Re: [Pw_forum] QHA Compile: Using gfortran instead of ifort

[W2AGZ]

Alberto, thanks for the pointer to gibbs2.  I've heard anecdotally about the
package, and I will now indeed have a look.  -Paul

-Original Message-
From: pw_forum-boun...@pwscf.org [mailto:pw_forum-boun...@pwscf.org] On
Behalf Of Alberto Otero de la Roza
Sent: Thursday, November 27, 2014 9:58 AM
To: PWSCF Forum
Subject: Re: [Pw_forum] QHA Compile: Using gfortran instead of ifort

Hi Paul,

> I believe I may have raised this question in the far distant past.
>
> It appears that under QE-5.1.1, it is still necessary to compile the 
> source code within QHA using ifort.  Are any in the QE community aware 
> of a QHA package compile-able with gfortran, or object code resulting 
> from such?  Is there an equivalent to QHA somewhere within the QE 
> package (or outside!) capable of yielding similar results such as, e.g.,
Debye temperatures?

There is gibbs2:

http://azufre.quimica.uniovi.es/software.html#gibbs2

It's free software, as far as I know you can build it with any compiler
conforming to the Fortran 90/95 standard, and gives you the Debye
temperature as well as lots of other stuff. If you run, for instance, the
example 01_simple.ing in the tests you'll get the Debye temperature as field
14 in 01_simple.eos.

Best,

A.

---
Dr. Alberto Otero de la Roza
National Institute for Nanotechnology,
National Research Council of Canada,
11421 Saskatchewan Drive, Edmonton,
Alberta T6G 2M9, Canada

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Re: [Pw_forum] QHA Compile: Using gfortran instead of ifort

[W2AGZ]

Alex, thanks for your quick and wise response!  

I did a cursory pass through of the source code, matdyn.f90 and lambda.f90,
used in QHA (matdyn) and the general phonon packages within QE, and didn't
find any obvious uses of floating point loop variables.  Frankly, I can't
imagine why such assignments would ever be done!  On the other hand,
occasionally posted on the forum are reports of NaN errors embedded in
phonon calculation output.  I wonder if such result from the "very bad"
programming practices you describe.

Hope to see you at the March Meeting upcoming in San Antonio.

-Paul
-Original Message-
From: pw_forum-boun...@pwscf.org [mailto:pw_forum-boun...@pwscf.org] On
Behalf Of Axel Kohlmeyer
Sent: Thursday, November 27, 2014 6:24 AM
To: PWSCF Forum
Subject: Re: [Pw_forum] QHA Compile: Using gfortran instead of ifort

On Wed, Nov 26, 2014 at 11:27 PM, W2AGZ  wrote:
> To the Community:
>
>
>
> I believe I may have raised this question in the far distant past.
>
>
>
> It appears that under QE-5.1.1, it is still necessary to compile the 
> source code within QHA using ifort.  Are any in the QE community aware 
> of a QHA package compile-able with gfortran, or object code resulting 
> from such?  Is there an equivalent to QHA somewhere within the QE 
> package (or outside!) capable of yielding similar results such as, e.g.,
Debye temperatures?
>
>
>
> As always, thanks for any advice/guidance.

for the most part it seems as if all it needs is somebody with a little bit
to time to sit down and replace the loops using floating point variables
with the equivalent using integral loop variables.

using floating point loop variables is very, *very*, *VERY* bad programming
style (due to limitations of floating point math) and as of the last decade
removed from the fortran standard.

not really rocket science...

axel.

>
>
>
> Paul Michael Grant, PhD
>
> Physicist and Science Writer
>
> Senior Life Fellow, American Physical Society
>
> Fellow, Institute of Physics, United Kingdom
>
> w2...@w2agz.com
>
> http://www.w2agz.com
>
>
>
>
>
>
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--
Dr. Axel Kohlmeyer  akohl...@gmail.com  http://goo.gl/1wk0 College of
Science & Technology, Temple University, Philadelphia PA, USA International
Centre for Theoretical Physics, Trieste. Italy.
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Re: [Pw_forum] Help with QE compilation

[Filippo Spiga]

Elliot, try the following simple way to configure

./configure --enable-parallel --disable-openmp --without-scalapack
make all

Every time you run using 4 MPI you should set "-ndiag 4" as parameter of pw.x 
(or cp.x or other executables). "make install" & "--prefix" do not work 
perfectly in QE-5.0.2, they have been fixed only recently. You can avoid the 
FFTW3 library, QE will use its internal driver and for a quad-core system is 
more than enough.

HTH
F


> On Nov 25, 2014, at 12:13 PM, Elliot Menkah  wrote:
> 
> 
> Signed PGP part
> Hello Everyone,
> 
> 
> I've compiled a parallel version of QE-5.0.2 on a quad-core workstation
> along with other dependencies such as openmpi-1.8.1 and fft-3.3.4 but
> when i run my calculations with it, I seem not to get the optimized
> computing power and efficiency as I expect.
> 
> The time line and factor for the same jobs is no different from when I
> run them with a serial version.
> 
> Could it be that I didn't compile it well or some dependencies are missing?
> 
> Can anyone please help me out.
> 
> Below is how I compiled the packages.
> -
> 
> #openmpi
> -
> ./configure --prefix=3D/usr
> make all
> make install
> -
> 
> 
> 
> #Configuring fftw
> -
> ./configure CC=3Dmpicc FC=3Dmpif90
> make
> make install
> -
> 
> 
> #Quantum espresso 5.0.2
> -
> ./configure --with-internal-blas --with-internal-lapack --enable-openmp
> --enable-parallel FFT_LIBS=3D/usr/lib/libfftw3.a --with-scalapack 2>&1|
> tee make_out3
>   =20
> make all 2>&1 | tee make_out4
> 
> 
> Thank you,
> 
> Kind Regards
> Elliot
> 
> 
> --
> Elliot S. Menkah
> Research Student - Computational Chemistry/ Computational Material Science
> Theoretical and Computational Chemistry
> Dept. of Chemistry
> Kwame Nkrumah UNiversity of Sci. and Tech.
> Kumasi
> Ghana
> 
> Tel: +233 243-055-717
> 
> Alt Email: elliotsmen...@gmail.com
>elliotsmen...@hotmail.com
> 
> 
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http://filippospiga.info ~ skype: filippo.spiga

«Nobody will drive us out of Cantor's paradise.» ~ David Hilbert

*
Disclaimer: "Please note this message and any attachments are CONFIDENTIAL and 
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Re: [Pw_forum] QHA Compile: Using gfortran instead of ifort

[Alberto Otero de la Roza]

Hi Paul,

> I believe I may have raised this question in the far distant past.
>
> It appears that under QE-5.1.1, it is still necessary to compile the source
> code within QHA using ifort.  Are any in the QE community aware of a QHA
> package compile-able with gfortran, or object code resulting from such?  Is
> there an equivalent to QHA somewhere within the QE package (or outside!)
> capable of yielding similar results such as, e.g., Debye temperatures?

There is gibbs2:

http://azufre.quimica.uniovi.es/software.html#gibbs2

It's free software, as far as I know you can build it with any
compiler conforming to the Fortran 90/95 standard, and gives you the
Debye temperature as well as lots of other stuff. If you run, for
instance, the example 01_simple.ing in the tests you'll get the Debye
temperature as field 14 in 01_simple.eos.

Best,

A.

---
Dr. Alberto Otero de la Roza
National Institute for Nanotechnology,
National Research Council of Canada,
11421 Saskatchewan Drive, Edmonton,
Alberta T6G 2M9, Canada

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[Pw_forum] problem in vc-relax/ relax

[Elio Physics]

Dear all,
I am trying to optimize a structure I am working on. Firstly, I try to find 
what is the lattice constant that gives the minimum energy. When this value is 
used and an scf calculation is performed, The pressure is not exactly zero ( ~ 
- 2.45 Kbars) and the forces on individual atoms are still large. So I try to 
relax the structure using calculation =' relax'., which works pretty fine. 
However, due to the differences in the scf calculation performed by 'relax' and 
by 'scf', I again get a pressure of -2.45 and a large force when I run an scf 
calculation.  I also realized that  P ~ 0 and forces are pretty low at a value 
of the lattice constant different from the one above (which gives the minimum 
energy). Can anyone tell me what can be done? how can i get low forces keeping 
the equilibrium lattice constant intact? Is it possible to use a lattice 
constant which does give a minimum energy structure but retains both P and 
Forces almost zero?
Any advice is highly appreciated.
ElioDerby university 
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Re: [Pw_forum] QHA Compile: Using gfortran instead of ifort

[Axel Kohlmeyer]

On Wed, Nov 26, 2014 at 11:27 PM, W2AGZ  wrote:
> To the Community:
>
>
>
> I believe I may have raised this question in the far distant past.
>
>
>
> It appears that under QE-5.1.1, it is still necessary to compile the source
> code within QHA using ifort.  Are any in the QE community aware of a QHA
> package compile-able with gfortran, or object code resulting from such?  Is
> there an equivalent to QHA somewhere within the QE package (or outside!)
> capable of yielding similar results such as, e.g., Debye temperatures?
>
>
>
> As always, thanks for any advice/guidance.

for the most part it seems as if all it needs is somebody with a
little bit to time to sit down and replace the loops using floating
point variables with the equivalent using integral loop variables.

using floating point loop variables is very, *very*, *VERY* bad
programming style (due to limitations of floating point math) and as
of the last decade removed from the fortran standard.

not really rocket science...

axel.

>
>
>
> Paul Michael Grant, PhD
>
> Physicist and Science Writer
>
> Senior Life Fellow, American Physical Society
>
> Fellow, Institute of Physics, United Kingdom
>
> w2...@w2agz.com
>
> http://www.w2agz.com
>
>
>
>
>
>
> ___
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-- 
Dr. Axel Kohlmeyer  akohl...@gmail.com  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.
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[Pw_forum] No space left on device

[robert.guzman]

Dear users and owners of wannier90.

To plot the wannier functions is necessary to obtain the UNK archives. 
Someone of yours know if is possible to reduce the size of the archive 
UNK? I used 4 pools in pw2wannier90.x

The last message in my calculation was:

forrtl: No space left on device
forrtl: severe (38): error during write, unit 98, file 
/state/partition1/25931.1.utopia/UNK00037.1

Best Regards.

Mgter. R. M. Guzmán A.
Insituto Balseiro. Argentina.

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[Pw_forum] Fwd: [Wannier] Incompatibility between Wannier Functions and Hamiltonian

[robert.guzman]

Hi everyone.

I solved my problem. I made the calculation one more time, but in this 
case firstly I calculate the wannier functions, only the wannier 
functions. After that I changed the keys in order to calculate the bands 
and the hamiltonian, only the bands an the hamiltonian (Here I extracted 
"wannier_plot = .true." and
"wannier_plot_supercell = 1). In this case the simetry of the wannier 
functions was consistently with the value of the locals hoppings.

Best Regards

Mgter. R. M. Guzmán A.
Insituto Balseiro. Argentina.

 Original Message 
Asunto: [Wannier] Incompatibility between Wannier Functions and 
Hamiltonian
Fecha: 2014-11-21 18:57
Remitente: "robert.guzman" 
Destinatario: wann...@quantum-espresso.org

I am trying to understand the results of wannier90. I looked the 
Hamiltonian and found that the symmetry of the hoppings are incompatible 
with the simmetry of the wannier functions. Mi system is graphene with 
an absorbate and this problem appears around the vecinity of the 
absorbate. More specifically the problem is the hopping between the 
absorbate orbital's  and the Pz orbitals of graphene.

I would like to know in which basis the hamiltonian was written. I dont 
know if exist an order to run the wannier90 code to get a hamiltonian 
compatible with the wannier orbitals.

I attached my code, I calculated the wannier orbitals, the bands, and 
the hamiltonian in the same run.

First I runned in wannier90.x:

num_bands =   154
num_wann  =   84

dis_win_min   = -26.d0
dis_win_max   = 11.d0
dis_froz_min  = -3.5d0
dis_froz_max  = 0.0d0
dis_num_iter  = 5
num_iter  = 5
num_print_cycles  = 10
search_shells = 64

conv_window = 3
guiding_centres = .true.
num_guide_cycles = 1

begin Unit_Cell_Cart
ang
9.8440.   0.
-4.9220   8.52515403   0.
0.   0.   12.0
end Unit_Cell_Cart

begin atoms_cart
ang
C1   1.229841053   0.709179359   5.949551118
C2   0.003577193   1.417300393   5.971868458
C1   0.006453278   2.843322235   5.981616971
C2  -1.229967481   3.553838312   5.971829025
C1  -1.230087047   4.969845443   5.949447950
C2  -2.461079646   5.682654655   5.953819305
C1  -2.460577041   7.102342988   5.941465227
C2  -3.690326679   7.811854582   5.953792147
C1   3.692094571   0.708569867   5.939801486
C2   2.462694369   1.418753377   5.951481237
C1   2.467689321   2.838561588   6.012420305
C2   1.228679112   3.548967457   6.014926017
C1   1.232952473   4.977177166   6.012008170
C2   0.000867285   5.682686605   5.951142664
C1   0.000642173   7.102386194   5.939523436
C2  -1.229932568   7.812781386   5.930948597
C1   6.154256791   0.709329937   5.948937623
C2   4.921410432   1.418883570   5.951696238
C1   4.916283497   2.838706807   6.013721556
C2   3.691912958   3.529553852   6.086993249
C1   3.690871576   4.970687568   6.411918947
C2   2.443425473   5.691968784   6.086288746
C1   2.457366207   7.097708901   6.013074588
C2   1.230338108   7.812030829   5.951324345
C1   8.614084178   0.701792359   5.982359578
C2   7.380585470   1.417354319   5.971609160
C1   7.377633868   2.843368084   5.982465512
C2   6.155355649   3.548972234   6.017453485
C1   6.150769009   4.977154471   6.016715345
C2   4.940071807   5.691778083   6.091799000
C1   4.926577605   7.097574480   6.016512018
C2   3.692016477   7.815626632   6.017107835
F3.682906044   4.967145771   7.963469359
end atoms_cart

begin projections
ang
c=   1.229841053, -0.000820641,  5.949551118   : s
c=   1.844841053,  1.064179359,  5.949551118   : s
c=   0.614841053,  1.064179359,  5.949551118   : s
c=   0.006453278,  2.133322235,  5.981616971   : s
c=   0.621453278,  3.198322235,  5.981616971   : s
c=  -0.608546722,  3.198322235,  5.981616971   : s
c=  -1.230087047,  4.259845443,  5.949447950   : s
c=  -0.615087047,  5.324845443,  5.949447950   : s
c=  -1.845087047,  5.324845443,  5.949447950   : s
c=  -2.460577041,  6.392342988,  5.941465227   : s
c=  -1.845577041,  7.457342988,  5.941465227   : s
c=  -3.075577041,  7.457342988,  5.941465227   : s
c=   3.692094571, -0.001430133,  5.939801486   : s
c=   4.307094571,  1.063569867,  5.939801486   : s
c=   3.077094571,  1.063569867,  5.939801486   : s
c=   2.467689321,  2.128561588,  6.012420305   : s
c=   3.082689321,  3.193561588,  6.012420305   : s
c=   1.852689321,  3.193561588,  6.012420305   : s
c=   1.232952473,  4.267177166,  6.012008170   : s
c=   1.847952473,  5.332177166,  6.012008170   : s
c=   0.617952473,  5.332177166,  6.012008170   : s
c=   0.000642173,  6.392386194,  5.939523436   : s
c=   0.615642173,  7.457386194,  5.939523436   : s
c=  -0.614357827,  7.457386194,  5.939523436   : s
c=   6.154256791, -0.000670063,  5.948937623   : s
c=   6.769256791,  1.064329937,  5.948937623   : s
c=   5.539256791,  1.064329937,  5.948937623   : s
c=   

Re: [Pw_forum] Symmetry not recognized in spin-orbit calculations

[Andrea Dal Corso]

Thank you for reporting this. There was actually a problem with rounding
errors in the search of point group symmetry. Now I corrected the bug in
the SVN version.

Andrea 


On Wed, 2014-11-26 at 17:27 -0500, Lin, Yangzheng wrote:
> Thanks Paolo, I got another solution too by modifying the lattice
> parameters a little bit to,
> 
> CELL_PARAMETERS (alat=  1.)
>0.0   5.440045000   5.440045000
>5.440045000   0.0   5.440045000
>5.440045000   5.440045000   0.0
> 
> I don't know the reason, but the symmetry problem was solved.
> 
> Yangzheng
> 
> 
> On Wed, Nov 26, 2014 at 4:26 PM, Paolo Giannozzi 
> wrote:
> 
> > On Wed, 2014-11-26 at 13:09 -0500, Lin, Yangzheng wrote:
> >
> > >  Error in routine tipo_sym (1):
> > >  symmetry not recognized
> > > Does anyone know how to solve this problem?
> >
> > not really a solution but a workaround: remove the following line
> >
> > >   verbosity = 'high',
> >
> > P.
> >
> > --
> > Paolo Giannozzi, Dept. Chemistry,
> > Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
> > Phone +39-0432-558216, fax +39-0432-558222
> >
> > ___
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> >
> 
> 
> 
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-- 
Andrea Dal CorsoTel. 0039-040-3787428
SISSA, Via Bonomea 265  Fax. 0039-040-3787249
I-34136 Trieste (Italy) e-mail: dalco...@sissa.it


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Re: [Pw_forum] Fwd: Re: Fwd: Re: parameteres of quantum dots

[Giuseppe Mattioli]

Dear Pablo

> I have read a
> few articles these two days and know I have things more clear. My last
> doubt is about The energy cutoff I have to choose. The total energy of
> my system is about 34 ry. The question is: Shall i used a energy
> cutoff of 300.0 ry or so?

You still have a vague idea of what is a plane wave basis set for ab initio 
calculations... :-)
The brute answer to your question is: increase separately ecutwfc and ecutrho 
until a given parameter of your calculation (total energy, lattice 
parameters, forces on atoms, whatever...) becomes stationary within an 
arbitrary range of values, let us say, for instance, 0.001 Ry in the case of 
total energy. Of course there are common ranges of ecutwfc and ecutrho values 
usually suitable for a given kind of calculation, and they depend 
(mainly) on the pseudopotentials used in such calculation. You *should not* 
perform plane-wave calculations if you don't know (possibly quite well) 
what is a pseudopotential and which are the theoretical and practical 
differences between the ultrasoft, norm-conserving and PAW approaches. You may 
start from this treasure "hidden" in the QE distribution :-)

YourEspresso/5.1/atomic/Doc/pseudo-gen.pdf

and from all the references cited therein.

HTH

Giuseppe

On Thursday, November 27, 2014 12:49:13 AM pablohi wrote:
> Thanks for your help!
> 
> I'm learning this by my own in order to do my master thesis. I didn't
> choose the atom positions, my supervisors did it for me. I have read a
> few articles these two days and know I have things more clear. My last
> doubt is about The energy cutoff I have to choose. The total energy of
> my system is about 34 ry. The question is: Shall i used a energy
> cutoff of 300.0 ry or so?
> 
> Thanks in advance, your help was very usefull for me!
> 
> Regards
> 
> Pablo Hidalgo Romera
> Computer architecture and electronics department(student)
> University of Granada(Spain)
> 
>  Mensaje original 
> Asunto: Re: [Pw_forum] Fwd: Re:  parameteres of quantum dots
> Fecha: 2014-11-24 11:34
> Remitente: Giuseppe Mattioli 
> Destinatario: PWSCF Forum 
> Respuesta a: PWSCF Forum 
> 
> 
> 
> Dear Pablo
> 
> It seems that you are attempting to perform complex calculations
> without
> going through a proper training and without supervision. There are
> several critical issues in your input file, and this forum is generally
> not intended for training. I can only point out the bad mistakes, but
> you should take your time to learn the hard way...
> 
> > I want to simulate the energies spectrum of CdSe Quantum Dots
> 
> What is it? Are you talking about optical absorption spectrum? Are you
> aware of the difference between DFT and TD-DFT?
> 
> >  ibrav = 0,
> > 
> > CELL_PARAMETERS {bohr}
> > 
> > 
> > 
> >32.5033024000 0.00 0.00
> > 
> >-16.251651200028.1486855853 0.00
> > 
> >  0.00 0.0039.8082529177
> 
> why a monoclinic cell?
> 
> >  ecutwfc = 10.0,ecutrho = 80.0,
> 
> poorly unconverged plane wave basis set
> 
> > ATOMIC_POSITIONS  {bohr}
> 
> find attached an image representing your system, as obtained by opening
> your input with xcrysden. There is clearly something wrong, and apart
> from the position of H atoms, too close to the Cd and Se atoms, the
> structure seems to be the right one. A hint: look for the options of
> ATOMIC_POSITIONS in the pw.x manual.
> 
> >  occupations='smearing', smearing='marzari-vanderbilt',
> 
> degauss=0.05
> 
> Is your system a metal?
> 
> >  noncolin = .false.
> 
> useless
> 
> > calculation='bands'
> 
> why do you need it?
> 
> HTH
> 
> Giuseppe
> 
> 
> 
> - Article premier - Les hommes naissent et demeurent
> 
> libres et ègaux en droits. Les distinctions sociales
> 
> ne peuvent être fondèes que sur l'utilitè commune
> 
> - Article 2 - Le but de toute association politique
> 
> est la conservation des droits naturels et
> 
> imprescriptibles de l'homme. Ces droits sont la libertè,
> 
> la propriètè, la sùretè et la rèsistance à l'oppression.
> 
> 
> 
>   Giuseppe Mattioli
> 
>   CNR - ISTITUTO DI STRUTTURA DELLA MATERIA
> 
>   v. Salaria Km 29,300 - C.P. 10
> 
>   I 00015 - Monterotondo Stazione (RM)
> 
>   Tel + 39 06 90672836 - Fax +39 06 90672316
> 
>   E-mail: 
> 
>   http://www.ism.cnr.it/english/staff/mattiolig
> 
>   ResearcherID: F-6308-2012


- Article premier - Les hommes naissent et demeurent
libres et ègaux en droits. Les distinctions sociales
ne peuvent être fondèes que sur l'utilitè commune
- Article 2 - Le but de toute association politique
est la conservation des droits naturels et 
imprescriptibles de l'homme. Ces droits sont la libertè,
la 

Re: [Pw_forum] Issue with PAW-BLYP pseudopots and spin-polarized calculations.

[Lorenzo Paulatto]

Dear Gisela,
I have not implemented BLYP + PAW + spin. It is simple but not 
completely straightforward as it has a few more terms than most functionals.

I can do it, it won't take long, but I cannot test it.

If you agree to properly test it, I'll send you the file when it is done.

kind regards


On 27/11/14 02:37, Gisela Bocan wrote:
> Already tried that. Did not work :-(
>
> The output I always get looks like this:
>
>   Program PWSCF v.5.1 starts on 21Nov2014 at 13:48:22
>
>   This program is part of the open-source Quantum ESPRESSO suite
>   for quantum simulation of materials; please cite
>   "P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 (2009);
>URL http://www.quantum-espresso.org;,
>   in publications or presentations arising from this work. More
> details at
> http://www.quantum-espresso.org/quote
>
>   Parallel version (MPI), running on 9 processors
>   R & G space division:  proc/nbgrp/npool/nimage =   9
>   Waiting for input...
>   Reading input from standard input
>
>   Current dimensions of program PWSCF are:
>   Max number of different atomic species (ntypx) = 10
>   Max number of k-points (npk) =  4
>   Max angular momentum in pseudopotentials (lmaxx) =  3
> file F.blyp-n-kjpaw_t_psl.1.0.0.UPF: wavefunction(s)  2S
> 2P renormalized
> file H.blyp-kjpaw_t_psl.1.0.0.UPF: wavefunction(s)  1S
> renormalized
>
>   Subspace diagonalization in iterative solution of the eigenvalue
> problem:
>   scalapack distributed-memory algorithm (size of sub-group:  2*  2
> procs)
>
>
>   Parallelization info
>   
>   sticks:   dense  smooth PW G-vecs:dense   smooth  PW
>   Min 105  41 1213435 3379 554
>   Max 106  42 1313454 3414 567
>   Sum 949 373113   120995305655019
>
>   Generating pointlists ...
>   new r_m :   0.2063 (alat units)  1.5922 (a.u.) for type1
>   new r_m :   0.2063 (alat units)  1.5922 (a.u.) for type2
>   new r_m :   0.4125 (alat units)  3.1845 (a.u.) for type3
>
>
>   bravais-lattice index =8
>   lattice parameter (alat)  =   7.7200  a.u.
>   unit-cell volume  =2530.5481 (a.u.)^3
>   number of atoms/cell  =   17
>   number of atomic types=3
>   number of electrons   =81.00
>   number of Kohn-Sham states=   49
>   kinetic-energy cutoff =  20.  Ry
>   charge density cutoff = 200.  Ry
>   convergence threshold =  1.0E-08
>   mixing beta   =   0.7000
>   number of iterations used =8  plain mixing
>   Exchange-correlation  =  SLA  LYP  B88  BLYP ( 1  3  1  3 0)
>
>   celldm(1)=   7.72  celldm(2)=   1.00  celldm(3)=   5.50
>   celldm(4)=   0.00  celldm(5)=   0.00  celldm(6)=   0.00
>
>   crystal axes: (cart. coord. in units of alat)
> a(1) = (   1.00   0.00   0.00 )
> a(2) = (   0.00   1.00   0.00 )
> a(3) = (   0.00   0.00   5.50 )
>
>   reciprocal axes: (cart. coord. in units 2 pi/alat)
> b(1) = (  1.00  0.00  0.00 )
> b(2) = (  0.00  1.00  0.00 )
> b(3) = (  0.00  0.00  0.181818 )
>
>
>   PseudoPot. # 1 for  F read from file:
>   /home/gbocan/HLiF001/PseudoPots/F.blyp-n-kjpaw_t_psl.1.0.0.UPF
>   MD5 check sum: ab51591266cfe6c1355604df55a98c19
>   Pseudo is Projector augmented-wave + core cor, Zval =  7.0
>   Generated using "atomic" code by A. Dal Corso  v.5.1
>   Shape of augmentation charge: PSQ
>   Using radial grid of 1105 points,  4 beta functions with:
>  l(1) =   0
>  l(2) =   0
>  l(3) =   1
> l(4) =   1
>   Q(r) pseudized with 0 coefficients
>
>
>   PseudoPot. # 2 for Li read from file:
>   /home/gbocan/HLiF001/PseudoPots/Li.blyp-s-kjpaw_t_psl.1.0.0.UPF
>   MD5 check sum: aa34437da800ee119838ddb9a2ae
>   Pseudo is Projector augmented-wave, Zval =  3.0
>   Generated using "atomic" code by A. Dal Corso  v.5.1
>   Shape of augmentation charge: PSQ
>   Using radial grid of 1017 points,  4 beta functions with:
>  l(1) =   0
>  l(2) =   0
>  l(3) =   1
>  l(4) =   1
>   Q(r) pseudized with 0 coefficients
>
>
>   PseudoPot. # 3 for  H read from file:
>   /home/gbocan/HLiF001/PseudoPots/H.blyp-kjpaw_t_psl.1.0.0.UPF
>   MD5 check sum: ab4c408302926066b4b306e7e4129f31
>   Pseudo is Projector augmented-wave, Zval =  1.0
>   Generated using "atomic" code 

Re: [Pw_forum] xcrysden shows only primitive structure for output of QE

[Tone Kokalj]

On Sat, 2014-11-22 at 20:40 -0800, James Lee wrote:
> Hi 
> When I use ibrav=0 and conventional cell coordinates, xcrysden shows 
> conventional cell for vc-relax
> output, and everything is ok.

When ibrav=0, xcrysden shows the lattice as specified by
CELL_PARAMETERS ...

> when I use ibrav=2, xcrysden can show both primitive and conventional cell
> for input file, but for its vc-relax output, xcrysden only shows optimized 
> primitive cell. 

This is correct. For output, xcrysden relies only on the data stored in
the output file. Because only the primitive vectors are printed in the
output, xcrysden shows only primitive lattice.

If you want to see also the conventional lattice then transform pw.x
output file to XSF file (using pwo2xsf.sh filter) and then supplement
the XSF file with the corresponding convetional vectors, specified by
the CONVVEC card (see: http://www.xcrysden.org/doc/XSF.html#__toc__4 )

Regards, Tone

-- 
Anton Kokalj
J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia 
(tel: +386-1-477-3523 // fax:+386-1-477-3822)

Please, if possible, avoid sending me Word or PowerPoint attachments.
See:  http://www.gnu.org/philosophy/no-word-attachments.html

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Re: [Pw_forum] Symmetry not recognized in spin-orbit calculations

[Paolo Giannozzi]

On Wed, 2014-11-26 at 17:27 -0500, Lin, Yangzheng wrote:

> Thanks Paolo, I got another solution too by modifying the lattice
> parameters a little bit to,
> 
> CELL_PARAMETERS (alat=  1.)

unrelated to your problem: The code can in principle work with 
any value of the lattice parameter, but it is a good habit to
use a sensible value, not 1, or the conversion factor from A 
to a.u., as often done for no good reason (both lattice vectors
and atomic positions can be provided in a.u. or in A)

>0.0   5.440045000   5.440045000
>5.440045000   0.0   5.440045000
>5.440045000   5.440045000   0.0

> I don't know the reason, but the symmetry problem was solved.

nor do I, but the code shouldn't have stopped, since the computed
information on space groups is used only for printout and not for
computations

Paolo
> 
> Yangzheng
> 
> 
> On Wed, Nov 26, 2014 at 4:26 PM, Paolo Giannozzi
>  wrote:
> On Wed, 2014-11-26 at 13:09 -0500, Lin, Yangzheng wrote:
> 
> >  Error in routine tipo_sym (1):
> >  symmetry not recognized
> > Does anyone know how to solve this problem?
> 
> not really a solution but a workaround: remove the following
> line
> 
> >   verbosity = 'high',
> 
> P.
> 
> --
> Paolo Giannozzi, Dept. Chemistry,
> Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
> Phone +39-0432-558216, fax +39-0432-558222
> 
> ___
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> 
> 
> 
> -- 
> Yangzheng Lin
> 
> Postdoctoral Associate
> 
> Geophysical Laboratory, Carnegie Institution for Science
> 
> 5251 Broad Branch Rd. NW, Washington, DC 20015, USA
> 
> ___
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-- 
 Paolo Giannozzi, Dept. Chemistry, 
 Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
 Phone +39-0432-558216, fax +39-0432-558222 

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