?a siempre una felicidad situada m?s all? de la porci?n
que le es otorgada. Pero la grandeza del hombre est? precisamente en querer
mejorar lo que es. En imponerse Tareas. En el Reino de los Cielos no hay
grandeza que conquistar, puesto que all? todo es jerarqu?a establecida,
inc?gnita despejada, existir sin t?rmino, imposibilidad de sacrificio,
reposo y deleite. Por ello, agobiado de penas y de Tareas, hermoso dentro
de su miseria, capaz de amar en medio de las plagas, el hombre puede hallar
su grandeza, su m?xima medida en el Reino de este Mundo*".
Alejo Carpentier, El reino de este mundo, (1949).

"...man never knows for who he suffers and waits. He suffers and waits and
works for peoples he will never meet, and who at the same time will suffer
and wait and work for others who will also not be happy, as man always
desires a happiness that is beyond the lot that he is given. But the
greatness of man is precisely in wanting to improve what he is. In
assigning himself Tasks. In the Kingdom of Heaven there is no greatness to
conquer, for everything there is an established hierarchy, the unknown is
unobscured, existence is without end, sacrifice, rest, and delight are
impossibilities. Therefore, overwhelmed with hardships and Tasks, beautiful
within his misery, capable of loving in the middle of calamity, man can
only find his greatness, his full self-realization, in the Kingdom of this
World." - Alejo Carpentier
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[Pw_forum] optical properties (bhabya sahoo)

[Eduardo Ariel Menendez Proupin]

Dear Bhabya

Optical properties in RPA
make pp
use bin/epsilon.x
read Doc/eps_man.pdf
no example, but it is straightforward reading the manual.

Optical properties by TDDFPT (absolutely better than RPA for isolated
systems, buy still in progress for periodical systems)
make tddfpt
read documentation at TDDFPT/Doc/
and see examples in
TDDFPT/Examples/

For more advanced methods to calculate optical properties you can use other
codes like YAMBO, that use the output of PWSCF and produce optical
properties un several approximations. http://www.yambo-code.org/
YAMBO can de downloaded and compiled within QE, but it is a bit tricky to
compile ( by my own experience two weeks ago).

Good luck
Eduardo


> -- Mensaje reenviado --
> From: bhabya sahoo 
> To: PWSCF Forum 
> Cc:
> Date: Mon, 30 Apr 2012 11:40:50 +0530
> Subject: [Pw_forum] optical properties
> can any one help me to find the optical properies by espresso code
> is there any example in espresso
> but i know  ev.x command can do this but i donot what should be the input
> file for this
>
>
> any suggetions are highly appricieted
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>  b sahoo
> mumbai
> reserch scholar
>
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>


-- 


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

On leave from: Departamento de Fisica, Facultad de Ciencias, Universidad de
Chile URL: http://fisica.ciencias.uchile.cl/~emenendez

"*Padece, espera y trabaja para gentes que nunca conocer? y que a su vez
padecer?n, esperar?n y trabajar?n para otros, que tampoco ser?n felices,
pues el hombre ans?a siempre una felicidad situada m?s all? de la porci?n
que le es otorgada. Pero la grandeza del hombre est? precisamente en querer
mejorar lo que es. En imponerse Tareas. En el Reino de los Cielos no hay
grandeza que conquistar, puesto que all? todo es jerarqu?a establecida,
inc?gnita despejada, existir sin t?rmino, imposibilidad de sacrificio,
reposo y deleite. Por ello, agobiado de penas y de Tareas, hermoso dentro
de su miseria, capaz de amar en medio de las plagas, el hombre puede hallar
su grandeza, su m?xima medida en el Reino de este Mundo*".
Alejo Carpentier, El reino de este mundo, (1949).

"...man never knows for who he suffers and waits. He suffers and waits and
works for peoples he will never meet, and who at the same time will suffer
and wait and work for others who will also not be happy, as man always
desires a happiness that is beyond the lot that he is given. But the
greatness of man is precisely in wanting to improve what he is. In
assigning himself Tasks. In the Kingdom of Heaven there is no greatness to
conquer, for everything there is an established hierarchy, the unknown is
unobscured, existence is without end, sacrifice, rest, and delight are
impossibilities. Therefore, overwhelmed with hardships and Tasks, beautiful
within his misery, capable of loving in the middle of calamity, man can
only find his greatness, his full self-realization, in the Kingdom of this
World." - Alejo Carpentier
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[Pw_forum] Ba pseudopotential for spin-orbit calculations

[Eduardo Ariel Menendez Proupin]

Hi,
Is there any Ba pseudopotential available that can be used for spin-orbit
calculations (generated with fully relativistic hamiltonian).
Thanks,
-- 


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

On leave from: Departamento de Fisica, Facultad de Ciencias, Universidad de
Chile URL: http://fisica.ciencias.uchile.cl/~emenendez

"*Padece, espera y trabaja para gentes que nunca conocer? y que a su vez
padecer?n, esperar?n y trabajar?n para otros, que tampoco ser?n felices,
pues el hombre ans?a siempre una felicidad situada m?s all? de la porci?n
que le es otorgada. Pero la grandeza del hombre est? precisamente en querer
mejorar lo que es. En imponerse Tareas. En el Reino de los Cielos no hay
grandeza que conquistar, puesto que all? todo es jerarqu?a establecida,
inc?gnita despejada, existir sin t?rmino, imposibilidad de sacrificio,
reposo y deleite. Por ello, agobiado de penas y de Tareas, hermoso dentro
de su miseria, capaz de amar en medio de las plagas, el hombre puede hallar
su grandeza, su m?xima medida en el Reino de este Mundo*".
Alejo Carpentier, El reino de este mundo, (1949).

"...man never knows for who he suffers and waits. He suffers and waits and
works for peoples he will never meet, and who at the same time will suffer
and wait and work for others who will also not be happy, as man always
desires a happiness that is beyond the lot that he is given. But the
greatness of man is precisely in wanting to improve what he is. In
assigning himself Tasks. In the Kingdom of Heaven there is no greatness to
conquer, for everything there is an established hierarchy, the unknown is
unobscured, existence is without end, sacrifice, rest, and delight are
impossibilities. Therefore, overwhelmed with hardships and Tasks, beautiful
within his misery, capable of loving in the middle of calamity, man can
only find his greatness, his full self-realization, in the Kingdom of this
World." - Alejo Carpentier
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[Pw_forum] runtime error for GWW in example01-benzene

[Eduardo Ariel Menendez Proupin]

Hi,
I have found runtime errors running pw4gww.x in the example01 (benzene)
when the code is compiled with gfortran, either serially or parallel.
Using Intel compiler and OpenMPI bilt with Intel compilers, the problem is
solved. I report this error because of my system is quite extended, I
guess, and allows the easiest installation. Before this problem, in the
same machine, I had used the phonon, TDDFT, and epsilon programs without
any problem. Follows the stdout and stderr output

 
 114   10.578069863696490
 115   10.626629777342377
FUNCTION WFC_REAL
 IBND:   1
 lbound and ubound of psic:1  884736
 before
 after
*** glibc detected *** ../../../../bin/pw4gww.x: malloc(): memory
corruption: 0x024614d0 ***
=== Backtrace: =
/lib/x86_64-linux-gnu/libc.so.6(+0x7a87a)[0x7fc65433487a]
/lib/x86_64-linux-gnu/libc.so.6(__libc_malloc+0x6e)[0x7fc654336e1e]
/usr/lib/x86_64-linux-gnu/libgfortran.so.3(+0x167c9)[0x7fc654b007c9]
/usr/lib/x86_64-linux-gnu/libgfortran.so.3(+0xa3a90)[0x7fc654b8da90]
/usr/lib/x86_64-linux-gnu/libgfortran.so.3(+0xb0800)[0x7fc654b9a800]
../../../../bin/pw4gww.x[0x582b3e]
../../../../bin/pw4gww.x[0x5974a7]
../../../../bin/pw4gww.x[0x43c0ce]
../../../../bin/pw4gww.x[0x411e63]
../../../../bin/pw4gww.x[0x404ad6]
..(enough, I guess)


My system is Ubuntu 11.04
Linux version 2.6.38-13-generic (buildd at yellow) (gcc version 4.5.2
(Ubuntu/Linaro 4.5.2-8ubuntu4) ) #56-Ubuntu SMP Tue Feb 14 12:39:59 UTC 2012

gcc version 4.5.2

I hope it helps

-- 


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

On leave from: Departamento de Fisica, Facultad de Ciencias, Universidad de
Chile URL: http://fisica.ciencias.uchile.cl/~emenendez

"*Padece, espera y trabaja para gentes que nunca conocer? y que a su vez
padecer?n, esperar?n y trabajar?n para otros, que tampoco ser?n felices,
pues el hombre ans?a siempre una felicidad situada m?s all? de la porci?n
que le es otorgada. Pero la grandeza del hombre est? precisamente en querer
mejorar lo que es. En imponerse Tareas. En el Reino de los Cielos no hay
grandeza que conquistar, puesto que all? todo es jerarqu?a establecida,
inc?gnita despejada, existir sin t?rmino, imposibilidad de sacrificio,
reposo y deleite. Por ello, agobiado de penas y de Tareas, hermoso dentro
de su miseria, capaz de amar en medio de las plagas, el hombre puede hallar
su grandeza, su m?xima medida en el Reino de este Mundo*".
Alejo Carpentier, El reino de este mundo, (1949).

"...man never knows for who he suffers and waits. He suffers and waits and
works for peoples he will never meet, and who at the same time will suffer
and wait and work for others who will also not be happy, as man always
desires a happiness that is beyond the lot that he is given. But the
greatness of man is precisely in wanting to improve what he is. In
assigning himself Tasks. In the Kingdom of Heaven there is no greatness to
conquer, for everything there is an established hierarchy, the unknown is
unobscured, existence is without end, sacrifice, rest, and delight are
impossibilities. Therefore, overwhelmed with hardships and Tasks, beautiful
within his misery, capable of loving in the middle of calamity, man can
only find his greatness, his full self-realization, in the Kingdom of this
World." - Alejo Carpentier
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[Pw_forum] Small value of stress at equilibrium (T=0,P=0)

[Eduardo Ariel Menendez Proupin]

Relax again from the last structure and you should get smaller residual
stress. Otherwise, increase the cutoffs.
Please, read this
http://www.quantum-espresso.org/wiki/index.php/Methodological_Background#Stress

Stress smaller than 10 kbar in a solid generally have little effect.

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



-- Mensaje reenviado --
From: bramha pandey 
To: PWSCF Forum 
Cc:
Date: Thu, 22 Mar 2012 19:08:56 +0530
Subject: [Pw_forum] Small value of stress at equilibrium (T=0,P=0)
Dear all,
I am using AlN with zincblede structure using USPP (PBE xc).
After completing convergence test of ecut and k-point, i calculated the
equilibrium lattice constant(at T=0, P=0).
But i wondered if i put this equilibrium lattice constant in calculation i
got, small value of stress(-7.36kbar).
i know this is Pulay stress and think it may be zero (may be i am wrong if
so please correct me) at equilibrium but here it is not the case.
i want to know whether this will affect the other property like bulk
modulus, lattice constant calculation etc at different pressure and
temperature.
How can i fix it.
Your valuable comment is highly aappriciable.

-- 
Thanks and Regards
Bramha Prasad Pandey
GLA University, Mathura.
INDIA.

--
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[Pw_forum] Rydberg to kJ/mole

[Eduardo Ariel Menendez Proupin]

>Is there any normalisation to be made? Dividing by the number of molecules
per unit cell (if there is one per >asymmetric unit, this would refer to 8
for an orthorombic case, e.g.)?

QE gives the energy of the cell defined in the input.

>I'm not sure, what the "reference" of the calculated Rydberg value is - if
it would be the whole cell, I would get >doubled energy values and
differences when I calculate a 2x1x1 supercell...

 Yes. Yo can make the test. there my be a few details.  If you double the
cell in X direction, divide by 2 the number of k-points in the first
direction. If the number of electron is odd, it may be necessary to do a
spin polarised calculation.


>The other way round: what does "per mole" really mean in a conversion of
"some amount" to "a mole" (e.g.: >Joule to Joule/mol)...
Take the energy in Ry, multiply by the number of Avogadro, and convert to
kJ. My only doubt is per mole o what ? Moles of supercells, molecules or
atoms? I do not know.


-- 


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

On leave from: Departamento de Fisica, Facultad de Ciencias, Universidad de
Chile URL: http://fisica.ciencias.uchile.cl/~emenendez
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[Pw_forum] mathematical method for computing in quantm espresso

[Eduardo Ariel Menendez Proupin]

Read this
espresso-4.3.2/TDDFPT/Doc/turboTDDFT-CPC.pdf
or Comput. Phys. Commun. 182 (2011) 1744-1754.

and the user guide at www.quantum-espresso.org

For the optical properties there is also a less sophisticated approach
implemented in the epsilon.x code, the manual is in the file
espresso-4.3.2/Doc/eps_man.pdf

Enjoy,
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


-- Mensaje reenviado --

> From: F Anis 
> To: pw_forum at pwscf.org
> Cc:
> Date: Thu, 8 Mar 2012 00:32:04 -0800 (PST)
> Subject: [Pw_forum] mathematical method for computing in quantm espresso
> Hi,
> What mathematical method for computing the optical properties and self
> consist cycle in the quantum espresso is used.
> thanks.
>
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>
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[Pw_forum] Eyvaz Isaev

[Eduardo Ariel Menendez Proupin]

I wish to express my sadness from Prof. Eyvaz Isaev departure. At the
beginning I was reluctant to use the forum byte allowance to express my
private condolence and thought that the obituary by Paolo was enough.
Although I did not have much interaction with him, I appreciated him as one
of the most helpful and kind guys of this community. He belonged plenty to
this community of persons that sacrifice a non-neglgible amount of time and
productivity to help the fellows and make science a delightful activity.

-- 
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

"...man never knows for who he suffers and waits. He suffers and waits and
works for peoples he will never meet, and who at the same time will suffer
and wait and work for others who will also not be happy, as man always
desires a happiness that is beyond the lot that he is given. But the
greatness of man is precisely in wanting to improve what he is. In
assigning himself Tasks. In the Kingdom of Heaven there is no greatness to
conquer, for everything there is an established hierarchy, the unknown is
unobscured, existence is without end, sacrifice, rest, and delight are
impossibilities. Therefore, overwhelmed with hardships and Tasks, beautiful
within his misery, capable of loving in the middle of calamity, man can
only find his greatness, his full self-realization, in the Kingdom of this
World." - Alejo Carpentier- The kingdom of this world
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[Pw_forum] doubt on TDDFPT output

[Eduardo Ariel Menendez Proupin]

Hi,
I am rather confused with the TDDFPT output. In the turbo_spectrum run I
pretend to obtain the polarizabilty \alpha_{33}, and I set the input as

_input
  prefix='cnt_21',
  outdir='./temp',
  itermax=1
  itermax0=4000
  extrapolation="osc"
  epsil=0.0073495
  units=1
  start=0.d0
  end=5.0d0
  increment=0.01d0
  start=0.0d0
  ipol=3
  verbosity=1


In the output I get references only to the direction 1, as seen below

 Program TDDFPT_PP v.4.3.1  starts on 11Jan2012 at 12: 6:32
.
 Parallel version (MPI), running on56 processors
 R & G space division:  proc/pool =   56

 Reading  1 Lanczos steps for direction 1
   3500 steps will be considered
.
 Polarization direction:1

Static dipole polarizability Tensor:
 chi_1_1=  0.523359728355224E+03 + i0.000E+00


I check that the chi_1_1 values in the output are different the results
when I set ipol=3. Is it a bug of the output or is somehing different to
the \alpha_{33} that I want to obtain ?

Thanks

-- 


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

On leave from: Departamento de Fisica, Facultad de Ciencias, Universidad de
Chile URL: http://fisica.ciencias.uchile.cl/~emenendez

"*Padece, espera y trabaja para gentes que nunca conocer? y que a su vez
padecer?n, esperar?n y trabajar?n para otros, que tampoco ser?n felices,
pues el hombre ans?a siempre una felicidad situada m?s all? de la porci?n
que le es otorgada. Pero la grandeza del hombre est? precisamente en querer
mejorar lo que es. En imponerse Tareas. En el Reino de los Cielos no hay
grandeza que conquistar, puesto que all? todo es jerarqu?a establecida,
inc?gnita despejada, existir sin t?rmino, imposibilidad de sacrificio,
reposo y deleite. Por ello, agobiado de penas y de Tareas, hermoso dentro
de su miseria, capaz de amar en medio de las plagas, el hombre puede hallar
su grandeza, su m?xima medida en el Reino de este Mundo*".
Alejo Carpentier, El reino de este mundo, (1949).

Translate from spanish here
http://translate.google.com/?hl==UTF-8==es=en
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[Pw_forum] Dynamic polarizability of C60

[Eduardo Ariel Menendez Proupin]

Hi Anne, and everybody,

My question about the dynamical polarizability was more for the developers,
because I don not find it clear in the documentation.
Let me focus my question

The electronic dynamical  polarizability is calculated with the
turbo-TDDFPT code. Then, what dynamic polarizability is calculated with
PHONON ? Knowing some of he applications of the PHONON code, I foresee two
logical answers
a) the polarizabilty due to phonon excitations, plus the electronic
polarizabilty in the static limit, i.e., for energy much smaller than the
electronic transition energies.
b) the same, but with the frequency dependent electronic contributions,
calculated with ground state DFT instead of TDDFT.
and the answer is c)  ...?

I do not believe that the frequencies in the example 33 are in Ry. They are
too high if the units are Ry, and PHONON is esentially a code to calculate
phonons and derived properties. I would bet for THz.

best regards
Eduardo


DearEduardo You wanted to know What exactly this dynamical polarizability
is? In fact, when a system (atomic, molecule,...) is submitted to an
external field, its electrons are reorganised according to the frequence of
that external field. One can then evaluate the aptitude of the system to be
subject to that reorganisation by evaluating the polarizability.
Particularly when the phenomenon is time dependent, one evaluate the
dynamical polarizability.is it include the electronic , phonon or both
contributions?   For my case, I want to consider C60 as a dielectric sphere
of finite or infinite thickness, I don't know exactly if the phonon
contribution is relevant, but I am mostly evolved in electronic
calculations.  What are the frequency units (THz, eV? ) in the example 33.
 As I see in output of that example 33 (it is also the case for almost all
the other input and output files of espresso-4.3.1), the energies and
frequencies are in Ry Kind regard
-- 


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

On leave from: Departamento de Fisica, Facultad de Ciencias, Universidad de
Chile URL: http://fisica.ciencias.uchile.cl/~emenendez

"*Padece, espera y trabaja para gentes que nunca conocer? y que a su vez
padecer?n, esperar?n y trabajar?n para otros, que tampoco ser?n felices,
pues el hombre ans?a siempre una felicidad situada m?s all? de la porci?n
que le es otorgada. Pero la grandeza del hombre est? precisamente en querer
mejorar lo que es. En imponerse Tareas. En el Reino de los Cielos no hay
grandeza que conquistar, puesto que all? todo es jerarqu?a establecida,
inc?gnita despejada, existir sin t?rmino, imposibilidad de sacrificio,
reposo y deleite. Por ello, agobiado de penas y de Tareas, hermoso dentro
de su miseria, capaz de amar en medio de las plagas, el hombre puede hallar
su grandeza, su m?xima medida en el Reino de este Mundo*".
Alejo Carpentier, El reino de este mundo, (1949).

Translate from spanish here
http://translate.google.com/?hl==UTF-8==es=en
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[Pw_forum] Regarding raman spectra

[Eduardo Ariel Menendez Proupin]

Hi,
save the data in a file, let's name it archive.dat

call gnuplot with the command of the same name. Inside the gnuplot
terminal,
plot "archive.dat"  using 2:5  with impulses
or
plot "archive.dat"  u 2:5  w i

that will produce a plot of vertical lines. If you want a continuous curve,
you need to write your own program. I know no utility in Quantum ESRESSO to
do that. Any user of Quantum ESPRESSO and similar non-commercial packages
needs to write, and enjoy doing it :-),  some small programs to analize the
output data.

Yoy have asked for a GGA pseudopotential, but take into account that the
PHONON  code calculates the Raman spectra only for LDA and norm conserving
pseudopotentials.

I guess that vdW interaction is important for soft modes, or at least to
have an apropriate strucuture with minimal energy, otherwise there are
imaginary frequencies. Graphene is a famous case where vdW is important.

best regards
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



-- Mensaje reenviado --
From: Kondaiah Samudrala 
To: pw_forum at pwscf.org
Cc:
Date: Mon, 23 Jan 2012 15:45:23 +0530
Subject: [Pw_forum] Regarding raman spectra

   Dear all,
   I get the result of cross section of Raman and IR. The results are:

#  mode   [cm-1] [THz]  IR   Raman depol
1  0.00   -0.00010. 0.0.7298
2  0.000.0. 0.0.4596
3  0.000.0. 0.0.3769
4 72.482.17280.2093 0.0.7221
5181.805.45030.  1725.78320.7500
6216.896.50230.  2083.45000.7500
7363.65   10.90210. 91729.50390.2795
8396.95   11.90010.104976.37800.7500
9420.27   12.59920. 0.0.6389
   10425.05   12.74270.  1248.54190.7500
   11451.38   13.53210.329620.46540.3306
   12460.15   13.79490.1942 0.0.3225


   The result of raman data are very well compared with the experimental
result. But I am not able to plot Raman spectrum with this o/p using
XMGRACE.

   Please give me suggetion for plot raman spectra. Here with i attached
direct plot of my trail with xmgrace (2 and 5th colums) .

   What is the meaning of cross section in this calculation?

   Please provide norm conserving pseudopotential for phosphorus using GGA
(PBE or PW91) XC-functional ( Using LDA-CAPZ is already in website).

   Finally, for structural properties semiemperical correction of Vdw
interactions plays very importent role. But, Is there any  influence of
semiemperical  correction  to Vdw interaction on vibrational properties
.

  I appreciate to all your instructions.

  with regards
  S.Appalakondaiah
  Research Schloar
  University of hyderabad
  Hyderabad
  India

-- 




On leave from: Departamento de Fisica, Facultad de Ciencias, Universidad de
Chile URL: http://fisica.ciencias.uchile.cl/~emenendez

"*Padece, espera y trabaja para gentes que nunca conocer? y que a su vez
padecer?n, esperar?n y trabajar?n para otros, que tampoco ser?n felices,
pues el hombre ans?a siempre una felicidad situada m?s all? de la porci?n
que le es otorgada. Pero la grandeza del hombre est? precisamente en querer
mejorar lo que es. En imponerse Tareas. En el Reino de los Cielos no hay
grandeza que conquistar, puesto que all? todo es jerarqu?a establecida,
inc?gnita despejada, existir sin t?rmino, imposibilidad de sacrificio,
reposo y deleite. Por ello, agobiado de penas y de Tareas, hermoso dentro
de su miseria, capaz de amar en medio de las plagas, el hombre puede hallar
su grandeza, su m?xima medida en el Reino de este Mundo*".
Alejo Carpentier, El reino de este mundo, (1949).

Translate from spanish here
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[Pw_forum] Dynamic polarizability of C60

[Eduardo Ariel Menendez Proupin]

What is exactly this dynamical polarizability? Does it include  the
electronic , phonon or both contributions?

What are the frequency units (THz, eV? ) in the example 33.


  tr2_ph=1.0d-14,
  prefix='ch4',
  epsil=.true.,
  trans=.false.,
  fpol=.true.,
  amass(1)=12.0107,
  amass(2)=1.00794,
  outdir='/home/giannozz/tmp/',
  fildyn='ch4.dynG',
 /
0.0 0.0 0.0

FREQUENCIES
 2
 0.0d0
 1.5d0

Best regards
eduardo


-- Mensaje reenviado --
From: anne etindele 
To: "pw_forum at pwscf.org" 
Cc:
Date: Tue, 17 Jan 2012 16:23:52 + (GMT)
Subject: [Pw_forum] Dynamic polarizability of C60
Dear all

I am a new user of Quantum espresso (espresso-4.3.1), and I have found that
it is possible,
as it is done in example 33, to calculate dynamic polarizability of
molecules using pw.x
and ph.x.

I am interested on the description of properties of C60 complex. I tried to
modify the script of example 33
in order to get its dynamic polarizability but I couldn't even run self
consistent calculation as the code signals "MPI abort..".


-- 


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

On leave from: Departamento de Fisica, Facultad de Ciencias, Universidad de
Chile URL: http://fisica.ciencias.uchile.cl/~emenendez
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[Pw_forum] scaling of turbo_lanczos.x

[Eduardo Ariel Menendez Proupin]

I have one more question ? What is nipol ? The manual reads

nipol   1 if ipol < 4; 3 if ipol=4
Determines the number of zeta coefficients to be calculated
for
 a given polarization direction.
I think this z is the $^{m}z_{ij}$ present in Eqs. 33, 34-36 of the article
included in the Doc directory. What parameter in the Eq. correspond to
nipol ?


--

Hi
I am calculating optical spectra of a carbon nanotube with turbo-TDDFPT. I
would like to know how scales the cost and the needed parameters with the
size of the unit cell. As only the gamma point is allowed I need to
replicate the unit cell. for example, if I duplicate the unit cell, how
scales

a) the itermax parameter to achieve an equivalent resolution of the
spectrum (is the same or must be scaled)
b) RAM, CPU time for fixed itermax

Is there any advice to use efficiently multiple CPU systems that may differ
from the advices to use pw.x ? Are task groups implemented (-ntg or
similar) ?

Thank you
Eduardo
-- 


-- 


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

On leave from: Departamento de Fisica, Facultad de Ciencias, Universidad de
Chile URL: http://fisica.ciencias.uchile.cl/~emenendez

"*Padece, espera y trabaja para gentes que nunca conocer? y que a su vez
padecer?n, esperar?n y trabajar?n para otros, que tampoco ser?n felices,
pues el hombre ans?a siempre una felicidad situada m?s all? de la porci?n
que le es otorgada. Pero la grandeza del hombre est? precisamente en querer
mejorar lo que es. En imponerse Tareas. En el Reino de los Cielos no hay
grandeza que conquistar, puesto que all? todo es jerarqu?a establecida,
inc?gnita despejada, existir sin t?rmino, imposibilidad de sacrificio,
reposo y deleite. Por ello, agobiado de penas y de Tareas, hermoso dentro
de su miseria, capaz de amar en medio de las plagas, el hombre puede hallar
su grandeza, su m?xima medida en el Reino de este Mundo*".
Alejo Carpentier, El reino de este mundo, (1949).

Translate from spanish here
http://translate.google.com/?hl==UTF-8==es=en
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[Pw_forum] scaling of turbo_lanczos.x

[Eduardo Ariel Menendez Proupin]

Hi
I am calculating optical spectra of a carbon nanotube with turbo-TDDFPT. I
would like to know how scales the cost and the needed parameters with the
size of the unit cell. As only the gamma point is allowed I need to
replicate the unit cell. for example, if I duplicate the unit cell, how
scales

a) the itermax parameter to achieve an equivalent resolution of the
spectrum (is the same or must be scaled)
b) RAM, CPU time for fixed itermax

Is there any advice to use efficiently multiple CPU systems that may differ
from the advices to use pw.x ? Are task groups implemented (-ntg or
similar) ?

Thank you
Eduardo
-- 


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

On leave from: Departamento de Fisica, Facultad de Ciencias, Universidad de
Chile URL: http://fisica.ciencias.uchile.cl/~emenendez

"*Padece, espera y trabaja para gentes que nunca conocer? y que a su vez
padecer?n, esperar?n y trabajar?n para otros, que tampoco ser?n felices,
pues el hombre ans?a siempre una felicidad situada m?s all? de la porci?n
que le es otorgada. Pero la grandeza del hombre est? precisamente en querer
mejorar lo que es. En imponerse Tareas. En el Reino de los Cielos no hay
grandeza que conquistar, puesto que all? todo es jerarqu?a establecida,
inc?gnita despejada, existir sin t?rmino, imposibilidad de sacrificio,
reposo y deleite. Por ello, agobiado de penas y de Tareas, hermoso dentro
de su miseria, capaz de amar en medio de las plagas, el hombre puede hallar
su grandeza, su m?xima medida en el Reino de este Mundo*".
Alejo Carpentier, El reino de este mundo, (1949).

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[Pw_forum] why is the tetrahedron interpolated DOS step-like?

[Eduardo Ariel Menendez Proupin]

>Eduardo: you may want to rehearse the theory of critical points, such as 
>explained in many solid-state texts, my favorite one (at least in this field) 
>still being Bassani and Pastori Parravicini's. SB
Stefano,
Thank you. You are right if the system is 2D, but in this case it is
quasi-1D. The 1-D Van Hove singularitu is appreciated in the large
energy scale of the
plot between -6 and -4 eV.

Maybe the steps in the low energy scale reveal that a quasi-1D system
with a finite k-point sampling is an effective bi-dimensionality with
a smaller energy scale, with as many bands as k-points. I do not think
that you are meaning that,
as k-points sampling is not a matter of solid state textbooks.

Thanks, and nice weekend
Eduardo

On Dec 9, 2011, at 1:33 PM, Eduardo Ariel Menendez Proupin wrote:

>* Dear all,*>* *>* I would like to know if the step-like aspect of a DOS 
>calculated with the tetrahedron interpolation is what is expected to be. 
>Please, take a look at the figures attached. I would expect something soft or 
>at least a polygonal line with slope. *>* *>* I have looked at flib/dost.f90 
>and checked that the interpolation formulae are the same of the Bloechl's 
>article OK.*>* I am sorry to ask such a basic question, but I am puzzled since 
>a long time, and tired of soften the stepped line with an additional program. 
>*>* Thanks in advance*



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[Pw_forum] why is the tetrahedron interpolated DOS step-like?

[Eduardo Ariel Menendez Proupin]

Dear all,

I would like to know if the step-like aspect of a DOS calculated with the
tetrahedron interpolation is what is expected to be. Please, take a look at
the figures attached. I would expect something soft or at least a polygonal
line with slope.

I have looked at flib/dost.f90 and checked that the interpolation formulae
are the same of the Bloechl's article OK.
I am sorry to ask such a basic question, but I am puzzled since a long
time, and tired of soften the stepped line with an additional program.
Thanks in advance
-- 


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

On leave from: Departamento de Fisica, Facultad de Ciencias, Universidad de
Chile URL: http://fisica.ciencias.uchile.cl/~emenendez

"*Padece, espera y trabaja para gentes que nunca conocer? y que a su vez
padecer?n, esperar?n y trabajar?n para otros, que tampoco ser?n felices,
pues el hombre ans?a siempre una felicidad situada m?s all? de la porci?n
que le es otorgada. Pero la grandeza del hombre est? precisamente en querer
mejorar lo que es. En imponerse Tareas. En el Reino de los Cielos no hay
grandeza que conquistar, puesto que all? todo es jerarqu?a establecida,
inc?gnita despejada, existir sin t?rmino, imposibilidad de sacrificio,
reposo y deleite. Por ello, agobiado de penas y de Tareas, hermoso dentro
de su miseria, capaz de amar en medio de las plagas, el hombre puede hallar
su grandeza, su m?xima medida en el Reino de este Mundo*".
Alejo Carpentier, El reino de este mundo, (1949).

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[Pw_forum] change in Fermi Energy with ecutoff, Vacuum and degauss

[Eduardo Ariel Menendez Proupin]

Deepak,
Periodic calculations have several components of the electrostatic energy
that are separately infinite, but added they cancel. Instead of dealing
with infinites, they are usually eliminated in plane wave codes setting to
0 the G=0 components of the Fourier transforms. I guess that Quantum
ESPRESSO  satisfies this rule. A component V(G=0)  is just the spatial
average of V(r), meaning in practice that  the electrostatic potential (the
Hartree part) is adjusted to zero. The amount of vacuum volume in the
supercell represents a weight for the spatial averages. If you change from
10 to 20 angstroms of vacumm width, you are doubling the weight of the
vacuum part in the average.

If the average were not adjusted to zero,  then I would expect that the
average tends softly to cero for infinite vacuum volume, and the Fermi
level converge to a constant value. As the average potential is
artificially shifted to zero, the Fermi level experiments the opposite
shift. For more interesting details, take a look at PRB 77, 115139 (2008).

Best regards


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

-- Mensaje reenviado --
From: Dipak Thakur 
To: pw_forum at pwscf.org
Date: Tue, 29 Nov 2011 22:05:00 +0530
Subject: [Pw_forum] change in Fermi Energy with ecutoff, Vacuum and degauss
Hello every one.

I am perplexed by change in Fermi energy with change in ecutoff, Vacuum and
degauss.

I have done some calculations using a set of ecutoff, Vacuum and degauss
and then repeated the same for other set of ecutoff, Vacuum and degauss.

I have obtained a value of -0.756 eV for Fermi energy in case where the
ecutoff was 60 Ry., Vacuum was 20 A and degauss was 0.02, whereas for the
second set with ecutoff of 20 Ry., Vacuum of 10 A and degauss of 0.002 the
Fermi energy was 3.0097 eV.

Can anyone help me which value of Fermi energy is correct and why?

Please help me in understanding the what wrong am I doing?

The calculations are related to graphene with Aluminium dopant (one atom of
Al and 31 carbon atoms).

Thanks and regards
Deepak Thakur
Research student
Swami Ramanand Teerth Marathwada University, Nanded.
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[Pw_forum] Problem With Total-Energy Convergence vs. ecutwfc

[Eduardo Ariel Menendez Proupin]

As Nicola said, what matters are the energy differences. Please, check that
the forces and stresses are converged. From a practical point of view that
is enough. To be happy, I prefer that the energy also converge. I think the
non convergence is the (frequent) fault of the pseudopotential. If you are
worrried enough, try to generate a new pseudopotential, and chek that is
yet transferible.
Cheers
Eduardo Menendez
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[Pw_forum] starting charge 209.99992, renormalised to 240.00000

[Eduardo Ariel Menendez Proupin]

Hi,
I am calculating for fcc C60 I am puzzled by the message
starting charge  209.2, renormalised to  240.0, th

this is with the pseudopotential C.pbe-mt_gipaw.UPF. The difference between
209 and 240 looks a bit too great, it does not depend on the cutoff.

in contrast, using
with C.pbe-rrkjus.UPF
starting charge  239.99684, renormalised to  240.0

Is this difference of charges a problem? Can this pseudpotential be used for
ground state calculations ?



-- 


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

On leave from: Departamento de Fisica, Facultad de Ciencias, Universidad de
Chile URL: http://fisica.ciencias.uchile.cl/~emenendez

"*Padece, espera y trabaja para gentes que nunca conocer? y que a su vez
padecer?n, esperar?n y trabajar?n para otros, que tampoco ser?n felices,
pues el hombre ans?a siempre una felicidad situada m?s all? de la porci?n
que le es otorgada. Pero la grandeza del hombre est? precisamente en querer
mejorar lo que es. En imponerse Tareas. En el Reino de los Cielos no hay
grandeza que conquistar, puesto que all? todo es jerarqu?a establecida,
inc?gnita despejada, existir sin t?rmino, imposibilidad de sacrificio,
reposo y deleite. Por ello, agobiado de penas y de Tareas, hermoso dentro de
su miseria, capaz de amar en medio de las plagas, el hombre puede hallar su
grandeza, su m?xima medida en el Reino de este Mundo*".
Alejo Carpentier, El reino de este mundo, (1949).

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[Pw_forum] Finding effective mass

[Eduardo Ariel Menendez Proupin]

Dear Padmaja,
Quantum ESPRESSO calculates the band energies by a method different from
k.p. If you want to calculate an effective mass you can use QE to calculate
the band energies in the neighborhood of the desired k-point and then obtain
the effective mass doing numerical derivation.

If you want to get inside he code, you can extract the matrix elements of
the momentum operator and program the calculation of the effective mass.

Due to the non-locality of the pseudopotentials, as well as of the GGA
functionals, I am not sure if the expressions found in the  50's classic
papers (e.g. Kohn) can be applied. In presence of non local
hamiltonian it is not true that p/m=[H,r]/ihbar
 I know that  for optical properties, the momentum operator in the A.p
interaction hamiltonian has to be replaced by a generalized operator. See,
e.g., PRB48, 11789 (1993) and PRB 73, 045112 (2006). Hence, I suspect you
would have to repeat the derivation made in the classic papers, or find
where it is done (and let me know your findings).

Best regards
Eduardo

-- Mensaje reenviado --
From: Padmaja Patnaik 
To: "pw_forum at pwscf.org" 
Date: Tue, 27 Sep 2011 07:24:52 +0100 (BST)
Subject: [Pw_forum] Finding effective mass
Dear All

Is it possible to calculate effective mass using k.p method in quantum
espresso?



-- 


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

On leave from: Departamento de Fisica, Facultad de Ciencias, Universidad de
Chile URL: http://fisica.ciencias.uchile.cl/~emenendez

"*Padece, espera y trabaja para gentes que nunca conocer? y que a su vez
padecer?n, esperar?n y trabajar?n para otros, que tampoco ser?n felices,
pues el hombre ans?a siempre una felicidad situada m?s all? de la porci?n
que le es otorgada. Pero la grandeza del hombre est? precisamente en querer
mejorar lo que es. En imponerse Tareas. En el Reino de los Cielos no hay
grandeza que conquistar, puesto que all? todo es jerarqu?a establecida,
inc?gnita despejada, existir sin t?rmino, imposibilidad de sacrificio,
reposo y deleite. Por ello, agobiado de penas y de Tareas, hermoso dentro de
su miseria, capaz de amar en medio de las plagas, el hombre puede hallar su
grandeza, su m?xima medida en el Reino de este Mundo*".
Alejo Carpentier, El reino de este mundo, (1949).

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[Pw_forum] epsilon.x and scissor shift renormalization of momentum operator

[Eduardo Ariel Menendez Proupin]

Hi all,
Recently a  reviewer has warned me about a problem of the dielectric
function calculation that I performed using the epsilon code, where I
applied the scissor shift (option shift in the input) to correct the
infamous gap problem.  Following the referee's criticism I got to an article
by Rodolfo del Sole and Rafaello Girlanda, PRB 48, 11780 (1993), when a
scissor shift  is applied to correct the LDA underestimation of the
transition energies, the momentum matrix elements  must be
multiplied by (Ec-Ev)/(Ec0-Ev0), (see unnumbered equation after Eq. (15) in
the cited paper) , where Ec0-Ev0 is the LDA transition energy and
Ec-Ev=Ec0-Ev0 +\Delta  ( \Delta is the scissor shift). Equivalently, one can
replace the \omega^2 in the denominator by (\omega-\Delta/\hbar)^2  (Eq. 17
and 19 of the above article) . As shown by del Sole and Girlanda (and
repeated many times in the literature)  this is a simple approximation for
the fact that "exact" transition energies Ec-Ev arise from non-local
self-energy (e.g. from GW) and for non-local one electron hamiltonians the
interaction with an electromagnetivc wabe is not longer A.p.

It is very easy to set this correction in the code epsilon.x, for example ,
in subroutine eps_calc one can change

   etrans = ( et(iband2,ik) -et(iband1,ik) ) * RYTOEV + shift
...
   epsi(:,iw) = epsi(:,iw) + dipole(:,iband1,iband2) *
intersmear * w* &
 RYTOEV**3 * (focc(iband1,ik))/
&
  (( (etrans**2 -w**2 )**2 + intersmear**2 *
w**2 )* etrans )

   epsr(:,iw) = epsr(:,iw) + dipole(:,iband1,iband2) *
RYTOEV**3 * &
 (focc(iband1,ik)) * &
 (etrans**2 - w**2 ) / &
  (( (etrans**2 -w**2 )**2 + intersmear**2 *
w**2 )* etrans )

by the following

   etrans = ( et(iband2,ik) -et(iband1,ik) ) * RYTOEV + shift
   shift_renorm = ( etrans/(etrans-shift) )**2

   epsi(:,iw) = epsi(:,iw) + dipole(:,iband1,iband2)
*shift_renorm* intersmear * w* &
 RYTOEV**3 * (focc(iband1,ik))/
&
  (( (etrans**2 -w**2 )**2 + intersmear**2 *
w**2 )* etrans )

   epsr(:,iw) = epsr(:,iw) + dipole(:,iband1,iband2)
*shift_renorm* RYTOEV**3 * &
 (focc(iband1,ik)) * &
 (etrans**2 - w**2 ) / &
  (( (etrans**2 -w**2 )**2 + intersmear**2 *
w**2 )* etrans )

and similarly in a few other parts of the code.

This is equivalent to replace epsilon_2(omega) by epsilon2(omega-
shift/hbar) , at least for small broadening parameter so that the "delta
function" is sharp  ,  and it corrects automatically the real part of the
dielectric function.

This is valid for LDA, and in principle not valid for GGA, although I
suspect that in practice gives the same results. In fact

I would appreciate a feedback to this comment.

Best regards

-- 


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

On leave from: Departamento de Fisica, Facultad de Ciencias, Universidad de
Chile URL: http://fisica.ciencias.uchile.cl/~emenendez

"*Padece, espera y trabaja para gentes que nunca conocer? y que a su vez
padecer?n, esperar?n y trabajar?n para otros, que tampoco ser?n felices,
pues el hombre ans?a siempre una felicidad situada m?s all? de la porci?n
que le es otorgada. Pero la grandeza del hombre est? precisamente en querer
mejorar lo que es. En imponerse Tareas. En el Reino de los Cielos no hay
grandeza que conquistar, puesto que all? todo es jerarqu?a establecida,
inc?gnita despejada, existir sin t?rmino, imposibilidad de sacrificio,
reposo y deleite. Por ello, agobiado de penas y de Tareas, hermoso dentro de
su miseria, capaz de amar en medio de las plagas, el hombre puede hallar su
grandeza, su m?xima medida en el Reino de este Mundo*".
Alejo Carpentier, El reino de este mundo, (1949).

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[Pw_forum] about raman?

[Eduardo Ariel Menendez Proupin]

Neither do I know if the values are correct, it depends on the units, and
very details.  You should  search for experimental values of Raman cross
sections in ZnO and compare with yur numbers.

However, it is crucial to know what is printed at the output.
Regarding the units, in dynmat.f90 I can read
 !   Raman cross sections are in units of bohr^4/(Ry mass unit)
write (6,'(5x,"Raman cross sections are in A^4/amu units")').
I guess A means Angstrom, but I am not sure that the comment and the write
statement are consisten. Also,  I think that  cross section should have
units of area. In any case, it is quite common to report Raman cross
sections in "arbitrary units" due to experimental difficulties to precisely
determine them.

please, see PRB 54, 7830 (1996) and take a look at dynmat.f90 to see exactly
what is printed on the column Raman. It corresponds to a particular
configuration of incoming and outgoing polarisations and scattering
direction.
Pay attentio to this part of dynmat.f90

   alpha = (raman(1,1,nu) + raman(2,2,nu) + raman(3,3,nu))/3.d0
   beta2 = ( (raman(1,1,nu) - raman(2,2,nu))**2 + &
 (raman(1,1,nu) - raman(3,3,nu))**2 + &
 (raman(2,2,nu) - raman(3,3,nu))**2 + 6.d0 * &
  (raman(1,2,nu)**2 + raman(1,3,nu)**2 + raman(2,3,nu)**2) )/2.d0
   write (6,'(i5,f10.2,2f10.4,f15.4,f10.4)') &
nu, freq, freq*cm1thz, infrared(nu), &
(45.d0*alpha**2 + 7.0d0*beta2)*r1fac, &
 3.d0*beta2/(45.d0*alpha**2 + 4.0d0*beta2)

(45.d0*alpha**2 + 7.0d0*beta2)*r1fac is what is written on column "Raman"

Good luck


-- 


Eduardo Menendez Proupin
Departamento de Qu?mica Fisica Aplicada
Facultad de Ciencias
Universidad Aut?noma de Madrid
Phone: +34 91 497 6706

On leave from: Departamento de Fisica, Facultad de Ciencias, Universidad de
Chile URL: http://fisica.ciencias.uchile.cl/~emenendez

"*Padece, espera y trabaja para gentes que nunca conocer? y que a su vez
padecer?n, esperar?n y trabajar?n para otros, que tampoco ser?n felices,
pues el hombre ans?a siempre una felicidad situada m?s all? de la porci?n
que le es otorgada. Pero la grandeza del hombre est? precisamente en querer
mejorar lo que es. En imponerse Tareas. En el Reino de los Cielos no hay
grandeza que conquistar, puesto que all? todo es jerarqu?a establecida,
inc?gnita despejada, existir sin t?rmino, imposibilidad de sacrificio,
reposo y deleite. Por ello, agobiado de penas y de Tareas, hermoso dentro de
su miseria, capaz de amar en medio de las plagas, el hombre puede hallar su
grandeza, su m?xima medida en el Reino de este Mundo*".
Alejo Carpentier, El reino de este mundo, (1949).

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[Pw_forum] Raman on DFT-false-metals

[Eduardo Ariel Menendez Proupin]

Hi,
I would like to calculate a Raman spectrum with PHONON for an insulator that
is metallic in LDA and GGA. Is it possible to introduce easily a scissors
shift to open the gap and allow the Raman calculation?

-- 


Eduardo Menendez Proupin
Departamento de Qu?mica Fisica Aplicada
Facultad de Ciencias
Universidad Aut?noma de Madrid
Phone: +34 91 497 6706

On leave from: Departamento de Fisica, Facultad de Ciencias, Universidad de
Chile URL: http://fisica.ciencias.uchile.cl/~emenendez

"*Padece, espera y trabaja para gentes que nunca conocer? y que a su vez
padecer?n, esperar?n y trabajar?n para otros, que tampoco ser?n felices,
pues el hombre ans?a siempre una felicidad situada m?s all? de la porci?n
que le es otorgada. Pero la grandeza del hombre est? precisamente en querer
mejorar lo que es. En imponerse Tareas. En el Reino de los Cielos no hay
grandeza que conquistar, puesto que all? todo es jerarqu?a establecida,
inc?gnita despejada, existir sin t?rmino, imposibilidad de sacrificio,
reposo y deleite. Por ello, agobiado de penas y de Tareas, hermoso dentro de
su miseria, capaz de amar en medio de las plagas, el hombre puede hallar su
grandeza, su m?xima medida en el Reino de este Mundo*".
Alejo Carpentier, El reino de este mundo, (1949).

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[Pw_forum] Why dielectric function of only interband contribution has the features of intraband?

[Eduardo Ariel Menendez Proupin]

Hi Gui-Bin

To avoid intraband contribution it is not enough to use intrasmear=0, you
also need to set occupations='fixed' in the PW calculations, at least for
the nscf one. The following reads in the manual of epsilon.

\emph{intrasmear} is the broadening parameter for the intraband, i.e. metal
Drude like term (again in eV),
the intraband contribution is calculated only if a Gaussian broadening or
tetrahedron method it's been
applied in PW calculations.


On the other hand, it seems from the epsi plot,  that the Wien calculation
considers automatically a larger number of bands. You must set manually the
parameter nbnd in the  nscf calculations, and increase it until the
dielectric function is converged. Check specially the convergence of epsr.
nbnd determine the number of transitions (the peaks) observed in epsri. High
energy transitions contribute in shifting the low energy values of epsr, as
you can see looking at the Kramers-Kronig relations.

Best wishes
Eduardo



>
> "
>>
>> Today's Topics:
>>
>>   1. Why dielectric function of only interband contribution has
>>  the features of intraband? (gbliu)
>>
>>
>> -- Mensaje reenviado --
>> From: gbliu 
>> To: PWSCF Forum 
>> Date: Wed, 13 Jul 2011 01:04:28 +0800
>> Subject: [Pw_forum] Why dielectric function of only interband contribution
>> has the features of intraband?
>> **
>> Dear PW users,
>>
>> I calculated the dielectric function of (3,3) Carbon nanotube (CNT).
>> However, the results for only interband contribution has the features of
>> intraband contribution! Attached figures show the results of parallel
>> polarization compared with wien2k (a FP-LAPW software). Using "intrasmear =
>> 0", the direct result of epsi.dat should gives out only interband
>> contributions, while epsr.dat is added by  "omega_p^2/omega^2" to get the
>> interband contributions only.  And omega_p is obtained as *3.5679eV* by
>> fitting the difference of data with intrasmear=0 and intrasmear=0.1 using
>> Drude model  "\epsilon_{intra}=1- omega_p^2/(omega^2+i*omega*intrasmear)".
>> How to understand this?
>>
>> Another problem is, fitted omega_p = 3.5679eV. This is far from the
>> result given by wien2k, 24.5eV!  Which one is more reasonable? And why?
>>
>>Can anyone help me?  Thanks in advance!
>>
>> Best wishes,
>>
>> Liu Gui-Bin
>> Dept. of Physics, The University of Hong Kong
>>
>> ---input file for epsilon.x--
>>  
>>outdir='./work'
>>prefix='cnt33'
>>calculation='eps'
>> /
>> _grid
>>smeartype='gauss'
>>intersmear=0.1d0
>>intrasmear=0d0
>>wmax=30d0
>>wmin=0d0
>>nw=2000
>>shift=0d0
>> /
>> --
>>
>> ___
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>>
>> http://www.democritos.it/mailman/listinfo/pw_forum
>>
>>
>
>
> --
>
>
> Eduardo Menendez Proupin
> Departamento de Qu?mica Fisica Aplicada
> Facultad de Ciencias
> Universidad Aut?noma de Madrid
> Phone: +34 91 497 6706
>
> On leave from: Departamento de Fisica, Facultad de Ciencias, Universidad de
> Chile URL: http://fisica.ciencias.uchile.cl/~emenendez
>
> "*Padece, espera y trabaja para gentes que nunca conocer? y que a su vez
> padecer?n, esperar?n y trabajar?n para otros, que tampoco ser?n felices,
> pues el hombre ans?a siempre una felicidad situada m?s all? de la porci?n
> que le es otorgada. Pero la grandeza del hombre est? precisamente en querer
> mejorar lo que es. En imponerse Tareas. En el Reino de los Cielos no hay
> grandeza que conquistar, puesto que all? todo es jerarqu?a establecida,
> inc?gnita despejada, existir sin t?rmino, imposibilidad de sacrificio,
> reposo y deleite. Por ello, agobiado de penas y de Tareas, hermoso dentro de
> su miseria, capaz de amar en medio de las plagas, el hombre puede hallar su
> grandeza, su m?xima medida en el Reino de este Mundo*".
> Alejo Carpentier, El reino de este mundo, (1949).
>
> Translate from spanish here
> http://translate.google.com/?hl==UTF-8==es=en
>
>


-- 


Eduardo Menendez Proupin
Departamento de Qu?mica Fisica Aplicada
Facultad de Ciencias
Universidad Aut?noma de Madrid
Phone: +34 91 497 6706

On leave from: Departamento de Fisica, Facultad de Ciencias, Universidad de
Chile URL: http://fisica.ciencias.uchile.cl/~emenendez

"*Padece, espera y trabaja para gentes que nunca conocer? y que a su vez
padecer?n, esperar?n y trabajar?n para otros, que tampoco ser?n felices,
pues el hombre ans?a siempre una felicidad situada m?s all? de la porci?n
que le es otorgada. Pero la grandeza del hombre est? precisamente en querer
mejorar lo que es. En imponerse Tareas. En el Reino de los Cielos no hay
grandeza que conquistar, puesto que all? todo es jerarqu?a establecida,
inc?gnita despejada, existir sin t?rmino, imposibilidad de sacrificio,
reposo y deleite. Por ello, agobiado de penas y de Tareas, hermoso dentro de
su miseria, capaz de amar en medio de las plagas, el 

[Pw_forum] Pw_forum Digest, Vol 49, Issue 33

[Eduardo Ariel Menendez Proupin]

Hi Gui-Bin

To avoid intraband contribution it is not enough to use intrasmear=0, you
also need to set occupations='fixed' in the PW calculations, at least for
the nscf one. The following reads in the manual of epsilon.

\emph{intrasmear} is the broadening parameter for the intraband, i.e. metal
Drude like term (again in eV),
the intraband contribution is calculated only if a Gaussian broadening or
tetrahedron method it's been
applied in PW calculations.


On the other hand, it seems from the epsi plot,  that the Wien calculation
considers automatically a larger number of bands. You must set manually the
parameter nbnd in the  nscf calculations, and increase it until the
dielectric function is converged. Check specially the convergence of epsr.
nbnd determine the number of transitions (the peaks) observed in epsri. High
energy transitions contribute in shifting the low energy values of epsr, as
you can see looking at the Kramers-Kronig relations.

Best wishes
Eduardo


"
>
> Today's Topics:
>
>   1. Why dielectric function of only interband contribution has
>  the features of intraband? (gbliu)
>
>
> -- Mensaje reenviado --
> From: gbliu 
> To: PWSCF Forum 
> Date: Wed, 13 Jul 2011 01:04:28 +0800
> Subject: [Pw_forum] Why dielectric function of only interband contribution
> has the features of intraband?
> **
> Dear PW users,
>
> I calculated the dielectric function of (3,3) Carbon nanotube (CNT).
> However, the results for only interband contribution has the features of
> intraband contribution! Attached figures show the results of parallel
> polarization compared with wien2k (a FP-LAPW software). Using "intrasmear =
> 0", the direct result of epsi.dat should gives out only interband
> contributions, while epsr.dat is added by  "omega_p^2/omega^2" to get the
> interband contributions only.  And omega_p is obtained as *3.5679eV* by
> fitting the difference of data with intrasmear=0 and intrasmear=0.1 using
> Drude model  "\epsilon_{intra}=1- omega_p^2/(omega^2+i*omega*intrasmear)".
> How to understand this?
>
> Another problem is, fitted omega_p = 3.5679eV. This is far from the
> result given by wien2k, 24.5eV!  Which one is more reasonable? And why?
>
>Can anyone help me?  Thanks in advance!
>
> Best wishes,
>
> Liu Gui-Bin
> Dept. of Physics, The University of Hong Kong
>
> ---input file for epsilon.x--
>  
>outdir='./work'
>prefix='cnt33'
>calculation='eps'
> /
> _grid
>smeartype='gauss'
>intersmear=0.1d0
>intrasmear=0d0
>wmax=30d0
>wmin=0d0
>nw=2000
>shift=0d0
> /
> --
>
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>


-- 


Eduardo Menendez Proupin
Departamento de Qu?mica Fisica Aplicada
Facultad de Ciencias
Universidad Aut?noma de Madrid
Phone: +34 91 497 6706

On leave from: Departamento de Fisica, Facultad de Ciencias, Universidad de
Chile URL: http://fisica.ciencias.uchile.cl/~emenendez

"*Padece, espera y trabaja para gentes que nunca conocer? y que a su vez
padecer?n, esperar?n y trabajar?n para otros, que tampoco ser?n felices,
pues el hombre ans?a siempre una felicidad situada m?s all? de la porci?n
que le es otorgada. Pero la grandeza del hombre est? precisamente en querer
mejorar lo que es. En imponerse Tareas. En el Reino de los Cielos no hay
grandeza que conquistar, puesto que all? todo es jerarqu?a establecida,
inc?gnita despejada, existir sin t?rmino, imposibilidad de sacrificio,
reposo y deleite. Por ello, agobiado de penas y de Tareas, hermoso dentro de
su miseria, capaz de amar en medio de las plagas, el hombre puede hallar su
grandeza, su m?xima medida en el Reino de este Mundo*".
Alejo Carpentier, El reino de este mundo, (1949).

Translate from spanish here
http://translate.google.com/?hl==UTF-8==es=en
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[Pw_forum] total energy with GW

[Eduardo Ariel Menendez Proupin]

Hi,
I wish to know if the GWW code calculates total energies of the ground
state, such that can be used to obtain defect formation energies or elastic
constants.
If not GWW, is there any code with that capability?

-- 


Eduardo Menendez
Departamento de Fisica
Facultad de Ciencias
Universidad de Chile
Phone: (56)(2)9787439
URL: http://fisica.ciencias.uchile.cl/~emenendez
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[Pw_forum] LO-TO splitting in dynmat.x

[Eduardo Ariel Menendez Proupin]

Just to add a reference, an analysis of the polaritons in non cubic crystals
can be found in this article.

R. Loudon, Advances in Physics, 2001, Vol. 50, No. 7, 813-864



This article was originall y published in Advances in Physics, volume 13,
1964 . It attracted 1147 citations by October 2001, and is ranked 2 in the
index of articles attracting more than 100 citations.

-- 


Eduardo Menendez
Departamento de Fisica
Facultad de Ciencias
Universidad de Chile
Phone: (56)(2)9787439
URL: http://fisica.ciencias.uchile.cl/~emenendez
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[Pw_forum] About band plot

[Eduardo Ariel Menendez Proupin]

Hi Padmaja,

Please, study the example05
example05:
This example shows how to use pw.x and postprocessing codes to
make a contour plot in the [110] plane of the charge density for
Si, and to plot the band structure of Si.


The code is not aware of the name of the symmetry points (as far as I know).
You should. If you are studying a cubic material, you can find the names and
coordinates of the high symmetry points in a solid state physics or
semiconductor textbook or in one of the hundreds of articles on band
calculations.
If your crystal  has a not so usual lattice, you can use the names defined
in the book
The Mathematical Theory of Symmetry in Solids: Representation Theory for
Point Groups and Space Groups
[image: Cubierta
delantera]
Christopher 
Bradley,
Arthur 
Cracknell

http://books.google.com/books?id=lMdNv_wbu2IC=frontcover=bradley+symmetry=bl=Nle4sptJFT=68EASNmZCFBcppbWHbe3_1gSq0c=es=X5W5TYDRBIfe0QGLsaTgDw=X=book_result=result=1=0CBYQ6AEwAA#v=onepage=false

or define your own names, i.e, A,B,C, ... , specifying the coordinates of
the points.

Personally I do not like the postscript file generated with plot bands. I
generally use the data file, and make my band diagram with gnuplot (a heavy
of work). If you just want to add the letters, you may edit the postcript
file.

pstoedit - f xfig file.ps file.fig

edit it with xfig, and export to EPS.


-- Mensaje reenviado --
From: Padmaja Patnaik 
To: pw_forum at pwscf.org
Date: Thu, 28 Apr 2011 05:34:15 +0100 (BST)
Subject: [Pw_forum] About band plot
Hi All
I had put this query last tuesday but didnt get any response. Thats why
asking it again. While plotting band structure, in the output ps file the
code doesn't mention the high symmetry points Gamma, K, L etc. along the X
axis. How to do that?

Thanks in advance

Padmaja Patnaik
Research Scholar
Dept of Physics
IIT Bombay
Mumbai, India

-- 


Eduardo Menendez
Departamento de Fisica
Facultad de Ciencias
Universidad de Chile
Phone: (56)(2)9787439
URL: http://fisica.ciencias.uchile.cl/~emenendez
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[Pw_forum] k-point

[Eduardo Ariel Menendez Proupin]

Abolore,I do not know any standard set of k-points for monoclinic system.
Chose the points that you think are representative, e.g, half of every
reciprocal lattice vectors, and path between them. I suggest you first
calculate the DOS, locate the points of the valence band maximum and
conduction band minimum, and be sure that they are in included in the
k-points path of the band diagram. Some maxima of the DOS are related to
lines were some bands are flat. Assure that these lines are included in the
path. A good method is to explain the DOS features with the band diagram. If
some feature cannot be explained with the band diagram, investigate the
reason.
It is like choosing 4 or 5 cities to visit in a tour by Italy, with a good
choice you will get some idea about the country and you can explain some of
the history from the monuments and museum, or the cafes that you visited.
As there is no convention for the letters that design the k-points in a
monoclinic crystal, PLEASE, indicate the coordinates of the points in the
figure caption or in the text.  [Pw_forum] k-point
*Abolore Musari* abmus007 at gmail.com

*Mon Apr 25 23:57:21 CEST 2011*

   - Previous message: [Pw_forum] why are there two Fermi energies?
   
   - *Messages sorted by:* [ date
]
[
   thread 
]
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   author 
]

--

Dear QE User,
I am having a problem as regard (k-point)
I am working on monoclinic system, and am using xcrysden to get my k-point
and my question is how do I know the special points (k-points) to select
from the Brillion zone in the xcrysden k path selection?

Thanks in anticipation of your favourable assistance

Musari Abolore
Dept Of Physics
University of Agriculture, Abeokuta
Nigeria
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-- 


Eduardo Menendez
Departamento de Fisica
Facultad de Ciencias
Universidad de Chile
Phone: (56)(2)9787439
URL: http://fisica.ciencias.uchile.cl/~emenendez
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[Pw_forum] why are there two Fermi energies?

[Eduardo Ariel Menendez Proupin]

I am sorry, Murphy's law has just acted. Find the figures here

http://www.gnm.cl/emenendez/uploads/Temp/impurity-energy.eps
http://www.gnm.cl/emenendez/uploads/Temp/impurity-fermi.eps

Finally, I plotted Energy vs magnetization. Indeed, I have a minimum
at total magnetization equal 1. However, the
behavior is strange. The plot of E vs M is linear at each side of the

minimum, with a kink at M=1. Should'n it be rather like a parable ?
Please, see the plots here (above)




Eduardo Menendez
Departamento de Fisica
Facultad de Ciencias
Universidad de Chile
Phone: (56)(2)9787439
URL: http://fisica.ciencias.uchile.cl/~emenendez
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[Pw_forum] why are there two Fermi energies?

[Eduardo Ariel Menendez Proupin]

Hi Paolo,



>>* the restriction is in this code
*>>*  if ( ((MOD(NINT(tot_magnetization_),2) == 0) .and. (MOD
*>>* (NINT(nelec_),2)==1)) .or.   &
*>>*   ((MOD(NINT(tot_magnetization_),2) == 1) .and. (MOD
*>>* (NINT(nelec_),2)==0))  ) &
*>>*   CALL errore(' set_nelup_neldw
*>>* ',  &
*>>*  'tot_magnetization is inconsistent with total number
*>>* of electrons ', 2 )
*
>in the new version, this restriction (now a warning, no longer an
>error) applies only if the
>number of electrons is integer and if the magnetization is integer.
>For noninteger charge
>or magnetization, it doesn't make sense.


In fact, increasing the k-point sampling, the unrestricted calculation
converges towards
0 total magnetization, with a lower energy than magnetization =1, but
setting tot_magnetization=0, or 0.1, 0.2, etc, stops due to the above
instruction in versiom 4.2.1.
This is one more reason to change to the newest version.


*You stated something in a previous post*

>The "two Fermi energies" of the constrained
>case need not to be exactly the same as the (single)
>Fermi energy of the unconstrained case, as long as the
>occupancies for spin-up and spin-down are the same in the
>two cases.

Why not? Aren't the the energies and occupations related by
the Fermi-Dirac function? I verified that the occupations are the
same, then I do not understand
why it is possible with different Fermi energies.
These are my KS energies and the occupations, using degauss=0.00019. I
think the differences are just numerical noise.

1)  tot_magnetization unset
 the Fermi energy is 6.1614 ev
!total energy  =-502.92571441 Ry total
magnetization   = 1.00 Bohr mag/cell
up: 4.8593   4.8594   5.2221   5.2221   5.   6.1335   6.1336   6.1338


  1.   1.   1.   1.   1.   1.   1.   1.

dw: 4.8796   4.8796   5.2528   5.2530   5.2531   6.1595   6.1596   6.1596
  1.   1.   1.   1.   1.   0.6709   0.6661   0.6631

2) tot_magnetization=1
 the spin up/dw Fermi energies are 6.38536.1614 ev
!total energy  =-502.92571439 Ry total
magnetization   = 1.00 Bohr mag/cell
up: 4.8593   4.8594   5.2221   5.2221   5.2221   6.1335   6.1337   6.1338


  1.   1.   1.   1.   1.   1.   1.   1.

dw: 4.8796   4.8796   5.2528   5.2530   5.2531   6.1595   6.1596   6.1596
  1.   1.   1.   1.   1.   0.6715   0.6660   0.6625

Finally, I plotted Energy vs magnetization. Indeed, I have a minimum
at total magnetization equal 1. However, the
behavior is strange. The plot of E vs M is linear at each side of the
minimum, with a kink at M=1. Should'n it be rather like a parable ?
Please, see the plots here

http://www.gnm.cl/emenendez/pmwiki.php/Temp/Plots?action=upload=impurity-energy.eps

http://www.gnm.cl/emenendez/pmwiki.php/Temp/Plots?action=upload=impurity-fermi.eps


This was using gamma point fo sample the Brillouin zone. That is not
converged, using a 3x3x3 grid the lowest energy seems to be
for null magnetization (I am doing more calculations). Maybe the kinks
are due to insufficient Brillouin zone sampling.



Best regards


-- 


Eduardo Menendez
Departamento de Fisica
Facultad de Ciencias
Universidad de Chile
Phone: (56)(2)9787439
URL: http://fisica.ciencias.uchile.cl/~emenendez
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[Pw_forum] why are there two Fermi energies?

[Eduardo Ariel Menendez Proupin]

Alexander
>Shift in eigenvalues can be seen as produced by external magnetic fiels (a
>Zeeman term) then the state with two different Fermi energies may be
thought of a >true ground state with only one Fermi level but in the
presence of this stabilizing >magnetic field proportional to the difference
in Fermi energies.

Why not a true ground state with one Fermi level and an external plus an
internal magnetic field that is due to the spin polarization, causes a shift
ib the KS energies, and is self adjusted to have  thermodynamical
equilibrium, i.e., one Fermi level.

Fixing total magnetization would be equivalent to setting and external
magnetic field, and shifting the eigenvalues would be equivalent to an
internal magnetic field.

By the way, what are the physical restrictions to the values of
tot_magnetization ?
In my system, having 255 electrons, I can fix tehe tot_magnetization  to
0.5, 0.7, 1, 1.2, 1.3, 3.0

For 1.5 <= tot_magnetization<2.5 I get error

 from  set_nelup_neldw  : error # 2
 tot_magnetization is inconsistent with total number of electrons

well I see the restriction is in this piece of code
the restriction is in this code
 if ( ((MOD(NINT(tot_magnetization_),2) == 0) .and.
(MOD(NINT(nelec_),2)==1)) .or.   &
  ((MOD(NINT(tot_magnetization_),2) == 1) .and.
(MOD(NINT(nelec_),2)==0))  ) &
  CALL errore(' set_nelup_neldw ',  &
 'tot_magnetization is inconsistent with total number of
electrons ', 2 )

I understand that with integer occupations the magnetization could have only
even or odd integer values values depending on the number of electrons. But,
with smearing, allowing real occupations, what is the problem with having
even magnetization with odd number of electrons or close real values?


Best wishes

-- 


Eduardo Menendez
Departamento de Fisica
Facultad de Ciencias
Universidad de Chile
Phone: (56)(2)9787439
URL: http://fisica.ciencias.uchile.cl/~emenendez
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[Pw_forum] why are there two Fermi energies?

[Eduardo Ariel Menendez Proupin]

Hi,
Let me clarify that I found no difference between version 4.2.1 and others.
I have used only 4.2.1.

I suspected that the Fermi level was a way to control the occupations.
However, using different fermi levels will produce different charge
densities because the occupation numbers will be different. If both types of
calculations produce the same energy, then the ground state is degenerate,
but the one with two Fermi energies seems incompatible with thermodynamics.
I used Fermi smearing, by the way.

I am committed to teaching duties today. Thanks for your answers, and I will
come back tomorrow, or maybe late today, and I will look at the occupations
using verbosity = .true.

Mathematically it seems logical that to control  the number of electron (one
degree of freedom) one needs one parameter, which is the Fermi level. To
control an additional degree of freedom, the magnetization, one needs an
additional parameter, then it is reasonable to use two Fermi levels or an
equivalent set of two parameters.
For example, one could define a single Fermi level and apply a shift to the
spin down eigenvalues. This needs a physical interpretation, as well as
having to Fermi levels.

Moreover, reversing the reasoning, I wonder why or how one gets the same
number of electrons and magnetization using only one parameter (Fermi level)
in the case of not using tot_magnetization. Is it a hazard or is there a
trick that bias the calculation to the integer magnetization?

Best regards
-- 


Eduardo Menendez
Departamento de Fisica
Facultad de Ciencias
Universidad de Chile
Phone: (56)(2)9787439
URL: http://fisica.ciencias.uchile.cl/~emenendez
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[Pw_forum] new bfgs: strange behavior doing vc-relax

[Eduardo Ariel Menendez Proupin]

>Dear Dr. Giannozzi,
>thank you for the answer! I could find it myself looking in the output file
a bit >more carefully...
>One thing, which is somehow contrary to my expectations, is that the final
scf >energy is higher
>than the last one from vc-relax. Could you, please, elaborate a bit on the
>matter?

Dear Maxim,

I followed this discussion with interest, and thanks to that I learned about
the new scf calculation with final G-vectors. Concerning your last question,

the energy is higher because the vc-relaxed energy was optimized for a
different basis set, than the final scf calculation (different G-vectors).
Hence, the energy of the final scf calculation is is made for a structure
that is slightly out of the minimum for the new basis set. Remember than the
G-vectors used in a scf calculation are all the reciprocal lattice vectors
 contained in a sphere that has a radius determined by the cutoff. These
vectors are selected at the first step of the vc-relaxation. When the unit
cell gets deformed, the G-vectors vary accordingly, and the region that the
G-vectors occupy is a deformation from the initial sphere, maybe an
elipsoid. When the vc-relax stops, the final scf calculation takes the
G-vectors contained inside a sphere. Hence, some of the old G-vectors that
were in the border of the deformed sphere may be eliminated, and some that
were absent are now included.
If you had used an (impossible) infinite cutoff, the basis set would be
complete in both cases (G-vectors contained in an infinite sphere or in an
infinite elipsoid) and there would be no difference. Usually, I repeat the
vc-relax procedure starting 'from_scratch' with the last structure
(coordinates and lattice vectors) in the new input file, until the vc-relax
procedure performs only one step. In this case there is no difference. If it
never happens that vc-relax stops at the first step, then I increase the
cutoffs. In your case, the energy difference of 0.5 mRy may be small enough
and do not need to do that. It depends on the property that you want. E.g.,
if you are interested in elastic properties,  you may need that the minimal
energy structure also gives a stress tensor below 0.1 kbar or so. If you
cannot get it, increase the cutoff.

The following link may help

http://www.quantum-espresso.org/wiki/index.php/Methodological_Background#Stress

Best regards

-- 


Eduardo Menendez
Departamento de Fisica
Facultad de Ciencias
Universidad de Chile
Phone: (56)(2)9787439
URL: http://fisica.ciencias.uchile.cl/~emenendez
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[Pw_forum] npool in nscf calculation

[Eduardo Ariel Menendez Proupin]

Hi,
Does it makes sense to use npool in a non self consistent calculation (for
DOS) with pw.x ?


-- 


Eduardo Menendez
Departamento de Fisica
Facultad de Ciencias
Universidad de Chile
Phone: (56)(2)9787439
URL: http://fisica.ciencias.uchile.cl/~emenendez
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[Pw_forum] how to get the Eigendisplacements by ph.x

[Eduardo Ariel Menendez Proupin]

> want to know how to get the Eigendisplacements  by ph.x . what i found in
the dyn_G file is just "Diagonalizing the dynamical matrix"

Use dynmat.x after ph.x.

In the source file you will find the keywords explained
PH/dynmat.f90

Good luck,
-- 


Eduardo Menendez
Departamento de Fisica
Facultad de Ciencias
Universidad de Chile
Phone: (56)(2)9787439
URL: http://fisica.ciencias.uchile.cl/~emenendez
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[Pw_forum] Problems with electrostatic corrections (Makov-Payne or density counter charge) for aperiodic systems in 4.2 version

[Eduardo Ariel Menendez Proupin]

2) Why the DCC correction is disabled in version 4.2? Indeed when setting
asume_isolated = 'dcc' and  input parameters to their default  values, I
obtain an error message "DCC correction is disabled". Looking in the
PW/input.f90 subroutine, one found that the dcc correction is disabled by an
immediate call to errore subroutine.

I guess some bug was discovered ans is not fixed yet.
I take the occasion to ask if the DCC correction has been or will be
available for slab calculations.
-- 


Eduardo Menendez
Departamento de Fisica
Facultad de Ciencias
Universidad de Chile
Phone: (56)(2)9787439
URL: http://fisica.ciencias.uchile.cl/~emenendez
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[Pw_forum] Pw_forum] Shift of Energy

[Eduardo Ariel Menendez Proupin]

Hi Pari,

I think you should read this book.

Density functional theory: a practical introduction  David S. Sholl,Janice
A. Steckel

http://books.google.com/books?id=Q8iNmtswLWYC=frontcover=Janice+Steckel++Sholl=bl=BBHL-SfWoi=HLO4FmyafC7bKh22C0Qf1353Lug=es=KfaZTaajFImatwfQ95iVDA=X=book_result=result=1=0CBcQ6AEwAA#v=onepage=false

72/8
9.
694/9
77.
694/9-76.276
.8351
So, where does the 7 Ry difference arise?

Best regards

Eduardo Menendez
Departamento de Fisica
Facultad de Ciencias
Universidad de Chile
Phone: (56)(2)9787439
URL: http://fisica.ciencias.uchile.cl/~emenendez


>
>
> -- Mensaje reenviado --
> From: pari shok 
> To: pw_forum at pwscf.org
> Date: Mon, 4 Apr 2011 10:32:53 -0400
> Subject: [Pw_forum] Shift of Energy
> 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.
> 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.
> 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
> any relation between scaling the cell and cut off energy.
> As you know, I need to find a reference for my further calculations.
> I really really appreciate your help.
> Yours
> P Shok
>
>
> --
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[Pw_forum] Wrong ELF values

[Eduardo Ariel Menendez Proupin]

*
Hi,
0
z

what happens is that 1 and 0.5 are values with interpretation, and values
close to 0 not, as far (rather near) as I know.

Paolo Giannozzi* giannozz at democritos.it

*Tue Feb 8 20:43:44 CET 2011*


   - Previous message: [Pw_forum] Wrong ELF
values
   - Next message: [Pw_forum] Why does dos.x look for evc.dat
files?
   - *Messages sorted by:* [ date
]
[ thread 
]
[ subject 
]
[ author 
]

--

On Feb 8, 2011, at 18:42 , Claudia Loyola wrote:

>* the problem is that the ELF values are between -0.2092 and 1.2504*>* for one 
>case and for the others is like the same, and not between 0*>* and 1 as the 
>theory goes. I do not understand what I am doing wrong...*
maybe nothing: there have been other reports of funny results with elf.
In 
particular:http://www.democritos.it/pipermail/pw_forum/2010-October/018460.html
So, who is right: 0

[Pw_forum] why don't I get an integer magnetization in a finite system

[Eduardo Ariel Menendez Proupin]

Hi,
I am making calculations for a nanocrystal, isolated system in a supercell,
only gamma point. I have 10 angstrom separation between a nanocrystal border
and the border of the closest image.
 I am a bit surprised to obtain a non integer value of the total
magnetization.

total energy  =   -9085.20537799 Ry
 Harris-Foulkes estimate   =   -9085.20537567 Ry
 estimated scf accuracy<   0.1138 Ry

 total magnetization   = 2.79 Bohr mag/cell
 absolute magnetization= 3.11 Bohr mag/cell

There is not SCF convergence yet, but the restart is waiting in a queue. I
think that the magnetization should be integer.
Should be?
In this case, with an even number of electrons, it should be 0, 2, 4, or 2N.
The reason for getting a non integer magnetization may be
a) supercell not large enough
b) smearing.  occupations = 'smearing', smearing = 'cold', degauss = 0.02,
c) other?

And the solution is
a) Larger supercell
b) fixed occupation, but not if the system is metallic
c) tot_magnetization = 2, ! or any even numbe
d) other

Thanks for the help

Best regards




Eduardo Menendez
Departamento de Fisica
Facultad de Ciencias
Universidad de Chile
Phone: (56)(2)9787439
URL: 
http://fisica.ciencias.uchile.cl/~emenendez
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[Pw_forum] Restarting nscf calculations

[Eduardo Ariel Menendez Proupin]

Hi all,

I need to do a PW nscf calculation with many k-points, so many that the wave
functions files fill the hard disk. I think the only way to avoid filling
the hard disk is using disk_io='none' . However, I need to do a few
restarts, because the queue system does not allows such long calculation at
once.

However, when I restart, the calculation begin again by the first k-point.
(I checked that if disk_io='default', the calculation restarts by the first
non computed k-point).
I assume that in order to compute the DOS, the wavefunctions are not needed,
just the energies and weights are needed. Hence, I wonder if  this behaviour
is  a bug or if this is the intended procedure.

The version of espresso is 4.0.4.

Thanks

Eduardo


-- 


Eduardo Menendez
Departamento de Fisica
Facultad de Ciencias
Universidad de Chile
Phone: (56)(2)9787439
URL: http://fisica.ciencias.uchile.cl/~emenendez
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[Pw_forum] PDOS for P symmetry lacking in Ni

[Eduardo Ariel Menendez Proupin]

Hi Gabriele,
Thank you for your comments.
I think that better than adding new capabilities to the ld1 program, and a
new "opportunity" to  users to curse pseudopotentials, it is easier to add
to projwfc.x the capability to project onto a Slater or Gaussian orbital
that the user can define giving a covalent or ionic radius. I know a popular
code that uses just a constant function up to a given radius.

Have a nice weekend
Eduardo

-- 


Eduardo Menendez
Departamento de Fisica
Facultad de Ciencias
Universidad de Chile
Phone: (56)(2)9787439
URL: http://fisica.ciencias.uchile.cl/~emenendez

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[Pw_forum] OPTIONAL VARIABLES FOR RAMAN

[Eduardo Ariel Menendez Proupin]

Hi, Where can I read the meaning of these options of the PHONON code ?
   ///---
  OPTIONAL VARIABLES FOR RAMAN:

  +
  Variable:   eth_rps

  Type:   REAL
  Default:1.0d-9
  Description:Threshold for calculation of  Pc R |psi>.
  +

  +
  Variable:   eth_ns

  Type:   REAL
  Default:1.0e-12
  Description:Threshold for non-scf wavefunction calculation.
  +

  +
  Variable:   dek

  Type:   REAL
  Default:1.0e-3
  Description:Delta_xk used for wavefunction derivation wrt k.

-- 


Eduardo Menendez
Departamento de Fisica
Facultad de Ciencias
Universidad de Chile
Phone: (56)(2)9787439
URL: http://fisica.ciencias.uchile.cl/~emenendez

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[Pw_forum] PDOS for P symmetry lacking in Ni

[Eduardo Ariel Menendez Proupin]

Hi,
I am doing a tutorial example of calculation of the projected DOS in Ni. It
produces the PDOS projected on S and D states, but not on P.
There are no bound P valence states in nickel. Is that the cause for not
having a P partial DOS?

States with P-symmetry component may be present in an empty band. Is there
an option to produce the P-PDOS?


Support information:
this is from the help file INPUT_PROJWFC.txt

  In the collinear case and the non-collinear, non spin-orbit case
  projected DOS are written to file "filpdos".pdos_atm#N(X)_wfc#M(l),
  where N = atom number , X = atom symbol, M = wfc number, l=s,p,d,f
  (one file per atomic wavefunction found in the pseudopotential file)


this is the head of the pseudopotential

Generated using Andrea Dal Corso code (rrkj3)

Author: Andrea Dal Corso   Generation date: unknown

Info:  Ni

1The Pseudo was generated with a Scalar-Relativistic Calculation
  1.700E+00Local Potential cutoff radius
nl pn  l   occ   RcutRcut US E pseu
4S  1  0  1.00  2.000  2.500  0.000
4S  1  0  0.00  2.000  2.500  0.000
4P  2  1  0.00  2.400  2.600  0.000
4P  2  1  0.00  2.400  2.600  0.000
3D  3  2  9.00  1.600  2.500  0.000
3D  3  2  0.00  1.600  2.500  0.000



Thanks
-- 


Eduardo Menendez
Departamento de Fisica
Facultad de Ciencias
Universidad de Chile
Phone: (56)(2)9787439
URL: http://fisica.ciencias.uchile.cl/~emenendez

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[Pw_forum] distributed computing

[Eduardo Ariel Menendez Proupin]

Wonderfull!! It looks like the silicon calculation of example1.

Can anyone provide the historical reference of the date and kind of computer
that hosted the original calculation?

> bit of hubris today - I got QE running on my cell phone...

> http://mml.materials.ox.ac.uk/Main/QEN900

-- 


Eduardo Menendez
Departamento de Fisica
Facultad de Ciencias
Universidad de Chile
Phone: (56)(2)9787439
URL: http://fisica.ciencias.uchile.cl/~emenendez

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[Pw_forum] GDIS

[Eduardo Ariel Menendez Proupin]

Hi Koa,
I use GDIS to visualize and modify some structures, and to produce  images.
GDIS can read XYZ files, and a number of other formats, but not a format of
Quantum ESPRESSO. GDIS is the preferred interface of GULP and have
capabilities for other packages, like SIESTA. It would be nice to have, and
it may be easy to write, a script to transfom from and for PWSCF format. One
advantage for Debian and Ubuntu users is that it is included in the
distribution, hence apt-get install gdis, and it gets installs in your box.
If you do not use GULP, or SIESTA, or other supported code, you may live
without it. For my taste, the images of XCRYSDEN are prettier. GDIS has
certain capabilities to generate supercells and surfaces, what is call, a
builder. XCRYSDEN can do the same, but only if you also have CRYSTAL.


Regards

-- 


Eduardo Menendez
Departamento de Fisica
Facultad de Ciencias
Universidad de Chile
Phone: (56)(2)9787439
URL: http://fisica.ciencias.uchile.cl/~emenendez

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[Pw_forum] 'Tetrahedra' and 'scf'

[Eduardo Ariel Menendez Proupin]

Hi,
I think it would be helpful and appreciated to keep scf with tetrahedron
method, at least to make accurate SCF calculations.

It would also be fine if the program just don't calculate the forces when
the tetrahedron methos is chosen, and give a  warning for the beginners
"forces are not variational. Use other smearing method"


> according to changelog-4.2, the tetrahedron method was forbidden to be used
> for scf at *2010-03-25.*
> What is the reason?
>

>forces are not variational, i.e. are not the derivative of the energy.
>This shouldn't be a big problem if you do not calculate forces, though.


Best regards
-- 


Eduardo Menendez
Departamento de Fisica
Facultad de Ciencias
Universidad de Chile
Phone: (56)(2)9787439
URL: http://fisica.ciencias.uchile.cl/~emenendez

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[Pw_forum] A Quastion about stress

[Eduardo Ariel Menendez Proupin]

> How can we exert a shear force?
A short list of readings

Introduction to Solid State Physics, C. Kittel,
Theory of Elasticity,  Landau 

For simulation with Quantum ESPRESSO, you define a strain and the code
calculates stress.
You must obtain a relaxed structure (calculation='vc-relax'), then you apply
deformations to the lattice vectors, but relaxing the atom positions
(calculation='relax')

 One simple example of how to deform the lattice vectors is explained in
J. Appl. Phys. 99, 103504 (2006). See also Phys Rev B 1995; 51: 17431.



An explanation on the theory of ab initio stress calculations is  in

Nielsen OH, Richard M. First?Principles Calculation of Stress. Phys
Rev Lett 1983;50: 697,
and more detailed in PRB 32, 3780 (1985)

Good luck
-- 


Eduardo Menendez
Departamento de Fisica
Facultad de Ciencias
Universidad de Chile
Phone: (56)(2)9787439
URL: http://fisica.ciencias.uchile.cl/~emenendez

Let's pray for the 33 trapped miners! Four months to rescue.
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[Pw_forum] Young's Modulus

[Eduardo Ariel Menendez Proupin]

Dear Mohsen

Let me comment on your procedure

>At first i relaxed nano-tube and obtain the position of carbon atoms in the
>ground state. Then i decrease the tube length. A in the relation is the
area of >nano-tube (A=pi*R*R which R is the radius of tube). F is the atomic
force in >the Z axis which can be calculated by using Q.E.
>I think it is better to calculate total energy in some configuration and
use >(F=dE/dz, where E is the total energy in different configuration).
>Is there any problem in this procedure?

First, are you calculating the Young modulus of an isolated nanotube, or of
a material composed of (3,3) nanotubes perfectly oriented and with a well
defined density ?

The Young modulus is a concept that is well suited for a homogeneous
material, e.g., a bulk of nanotubes. It will depend on the density and
orientations of the nanotubes, but will be indendent of the transverse area
(the force and the energy of deformation is prportional to the area). In a
bulk of nanotubes perfectly oriented, the relevant area A would be the
transverse area of the unit cell, and the size and shape of the  unit cell
depends on the density of nanotubes, or must be optimized by a mimimum
energy criterium. If you are studying the Young modulus of a single isolated
nanotube, then note that the Young modulus is well defined only if everybody
use the same definition of A. Hence, be sure of considering the same
definition as the other results that you compare. Second, be sure to use a
unit cell sufficiently wide,  so that the preriodic replicas of the nanotube
are far enough and  the results do not depend on the transversal dimensions
of the unit cell.


>If we relaxed the tube after compression there is no net force on carbon
>atoms so I did not relax the system after compression.
*>Have you used a finite nanotube and computed the forces upon the >atoms of
the edge?*.> A finite nano-tube? I consider a unit cell (which can >make
an infinite tube ) and calculate force between atoms.
>Is there any problem?
Yes. The state with the atoms not relaxed is not a state of equilibrium, and
according to Boltzmann law, if its energy difference with the relaxed state
is larger than kT (0.026 eV at 300 K), this state may happen only once in
the lifetime of the universe. Then, the property you calculate may have
nothing to do with a real situation. Hence, relax the atoms.

If you relax, of course  there will be no net force upon the atoms, but the
tube have stress. Use tstress=.true. and use the appropriate  component of
the stress tensor as F/A. Remember to do it for various transverse sizes of
the simulation cell and be sure that the stress is independent of the cell
size, or extrapolate. Of course, also must be independent of the cutoffs and
smearing parameters (degauss). Alternatively, you may use the second
derivative of the total energy to obtain the Young modulus. It is healthy to
use both methods to check that the results are fine. The numbers will not be
exactly equal due to numerical reasons, and you can systematically improve
the agreement increasing the cutoffs and the number of kpoints.


When I asked about a finite nanotube, I was thinking in an alternative way
to do it. Use a large cubic cell, with a finite nanotube inside, made a
constrained relaxation fixing the z coordinate (I assume that z is the
nanotube axis) of the edge atoms, relax the other atoms, and sum the forces
acting upon the atoms at one edge (that must be the negative of the total
force upon the other edge). With that you can obtain the Young modulus of a
finite nanotube. If you want it for the infinite nanotube you must do it
with several lengths and extrapolate to infinite length. Of course this is
much more  expensive (really brute force) if your goal is the infinite
nanotube, but is is what you should do if your interest is in short
nanotubes.

Best regards
Eduardo

-- 


Eduardo Menendez
Departamento de Fisica
Facultad de Ciencias
Universidad de Chile
Phone: (56)(2)9787439
URL: http://fisica.ciencias.uchile.cl/~emenendez

Let's pray for the 33 trapped miners! Four months to rescue.
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[Pw_forum] Young's Modulus

[Eduardo Ariel Menendez Proupin]

Hi,
I think we always know what WE do, but not all of what computers do :-(.

Mohsen, did you relaxed the atoms after the compression? Why did you
calculate force and not stress. Have you used a finite nanotube and computed
the forces upon the atoms of the edge? Finally, how is defined A in
E=(F/A)/((L-L0)/L0)
for the case of a single nonotube?
Best regards
Eduardo

Eduardo Menendez
Departamento de Fisica
Facultad de Ciencias
Universidad de Chile
Phone: (56)(2)9787439
URL: http://fisica.ciencias.uchile.cl/~emenendez

Let's pray for the 33 trapped miners! Four months to rescue



> -- Mensaje reenviado --
> From: Stefano Baroni 
> To: PWSCF Forum 
> Date: Wed, 22 Sep 2010 19:43:15 +0200
> Subject: Re: [Pw_forum] Young's Modulus
> For that, also LRT akkows one to know what one is doing ... ;-)
> SB
>
> On Sep 22, 2010, at 7:30 PM, Mehmet Topsakal wrote:
>
> Dear Eyvaz,
>
> I think you omitted one more thing to mention. Brute-force method also
> allows one to know what he is doing.
>
>
>
> On Wed, Sep 22, 2010 at 8:14 PM, Eyvaz Isaev wrote:
>
>> Hi,
>>
>> Yes, you are right about Abinit for elastic constants calculations. The
>> main question is which method (Abinit or via total energy) is easier
>> and less time-consuming.
>>
>> Bests,
>> 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
>>
>
>>
-- 


.
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[Pw_forum] projector for local channel in ultrasoft pseudopotential

[Eduardo Ariel Menendez Proupin]

Hi Alaska,
I recently made a norm conserving Bi pseudo without the 5d semicore states.
This can be used with low cutoffs as the ultrasofts.
The 5d states has energy of -2.58 Ry, I have seen a recipe in the manual of
other code, that states over -3 Ry need to be included in the valence.
Hence, this pseudo does not fulfill this recipe and the transferibility must
be checked.
 You can check the transferibility making tests and comparisons with the
other norm conserving pseudos that are on the web site. You may also modify
the input to generate an ultrasoft that includes the 5d states. Change the
line "6D  3  2  0.00  0.00  2.60  2.6" by "5D , etc ".

 
title='Bi ultrasofts pp',
zed=83.0,
iswitch=3,
rel=1,
dft='PBE'
config='[Xe] 4f14 5d10 5f0 6s2 6p2 6d0',
 /
 
pseudotype=2,
upf_v1_format=.true.,
file_pseudopw='Bi.UPF',
lloc=1,
nlcc=.true.,
rho0=0.01,
author='EMP',
 /
4
6S  1  0  2.00  0.00  2.40  2.40
6D  3  2  0.00  0.00  2.60  2.60
5F  4  3  0.00  0.00  2.40  2.40
6P  2  1  2.00  0.00  2.40  2.40

   nconf=1,
   ecutmin=20.0,
   ecutmax=100.0,
   configts(1)='[Xe] 4f14 5d10 5f0 6s2 6p3 6d0',

Below is a summary of the cutoff study made with a ficticious BiO structure
bcc-like (Bi at a corner and O at the center of a cubic cell). You must make
your own study. I think it is safe to use a cutoff of  30 Ry, or 35 Ry if
you need to do variable cell relaxations or dynamics.

#alat   vol(a.u.) ecut(Ry)  total_E(Ry) P(kbar)
5.9995 215.9460 25 -50.64005577 -40.42
5.9995 215.9460 30 -50.65420993 21.02
5.9995 215.9460 35 -50.65484781 27.84
5.9995 215.9460 40 -50.65563353 27.21
5.9995 215.9460 45 -50.65607150 26.15
5.9995 215.9460 50 -50.65655203 26.54
5.9995 215.9460 60 -50.65685079 27.84
5.9995 215.9460 70 -50.65691919 28.3
5.9995 215.9460 80 -50.65703269 28.14
5.9995 215.9460 100 -50.65709652 28.48
5.9995 215.9460 110 -50.65709881 28.18
5.9995 215.9460 120 -50.65710837 28.33


Best regards,
-- 
Eduardo Menendez
Departamento de Fisica
Facultad de Ciencias
Universidad de Chile
Phone: (56)(2)9787439
URL: http://fisica.ciencias.uchile.cl/~emenendez
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[Pw_forum] generating pseudopotential for Ti

[Eduardo Ariel Menendez Proupin]

Hello,
I am trying to make an alternative pseudopotential for Ti, and I have the
following wanrings and errors, that I have not been able to avoid changing
parameters


 - Generating NC pseudopotential -


  Generating local potential from pseudized AE potential:
  Matching radius rcloc =   1.1000

  Local pseudo, rcloc= 1.088 Estimated cut-off energy=20.72 Ry


  Wfc   3S  rcut= 1.088  Estimated cut-off energy=   40.68 Ry
  Using 4 Bessel functions for this wfc, rho(0) = 0.010
  This function has0 nodes for 0 < r <1.088


  Wfc   3P  rcut= 1.088  Estimated cut-off energy=  149.03 Ry
  This function has0 nodes for 0 < r <1.088


  Wfc   3D  rcut= 1.088  Estimated cut-off energy=  194.63 Ry
  This function has0 nodes for 0 < r <1.088


  Wfc   4S  rcut= 3.031  Estimated cut-off energy=4.89 Ry
  Using 4 Bessel functions for this wfc, rho(0) = 0.010
 This function has0 nodes for 0 < r <3.031


   WARNING! Expected number of nodes:   0= 1-  0-  1, number of
nodes found:  2.
   Setting wfc to zero for this iteration.
   (This warning will only be printed once per wavefunction)


   WARNING! Expected number of nodes:   1= 2-  0-  1, number of
nodes found:  2.
   Setting wfc to zero for this iteration.
   (This warning will only be printed once per wavefunction)
.

   End of All-electron run 


   WARNING! Expected number of nodes:   0= 2-  1-  1, number of
nodes found:  1.
   Setting wfc to zero for this iteration.
   (This warning will only be printed once per wavefunction)


   WARNING! Expected number of nodes:   0= 3-  2-  1, number of
nodes found:  1.
   Setting wfc to zero for this iteration.
   (This warning will only be printed once per wavefunction)


 %%
 from run_pseudo : error # 1
 Errors in PS-KS equation
 %%


The input is the following

title='Ti ultrasofts pp',
zed=22.0,
iswitch=3,
rel=1,
dft='PBE'
config='[Ne] 3s2 3p6 3d2 4s2 4p0',
!nld=2,
 /
 
pseudotype=2,
upf_v1_format=.true.,
file_pseudopw='Ti-pbe-rrkjus.UPF',
lloc=-1,
rcloc=1.10,
nlcc=.false.,
rho0=0.01,
author='EMP',
 /
4
3S  1  0  2.00  0.00  1.10  1.10
3P  2  1  6.00  0.00  1.10  1.10
3D  3  2  2.00  0.00  1.10  1.10
4S  2  0  2.00  0.00  3.00  3.00

   nconf=1,
   ecutmin=20.0,
   ecutmax=100.0,
   configts(1)='[Ne] 3s2 3p6 3d2 4s2 4p0',

In fact, I want to make an ultrasoft, this input is for norm conserving hust
ti isolate the source of the error.

thanks

-- 
Eduardo Menendez
Departamento de Fisica
Facultad de Ciencias
Universidad de Chile
Phone: (56)(2)9787439
URL: http://fisica.ciencias.uchile.cl/~emenendez
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[Pw_forum] elastic constants and internal strain

[Eduardo Ariel Menendez Proupin]

Hi all,

As far as I understand, PWSCF calculates the stress following Nielsen and
Martin, PRL 50, 697 (1985), with expressions updated for ultrasoft
pseudopotentials and maybe other thechnical upgrades. In the formalism of
Nielsen and Martin, the stress is calculated as a partial derivative of the
energy versus the strain tensor, hence keeping frozen the atomic
coordinates. The effect of keeping frosen the atomic fractional coordinates
have a large effect in the paradigmatic case of the C44 elastic modulus of
silicon, where there is a large internal strain when the cristal is strained
along the [111] direction. In the times of 1985, the internal strain
contribution to the stress was evaluated using more theory and the (I guess,
experimental) values of the TO phonon frequency.

In modern times, I would instead relax the atomos in the strained cell, and
take the value of the stress tensor at the relaxed geometry. Doing so, I
think I still lose
part of the stress, related with the derivative of the atomic positions with
respect to the strain.  On the other hand, the internal strain can be
accounted for, calculating the elastic moduli from the second derivative of
the energy with respect to the strain.

I tested both methods to obtain the C44 constant of silicon, using the
strain long the [111] direction. With both methods I obtain the same value
of 77.1 GPa. I expected to obtain different values. What am I missing?

 I checked that not allowing relaxation, I also obtained the same value for
the C44(0) using the energy and the stress data. I also checked that the
constant C11 give consistent values.


-- 
Eduardo Menendez
Departamento de Fisica
Facultad de Ciencias
Universidad de Chile
Phone: (56)(2)9787439
URL: http://fisica.ciencias.uchile.cl/~emenendez
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[Pw_forum] plane averaged local potential

[Eduardo Ariel Menendez Proupin]

Hello,
I need to calculate plane averaged local potentials, and charges, for a
heterostructure. I.e.,
V(z)=1/(Lx*Ly) \int\int V(x,y,z) dx dy

I think I  can do it using PP to get V(x,y,z) in the 3D FFT grid and a write
a program that makes the average. Then I want to obtain the macroscopic
average, as defined in a triestine paper by Baldereschi, Baroni and Resta
PRL 61 ,734 (1988).

Before spending one or two days  writing the program and become sure that is
works fine, I would like to confirm that this is not already implemented in
PP or in other utility of Quantum-ESPRESSO.

Thank you

-- 
Eduardo Menendez
Departamento de Fisica
Facultad de Ciencias
Universidad de Chile
Phone: (56)(2)9787439
URL: http://fisica.ciencias.uchile.cl/~emenendez
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[Pw_forum] about potentials given by PP

[Eduardo Ariel Menendez Proupin]

Hello,

I have some doubts about the input of the postprocessing code PP

   Variable:   plot_num


 Type:   INTEGER
   Description:selects what to save in filplot:

  0  = charge

  1  = total potential V_bare+V_H + V_xc

  2  = local ionic potential

 11 = the V_bare + V_H potential

  12 = the electric field potential

Doubt one: "local ionic potential" = V_bare ?
Doubt two: " the electric field potential" = V_H?
Doubt three "Does V_bare" includes only the local part of the
pseudopotentials?

Thank you

-- 
Eduardo Menendez
Departamento de Fisica
Facultad de Ciencias
Universidad de Chile
Phone: (56)(2)9787439
URL: http://fisica.ciencias.uchile.cl/~emenendez
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[Pw_forum] failure with npool

[Eduardo Ariel Menendez Proupin]

Dear Paolo,
Here is the answer to your suggestion a few days ago, concerning the
use of versions of  zhpev_drv.f90

echo "4.0.4/bin-hpmpi/pw.x"
/opt/hpmpi/bin/mpirun -np ${NCPUS} -hostfile nodelist /discolocal/app/Espresso/e
spresso-4.0.4/bin-hpmpi/pw.x -in ${inputfile} >> ${outputfile}
 PWSCF: 34m15.70s CPU time,36m14.28s wall time


echo "bin-speed/pw-1.4.x"
/opt/hpmpi/bin/mpirun -np ${NCPUS} -hostfile nodelist  /discolocal/emenendez/Che
mUtils/Espresso/espresso-4.1/bin-speed/pw-1.3.x -in ${inputfile} >> ${outputfile
}
 PWSCF: 35m 4.30s CPU time,40m17.14s wall time

echo "bin-speed/pw-1.3.x"
/opt/hpmpi/bin/mpirun -np ${NCPUS} -hostfile nodelist  /discolocal/emenendez/Che
mUtils/Espresso/espresso-4.1/bin-speed/pw-1.3.x -in ${inputfile} >> ${outputfile
}
 PWSCF: 32m15.69s CPU time,37m13.17s wall time

echo "bin-speed/pw-1.2.x"
/opt/hpmpi/bin/mpirun -np ${NCPUS} -hostfile nodelist  /discolocal/emenendez/Che
mUtils/Espresso/espresso-4.1/bin-speed/pw-1.2.x -in ${inputfile} >> ${outputfile
}
 PWSCF: 30m13.87s CPU time,35m22.95s wall time


>< cdiaghg : 605.99s CPU ( 1419 calls, 0.427 s avg)
>
>>* cdiaghg : 893.34s CPU ( 1593 calls, 0.561 s avg)
*>
>here it is: subspace diagonalization. Are you sure that the two
>codes were compiled in the same way? and that you are running
>under the same conditions? If so, please get the previous version
>of Modules/zhpev_drv.f90:
>http://qe-forge.org/cgi-bin/cvstrac/q-e/fileview?f=espresso/Modules/zhpev_drv.f90=1.4
> 
>
>then 1.3 and 1.2, and please let us know if and when you notice a
>difference.  If you get errors related to nonexistent routines
>'numroc' and 'indxl2g', just remove the line
>  INTEGER :: numroc, INDXL2G
>Some changes that were needed to ensure statibility on weird
>machines may have slowed down the general performances. If
>you have scalapack, it mighy be interesting to try it.







-- 
Eduardo Menendez
Departamento de Fisica
Facultad de Ciencias
Universidad de Chile
Phone: (56)(2)9787439
URL: http://fisica.ciencias.uchile.cl/~emenendez
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[Pw_forum] failure with npool

[Eduardo Ariel Menendez Proupin]

>are you REALLY sure that you made the correct correction? this is the
>correct file:
>http://qe-forge.org/cgi-bin/cvstrac/q-e/getfile?f=espresso/PW/realus.f90=1.38
> 
>

>(by the way, in my previous message, replace "fileview" with "getfile")

>P.

Not REALLY sure. I had changed the line 1526, instead of adding it. Now it
works fine. Thank you.

The tests runs for zhpev_drv.f90 are queued.



-- 
Eduardo Menendez
Departamento de Fisica
Facultad de Ciencias
Universidad de Chile
Phone: (56)(2)9787439
URL: 
http://fisica.ciencias.uchile.cl/~emenendez
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[Pw_forum] how to keep mails in the same thread

[Eduardo Ariel Menendez Proupin]

Hi,
I made a question yesterday. There are replies in the same thread, but after
my reply, there are two threads in the Forum archive. Then it will be hard
to trace this issue in the future.
It has happened to me before and I do not discover the correct way yet :-((.


If the original message that I sent to pw_forum at pwscf.org had the Subject
"failure with npool", what is the subject for the replies?
Any one of the followings

failure with npool
[Pw_forum] failure with npool
Re: [Pw_forum] failure with npool
Re: Re: [Pw_forum] failure with npool

I apologize
-- 
Eduardo Menendez
Departamento de Fisica
Facultad de Ciencias
Universidad de Chile
Phone: (56)(2)9787439
URL: 
http://fisica.ciencias.uchile.cl/~emenendez
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[Pw_forum] failure with npool

[Eduardo Ariel Menendez Proupin]

Dear Paolo, Axel, and every one,

Regarding the timings of 4.1 and 4.0.4, I sent yesterday the outputs
produced by both codes.
Due to the size of the attachements, the message is awaiting for moderation.
I am not sure if I can send attachments to the forum :-(. In any case, find
below a summary of the differences of the outputs.I see 4.1 mades 8 SCF
iterations, while, 4.0.4 made 9, but in shorter time. Here is a collection
of most noticeable differences. I hope it helps
tuning.

< Program PWSCF v.4.0.4 starts ...
< Today is 25Jul2009 at 11:19:38
---
> Program PWSCF v.4.1 starts ...
> Today is 26Jul2009 at 12:15:35
16,26c16
< Found additional translation: 0. 0. 0.1000
< Found additional translation: 0. 0. 0.2000
< Found additional translation: 0. 0. 0.3000
< Found additional translation: 0. 0. 0.4000
< Found additional translation: 0. 0. -0.5000
< Found additional translation: 0. 0. -0.4000
< Found additional translation: 0. 0. -0.3000
< Found additional translation: 0. 0. -0.2000
< Found additional translation: 0. 0. -0.1000
<
< Iterative solution of the eigenvalue problem
---
> Waiting for input...
27a18
> Subspace diagonalization in iterative solution of the eigenvalue problem:
31a23,24
> Found symmetry operation: I + ( 0. 0. 0.1000)
> This is a supercell, fractional translation are disabled


1389c1370
< convergence has been achieved in 9 iterations
---
> convergence has been achieved in 8 iterations
1393c1374
< PWSCF : 30m58.57s CPU time, 36m 1.09s wall time
---
> PWSCF : 34m36.46s CPU time, 39m42.87s wall time
1395,1396c1376,1377
< init_run : 37.43s CPU
< electrons : 1818.18s CPU
---
> init_run : 38.88s CPU
> electrons : 2034.45s CPU
1399,1401c1380,1382
< wfcinit : 36.15s CPU
< potinit : 0.36s CPU
< realus : 0.20s CPU
---
> wfcinit : 37.84s CPU
> potinit : 0.37s CPU
> realus : 0.18s CPU
1404,1408c1385,1389
< c_bands : 1690.30s CPU ( 10 calls, 169.030 s avg)
< sum_band : 126.80s CPU ( 10 calls, 12.680 s avg)
< v_of_rho : 0.35s CPU ( 10 calls, 0.035 s avg)
< newd : 0.07s CPU ( 10 calls, 0.007 s avg)
< mix_rho : 0.06s CPU ( 10 calls, 0.006 s avg)
---
> c_bands : 1920.64s CPU ( 9 calls, 213.404 s avg)
> sum_band : 112.93s CPU ( 9 calls, 12.547 s avg)
> v_of_rho : 0.30s CPU ( 9 calls, 0.033 s avg)
> newd : 0.06s CPU ( 9 calls, 0.007 s avg)
> mix_rho : 0.04s CPU ( 9 calls, 0.005 s avg)
1411,1412c1392,1393
< init_us_2 : 3.62s CPU ( 714 calls, 0.005 s avg)
< cegterg : 1677.69s CPU ( 340 calls, 4.934 s avg)
---
> init_us_2 : 3.22s CPU ( 646 calls, 0.005 s avg)
> cegterg : 1909.07s CPU ( 306 calls, 6.239 s avg)
415,1418c1396,1399
< h_psi : 736.21s CPU ( 1487 calls, 0.495 s avg)
< s_psi : 79.33s CPU ( 1487 calls, 0.053 s avg)
< g_psi : 2.70s CPU ( 1113 calls, 0.002 s avg)
< cdiaghg : 605.99s CPU ( 1419 calls, 0.427 s avg)
---
> h_psi : 695.24s CPU ( 1661 calls, 0.419 s avg)
> s_psi : 72.59s CPU ( 1661 calls, 0.044 s avg)
> g_psi : 2.17s CPU ( 1321 calls, 0.002 s avg)
> cdiaghg : 893.34s CPU ( 1593 calls, 0.561 s avg)
1421c1402
< add_vuspsi : 78.47s CPU ( 1487 calls, 0.053 s avg)
---
> add_vuspsi : 73.58s CPU ( 1661 calls, 0.044 s avg)
1424,1427c1405,1408
< calbec : 126.54s CPU ( 1827 calls, 0.069 s avg)
< cft3s : 633.97s CPU ( 505734 calls, 0.001 s avg)
< interpolate : 0.09s CPU ( 20 calls, 0.005 s avg)
< davcio : 0.02s CPU ( 1054 calls, 0.000 s avg)
---
> calbec : 127.38s CPU ( 1967 calls, 0.065 s avg)
> cft3s : 583.31s CPU ( 468124 calls, 0.001 s avg)
> interpolate : 0.08s CPU ( 18 calls, 0.005 s avg)
> davcio : 0.02s CPU ( 952 calls, 0.000 s avg)
430c1411
< fft_scatter : 411.50s CPU ( 505734 calls, 0.001 s avg)
---
> fft_scatter : 396.13s CPU ( 468124 calls, 0.001 s avg)


Note that I repeated the tests and the timings changes less than 10 seconds
in 35 min.
Best regards,


-- 
Eduardo Menendez
Departamento de Fisica
Facultad de Ciencias
Universidad de Chile
Phone: (56)(2)9787439
URL: http://fisica.ciencias.uchile.cl/~emenendez
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[Pw_forum] failure with npool

[Eduardo Ariel Menendez Proupin]

Dear Paolo,
I made the correction and recompiled. Regretfully, it fails with the same
error.
Commenting the tqr input  keyword it works, however much slower.

 %%
 from addusdens_r : error # 1
 expected  360., found  180.00057894: wrong charge, increase
ecutrho
 %%

Best regards
Eduardo


> -- Mensaje reenviado --
> From: Paolo Giannozzi 
> To: PWSCF Forum 
> Date: Mon, 27 Jul 2009 18:45:53 +0200
> Subject: Re: [Pw_forum] failure with npool
> Eduardo Ariel Menendez Proupin wrote:
>   1
>
>> from addusdens_r : error # 1
>> expected  360., found  101.25021916: wrong charge
>>
>
> actually it looks like the charge is good: it is the test that is
> wrong! quick fix:
>
> diff -w -i -b -r1.37 PW/realus.f90
> 1472c1472
> <   USE mp_global,ONLY : intra_pool_comm
> ---
> >   USE mp_global,ONLY : intra_pool_comm, inter_pool_comm
> 1526a1527
> >   CALL mp_sum(  charge , inter_pool_comm )
>
> P.
> --
> Paolo Giannozzi, Democritos and University of Udine, Italy
>
>
>
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[Pw_forum] failure with npool

[Eduardo Ariel Menendez Proupin]

Hi,
I have found a problem with a benchmark calculation with pw.x . It aborts
when running with the -npool option.

However, it runs normally without the npool option. The calculation uses 34
k-points.


I have tried with
mpirun -np 32 pw.x -npool 2
mpirun -np 32 pw.x -npool 4
mpirun -np 4 pw.x -npool 2
mpirun -np 4 pw.x -npool 2

in two machines, using OpenMPI and HPMPI, single nodes and multiples nodes.
All the times it fails.

Looking at the output I see the following messages

%%
 %%
 from addusdens_r : error # 1
 from addusdens_r : error # 1
 expected  360., found  101.25021916: wrong charge, increase
ecutrho
 from addusdens_r : error # 1
 expected  360., found  101.25021916: wrong charge, increase
ecutrho
 expected  360., found  101.25021916: wrong charge, increase
ecutrho
 %%

 %%
 %%
 stopping ...


 stopping ...
 stopping ...
 %%
 from addusdens_r : error # 1
 expected  360., found  101.25021916: wrong charge, increase
ecutrho
 %%

 stopping ...

the previous output was with -npool 4. Using -npool 2 I get outpits like
this

 %%
 %%
 from addusdens_r : error # 1
 expected  360., found  180.00040683: wrong charge, increase
ecutrho
 from addusdens_r : error # 1
 expected  360., found  180.00040683: wrong charge, increase
ecutrho

It looks like hving problems to sum the charge densities of the pools.

Here is the input (the pseudos are from the web site)

 
 calculation = 'scf' ,
restart_mode = 'from_scratch' ,
   outdir = '.' ,
   pseudo_dir = '.'
  prefix = 'cdsebench' ,
  wfcdir = '/tmp',
 /
 
   ibrav = 0,
   celldm(1) = 1.8897261,
 nat = 40,
ntyp = 2,
 ecutwfc = 30.0 ,
 ecutrho = 180.0 ,
 occupations = 'smearing' ,
 degauss = 0.02 ,
smearing = 'gaussian' ,
!   qcutz=150., q2sigma=2.0, ecfixed=24.0
 /
 
electron_maxstep = 60,
conv_thr = 1.0D-6 ,
 startingpot = 'atomic' ,
 startingwfc = 'random' ,
! mixing_mode = 'TF' ,
 mixing_beta = 0.7D0,
 mixing_beta = 0.7D0,
  diagonalization = 'david' ,
tqr = .true.
 /

CELL_PARAMETERS hexagonal
 4.373836756  0.0  0.0
-2.187115631  3.787739854  0.0
 0.0  0.0 71.411016248

ATOMIC_SPECIES
   Cd  112.41000  Cd.pbe-van.UPF
   Se  78.96  Se.pbe-van.UPF

ATOMIC_POSITIONS (crystal)
Cd0.00.00.0
Cd0.00.00.1
Cd0.00.00.2
Cd0.00.00.3
Cd0.00.00.4
Cd0.00.00.5
Cd0.00.00.6
Cd0.00.00.7
Cd0.00.00.8
Cd0.00.00.9
Cd0.638210.129080.05151
Cd0.638210.129080.15151
Cd0.638210.129080.25151
Cd0.638210.129080.35151
Cd0.638210.129080.45151
Cd0.638210.129080.55151
Cd0.638210.129080.65151
Cd0.638210.129080.75151
Cd0.638210.129080.85151
Cd0.638210.129080.95151
Se0.00.00.037565413
Se0.00.00.137565413
Se0.00.00.237565413
Se0.00.00.337565413
Se0.00.00.437565413
Se0.00.00.537565413
Se0.00.00.637565413
Se0.00.00.737565413
Se0.00.00.837565413
Se0.00.00.937565413
Se0.652900.19516

[Pw_forum] parallel execution of PWscf

[Eduardo Ariel Menendez Proupin]

>I am using LG Quad core processor machine with PWscf running on linux. I
want to know >whether there is any command to run it parallely on the four
processors or by default with >simple installation (i.e.,  ./configure and
make all) it uses all the four processors?

It depends. configure detects your environment and set the options for an
optimal "compilation".

If you have MPI well installed, then configure detects it , and you run it
as Lorenzo explained (mpirun -np path-to-executables/pw.x )

There is another paralellism that you can exploit, although it is not from
espresso, but from the Intel MKL implementation of the BLAS/LAPACK
libraries. With ifort compiler (or other OpenMP capable compiler) and the
Intel MKL libraries well installed, configure detects the MKL and sets the
compilation options automatically to use the MKL. The MKL have OpenMP
parallelism implemented, and you run pw.x like a serial program, but the
matrix operations made by MKL libraries will run parallel. If it works, with
the command top you will see
CPU use higher than 100%, near 400 % if you have a QuadCore.

Take it into account if you compare performance of mpi vs "serial". When I
was unaware of the MKL built-in parallelism got unhappy because mpirun -np 2
pw.x (in a Dual Xeon) was only 30 % faster than just pw.x

Generally, this is slower than paralellization with MPI, but there is at
least one example where OpenMP runs faster.
http://www.democritos.it/pipermail/pw_forum/2008-May/008870.html
and
http://www.democritos.it/pipermail/pw_forum/2008-May/008884.html


If you have Intel or AMD CPU, try to compile espresso with the MKL. For
large calculations, the one for which speed is really important, using the
MKL can provide a factor of 5 in speed.

In summary,
If you just want to do fast calculations for small systems, do not care of
installing the parallel environment.
If you want to calculate large systems, take your time to study the manual.
After some training one can set the system to run efficiently in half a day,
i.e., install Fortran compiler, MKL libraries, MPI, ESPRESSO an do some
tests. Note that the latests distributions of Intel Fortran Compiler include
the MKl, then it is one step less.

Regards
Eduardo

-- Mensaje reenviado --
> From: Neel Singh 
> To: pw_forum at pwscf.org
> Date: Fri, 24 Jul 2009 17:06:10 +0530 (IST)
> Subject: [Pw_forum] parallel execution of PWscf
> Hi
> I am using LG Quad core processor machine with PWscf running on linux. I
> want to know whether there is any command to run it parallely on the four
> processors or by default with simple installation (i.e.,  ./configure and
> make all) it uses all the four processors?
>
> Neel
> University of Delhi
>
> --
>
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[Pw_forum] Fwd: Mixed MPI-OpenMP

[Eduardo Ariel Menendez Proupin]

Hi,
I read the following in Paolo's announcement of version 4.1

 * mixed openMP-MPI parallelization: both CP and PWscf have been
   demonstrated to run on 65536 processors

1) How should one compile and run? I could not find it on the manual.

2)  Could someone, please, suggest a strategy to mix OpenMP and MPI
efficiently? How many OpenMP threads per node, how many MPI processes per
node? Just not to begin experimenting from the ground. For a test case, I
have a cluster infiniband-connected, where each node have two Quadcore
Xeons, i.e., 8 cores per node.

Thanks,





-- 
Eduardo Menendez
Departamento de Fisica
Facultad de Ciencias
Universidad de Chile
Phone: (56)(2)9787439
URL: http://fisica.ciencias.uchile.cl/~emenendez
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[Pw_forum] Strain calculation through quantum espresso (Giovanni Cantele)

[Eduardo Ariel Menendez Proupin]

Hi DS

Strain is a geometrical property. If you want a fast calculation, just use
the Bilbao Crystallographic Server.
http://www.cryst.ehu.es/cryst/strain.html
there you may input two sets of lattice parameters and get the strain
relating both lattices.

Take a look at Fast et al, PRB 51, 17431 (1995). In equations (1) and (2)
are explained the relation between lattice vectors and strain. In  Kittel's
textbook it is explained too, but I am not sure if in all the editions. In
the article of Fast it explains what you can do with Q-E and similar codes.

In Q-E you input the lattice parameters or the lattice vectors, and all the
other stuff, and get the stress tensor as explained in previous posts.

Maybe what you need is to find the strain of a crystal under an specified
stress tensor. As far as I know, with Q-E you cand do it only in the case of
hydrostatic stress (when the stress tensor is the pressure times the
identity matrix), using calculation='vc-relax'  and setting the variable
press. E.g.
 
calculation = 'vc-relax'
..

cell_dynamics='damp-pr',
press = 35.0, (the value of pressure in kbars)
cell_dofree='all',


For a non-hydrostatic stress, you may need to find the elastic constants (as
in Fasts's paper) first and then solve the equations of elasticity. If the
stress is big, you may need an iterative process.

If you need the strain under a fully specified stress tensor, i.e., the six
independent components of the tensor, you may device a minimization
algorithm implemented in a shell or python script, that run pw.x  to get the
energies and stress.
An alternative is  to find the elastic constants (as in Fasts's paper) first
and then solve the equations of elasticity. If the stress is big, you may
need an iterative process to find the elastic constants under a stress that
is close to your derired stress.

In simple cases, such as uniaxial stress and orthorombic lattices, you do
cell relaxations with constraints (cell_dofree='x' ) keeping one lattice
vector fixed, and by trial and error you can obtain the lattice that produce
the desired component of the stress.




-- 
Eduardo Menendez
Departamento de Fisica
Facultad de Ciencias
Universidad de Chile
Phone: (56)(2)9787439
URL: http://fisica.ciencias.uchile.cl/~emenendez
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[Pw_forum] -nimage -npool -ntg -ndiag

[Eduardo Ariel Menendez Proupin]

Hi, I found in the new, or maybe not so new, users guide, that 1000 atoms or
so can be calculated, and new ways to paralelize.

The example in the manual is

 mpirun -np 4096 ./pw.x -nimage 8 -npool 2 -ntg 8 -ndiag 144 -input myinput.in

I have played a bit, but not with a massive computer, and I have found that
the default options are always better than my unexpert  choices.

So, I would like to see some hints, in addition to what  is reproduced below
(from the users guide), about the good choices of -ntg and -ndiag. Maybe
some examples is enough to understand it.

[Pw_forum] ensemble DFT vs "PWSCF" DFT in metals

[Eduardo Ariel Menendez Proupin]

Hi,
I am curious about the difference between the ensemble DFT method
implemented in CP and the smeared DFT used in PWSCF with Methfessel-Paxton
smearing. ?What is better for what system?

-- 
Eduardo Menendez
Departamento de Fisica
Facultad de Ciencias
Universidad de Chile
Phone: (56)(2)9787439
URL: http://fisica.ciencias.uchile.cl/~emenendez
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[Pw_forum] new unit-cell volume in variable cell relaxation

[Eduardo Ariel Menendez Proupin]

Hi,
When doing variable cell relaxation it is useful to have the current volume
of the variable cell. This is reported in the output when
cell_dynamics='damp-w', e.g. in a line as the following
 new unit-cell volume =   3705.0385 (a.u.)^3

However, when cell_dynamics='bfgs' the cell volume is not reported (pw.x of
version 4.0.4 ).

I see in the text that bfgs is still experimental. If interesting for
debuging the code, I can supply an input  case where the relaxation fails .
In this case, in the 3rd bfgs step,

   WARNING: integrated charge=   140.52433035, expected=   288.

 %%
 from electrons : error # 1
 charge is wrong

I suspect the bgfs made drastic change and the electronic calculation went
crazy. With damped dynamics it works smoothly.

Best regards

-- 
Eduardo Menendez
Departamento de Fisica
Facultad de Ciencias
Universidad de Chile
Phone: (56)(2)9787439
URL: http://fisica.ciencias.uchile.cl/~emenendez
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[Pw_forum] band and dos input files in xcrysden

[Eduardo Ariel Menendez Proupin]

Well, I also like the way the tasks are distributed, it is conceptually very
clear. I know a different code that saves a DOS file after a band
calculation and the newbies come to me with strange peaks in DOS that are
caused by a flat band along a line.
Calling dos from pw.x  or pw from dos.x masks that conceptual clarity.
However, we have to be practical and run the frequent calculations as easily
as possible. I would prepend a nscf calculation with "standard options" ,
and give warning in the otput file that non-standard options can be done
doing the nscf calculation separately.

Also, I would alway make pw.x to write the self-consistent DOS in a file
after an scf calculation, no matter how coarse is the k-points grid. I find
this useful for checking purposes (e.g. to know if an impurity have levels
in the gaps). Also, for simple metals the k-points grid needed to have
converged energies and forces also is enough to have a good DOS. Then let
the user the choice to do post processing if want a DOS with an occupation
scheme different than the SCF. I would put this file in the .save directory
and name it prefix.scfdos or something like that.

Boris, thank for your script. I will soon test it. Maybe it can be embedded
in PWGUI.

Best regards
Eduardo

-- Mensaje reenviado --

> From: Paolo Giannozzi 
> To: PWSCF Forum 
> Date: Thu, 26 Feb 2009 10:34:30 +0100
> Subject: Re: [Pw_forum] band and dos input files in xcrysden
>
> On Feb 21, 2009, at 17:05 , Eduardo Ariel Menendez Proupin wrote:
>
>  Let me remind how is the process to obtain the DOS. It has three
>> calculations
>> and 3 input files
>>
>> pw.x < si.scf.in > si.scf.out   # self consistent
>> pw.x  si.dos.out  # non selfconsistent dense k-points mesh
>> and a few options
>> dos.x   si.dos2.out  # postprocessing
>>
>
> Hi Eduardo,  the issue you raise is a serious one and requires some though.
> Right now several standard calculations in q-e are clumsy because they
> require separate steps. While I think that it is a good idea to keep
> separate
> steps separate, I also think that at least the most common calculations
> might
> be streamlined. I am not convinced that the PWGui is the right tool for
> this,
> though, at least not in the present form (a tool to produce input data).
> The ideal  solution would be the usage of a high-level scripting language
> like
> python to "glue" the various pieces together, but this is highly nontrivial
> (at least for me and for 99% of q-e users).
> A simpler option could be to collapse some calculations into the same
> executable:
> for instance
> - add a call to dos after a nscf calculation in pw.x,
>  add a call to bands after a bands calculation in pw.x
> or
> - prepend a nscf calculation to dos.x,
>  prepend a band calculation to bands.x
> Suggestions are welcome
>
> Paolo
> ---
> Paolo Giannozzi, Democritos and University of Udine, Italy
>
>
>
>
>
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[Pw_forum] [Fwd: dielectric tensor]

[Eduardo Ariel Menendez Proupin]

Dear Vivek,
I think you can calculate the low frequency dielectric tensor using the
PHONON output and a formula.
Please, see PHYSICAL REVIEW B 76, 245110 (2007), eq. (1).

Maybe PHONON can calculate directly, but I don not find how.
Best regards
Eduardo

-- 
Eduardo Menendez
Departamento de Fisica
Facultad de Ciencias
Universidad de Chile
Phone: (56)(2)9787439
URL: http://fisica.ciencias.uchile.cl/~emenendez



>
> -- Mensaje reenviado --
> From: "Vivek Ranjan" 
> To: pw_forum at pwscf.org
> Date: Mon, 23 Feb 2009 10:05:03 -0500 (EST)
> Subject: [Pw_forum] [Fwd: dielectric tensor]
>
>
>  Original Message 
> Subject: dielectric tensor
> From:"Vivek Ranjan" 
> Date:Fri, February 20, 2009 4:54 pm
> To:  pw_forum at pwscf.org
> --
>
> Hello,
>
> I was wondering if PWSCF can calculate low frequency dielectric
> permittivity tensor. I would like to calculate dielectric constant in KHz
> frequency range.
>
> Thank you,
>
> Vivek Ranjan
> NCSU
>
>
> __
> web : http://www.geocities.com/vivekranjanweb
> __
> Vivek Ranjan Email : vranjan at chips.ncsu.edu
> Center for High Performance Simulation : vranjan at ncsu.edu
> Department of Physics
> NC State University  Phone : +1-919-513-0613 (Office)
> Campus Box 7518  Fax   : +1-919-513-4804
> Raleigh, NC 27695
> --
>
>
>
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[Pw_forum] band and dos input files in xcrysden

[Eduardo Ariel Menendez Proupin]

Dear Tone,
Thanks for your interest in my request.

>Don't know what exactly you mean for Emin and Emax, however, as far as
>the outdir and prefix are concerned, how should pwgui know which is the
>corresponding pw.x input file? (this would be needed for the
>inheritance).

Let me remind how is the process to obtain the DOS. It has three
calculations and 3 input files

pw.x < si.scf.in > si.scf.out   # self consistent
pw.x  si.dos.out  # non selfconsistent dense k-points mesh and a
few options
dos.x   si.dos2.out  # postprocessing


At present, pwgui has a Menu File/New, where one can define the input files
from the scratch.

A typical input for dos.x looks like this

 outdir='./temp',
 prefix='silicon'
 fildos='silicon.dos',
 Emin=-10.0, Emax=25.0, DeltaE=0.1
/
One simple idea is to add a submenu to the menu  "File/New from here"
So, if I have an open pw.x input, when I select "File/New from here" it will
make the new file inheriting all the properties: in this case outdir and
prefix. I would also set by default fildos = prefix.dos.

Emin and Emax are the minumum and maxima of the Kohn-Sham eigenvalues that
can be taken from the pw.x outputs. pwgui may run an script to take these
values from the pw.x output if this exists (I may want to run the files
interactvely or just to make the input files and copy them to a server). We
may ask Paolo  to put Emin and Emax, and Efermi or HOMO in a single line of
the output.

NSCF calculation inherits many more fields from the SCF, so it makes more
sense to generate the *.dos.in file from the .scf.in file. Let see the
differences

diff si.scf.in si.dos.in
2c2
<  calculation = 'scf' ,
---
>  calculation = 'nscf' ,
15a16,17
> nbnd = 8,
> occupations='tetrahedra',
29c31
<   5 5 5   1 1 1
---
>   20 20 20   0 0 0

This I make simply saving the si.scf.in with the name si.dos.in and changing
the variables. However, it may be nice to make the changes automatically.
The keywords nbnd, occupations, and the k-point mesh (20 20 20) are
difficult to set automagically. I propose some maybe good default values

nbnd can be searched in the output file.

grep 'number of Kohn-Sham states' si.scf.out
 number of Kohn-Sham states=4
and just double the number 4. It would be a different recipe if we deal with
a  metal, but let's keep simple and let the user to reduce it.

I would set occupations='tetrahedra' by default.

>   20 20 20   0 0 0
I would make a contest to select the winning idea. I have one recipe
If I have in the scf input calculation
K_POINTS automatic
N1 N2 N3 1 1 1  or 'N1 N2 N3 0 0 0'
then for the nscf calculation I would set
N1n N2n N3n 0 0 0

such that
N1n/N1 = N2n/N2 = N3n/N3 and
N1n*N2n*N3n = (30^3)/nat   (nat the number of atoms)

A different strategy may be to have a menu Project and from the Project
menu, select kinds of input fiiles or tasks. If one selects task  DOS, for
example, then pwgui can  create the three input files and display a reminder
of the sequence of calculations to be done.


Best regards
Eduardo


> -- Mensaje reenviado --
> From: Tone Kokalj 
> To: PWSCF Forum 
> Date: Fri, 20 Feb 2009 12:08:43 +0100
> Subject: Re: [Pw_forum] band and dos input files in xcrysden
> On Thu, 2009-02-19 at 23:48 -0300, Eduardo Ariel Menendez Proupin wrote:
> > Hi Tone,
> >
> > Do you have plans to add the capability in PWGUI to generate inputs
> > for bands.x and dos.x ?
>
> Actually, I didn't have, but this can be easily done. Due to your
> request I will do so in the future.
>
> > It would be goood to operate it in an easy way, i.e. inheriting
> > outdir and prefix from the parent pw.x input and Emin=-10.0, Emax=25.0
> > from the pw.x output.
>
> Don't know what exactly you mean for Emin and Emax, however, as far as
> the outdir and prefix are concerned, how should pwgui know which is the
> corresponding pw.x input file? (this would be needed for the
> inheritance).
>
> Regards, Tone
>
>
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[Pw_forum] band and dos input files in xcrysden

[Eduardo Ariel Menendez Proupin]

Hi Tone,

Do you have plans to add the capability in PWGUI to generate inputs for
bands.x and dos.x ?
It would be goood to operate it in an easy way, i.e. inheriting  outdir and
prefix from the parent pw.x input and Emin=-10.0, Emax=25.0 from the pw.x
output.

Best regards

-- 
Eduardo Menendez
Departamento de Fisica
Facultad de Ciencias
Universidad de Chile
Phone: (56)(2)9787439
URL: http://fisica.ciencias.uchile.cl/~emenendez
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[Pw_forum] poor k-points convergence, ghost states ?

[Eduardo Ariel Menendez Proupin]

Hi,
I am trying to reproduce a paper on AgSbTe. I am having problems to obtain
convergence against the number of k-points. With a supercell of 8 atoms, I
do not have convergence with 26x26x26 Monkhorst-Pack mesh. I think that this
is a quite dense mesh and I should have obtained convergence much before. My
student  is also having troble to complete the band calculations.
I am using BHS pseudopotentials for Sb and Te, and US for Ag.  I suspect
that I have ghost states. Is there other possible reasonable cause?
Thanks
-- 
Eduardo Menendez
University of Chile
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[Pw_forum] OpenMPI on mac

[Eduardo Ariel Menendez Proupin]

Hi,
I am new with Macs. I am learning to compile in it. Frankly, I have been
happy after installing fink, so I am still Linux minded. I installed g95,
and with it I could compile QE serially. The problem is to use mpif90. There
is an mpif90 that comes with Xcode version 3, but it is not configured. When
I run it I have this message.

Macintosh:Developer eariel$ mpif90
--
Unfortunately, this installation of Open MPI was not compiled with
Fortran 90 support.  As such, the mpif90 compiler is non-functional.

Obviously I would have to configure it, but I do not find any file named
configure. Is there an option to reconfigure it within Xcode, without
downloading OpenMPI independently of Xcode?

Other question, is there a gfortran in Xcode? How to install it?
Thanks

-- 
Eduardo Menendez
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[Pw_forum] problem changing the time step with pwscf

[Eduardo Ariel Menendez Proupin]

Hi,
I noticed that running molecular dynamic calculations , the time step (dt)
cannot be changed if one restarts from a previous run
(restart_mode='restart'). This happens at least in versions 4.0 and 3.2.
If it is done, pw.x runs without complain (see note below), but the
velocities and the kinetic energies are not correctly calculated. Also, in
the prefix.msd.dat file, the times are calculated as dt*istep, producing a
jump in time if dt is changed. The time should be something like
previous_final_time+(istep-previous_nstep)*dt. Note that the time is
correctly reported in the standard output.

This can be tested with example04, running it mannually to avoid deletion of
the temporary save, and restarting wiht a modified input file
si.md8.in  using
restart_mode='restart',
dt=10,
nstep=150,

Note: There is also a warning message when restarting in example 4: RECOVER
from restart file failed: file not found.

Here is my bash script (just one more) to extract the temperature and the
energies from the output file. The jumps are seen plotting the dat files.

INFILE=si.md8.out
SUFFIX=si8.dat
grep kbar $INFILE |awk '{print $6}' >>p_${SUFFIX}
grep 'temperature   =' $INFILE |awk '{print $3}' >>t_${SUFFIX}
grep 'Ekin + Etot (const)' $INFILE |awk '{print $6}' >>etotal_${SUFFIX}
grep 'kinetic energy (Ekin) =' $INFILE |awk '{print $5}' >>ekin_${SUFFIX}
paste etotal_${SUFFIX} ekin_${SUFFIX}|awk '{printf("%7.7f \n", $1-$2)}'
>epot_${SUFFIX}

Why change the time step? Maybe just to check the stability of the
simulations. Or maybe a large dt is enough for driving the system to a
certain temperature near equilibrium, but a smaller one is need after the
thermostat is switched off.

-- 
Eduardo Menendez
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[Pw_forum] acml-mkl

[Eduardo Ariel Menendez Proupin]

Dear Sagar,
Please, run the following commands and let me know the output

uname -a
ifort -V
./configure (in the ESPRESSO directory)
Eduardo


> -- Mensaje reenviado --
> From: ambavale sagar 
> To: pwforum que-ans 
> Date: Fri, 16 May 2008 11:15:23 +0530 (IST)
> Subject: Re: [Pw_forum] acml-mkl
> AS> I have x86_64 (i.e. AMD64) architacture machine with Xeon
> AS> (x5450-quad core) processors having dual cpu. I have installed intel
> AS> fortran compiler, c compiler and mkl. But as i compile espresso4cvs2
> AS> version it does not recognise BLAS,LAPACK libraries.
>
> AK>if configure does not find MKL, it either means you have not
> AK>installed it correctly or to a location that configure does not
> AK>know about. check the config.log file and simply adapt the make.sys
> AK>file manually according to the MKL user's guide (RTFM!!).
>
> hi,
> My config.log file shows that it detect the mkl library at a standard place
> but finds it incompatible. The part of config.log file looks like :
> .
> ..
> configure:5894: checking for library containing dgemm
> configure:5907: ifort -o conftest -O2 -assume byterecl  -nomodule -i-static
> -openmp  -L/opt/intel/mkl/10.0.1.014/lib/em64t conftest.f   >&5
> ld: skipping incompatible /opt/intel/mkl/10.0.1.014/lib/em64t/libguide.awhen 
> searching for -lguide
> /tmp/ifortMq0fkI.o: In function `MAIN__':
> conftest.f:(.text+0x2b): undefined reference to `dgemm_'
> configure:5913: $? = 1
> configure: failed program was:
> |   program main
> |   call dgemm
> |   end
> configure:5945: ifort -o conftest -O2 -assume byterecl  -nomodule -i-static
> -openmp  -L/opt/intel/mkl/10.0.1.014/lib/em64t conftest.f -lmkl_em64t
> >&5
> ld: skipping incompatible /opt/intel/mkl/
> 10.0.1.014/lib/em64t/libmkl_intel_lp64..a when searching for
> libmkl_intel_lp64.a
> ld: cannot find libmkl_intel_lp64.a
> configure:5951: $? = 1
> configure: failed program was:
> |   program main
> |   call dgemm
> |   end
> configure:5979: result: no
> configure:5894: checking for library containing dgemm
> configure:5907: ifort -o conftest -O2 -assume byterecl  -nomodule -i-static
> -openmp  -L/opt/intel/mkl*/lib/em64t conftest.f   >&5
>
> ...
>
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[Pw_forum] acml - mkl

[Eduardo Ariel Menendez Proupin]

Dear Sagar,

I am not sure if configure detects the acml library. Recently it did not
work for me. In case that configure does not detect the ACML, after you run
./configure,  edit the file  make.sys
and modify the last line, to appear like this

LIBS   = /opt/acml4.1.0/ifort64/lib/libacml.a $(MPI_LIBS)
$(MASS_LIBS) $(PGPLOT_LIBS) $(LD_LIBS)

Note that /opt/acml4.1.0 is the directory where I placed the ACML in my PC.
Use the appropriate directory in your system.

I also have one PC with  processor AMD 64 X2, the operating system has a
strange architecture x86_64 (as given by the command uname -a),  but the
intel compiler that works is 32bits ,  the emt64 version does not work for
me in this machine. In this machine, I compiled using

LIBS   = /opt/acml4.1.0/ifort32/lib/libacml.a $(MPI_LIBS)
$(MASS_LIBS) $(PGPLOT_LIBS) $(LD_LIBS)

Regards
Eduardo

-- Mensaje reenviado --

> From: ambavale sagar 
> To: pwforum que-ans 
> Date: Tue, 13 May 2008 12:01:16 +0530 (IST)
> Subject: [Pw_forum] acml - mkl
> Dear Pwscf users,
> I have x86_64 (i.e. AMD64) architacture machine with Xeon (x5450-quad core)
> processors having dual cpu. I have installed intel fortran compiler, c
> compiler and mkl. But as i compile espresso4cvs2 version it does not
> recognise BLAS,LAPACK libraries. Must i install ACML as i have AMD
> architacture? During compilation of acml i couldn't find driver.f( They say
> that driver.f is application program). What should be the procedure?
> One more question: Is it possible to have Xeon processors with ia-64
> architacture?
>
> regards
> Sagar Ambavale
> Research Student
> The M.S.University of Baroda
> India
>
>
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[Pw_forum] openmp vs mpich performance with MKL 10.x

[Eduardo Ariel Menendez Proupin]

Thank you Axel, for all the time and the explanations of the deep numerical
details.
I will give up at his point. I am satisfied to know that I am not
wasting CPU resources due to bad configuration, and I will keep both MPI and
OpenMP compilations.. I will try to add to the benchmark of Nicola with CP.
Best regards
-- 
Eduardo Menendez
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[Pw_forum] Fwd: openmp vs mpich performance with MKL 10.x

[Eduardo Ariel Menendez Proupin]

-- Forwarded message --
From: Eduardo Ariel Menendez Proupin <earie...@gmail.com>
Date: 2008/5/7
Subject: Re: [Pw_forum] openmp vs mpich performance with MKL 10.x
To: Axel Kohlmeyer 


Hi,


 with serial MKL, serial FFTW-2.1.5 and OpenMPI with 4 mpi tasks.
> i get a wall time of 12m12s and cpu time of 10m40s.
>
I GET
OMP_NUM_THREADS=1
MKL_NUM_THREADS=1
 DFLAGS =  -D__INTEL -D__FFTW -D__USE_INTERNAL_FFTW -D__MPI -D__PARA
mpiexec -n 4 /home/emenendez/ChemUtils/Espresso/espresso4.0cvs3/bin4/pw.x <
cdteo0.2.md.in >> cdteo0.2.md.out
 PWSCF: 12m33.73s CPU time,12m43.31s wall time


> changing MKL to threaded MKL using 4 threads and 1 mpi task
> i get a wall time of 18m8s and cpu time of 28m30s
> (which means that roughly 40% of the time the code
> was running multi-threaded BLAS/LAPACK).

OMP_NUM_THREADS=4
MKL_NUM_THREADS=4
mpiexec -n 1 /home/emenendez/ChemUtils/Espresso/espresso4.0cvs3/bin4/pw.x <
cdteo0.2.md.in >> cdteo0.2.md.out
 PWSCF: 27m40.02s CPU time,17m 2.73s wall time



>
> with serial FFT, threaded MKL using 2 threads and 2 mpi tasks
> i get a wall time of 12m45s and cpu time of 14.42s

UNTESTED IN THIS MACHINE, BUT WORSE IN OTHERS.

>
> now when i swap the serial FFTW2 against the
> intel MKL FFTW2 wrapper i get with 2 threads and 2 MPI tasks
> a wall time of 15m2s and a cpu time of 24m11s.

 UNTESTED IN THIS MACHINE, BUT WORSE IN OTHERS.


> and with 4 threads and 1 MPI task i get
> a wall time of 0h19m   and a cpu time of 1h 2m


OMP_NUM_THREADS=4
MKL_NUM_THREADS=4
mpiexec -n 1 /home/emenendez/ChemUtils/Espresso/espresso4.0cvs3/bin5/pw.x <
cdteo0.2.md.in >> cdteo0.2.md.out
 PWSCF: 58m50.42s CPU time,17m55.90s wall time



> and finally when disabling threading and with
> 4 MPI tasks i get 12m38 wall time and 11m14s cpu time.

 OMP_NUM_THREADS=1
MKL_NUM_THREADS=1
 DFLAGS =  -D__INTEL -D__FFTW  -D__MPI -D__PARA (using fftw2_intel)
mpiexec -n 4 /home/emenendez/ChemUtils/Espresso/espresso4.0cvs3/bin5/pw.x <
cdteo0.2.md.in >> cdteo0.2.md.out
 PWSCF: 13m 2.54s CPU time,13m16.11s wall time
IT IS WORSE THAN USING THE INTERNAL FFTW.

HOWEVER, RUNNING SERIAL

OMP_NUM_THREADS=4
MKL_NUM_THREADS=4
DFLAGS =  -D__INTEL -D__FFTW
BLAS_LIBS  = -lfftw2xf_intel -lmkl_em64t
/home/emenendez/ChemUtils/Espresso/espresso4.0cvs3/bin2/pw.x <
cdteo0.2.md.in >> cdteo0.2.md.out
 PWSCF: 36m58.97s CPU time,11m36.11s wall time


OMP_NUM_THREADS=4
MKL_NUM_THREADS=4
DFLAGS =  -D__INTEL -D__FFTW3
BLAS_LIBS  = -lfftw3xf_intel -lmkl_em64t
/home/emenendez/ChemUtils/Espresso/espresso4.0cvs3/bin3/pw.x <
cdteo0.2.md.in >> cdteo0.2.md.out
 PWSCF: 36m44.64s CPU time,11m29.59s wall time



>
> obviously, switching to the intel fft didn't help.

FOR ME, IT HELPS ONLY WHEN RUNNING SERIAL.

>
>
> your system with many states and only gamma point
> is definitely a case that benefits the most from
> multi-threaded BLAS/LAPACK.

TYPICAL FOR BO MOLECULAR DYNAMICS.

I WOULD SAY, AVOID MIXING MPI AND OPENMP. ALSO AVOID INTEL  FFTW WRAPPERS
WITH MPI, EVEN IF OMP_NUM_THREADS=1.
USE THREADED BLAS/LAPACK/FFTW2(3) FOR SERIAL RUNS.

ANYWAY, THE DIFFERENCE BETWEEN THE BEST MPI AND THE BEST OPENMP IS LESS THAN
10% (11m30s vs 12m43s)

>
>
> i'm curious to learn how these number match up
> with your performance measurements.
>
> cheers,
>   axel.
>
>
>


-- 
Eduardo Menendez



-- 
Eduardo Menendez
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[Pw_forum] openmp vs mpich performance with MKL 10.x

[Eduardo Ariel Menendez Proupin]

> there are two issue that need to be considered.
>
> 1) how large are your test jobs? if they are not large enough, timings are
> pointless.


about 15 minutes in Intel Quadcore. 66 atoms: Cd_30Te_30O_6. 576 electrons
in total.
My test may be very particular. If you a have a balanced benchmark, I would
like to run it.


> 2) it is most likely, that you are still tricked by the
>   auto-parallelization of intel MKL. the export OMP_NUM_THREADS
>   will usually only work for the _local_ copy, for some
>   MPI startup mechanisms not at all. thus your MPI jobs will
>   be slowed down.

I am using only SMP. Sorry, I still haven't a cluster of Quadcores.

>
>
>   to make certain that you only like the serial version of
>   MKL with your MPI executable, please replace  -lmkl_em64t
>   in your make.sys file with
>   -lmkl_intel_lp64 -lmkl_sequential -lmkl_core


Yes, I also tried that. The test runs in 14m2s. Using only -lmkl_em64t it
runs in 14m31s. Using serial compilations it ran in 12m20s.



Thanks,
Eduardo
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[Pw_forum] comparing gaussian03 with pwscf

[Eduardo Ariel Menendez Proupin]

If there is doubt on the approximations for lantanides, I suggest to make
some tests with something more "classic", such as NaCl or MgO and then
compare PWSCF vs GAUSSIAN with complete basis sets.

One question? What is the useful information provided by the knowledge of
the charge transfer? Can it be correlated to any measurable property
(reactivity, entropy, adsorcion enrgy, ) or with any measurable and
difficult to calculate property?

Some years ago I calculated and reported some charge transfer and said
something about the ionicity. To know better, I calculated the charge
transfer in NaCl. For this, I integrated the charge density in the Voronoi
cells of Na and Cl, using the self consisten charge density and the
superposition of atomic densities. The difference is the charge transfer or,
more precisely, the charge that crosses the boundary of the Voronoi cells.
To my surprise, the charge transfer in NaCl is 0.1 electron, and not 1
electron as the textbooks suggest. I also tested it with MgO (0.2 instead of
2). So, where is hidden  the truth of the ionic bond?



-- 
Eduardo Menendez
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[Pw_forum] openmp vs mpich performance with MKL 10.x

[Eduardo Ariel Menendez Proupin]

Hi,
I have noted recently that I am able to obtain faster binaries of pw.x using
the the OpenMP paralellism implemented in the Intel MKL libraries of version
10.xxx, than using MPICH, in the Intel cpus. Previously I had always gotten
better performance using MPI. I would like to know of other experience on
how to make the machines faster. Let me explain in more details.

Compiling using MPI means using mpif90 as linker and compiler, linking
against mkl_ia32 or mkl_em64t, and using link flags -i-static -openmp. This
is just the  what appears in the make.sys after running configure in version
4cvs,

At runtime, I set
export OMP_NUM_THREADS=1
export MKL_NUM_THREADS=1
and run using
mpiexec -n $NCPUs pw.x output
where NCPUs  is the number of cores available in the system.

The second choice is
./configure --disable-parallel

and at runtime
export OMP_NUM_THREADS=$NCPU
export MKL_NUM_THREADS=$NCPU
and run using
pw.x output

I have tested it in Quadcores (NCPU=4) and with an old Dual Xeon B.C.
(before cores) (NCPU=2).

Before April 2007, the first choice had always workes faster. After that,
when I came to use the MKL 10.xxx, the second choice is working faster. I
have found no significant difference between version 3.2.3 and 4cvs.

A special comment is for the FFT library. The MKL has a wrapper to the FFTW,
that must be compiled after instalation (it is very easy). This creates
additional libraries named like libfftw3xf_intel.a and libfftw2xf_intel.a
This allows improves the performance in the second choice, specially with
libfftw3xf_intel.a.

Using MPI, libfftw2xf_intel.a is as fast as using the FFTW source
distributed with espresso, i.e., there is no gain in using
libfftw2xf_intel.a. With  libfftw3xf_intel.a and MPI, I have never been able
to run pw.x succesfully, it just aborts.

I would like to hear of your experiences.

Best regards
Eduardo Menendez
University of Chile
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[Pw_forum] questions on the acoustic sum rule crystal

[Eduardo Ariel Menendez Proupin]

Hi,

Question 1. This question is about the Acoustic Sum Rule in phonon
calculations. Is there a reference to learn about the option zasr='crystal'?

Is 'crystal' always better than 'simple' ?

  ! zasr   :  Indicates type of Acoustic Sum Rules used for the Born
  !   effective charges (character):
  !   - 'no': no Acoustic Sum Rules imposed (default)
  !   - 'simple':  previous implementation of the asr used
  ! (3 translational asr imposed by correction of
  ! the diagonal elements of the force-constants matrix)
  !   - 'crystal': 3 translational asr imposed by optimized
  !  correction of the IFC (projection).

Question 2. Consider the calculation of the phonon DOS, as in example 06.
The ASR can be imposed in the run of q2r and/or in the run of matdyn, let's
say
There are four combinations of zasr-asr in q2r an matdyn
q2r  matdyn
 1   no no
 2   no crystal
 3  crystalno
 4  crystalcrystal

Should  there be  differences in the final DOS in the combinations 2, 3, and
4?

-- 
Eduardo Menendez
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