Re: [QE-users] NEB: Atoms do not get relaxed

[Ari P Seitsonen]

I think that I found it: Switching the 'restart_mode' from 'restart' to 
'from_scratch' in the name list '' "released" the atoms to relax 
properly.


  I have no idea why this should have an effect on the relaxation: I 
always keep it as 'restart' in the calculations with the NEB, and the code 
'pw.x' performs the restart if the files needed for a restart are present, 
otherwise the calculation starts from the given configuration and with the 
same initialisation of the electronic structure as with 'from_scratch', so 
I was expecting the same to happen with the NEB. My mistake, "never expect 
the logic of the developer to be the same as your own". Now happily 
computing all kinds of barriers and paths! :)


Greetings from Paris and Grazie a Giuseppe again,

   apsi

-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-
  Ari Paavo Seitsonen / ari.p.seitso...@iki.fi / http://www.iki.fi/~apsi/
Слава Україні


On Thu, 27 Apr 2023, Ari P Seitsonen wrote:



Dear Giuseppe,

 Thank you for the comment. One of my concerns was that the energy in the 
images does not really change:


grep -w '  4  ' neb.out
4 -78481.6171806   29.739170F
4 -78481.6171811   29.738137F
4 -78481.6171811   29.736993F
4 -78481.6171811   29.734436F
4 -78481.6171812   29.727381F
4 -78481.6171809   29.718296F
4 -78481.6171808   29.712880F
4 -78481.6171810   29.713046F
4 -78481.6171810   29.719086F
4 -78481.6171811   29.729326F
4 -78481.6171812   29.740800F
4 -78481.6171805   29.752151F
4 -78481.6171812   29.761356F
4 -78481.6171812   29.769083F
4 -78481.6171805   29.774024F
4 -78481.6171812   29.776518F
4 -78481.6171800   29.776688F
4 -78481.6171811   29.773882F

There are forces on the atoms, here again on one of them on the fourth image:

atom   84 type  2   force =-0.004078720.00078289   -0.00018719
atom   84 type  2   force =-0.004074940.00078224   -0.00018711
atom   84 type  2   force =-0.004075540.00078237   -0.00018713
atom   84 type  2   force =-0.004075600.00078248   -0.00018709
atom   84 type  2   force =-0.004075110.00078229   -0.00018712
atom   84 type  2   force =-0.004076190.00078255   -0.00018726
atom   84 type  2   force =-0.004076230.00078272   -0.00018718
atom   84 type  2   force =-0.004075280.00078225   -0.00018721
atom   84 type  2   force =-0.004075640.00078257   -0.00018705
atom   84 type  2   force =-0.004075000.00078222   -0.00018713
atom   84 type  2   force =-0.004075770.00078249   -0.00018711
atom   84 type  2   force =-0.004069050.00078120   -0.00018643
atom   84 type  2   force =-0.004075510.00078243   -0.00018722
atom   84 type  2   force =-0.004072710.00078203   -0.00018711
atom   84 type  2   force =-0.004077960.00078294   -0.00018727
atom   84 type  2   force =-0.004076070.00078266   -0.00018716
atom   84 type  2   force =-0.004074370.00078207   -0.00018715
atom   84 type  2   force =-0.004076420.00078274   -0.00018719

The 'path length' indeed keeps on increasing - what is this, if the energies 
of the images remain the same?


initial path length   =  5. bohr
path length  =  5.000 bohr
path length  =  5.000 bohr
path length  =  5.003 bohr
path length  =  5.013 bohr
path length  =  5.094 bohr
path length  =  5.337 bohr
path length  =  5.702 bohr
path length  =  6.163 bohr
path length  =  6.695 bohr
path length  =  7.277 bohr
path length  =  7.897 bohr
path length  =  8.546 bohr
path length  =  9.216 bohr
path length  =  9.904 bohr
path length  = 10.606 bohr
path length  = 11.321 bohr
path length  = 12.047 bohr
path length  = 12.783 bohr

Probably I am doing something really stupid somewhere... I will try to look 
at the source code next and try to understand somewhat better for what is 
done in the code, the meaning of the variables and so on.


   Greetings,

  apsi

-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-
 Ari Paavo Seitsonen / ari.p.seitso...@iki.fi / htt

Re: [QE-users] NEB: Atoms do not get relaxed

[Ari P Seitsonen]

Dear Giuseppe,

  Thank you for the comment. One of my concerns was that the energy in the 
images does not really change:


grep -w '  4  ' neb.out
 4 -78481.6171806   29.739170F
 4 -78481.6171811   29.738137F
 4 -78481.6171811   29.736993F
 4 -78481.6171811   29.734436F
 4 -78481.6171812   29.727381F
 4 -78481.6171809   29.718296F
 4 -78481.6171808   29.712880F
 4 -78481.6171810   29.713046F
 4 -78481.6171810   29.719086F
 4 -78481.6171811   29.729326F
 4 -78481.6171812   29.740800F
 4 -78481.6171805   29.752151F
 4 -78481.6171812   29.761356F
 4 -78481.6171812   29.769083F
 4 -78481.6171805   29.774024F
 4 -78481.6171812   29.776518F
 4 -78481.6171800   29.776688F
 4 -78481.6171811   29.773882F

There are forces on the atoms, here again on one of them on the fourth 
image:


 atom   84 type  2   force =-0.004078720.00078289   -0.00018719
 atom   84 type  2   force =-0.004074940.00078224   -0.00018711
 atom   84 type  2   force =-0.004075540.00078237   -0.00018713
 atom   84 type  2   force =-0.004075600.00078248   -0.00018709
 atom   84 type  2   force =-0.004075110.00078229   -0.00018712
 atom   84 type  2   force =-0.004076190.00078255   -0.00018726
 atom   84 type  2   force =-0.004076230.00078272   -0.00018718
 atom   84 type  2   force =-0.004075280.00078225   -0.00018721
 atom   84 type  2   force =-0.004075640.00078257   -0.00018705
 atom   84 type  2   force =-0.004075000.00078222   -0.00018713
 atom   84 type  2   force =-0.004075770.00078249   -0.00018711
 atom   84 type  2   force =-0.004069050.00078120   -0.00018643
 atom   84 type  2   force =-0.004075510.00078243   -0.00018722
 atom   84 type  2   force =-0.004072710.00078203   -0.00018711
 atom   84 type  2   force =-0.004077960.00078294   -0.00018727
 atom   84 type  2   force =-0.004076070.00078266   -0.00018716
 atom   84 type  2   force =-0.004074370.00078207   -0.00018715
 atom   84 type  2   force =-0.004076420.00078274   -0.00018719

The 'path length' indeed keeps on increasing - what is this, if the 
energies of the images remain the same?


 initial path length   =  5. bohr
 path length  =  5.000 bohr
 path length  =  5.000 bohr
 path length  =  5.003 bohr
 path length  =  5.013 bohr
 path length  =  5.094 bohr
 path length  =  5.337 bohr
 path length  =  5.702 bohr
 path length  =  6.163 bohr
 path length  =  6.695 bohr
 path length  =  7.277 bohr
 path length  =  7.897 bohr
 path length  =  8.546 bohr
 path length  =  9.216 bohr
 path length  =  9.904 bohr
 path length  = 10.606 bohr
 path length  = 11.321 bohr
 path length  = 12.047 bohr
 path length  = 12.783 bohr

Probably I am doing something really stupid somewhere... I will try to 
look at the source code next and try to understand somewhat better for 
what is done in the code, the meaning of the variables and so on.


Greetings,

   apsi

-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-
  Ari Paavo Seitsonen / ari.p.seitso...@iki.fi / http://www.iki.fi/~apsi/
Слава Україні


On Thu, 27 Apr 2023, Giuseppe Mattioli wrote:



Dear Ari
The NEB is not exactly "stuck"


 path length  =  8.546 bohr
 path length  =  9.216 bohr
 path length  =  9.904 bohr


The MEP length keeps increasing. Maybe a look into the trajectory 
files can tell you what's happening. If any other source of 
misbehavior can be excluded, try to go ahead (maybe fixing the 
position of "useless" atoms). I've experienced NEB in large systems 
converged after several hundreds steps.

HTH
Giuseppe

Quoting Ari P Seitsonen :


Dear Users,

  I have a problem in the calculations with the method NEB: The 
atoms do not get relaxed even if there are clearly forces on the 
atoms. The electronic structure converges well, and the relaxation 
of the ions follows nicely when the NEB is not used.


  I have in the input

BEGIN
BEGIN_PATH_INPUT

  restart_mode  = 'restart'
  string_method 

[QE-users] NEB: Atoms do not get relaxed

[Ari P Seitsonen]

Dear Users,

  I have a problem in the calculations with the method NEB: The atoms do 
not get relaxed even if there are clearly forces on the atoms. The 
electronic structure converges well, and the relaxation of the ions 
follows nicely when the NEB is not used.


  I have in the input

BEGIN
BEGIN_PATH_INPUT

  restart_mode  = 'restart'
  string_method = 'neb'
  nstep_path=  30
  ds= 0.2
  opt_scheme= "broyden"
  num_of_images = 8
  k_max = 0.3
  k_min = 0.2
  CI_scheme = "auto"
!  minimum_image = .true.
  first_last_opt= .true.
  path_thr  = 0.1
/
END_PATH_INPUT

and

 
 /

I have tried with different values of 'num_of_images', 'k_min' and 
'k_max', with the climbing image and without. One calculation - a 
diffusion path of one ad-atom on a surface - worked well, all other become 
stuck with the output like:



 -- iteration  12 --

 cpu =  0   tcpu =   9589.5self-consistency for image   1
 cpu =  0   tcpu =   9656.9self-consistency for image   3
 cpu =  0   tcpu =   9823.9self-consistency for image   5
 cpu =  0   tcpu =  10043.8self-consistency for image   7

 activation energy (->) =  10.012055 eV
 activation energy (<-) =   6.833374 eV

 imageenergy (eV)error (eV/A)frozen

 1 -78491.59206780.000987F
 2 -78490.33340357.018378F
 3 -78486.4101831   18.058881F
 4 -78481.6171805   29.752151F
 5 -78481.5800131   29.996389F
 6 -78485.0169815   13.489042F
 7 -78487.70206497.675245F
 8 -78488.41338728.072137F

 climbing image =  5

 path length  =  8.546 bohr
 inter-image distance =  1.221 bohr

 -- iteration  13 --

 cpu =  0   tcpu =  10165.0self-consistency for image   1
 cpu =  0   tcpu =  10267.1self-consistency for image   3
 cpu =  0   tcpu =  10487.8self-consistency for image   5
 cpu =  0   tcpu =  10710.2self-consistency for image   7

 activation energy (->) =  10.011390 eV
 activation energy (<-) =   6.833374 eV

 imageenergy (eV)error (eV/A)frozen

 1 -78491.59140280.000493F
 2 -78490.33340367.099250F
 3 -78486.4101837   17.820470F
 4 -78481.6171812   29.761356F
 5 -78481.5800130   29.998875F
 6 -78485.0169810   13.636010F
 7 -78487.70206487.675132F
 8 -78488.41338708.071850F

 climbing image =  5

 path length  =  9.216 bohr
 inter-image distance =  1.317 bohr

 -- iteration  14 --

 cpu =  0   tcpu =  10843.3self-consistency for image   1
 cpu =  0   tcpu =  10962.6self-consistency for image   3
 cpu =  0   tcpu =  11183.6self-consistency for image   5
 cpu =  0   tcpu =  11420.4self-consistency for image   7

 activation energy (->) =  10.011390 eV
 activation energy (<-) =   6.833374 eV

 imageenergy (eV)error (eV/A)frozen

 1 -78491.59140320.000582F
 2 -78490.33340347.139704F
 3 -78486.4101836   17.548234F
 4 -78481.6171812   29.769083F
 5 -78481.5800132   29.998295F
 6 -78485.0169814   13.849319F
 7 -78487.70206427.669197F
 8 -78488.41338718.072137F

 climbing image =  5

 path length  =  9.904 bohr
 inter-image distance =  1.415 bohr

 -- iteration  15 --

...

  So the atoms do not move, the electronic structure is converged in few 
iterations, but the energies of individual images change in the micro-eVs.


  Any idea would be appreciated; thank you in advance for any hints.

Greetings,

   apsi

-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-
  Ari Paavo Seitsonen / ari.p.seitso...@iki.fi / http://www.iki.fi/~apsi/
Слава Україні___
The Quantum ESPRESSO community stands by the Ukrainian
people and expresses its concerns about the devastating
effects that the Russian military offensive has 

Re: [QE-users] Optimizing QE Install

[Ari P Seitsonen]

Dear Robert,

  Adding to the comments and hints by Lorenzo and Paolo, I would just like 
to add that i) I usually use OpenBLAS (https://www.OpenBLAS.net/) instead 
of the NetLib versions of BLAS+LAPACK (compiled from source, it easily 
adapts to the underlying hardware, with few options and it seems to me to 
be close to the performance of Intel MKL et co; despite its name it also 
contains LAPACK, not only BLAS) and ii) why OpenMPI 1.x.y, as the latest 
versions are at 4.x.y?


  I would also ensure that the environmental variable 'OMP_NUM_THREADS' is 
indeed set correctly, even if at '1', to avoid a burst of OpenMP threads. 
The correct number of course depends on the number of cores available, 
hyper-threading or not (or how is it called on the AMD EPYC), the number 
of MPI tasks and the amount of memory available, should the latter become 
a bottleneck.


Greetings from Paris,

   apsi

-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-
  Ari Paavo Seitsonen / ari.p.seitso...@iki.fi / http://www.iki.fi/~apsi/


On Sat, 23 Jan 2021, Robert Stanton wrote:


Dear all,
     I am able to successfully install parallel QE and get everything to run 
smoothly, however after testing against an install on an
externally maintained cluster I'm finding my speed to be slower by a factor of 
5-10x when keeping the system, core number, QE version,
etc. the same. 

    I'm not sure the degree to which this could be a hardware discrepancy (Xeon 
Silvers vs new EPYCs), v.s. how much could be a
sub-optimal compilation of QE. The slower QE install is being done with 
blas/lapack 3.8.0 and openmpi 1.10.7. I'm just curious if
there is anything very clearly not ideal about this environment, or if it is 
likely something I'll just need to troubleshoot with
smaller settings? Thanks so much in advance for any insights you can provide!

Regards, 
Robert Stanton
Graduate Student
Clarkson University

___
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] SCF calculations on WN supercell not converging

[Ari P Seitsonen]

Dear Coralie,

  Besides the concern of the possibly errorneous pseudo potential, I 
would recommend that you begin with a simpler system at the beginning if 
you are not yet familiar with the (periodic) DFT calculations, in 
particular the broadening, empty bands, choice of k points and so on.


  In particular here, it seems that you have been trying to use quite many 
k points in the directions corresponding to the surface plane (earlier 
2x2, now 4x4 will consume plenty of computing time), and in particular in 
the direction corresponding to the surface normal, where you have (in 
principle) no periodicity there is no need to specify more than "1" in the 
k points. I would also recommend to try if you can make the laterally 1x1 
unit cell, without the adsorbate to converge, before going to such large a 
slab. Are you sure about the values of the 'starting_magnetization()' on 
the nitrogen and tungsten atoms - 60 % polarisation on the latter for 
example (please notice that this is in _relative_ units, so the tungsten 
atoms have a magnetic moment of 0.6 * 14 valence electrons in the 
initial electron density - the magnetisation is larger than the "true 
valence" of four electrons of W)? The initial electronic structure might 
be very far from the final, self-consistent one that you are trying to 
reach. What is the magnetic ordering in the bulk, is it ferro-magnetic?


Greetings from Paris,

   apsi

-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-
  Ari Paavo Seitsonen / ari.p.seitso...@iki.fi / http://www.iki.fi/~apsi/


On Fri, 19 Jun 2020, Coralie Khabbaz wrote:


Hello,
Thank you so much for your response. Do you think it will converge if I use the 
PAW pseudopotential instead of
the ultrasoft?

On Fri, 19 Jun 2020 at 04:15, Andrea Urru  wrote:
  Dear Coralie, 
the issue you are facing is most likely due to the W pseudopotential, which 
gives convergence issues if
used in slab systems 
with vacuum space, as reported here: 
https://dalcorso.github.io/pslibrary/PP_list.html

The behavior you describe might be due to a ghost state, but I am not deeply 
expert in pseudopotentials
and I cannot swear. 
I would suggest you to try a different pseudopotential. If you wish to use 
Ultrasoft pseudopotentials you
may try the one from 
Pslibrary 0.3.1. 

Best regards, 

Andrea Urru

Ph. D. Student in Condensed Matter 
SISSA - Trieste (Italy)  

  Il giorno 17 giu 2020, alle ore 23:31, Coralie Khabbaz 
 ha
  scritto:

Hello,
I am doing an scf calculation on a tungsten nitride (WN) slab (catalyst), with 
a methane molecule 5
Angstrom away from the surface. The energy values are not converging, even 
after 533 iterations.
The energy values are very negative, and then they increase to a positive value 
then decrease a lot
again. Before building the supercell, I had a WN unit cell with 433 K-points. 
Then, I built the
super cell by using a scaling of 333 and miller indices of 100. I tried using K 
points of 111 and
222 for my super cell, but the calculations didn't converge for both. 

This is the input file I am using:


    calculation  = "scf"
    max_seconds  =  1.72800e+05
    pseudo_dir   = "/home/coralee/projects/def-jkopysci/coralee/.pseudopot"
    restart_mode = "from_scratch"
/


    a                         =  1.24907e+01
    angle1(1)                 =  0.0e+00
    angle1(2)                 =  0.0e+00
    angle2(1)                 =  0.0e+00
    angle2(2)                 =  0.0e+00
    b                         =  1.34803e+01
    c                         =  2.52767e+01
    cosab                     =  6.12323e-17
    cosac                     =  6.12323e-17
    cosbc                     = -1.85547e-01
    degauss                   =  1.0e-02
    ecutrho                   =  4.5e+02
    ecutwfc                   =  5.0e+01
    ibrav                     = 14
    nat                       = 113
    nspin                     = 2
    ntyp                      = 4
    occupations               = "smearing"
    smearing                  = "gaussian"
    starting_magnetization(1) =  2.0e-01
    starting_magnetization(2) =  6.0e-01
    starting_magnetization(3) =  0.0e+00
    starting_magnetization(4) =  0.0e+00
/


    conv_thr         =  1.0e-06
    diagonalization  = "david"
    electron_maxstep = 528
    mixing_beta      =  4.0e-01
    startingpot      = "atomic"
    startingwfc      = "atomic+random"
/

K_POINTS {automatic}
 4  4  2  0 0 0

ATOMIC_SPECIES
N      14.00674  N.pbe-n-rrkjus_psl.1.0.0.UPF
W     183.84000  W.pbe-spn-rrkjus_psl.1.0.0.UPF
C      12.01070  C.pbe-n-rrkjus_psl.1.0.0.UPF
H       1.00794  H.pbe-rrkjus_psl.1.0.0.UPF

ATOMIC_POSITIONS {angstrom}
N       2.481849   0.418242  14.837784
N       6.645429   0.418242  14.837784
N      10.809008   0.418242  14.837784
N       2.481849   4.911686  14.837784
N       6.645429   4.911686  14.837784
N      10.809008   4.911686  14.837784
N       

Re: [QE-users] [Pw_forum] input file for isolated atom

[Ari P Seitsonen]

Dear Ajmalghan,

  Some quick comments:

 - Why do you use k point in the case of an isolated atom?? Well, that 
should not matter, just that you are wasting computing time


 - I guess that the spherical symmetry of the atom is broken; thus I would 
use a non-cube cell, preferably the orthorhombic cell, with slightly 
different lengths of the basis vectors of the unit cell. Then to break the 
symmetry, you can use some randomisation of the initial wave functions. 
And still, the convergence is probably going to be very difficult... You 
can indeed try to fix the magnetisation; and I would reduce the 
'mixing_beta' to something (very) small - in principle already at the 
first step the electron density should be close to the self-consistent 
one, bar the loss of sphericality and the randomised wave function


 - Please remember that the scale of 'starting_magnetisation' is from -1 
to +1, meaning that all the electrons are spin-polarised either up or 
down, whereas in your case you only want to polarise the two valence 
electrons out of the valence of the pseudo potential that seems to be 12 
electrons


  Well, Good Luck. :)

Greetings from Paris,

   apsi

-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-
  Ari Paavo Seitsonen / ari.p.seitso...@iki.fi / http://www.iki.fi/~apsi/
Ecole Normale Supérieure (ENS), Département de Chimie, Paris
Mobile (F) : +33 789 37 24 25(CH) : +41 79 71 90 935


On Sat, 9 Nov 2019, Ajmal Ghan wrote:


Hello all,

I have gone through all the archived discussion about cohesive energy 
calculation.

I am trying to calculate the cohesive energy of Ti which is  4.85eV. But I am 
getting 5.23 eV which is closer. But I have found from a previous discussion
here ( 
https://www.mail-archive.com/users@lists.quantum-espresso.org/msg11410.html ) 
that, the final magnetization should be 2 Bohr mag/ cell at the end
of calculation for Ti and smearing contribution of energy should be 0.0Ry. 
But I am getting to get 3.83 Bohr mag/cell and a significant smearing 
contribution = -0.03295688 Ry.

Anyone help me to sort this. what should I change in the input?


here is my input,


   calculation      = 'scf'
   restart_mode     = 'from_scratch'
   pseudo_dir       = '/work/shared/s-tih/pseudo/'
   prefix           = 'Tifree_deg1_50_8k_1'
   wf_collect       = .true.
   tstress          = .true.
   tprnfor          = .true.
   forc_conv_thr    = 1.0d-6
   verbosity        = 'high'
 /

   ibrav            = 1
   celldm(1)     = 20
   nat              = 1
   ntyp            = 1
   ecutwfc       = 50      //( I have performed convergence study. But since 
degauss is reduced to 0.01, i increased ecut) 
   ecutrho       = 400
   nspin          = 2
   starting_magnetization(1) = 1        // I think, the final magnetisation 
should be 2 bohr mag/ cell at the end of calculation.
   nosym            = .true                    /// I hope this is enough to 
break the symmetry
   nbnd             = 100
   occupations      = 'smearing',  smearing='mp', degauss=0.01D0
 /

   diagonalization  = 'cg'
   mixing_beta      = 0.7d00
   conv_thr         = 1.0d-8     // I used even higher convergence since 
smearing is reduced.
/
ATOMIC_SPECIES
  Ti  47.8670  Ti.pbe-spn-rrkjus_psl.1.0.0.UPF


ATOMIC_POSITIONS (crystal)
   Ti     0.5 0.5 0.5

K_POINTS {automatic}
  8  8  5  0  0  0


I don't really know this is the correct way to post a reply. All input is 
welcome. 

Thanks & Regards,
--
Ajmalghan MUTHALI

Post doctorate researcher
Laboratoire ICB 
UMR 6303 CNRS-Université de Bourgogne 
9 Avenue Alain Savary, BP 47870 
F-21078 DIJON Cedex, France 
Tel: +33-(0)7.69.28.19.91 
Email : ajmalghan.muth...@u-bourgogne.fr

___
Quantum ESPRESSO is supported by MaX (www.max-centre.eu/quantum-espresso)
users mailing list users@lists.quantum-espresso.org
https://lists.quantum-espresso.org/mailman/listinfo/users

Re: [QE-users] DFT + U not working on Sn 4d

[Ari P Seitsonen]

Dear ?, (please read the instructions about posting to this Forum, signing
 and affiliation)

  Does your pseudo potential or PAW data set include the d orbital in the 
valence of the atomic species? If yes, did you check in the file 
'Modules/set_hubbard_l.f90' that the l for the element in question is set? 
At least in version 6.4 of QE I did not find 'Sn'. If needed, please 
modify the file, recompile and try again.


  Well, I am just guessing...

Greetings,

   apsi

-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-
  Ari Paavo Seitsonen / ari.p.seitso...@iki.fi / http://www.iki.fi/~apsi/
Ecole Normale Supérieure (ENS), Département de Chimie, Paris
Mobile (F) : +33 789 37 24 25(CH) : +41 79 71 90 935


On Sat, 2 Nov 2019, 후신 부지드 wrote:



Hello,

As indicated in the literature (for example 
https://www.sciencedirect.com/science/article/pii/S0927025616300672) people 
apply a Hubbard potential around 8
or 9 eV to correct the band gap of pure SnS2 from around 1.3 eV with only GGA 
to around 2 eV after applying U.

Knowing that Sn d orbital is closed shell orbital (d10), I applied U of 9 eV 
but band gap is not changing unlike what is reported in the literature, is it
because it is closed shell, if so why it worked for other people ?

I'm attaching the result of the calculation with and without U, and the density 
of states for both which look the same.

Best

[mdnform?OpenForm=bou...@skku.edu=users@lists.quantum-espresso.org=E455F3F7280BDC0A492584A6004F55D7]
___
Quantum ESPRESSO is supported by MaX (www.max-centre.eu/quantum-espresso)
users mailing list users@lists.quantum-espresso.org
https://lists.quantum-espresso.org/mailman/listinfo/users

Re: [QE-users] charge is wrong: smearing is needed

[Ari P Seitsonen]

Dear Mohamed,

  At least you have an odd number of electrons but you do not specify a 
spin polarisation in your input. The system might well be a doublet or a 
quartet...


  You can also try using with the smearing/broadening of the occupation 
numbers: It does not harm, and if and when the self-consistent cycle has 
converged you can investigate if there is indeed a gap between the 
occupied and unoccupied orbitals or not.


  (Usually in a system with vacuum I use the mixing mode 'local-TF')

Greetings from Paris,

   apsi

-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-
  Ari Paavo Seitsonen / ari.p.seitso...@iki.fi / http://www.iki.fi/~apsi/
Ecole Normale Supérieure (ENS), Département de Chimie, Paris
Mobile (F) : +33 789 37 24 25(CH) : +41 79 71 90 935


On Sat, 2 Nov 2019, Mohamed Ahmed Abd-Elati wrote:


Dear all I am tried many times to do relax step for  GQDs structures using an 
attached input file but I faced the error attached also here. I am used the
same input file for the same structure in case of oxygen passivation ( not 
nitrogen ) and no errors appeared.
thanks
Mohammed A. Abdelati 
Assistant Lecturer
Laser Applications in Metrology Photochemistry and Agriculture (LAMPA) 
Department, National Institute of Laser Enhanced Sciences (NILES), Cairo
University, Giza, Egypt. 
Mobile   +20 1009752922 
Home    +201152605076
E-mail    ma198...@yahoo.com

___
Quantum ESPRESSO is supported by MaX (www.max-centre.eu/quantum-espresso)
users mailing list users@lists.quantum-espresso.org
https://lists.quantum-espresso.org/mailman/listinfo/users

Re: [QE-users] inaccurate LDA bandstructure compared to VASP in FeSe system

[Ari P Seitsonen]

Dar Tiagang,

  I guess that the value 'celldm(3)= 10.431292329' should actually be 
1.46419098375312488028, as it is interpreted as c/a, not simply c. If you 
use the variables 'a' and 'c' in the input they are the absolute lengths 
of the cell vectors and in Ångström. Just my guess...


Greetings from Paris,

   apsi

-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-
  Ari Paavo Seitsonen / ari.p.seitso...@iki.fi / http://www.iki.fi/~apsi/
Ecole Normale Supérieure (ENS), Département de Chimie, Paris
Mobile (F) : +33 789 37 24 25(CH) : +41 79 71 90 935


On Sat, 23 Mar 2019, Tiangang Zhou wrote:



Hello all,

I'm working on the beta-FeSe system. In the first step I have done a simple LDA 
calculation. Unfortunately, after
adjusting ecutwfc and scf K_POINTS, I can’t get the relatively accurate result 
compared to VASP and wien2k (the
result of VASP and wien2k agree well on the fermi surface). It’s likely that 
the pseudopotential has some problem
or I miss some key steps. The input files are listed below.

fe_se.scf.in
```

calculation = 'scf'
restart_mode='from_scratch',
prefix='fe_se',
pseudo_dir = '/home/tgzhou/softwares/qe_release_6.4/pseudo/',
outdir='tempdir/'
/

ibrav=  6, celldm(1)= 7.124270293115536, celldm(3)= 10.431292329,
nat=  4, ntyp= 2,
ecutwfc = 120.0,
localization_thr = 0.01,
occupations='smearing', smearing='mp', degauss=0.02
/

mixing_beta = 0.7,
conv_thr =  1.0d-10
/
ATOMIC_SPECIES
Fe  55.845  Fe.pz-n-kjpaw_psl.1.0.0.UPF
Se  78.96   Se.pz-n-kjpaw_psl.1.0.0.UPF
ATOMIC_POSITIONS crystal
Fe       0.0   0.0   0.0
Fe       0.5   0.5   0.0
Se       0.0   0.5   0.768115942
Se       0.5   0.0   0.231884057
K_POINTS automatic
8 8 4 0 0 0
```

fe_se.band.in
```

calculation='bands'
pseudo_dir = '/home/tgzhou/softwares/qe_release_6.4/pseudo/',
outdir='tempdir/',
prefix='fe_se'
/

ibrav=  6, celldm(1)= 7.124270293115536, celldm(3)= 10.431292329,
nat=  4, ntyp= 2,
ecutwfc = 120.0,
nbnd=20
/

/
ATOMIC_SPECIES
Fe  55.845  Fe.pz-n-kjpaw_psl.1.0.0.UPF
Se  78.96   Se.pz-n-kjpaw_psl.1.0.0.UPF
ATOMIC_POSITIONS crystal
Fe       0.0   0.0   0.0
Fe       0.5   0.5   0.0
Se       0.0   0.5   0.768115942
Se       0.5   0.0   0.231884057
K_POINTS crystal_b
4
0.0 0.0 0.0 50
0.5 0.0 0.0 50
0.5 0.5 0.0 50
0.0 0.0 0.0 1
```


The band structure is in the path \Gamma-X-M-\Gamma. And those two have some 
similarity but the qe FeSe band are
much more narrow.

qe FeSe band structure 
https://drive.google.com/file/d/1wG1Nm-f5v03-kfefJoPZ4gSD4rYaJSQa/view
vasp FeSe band structure 
https://drive.google.com/file/d/1T0iNg7oecpey2dD6BB9iNrvjS6rm7Mnr/view 


Best,

Tiangang Zhou
School of Physics
Peking University


___
users mailing list
users@lists.quantum-espresso.org
https://lists.quantum-espresso.org/mailman/listinfo/users

Re: [QE-users] error

[Ari P Seitsonen]

Hello Sabike,

  Is there a reason why you do not want to use a more modern version of 
Quantum ESPRESSO? I seem to remember such errors myself on some computers, 
but it was some time ago (and vanished when the 6.x versions came 
available and I used GCC/GFORTRAN/Open-MPI/OpenBLAS to compile the code).


  You did not provide any input file - it is still up to us to guess for 
what you have in your input file.


Greetings,

   apsi

-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-
  Ari Paavo Seitsonen / ari.p.seitso...@iki.fi / http://www.iki.fi/~apsi/
Ecole Normale Supérieure (ENS), Département de Chimie, Paris
Mobile (F) : +33 789 37 24 25(CH) : +41 79 71 90 935


On Sun, 20 Jan 2019, Sabike Ghasemi wrote:


hi paolo
i use 5.2.0 and have 3 input,2 input for minimizing electron wave functional 
and 1 input for md, i did it on my cluster with version 5.0.2 without eror,but 
on the
other cluster with version 5.2.0 with erro.

___
From: "Paolo Giannozzi" 
To: "Quantum Espresso users Forum" 
Sent: Sunday, January 20, 2019 12:19:19 PM
Subject: Re: [QE-users] error

On Sun, Jan 20, 2019 at 4:35 AM Sabike Ghasemi  wrote:

  do everyone help me?


no, nobody will help you, because you did not provide enough information: your 
code version, how you run your code, with which input.

Paolo

# FROM IOTK LIBRARY, VERSION 1.2.0
# UNRECOVERABLE ERROR (ierr=1)
# ERROR IN: iotk_write_dat (iotk_dat+COMPLEX2_0.f90:1013)
# CVS Revision: 1.27 

application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
[unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=1
:
system msg for write_line failure : Bad file descriptor

# FROM IOTK LIBRARY, VERSION 1.2.0
# UNRECOVERABLE ERROR (ierr=1)
# ERROR IN: iotk_getline (iotk_scan.f90:947)
# CVS Revision: 1.23 
# 
iostat=-1
# ERROR IN: iotk_scan_tag (iotk_scan.f90:593)
# CVS Revision: 1.23 
# ERROR IN: iotk_scan (iotk_scan.f90:821)
# CVS Revision: 1.23 
# ERROR IN: iotk_scan_end (iotk_scan.f90:241)
# CVS Revision: 1.23 
# foundl
# ERROR IN: iotk_close_read (iotk_files.f90:746)
# CVS Revision: 1.20 

application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
[unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=1
:
system msg for write_line failure : Bad file descriptor


best regards,
sabike ghasemi,phd student,iran
___
users mailing list
users@lists.quantum-espresso.org
https://lists.quantum-espresso.org/mailman/listinfo/users


--
Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222


___
users mailing list
users@lists.quantum-espresso.org
https://lists.quantum-espresso.org/mailman/listinfo/users

___
users mailing list
users@lists.quantum-espresso.org
https://lists.quantum-espresso.org/mailman/listinfo/users

Re: [QE-users] vdw_corr

[Ari P Seitsonen]

Dear Sabike,

  QE v5.0.2 is most likely too old, it does not contain the DFT+D3 method.

Greetings,

   apsi

-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-
  Ari Paavo Seitsonen / ari.p.seitso...@iki.fi / http://www.iki.fi/~apsi/
Ecole Normale Supérieure (ENS), Département de Chimie, Paris
Mobile (F) : +33 789 37 24 25(CH) : +41 79 71 90 935


On Tue, 1 Jan 2019, Sabike Ghasemi wrote:


Hi Proff Ari
Thanks, I think that problem is qe version.it is 5.0.2.
input file:


calculation  = "scf"
 dipfield = .TRUE.
 disk_io  = "default"
iprint   = 1
max_seconds  =  8.64000e+04
nstep= 100
outdir   = "./tmp3/"
prefix   = "H2Otest"
dipfield =.TRUE.
pseudo_dir   = "./"
restart_mode = "from_scratch"
tefield  = .TRUE.
title= "H2Otest"
tprnfor  = .TRUE.
verbosity= "high"
/

a =   12.2720003128052
b =   12.763389648
c =  30
cosab =  6.12323e-17
cosac =  6.12323e-17
cosbc =  6.12323e-17
ibrav = 14
nat   = 96
ntyp  = 2
degauss =  1.0e-02
ecutrho = 300
ecutwfc = 25
occupations = "smearing"
smearing= "gaussian"
edir= 3
emaxpos =  0.9
eopreg  =  0.2
eamp=  0.0e+00
vdw_corr = "Grimme-D3"
dftd3_version = 3
dftd3_threebody = .TRUE.
/

conv_thr =  1.0e-06
electron_maxstep = 200
mixing_beta  =  7.0e-01
startingpot  = "atomic"
startingwfc  = "atomic+random"
 /
K_POINTS {automatic}
6  6  1  0 0 0
ATOMIC_SPECIES
O  15.99940  O.pbe-rrkjus.UPF
H   1.00794  H.pbe-rrkjus.UPF
ATOMIC_POSITIONS {angstrom}





and my output is:
 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.php

Parallel version (MPI), running on40 processors
R & G space division:  proc/nbgrp/npool/nimage =  40

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
Reading input from 
/share/users/mneek/espresso/Gasemi/proposal/withoutgraphene-vdw/1.in
Cannot match namelist object name vdw_corr
namelist read: misplaced = sign
Cannot match namelist object name "grimme-d3"
Cannot match namelist object name dftd3_version
namelist read: misplaced = sign
Cannot match namelist object name 3
Cannot match namelist object name dftd3_threebody
namelist read: misplaced = sign
Cannot match namelist object name .true.
Presently no symmetry can be used with electric field

  file O.pbe-rrkjus.UPF: wavefunction(s)  2S renormalized
  file H.pbe-rrkjus.UPF: wavefunction(s)  1S renormalized

Subspace diagonalization in iterative solution of the eigenvalue problem:
a serial algorithm will be used




- Original Message -
From: "Ari Paavo Seitsonen" 
To: "Quantum Espresso users Forum" 
Sent: Tuesday, January 1, 2019 1:48:12 PM
Subject: Re: [QE-users] vdw_corr

Dear Sabike,

  What do you mean with "result does not change"? What do you try to
calculate? Can you provide your input file on this forum?

Greetings & Happy 2019 from Paris,

   apsi

-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-
  Ari Paavo Seitsonen / ari.p.seitso...@iki.fi / http://www.iki.fi/~apsi/
Ecole Normale Supérieure (ENS), Département de Chimie, Paris
Mobile (F) : +33 789 37 24 25(CH) : +41 79 71 90 935


On Tue, 1 Jan 2019, Sabike Ghasemi wrote:


hi all,
i want to apply van der waals correction to bulk water. i use  vdw_corr = 
"Grimme-D3", dftd3_version =
3, dftd3_threebody = .TRUE. in 

but result don't change with and without vanderwals.
do everybody help me?




best regards,
sabike ghasemi
phd student, damghan university, Iran



___
users mailing list
users@lists.quantum-espresso.org
https://lists.quantum-espresso.org/mailman/listinfo/users
___
users mailing list
users@lists.quantum-espresso.org
https://lists.quantum-espresso.org/mailman/listinfo/users

Re: [QE-users] vdw_corr

[Ari P Seitsonen]

Dear Sabike,

  What do you mean with "result does not change"? What do you try to 
calculate? Can you provide your input file on this forum?


Greetings & Happy 2019 from Paris,

   apsi

-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-
  Ari Paavo Seitsonen / ari.p.seitso...@iki.fi / http://www.iki.fi/~apsi/
Ecole Normale Supérieure (ENS), Département de Chimie, Paris
Mobile (F) : +33 789 37 24 25(CH) : +41 79 71 90 935


On Tue, 1 Jan 2019, Sabike Ghasemi wrote:


hi all,
i want to apply van der waals correction to bulk water. i use  vdw_corr = 
"Grimme-D3", dftd3_version =
3, dftd3_threebody = .TRUE. in 

but result don't change with and without vanderwals.
do everybody help me?




best regards,
sabike ghasemi
phd student, damghan university, Iran

___
users mailing list
users@lists.quantum-espresso.org
https://lists.quantum-espresso.org/mailman/listinfo/users

Re: [QE-users] dipole moment

[Ari P Seitsonen]

Dear Sabike, [your affiliation please?]

  If I understand correctly your question, looking in the code in 
'add_efield.f90':


...
 tot_dipole  = -el_dipole + ion_dipole
...

  IF ( iverbosity > 0 ) THEN
WRITE( stdout, '(8X,"Elec. dipole ",1F15.4," Ry au, ", 1F15.4," Debye")' ) &
el_dipole, (el_dipole*au_debye)
WRITE( stdout, '(8X,"Ion. dipole  ",1F15.4," Ry au, ", 1F15.4," Debye")' ) &
  ion_dipole, (ion_dipole*au_debye)
  END IF

  WRITE( stdout, '(8X,"Dipole   ",1F15.4," Ry au, ", 1F15.4," Debye")' ) &
  (tot_dipole* (omega/fpi)), ((tot_dipole* 
(omega/fpi))*au_debye)

  WRITE( stdout, '(8x,"Dipole field ", 1F15.4," Ry au, ")') tot_dipole


Do those lines help? So something like
"Dipole = (-el_dipole + ion_dipole) * volume / (4 pi)". Was this what you 
were looking for?


Greetings from Lviv,

   apsi

-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-
  Ari Paavo Seitsonen / ari.p.seitso...@iki.fi / http://www.iki.fi/~apsi/
Ecole Normale Supérieure (ENS), Département de Chimie, Paris
Mobile (F) : +33 789 37 24 25(CH) : +41 79 71 90 935


On Sat, 17 Nov 2018, Sabike Ghasemi wrote:


hi all,
i am calculating dipole moment of water by pw.x.
i do it correctly.but i don't understand "Elec. dipole" and " ion. dipole" in 
out put and relation them wit
dipole. can i help me ?
input :

    calculation  = "scf"
    dipfield = .TRUE.
    disk_io  = "default"
    iprint   = 1
    max_seconds  =  8.64000e+04
    nstep    = 100
    outdir   = "./tmp1/"
    prefix   = "H2Otest"
    pseudo_dir   = "./"
    restart_mode = "from_scratch"
    tefield  = .TRUE.
    title    = "H2Otest"
    tprnfor  = .TRUE.
    verbosity    = "high"
/


    a   =  10
    degauss =  1.0e-02
    ecutrho =  520
    ecutwfc = 130
    ibrav   = 1
    nat = 3
    ntyp    = 2
    occupations = "smearing"
    smearing    = "gaussian"
  edir    = 1
    emaxpos =  0.9
    eopreg  =  0.2
 eamp    =  0.0e+00
input_dft = "PBE"
vdw_corr = "Grimme-D2"
/


    conv_thr =  1.0e-06
    electron_maxstep = 200
    mixing_beta  =  7.0e-01
    startingpot  = "atomic"
    startingwfc  = "atomic+random"
/

K_POINTS {automatic}
 3  3  3  0 0 0

ATOMIC_SPECIES
O  15.99940  O.pbe-rrkjus.UPF
H   1.00794  H.pbe-rrkjus.UPF

ATOMIC_POSITIONS {angstrom}
O   5   5   5
H   5   4.209   5.563
H   5   5.791   5.563



output:
 

 iteration #  6 ecut=   130.00 Ry beta=0.70
 Davidson diagonalization with overlap
 c_bands:  1 eigenvalues not converged
 ethr =  7.81E-08,  avg # of iterations =  6.6

 negative rho (up, down):  0.438E-04 0.000E+00

 Adding external electric field

 Computed dipole along edir(3) :
    Elec. dipole  0.0027 Ry au,   0.0068 Debye
    Ion. dipole   0.0040 Ry au, 0.0101 Debye
    Dipole    0.6902 Ry au,  1.7543 Debye
    Dipole field  0.0013 Ry au

    Potential amp.   -0.0389 Ry
    Total length 15.1178 bohr


 total cpu time spent up to now is  152.0 secs

 End of self-consistent calculation



best regards,
sabike ghasemi
phd student

___
users mailing list
users@lists.quantum-espresso.org
https://lists.quantum-espresso.org/mailman/listinfo/users

Re: [QE-users] Raman spectra with GGA

[Ari P Seitsonen]

Dear Karolina, Giuseppe et co,

  Indeed the "standard solution" has been to switch off the test and 
continue the calculation, yielding the intensities calculated with LDA 
(the frequencies are consistent with the ground-state calculation, GGA 
that is). Just last week I discussed with one Developer of the 
PHonon/Raman codes, who mentioned he had basically implemented also the 
third order derivatives, but they are not yet included in the 
distribution.


-
#$ grep -n -B 1 apsi /sw/source/intel/app/qe/qe-6.3/PHonon/PH/phq_setup.f90
123- 'third order derivatives not implemented with GGA', 0)
124:!apsi 'third order derivatives not implemented with GGA', 1)
-

This tells the code to write out the warning but continue, whereas the 
original code stops with the same (error) message.


Greetings from Sunny Paris,

   apsi

-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-
  Ari Paavo Seitsonen / ari.p.seitso...@iki.fi / http://www.iki.fi/~apsi/
Ecole Normale Supérieure (ENS), Département de Chimie, Paris
Mobile (F) : +33 789 37 24 25(CH) : +41 79 71 90 935


On Thu, 4 Oct 2018, Giuseppe Mattioli wrote:



Dear Karolina

AFAIK gradient corrections have been never "officially" implemented in ph.x 
RAMAN calculations and you are stuck at LDA level. I saw Ari Seitsonen's 
slides you mention (I suppose), and in the last slide there is actually this 
caveat


Limitations: Beyond LDA only with shortcuts

If you want to know such shortcuts you should ask Ari, or the Authhors of the 
graphene nanoribbon paper (if you find it, because it is not cited in the 
slides).


HTH
Giuseppe

Karolina Milowska  ha scritto:


Dear All,

Recently, I have came across files and slides from MASTANI Summer School
from 2014, in particular - the calculation of Raman spectrum of graphene
nanoribbon. I would like to reproduce this example. Unfortunately, version
6.3 doesn't allow me to do that.

This is he error message:
%%
Error in routine phq_setup (1):
third order derivatives not implemented with GGA
%%

May I ask you where can I find the version of qe which has this
implementation?

Kind regards,
Karolina




GIUSEPPE MATTIOLI
CNR - ISTITUTO DI STRUTTURA DELLA MATERIA
Via Salaria Km 29,300 - C.P. 10
I-00015 - Monterotondo Scalo (RM)
Mob (*preferred*) +39 373 7305625
Tel + 39 06 90672342 - Fax +39 06 90672316
E-mail: 

___
users mailing list
users@lists.quantum-espresso.org
https://lists.quantum-espresso.org/mailman/listinfo/users___
users mailing list
users@lists.quantum-espresso.org
https://lists.quantum-espresso.org/mailman/listinfo/users

Re: [QE-users] Meta-GGA not implemented with USPP/PAW

[Ari P Seitsonen]

Dear Michal,

  Just a small note: PSlibrary does contain the inputs for the creation of 
norm-conserving pseudo potentials as well, they are just not created by 
default; from 'make_ps':


#  Uncomment the following line to generate the NC-PPs. Be very careful
#  these PPs are completely untested.
#
#. ../nc_ps_collection.job

Greetings from Paris,

   apsi

-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-
  Ari Paavo Seitsonen / ari.p.seitso...@iki.fi / http://www.iki.fi/~apsi/
Ecole Normale Supérieure (ENS), Département de Chimie, Paris
Mobile (F) : +33 789 37 24 25(CH) : +41 79 71 90 935


On Thu, 6 Sep 2018, Michal Krompiec wrote:


Dear All,I'm trying to use a meta-GGA functional and I got this error:  
Meta-GGA not implemented with USPP/PAW. Does it mean that
ultra-soft pseudopotentials or PAW cannot be used in conjunction with meta-GGA 
in QE? It is a bit confusing as all pseudopotentials from
the PS library are USPP or PAW. Am I missing something?
Thanks in advance,
Michal Krompiec

___
users mailing list
users@lists.quantum-espresso.org
https://lists.quantum-espresso.org/mailman/listinfo/users

Re: [QE-users] EXX+soc in QE 6.3 ?

[Ari P Seitsonen]

Dear Malte,

  Hmm, there seems to be the space inversion symmetry present in your 
system, thus no splitting...?


Greetings,

   apsi

-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-
  Ari Paavo Seitsonen / ari.p.seitso...@iki.fi / http://www.iki.fi/~apsi/
Ecole Normale Supérieure (ENS), Département de Chimie, Paris
Mobile (F) : +33 789 37 24 25(CH) : +41 79 71 90 935


On Wed, 15 Aug 2018, Malte Sachs wrote:


Dear all,

I've tried to perform a calculation of PbF2 with QE-6.3 using the hybrid 
functional PBE0 together with spin-orbit coupling and the sg15-ONCP NCPPs. 
The calculation starts and ends without errors. However, inspecting the 
eigenvalues I cannot see any influence of the spin-orbit coupling. E.g. for 
the Gamma-Point:


  k = 0. 0. 0. (  2085 PWs)   bands (ev):

   -19.4836 -19.4836 -18.9442 -18.9442 -11.4661 -11.4661 -11.4661 -11.4661
    -8.9347  -8.9347  -8.8598  -8.8598  -8.8598  -8.8598  -0.4010 -0.4010
 1.0062   1.0062   1.0062   1.0062   1.0504   1.0504 1.4205   1.4205
 1.5548   1.5548   1.5548   1.5548

At least for the lowest Pb d-semi core states I would expect to see an 
effect. Is exx+soc implemented in version 6.3?


Best regards,

Malte

--
Malte Sachs
Anorganische Chemie, Fluorchemie
Philipps-Universität Marburg
Hans-Meerwein-Straße 4
35032 Marburg (Paketpost: 35043 Marburg)
Tel.: +49 (0)6421 28 - 25 68 0
http://www.uni-marburg.de/fb15/ag-kraus/

___
users mailing list
users@lists.quantum-espresso.org
https://lists.quantum-espresso.org/mailman/listinfo/users

Re: [QE-users] HSE calculation for ZnO band structure converges slow

[Ari P Seitsonen]

Dear Tan,

  Adding to the answer of Stefano (Baroni; only the latest versions of QE 
have the ACE algorithm implemented which speeds up the calculations) two 
notes: Probably you are not interested in having the natural symmetries in 
the lattice (avoiding the symmetrisation might make sense in calculation 
of a band structure with hybrid functionals indeed), but providing only 
three digits to the lattice parametre a[1,1] = 2.814 (Å) ensures that the 
hexagonal symmetry is not found (it would be easier to provide 'ibrav = 4 
/ a = 3.249 / c = 5.205' than the explicit lattice vectors); you could 
avoid the symmetrisation also with the keyword 'nosym'. Secondly, the 
cut-off energy could be still insufficient, at least with 
Troullier-Martins-type pseudo potentials 80 Ry and above is needed for 
good convergence; yet maybe the band structure converges faster.


  About other parametres, maybe 'ecutfock' would be useful too; I do not 
know/remember which one is the standard method of treating the divergence 
in the Fourier transform in the Fock operator, but that probably does not 
affect the computing time.


Greetings from Sunny Paris,

   apsi

-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-
  Ari Paavo Seitsonen / ari.p.seitso...@iki.fi / http://www.iki.fi/~apsi/
Ecole Normale Supérieure (ENS), Département de Chimie, Paris
Mobile (F) : +33 789 37 24 25(CH) : +41 79 71 90 935


On Wed, 15 Aug 2018, Tan Hengxin wrote:


Dear Users,

I am doing HSE calculations on wurtzite ZnO for the band structure.
However, the run converges slowly:
I use a 6*6*4 k-mesh. The cutoff energy is 60 Ry. Norm-conversing 
pseudopotentials are used, and there are 12 and 6 valence electrons for
Zn and O respectively.
The job was run with 2 nodes (48 processors) with npool = 2. The run takes 45 
hours.

Is this seems normal? Or what would be done to reduce the run time? Are there 
any tricks that need to be paid special attention to ZnO? 
Thanks for your help.

The input parameters and the tail of the output are copied below.
input:

  calculation   = 'scf',
  prefix        = 'ZnO',
  pseudo_dir    = './',
  verbosity     = 'high',
  wf_collect    = .true.
  etot_conv_thr = 1.0D-6,
  forc_conv_thr = 1.0D-4,
  restart_mode  = 'from_scratch',
  outdir        = './temp_out',
/

  ibrav         = 0,
  nat           = 4,
  ntyp          = 2,
  ecutwfc       = 60,
  nbnd          = 36,
  input_dft     = 'hse',
  exx_fraction  = 0.25,
  nqx1 = 6, nqx2 = 6, nqx3 = 6,
/

  mixing_mode   = 'plain',
  mixing_beta   = 0.7,
  conv_thr      = 1.D-8,
/

ATOMIC_SPECIES
 Zn 65.38     Zn_fan_nc_pbe_srl.upf
 O  15.999    O_web_nc_pbe.upf

CELL_PARAMETERS (angstrom)
     3.249         0.000         0.000
    -1.625         2.814         0.000
     0.000         0.000         5.205

ATOMIC_POSITIONS (crystal)
Zn    0.33343         0.66687         0.0
Zn    0.66627         0.33313         0.5
O     0.33343         0.66687         0.38269
O     0.66627         0.33313         0.88269

K_POINTS {crystal}
216
  (The 216 k points with weights (from 6*6*6 k-mesh))
output:
..

!    total energy              =    -269.06624688 Ry
     Harris-Foulkes estimate   =    -277.03747208 Ry
     estimated scf accuracy    <          3.7E-09 Ry

     convergence has been achieved in   1 iterations

!    total energy              =    -269.06624688 Ry
     Harris-Foulkes estimate   =    -269.06624688 Ry
     est. exchange err (dexx)  =       0. Ry
     - averaged Fock potential =      15.94246020 Ry
     + Fock energy             =      -7.97123500 Ry

     EXX self-consistency reached

     Writing output data file ZnO.save

     init_run     :      1.05s CPU      1.15s WALL (       1 calls)
     electrons    : 150333.27s CPU 152710.02s WALL (       5 calls)

     Called by init_run:
     wfcinit      :      1.01s CPU      1.11s WALL (       1 calls)
     wfcinit:atom :      0.00s CPU      0.00s WALL (     108 calls)
     wfcinit:wfcr :      1.00s CPU      1.03s WALL (     108 calls)
     potinit      :      0.01s CPU      0.02s WALL (       1 calls)

     Called by electrons:
     c_bands      : 150323.40s CPU 152695.15s WALL (      25 calls)
     sum_band     :      7.77s CPU      8.01s WALL (      25 calls)
     v_of_rho     :      0.12s CPU      0.13s WALL (      27 calls)
     v_h          :      0.00s CPU      0.00s WALL (      27 calls)
     v_xc         :      0.12s CPU      0.12s WALL (      27 calls)
     mix_rho      :      0.01s CPU      0.01s WALL (      25 calls)

     Called by c_bands:
     init_us_2    :      0.21s CPU      0.24s WALL (    6480 calls)
     cegterg      : 149815.07s CPU 152046.20s WALL (    2700 calls)

     Called by sum_band:

     Called by *egterg:
     h_psi        : 149780.99s CPU 152011.56s WALL (    9389 calls)
     g_psi        :      0.08s CPU      0.13s WALL (    6581 calls)
     cdiaghg      :     29.34s 

Re: [QE-users] Band Structure and DOS contradiction in doped graphene

[Ari P Seitsonen]

Dear B S Bhushan,

  To me it looks like

 1) QE/PWscf sets the Fermi level in the band gap, at some arbitrary 
energy just so that the number of electrons is conserved: It could be 
higher (but hardly lower). This is normal, as the energy position is not 
specifically defined so long as the number of electrons is correct (or, 
the Fermi level can be anywhere in the band gap just as it is far enough 
from the valence and conduction band edges)


 2) the program to calculate DOS does not realign the Fermi energy, so 
with the broadening there appears some intensity at the Fermi energy


  After you check that this is the correct assumption (for example that 
the occupation of all bands is either 0 or 1), you can manually 
shift the Fermi energy to mid-gap in the plots; or, some people do not 
show the Fermi energy at all in systems with gap but align the energy 
scale so that the top of the valence band ("valence band maximum", "VBM") 
is at zero.


  Which value of Fermi energy do you use actually, the one from the 
self-consistent or non-self-consistent calculation?


Greetings from Sunny Paris,

   apsi

-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-
  Ari Paavo Seitsonen / ari.p.seitso...@iki.fi / http://www.iki.fi/~apsi/
Ecole Normale Supérieure (ENS), Département de Chimie, Paris
Mobile (F) : +33 789 37 24 25(CH) : +41 79 71 90 935


On Mon, 21 May 2018, B S Bhushan wrote:


Dear Experts,
I am analyzing doped graphene using pbe functional.
Where, I end up having contradictory DOS and Band structure.

The Band structure shows a small band gap at the fermi level, however, the DOS 
shows few states on the fermi level.

What should I call the system in such cases, metallic or semi-metallic or 
semi-conducting ???

or have I done something wrong ???

The link below contains the figures and input scripts used by me.
https://drive.google.com/open?id=11Q7xfMGCHJDUlPK0amTnWO-y4R70ZQWj 

Please suggest.


Sincerely,
B S Bhushan,
Ph.D Scholar,
ABV- Indian Institute of Information Technology and Management, Gwalior.
www.bsbhushan.com


___
users mailing list
users@lists.quantum-espresso.org
https://lists.quantum-espresso.org/mailman/listinfo/users

Re: [QE-users] Problem compiling QE 6.2.1

[Ari P Seitsonen]

Dear Marcos,

  Were you running a parallel compilation ("make -jN ...")? This usually 
fails for me. Otherwise, is the directory '/software/q-e-qe-6.2.1/' 
correct? Personally I have not had any other problems in compilation with 
6.2.1, with gcc/gfortran, OpenMPI, OpenBLAS, ScaLAPACK etc.


Greetings from Rainy Paris,

   apsi

-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-
  Ari Paavo Seitsonen / ari.p.seitso...@iki.fi / http://www.iki.fi/~apsi/
Ecole Normale Supérieure (ENS), Département de Chimie, Paris
Mobile (F) : +33 789 37 24 25(CH) : +41 79 71 90 935


On Sun, 13 May 2018, Marcos Veríssimo Alves wrote:


Hi all,

I am trying to compile QE 6.2.1, and I'm running into troubles because of the 
compilation of the FoX library.
basically, compilation runs with lots of warnings:

f951: Warning: Nonexistent include directory 
‘/software/q-e-qe-6.2.1//FoX/finclude’ [-Wmissing-include-dirs]

and when read_upf_schema.f90 is to be compiled, it crashes:

mpif90 -O3 -g -x f95-cpp-input -D__FFTW3 -D__MPI  
-I/software/q-e-qe-6.2.1//include
-I/software/q-e-qe-6.2.1//FoX/finclude -I../include/ -I../iotk/src 
-I../ELPA/src -I../FFTXlib -I../LAXlib
-I../UtilXlib -I../KS_Solvers/CG -I/software/q-e-qe-6.2.1//include 
-I/software/q-e-qe-6.2.1//FoX/finclude
-I../include/ -I. -c read_upf_schema.f90
f951: Warning: Nonexistent include directory 
‘/software/q-e-qe-6.2.1//FoX/finclude’ [-Wmissing-include-dirs]
f951: Warning: Nonexistent include directory ‘../ELPA/src’ 
[-Wmissing-include-dirs]
f951: Warning: Nonexistent include directory 
‘/software/q-e-qe-6.2.1//FoX/finclude’ [-Wmissing-include-dirs]
read_upf_schema.f90:18:12:

 USE FoX_Dom
    1
Fatal Error: Can't open module file ‘fox_dom.mod’ for reading at (1): No such 
file or directory
compilation terminated.
../make.inc:16: recipe for target 'read_upf_schema.o' failed
make[1]: *** [read_upf_schema.o] Error 1
make[1]: Leaving directory '/software/q-e-qe-6.2.1/Modules'
Makefile:183: recipe for target 'mods' failed
make: *** [mods] Error 1

At this point of the compilation, the FoX directory is empty. Am I missing 
something? I searched the mail archives
but found nothing about this kind of error.

Best regards,

Marcos

___
users mailing list
users@lists.quantum-espresso.org
https://lists.quantum-espresso.org/mailman/listinfo/users

Re: [QE-users] Eigenvalues for vc relax not converging

[Ari P Seitsonen]

Dear Priya,

  Some quick comments:

 - Are you sure that the ecutwfc = 20 Ry is sufficient? The 40 Ry that you 
mention sounds much more realistic, if not even higher value would be 
needed; the calculation of the stress tensor ("vc-relax") requires a 
stricter convergence with respect to the cut-off energy/basis set than for 
example total energy as the former is a (second) derivative of the latter, 
and the basis set would in principle be a function of the lattice 
constant, so better be well converged in the basis set


 - Since you have an FCC lattice you could easily calculate the total 
energy of the ("relax"'ed) system as a function of the lattice parametre 
and check if you converge toward the same value as the 'vc-relax'


 - Do I understand you correctly that you can reach convergence in the 
self-consistent loop, but in the subsequent loops the electronic structure 
does not convergence (as the D3 does not affect the electronic structure 
explicitly, only via the modified lattice constant)


 - Your value for smearing is quite small; you could at least temporarily 
try to increase it


 - What is the lowest value of convergence that you reach in, say 100 
iterations?


Good Luck, Greetings from Helsinki,

   apsi

-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-
  Ari Paavo Seitsonen / ari.p.seitso...@iki.fi / http://www.iki.fi/~apsi/
Ecole Normale Supérieure (ENS), Département de Chimie, Paris
Mobile (F) : +33 789 37 24 25(CH) : +41 79 71 90 935


On Tue, 8 May 2018, Priya Shrivastava wrote:



Dear All,

I am trying to reproduce published data but wihtout Vdw i got wrong results and 
then after including DFT-D3 , my
calculations are not converging for vc-relax.Please see my i/p  file. I have 
just started using QE so i am not
sure whats wrong however i have read threads containing similar problems. I 
tried reducing beta to 0.2 and change
nbnd and diagonalization but to no avail . I have also used the suggested 
ecutwfc=40 in the paper  but my
calculations didnt converge even after 500 iterations. Please help me.

 calculation='vc-relax',
 restart_mode='from_scratch',
 prefix='Cs',
 pseudo_dir="/home/external/iitb/priyas/PSEUDOPOTENTIALS_PBE",
 tstress = .true.
 tprnfor = .true.
 verbosity= 'high',
 forc_conv_thr=1.0d-3,
 etot_conv_thr=1.0d-5,
/

 a   = 10.6212,
 ibrav   = 2,
 nat = 3,
 ntyp    = 3,
 ecutwfc= 20.0,
 ecutrho=400.0,
 vdw_corr='DFT-D3',
 nbnd=35,
 occupations='smearing',
 degauss=0.001, 
/

 mixing_beta=0.2,
 diagonalization='cg',
 conv_thr=1d-8,
 electron_maxstep=500,
/

 ion_dynamics='bfgs',
/

 cell_dynamics='bfgs'
 press=0.0,
 press_conv_thr=0.5,
/
ATOMIC_SPECIES
Cs 132.905 Cs.pbe-spn-kjpaw_psl.1.0.0.UPF
Ti 47.867  Tl.pbe-dn-kjpaw_psl.1.0.0.UPF
Br 79.904  Br.pbe-n-kjpaw_psl.1.0.0.UPF
ATOMIC_POSITIONS crystal
Cs  0.25   0.25   0.25
Ti  0.00   0.00   0.00
Br  0.234000   0.00   0.00
K_POINTS automatic
4 4 4 1 1 1
,
Regards,
Priya,IITB


___
users mailing list
users@lists.quantum-espresso.org
https://lists.quantum-espresso.org/mailman/listinfo/users

Re: [QE-users] NVE simulation in cp.x - large fluctuation in temperature

[Ari P Seitsonen]

Dear Jie,

  I do not know about the other options, but

 1) simulating a periodic system of only three atoms with only the Gamma 
point cannot lead to an accurate description of the electronic structure, 
and thus the forces on the ionic cores,


 2) the standard deviation in the fluctuations is supposed to be 
~sqrt[2/(3*N_atoms)) * T_average ~= 350 K in your case, and the 
instantaneous fluctuations are of course larger


  Just my quick thoughts...

Greetings from Sunny Zurich,

   apsi

-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-
  Ari Paavo Seitsonen / ari.p.seitso...@iki.fi / http://www.iki.fi/~apsi/
Ecole Normale Supérieure (ENS), Département de Chimie, Paris
Mobile (F) : +33 789 37 24 25(CH) : +41 79 71 90 935


On Fri, 13 Apr 2018, Jie Peng wrote:


Dear all
I have been running MD simulations on HfS2 using cp.x code in Quantum espresso. 
I start from initial
configuration obtained from pwscf vc-relax, and relax the system using cp.x by 
consecutive steps of:
electron relaxation->ionic relaxation->cell relaxation. Then, I just directly 
start a NVE simulation
starting from the equilibrium configuration. I expect the system to almost stay 
stationary or the
temperature should be very small since I am allowing dynamics in a system that 
is already in
equilibrium. However, what I see is a huge fluctuation in the tmpp output of 
cp.x, as I attach a figure
showing variation of tmpp (Ionic temperature) with simulation time
[IMAGE]

I did this because it is suggested in the user guide you should apply an 
initial displacement to the
atoms in your system after the relaxation since otherwise there will not be any 
dynamics. But what I
see here is a large fluctuation of the system temperature.

The thinking or questions here are

1.Does the tmpp represents the physical temperature of the system here? I think 
it should be since it
is the temperature corresponding to kinetic energy of the ions.

2.It above point is true, why is the temperature varying so fiercely? Am I 
setting incorrect
parameters, for instance the timestep or the fictitious mass? But I took those 
from previous simulation
steps where I did the relaxation, and they all worked well since they 
successfully drived my system to
equilibrium, satisfying the convergence threshold on total energy, forces 
acting on atoms, and the
fictitious electron kinetic energy. I am confused at this point.

The input file for NVE simulation is attached here:


    calculation='cp',
    title='Halfnium disulfide'
    restart_mode='restart',
    ndr=53,
    ndw=54,
    nstep=5,
    iprint=10
    isave=100,
    tstress = .true.
    tprnfor = .true.
    dt=10,
    wf_collect=.true.
    etot_conv_thr=1e-6
    forc_conv_thr=1e-3
    ekin_conv_thr=1e-5
    prefix='HfS2',
    pseudo_dir='/home/jpeng/HfS2/potential'
    outdir='./tmp/',
 /
 
    ibrav= 4,
    a=3.6529
   c=5.6544
    nat=  3, ntyp= 2,
    ecutwfc =50
    vdw_corr='DFT-D',
 !   lspinorb=.true.
 !   noncolin=.true.
 !   ecutrho=300
 !   nbnd=14
!    occupations='smearing'
!    smearing='gaussian'
!   degauss=0.01
 !  nspin=2
 !   starting_magnetization(1)=0.1
! Hf  95.94  Hf.pbe-mt_fhi.UPF
! S  32.065  S.pbe-mt_fhi.UPF
/
 
    electron_dynamics='verlet'
    electron_velocities='zero'
    emass=400
    emass_cutoff=1
/
 
    ion_dynamics = 'verlet'
    ion_damping=0.1
!    ion_nstepe=10
 /
 
    cell_dynamics = 'none'
 
/
ATOMIC_SPECIES
 Hf  95.94  Hf.pbe-mt_fhi.UPF
 S  32.065  S.pbe-mt_fhi.UPF
ATOMIC_POSITIONS (crystal)
Hf      -0.0  -0.0  -0.0
S        0.7   0.3   0.257234636
S        0.3   0.7  -0.257234636

Anyone could help me on it? Thank you very much.

Best
Jie
--
--
--
Jie Peng
PhD student
2134 Glenn Martin Hall, Mechanical Engineering, University of Maryland
College Park, Maryland, USA
Phone:(+1) 240-495-9445
Email: jiep...@umd.edu


___
users mailing list
users@lists.quantum-espresso.org
https://lists.quantum-espresso.org/mailman/listinfo/users

Re: [QE-users] O_ad(O-adsorption) is not binding at bridge position on Pt-surface

[Ari P Seitsonen]

Dear Venkataramana Imandi,

  Since you have fixed the lowest layers of the substrate, it sounds quasi 
impossible that only few layers would have moved that much (the 
interaction between the layers should be larger than the corrugation of 
the potential energy surface of the oxygen). Of course the coverage is 
quite high (1/2), but still I am surprised... Otherwise, I do not see 
anything "obviously wrong" in your input now.


Greetings,

   apsi

-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-
  Ari Paavo Seitsonen / ari.p.seitso...@iki.fi / http://www.iki.fi/~apsi/
Ecole Normale Supérieure (ENS), Département de Chimie, Paris
Mobile (F) : +33 789 37 24 25(CH) : +41 79 71 90 935


On Tue, 10 Apr 2018, Venkataramana Imandi wrote:


Dear Ari,

Sorry, I didn't mention that I also tried by fixing coordinate of O_ad at a 
bridge position.
It resulted the Pt atoms moving, in such way that O_ad becomes three-fold 
site(either fcc or hcp).

With best regards
Venkataramana Imandi
Postdoctoral fellow
IIT Madras, India.


On Tue, Apr 10, 2018 at 2:44 PM, Venkataramana Imandi 
 wrote:

  Dear QE community,

  I am a new user of Quantum espresso simulation package. I installed 6.2.1 
Quantum espresso
  in the Linux-X86_64-INTEL-MPI. I want to find out the binding energy of 
O_ad at various
  sites(top,bridge,hcp and fcc) on Pt-surface and Pt-Ni alloy surface. In 
the beginning, i
  have tried on Pt-surface, and I got O_ad at top, hcp and fcc sites on 
Pt-surface, however,
  i couldn't find O_ad at bridge position.
  I have tried all possible ways of getting O_ad at the bridge 
position(between Pt-Pt). None
  of them were given succussful results, and the resulted O_ad comes to 
either fcc or hcp
  position. All possible ways: using with and without spin-polarization, 
davidson
  diagonalization anc cg, option (nosym = .TRUE. and .FALSE.), mixing 
mode(plain, local-TF
  and TF), changing mixing-beta(0.2, 0.3 and 0.5), neutral, negative 
charge(-2) and different
  simulation setup (present 24 atoms to 48 Pt atoms). The last option, i 
used different
  pseudopotential(Pt.pw91-n-van.UPF and O.pw91-van_ak.UPF), herein, i got 
error as follows
  (Error in scalartorealdp  Too few elements found). Now i stopped trials.
  I ask you can anyone do calculation in your simulation setup with the 
given input file,
  tell me the where the problem is.

  I really thanks to you in advance for any suggestions regarding this.
  For information, i used VASP in the last year, therein, i obtained O_ad 
at all sites on
  Pt-surface.

   
      calculation='relax'
      restart_mode='from_scratch',
      pseudo_dir = '/home2/oth/ch18ipf01/pseudopotential2/',
      prefix='pt'
      tprnfor = .true.,
      nstep = 200
   /
   
      ibrav=0,
      nat=25,
      ntyp=2,
      ! nspin = 2,
      ! starting_magnetization(1)=0.7,
      ecutwfc = 32.0,
      ecutrho = 320.0,
      occupations='smearing',
      smearing='methfessel-paxton',
      degauss=0.02
     ! tot_charge = -2,
      nosym = .TRUE.
   /
   
      diagonalization='cg'
      conv_thr = 1.0e-6
      mixing_beta = 0.3
     electron_maxstep = 1000
   /
  
  ion_dynamics='bfgs',
   /
  ATOMIC_SPECIES
  Pt  195.084  Pt.pbe-nd-rrkjus.UPF
  O    15.999  O.pbe-rrkjus.UPF

  ATOMIC_POSITIONS {angstrom}
  O 3.45091550  1.17466050 13.69732100  1 1 1
  Pt    4.84778787  1.20016667 12.44963917  1 1 1
  Pt    3.46185858  3.60066659 12.44963917  1 1 1
  Pt    2.07592929  1.20016667 12.44963917  1 1 1
  Pt    0.6900  3.60066659 12.44963917  1 1 1
  Pt    3.46185858  0.4000 10.18642611  1 1 1
  Pt    4.84778787  2.80049996 10.18642611  1 1 1
  Pt    0.6900  0.4000 10.18642611  1 1 1
  Pt    2.07592929  2.80049996 10.18642611  1 1 1
  Pt    3.46185858  2.0000  7.92321305  1 1 1
  Pt    4.84778787  4.40083326  7.92321305  1 1 1
  Pt    0.6900  2.0000  7.92321305  1 1 1
  Pt    2.07592929  4.40083326  7.92321305  1 1 1
  Pt    4.84778787  1.20016667  5.6600  1 1 1
  Pt    3.46185858  3.60066659  5.6600  1 1 1
  Pt    2.07592929  1.20016667  5.6600  1 1 1
  Pt    0.6900  3.60066659  5.6600  1 1 1
  Pt    3.46185858  0.4000  3.39678694  0 0 0
  Pt    4.84778787  2.80049996  3.39678694  0 0 0
  Pt    0.6900  0.4000  3.39678694  0 0 0
  Pt    

Re: [QE-users] O_ad(O-adsorption) is not binding at bridge position on Pt-surface

[Ari P Seitsonen]

Dear Venkataramana Imandi,

  Possibly the bridge site is a saddle point but the symmetry is not 
perfect, so the symmetry constrain does not fix the atom from moving 
toward a lower-energy site. I would try arranging the surface so that for 
example the x axis is the reaction coordinate for diffusion from a 
three-fold site to the other three-fold site, and then fixing the value of 
that coordinate (well, I do not remember if the fixed coordinates in the 
input are for relative or Cartesian coordinates, but you could try fixing 
a Cartesian one). If the bridge would be, however, a in-principle fully 
symmetric coordinate it does not get fixed because the symmetries are not 
found.


Greetings from Rüschlikon (ZH),

   apsi

-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-
  Ari Paavo Seitsonen / ari.p.seitso...@iki.fi / http://www.iki.fi/~apsi/
Ecole Normale Supérieure (ENS), Département de Chimie, Paris
Mobile (F) : +33 789 37 24 25(CH) : +41 79 71 90 935


On Tue, 10 Apr 2018, Venkataramana Imandi wrote:



Dear QE community,

I am a new user of Quantum espresso simulation package. I installed 6.2.1 
Quantum espresso in the
Linux-X86_64-INTEL-MPI. I want to find out the binding energy of O_ad at 
various sites(top,bridge,hcp
and fcc) on Pt-surface and Pt-Ni alloy surface. In the beginning, i have tried 
on Pt-surface, and I got
O_ad at top, hcp and fcc sites on Pt-surface, however, i couldn't find O_ad at 
bridge position.
I have tried all possible ways of getting O_ad at the bridge position(between 
Pt-Pt). None of them were
given succussful results, and the resulted O_ad comes to either fcc or hcp 
position. All possible ways:
using with and without spin-polarization, davidson diagonalization anc cg, 
option (nosym = .TRUE. and
.FALSE.), mixing mode(plain, local-TF and TF), changing mixing-beta(0.2, 0.3 
and 0.5), neutral,
negative charge(-2) and different simulation setup (present 24 atoms to 48 Pt 
atoms). The last option,
i used different pseudopotential(Pt.pw91-n-van.UPF and O.pw91-van_ak.UPF), 
herein, i got error as
follows (Error in scalartorealdp  Too few elements found). Now i stopped trials.
I ask you can anyone do calculation in your simulation setup with the given 
input file, tell me the
where the problem is.

I really thanks to you in advance for any suggestions regarding this.
For information, i used VASP in the last year, therein, i obtained O_ad at all 
sites on Pt-surface.

 
    calculation='relax'
    restart_mode='from_scratch',
    pseudo_dir = '/home2/oth/ch18ipf01/pseudopotential2/',
    prefix='pt'
    tprnfor = .true.,
    nstep = 200
 /
 
    ibrav=0,
    nat=25,
    ntyp=2,
    ! nspin = 2,
    ! starting_magnetization(1)=0.7,
    ecutwfc = 32.0,
    ecutrho = 320.0,
    occupations='smearing',
    smearing='methfessel-paxton',
    degauss=0.02
   ! tot_charge = -2,
    nosym = .TRUE.
 /
 
    diagonalization='cg'
    conv_thr = 1.0e-6
    mixing_beta = 0.3
   electron_maxstep = 1000
 /

ion_dynamics='bfgs',
 /
ATOMIC_SPECIES
Pt  195.084  Pt.pbe-nd-rrkjus.UPF
O    15.999  O.pbe-rrkjus.UPF

ATOMIC_POSITIONS {angstrom}
O 3.45091550  1.17466050 13.69732100  1 1 1
Pt    4.84778787  1.20016667 12.44963917  1 1 1
Pt    3.46185858  3.60066659 12.44963917  1 1 1
Pt    2.07592929  1.20016667 12.44963917  1 1 1
Pt    0.6900  3.60066659 12.44963917  1 1 1
Pt    3.46185858  0.4000 10.18642611  1 1 1
Pt    4.84778787  2.80049996 10.18642611  1 1 1
Pt    0.6900  0.4000 10.18642611  1 1 1
Pt    2.07592929  2.80049996 10.18642611  1 1 1
Pt    3.46185858  2.0000  7.92321305  1 1 1
Pt    4.84778787  4.40083326  7.92321305  1 1 1
Pt    0.6900  2.0000  7.92321305  1 1 1
Pt    2.07592929  4.40083326  7.92321305  1 1 1
Pt    4.84778787  1.20016667  5.6600  1 1 1
Pt    3.46185858  3.60066659  5.6600  1 1 1
Pt    2.07592929  1.20016667  5.6600  1 1 1
Pt    0.6900  3.60066659  5.6600  1 1 1
Pt    3.46185858  0.4000  3.39678694  0 0 0
Pt    4.84778787  2.80049996  3.39678694  0 0 0
Pt    0.6900  0.4000  3.39678694  0 0 0
Pt    2.07592929  2.80049996  3.39678694  0 0 0
Pt    3.46185858  2.0000  1.13357388  0 0 0
Pt    4.84778787  4.40083326  1.13357388  0 0 0
Pt    0.6900  2.0000  1.13357388  0 0 0
Pt    2.07592929  4.40083326  1.13357388  0 0 0

K_POINTS {automatic}
3 3 1 0 0 0
CELL_PARAMETERS {angstrom}
5.5437171600 0.00 0.00
0.00 4.800000 0.00
0.00 0.00    25.5792783300


With best regards
Venkataramana 

Re: [QE-users] QE and BoltzTraP

[Ari P Seitsonen]

Hello,

  If one wants to invest some time into learning a very flexible 
environment, I would go for Jupyter Notebooks, NumPy et co: Not only 
producing vector graphics (.eps for example), it provides the full (ie 
almost unlimited) capacity of Python for processing the data.


Greetings from Dublin,

   apsi

-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-
  Ari Paavo Seitsonen / ari.p.seitso...@iki.fi / http://www.iki.fi/~apsi/
Ecole Normale Supérieure (ENS), Département de Chimie, Paris
Mobile (F) : +33 789 37 24 25(CH) : +41 79 71 90 935


On Thu, 22 Mar 2018, Bramha Pandey wrote:


GNUPLOT tools is a best for ploting. If you would like to some time spent with 
GNUPLOT to learn.

--
Regards
Dr. Bramha P Pandey
Asstt. Prof. ECE Deptt.
MMM University of Technology, Gorakhpur (U.P)
India-273010.

On Thu, Mar 22, 2018 at 1:42 PM, NEELESH GUPTA  wrote:
  Dear PWSCF users/experts,
 I have run boltztrap calculations 
(after nscf
calculations with dense k mesh in quantum espresso). Now I need to plot 
electrical, thermal
conductivities, Seebeck coefficient, figure of merit etc (vs. Temp.) from 
output files. Now I
have .trace file with 10 columns in total.  Could you please tell me the 
procedure of plotting
them? Which software is good here for plotting?






Thank you very much.



Warm regards[IMAGE]
Neelesh Gupta
Research Scholar,ECE
IIIT Allahabad, India.

___
users mailing list
users@lists.quantum-espresso.org
https://lists.quantum-espresso.org/mailman/listinfo/users



___
users mailing list
users@lists.quantum-espresso.org
https://lists.quantum-espresso.org/mailman/listinfo/users

Re: [Pw_forum] Phonon calculation of Silicene: ph.x

[Ari P Seitsonen]

Dear Neelesh,

  Adding to the answer of Jagdish, there is a fixed dimension:

qe-6.2/Modules/parameters.f90:   npk= 4,  &! max number of k-points

(This in version 6.2)
As pointed our in the previous answer, the number of actual k points will 
be reduced significantly if you do not apply k point beyond one value in 
the direction without periodicity (assuming that you have indeed a 
single, isolated layer in question).


Greetings,

   apsi

-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-
  Ari Paavo Seitsonen / ari.p.seitso...@iki.fi / http://www.iki.fi/~apsi/
Ecole Normale Supérieure (ENS), Département de Chimie, Paris
Mobile (F) : +33 789 37 24 25(CH) : +41 79 71 90 935


On Thu, 11 Jan 2018, Jagdish verma wrote:


Dear Neelesh,

I don't know about the error. But in scf input , I think you should have 36 36 
1 0 0 0 k grid because silicene  has 2D structure. It will
decrease k points in scf.out. Please correct me if I said anything wrong. 

On Thu, Jan 11, 2018 at 5:50 PM, NEELESH GUPTA  wrote:
  Dear All ,
   
I'm trying to perform a phonon calculation of silicne using using ph.x on QE v 
6.0.

I running this simulation using parallelzation
mpirun -np 32 -hostfile machine ph.x -ndiag4  -nk 2  ph.out



Error generated...

 %%
 Error in routine set_kplusq (23976):
 too many k points
 %%

 stopping ...

:

##I have done the scf calculation is done with k-points
  36  36  36  0 0 0

##  Detailed paramters
  ibrav=4,
  celldm(1)=7.3321373633d0, celldm(3)=12.8865979381d0,
  nat=2,
  ntyp=1,


## the ph code is
Ph
 
    prefix='calc'
    outdir='Xe',
    fildyn='calc.dyn',
    tr2_ph=1.0d-16,
    alpha_mix=0.7,
    verbosity='high',
    ldisp=.true.,
    epsil= .false.
    trans=.true,
    nq1=4,nq2=4,nq3=1,



I have tried with -nimage in mpi run  but it stops and in crash files it shows error of too many k-points. 


Thanks in advance!



Warm regards
Neelesh Gupta
Research Scholar,ECE









___
Pw_forum mailing list
Pw_forum@pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum




--
With best regards,
Jagdish Verma,



___
Pw_forum mailing list
Pw_forum@pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum

Re: [Pw_forum] Is it possible to calculated IR and Raman spectra for molecules adsorbed on metal surfaces

[Ari P Seitsonen]

Dear Jibiao Li,

  A late reply, but: It is not possible to "isolate" the molecule in the 
calculation nor in the experiment, as any photon hitting the system might 
cause an electronic excitation, either at the molecule or the surface, so 
the intensity of the spectrum would be beyond the non-resonant regime.


  The crude approximation is to calculate the vibrational modes and try to 
correlate those with experiments - without the intensity (but maybe with 
the selection rules from symmetry). Next, you might try to move the atoms 
along the normal modes and see if you get something useful from the 
variation/derivative of the dipole/polarisability. But, as said, also in 
the experiment there could be any excitations, thus smearing the 
intensities.


Greetings from Paris,

   apsi

-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-
  Ari Paavo Seitsonen / ari.p.seitso...@iki.fi / http://www.iki.fi/~apsi/
Ecole Normale Supérieure (ENS), Département de Chimie, Paris
Mobile (F) : +33 789 37 24 25(CH) : +41 79 71 90 935


On Tue, 9 Jan 2018, jibiaoli wrote:


Dear All,

I learned from the maillist that pure metallic systems do not have IR and Raman 
active modes, thereby it's meaningless to calculated IR and Raman
spectra for those systems. However, I am very much interested in molecules 
adsorbed on metal surfaces, is it possible to get IR and Raman spectra
for molecules/metal systems through QE calculations?

Best

Jibiao Li

Yangtze Normal University, China

___
Pw_forum mailing list
Pw_forum@pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum

Re: [Pw_forum] Pseudopotential Radius for K

[Ari P Seitsonen]

Dear Lance Kavalsky,

  A wild guess: s was the local component of the pseudo potential? I 
agree, the cut-off radius should have been listed though.


Greetings from Rainy Paris,

   apsi

-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-
  Ari Paavo Seitsonen / ari.p.seitso...@iki.fi / http://www.iki.fi/~apsi/
Ecole Normale Supérieure (ENS), Département de Chimie, Paris
Mobile (F) : +33 789 37 24 25(CH) : +41 79 71 90 935


On Tue, 9 Jan 2018, Lance Kavalsky wrote:



Hello all,


For the Potassium pseudopotential K.pbe-mt_fhi.UPF from the website, I am 
trying to find the cutoff
radius.


When reading through the file, I see that in the Nonlocal section, cutoff radii 
are provided for each of
the angular momenta (except for the s-orbitals), but what units are these in? 
Also, I noticed that the
s-orbital is not listed in either this section, nor in the semilocal section 
where the beta projectors for
calculating the nonlocal component are listed (no L=0).


Why might the L=0 projector not be detailed within the file? And is it safe to 
assume that for all L the
cutoff radius applied would be the same?


I would very much appreciate any clarification on this matter.


Thanks,

Lance Kavalsky

HBSc., MASc. student

Dept. of Materials Science and Engineering

University of Toronto


___
Pw_forum mailing list
Pw_forum@pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum

Re: [Pw_forum] Force is fluctuating for water system

[Ari P Seitsonen]

Dear Narendra Nath Ghosh,

  Adding to Lorenzo's answer, a small note: You seem to have an odd number 
of electrons but you do not specify 'nspin = 2' - are you sure that this 
is what you intended to do (physically)? 70 Ry with a pseudo potential à 
la Troullier-Martins for oxygen, it might be at the lower limit (it 
depends on the core radii, usually I would go for 80-90 Ry minimum). And, 
do you know if the electron gets localised or remains delocalised - this 
is an open question to my knowledge, and might well depend on the kind of 
exchange-correlation functional used (GGA like BLYP probably delocalise it 
- with the highest occupied orbital in the conduction band - and hybrid 
functionals might localise it).


Greetings from Helsinki/Finland,

   apsi

-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-
  Ari Paavo Seitsonen / ari.p.seitso...@iki.fi / http://www.iki.fi/~apsi/
Ecole Normale Supérieure (ENS), Département de Chimie, Paris
Mobile (F) : +33 789 37 24 25(CH) : +41 79 71 90 935


On Tue, 19 Dec 2017, Narendranath Ghosh wrote:


Dear all 

I am relaxing a system of 128 water molecule with extra electron.The force is 
fluctuating even after bfgs
steps   =  48.



Input:


  calculation='relax',
  outdir='/share_home/hpc/NEGATIVE_HYDRATED_ELECTRON/OUTPUT',
  prefix='water-128-negative',
  pseudo_dir='/share_home/hpc/RESEARCH_SCHOLAR/HYDRATED-ELECTRON/pseudo',
  verbosity='high',
  restart_mode='restart',
/

  ibrav=0,
  celldm(1)=29.8576727681d0,
  nat=384,
  tot_charge=-1,
  ntyp=2,
  ecutwfc=70,
  ecutrho=280,
  input_dft='BLYP',
  occupations='smearing',
  degauss=0.05d0,
/

  mixing_beta=0.500d0,
  electron_maxstep=500,
/

/
ATOMIC_SPECIES
 O  16.0d0   O.blyp-mt.UPF
 H  1.0079d0 H.blyp-vbc.UPF

K_POINTS {automatic}
  1 1 1 0 0 0
CELL_PARAMETERS {alat}
  1.d0  0.d0  0.d0
  0.d0  1.d0  0.d0
  0.d0  0.d0  1.d0

Output

    Total force = 0.030447 Total SCF correction = 0.001115
 Total force = 0.033732 Total SCF correction = 0.000223
 Total force = 0.042921 Total SCF correction = 0.000171
 Total force = 0.032971 Total SCF correction = 0.000165
 Total force = 0.032983 Total SCF correction = 0.000266
 Total force = 0.036132 Total SCF correction = 0.000252
       Total force = 0.040191 Total SCF correction = 0.000833
 Total force = 0.032897 Total SCF correction = 0.001663
 Total force = 0.025425 Total SCF correction = 0.000288
 Total force = 0.019869 Total SCF correction = 0.000279
 Total force = 0.020382 Total SCF correction = 0.000102
 Total force = 0.025164 Total SCF correction = 0.000109
 Total force = 0.027580 Total SCF correction = 0.000141
 Total force = 0.026211 Total SCF correction = 0.000188
 Total force = 0.023574 Total SCF correction = 0.000139
 Total force = 0.024877 Total SCF correction = 0.000103
 Total force = 0.027597 Total SCF correction = 0.000131
 Total force = 0.027563 Total SCF correction = 0.000169
 Total force = 0.023015 Total SCF correction = 0.000195
 Total force = 0.02 Total SCF correction = 0.000109
 Total force = 0.021345 Total SCF correction = 0.92
 Total force = 0.023793 Total SCF correction = 0.000129
 Total force = 0.024400 Total SCF correction = 0.000145
 Total force = 0.025073 Total SCF correction = 0.000243
 Total force = 0.022300 Total SCF correction = 0.000376
 Total force = 0.020060 Total SCF correction = 0.97
 Total force = 0.021991 Total SCF correction = 0.000134
 Total force = 0.022541 Total SCF correction = 0.000132
 Total force = 0.023051 Total SCF correction = 0.000158
 Total force = 0.023734 Total SCF correction = 0.000168


 Total force = 0.023734 Total SCF correction = 0.000168
 number of scf cycles    =  49
 number of bfgs steps    =  48
 energy   old    =   -4400.3520443575 Ry
 energy   new    =   -4400.3528674259 Ry
 CASE: energy  _new < energy  _old
 new trust radius    =   0.0602516409 bohr
 new conv_thr    =   0.000591 Ry

Please help me.

Dr. Narendra Nath Ghosh

Research Associate

University of Gour  Banga

Malda-732102

India

Phone No : 09126667601


___
Pw_forum mailing list
Pw_forum@pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum

Re: [Pw_forum] problem in relaxing gold cluster

[Ari P Seitsonen]

Dear Haja Zareyi,

  [Next time with affiliation please :) ]

  'hgh' in the name of the pseudo potential => it is norm-conserving, no 
need to specify 'ecutrho'. Did you check that the 'ecutwfc' was 
sufficient for a reasonable convergence?


Greetings from Lviv/Lemberg,

   apsi

-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-
  Ari Paavo Seitsonen / ari.p.seitso...@iki.fi / http://www.iki.fi/~apsi/
Ecole Normale Supérieure (ENS), Département de Chimie, Paris
Mobile (F) : +33 789 37 24 25(CH) : +41 79 71 90 935


On Sun, 3 Dec 2017, hajar zareyi wrote:


Dear all,

I am trying to relax gold cluster but the structure is going to break apart. 
there is my input file

 
calculation = 'relax' ,
restart_mode = 'from_scratch' ,
outdir="./TMP",
pseudo_dir ="./",         
tprnfor   = .true.
tstress = .true.
prefix = 'AU',
/

ibrav = 1,
celldm(1) = 34.75,
nat = 13,
ntyp = 1,
ecutwfc = 45 ,
ecutrho = 500,                       
occupations = 'smearing' ,
degauss= 0.01 ,
smearing= 'gaussian',
/
 
mixing_mode = 'local-TF'                                 
mixing_beta = 0.7
conv_thr = 1.D-6 , 
/
 
/
 
/
ATOMIC_SPECIES
Au    196.966657   Au.blyp-d-hgh.UPF
ATOMIC_POSITIONS (angstrom)
Au 7.000 10.000 10.000
Au 8.360 7.644 10.000
Au 11.080 7.644 10.000
Au 12.440 10.000 10.000
Au 11.080 12.356 10.000
Au 8.360 12.356 10.000
Au 9.720 10.000  10.000
Au 9.7238155 8.4315277  7.777622
Au 8.3424810 10.7842271  7.780175
Au 11.0523480 10.8179223  7.78000
Au 9.7238155 8.4315277  12.2223780
Au 8.3328179 10.7673656  12.220
Au 11.0523480 10.8179223  12.220

K_POINTS gamma

is there any one to help me to correct it

 


--
This message has been scanned for viruses and dangerous content by
KNTU Antispam System (E.F.A. Project), and is believed to be clean.
___
Pw_forum mailing list
Pw_forum@pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum

Re: [Pw_forum] Phonon negative Frequency

[Ari P Seitsonen]

Dear Suresh,

  Adding to the comment of Isaiah, did you check the FAQ?
http://www.quantum-espresso.org/faq/phonons/#7.3

Greetings,

   apsi

PS Why running in serial...? I guess basically any CPU nowadays has at 
least two cores.


-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-
  Ari Paavo Seitsonen / ari.p.seitso...@iki.fi / http://www.iki.fi/~apsi/
Ecole Normale Supérieure (ENS), Département de Chimie, Paris
Mobile (F) : +33 789 37 24 25(CH) : +41 79 71 90 935


On Wed, 29 Nov 2017, Isaiah Moses wrote:


Dear Suresh,
I doubt if there is any way you can know if you'll have negative frequency 
while the calculation is on.
However you can take note of some of the information in phonon user's guide on 
how to avoid negative frequency.

Also, you can do a test run with a single q-point splitted among irreps in 
order to save your time and computational resources.
Check example on how to split phonon calculation in case you are not familiar 
with that.

All the best,
Isaiah.

On Wed, Nov 29, 2017 at 6:24 AM, Suresh A  wrote:
  Dear All,
 I am ran phonon calculation for anatase previously and got 
negative frequencies. I was install QE-5.2.0 in serial mode and
took days to finish the calculation in my desktop.

Is there any way to know the negative frequency before the calculation ends? So 
that the time can be saved.
                                 Thank You
  
 Yours Sincerly,

A.Suresh,
Research Scholar,
School of Physics,
Madurai Kamaraj University,
Madurai.

___
Pw_forum mailing list
Pw_forum@pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum




--
Isaiah Abu Moses
Graduate Student,
Physics Department,
University of Ibadan,
Nigeria

___
Pw_forum mailing list
Pw_forum@pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum

Re: [Pw_forum] convergence problem in scf calculation in rare earth oxide Sm2O3

[Ari P Seitsonen]

Dear Mohammed,

  I do not not know anything about the compound, but one note: Did you 
notice that the keyword 'starting_magnetization' expects values between -1 
and 1, those limits meaning full spin polarisation of the valence 
electrons (or, a relative polarisation)? If this is not what you wanted, 
the guess (ferro-magnetic, apparently) for the initial density can be 
quite far from the final value. And indeed all the lanthanides are 
difficult to handle, I do not know how accurate the available PAW/pseudo 
potentials are; one might consider starting initially with a fixed 
total magnetisation to see if one can converge then. Yet in some cases I 
am still fighting to get the electronic structure to converge, even in 
molecules.


  Sorry, I have no better suggestions.

Greetings,

   apsi

-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-
  Ari Paavo Seitsonen / ari.p.seitso...@iki.fi / http://www.iki.fi/~apsi/
Ecole Normale Supérieure (ENS), Département de Chimie, Paris
Mobile (F) : +33 789 37 24 25(CH) : +41 79 71 90 935


On Sat, 25 Nov 2017, Mohammed Khalafalla wrote:


Dear all,
I could not achieve scf convergence in Sm2La2O6 (the input file is attached 
herewith). This was the case even after several 'restart' of the
calculation with different pseudpotentials specially for 'O' atom. I guess I 
used well tested PAW psedu for rare earth from
http://www.vlab.msi.umn.edu/resources/repaw/index.shtml
I used recommended hubbard potentials and spin polarization, but no change. 
Generally I found convergence in (Sm,O) system to be difficult. Can
you kindly let me know which parameter set-up would determine successful 
convergence in (Sm,O) system?
Regards,
Mohammed A. H. Khalafalla (PhD)
Taibah University
KSA


___
Pw_forum mailing list
Pw_forum@pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum

Re: [Pw_forum] Convergence test, vc-relax calculation

[Ari P Seitsonen]

Dear Mondol Anik Kumar,

 1) It depends on which quantities you mean hear: The ecutwfc (and 
ecutrho, if using Vanderbilt/USPP or PAW) are universal so long as you 
have not added or changed new pseudo potentials/PAW data sets; k points, 
one can in general estimate the spacing (in reci-procal space, naturally) 
from the bulk, unless the physics is radically different (for example one 
system metallic, the other one insulating)


 2) You can use "restart_mode = 'restart'" and you do not have to update 
the geometry or cell in the input file; I tend to do this anyway, in case 
I once want to do a "restart_mode = 'from_scratch'"


Greetings from Paris,

   apsi

-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-
  Ari Paavo Seitsonen / ari.p.seitso...@iki.fi / http://www.iki.fi/~apsi/
Ecole Normale Supérieure (ENS), Département de Chimie, Paris
Mobile (F) : +33 789 37 24 25(CH) : +41 79 71 90 935


On Sun, 26 Nov 2017, Anik Mondol wrote:


Dear Users,I am new to quantum espresso. I appreciate the things that can be 
done by quantum espresso. I have  some specific queries. I will get
to the points

My intention is to calculate bandstructure of GaN nanowire. I have carried 
convergence test ( ecutwfc, kpoint , lattice parameters( a,c)) for GaN
supercell.
Then I constructed a nanowire supercell by adding vacuum . Then I have 
performed a self-consistent and vc-relax calculation

Now my confusion is this :

1. Did I need to carry out convergence test for the supercell as well ?

2.After the vc -relax calculation, I want to do a final scf calculation do I 
need to update my input file with the optimized results  from the
outputs of vc-relaxation or QE reads data from the saved directory ?

Regards

Mondol Anik Kumar
Department of Electrical and Electronic Engineering
Bangladesh University of Engineering and Technology 
___
Pw_forum mailing list
Pw_forum@pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum

Re: [Pw_forum] Error while running VASP 5.4.1 with wannier90-1.2

[Ari P Seitsonen]

Dear Pachineela,

  Well, there is an on-line copy: 
https://depositonce.tu-berlin.de/handle/11303/547

  A short historical note on shifting the k point mesh, Monkhorst and Pack 
published their initial algorithm to obtain the equidistant mesh, which 
avoided the Gamma; then there was a Comment (by Chadi and Cohen, if I 
remember well) on their Article pointing out the problem indeed in the 
hexagonal cell, and Monkhorst and Pack responded introducing this shift, 
which they used to shift the initial mesh so that one point is at Gamma - 
and this was introduced in the DFT codes as a general shift.


Greetings,

   apsi

-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-
  Ari Paavo Seitsonen / ari.p.seitso...@iki.fi / http://www.iki.fi/~apsi/
Ecole Normale Supérieure (ENS), Département de Chimie, Paris
Mobile (F) : +33 789 37 24 25(CH) : +41 79 71 90 935


On Tue, 14 Nov 2017, pachineela rambabu wrote:


Dear Sir,
   thanks for the reply. Can I get a copy of your thesis?
thanks,

On Tue, Nov 14, 2017 at 1:23 AM, Ari P Seitsonen <ari.p.seitso...@iki.fi> wrote:

  1) rm -rf ${VASP_DIR}
  2) wget qe-6.2.tar.gz
  3) Compile and compute

   ;)

    Well, my guess is that this is a cell - for example hexagonal - where 
the k point grid
  better contain the Gamma point (or at least [0,0,k_z] laterally), because 
otherwise the
  initial Monkhorst-Pack grid of k points has a lower symmetry than the 
cell; further
  explanation for example in the Appendix of my PhD thesis.

      Greetings,

         apsi

  
-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-
    Ari Paavo Seitsonen / ari.p.seitso...@iki.fi / http://www.iki.fi/~apsi/
      Ecole Normale Supérieure (ENS), Département de Chimie, Paris
      Mobile (F) : +33 789 37 24 25    (CH) : +41 79 71 90 935


  On Mon, 13 Nov 2017, pachineela rambabu wrote:

Hi,
   I am trying to run the bandstructure of Bi2Se3 with VASP5.4.1 
compiled with
wannier90-1.2. In INCAR
file I added "LWANNIER90=.TRUE.. However I am getting the following 
error:



 KPOINTS: Kpoints for band structure 
  interpolating k-points between supplied coordinates
  k-points in reciprocal lattice
Space group operators:
 irot   det(A)    alpha  n_x  n_y  
n_z   
tau_x    tau_y   
tau_z
    1 1.00 0.00 1.00 0.00 
0.00
0.00 0.00
0.00

 
-
|   
  |
|   W    W    AA    R   N    N  II  N    N      !!! 
  |
|   W    W   A  A   R    R  NN   N  II  NN   N  G    G  !!! 
  |
|   W    W  A    A  R    R  N N  N  II  N N  N  G   !!! 
  |
|   W WW W  AA  R   N  N N  II  N  N N  G  GGG   !  
  |
|   WW  WW  A    A  R   R   N   NN  II  N   NN  G    G  
  |
|   W    W  A    A  R    R  N    N  II  N    N      !!! 
  |
|   
  |
|  Your generating k-point grid is not commensurate to the 
symmetry   |
|  of the lattice.  This can cause   slow convergence with 
respect    |
|  to k-points for HF type calculations 
  |
|  suggested SOLUTIONS: 
  |
|   ) if not already the case, use automatic k-point generation 
  |
|   ) shift your grid to Gamma (G) (e.g. required for hex or 
fcc lattice) |
|   
  |
 
-


I am unable to find where the error is? Please address my problem.

thanks,
--
P. Rambabu
PhD Scholor
Physics, IIT Hyderabad
Mobile: 9074508220.


___
Pw_forum mailing list
Pw_forum@pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum




--
P. Rambabu
PhD Scholor
Physics, IIT Hyderabad
Mobile: 9074508220.

___
Pw_forum mailing list
Pw_forum@pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum

Re: [Pw_forum] Error while running VASP 5.4.1 with wannier90-1.2

[Ari P Seitsonen]

1) rm -rf ${VASP_DIR}
2) wget qe-6.2.tar.gz
3) Compile and compute

 ;)

  Well, my guess is that this is a cell - for example hexagonal - where 
the k point grid better contain the Gamma point (or at least [0,0,k_z] 
laterally), because otherwise the initial Monkhorst-Pack grid of k points 
has a lower symmetry than the cell; further explanation for example in the 
Appendix of my PhD thesis.


Greetings,

   apsi

-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-
  Ari Paavo Seitsonen / ari.p.seitso...@iki.fi / http://www.iki.fi/~apsi/
Ecole Normale Supérieure (ENS), Département de Chimie, Paris
Mobile (F) : +33 789 37 24 25(CH) : +41 79 71 90 935


On Mon, 13 Nov 2017, pachineela rambabu wrote:


Hi,
   I am trying to run the bandstructure of Bi2Se3 with VASP5.4.1 compiled with 
wannier90-1.2. In INCAR
file I added "LWANNIER90=.TRUE.. However I am getting the following error:



 KPOINTS: Kpoints for band structure 
  interpolating k-points between supplied coordinates
  k-points in reciprocal lattice
Space group operators:
 irot   det(A)    alpha  n_x  n_y  n_z    
tau_x    tau_y   
tau_z
    1 1.00 0.00 1.00 0.00 0.00 
0.00 0.00
0.00

 -
| |
|   W    W    AA    R   N    N  II  N    N      !!!   |
|   W    W   A  A   R    R  NN   N  II  NN   N  G    G  !!!   |
|   W    W  A    A  R    R  N N  N  II  N N  N  G   !!!   |
|   W WW W  AA  R   N  N N  II  N  N N  G  GGG   !    |
|   WW  WW  A    A  R   R   N   NN  II  N   NN  G    G    |
|   W    W  A    A  R    R  N    N  II  N    N      !!!   |
| |
|  Your generating k-point grid is not commensurate to the symmetry   |
|  of the lattice.  This can cause   slow convergence with respect    |
|  to k-points for HF type calculations   |
|  suggested SOLUTIONS:   |
|   ) if not already the case, use automatic k-point generation   |
|   ) shift your grid to Gamma (G) (e.g. required for hex or fcc lattice) |
| |
 -


I am unable to find where the error is? Please address my problem.

thanks,
--
P. Rambabu
PhD Scholor
Physics, IIT Hyderabad
Mobile: 9074508220.

___
Pw_forum mailing list
Pw_forum@pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum

Re: [Pw_forum] Fw: Contracting cell volume for supercell in vc-relax

[Ari P Seitsonen]

Dear Amar,

  A general comment: Have you considered why your cell changes so much 
from the initial one? It is hard to say without seeing the input. If you 
think that the job is meaningful, you could take the latest cell vectors 
and atomic positions and start with 'from_scratch' again. But usually when 
I have had this messsage, I have ended up realising that my initial 
structure was somehow errorneous.


Greetings from Paris,

   apsi

-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-
  Ari Paavo Seitsonen / ari.p.seitso...@iki.fi / http://www.iki.fi/~apsi/
Ecole Normale Supérieure (ENS), Département de Chimie, Paris
Mobile (F) : +33 789 37 24 25(CH) : +41 79 71 90 935


On Sat, 28 Oct 2017, Amar Singh wrote:


Hi Friends,
​I am trying to optimize a supercell using vc-relax using ibrav = 14, unit cell 
volume keeps on shrinking and finally ends up with an error "Not
enough space allocated for radial FFT: try restarting with a larger 
cell_factor". Using cell factor = 8 and ecutrho = 10 X ecutwfc helped a bit
in reducing the rate at which volume of cell decreases / SCF cycle, but not 
solved the problem completely. Can these variables be increased
further ?
Would be thankful for any suggestion on it.
Thanks
​Amar
​MGRU, Chennai

___
Pw_forum mailing list
Pw_forum@pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum

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

[Ari P Seitsonen]

Dear Saif Ullah,

  (Next time with your affiliation, please)

  I wonder why you have commented out the spin polarisation; did you do 
the same witht eh other codes? Since your system is neutral, it looks to 
me as if your system would have an odd number of electrons, but the spin 
polarisation is not accounted for. Did you check that your energies are 
well converged, considering that you are performing calculations 
with 'vc-relax'?


Greetings from Sunny Paris,

   apsi

-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-
  Ari Paavo Seitsonen / ari.p.seitso...@iki.fi / http://www.iki.fi/~apsi/
Ecole Normale Supérieure (ENS), Département de Chimie, Paris
Mobile (F) : +33 789 37 24 25(CH) : +41 79 71 90 935


On Wed, 4 Oct 2017, Saif Ullah wrote:


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


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


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


   diagonalization='cg',
  conv_thr=1d-08,
  mixing_mode='local-TF',
  mixing_beta=0.500d0,
 electron_maxstep=2000
/

ion_dynamics='bfgs'
/

   cell_dynamics = 'bfgs' ,
  cell_dofree='2Dxy'
/
ATOMIC_SPECIES
C 12.010700d0 C.pbe-van_ak.UPF
Li  6.941000d0 Li.pbe-n-van.UPF 
CELL_PARAMETERS (angstrom)
  12.353060724   0.000889035  -0.20145
  -6.175669462  10.698563666   0.20131
  -0.49454   0.28549  20.0

ATOMIC_POSITIONS (angstrom)
C       -0.123777599   0.044352021   0.750813339
C        2.347139643   0.044536664   0.710530839
C        4.816959818   0.046608474   0.671588196
C        7.288030852   0.047974520   0.631371477
C        9.759254756   0.046949526   0.590970165
C       -1.361324273   2.182837743   0.784592128
C        1.111661447   2.176898866   0.738849472
C        3.584693057   2.183131578   0.703985603
C        6.053702309   2.186196980   0.671658550
C        8.522771292   2.186413475   0.631364175
C       -2.598243992   4.325485482   0.824910219
C       -0.131078480   4.322022349   0.764237921
C        2.354133011   4.322141066   0.723759919
C        4.821870209   4.325914119   0.703967494
C        7.288439627   4.327051393   0.671562970
C       -3.831089225   6.466525503   0.871657296
C       -1.366959478   6.470638409   0.819586551
C        1.111648295   6.474564682   0.764205441
C        3.590771165   6.470877940   0.738791095
C        6.055337825   6.467163164   0.710460311
C       -5.064123742   8.605360424   0.914570582
C       -2.595447017   8.606844025   0.871611006
C       -0.124940436   8.609595937   0.824824937
C        2.349153535   8.609719150   0.784488796
C        4.820054590   8.607291549   0.750697179
C       -0.125510159   1.469181337   0.757732918
C        2.348583973   1.469399905   0.717413261
C        4.819499832   1.472058312   0.683659878
C        7.288388407   1.473415839   0.646082581
C        9.757057163   1.472349661   0.603098319
C       -1.367183927   3.608059861   0.792700719
C        1.111411672   3.604765482   0.737260404
C        3.590550668   3.608523771   0.711920217
C        6.055141240   3.612373570   0.683651546
C        8.521773207   3.612481509   0.643390074
C       -2.598108408   5.752895502   0.838312859
C       -0.130966528   5.757101185   0.12574
C        2.354245670   5.757343547   0.737229826
C        4.822007602   5.753541812   0.717366687
C        7.288591341   5.752608946   0.684948021
C       -3.829804361   7.892507839   0.886438561
C       -1.360854441   7.895696352   0.838263118
C        1.112121068   7.902104754   0.792620096
C        3.585162055   7.896134775   0.757637017
C        6.054187493   7.893269674   0.725270353
C        1.111459010  -0.667769729   0.725378109
C        3.582681447  -0.666400412   0.685002360
C        6.052708940  -0.664305301   0.643406933
C        8.523624623  -0.664119335   0.603107212
C       10.993446884  -0.665855193   0.564139854
Li       1.142006551   5.022080560   2.622103194
K_POINTS automatic
 6 6 1 0 0 0

___
Pw_forum mailing list
Pw_forum@pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum

Re: [Pw_forum] Graphene

[Ari P Seitsonen]

@Ankita,

  Please learn the concept of a "slab": Adding vacuum in the third 
direction (and you can use the [surface] dipole correction if the two 
surfaces/sides do not have the same asymptotic potential).


@Brahma,

  Please provide your afficialtion too. ;)

Greetings from the Aeroport of Zurich,

   apsi

-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-
  Ari Paavo Seitsonen / ari.p.seitso...@iki.fi / http://www.iki.fi/~apsi/
Ecole Normale Supérieure (ENS), Département de Chimie, Paris
Mobile (F) : +33 789 37 24 25(CH) : +41 79 71 90 935


On Sun, 10 Sep 2017, Bramha Pandey wrote:


Dear Ankita, You may use virtual nanolab(vnl) which is the part of Quantum 
wise. It is free for academic
community. 
Bdw kindly provide your affiliation for future communication on this forum. 

On Sep 10, 2017 11:36 AM, "ankita jangir"  wrote:

  Dear qe users
  I want to run scf for graphene but dont have idea about how to form 
structure of a 2D
  material in QE. I  run many 3D crystalline materials on QE.
  Please suggest.


  ___
  Pw_forum mailing list
  Pw_forum@pwscf.org
  http://pwscf.org/mailman/listinfo/pw_forum


___
Pw_forum mailing list
Pw_forum@pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum

Re: [Pw_forum] Relax or vc-relax

[Ari P Seitsonen]

Dear Rajesh,

  I do not know about the ESM, but please check the keyword 'cell_dofree' 
in the namelist ''.


Greetings from Dublin,

   apsi

-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-
  Ari Paavo Seitsonen / ari.p.seitso...@iki.fi / http://www.iki.fi/~apsi/
Ecole Normale Supérieure (ENS), Département de Chimie, Paris
Mobile (F) : +33 789 37 24 25(CH) : +41 79 71 90 935


On Mon, 24 Jul 2017, Rajesh wrote:


Dear Dr Kumar
Thank you for your reply. Actually, in publications related to 2D materials I 
find that a vacuum is
applied in perpendicular direction to the plane of nanohseet, say graphene. In 
vc-relax the change in
dimension may affect the vacuum thickness. I there any option to address this? 
What about esm?


Thanks 
Rajesh

On Mon, Jul 24, 2017 at 3:39 PM, Sonu Kumar <1009uku...@gmail.com> wrote:
  Relax will only relax your atomic positions, while vc-relax will relax 
atomic positions
as well lattice parameters. Please read the documentation of pw.x for
detail.

bests, sonu

===
With kind regards,
Dr. S Kumar, Post doctoral fellow
Physical Sciences and Engineering  Divison,
IBN Sina Building, KAUST,
Thuwal, KSA
===

On Sun, Jul 23, 2017 at 10:36 PM, Rajesh  wrote:
  Dear users
Which option is better for geometry optimisation: relax or vc-relax. Please 
suggest I am new
to quantum espresso.

Thank you

Rajesh

___
Pw_forum mailing list
Pw_forum@pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum



___
Pw_forum mailing list
Pw_forum@pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum



___
Pw_forum mailing list
Pw_forum@pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum

Re: [Pw_forum] Pseudopotential generation of Silicon in [Ne] 3s2 3p2 3d0 configuration

[Ari P Seitsonen]

Dear Harshit Bharti,

  Indeed this is the standard procedure, the method of Don Hamann (PRB 
from 1990's) for unbound states. Do you need the orbital wave function 
somewhere else than in the DFT Hamiltonian? There the discontinuity does 
not matter, because i) the d channel is usually the local one for Si and 
thus the wave function is not used and ii) in the Kleinman-Bylander 
operator (V_l - V_local) |phi_l> the Delta V_l = (V_l - V_local) vanishes, 
or goes to zero, at the core radius, thus making the operator approach 
zero, and the discontinuity in phi_l does not matter.


Greetings from Lviv/Lemberg/Lwow/Lvov,

   apsi

-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-
  Ari Paavo Seitsonen / ari.p.seitso...@iki.fi / http://www.iki.fi/~apsi/
Ecole Normale Supérieure (ENS), Département de Chimie, Paris
Mobile (F) : +33 789 37 24 25(CH) : +41 79 71 90 935


On Tue, 20 Jun 2017, harshit bharti wrote:


Dear all,

The pseudo wave function that I have produced of the 3d orbital in the above 
configuration has a sharp
spike in the plot.
My main objective is to remove this spike which I have been unable to do even 
upon varying the
parameters.

The input file is as follows:


 
   iswitch=3,
   rlderiv=1.8,  
   rel=0,
   zed=14.0,
   config="[Ne] 3s2 3p2 3d0",
   dft='PBE',
/



   lloc=2,
   pseudotype=1,
   file_pseudopw='Si.UPF',
   zval=4.0,
   tm=.true.,
  
 
/

3
3S 1 0 2.00 0.00 2.20 2.20
3P 2 1 2.00 0.00 2.20 2.20
3D 3 2 0.00 0.00 1.20 2.20

It would be a pleasure if anyone could look into this problem and give some 
suggestions.

Thanking You

Yours sincerely,
Harshit Bharti
Visvesvaraya National Institute of Technology,
Nagpur

___
Pw_forum mailing list
Pw_forum@pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum

Re: [Pw_forum] Pseudopotential generation of Silicon in [Ne] 3s2 3p2 3d0 configuration

[Ari P Seitsonen]

Dear Harshit Bharti,

  What do you mean with "wrong pseudo potential for 3d orbital"? Please 
provide more information, about your input and why you say that the pseudo 
potential is "rong"? It is possible to generate a pseudo potential in the 
neutral or an ionised configuration; actually Si is one of the easiert 
elements to create a pseudo potential for.


Greetings,

   apsi

-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-
  Ari Paavo Seitsonen / ari.p.seitso...@iki.fi / http://www.iki.fi/~apsi/
Ecole Normale Supérieure (ENS), Département de Chimie, Paris
Mobile (F) : +33 789 37 24 25(CH) : +41 79 71 90 935


On Fri, 16 Jun 2017, harshit bharti wrote:


Dear all,

SInce the last few days, I have been trying to produce pseudo wave function for 
Silicon in the ground
state. However, I am always getting wrong pseudopotential for 3d orbital.
I have found out via some research papers and books that the configuration used 
for Silicon is in
excited state.
It would be a pleasure if I could get more information about the ground state 
pseudopotential generation
of silicon especially the 3d orbital.

Thanking you

Yours sincerely,
Harshit Bharti
Visvesvaraya National Institute of Technology,
Nagpur

___
Pw_forum mailing list
Pw_forum@pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum

Re: [Pw_forum] Error ortho went bananas

[Ari P Seitsonen]

Adding oto Giovanni's response,

  If this is the same GTH/HTH pseudo potential that we used recently 
(I-Chun Lin et alia x2) to simulate liquid water, we found that at least 
120 Ry was required for reasonable converergence (NVT; NPT would have 
required much more). 80-90 Ry is more or less sufficient for a 
Troullier-Martins-type pseudo potential. Oh, and PBE requires somewhat 
less than BLYP, that we used actually.


Greetings from Paris 6e,

   apsi

-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-
  Ari Paavo Seitsonen / ari.p.seitso...@iki.fi / http://www.iki.fi/~apsi/
Ecole Normale Supérieure (ENS), Département de Chimie, Paris
Mobile (F) : +33 789 37 24 25(CH) : +41 79 71 90 935


On Fri, 16 Jun 2017, Giuseppe Mattioli wrote:



 

Dear Kartikeya Dixit

 

> ecutwfc=20.0

> O 16.00 O.pbe-hgh.UPF

 

20.0 Ry seems to be a poorly unconverged value for this hard 
Hartwigsen-Goedecker-Hutter O.pbe-hgh.UPF
norm conserving pseudopotential. I would rather expect a converged value of 
80.0 Ry.

*N.B.*: If you do not understand this comment you should start from tutorials 
before performing actual
simulations.

 

Moreover

 

Variables: nr1b, nr2b, nr3b

 

Type: INTEGER

Description: dimensions of the "box" grid for Ultrasoft pseudopotentials

must be specified if Ultrasoft PP are present

 

There are no ultrasoft PP in your calculation

 

Variable: q2sigma

 

Type: REAL

Default: 0.1

Description: ecfixed, qcutz, q2sigma: parameters for modified functional to be

used in variable-cell molecular dynamics (or in stress calculation).

"ecfixed" is the value (in Rydberg) of the constant-cutoff;

"qcutz" and "q2sigma" are the height and the width (in Rydberg)

of the energy step for reciprocal vectors whose square modulus

is greater than "ecfixed". In the kinetic energy, G^2 is

replaced by G^2 + qcutz * (1 + erf ( (G^2 - ecfixed)/q2sigma) )

See: M. Bernasconi et al, J. Phys. Chem. Solids 56, 501 (1995)

 

You are not performing a variable-cell molecular dynamics simulation.

 

HTH

Giuseppe

 

On Thursday, June 15, 2017 05:21:52 PM dkartik wrote:

> Hello everyone

>

> I am getting an error ortho went bananas while running the following

> code. As it was discussed in various pw forums we can get rid of this

> problem by reducing dt or increasing ortho_max. But none of them helped.

> Any small hint or help is welcomed.

>

> Thanks

> Kartikeya Dixit

> Ph.D Scholar

> IIT Kanpur, India

>

> 

> calculation='cp',

> restart_mode='from_scratch',

> nstep=10, iprint=20, isave=20,

> dt=2,

> ndr=90, ndw=91,

> pseudo_dir='/home/bmrl/qe-6.0/pseudo/',

> outdir='/home/bmrl/qe-6.0/tempdir/',

> /

> 

> ibrav=2, celldm(1)=14, celldm(2)=14, celldm(3)=14,

> nat=96, ntyp=2, nbnd=256, nspin=1,

> ecutwfc=20.0, ecutrho=80.0,

> nr1b=16, nr2b=16, nr3b=16,

> qcutz=150., q2sigma=2.0, ecfixed=16.0,

> /

> 

> electron_dynamics='damp', electron_damping=0.0002,

> startingwfc='random', ampre=0.01,

> emass=700., emass_cutoff=3.,

> orthogonalization='ortho',ortho_eps=1.D-4,ortho_max=20

>

> /

> 

> ion_dynamics='none',

> ion_radius(1)=1.0, ion_radius(2)=1.0,

> /

> ATOMIC_SPECIES

> O 16.00 O.pbe-hgh.UPF

> Si 28.00 Si.pbe-hgh.UPF

> ATOMIC_POSITIONS angstrom

> Si 9.97400 6.18200 10.09600

> O 10.73300 7.57300 9.81000

> O 9.21500 4.79100 10.38200

> Si 1.58400 4.73800 1.98600

> O 2.69700 3.91500 2.80700

> O 0.47000 5.56200 1.16400

> Si 8.91900 7.87100 14.01700

> O 10.26400 8.75600 14.02000

> O 7.57400 6.98600 14.01400

> Si 14.02300 5.59500 12.09600

> O 13.94600 6.40800 13.48400

> O 14.1 4.78300 10.70700

> Si 0.28400 1.63200 13.19600

> O 0.16300 3.02000 14.00300

> O 0.40500 0.24400 12.38800

> Si 8.04100 13.89100 4.94300

> O 9.64300 13.73600 4.88500

> O 6.43900 14.04500 5.0

> Si 9.73700 7.14700 5.54700

> O 9.33100 5.60800 5.78500

> O 10.14400 8.68800 5.30900

> Si 11.01100 14.02700 9.05600

> O 9.51100 14.01600 9.64300

> O 12.51100 14.03700 8.46900

> Si 12.27100 0.49400 4.99400

> O 11.35400 0.99800 3.77000

> O 13.18800 -0.00900 6.21900

> Si 3.33100 6.05100 13.38200

> O 2.64900 7.36400 14.01800

> O 4.01200 4.73700 12.74600

> Si 13.93200 12.22900 12.33800

> O 13.83300 10.64200 12.08500

> O 14.03100 13.81700 12.59100

> Si 2.91700 13.62900 2.13900

> O 1.69600 14.02100 3.11200

> O 4.13900 13.23700 1.16500

> Si 7.59600 0.62100 0.30500

> O 6.02600 0.78500 0.61900

> O 9.16800 0.45700 -0.01000

> Si 3.33900 0.25800 5.24900

> O 1.81800 0.51400 5.71000

> O 4.86100 0.00100 4.78900

> Si 14.02000 10.49300 6.34600

> O 14.02100 9.51000 7.62100

> O 14.01900 11.47600 5.07000

> Si 6.18400 0.91400 12.58900

> O 5.02200 -0.02300 11.98700

> O 7.34700 1.85300 13.19100

> Si 6.34900 9.75100 9.83900

> O 5.28500 9.24600 10.93600

> O 7.41500 10.25600 8.74100

> Si 13.06000 5.56100 -0.00200

> O 12.77900 7.14600 -0.03800

> O 13.34100 3.97600 0.03500

> Si 12.87400 0.93700 12.45700

> O 11.74500 1.91000 13.06600

> O 14.00300 

Re: [Pw_forum] problem in HSE band structure calculation

[Ari P Seitsonen]

Dear Clarence,

  How could we know, without having any details about your system, pseudo 
potentials, ...? If you could provide them, maybe also the output as 
attachment if it is not too large. Is the nqx1 = nqx2 = nqx3 = 1 
sufficient? 30 Ry, hmm, this must be some "easy element" for the pseudo 
potentials.


Greetings,

   apsi

-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-
  Ari Paavo Seitsonen / ari.p.seitso...@iki.fi / http://www.iki.fi/~apsi/
Ecole Normale Supérieure (ENS), Département de Chimie, Paris
Mobile (F) : +33 789 37 24 25(CH) : +41 79 71 90 935


On Fri, 2 Jun 2017, LEUNG Clarence wrote:



Dear all,

I use the HSE function to calculate the band structure of my system. However, I 
found that the band gap is much smaller than that of other
researchers(about 2eV obtained from vasp). I also calculated the PBE band gap, 
which agrees well with previous reports.

I also attached my scf input file. The pseudopotentials is Norm-conserving. 


  ecutwfc=30,
  input_dft='hse',
  occupations='smearing',
  smearing = 'gaussian' ,
  degauss = 0.02 ,
  nosym = .true. ,
  vdw_corr = 'DFT-D' ,
  nqx1 = 1,
  nqx2 = 1 ,
  nqx3 = 1 ,
/

  conv_thr=1d-06,
  mixing_beta=0.3d0,
  electron_maxstep = 1000 ,
/

  ion_dynamics = 'bfgs',
  bfgs_ndim = 3 ,
/
K_POINTS
84
0.000  0.000  0.000  0.03125
0.000  0.1443377  0.000  0.06250
0.000  0.2886754  0.000 0.06250
0.000  0.4330131  0.000 0.06250
0.000 -0.5773508  0.000 0.03125
0.125  0.0721689  0.000 0.0625
0.125  0.2165066  0.000 0.0625
0.125  0.3608443  0.000 0.0625
0.125  0.5051820  0.000 0.0625
0.125 -0.5051820  0.000 0.0625
0.125 -0.3608443  0.000 0.0625
0.125 -0.2165066  0.000 0.0625
0.125 -0.0721689  0.000 0.0625
0.250  0.1443377  0.000 0.0625
0.250  0.2886754  0.000 0.0625
0.250  0.4330131  0.000 0.0625
0.250  0.5773508  0.000 0.0625
0.250 -0.4330131  0.000 0.0625
0.250 -0.2886754  0.000 0.0625
0.250 -0.1443377  0.000 0.0625
0.250  0.000  0.000 0.0625
0.375  0.2165066  0.000 0.0625
0.375  0.3608443  0.000 0.0625
0.375  0.5051820  0.000  0.0625
0.375  0.6495197  0.000  0.0625
0.375 -0.3608443  0.000  0.0625
0.375 -0.2165066  0.000  0.0625
0.375 -0.0721689  0.000  0.0625
0.375  0.0721689  0.000  0.0625
-0.50 -0.2886754  0.000  0.03125
-0.50 -0.1443377  0.000  0.0625
-0.50  0.000  0.000  0.0625
-0.50  0.1443377  0.000  0.0625
-0.50 -0.8660262  0.000  0.03125
        0.00    0.00    0.00    0
        0.027778    0.00    0.00    0
        0.06    0.00    0.00    0
        0.08    0.00    0.00    0
        0.11    0.00    0.00    0
        0.138889    0.00    0.00    0
        0.17    0.00    0.00    0
        0.19    0.00    0.00    0
        0.22    0.00    0.00    0
        0.25    0.00    0.00    0
        0.28    0.00    0.00    0
        0.305556    0.00    0.00    0
        0.33    0.00    0.00    0
        0.36    0.00    0.00    0
        0.39    0.00    0.00    0
        0.416667    0.00    0.00    0
        0.44    0.00    0.00    0
        0.47    0.00    0.00    0
        0.50    0.00    0.00    0
        0.48    0.03    0.00    0
        0.46    0.06    0.00    0
        0.44    0.09    0.00    0
        0.42    0.12    0.00    0
        0.416665    0.15    0.00    0
        0.38    0.18    0.00    0
        0.383331    0.21    0.00    0
        0.34    0.24    0.00    0
        0.349997    0.27    0.00    0
        0.30    0.30    0.00    0
        0.3174571429    0.3174571429    0.00    0
        0.3015842857    0.3015842857    0.00    0
        0.2857114286    0.2857114286    0.00    0
        0.2698385714    0.2698385714    0.00    0
        0.2539657143    0.2539657143    0.00    0
        0.2380928571    0.2380928571    0.00    0
        0.20    0.20    0.00    0
        0.2063471429    0.2063471429    0.00    0
        0.1904742857    0.1904742857    0.00    0
        0.1746014286    0.1746014286    0.00    0
        0.1587285714    0.1587285714    0.00   

Re: [Pw_forum] Why NEGATIVE Density of State?

[Ari P Seitsonen]

Hello,

  Adding to Karim's answer, you should switch to a different broadening 
function, one does that not take negative values, if you want to be sure 
of remaining non-negative.


Greetings from Paris,

   apsi

-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-
  Ari Paavo Seitsonen / ari.p.seitso...@iki.fi / http://www.iki.fi/~apsi/
Ecole Normale Supérieure (ENS), Département de Chimie, Paris
Mobile (F) : +33 789 37 24 25(CH) : +41 79 71 90 935


On Fri, 2 Jun 2017, Karim Elgammal wrote:


try to specify a value for 'degauss'; maybe 0.01-0.03

Karim Elgammal
PhD student at KTH

___
Pw_forum mailing list
Pw_forum@pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum

Re: [Pw_forum] shape of the wave function in reciprocal space

[Ari P Seitsonen]

Dear Issam AD Issam,

 1) For the third time: PLEASE sign your posts to this forum with your 
affiliation,


 2) Like I wrote already, you do not close the first two namelists. I 
already managed to run your input after the minor modifications that I 
suggested earlier.


  I suggest that you start with the examples and tests that are available 
at the web site to familiarise with the code, and discuss the issues with 
your supervisor.


Good Luck,

   apsi

-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-
  Ari Paavo Seitsonen / ari.p.seitso...@iki.fi / http://www.iki.fi/~apsi/
Ecole Normale Supérieure (ENS), Département de Chimie, Paris
Mobile (F) : +33 789 37 24 25(CH) : +41 79 71 90 935


On Fri, 26 May 2017, Issam AD Issam wrote:


i tried again with high ecutrho this time (x 8) but without succes, the same 
error has been received i
checked the input , it's sems it's correct but the output file exhibits the 
error

2017-05-26 14:32 GMT+00:00 Ari P Seitsonen <ari.p.seitso...@iki.fi>:

  Dear Issam AD Issam,

    Like I already mentioned in the previous e-mail, please sign your 
e-mails to this forum
  with your affiliation.

    One of your pseudo potentials is of ultra-soft/Vanderbilt type, then 
one usually better
  use ecutrho = 6-8 x ecutwfc; please read the documentation.

    You do not close the first two namelists.

    One further possibility is that you have non-ASCII characters in your 
input, like
  TAB-characters; a good tool is 'dos2unix' applied to the input file.

      Greetings,

         apsi

  
-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-
    Ari Paavo Seitsonen / ari.p.seitso...@iki.fi / http://www.iki.fi/~apsi/
      Ecole Normale Supérieure (ENS), Département de Chimie, Paris
      Mobile (F) : +33 789 37 24 25    (CH) : +41 79 71 90 935


  On Fri, 26 May 2017, Issam AD Issam wrote:

thank you Ari Paavo Seitsonen for your observations, ibrav=5 means
bravais-lattice  Trigonal R and for ecutrho it's not worth to set 
it because
ecutrho=4*ecutwfc ,but despite all that  changes there is no succes 
i received
same error
thank you any way


2017-05-26 11:56 GMT+00:00 Ari P Seitsonen <ari.p.seitso...@iki.fi>:

      Dear Issam AD Issam,

        [Please start a new thread for your postings; and please 
sign your
postings together with your affiliation]

        A comma in the mass for Al?

        You have inconsistent GGA for the two elements, your 
'ecutwfc' is too
low, you do not set 'ecutrho', and why do you set nr1/2/3
      explicitly? Is 14x14x14 a good sampling of the Brillouin zone 
(I do not
remember what ibrav == 5 is)?

          Greetings from Sunny Paris,

             apsi

     

-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-
        Ari Paavo Seitsonen / ari.p.seitso...@iki.fi / 
http://www.iki.fi/~apsi/
          Ecole Normale Supérieure (ENS), Département de Chimie, 
Paris
          Mobile (F) : +33 789 37 24 25    (CH) : +41 79 71 90 935


      On Fri, 26 May 2017, Issam AD Issam wrote:

            Dear PWSCF users,
            I'm a beginner in quantum espresso,  i tried to run a 
relaxation
calculation of α-Al2O3. i always receive an error in
            relax.out i checked the
            atomic positions and the lattice parametters i made 
sure that they
are exactly saved in input, i will show you the input
            file if you can help me.

            Many thanks in advance,

            
                calculation      = 'relax'
                restart_mode  = 'from_scratch'
                prefix  = 'AlO'
                tstress        = .true.
                tprnfor         = .true.
                pseudo_dir = '/home/isam/Public/upf_files/'
                outdir          = './scratch/'
                verbosity        = 'high'
                etot_conv_thr = 1e-7
                forc_conv_thr = 1e-6
                nstep  = 5000
                wf_collect       = .true.

            
                ibrav        = 5
                celldm(1) = 9.6945
                celldm(4) = 0.56957
                nat       =  10
                ntyp 

Re: [Pw_forum] Looking for some guidance with failing tests

[Ari P Seitsonen]

Dear Barry,

  If you let me intervene a little bit; how did you(?) compile the code? 
Some (most?) recent Intel compiler suites are known to be very buggy, 
gcc/gfortran is much more reliable. Did you try first to create a serial 
executable, should your MPI have an issue?


Greetings from Paris,

   apsi

-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-
  Ari Paavo Seitsonen / ari.p.seitso...@iki.fi / http://www.iki.fi/~apsi/
Ecole Normale Supérieure (ENS), Département de Chimie, Paris
Mobile (F) : +33 789 37 24 25(CH) : +41 79 71 90 935


On Fri, 26 May 2017, Barry Moore wrote:


Basically, you aren't worried that the tests I mention would give different 
results, or non-convergence,
on differing number of cores or when running multiple times. If that is the 
case, I won't worry either
but as a non-user these "tests" are very misleading.
- Barry

On Fri, May 26, 2017 at 1:24 PM, Paolo Giannozzi  wrote:
  They are not "failing", they almost invariably give tiny differences that 
are almost always
  irrelevant.

Paolo

On Fri, May 26, 2017 at 6:58 PM, Barry Moore  wrote:
  Paolo,
I am hopeful someone can help me understand these failures. Are these tests 
expected to fail
in parallel?

- Barry

On Tue, May 23, 2017 at 9:26 AM, Barry Moore  wrote:
  Paolo,
pw_b3lyp
b3lyp-O
pw_dft
dft8
pw_noncolin
noncolin
noncolin-constrain_atomic
noncolin-constrain_total
pw_relax
relax-bfgs_ndim3
pw_pawatom
paw-vcbfgs
pw_vdw
vdw-d
vdw1
vdw2
vdw5
vdw6
pw_xdm
xdm

Above is a list of tests which look like convergence problems. I grabbed 
b3lyp-O.in
and ran this numerous times with different settings (conv_thr and 
electron_maxstep),
different numbers of processors (1-8), and larger cutoffs (doubled ecutwfc and
ecutfock). I get a different result every time AND on some numbers of 
processors the
SCF doesn't converge... I also noticed that the oxygen atom is slightly offset 
from
center and moving it to the origin helps (the convergence issues on differing
processors remains). I was hoping if you could comment on these tests too.

- Barry 

On Mon, May 15, 2017 at 3:10 PM, Paolo Giannozzi  wrote:
  On Mon, May 15, 2017 at 8:16 PM, Barry Moore  wrote:

  > Thank you. Is there any documentation where I can quickly see which
  tests
  > this issue would creep in?

  no, it's quite unpredictable

  > I will check the other failing tests with better conv_thr.

  you will need to re-run reference output as well

  Paolo
  --
  Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,
  Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
  Phone +39-0432-558216, fax +39-0432-558222
  ___
  Pw_forum mailing list
  Pw_forum@pwscf.org
  http://pwscf.org/mailman/listinfo/pw_forum




--
Barry E Moore II, PhD
E-mail: bmoor...@pitt.edu

Assistant Research Professor
Center for Simulation and Modeling
University of Pittsburgh
Pittsburgh, PA 15260




--
Barry E Moore II, PhD
E-mail: bmoor...@pitt.edu

Assistant Research Professor
Center for Simulation and Modeling
University of Pittsburgh
Pittsburgh, PA 15260

___
Pw_forum mailing list
Pw_forum@pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum




--
Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222


___
Pw_forum mailing list
Pw_forum@pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum




--
Barry E Moore II, PhD
E-mail: bmoor...@pitt.edu

Assistant Research Professor
Center for Simulation and Modeling
University of Pittsburgh
Pittsburgh, PA 15260

___
Pw_forum mailing list
Pw_forum@pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum

Re: [Pw_forum] shape of the wave function in reciprocal space

[Ari P Seitsonen]

Dear Issam AD Issam,

  Like I already mentioned in the previous e-mail, please sign your 
e-mails to this forum with your affiliation.


  One of your pseudo potentials is of ultra-soft/Vanderbilt type, then one 
usually better use ecutrho = 6-8 x ecutwfc; please read the documentation.


  You do not close the first two namelists.

  One further possibility is that you have non-ASCII characters in your 
input, like TAB-characters; a good tool is 'dos2unix' applied to the input 
file.


Greetings,

   apsi

-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-
  Ari Paavo Seitsonen / ari.p.seitso...@iki.fi / http://www.iki.fi/~apsi/
Ecole Normale Supérieure (ENS), Département de Chimie, Paris
Mobile (F) : +33 789 37 24 25(CH) : +41 79 71 90 935


On Fri, 26 May 2017, Issam AD Issam wrote:


thank you Ari Paavo Seitsonen for your observations, ibrav=5 means 
bravais-lattice  Trigonal R and for ecutrho it's not worth to set it because
ecutrho=4*ecutwfc ,but despite all that  changes there is no succes i received 
same error
thank you any way


2017-05-26 11:56 GMT+00:00 Ari P Seitsonen <ari.p.seitso...@iki.fi>:

  Dear Issam AD Issam,

    [Please start a new thread for your postings; and please sign your 
postings together with your affiliation]

    A comma in the mass for Al?

    You have inconsistent GGA for the two elements, your 'ecutwfc' is too 
low, you do not set 'ecutrho', and why do you set nr1/2/3
  explicitly? Is 14x14x14 a good sampling of the Brillouin zone (I do not 
remember what ibrav == 5 is)?

      Greetings from Sunny Paris,

         apsi

  
-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-
    Ari Paavo Seitsonen / ari.p.seitso...@iki.fi / http://www.iki.fi/~apsi/
      Ecole Normale Supérieure (ENS), Département de Chimie, Paris
      Mobile (F) : +33 789 37 24 25    (CH) : +41 79 71 90 935


  On Fri, 26 May 2017, Issam AD Issam wrote:

Dear PWSCF users,
I'm a beginner in quantum espresso,  i tried to run a relaxation 
calculation of α-Al2O3. i always receive an error in
relax.out i checked the
atomic positions and the lattice parametters i made sure that they 
are exactly saved in input, i will show you the input
file if you can help me.

Many thanks in advance,


    calculation      = 'relax'
    restart_mode  = 'from_scratch'
    prefix  = 'AlO'
    tstress        = .true.
    tprnfor         = .true.
    pseudo_dir = '/home/isam/Public/upf_files/'
    outdir          = './scratch/'
    verbosity        = 'high'
    etot_conv_thr = 1e-7
    forc_conv_thr = 1e-6
    nstep  = 5000
    wf_collect       = .true.


    ibrav        = 5
    celldm(1) = 9.6945
    celldm(4) = 0.56957
    nat       =  10
    ntyp         =  2

    nbnd        = 14

    ecutwfc   = 20
    nr1      = 30
    nr2          = 18
    nr3      = 72 


    diagonalization      = 'david'
    mixing_mode     = 'plain'
    mixing_beta       = 0.7
    conv_thr     = 1e-9
    electron_maxstep  = 999
/

    trust_radius_ini  = 0.100
    ion_dynamics  = 'bfgs'
/

    cell_dynamics = 'bfgs'
    wmass =  0.0001
    press =  0
    cell_factor   =  2
/

ATOMIC_SPECIES
O    15.99940 O.pw91-van_ak.UPF
Al   26,9815386   Al.pbe-mt_fhi.UPF

ATOMIC_POSITIONS crystal

   Al 0.352     0.352        0.352
   Al    -0.352    -0.352        0.352
   Al 0.852 0.852  0.852
   Al 0.148 0.148  0.148
   O  0.556    -0.056  0.250
   O -0.056 0.250  0.556
   O  0.250 0.556 -0.056
   O  0.556 1.056 -0.250
   O  1.056    -0.250 -0.556
   O -0.250    -0.556  1.050

K_POINTS automatic
 14 14 14   3*0


___
Pw_forum mailing list
Pw_forum@pwscf.org
http://pwscf.org/mailman/listinfo/pw

Re: [Pw_forum] shape of the wave function in reciprocal space

[Ari P Seitsonen]

Dear Issam AD Issam,

  [Please start a new thread for your postings; and please sign your 
postings together with your affiliation]


  A comma in the mass for Al?

  You have inconsistent GGA for the two elements, your 'ecutwfc' is too 
low, you do not set 'ecutrho', and why do you set nr1/2/3 explicitly? Is 
14x14x14 a good sampling of the Brillouin zone (I do not remember what 
ibrav == 5 is)?


Greetings from Sunny Paris,

   apsi

-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-
  Ari Paavo Seitsonen / ari.p.seitso...@iki.fi / http://www.iki.fi/~apsi/
Ecole Normale Supérieure (ENS), Département de Chimie, Paris
Mobile (F) : +33 789 37 24 25(CH) : +41 79 71 90 935


On Fri, 26 May 2017, Issam AD Issam wrote:


Dear PWSCF users,
I'm a beginner in quantum espresso,  i tried to run a relaxation calculation of 
α-Al2O3. i always receive an error in relax.out i checked the
atomic positions and the lattice parametters i made sure that they are exactly 
saved in input, i will show you the input file if you can help me.

Many thanks in advance,


    calculation      = 'relax'
    restart_mode  = 'from_scratch'
    prefix  = 'AlO'
    tstress        = .true.
    tprnfor         = .true.
    pseudo_dir = '/home/isam/Public/upf_files/'
    outdir          = './scratch/'
    verbosity        = 'high'
    etot_conv_thr = 1e-7
    forc_conv_thr = 1e-6
    nstep  = 5000
    wf_collect       = .true.


    ibrav        = 5
    celldm(1) = 9.6945
    celldm(4) = 0.56957
    nat       =  10
    ntyp         =  2

    nbnd        = 14

    ecutwfc   = 20
    nr1      = 30
    nr2          = 18
    nr3      = 72 


    diagonalization      = 'david'
    mixing_mode     = 'plain'
    mixing_beta       = 0.7
    conv_thr     = 1e-9
    electron_maxstep  = 999
/

    trust_radius_ini  = 0.100
    ion_dynamics  = 'bfgs'
/

    cell_dynamics = 'bfgs'
    wmass =  0.0001
    press =  0
    cell_factor   =  2
/

ATOMIC_SPECIES
O    15.99940 O.pw91-van_ak.UPF
Al   26,9815386   Al.pbe-mt_fhi.UPF

ATOMIC_POSITIONS crystal

   Al 0.352     0.352        0.352
   Al    -0.352    -0.352        0.352
   Al 0.852 0.852  0.852
   Al 0.148 0.148  0.148
   O  0.556    -0.056  0.250
   O -0.056 0.250  0.556
   O  0.250 0.556 -0.056
   O  0.556 1.056 -0.250
   O  1.056    -0.250 -0.556
   O -0.250    -0.556  1.050

K_POINTS automatic
 14 14 14   3*0
___
Pw_forum mailing list
Pw_forum@pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum

Re: [Pw_forum] Pw_forum Digest, Vol 118, Issue 12

[Ari P Seitsonen]

Dear Mohammadreza Hosseini,

  Please try to understand the concept of "back-folding" when using 
super-cells hen calculating band structures. There are programs to 
"unfold" the band structure, for example by Jonas Björk.


  And please do not reply directly to the Digest-messages; use an 
appropriate Subject and post only the relevant part of the Digest-message 
- or start a new thread, if there is nothing in the digested message that 
you refer to, like in your case. Thank you. :)


Greetings from the aeroport of Lisbon,

   apsi

-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-
  Ari Paavo Seitsonen / ari.p.seitso...@iki.fi / http://www.iki.fi/~apsi/
Ecole Normale Supérieure (ENS), Département de Chimie, Paris
Mobile (F) : +33 789 37 24 25(CH) : +41 79 71 90 935


On Sun, 14 May 2017, Mohammadreza Hosseini wrote:


Dear All

I am calculating the band structure of phagraphyne. First we computed for 
primitive unit cell and then for the 2X2 supercell. Although the bulk structure 
is same the band structure is different. What is the problem ?  Should 
parameters be optimized again for supercell?

Mohammadreza Hosseini
Tarbiat modares uiversity

From: pw_forum-boun...@pwscf.org  on behalf of 
pw_forum-requ...@pwscf.org 
Sent: Saturday, May 13, 2017 10:00 PM
To: pw_forum@pwscf.org
Subject: Pw_forum Digest, Vol 118, Issue 12

Send Pw_forum mailing list submissions to
   pw_forum@pwscf.org

To subscribe or unsubscribe via the World Wide Web, visit
   http://pwscf.org/mailman/listinfo/pw_forum
or, via email, send a message with subject or body 'help' to
   pw_forum-requ...@pwscf.org

You can reach the person managing the list at
   pw_forum-ow...@pwscf.org

When replying, please edit your Subject line so it is more specific
than "Re: Contents of Pw_forum digest..."


Today's Topics:

  1. Re: how to determine the symmetry of a given phonon mode  in
 quantum espresso (Lorenzo Paulatto)
  2. Re: Gipaw - Magnetic susceptibility (Davide Ceresoli)


--

Message: 1
Date: Sat, 13 May 2017 15:08:04 +0200
From: Lorenzo Paulatto 
Subject: Re: [Pw_forum] how to determine the symmetry of a given
   phonon mode in quantum espresso
To: PWSCF Forum 
Message-ID: <1728518.gkaUiGcZ5e@paulaxps>
Content-Type: text/plain; charset="iso-8859-1"

On Friday, 12 May 2017 23:44:33 CEST Mihiri Hewa bosthanthirige wrote:

Hi,
I am graduate student at Clemson university, currently working with Quantum
Espresso. I would like to know how to determine the symmetry of a given
phonon mode in quantum espresso.


Hello,
it is printed in the output of phonon at the end of the calculation, i.e.:
...
   End of self-consistent calculation


--
Dr. Lorenzo Paulatto
IdR @ IMPMC -- CNRS & Universit? Paris 6
+33 (0)1 44 275 084 / skype: paulatz
http://www.impmc.upmc.fr/~paulatto/
23-24/4?16 Bo?te courrier 115,
4 place Jussieu 75252 Paris C?dex 05
-- next part --
An HTML attachment was scrubbed...
URL: 
http://pwscf.org/pipermail/pw_forum/attachments/20170513/0ddc04ba/attachment-0001.html

--

Message: 2
Date: Sat, 13 May 2017 16:09:02 +0200
From: Davide Ceresoli 
Subject: Re: [Pw_forum] Gipaw - Magnetic susceptibility
To: PWSCF Forum 
Message-ID: <6933968b-d5f1-fb6b-c518-e47ca4ce6...@cnr.it>
Content-Type: text/plain; charset=windows-1252; format=flowed

Dear Alan,
I think that there is no problem in doing a G=0 response
with a shifted mesh. The response is at G=0, hence it couples
wfcs at the same k. The susceptibility depends a lot on k-points
sampling and if your system has a vanishing band gap, convergence
can be a nightmare.
By default the macroscopic shape is diagonal:
  nmr_macroscopic_shape(:,:) = 0.d0
  nmr_macroscopic_shape(1,1) = 2.d0 / 3.d0
  nmr_macroscopic_shape(2,2) = 2.d0 / 3.d0
  nmr_macroscopic_shape(3,3) = 2.d0 / 3.d0
You can change the component (demagnetizing field) in the input file.

Good luck for your calculations!

Best,
Davide



On 05/12/2017 07:47 PM, Ambrozio wrote:

Dear QE users and Developers,

I'm working with NMR calculations in Gipaw. Recently I did some shielding
calculations and I have some questions regarding the magnetic susceptibility.
The article from developers Mauri et al (*PRL 77, 26, 1996*) explain that the
shielding of a bulk of a periodic system is also periodic (i.e. has the same
periodicity of *G*, the reciprocal lattice vectors), and it is proportional to
the magnetic susceptibility matrix. In the paper Mauri did a short discussion
about the macroscopic susceptibility, which is calculated at *G=0*. Follow my
questions:

i) Assuming that the macroscopic susceptibility is calculating at gamma point
(*G=0*) and 

Re: [Pw_forum] Slow convergence of Fe-111 surface by QE

[Ari P Seitsonen]

Dear Naren,

  In addition to the (much) too low cut-off energy you wrote that you 
tried several parametres, but it is difficult to us to guess for what you 
tried: Clearly now there is no spin polarisation, the mixing parametre is 
probably much too large, the 'degauss' too small (personally I prefer the 
Fermi-Dirac broadening), is the system ferromagnetic, why 'nosym = 
.true.'...? Please try a systematic approach, starting from most 
"physical" values for the parametres and then try to switch to something 
simpler, trying to understand for what goes wrong.


Greetings,

   apsi

-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-
  Ari Paavo Seitsonen / ari.p.seitso...@iki.fi / http://www.iki.fi/~apsi/
Ecole Normale Supérieure (ENS), Département de Chimie, Paris
Mobile (F) : +33 789 37 24 25(CH) : +41 79 71 90 935


On Fri, 5 May 2017, Narendranath Ghosh wrote:


Dear all!

I am currently trying to optimize a Fe-111 surface.But I find very slow 
convergence even after 229
iteration it didn't get converged.I have changed some parameters like smearing 
, degauss
,nspin, K_POINTS but nothing happened. 
Input
 
  calculation='relax',
  outdir='/share_home/hpc/BONS_QE/Fe-111/OUTPUT',
  prefix='Fe-111',
  pseudo_dir='/share_home/hpc/BONS_QE/pseudo',
  verbosity='low',
  nstep=500,
/


  ibrav=0,
  celldm(1)=22.9819600668d0,
  nat=81,
  ntyp=1,
  ecutwfc=30.0d0,
  input_dft='PBE',
  nosym = .true.,
  occupations='smearing',
  smearing='mv',
  degauss=0.005000d0,
  starting_magnetization(1)=0.5
  

/


  mixing_mode='local-TF',
  mixing_beta=0.700d0,
  electron_maxstep=500,
/


/

ATOMIC_SPECIES
  Fe 55.845000d0 Fe.pbe-mt_fhi.UPF

ATOMIC_POSITIONS {alat}
Fe       0.16360   0.096224929   1.432718760
Fe       0.49991   0.096224958   1.432718812
Fe       0.83491   0.096224719   1.432718553


K_POINTS {automatic}
3 3 1 0 0 0
CELL_PARAMETERS {alat}
  1.d0  0.d0  0.d0
  -0.5000d0  0.866025403784d0  0.d0
  0.d0  0.d0  3.339792528637d0


...
 

Any comment to help me getting started is very much appreciated!

 

Best regards,

Naren

 

 

Dr. Narendra Nath Ghosh
Research Associate
University of Gour Banga
Department of Chemistry
Malda-732102
India
Phone: +919126667601
___
Pw_forum mailing list
Pw_forum@pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum

Re: [Pw_forum] Need help with Supercell calculation

[Ari P Seitsonen]

Dear Sayan Chaudhuri,

  At least both the cut-off energies should be the same in both 
calculations. I did not check the inputs in more detail, for example if 
the k point sets are consistent. If yes, the total energy in the larger 
system should be very close to four times the total energy of the 
primitive cell.


Greetings,

   apsi

-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-
  Ari Paavo Seitsonen / ari.p.seitso...@iki.fi / http://www.iki.fi/~apsi/
Ecole Normale Supérieure (ENS), Département de Chimie, Paris
Mobile (F) : +33 789 37 24 25(CH) : +41 79 71 90 935


On Thu, 4 May 2017, sayan chaudhuri wrote:


Sir,
  
  Thanks for the quick response. I will make the correction. Is there anything 
other correction I have
to make?

Thanking you,
  Sayan Chaudhuri

On Thu, May 4, 2017 at 9:48 AM, Ari P Seitsonen <ari.p.seitso...@iki.fi> wrote:

  Dear Sayan Chaudhuri,

    If you multiply the number of cells by four, shouldn't you also multiply
  'tot_magnetization' by four too?

      Greetings from Rabat/Morocco,

         apsi

  
-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-
    Ari Paavo Seitsonen / ari.p.seitso...@iki.fi / http://www.iki.fi/~apsi/
      Ecole Normale Supérieure (ENS), Département de Chimie, Paris
      Mobile (F) : +33 789 37 24 25    (CH) : +41 79 71 90 935


  On Thu, 4 May 2017, sayan chaudhuri wrote:

Hi all,

   I am calculating DOS structure for a heusler alloy Fe2TiSb. When 
I am not
using a supercell I am
getting the same result reported previously, but after using a 
supercell I am
getting very different
result.
 I am attaching the scf files and DOS output for both the cases. 
Please tell me
what mistakes I am doing
while considering the supercell. The one with _sup in the name, 
contains
supercell.

Thanking you in advance,
   Sayan Chaudhuri


___
Pw_forum mailing list
Pw_forum@pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum



___
Pw_forum mailing list
Pw_forum@pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum

Re: [Pw_forum] Need help with Supercell calculation

[Ari P Seitsonen]

Dear Sayan Chaudhuri,

  If you multiply the number of cells by four, shouldn't you also multiply 
'tot_magnetization' by four too?


Greetings from Rabat/Morocco,

   apsi

-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-
  Ari Paavo Seitsonen / ari.p.seitso...@iki.fi / http://www.iki.fi/~apsi/
Ecole Normale Supérieure (ENS), Département de Chimie, Paris
Mobile (F) : +33 789 37 24 25(CH) : +41 79 71 90 935


On Thu, 4 May 2017, sayan chaudhuri wrote:


Hi all,

   I am calculating DOS structure for a heusler alloy Fe2TiSb. When I am not 
using a supercell I am
getting the same result reported previously, but after using a supercell I am 
getting very different
result.
 I am attaching the scf files and DOS output for both the cases. Please tell me 
what mistakes I am doing
while considering the supercell. The one with _sup in the name, contains 
supercell.

Thanking you in advance,
   Sayan Chaudhuri

___
Pw_forum mailing list
Pw_forum@pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum

Re: [Pw_forum] vc-relax

[Ari P Seitsonen]

Dear mohammadreza hosseini,

  Next time please do not forget your affiliation. :)

  Please check the variable 'cell_dofree' for the different options that 
can be chosen for the kind of deformation of the cell.


  As for the algorithms, please check the keywords 'ion_dynamics' (you can 
have either "bfgs" or "damp"'ed dyanmics) for the ions and 'cell_dynamics' 
for the cell itself.


Greetings from Paris,

   apsi

-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-
  Ari Paavo Seitsonen / ari.p.seitso...@iki.fi / http://www.iki.fi/~apsi/
Ecole Normale Supérieure (ENS), Département de Chimie, Paris
Mobile (F) : +33 789 37 24 25(CH) : +41 79 71 90 935


On Fri, 31 Mar 2017, mohammadreza hosseini wrote:


    Dear All
 
I am going to perform vc-relax calculations on MOF's. Is it possible to 
describe the algorithm of vc-relax in quantum espresso? does volume change
during vc-relax ?
 
Thanks

___
Pw_forum mailing list
Pw_forum@pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum

Re: [Pw_forum] Compiling QE 6.1 with Intel

[Ari P Seitsonen]

Dear Carlo,

  I do not have direct experience nor with QE, but I have seen this from 
another code:


--
Date: Fri, 27 Jan 2017 14:37:06 +
From: Iain Bethune 
Reply-To: c...@googlegroups.com
To: c...@googlegroups.com
Subject: Re: [CP2K:8598] error in qs_ks_methods.F depending on number of cores 
(intel compiler)

Further to what I reported this morning, I found that the MKL release 
2017.1.132 is buggy.  I was able to get a successful build using the compiler 
from the 2017.1.132 release and MKL from the previous (2017.0.098) release.
--

  Personally I had similar issues (again with CP2K), but I do not remember 
if it was with exactly that version; in any case I reverted from Intel 
v2017 to v2017 and I was able to run the code.


  Maybe not very useful, but... I would try with 'gfortran' (and OpenMPI, 
if possible).


Greetings,

   apsi

-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-
  Ari Paavo Seitsonen / ari.p.seitso...@iki.fi / http://www.iki.fi/~apsi/
Ecole Normale Supérieure (ENS), Département de Chimie, Paris
Mobile (F) : +33 789 37 24 25(CH) : +41 79 71 90 935


On Fri, 17 Mar 2017, Carlo Nervi wrote:


Dear QE community,a colleague of mine is using Intel compiler and libraries to 
compile QE 6.1.
We used

compilers_and_libraries_2017.1.132
and
parallel_studio_xe_2017.1.043

I got apparently normal results using "mpirun -np 21", but very different results using 
"mpirun -np 21 -nk 7", and relevant longer time of
calculations.
I suspect there is something wrong with libraries or mpi.
Before to dig more deep in the debugging, do anybody is aware of any 
inconsistencies/anomalies using the mentioned compiler/libraries?

We are using also docker...

Thank you,
Carlo

--


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

___
Pw_forum mailing list
Pw_forum@pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum

Re: [Pw_forum] how to do optimization with the lattice parameters in-plane being fixed

[Ari P Seitsonen]

Dear ???,

 [ Sorry, but did you read the instructions on how to post to the forum? 
Name and affiliation in the posts are a sign of respect to the other 
subscribers of the forum ]


  It sounds as you are looking for the keyword 'cell_dofree' in the 
documentation, is that correct?


Greetings from Sunny Paris,

   apsi

-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-
  Ari Paavo Seitsonen / ari.p.seitso...@iki.fi / http://www.iki.fi/~apsi/
Ecole Normale Supérieure (ENS), Département de Chimie, Paris
Mobile (F) : +33 789 37 24 25(CH) : +41 79 71 90 935


On Mon, 13 Mar 2017, 朱林光 wrote:


Dear all qe users:
Im a new user to qe,and i want to do some optimizations on tetragonal phase 
PbTiO3 with constraints in-plane to study the phase transition under different 
epitaxial  strain ,but i dont know how to do optimization with the lattice 
parameters in-plane being fixed and all atoms  the lattice parameter 
out-of-plane being relaxed in qe. Can anyone help me?
___
Pw_forum mailing list
Pw_forum@pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum
___
Pw_forum mailing list
Pw_forum@pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum

Re: [Pw_forum] Error in Ph.x for calculation Raman spectrum

[Ari P Seitsonen]

Dear LIANG Xiongyi,

  Some answers:

 - Yes, one needs fixed occupations, because the implementation in PH is 
for non-resonant Raman scattering; the formalism in metallic systems is 
much more involved, there are some recent developments in the Quantum 
ESPRESSO Community at least by Michele Lazzeri and Francesco Mauri


 - About LDA, I somehow thought that the restriction is lifted in recent 
versions (or, one just neglects the error message by commenting it 
out...). But I do not know whether for example hybrid functionals would 
work/give reasonable results, GGA yes


 - If the problem appears in the self-consistent calculation, the problem 
is not in the calculation of Raman spectrum. Without more details about 
your system (input, pseudo potentials) we can only guess for what you are 
calculating, it is difficult to help, sorry


 - First one should of course achieve self-consistency, in principle 
having an odd number of electrons is not a problem. Whether the phonon 
code works with spin-polarised systems, sorry, I do not know but I would 
guess so


Greetings,

   apsi

-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-
  Ari Paavo Seitsonen / ari.p.seitso...@iki.fi / http://www.iki.fi/~apsi/
Ecole Normale Supérieure (ENS), Département de Chimie, Paris
Mobile (F) : +33 789 37 24 25(CH) : +41 79 71 90 935


On Wed, 8 Mar 2017, LEUNG Clarence wrote:



Dear QE users,


As far as I know, when using ph.x to calculate raman spectrum. We should use 
fixed occupation and LDA in scf, right?


However a error occur (charge is wrong, smearing is needed ) when I use fixed 
occupation in scf calculation because of my system is odd electrons.


what should I do to calculate the raman spectrum of odd electron system?


Thanks in advanced!


Best regards,

LIANG Xiongyi

Department of Physics and Materials Science

City University of Hong Kong


___
Pw_forum mailing list
Pw_forum@pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum

Re: [Pw_forum] Monolayer WSe2 band structure related problems

[Ari P Seitsonen]

Dear Anindya Bose,

  How does your input now look like? That you were able to run 'vc-relax' 
but after that the self-consistent loop does not converge sounds weird.


  I usually use 'local-TF' as the mixing mode in systems with vacuum.

Greetings,

   apsi

-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-
  Ari Paavo Seitsonen / ari.p.seitso...@iki.fi / http://www.iki.fi/~apsi/
Ecole Normale Supérieure (ENS), Département de Chimie, Paris
Mobile (F) : +33 789 37 24 25(CH) : +41 79 71 90 935


On Tue, 7 Mar 2017, Anindya Bose wrote:


I have done my vc-relax successfully but while performing scf calculation I am 
getting an error: convergence is not achieved in 100 steps.Please
help me in this issue.I have made ecutwfc=60.How to resolve this error.How can 
I converge my process.

regards,
Anindya Bose

On Mon, Mar 6, 2017 at 10:34 PM, Ari P Seitsonen <ari.p.seitso...@iki.fi> wrote:

  Dear Anindya,

    Please provide your affiliation - to respect the other subscribers of 
the forum (please go through the instructions on how to post
  to the forum).

    Adding to the other items mentioned in the previous responses, I would 
like to point out that apparently you want to relax the
  lateral lattice constant of the cell, but without further options also 
the vertical lattice constant is optimised, and probably the
  vacuum is either reducing or increasing (it never goes to zero, due to 
numerical precision if nothing else; also the DFT+D2 dispersion
  correction has a long tail): Please check the input option 'cell_dofree'.

    'cell_factor = 15' does not make much sense; your threhould variables 
'etot_conv_thr' and 'forc_conv_thr' look very loose to me. Are
  you sure about "disk_io = 'high'"?

      Greetings,

         apsi

  
-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-
    Ari Paavo Seitsonen / ari.p.seitso...@iki.fi / http://www.iki.fi/~apsi/
      Ecole Normale Supérieure (ENS), Département de Chimie, Paris
      Mobile (F) : +33 789 37 24 25    (CH) : +41 79 71 90 935


  On Mon, 6 Mar 2017, Anindya Bose wrote:

Dear Sir,
I have used this code but I didn't get the direct band gap 
structure of monolayer WSe2.

  calculation='vc-relax',
  outdir='monolayer WSe2',
  prefix='calc',
  pseudo_dir='/home/anindya/Desktop/pseudopotential',
  verbosity='high',
  disk_io='high',
  wf_collect=.true.,
  nstep = 50,
  etot_conv_thr=1d-02,
  forc_conv_thr=1d-02,
/


  ibrav=4,
  celldm(1)=6.2020811408d0, celldm(3)=4.3566118221d0,
  nat=3,
  ntyp=2,
  ecutwfc=40.0d0,
  ecutrho =130.0d0,
  nbnd=200,
  vdw_corr='Grimme-D2',
  force_symmorphic=.true.,
  input_dft='PBE',
  occupations='fixed',
/


  diagonalization='david',
  conv_thr=1d-08,
  mixing_mode='plain',
  mixing_beta=0.700d0,
/


  ion_dynamics ='bfgs',
/
 

  cell_dynamics ='bfgs',
  cell_factor=15,
/

ATOMIC_SPECIES
  Se 78.96d0 Se_ONCV_PBE-1.0_r.oncvpsp.upf
  W 183.84d0 W_ONCV_PBE-1.1_r.oncvpsp.upf

ATOMIC_POSITIONS {alat}
  W    0.50d0   0.2886751346d0   2.1782995738d0
  Se   0.50d0  -0.2886751346d0   1.6692977456d0
  Se   0.50d0  -0.2886751346d0   2.6873014019d0

K_POINTS {automatic}
  10 10 1 0 0 0

I have enclosed my output band structure with this mail.Can you 
please help me in this regard.How can I get the correct
band diagram of monolayer
WSe2(direct bandgap). I have used all the codes for spin 
calculation and I got the spin orbit coupling but didn't find
perfect band diagram.I will
be waiting for your response.


___
Pw_forum mailing list
Pw_forum@pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum



___
Pw_forum mailing list
Pw_forum@pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum

Re: [Pw_forum] Problem while compiling QE v5.3.0 with ELPA

[Ari P Seitsonen]

Dear Rolly Ng,

  First a question: Why do you try to compile v5.3.0, in particular with 
pre-processor options that are meaningful only in newer versions of QE 
("-D__EXX_ACE", probably also "-D__ELPA3" and "-D__ELPA_2016")?


  Indeed the directory where the files 'fft_defs.h' is not in the options 
with '-I'; if you want to enforce it, you can always add the options in 
'make.sys' (nowadays 'make.inc') with 
"-I/home/qeuser/QE530-CPU/espresso-5.3.0/include", but I would first 
recommend you to try to get a consistent set of pre-processor flags (and, 
preferably, v6.1 if you can).


  I also do not know/remember if "fft_defs.h" has anything to do with 
ELPA; which version of ELPA do you try to include, is it something that 
existed when Quantum ESPRESSO v5.3.0 was developed? It could be that 
something has changed in the interface to ELPA in the meantime too.


Greetings,

   apsi

-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-
  Ari Paavo Seitsonen / ari.p.seitso...@iki.fi / http://www.iki.fi/~apsi/
Ecole Normale Supérieure (ENS), Département de Chimie, Paris
Mobile (F) : +33 789 37 24 25(CH) : +41 79 71 90 935


On Tue, 7 Mar 2017, Rolly Ng wrote:


Dear QE users,

I am trying to compile QE v5.3.0 with ELPA by following the steps
instructed here,

https://software.intel.com/en-us/articles/quantum-espresso-for-the-intel-xeon-phi-processor

But I am having unexpected error that fft_scalar.f90 complains unable to
find fft_def.h?

It stops with:
mpiifort -O2 -align array64byte -threads -heap-arrays 4096 -xCORE-AVX2
-fp-model fast=2 -complex-limited-range -assume byterecl  -nomodule -fpp
-D__INTEL -D__FFTW3 -D__DFTI -D__NON_BLOCKING_SCATTER -D__EXX_ACE
-D__MPI -D__PARA -D__SCALAPACK -D__ELPA3 -D__ELPA_2016
-I../../iotk/src -I../../Modules -I../../FFTXlib -c print_ks_energies.f90
mpiifort -O2 -align array64byte -threads -heap-arrays 4096 -xCORE-AVX2
-fp-model fast=2 -complex-limited-range -assume byterecl  -nomodule -fpp
-D__INTEL -D__FFTW3 -D__DFTI -D__NON_BLOCKING_SCATTER -D__EXX_ACE
-D__MPI -D__PARA -D__SCALAPACK -D__ELPA3 -D__ELPA_2016
-I../../iotk/src -I../../Modules -I../../FFTXlib -c punch.f90
mpiifort -O2 -align array64byte -threads -heap-arrays 4096 -xCORE-AVX2
-fp-model fast=2 -complex-limited-range -assume byterecl  -nomodule -fpp
-D__INTEL -D__FFTW3 -D__DFTI -D__NON_BLOCKING_SCATTER -D__EXX_ACE
-D__MPI -D__PARA -D__SCALAPACK -D__ELPA3 -D__ELPA_2016
-I../../iotk/src -I../../Modules -I../../FFTXlib -c
../../FFTXlib/fft_scalar.f90
fft_scalar.f90(18): #error: can't find include file: fft_defs.h
make[2]: *** [../../FFTXlib/fft_scalar.o] Error 1
make[2]: Leaving directory `/home/qeuser/QE530-CPU/espresso-5.3.0/PW/src'
make[1]: *** [pw] Error 1
make[1]: Leaving directory `/home/qeuser/QE530-CPU/espresso-5.3.0/PW'
make: *** [pw] Error 1

But I am sure fft_def.h is located at
/home/qeuser/QE530-CPU/espresso-5.3.0/include, but what can't it be
located by the fft_scalar.f90?

Please have a look at my make.sys attached.

# make.sys.  Generated from make.sys.in by configure.

# compilation rules

.SUFFIXES :
.SUFFIXES : .o .c .f .f90

# most fortran compilers can directly preprocess c-like directives: use
# $(MPIF90) $(F90FLAGS) -c $<
# if explicit preprocessing by the C preprocessor is needed, use:
# $(CPP) $(CPPFLAGS) $< -o $*.F90
#$(MPIF90) $(F90FLAGS) -c $*.F90 -o $*.o
# remember the tabulator in the first column !!!

.f90.o:
$(MPIF90) $(F90FLAGS) -c $<

# .f.o and .c.o: do not modify

.f.o:
$(F77) $(FFLAGS) -c $<

.c.o:
$(CC) $(CFLAGS)  -c $<



# topdir for linking espresso libs with plugins
TOPDIR = /home/qeuser/QE530-CPU/espresso-5.3.0

# DFLAGS  = precompilation options (possible arguments to -D and -U)
#   used by the C compiler and preprocessor
# FDFLAGS = as DFLAGS, for the f90 compiler
# See include/defs.h.README for a list of options and their meaning
# With the exception of IBM xlf, FDFLAGS = $(DFLAGS)
# For IBM xlf, FDFLAGS is the same as DFLAGS with separating commas

# MANUAL_DFLAGS  = additional precompilation option(s), if desired
#  You may use this instead of tweaking DFLAGS and FDFLAGS
#  BEWARE: will not work for IBM xlf! Manually edit FDFLAGS
MANUAL_DFLAGS  =
DFLAGS =  -D__INTEL -D__FFTW3 -D__DFTI -D__NON_BLOCKING_SCATTER
-D__EXX_ACE -D__MPI -D__PARA -D__SCALAPACK -D__ELPA3 -D__ELPA_2016
$(MANUAL_DFLAGS)
FDFLAGS= $(DFLAGS) $(MANUAL_DFLAGS)

# IFLAGS = how to locate directories where files to be included are
# In most cases, IFLAGS = -I../include

IFLAGS = -I../include -I$(MKLROOT)/include/fftw
-I/home/qeuser/QE530-CPU/espresso-5.3.0/../elpa/default-hsw/include/elpa/modules


# MOD_FLAGS = flag used by f90 compiler to locate modules
# Each Makefile defines the list of needed modules in MODFLAGS

MOD_FLAG  = -I

# Compilers: fortran-90, fortran-77, C
# If a parallel compilation is desired, MPIF90 should be a fortran-90
# compiler that produces 

Re: [Pw_forum] Monolayer WSe2 band structure related problems

[Ari P Seitsonen]

Dear Anindya,

  Please provide your affiliation - to respect the other subscribers of 
the forum (please go through the instructions on how to post to the 
forum).


  Adding to the other items mentioned in the previous responses, I would 
like to point out that apparently you want to relax the lateral lattice 
constant of the cell, but without further options also the vertical 
lattice constant is optimised, and probably the vacuum is either reducing 
or increasing (it never goes to zero, due to numerical precision if 
nothing else; also the DFT+D2 dispersion correction has a long tail): 
Please check the input option 'cell_dofree'.


  'cell_factor = 15' does not make much sense; your threhould variables 
'etot_conv_thr' and 'forc_conv_thr' look very loose to me. Are you sure 
about "disk_io = 'high'"?


Greetings,

   apsi

-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-
  Ari Paavo Seitsonen / ari.p.seitso...@iki.fi / http://www.iki.fi/~apsi/
Ecole Normale Supérieure (ENS), Département de Chimie, Paris
Mobile (F) : +33 789 37 24 25(CH) : +41 79 71 90 935


On Mon, 6 Mar 2017, Anindya Bose wrote:


Dear Sir,
I have used this code but I didn't get the direct band gap structure of 
monolayer WSe2.

  calculation='vc-relax',
  outdir='monolayer WSe2',
  prefix='calc',
  pseudo_dir='/home/anindya/Desktop/pseudopotential',
  verbosity='high',
  disk_io='high',
  wf_collect=.true.,
  nstep = 50,
  etot_conv_thr=1d-02,
  forc_conv_thr=1d-02,
/


  ibrav=4,
  celldm(1)=6.2020811408d0, celldm(3)=4.3566118221d0,
  nat=3,
  ntyp=2,
  ecutwfc=40.0d0,
  ecutrho =130.0d0,
  nbnd=200,
  vdw_corr='Grimme-D2',
  force_symmorphic=.true.,
  input_dft='PBE',
  occupations='fixed',
/


  diagonalization='david',
  conv_thr=1d-08,
  mixing_mode='plain',
  mixing_beta=0.700d0,
/


  ion_dynamics ='bfgs',
/
 

  cell_dynamics ='bfgs',
  cell_factor=15,
/

ATOMIC_SPECIES
  Se 78.96d0 Se_ONCV_PBE-1.0_r.oncvpsp.upf
  W 183.84d0 W_ONCV_PBE-1.1_r.oncvpsp.upf

ATOMIC_POSITIONS {alat}
  W    0.50d0   0.2886751346d0   2.1782995738d0
  Se   0.50d0  -0.2886751346d0   1.6692977456d0
  Se   0.50d0  -0.2886751346d0   2.6873014019d0

K_POINTS {automatic}
  10 10 1 0 0 0

I have enclosed my output band structure with this mail.Can you please help me 
in this regard.How can I get the correct band diagram of monolayer
WSe2(direct bandgap). I have used all the codes for spin calculation and I got 
the spin orbit coupling but didn't find perfect band diagram.I will
be waiting for your response.
___
Pw_forum mailing list
Pw_forum@pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum

[Pw_forum] Alignment of total energy?

[Ari P Seitsonen]

Dear Colleagues,

  I tried to search the FAQ and archives but was not successful - sorry if 
this is already answered somewhere.


  I am trying to calculate core level binding energies of atoms, and for 
this I need to align the total energies of the two calculations, with and 
without the core hole; the calculations are on surfaces/slabs, so I could 
use either the Fermi energies or the value of (dipole-corrected) potential 
in the vacuum. But I have forgotten which term is needed still... (Sorry, 
it is some 25 years when I was doing similar things.) Was it something 
like the average potential in the cell times some factor...?


  Thank you in advance for any answer. :)

Greetings from Paris,

   apsi

-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-
  Ari Paavo Seitsonen / ari.p.seitso...@iki.fi / http://www.iki.fi/~apsi/
Ecole Normale Supérieure (ENS), Département de Chimie, Paris
Mobile (F) : +33 789 37 24 25(CH) : +41 79 71 90 935___
Pw_forum mailing list
Pw_forum@pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum

Re: [Pw_forum] homo and lumo

[Ari P Seitsonen]

Dear K Zahra (next time with the affiliation, please :)

  What properties of the HOMO and LUMO do you want to study? Eigenvalues, 
how they look like, their reactivity, ...? The eigenvalues you can get 
with 'pw.x' (for LUMO you need to include some unoccupied/virtual 
orbitals), the wave functions with 'pp.x'. If you go for the Wannier 
functions, please notice that CO has a double bond, and there is some 
ambiguity in the localisation of the Wannier functions ("banana bonds"), 
so in that case I would think twice before using them - and actually they 
are not for you, because via the localisation all the occupied orbitals 
are mixed, so there is no longer "HOMO" when using them.


Greetings from Tarragona,

   apsi

-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-
  Ari Paavo Seitsonen / ari.p.seitso...@iki.fi / http://www.iki.fi/~apsi/
Ecole Normale Supérieure (ENS), Département de Chimie, Paris
Mobile (F) : +33 789 37 24 25(CH) : +41 79 71 90 935


On Sun, 12 Feb 2017, zahra krim wrote:


Dear,

I am a beginner student with  quantum espresso code, I would like to study the 
boundary orbitals of the molecule of CO, I would be grateful if anyone can help 
me to show the steps to follow in
order to study the HOMO and LUMO of carbon monoxide;

Cordially
K.zahra

___
Pw_forum mailing list
Pw_forum@pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum

Re: [Pw_forum] problem about installing

[Ari P Seitsonen]

Hello Nasim Ha,

  you did not show the command line, but - are you using 'mpif90' from 
OpenMPI? I think that it should find the object in question automatically 
- or the MPI library is not fully compatible with the MKL library. Did you 
install a system library for OpenMPI or compile it yourself?


Greetings,

   apsi

PS Same error in 2012, also from Tehran: ;)

http://qe-forge.org/pipermail/pw_forum/2012-May/098640.html

(Also there the compilation line missing; please check also 'mpirun -show' 
and 'mpirun --version')


  In 2013: http://www.mail-archive.com/pw_forum@pwscf.org/msg21638.html

  In 2014: https://www.mail-archive.com/pw_forum@pwscf.org/msg24125.html

  In 2015: http://www.mail-archive.com/pw_forum@pwscf.org/msg24892.html

  Similar in 2016: 
http://superuser.com/questions/1059211/installing-quantum-espresso-trouble-with-make


PS^2 And 5.4.0 is the newest version... ... since a couple of months :)


PS^3 Louis, please write to the Forum with your affiliation :)

-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-
  Ari Paavo Seitsonen / ari.p.seitso...@iki.fi / http://www.iki.fi/~apsi/
Ecole Normale Supérieure (ENS), Département de Chimie, Paris
Mobile (F) : +33 789 37 24 25(CH) : +41 79 71 90 935


On Wed, 8 Feb 2017, Nasim Ha wrote:


Hi Dear
I want to instal the newest version of QE (5.4.0) with operating system CentOS.
but in the compilation it give an error as below :

/opt/intel/composer_xe_2013_sp1.2.144/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.a(BI_MPI_F77_to_c_trans_comm.o):
In function `BI_MPI_F77_to_c_trans_comm':
../../../../scalapack/BLACS/SRC/MPI/INTERNAL/BI_MPI_F77_to_c_trans_comm.c:(.text+0x6):
undefined reference to `MPI_Comm_f2c'
make[2]: *** [pw.x] Error 1
make[2]: Leaving directory `/home/hadian/soft1/espresso-5.4.0/PW/src'
make[1]: *** [pw] Error 1
make[1]: Leaving directory `/home/hadian/soft1/espresso-5.4.0/PW'
make: *** [pw] Error 1
please help me
thans
--
N.H.Jazi
PhD student of Physics.
Physics Department,Central Tehran Branch,Islamic Azad
University,Tehran,88074907,Iran.
___
Pw_forum mailing list
Pw_forum@pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum
___
Pw_forum mailing list
Pw_forum@pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum

Re: [Pw_forum] QE 6 compilation

[Ari P Seitsonen]

Dear Amir,

  You state "scalapack=opnmpi" on the command line and the linker(? Or 
run-time?) complains about "libmkl_blacs_inte...", which I interpret as 
"blacs_intelmpi" - a contradiction.


  Just my wild guess - you can check in 'make.inc' if the correct BLACS 
version is included.


Greetings,

   apsi

-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-
  Ari Paavo Seitsonen / ari.p.seitso...@iki.fi / http://www.iki.fi/~apsi/
Ecole Normale Supérieure (ENS), Département de Chimie, Paris
Mobile (F) : +33 789 37 24 25(CH) : +41 79 71 90 935


On Tue, 7 Feb 2017, Mofrad, Amir Mehdi (MU-Student) wrote:



Dear QE users and developers, 


I have been trying to compile QE 6.0 on a cluster for a couple of times but not 
have been successful yet. At first, I was getting
the PZUNMTR parameter number error that I think I fixed it using 

./configure --with-scalapack=openmpi 

However, in my error file I get the following error that don't know what it is about: 


forrtl: severe (174): SIGSEGV, segmentation fault occurred
Image              PC                   
  Routine            Line        Source
pw.x               00CC3265       
Unknown               Unknown  Unknown
pw.x               00CC0E87   
Unknown               Unknown  Unknown
pw.x               00C5B374    
Unknown               Unknown  Unknown
pw.x               00C5B186    
Unknown               Unknown  Unknown
pw.x               00BE3B46    
Unknown               Unknown  Unknown
pw.x               00BEABE0   
Unknown               Unknown  Unknown
libc.so.6          2B1DBD61A250      
Unknown               Unknown  Unknown
libmpi.so.20       2B1DBCCEEFC5     Unknown     
          Unknown  Unknown
libmkl_blacs_inte  2B1DB9601E09  Unknown    
           Unknown  Unknown
libmkl_blacs_inte  2B1DB960044D  Unknown    
           Unknown  Unknown
libmkl_blacs_inte  2B1DB95F19CC     Unknown     
          Unknown  Unknown
libmkl_blacs_inte  2B1DB95F1391   Unknown   
            Unknown  Unknown
pw.x               00838CAB  mp_diag_mp_mp_sta          78  mp_diag.f90
pw.x               0083A2DB  mp_global_mp_mp_s          96  
mp_global.f90
pw.x               0040D2B2  MAIN__                     24  pwscf.f90
pw.x               0040D25E  
Unknown               Unknown  Unknown
libc.so.6          2B1DBD606B35    
Unknown               Unknown  Unknown
pw.x               0040D169    
Unknown               Unknown  Unknown
forrtl: severe (174): SIGSEGV, segmentation fault occurred
Image              PC                Routine            Line        Source
pw.x               00CC3265   
Unknown               Unknown  Unknown
pw.x               00CC0E87   
Unknown               Unknown  Unknown
pw.x               00C5B374   
Unknown               Unknown  Unknown
pw.x               00C5B186  Unknown               Unknown  Unknown
pw.x               00BE3B46  Unknown               Unknown  Unknown
pw.x               00BEABE0  Unknown               Unknown  Unknown
libc.so.6          2B514C9CE250  Unknown               Unknown  Unknown
libmpi.so.20       2B514C0A2FC5  Unknown               Unknown  Unknown
libmkl_blacs_inte  2B51489B5E09  Unknown               Unknown  Unknown
libmkl_blacs_inte  2B51489B444D  Unknown               Unknown  Unknown
libmkl_blacs_inte  2B51489A59CC  Unknown               Unknown  Unknown
libmkl_blacs_inte  2B51489A5391  Unknown               Unknown  Unknown
pw.x               00838CAB  mp_diag_mp_mp_sta          78  mp_diag.f90
pw.x               0083A2DB  mp_global_mp_mp_s          96  
mp_global.f90
pw.x               0040D2B2  MAIN__                     24  pwscf.f90
pw.x               0040D25E  Unknown               Unknown  Unknown
libc.so.6          2B514C9BAB35  Unknown               Unknown  Unknown
pw.x               0040D169  Unknown               Unknown  Unknown
forrtl: severe (174): SIGSEGV, segmentation fault occurred
Image              PC                Routine            Line        Source
pw.x               00CC3265  Unknown               Unknown  Unknown

Re: [Pw_forum] Re : Learning TDDFT calculation in Atomic label (CH4 molecule) using turbo_lanczos.x and turbo_davidson.x

[Ari P Seitsonen]

Hello Prem Sen et alia,

  Just a tiny note: If I remember correctly, C_2 has a level crossing 
(very?) close to the minimum distance. So one might need to be careful to 
choose the "correct" electronic ground state; I found this:


[doi: 10.1063/1.3624383]

"A particularly challenging example of this is the dissociation of the 
carbon dimer, where due to its multiple bond and significant 
multireference character even at equilibrium geometries, many methods 
struggle.3


  So Kohn-Sham method (the usual, single-determinant variant) might not be 
very accurate - it depends on which level of accuracy you need.


Good Luck, :)

   apsi

-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-
  Ari Paavo Seitsonen / ari.p.seitso...@iki.fi / http://www.iki.fi/~apsi/
Ecole Normale Supérieure (ENS), Département de Chimie, Paris
Mobile (F) : +33 789 37 24 25(CH) : +41 79 71 90 935


On Wed, 1 Feb 2017, Timrov Iurii wrote:



Dear Prem Sen,


> I was trying in different way to converge scf calculation in case of carbon dimer 
without "smearing". First I converge the system using
"smearing" then again I performed the scf calculation by changing the "restart_mode" from 
"from_scratch" to "restart". In this condition, the scf
calculation for carbon dimer is converging & also turbo_davidson.x is possible. 
Do you think, this is a right approach ??

I am not sure, but I would probably not rely on this approach. I think that if 
the system is gapped, then it should be possible to converge the
ground state calculation without any intermediate calculation with a smearing.

> Also I have observed that if I am using hybrid functional, the system is 
converging normally (keeping the restart_mode = from_scratch & without
"smearing").

This seems to indicate that with a hybrid functional you open a gap, and hence 
no smearing is needed in the calculation.

> Can I compute the absorption spectra for a molecule having triplet ground 
state using turbo_davidson.x or turbo_lanczos.x ??


If this amounts to perform a spin-polarized calculation (and include 
magnetism), then these codes cannot be used because it is not
implemented (currently only spin-unpolarized calculations can be performed with 
turbo_davidson.x and turbo_lanczos.x).


Regards,

Iurii


--
Dr. Iurii Timrov
Postdoctoral Researcher
Swiss Federal Institute of Technology Lausanne (EPFL)
Laboratory of Theory and Simulation of Materials (THEOS)
CH-1015 Lausanne, Switzerland 

__
From: pw_forum-boun...@pwscf.org  on behalf of prem sen 

Sent: Tuesday, January 31, 2017 7:18 PM
To: pw_forum@pwscf.org
Subject: [Pw_forum] Re : Learning TDDFT calculation in Atomic label (CH4 
molecule) using turbo_lanczos.x and turbo_davidson.x  
Dear Dr. Iurii Timrov,
    Thanks for the reply.
I was trying in different way to converge scf calculation in case of carbon dimer without 
"smearing". First I converge the system using "smearing"
then again I performed the scf calculation by changing the "restart_mode" from 
"from_scratch" to "restart". In this condition, the scf calculation
for carbon dimer is converging & also turbo_davidson.x is possible. Do you 
think, this is a right approach ??


Also I have observed that if I am using hybrid functional, the system is converging 
normally (keeping the restart_mode = from_scratch & without
"smearing").


Can I compute the absorption spectra for a molecule having triplet ground state 
using turbo_davidson.x or turbo_lanczos.x ??











Thanks & regards,
Prem Sen
Ph.D. Student,
IIT Bombay,
Mumbai,India.

___
Pw_forum mailing list
Pw_forum@pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum

Re: [Pw_forum] CuBTC open metal organic frameworks CONVERGENCE

[Ari P Seitsonen]

Hello Francesco,

  Adding to the previous posts, I found a better convergence in systems 
with vacuum using


mixing_mode = 'local-TF'

  Personally I do not find using 'conv_thr = 1e-8' as very strict, this is 
what I usually use for relaxation (and a bit tighter still when going for 
phonons etc), but indeed one might save some iterations, in particular at 
the beginning of the relaxation. Did you check that your electronic 
structure (density of states for example) looks as expected, for example 
having a band gap if such is expected?


  And personal opinion again, I would be surprised if the bad convergence 
is due to 50 Ry being too low, as those elements, in particular C, H and 
O, should be fine already at 35-40 Ry, not to mention 50. I can just 
imagine that the vdW-DF is extremely sensitive to some noise that arises 
from the augmentation charges, that was maybe not an issue when those 
pseudo potentials were first adapted in calculation (ie using "plain GGA" 
or LDA).


Greetings,

   apsi

-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-
  Ari Paavo Seitsonen / ari.p.seitso...@iki.fi / http://www.iki.fi/~apsi/
Ecole Normale Supérieure (ENS), Département de Chimie, Paris
Mobile (F) : +33 789 37 24 25(CH) : +41 79 71 90 935


On Mon, 23 Jan 2017, Francesco Pelizza wrote:


Hello dear community,


Here in strathclyde some colleagues are using QE to relax and than study
some MOF's.

The problem starts from the beginning, no convergence in the first SCF
cycle before a fixed cell relaxation.


We took care of spin polarized calculation, switched to non polarized
calculation and many other things, WFC from 50 to 80 Ry and RHO cutoffs
10 times the WFC, with gamma sampling and 3 x 3 x 3.

Also checked the smearing, degauss values, nothing seemed to make the
convergence better.

Here you can find some input files and output files.


We used ultrasoft pseudopotentials applying PBE and then vdW-DF functionals.


No success at all.


Please some of you have better experience of us in these systems to tell
us what we do wrong?


BW

Francesco Pelizza and Chris Campbell


Strathclyde University


___
Pw_forum mailing list
Pw_forum@pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum

Re: [Pw_forum] Re^2: Band structure projected on atomic orbitals

[Ari P Seitsonen]

Dear KM Mohsin,

  Could this be the kind of analysis obtained with the keyword 
'kresolveddos' in 'projwfc.x'? At least this is what I understood in the 
Figure that you cited (I once implemented this kind of option in another 
code and obtained plots like this).


Greetings from Sunny Paris,

   apsi

-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-
  Ari Paavo Seitsonen / ari.p.seitso...@iki.fi / http://www.iki.fi/~apsi/
Ecole Normale Supérieure (ENS), Département de Chimie, Paris
Mobile (F) : +33 789 37 24 25(CH) : +41 79 71 90 935


On Sat, 21 Jan 2017, K.M. Mohsin wrote:


Dr. Nicola and Abu Raihan, 
Thank you very much for your suggestions. 
For others summarizing, I will try QE+wannier90 to get "Oribtal projected band 
structure". 

Thanks again. 

Date: Fri, 20 Jan 2017 19:24:55 -0800
From: Mohammad Abu Raihan Miah 
Subject: Re: [Pw_forum] Band structure projected on atomic orbitals
To: PWSCF Forum 
Message-ID:
        
Content-Type: text/plain; charset="utf-8"

Dear KM,

Wannier90 should do the job for you as suggested. If you have time you can
use localized basis set based DFT codes like SIESTA for this kind of figure
more easily.

Thanks.

On Fri, Jan 20, 2017 at 8:09 AM, Nicola Marzari 
wrote:

>
>
> Dear KM,
>
> not sure about the status re atomic orbitals - using QE+Wannier90
> you can do this on Wannier functions, using bands_plot_project
> (see http://www.wannier.org/doc/user_guide.pdf sec. 2.9.11).
>
>                         nicola
>
>
>
> On 20/01/2017 15:00, K.M. Mohsin wrote:
> > Hello everyone,
> >
> > I am wondering is there any program or utility in QE package to
> > calculate and plot band structure projected on atomic orbitals. In VASP
> > they call it "Orbital projected band structure".
> >
> > I have seen this question asked earlier but to the best of my knowledge,
> > previous answers were unfortunately referred to partial DOS calculation
> > with projwfc.x or referred to personal work which is not complete in
> > terms of code and documentation. To clarify, I wish to produce a figure
> > as in the bellow,
> >
> > http://www.nature.com/articles/ncomms10892/figures/6
> >
> > Thanks.
> >
> >
> > --
> >
> > K. M. MOHSIN
> > Ph. D. Candidate (Nanoelectronics area),
> > Dept. of Electrical Engineering and Computer Science,
> > Louisiana State University, Baton Rouge, LA. U.S.A.
> > Phone : +1 (832) 868 8371
> >
> >
> > ___
> > Pw_forum mailing list
> > Pw_forum@pwscf.org
> > http://pwscf.org/mailman/listinfo/pw_forum
> >
>
> --
> --
> Prof Nicola Marzari, Chair of Theory and Simulation of Materials, EPFL
> Director, National Centre for Competence in Research NCCR MARVEL, EPFL
> http://theossrv1.epfl.ch/Main/Contact http://nccr-marvel.ch/en/project
> ___
> Pw_forum mailing list
> Pw_forum@pwscf.org
> http://pwscf.org/mailman/listinfo/pw_forum
>



--
Mohammad Abu Raihan Miah
PhD Student
Department of Electrical and Computer Engineering (ECE)

University of California, San Diego 
-- next part --
An HTML attachment was scrubbed...
URL: 
http://pwscf.org/pipermail/pw_forum/attachments/20170120/8ffc76ad/attachment-0001.html



--

K. M. MOHSIN
Ph. D. Candidate, Nano-electronics
Division. of Electrical Engineering and Computer Science
Louisiana State University, Baton Rouge, LA. U.S.A.
Phone : +1 (832) 868 8371

___
Pw_forum mailing list
Pw_forum@pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum

Re: [Pw_forum] PbTiO3 Tetragonal phase optimization problem

[Ari P Seitsonen]

Dear ?? (Name and affiliation?),

  Adding to the first answers, it looks to me that you are using 
Vanderbilt ultra-soft pseudo potentials, but you do not specify a value 
for 'ecutrho'. Did you check that the 'ecutwfc' is sufficient, ie did you 
perform sufficient convergence studies?


Greetings from Paris,

   apsi

-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-
  Ari Paavo Seitsonen / ari.p.seitso...@iki.fi / http://www.iki.fi/~apsi/
Ecole Normale Supérieure (ENS), Département de Chimie, Paris
Mobile (F) : +33 789 37 24 25(CH) : +41 79 71 90 935


On Sun, 8 Jan 2017, 朱林光 wrote:



  I am a new qe user,and i have a problem about the PbTiO3 Tetragonal phase 
optimization using vc-relax, the output result is much less than the accurate 
one,i dont know how to do such optimization about tetragonal,can you give me 
some advice,i really appreciate it. this is my input file:

calculation = 'vc-relax',
restart_mode = 'from_scratch',
pseudo_dir = '$PSEUDO_DIR/'
outdir = '$OUTPUT_DIR/'
tstress = .true.
tprnfor = .true.
disk_io='high'
/

ibrav=6
celldm(1)=7.8
celldm(3)=1.04
nat=5
ntyp=3
ecutwfc=26
occupations = 'smearing'
smearing= "gauss",
degauss=0.05,
/

conv_thr = 1.D-8
diagonalization   =   'david'
mixing_beta=0.7D0,
/

/

cell_dynamics='bfgs'
press=0.00
/
ATOMIC_SPECIES
Pb 207.2  Pb.pz-d-van.UPF
Ti 47.867  Ti.pz-sp-van_ak.UPF
O 15.9994  O.pz-van_ak.UPF
ATOMIC_POSITIONS
Pb 0.000 0.000 0.000
Ti 0.500 0.500 0.500
O 0.000 0.500 0.500
O 0.500 0.000 0.500
O 0.500 0.500 0.000
K_POINTS {automatic}
4 4 4 1 1 1
and output result is :
Begin final coordinates
new unit-cell volume =401.80625 a.u.^3 (59.54154 Ang^3 )
CELL_PARAMETERS (alat=  7.8000)
  0.934542602   0.0   0.0
  0.0   0.934542602   0.0
  0.0   0.0   0.969470674
ATOMIC_POSITIONS (alat)
Pb   0.0   0.0   0.048659159
Ti   0.467271301   0.467271301   0.502840681
O0.0   0.467271301   0.439632316
O0.467271301   0.0   0.439632316
O0.467271301   0.467271301  -0.032489462
End final coordinates
the accurate result is 3.9,and c/a is about 1.04, i dont know why my result is 
smaller than it? please help me,i really appreciate!


___
Pw_forum mailing list
Pw_forum@pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum
___
Pw_forum mailing list
Pw_forum@pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum

Re: [Pw_forum] problem about inputfile

[Ari P Seitsonen]

Dear Nasim,

  Spelling of 'POSITIONS' maybe...?

Greetings from Paris,

   apsi

-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-
  Ari Paavo Seitsonen / ari.p.seitso...@iki.fi / http://www.iki.fi/~apsi/
Ecole Normale Supérieure (ENS), Département de Chimie, Paris
Mobile (F) : +33 789 37 24 25(CH) : +41 79 71 90 935


On Sun, 1 Jan 2017, Nasim Ha wrote:


I want run pw.x but it stopped with this eroor : Error in routine
read_cards_pw (1):
atomic position info missing
I insert inputfile.
--
N.H.Jazi
PhD student of Physics.
Physics Department,Central Tehran Branch,Islamic Azad
University,Tehran,88074907,Iran.
___
Pw_forum mailing list
Pw_forum@pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum

Re: [Pw_forum] Si pseudopotential for Silicene

[Ari P Seitsonen]

Dear Andrey,

  You are using units 2pi/a ("tpiba_b"), at least in crystal coordinates 
("crystal_b") it would indeed be 1/3 1/3 0, probably not with "tpiba_b".


  If nothing helps, I will try running your example later myself.

Greetings,

   apsi

-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-
  Ari Paavo Seitsonen / ari.p.seitso...@iki.fi / http://www.iki.fi/~apsi/
Ecole Normale Supérieure (ENS), Département de Chimie, Paris
Mobile (F) : +33 789 37 24 25(CH) : +41 79 71 90 935


On Fri, 4 Nov 2016, Andrey Chibisov wrote:


Dear Ari,
I performed a band structure calculation (16x16x16), with paths/points where 
the K is included.
But the band gap is about 0.7 eV, all the same.
K point is 0.333 0.333 0.000 coordinates. Am I wrong?
I attached my input and output for band calculations.
 
 
04.11.2016, 22:03, "Ari P Seitsonen" <ari.p.seitso...@iki.fi>:
> Dear Andrey,
>
>    This combination of number of unit cells and k points does not include
> the point K in the Brillouin zone; what if you try with "9 9 1" (or "6 6
> 1" is faster)? Or you could perform a band structure calculation, with
> paths/points where the K is included.
>
>  Greetings,
>
> apsi
>
> -=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-
>    Ari Paavo Seitsonen / ari.p.seitso...@iki.fi / http://www.iki.fi/~apsi/
>  Ecole Normale Supérieure (ENS), Département de Chimie, Paris
>  Mobile (F) : +33 789 37 24 25 (CH) : +41 79 71 90 935
>
> On Fri, 4 Nov 2016, Andrey Chibisov wrote:
>
>>  Dear  Ari,
>>  I attached my input file and pseudopotential.
>>  I used fully-relativistic case.
>>
>>  04.11.2016, 19:47, "Ari P Seitsonen" <ari.p.seitso...@iki.fi>:
>>>  Dear Andrey,
>>>
>>> It would be useful if you would tell somewhat more for what you did in
>>>  your calculations; for example the input file. Did you try a
>>>  non-relativistic case, do you obtain the correct Dirac cone? If not, you
>>>  might have a problem with your k points (or the structure). Just guessing
>>>  here...
>>>
>>>   Greetings from Paris,
>>>
>>>  apsi
>>>
>>>  
-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-
>>> Ari Paavo Seitsonen / ari.p.seitso...@iki.fi / http://www.iki.fi/~apsi/
>>>   Ecole Normale Supérieure (ENS), Département de Chimie, Paris
>>>   Mobile (F) : +33 789 37 24 25 (CH) : +41 79 71 90 935
>>>
>>>  On Fri, 4 Nov 2016, Andrey Chibisov wrote:
>>>
>>>>   Dear Colleagues,
>>>>   I can not get the correct band gap for silicene.
>>>>   I used the pseudopotential and all the parameters as in the work Appl. 
Phys. Lett. 106, 183107 (2015)
(http://dx.doi.org/10.1063/1.4919885).
>>>>   Please help me with pseudopotential.
>>>>   With ''Si.rel-pbesol-n-rrkjus-psl.0.1.UPF'' pseudopotential I got the 
band gap about 0.7 eV in K point, but according to work Appl. Phys.
Lett. 106, 183107 it was 1.5 meV.
>>>>
>>>>   --
>>>>   Best regards,
>>>>   Andrey Chibisov. Ph.D.
>>>>   Numerical method of mathematical physics Laboratory,
>>>>   Computational Center, Russian Academy of Sciences.
>>>>   Khabarovsk, Russia
>>>>   Web page: https://www.researchgate.net/profile/A_Chibisov
>>>>   http://ru.linkedin.com/pub/andrey-chibisov/55/253/986/en
>>>>   ___
>>>>   Pw_forum mailing list
>>>>   Pw_forum@pwscf.org
>>>>   http://pwscf.org/mailman/listinfo/pw_forum
>>>  ,
>>>
>>>  ___
>>>  Pw_forum mailing list
>>>  Pw_forum@pwscf.org
>>>  http://pwscf.org/mailman/listinfo/pw_forum
>>
>>  --
>>  Best regards,
>>  Andrey Chibisov. Ph.D.
>>  Numerical method of mathematical physics Laboratory,
>>  Computational Center, Russian Academy of Sciences.
>>  Khabarovsk, Russia
>>  Web page: https://www.researchgate.net/profile/A_Chibisov
>>  http://ru.linkedin.com/pub/andrey-chibisov/55/253/986/en
 
-- 
Best regards,
Andrey Chibisov. Ph.D.
Numerical method of mathematical physics Laboratory,
Computational Center, Russian Academy of Sciences.
Khabarovsk, Russia
Web page: https://www.researchgate.net/profile/A_Chibisov
http://ru.linkedin.com/pub/andrey-chibisov/55/253/986/en
 

___
Pw_forum mailing list
Pw_forum@pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum

Re: [Pw_forum] Si pseudopotential for Silicene

[Ari P Seitsonen]

Dear Andrey,

  This combination of number of unit cells and k points does not include 
the point K in the Brillouin zone; what if you try with "9 9 1" (or "6 6 
1" is faster)? Or you could perform a band structure calculation, with 
paths/points where the K is included.


Greetings,

   apsi

-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-
  Ari Paavo Seitsonen / ari.p.seitso...@iki.fi / http://www.iki.fi/~apsi/
Ecole Normale Supérieure (ENS), Département de Chimie, Paris
Mobile (F) : +33 789 37 24 25(CH) : +41 79 71 90 935


On Fri, 4 Nov 2016, Andrey Chibisov wrote:


Dear  Ari,
I attached my input file and pseudopotential.
I used fully-relativistic case.

04.11.2016, 19:47, "Ari P Seitsonen" <ari.p.seitso...@iki.fi>:

Dear Andrey,

   It would be useful if you would tell somewhat more for what you did in
your calculations; for example the input file. Did you try a
non-relativistic case, do you obtain the correct Dirac cone? If not, you
might have a problem with your k points (or the structure). Just guessing
here...

 Greetings from Paris,

apsi

-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-
   Ari Paavo Seitsonen / ari.p.seitso...@iki.fi / http://www.iki.fi/~apsi/
 Ecole Normale Supérieure (ENS), Département de Chimie, Paris
 Mobile (F) : +33 789 37 24 25 (CH) : +41 79 71 90 935

On Fri, 4 Nov 2016, Andrey Chibisov wrote:


 Dear Colleagues,
 I can not get the correct band gap for silicene.
 I used the pseudopotential and all the parameters as in the work Appl. Phys. 
Lett. 106, 183107 (2015) (http://dx.doi.org/10.1063/1.4919885).
 Please help me with pseudopotential.
 With ''Si.rel-pbesol-n-rrkjus-psl.0.1.UPF'' pseudopotential I got the band gap 
about 0.7 eV in K point, but according to work Appl. Phys. Lett. 106, 183107 it 
was 1.5 meV.

 --
 Best regards,
 Andrey Chibisov. Ph.D.
 Numerical method of mathematical physics Laboratory,
 Computational Center, Russian Academy of Sciences.
 Khabarovsk, Russia
 Web page: https://www.researchgate.net/profile/A_Chibisov
 http://ru.linkedin.com/pub/andrey-chibisov/55/253/986/en
 ___
 Pw_forum mailing list
 Pw_forum@pwscf.org
 http://pwscf.org/mailman/listinfo/pw_forum

,

___
Pw_forum mailing list
Pw_forum@pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum


--
Best regards,
Andrey Chibisov. Ph.D.
Numerical method of mathematical physics Laboratory,
Computational Center, Russian Academy of Sciences.
Khabarovsk, Russia
Web page: https://www.researchgate.net/profile/A_Chibisov
http://ru.linkedin.com/pub/andrey-chibisov/55/253/986/en
___
Pw_forum mailing list
Pw_forum@pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum

Re: [Pw_forum] Si pseudopotential for Silicene

[Ari P Seitsonen]

Dear Andrey,

  It would be useful if you would tell somewhat more for what you did in 
your calculations; for example the input file. Did you try a 
non-relativistic case, do you obtain the correct Dirac cone? If not, you 
might have a problem with your k points (or the structure). Just guessing 
here...


Greetings from Paris,

   apsi

-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-
  Ari Paavo Seitsonen / ari.p.seitso...@iki.fi / http://www.iki.fi/~apsi/
Ecole Normale Supérieure (ENS), Département de Chimie, Paris
Mobile (F) : +33 789 37 24 25(CH) : +41 79 71 90 935


On Fri, 4 Nov 2016, Andrey Chibisov wrote:


Dear Colleagues,
I can not get the correct band gap for silicene. 
I used the pseudopotential and all the parameters as in the work Appl. Phys. Lett. 106, 183107 (2015) (http://dx.doi.org/10.1063/1.4919885). 
Please help me with pseudopotential.

With ''Si.rel-pbesol-n-rrkjus-psl.0.1.UPF'' pseudopotential I got the band gap 
about 0.7 eV in K point, but according to work Appl. Phys. Lett. 106, 183107 it 
was 1.5 meV.

--
Best regards,
Andrey Chibisov. Ph.D.
Numerical method of mathematical physics Laboratory,
Computational Center, Russian Academy of Sciences.
Khabarovsk, Russia
Web page: https://www.researchgate.net/profile/A_Chibisov
http://ru.linkedin.com/pub/andrey-chibisov/55/253/986/en
___
Pw_forum mailing list
Pw_forum@pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum___
Pw_forum mailing list
Pw_forum@pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum

Re: [Pw_forum] QE-5.4.0 on hpc cluster w gfortran + MKL and other

[Ari P Seitsonen]

Dear Eugenia,

  If you have not your problem yet, here a recent reply from Paolo G.:

http://qe-forge.org/pipermail/pw_forum/2016-October/111293.html

Basically you have to include 
'/opt/intel/composerxe-2013.0.080/mkl/include' (or similar) in the 
directories where the module files are looked for, 'IFLAGS'. Hopefully 
this helps.


Greetings from Paris,

   apsi

-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-
  Ari Paavo Seitsonen / ari.p.seitso...@iki.fi / http://www.iki.fi/~apsi/
Ecole Normale Supérieure (ENS), Département de Chimie, Paris
Mobile (F) : +33 789 37 24 25(CH) : +41 79 71 90 935


On Tue, 1 Nov 2016, eugenia wetrowa wrote:


Dear all, please help. I'm trying to build parallel QE-5.4.0 on hpc cluster.  
System parameters:
20 nodes with
2* E5-2680 Intel Xeon CPU (8 n), 128GiB RAM 300 GiB HDD
arch: x86_64
Gentoo/Linux 3.2.59
GCC compilers, gfortran 4.8
OpenMPI, mpich-2 mpi-mpich2-1_5-x86_64

Autoconfig detects compilers and parallel environment correctly but  links 
libraries:

BLAS_LIBS  = -L/opt/intel/composerxe-2013.0.080/mkl/lib/intel64 
-lmkl_gf_lp64  -lmkl_sequential -lmkl_core
BLAS_LIBS_SWITCH = external
LAPACK_LIBS    =
LAPACK_LIBS_SWITCH = external
ELPA_LIBS_SWITCH = disabled
SCALAPACK_LIBS = -lmkl_scalapack_lp64 -lmkl_blacs_openmpi_lp64
FFT_LIBS   = -lfftw3
MPI_LIBS   =
MASS_LIBS  =
AR = ar
ARFLAGS    = ruv
RANLIB = ranlib
FLIB_TARGETS   = all
LIBOBJS    = ../clib/clib.a ../iotk/src/libiotk.a
LIBS   = $(SCALAPACK_LIBS) $(LAPACK_LIBS) $(FFT_LIBS) $(BLAS_LIBS) 
$(MPI_LIBS) $(MASS_LIBS) $(LD_LIBS)

In this configuration "make" fails:

_ _ _ _ _ _
test -d bin || mkdir bin
( cd FFTXlib ; make TLDEPS= all || exit 1 )
make[1]: Entering directory `/home/osvasilyev/QE/FFTXlib'
mpif90 -O3 -g -x f95-cpp-input -D__GFORTRAN -D__STD_F95 -D__DFTI -D__MPI 
-D__PARA -D__SCALAPACK  -I../include -I/include  -c fft_types.f90
Warning: Nonexistent include directory "/include"
mpif90 -O3 -g -x f95-cpp-input -D__GFORTRAN -D__STD_F95 -D__DFTI -D__MPI 
-D__PARA -D__SCALAPACK  -I../include -I/include  -c scatter_mod.f90
Warning: Nonexistent include directory "/include"
mpif90 -O3 -g -x f95-cpp-input -D__GFORTRAN -D__STD_F95 -D__DFTI -D__MPI 
-D__PARA -D__SCALAPACK  -I../include -I/include  -c fft_scalar.f90
Warning: Nonexistent include directory "/include"
In file included from fft_scalar.f90:27:0:
fft_scalar.DFTI.f90:20:0: fatal error: mkl_dfti.f90: No such file or directory
 #include "mkl_dfti.f90"
 ^
compilation terminated.
make[1]: *** [fft_scalar.o] Error 1
make[1]: Leaving directory `/home/osvasilyev/QE/FFTXlib'
make: *** [libfft] Error 1
_ _ _ _ _ _ _

Then i tryed to build QE with MKL libraries following the Intel's manual, linking 
explicitlly ./configure --LIBDIRS="
-L/opt/intel/composerxe-2013.0.080/mkl/lib/intel64 -Wl, -lmkl_scalapack_ilp64 
-lmkl_gf_ilp64 -lmkl_gnu_thread -lmkl_core
-lmkl_blacs_intelmpi_ilp64 -lgomp -lpthread -lm -ldl" .
Configure says
"The following libraries have been found:
  BLAS_LIBS=-L/opt/intel/composerxe-2013.0.080/mkl/lib/intel64 -lmkl_gf_lp64  
-lmkl_sequential -lmkl_core
  LAPACK_LIBS=
  SCALAPACK_LIBS=-lmkl_scalapack_lp64 -lmkl_blacs_openmpi_lp64
  FFT_LIBS=-lfftw3
parallel environments detected successfully"

But compilation crushed again with same log. It's not clear for me what the errors 
occure. Directory "include" existed. When linking MKL breafly,
the same. And there was any unsuccessful cases of configuration, with internal 
libs too.

QE was builded only in configuration: LAPACK_LIBS  = -latllapack, 
SCALAPACK_LIBS = , FFT_LIBS  =  -lfftw3,  MPI_LIBS  = 
-L/usr/lib/mpi/mpi-mpich2-1_5-x86_64/usr/lib64/ , but it works poorly.  
Examples go normally on -np 2..8, but jobs (scf, md, relax that start
normally on local)  always fail due to SEGFAULT. tryed -np 2..128.
 
So I ask for advice, has anyone dealt sucesfully with QE on cluster with 
GFORTRAN? I suspect that gfortran+mkl+QE is unlivable, who knows some
appropriate configurations?

PS. Sysadmin's advices didn't help that's why I'm here)

Sincerely,
Eugenia W.

Research engineer
NRNU, Moscow.

___
Pw_forum mailing list
Pw_forum@pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum

Re: [Pw_forum] Ge.pz-hgh.UPF

[Ari P Seitsonen]

Dear Gabriel,

  You find many GTH/HTH-type pseudo potential via Matthias Karck's site:

https://www.cp2k.org/static/potentials/

I could see pseudo potentials with LDA - in CPMD format, that you would 
then convert with the UPF tools of QE into the .UPF files - containing 
four or 14 valence electrons (the latter most likely being preferred). The 
parametrisation of the LDA is not Perdew-Zunger though, but probably the 
form with PADE interpolation is very close (experts please correct me).


Greetings from Paris,

   apsi

-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-
  Ari Paavo Seitsonen / ari.p.seitso...@iki.fi / http://www.iki.fi/~apsi/
Ecole Normale Supérieure (ENS), Département de Chimie, Paris
Mobile (F) : +33 789 37 24 25(CH) : +41 79 71 90 935


On Fri, 21 Oct 2016, Gabriel Greene wrote:


Dear QE community,
I am wondering if it is possible to retrieve the pseudopotential generation 
information of the Ge pseudopotential Ge.pz-hgh.UPF which can be
downloaded on the QE pseudopotential page?

In the PP_INFO section, it states

Generation configuration: not available.
Converted from CPMD format using cpmd2upf v.5.0.1 - PG 10Jul201

Which prompted me to check the CPMD website page

http://cpmd.org/downloadable-files/no-authentication/pseudo-potentials/germanium

but there I do not see a Ge Goedecker-Teter-Hutter PP generated with the PZ-LDA 
functional (the closest I can see is a GTH PP generated with the B
LYP functional). 


Thanks very much,

Gabriel Greene-Diniz

Research Associate,

Atomistic Simulation Centre,

School of Mathematics and Physics,

Queen's University Belfast


___
Pw_forum mailing list
Pw_forum@pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum

[Pw_forum] Possibility of obtaining l-dependent potentials from 'atomic'/'ld1'

[Ari P Seitsonen]

Dear Colleagues,

  Does some one know if it is possible to recover the l-dependent 
potentials from the 'atomic'/'ld1' code for educational, or plotting
purpose? This of course only in the norm-conserving, Troullier-Martins 
case. We tried to look up both the options in the input and the items 
written into the .UPF file (after I had already written a Python script 
to extract various fields), but could not find it in either of them. As 
the last resort, I guess that the 'beta' function would be


  beta(r) = [ V_l(r) - V_local(r) ] phi(r) ,

so as phi(r) is given, one could obtain the V_l(r) by inverting the 'beta' 
from this equation? And the normalisation, are the matrix elements D_ij 
contain the (Kleinman-Bylander) factors 1 / < psi(r) | V_l(r) - V_local(r) 
| psi(r) >, or are there some hidden coefficient for normalisations (à 
la 4pi).


  Sorry if this is a FAQ. :(

Greetings from van Beethoven-city Bonn,

   apsi

-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-
  Ari Paavo Seitsonen / ari.p.seitso...@iki.fi / http://www.iki.fi/~apsi/
Ecole Normale Supérieure (ENS), Département de Chimie, Paris
Mobile (F) : +33 789 37 24 25(CH) : +41 79 71 90 935___
Pw_forum mailing list
Pw_forum@pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum

Re: [Pw_forum] ERROR PROBLEM WITH SURFACE RELAXATION

[Ari P Seitsonen]

Dear Omamuyovwi Akemu,

  Please try breaking the symmetry, even slightly, in the top-most layer; 
the symmetry analysis apparently does not take into account the fixed 
coordinates. So initially the code thinks that the two surfaces are 
identical, but after the relaxation only the top-most layer is moved, 
making it different by symmetry from the other surface. I usually displace 
the surface layer atoms vertically just so much that the possible 
symmetries along the surface normal are broken.


  Or maybe this is not your problem...

Greetings from Paris,

   apsi

-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-
  Ari Paavo Seitsonen / ari.p.seitso...@iki.fi / http://www.iki.fi/~apsi/
Ecole Normale Supérieure (ENS), Département de Chimie, Paris
Mobile (F) : +33 789 37 24 25(CH) : +41 79 71 90 935


On Thu, 23 Jun 2016, Omamuyovwi Akemu wrote:


Dear QE User,
 
I'm  having trouble trying to relax the (100) surface of Mo.
I will be grateful if someone can help or give me a hint on how to fix this 
problem.
Thanks you all.

Below is my input file:

  calculation = "relax",
  prefix  = "Mo"
  pseudo_dir  = "/home/omamu/QE/espresso-5.0.1/pseudo",
  outdir  = "./tmp",
/

  ibrav   = 6,
  celldm(1)   = 5.952639665D0,
  celldm(3)   = 10.4D0,
  nat = 15,
  ntyp    = 1,
  ecutwfc = 32.D0,
  ecutrho = 320.D0,
  occupations = "smearing",
  smearing    = "m-v",
  degauss = 0.02D0,
/

  conv_thr    = 1.D-8,
  mixing_beta = 0.3D0,
/

  ion_dynamics   = 'bfgs'
/
ATOMIC_SPECIES
Mo  95.94  Mo.pw91-n-van.UPF

ATOMIC_POSITIONS
Mo   0. 0. 0.000   0  0  0
Mo   0.5000 0.5000 0.500   0  0  0
Mo   0. 0. 1.000   0  0  0
Mo   0.5000 0.5000 1.500   0  0  0
Mo   0. 0. 2.000   0  0  0
Mo   0.5000 0.5000 2.500   0  0  0
Mo   0. 0. 3.000   0  0  0
Mo   0.5000 0.5000 3.500   1  1  1
Mo   0. 0. 4.000   1  1  1
Mo   0.5000 0.5000 4.500   1  1  1
Mo   0. 0. 5.000   1  1  1
Mo   0.5000 0.5000 5.500   1  1  1
Mo   0. 0. 6.000   1  1  1
Mo   0.5000 0.5000 6.500   1  1  1
Mo   0. 0. 7.000   1  1  1

K_POINTS automatic
10  10   1   0  0  0

The error report is :
  BFGS Geometry Optimization

 number of scf cycles    =   1
 number of bfgs steps    =   0

 energy   new    =    -438.7514973224 Ry

 new trust radius    =   0.0549563359 bohr
 new conv_thr    =   0.000100 Ry


ATOMIC_POSITIONS (alat)
Mo   0.0   0.0   0.0    0   0   0
Mo   0.5   0.5   0.5    0   0   0
Mo   0.0   0.0   1.0    0   0   0
Mo   0.5   0.5   1.5    0   0   0
Mo   0.0   0.0   2.0    0   0   0
Mo   0.5   0.5   2.5    0   0   0
Mo   0.0   0.0   3.0    0   0   0
Mo   0.5   0.5   3.5
Mo   0.0   0.0   4.000135262
Mo   0.5   0.5   4.500756431
Mo   0.0   0.0   4.999615948
Mo   0.5   0.5   5.500355304
Mo   0.0   0.0   6.000329230
Mo   0.5   0.5   6.509232263
Mo   0.0   0.0   6.993885956



 %%
 Error in routine checkallsym (1):
 some of the original symmetry operations not satisfied
   
Jolayemi Omamuyovwi Rita


?? ? 

Research Student
University of Benin
Nigeria.


___
Pw_forum mailing list
Pw_forum@pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum

Re: [Pw_forum] Raman calculation of graphyne

[Ari P Seitsonen]

Dear Barnali,

  The symmetries stem from the self-consistent calculation, so the problem 
is there. Indeed it looks from the few coordinates in the input that you 
provided that they are not precisely - up to some 4-5 digits on the 
symmetric positions like 0.5; thus 'pw.x' does not consider these as 
symmetries and all the modes become labelled with the basic symmetry "A". 
Please try symmetrising the coordinates, checking already in the output of 
'pw.x' that you have the symmetry requested.


Greetings from Paris,

   apsi

-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-
  Ari Paavo Seitsonen / ari.p.seitso...@iki.fi / http://www.iki.fi/~apsi/
Ecole Normale Supérieure (ENS), Département de Chimie, Paris
Mobile (F) : +33 789 37 24 25(CH) : +41 79 71 90 935


On Thu, 23 Jun 2016, Barnali Bhattacharya wrote:



Dear Sir/Madam

I am trying to reproduce the Raman spectra of graphyne system reported by Zhang et al [J. Phys. Chem. C, 2016, 120 (19), pp 10605–10613]. 
In my calculated spectra, I have found the Raman peaks are located more or less on same frequency as observed in the paper of Zhang et al.  The position of the Raman peaks are given below-


………

 # mode   [cm-1]    [THz]  IR  Raman   depol.fact

    1 -0.00   -0.    0. 0.    0.7265

    2 -0.00   -0.    0. 0.    0.7498

    3  0.00    0.    0. 0.0001    0.5641

    4    180.32    5.4057    0. 1.4898    0.2967

    5    180.47    5.4103    0. 1.5604    0.7466

    6    232.43    6.9680    0.    51.4183    0.7500

    7    232.84    6.9804    0.    59.4666    0.7500

    8    249.23    7.4716    0.    955497.8547    0.1945

    9    333.27    9.9912    0.0276 6.5036    0.6017

   10    401.52   12.0373    0. 0.0027    0.3409

   11    413.75   12.4038    0.0589 0.0026    0.5983

   12    414.29   12.4201    0.0586 0.0128    0.2304

   13    465.96   13.9692    0.0003 0.0051    0.7477

   14    506.14   15.1738    0.   4286930.6335    0.1763

   15    506.61   15.1879    0.    153395.9276    0.3020

   16    557.47   16.7124    0.0001  3677.4093    0.7500

   17    557.63   16.7175    0.0001  4445.0962    0.7500

   18    672.04   20.1471    0. 0.0257    0.6204

   19    679.01   20.3562    0. 5.2659    0.6276

   20    679.11   20.3593    0.    10.5107    0.2863

   21    788.70   23.6446    0.  14647549.8132    0.1986

   22    793.96   23.8025    0. 0.0232    0.7498

   23    948.26   28.4280    0.   3919030.7925    0.2311

   24    948.36   28.4312    0.   1167947.1815    0.2501

   25   1059.37   31.7591    3.1810 4.7302    0.2109

   26   1059.64   31.7672    3.1760 0.1304    0.2298

   27   1205.12   36.1285    0.  56577350.6847    0.2012

   28   1388.64   41.6303    0. 0.0043    0.6020

   29   1465.22   43.9261    0.    710764.1488    0.6076

   30   1465.26   43.9274    0.   1596968.3457    0.3793

   31   1482.91   44.4565    0.0018 4.9641    0.3255

   32   1501.10   45.0019   23.8090 1.7968    0.3140

   33   1501.37   45.0098   23.7976 0.3151    0.3348

   34   2191.33   65.6945    0. 162172387.6538    0.1964

   35   2230.26   66.8616    0.   3616106.5565    0.1860

   36   2231.11   66.8870    0.   2730839.0109    0.1988

……….

  But the problem arises in the case of mode symmetry and irreducible representation calculation. 
 I am not able to generate same irreducible representation like Zhang has got. 
Of course, I have missed some technique or something wrong with my understanding.

 My calculated irreducible representations are presented below-

..

  Mode symmetry, C_1 (1) point group:

 

 freq (  1 -  1) =      0.6  [cm-1]   --> A   I+R

 freq (  2 -  2) =  3.2  [cm-1]   --> A   I+R

 freq (  3 -  3) = 17.3  [cm-1]   --> A   I+R

 freq (  4 -  4) =    180.3  [cm-1]   --> A   I+R

 freq (  5 -  5) =    180.5  [cm-1]   --> A   I+R

 freq (  6 -  6) =    232.4  [cm-1]   --> A   I+R

 freq (  7 -  7) =    232.8  [cm-1]   --> A   I+R

     freq (  8 -  8) =    249.2  [cm-1]   --> A   I+R

 freq (  9 -  9) =    333.3  [cm-1]   --> A   I+R

 freq ( 10 - 10) =    401.5  [cm-1]   --> A   I+R

 freq ( 11 - 11) =    413.7  [cm-1]   --> A   I+R

 freq ( 12 - 12) =    414.3  [cm-1]   --> A   I+R

 freq ( 13 - 13) =    466.0  [cm-1]   --> A   I+R

 freq ( 14 - 14) =    506.1  [cm-1]   --> A   I+R

 freq ( 15 - 15) =    506.6  [cm-1]   --> A 

Re: [Pw_forum] uf

[Ari P Seitsonen]

Dear Ashkan,

  I am aware of this:

https://www.ifm.liu.se/theomod/compphys/band-unfolding/

Greetings from Paris,

   apsi

-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-
  Ari Paavo Seitsonen / ari.p.seitso...@iki.fi / http://www.iki.fi/~apsi/
Ecole Normale Supérieure (ENS), Département de Chimie, Paris
Mobile (F) : +33 789 37 24 25(CH) : +41 79 71 90 935


On Fri, 27 May 2016, ashkan shekaari wrote:


Dear experts,
How could one unfold the folded band structure of a supercell?

Is there a code for this purpose in QE?

--
Best,
Ashkan Shekaari
Plasma Physics Research Center
Science and Research Branch
I A U, 14778-93855 Tehran, Iran.
___
Pw_forum mailing list
Pw_forum@pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum

Re: [Pw_forum] vc-relax doesn't seem to converged.

[Ari P Seitsonen]

Dear Amir,

  Well, rather the other way around: 1 2 2 in the k points, as the longer 
the cell in real space, the fewer the k points needed in the corresponding 
accuracy in the reci-procal space, or, the integration over the Brillouin 
zone? Why? Exactly because it is the _reci-procal_ space (the longer the 
real-space dimension, the shorter the one in reci-procal space, so one 
needs less sampling points == k points to achieve the same 
sampling distance in the integrand).


  Well, I just mentioned LDA, because my first thought was that it is so 
old, why not going for the GGA's plus possibly a correction for the 
missing London dispersions, but at the second thought LDA is known to give 
quite good results in the bulk, and it is less of the art of "fitting" the 
"correct" GGA to obtain good results. Some results on the LDA versus GGA 
versus other schemes were recently performed by Colleagues (my own
contribution was small but hopefully positive, ie non-destructive) in 
Henri Hay et alia, Phys. Rev. B 92, 144111 DOI: 10.1103/PhysRevB.92.144111
Maybe this gives you some thoughts. I guess that if going for bulk-like 
properties the GGA functionals such as PBEsol ("PBE-for-solids") might be 
quite good results. It is up to you, indeed LDA might give reasonable 
results, without all this fit-to-be-ab-initio-considerations of choosing 
the functional to use. :) (wasntme) - just my personal opinion.


Greetings,

   apsi

-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-
  Ari Paavo Seitsonen / ari.p.seitso...@iki.fi / http://www.iki.fi/~apsi/
Ecole Normale Supérieure (ENS), Département de Chimie, Paris
Mobile (F) : +33 789 37 24 25(CH) : +41 79 71 90 935


On Mon, 23 May 2016, Mofrad, Amir Mehdi (MU-Student) wrote:


Thank you Ari for your reply. Yes you were right about the number of atoms. It 
should be 72. I figured that out too right after I sent out the email. However, 
I wanted to ask about what you said at the end of your reply. So do you think 3 
2 2 or even 4 2 2 would be good enough to do the optimization? Also, would you 
please clarify a bit on the LDA part you mentioned?


Best,

Amir M. Mofrad
Graduate Research Assistant
Chemical Engineering Department
University of Missouri


From: pw_forum-boun...@pwscf.org <pw_forum-boun...@pwscf.org> on behalf of Ari P 
Seitsonen <ari.p.seitso...@iki.fi>
Sent: Monday, May 23, 2016 7:18:16 AM
To: PWSCF Forum
Subject: Re: [Pw_forum] vc-relax doesn't seem to converged.

Dear Amir,

  Did you check your geometry, for example visually (XCrysDen, VESTA,
...)? To me it looks as if there are some Si atoms missing in the
structure, and thus there are dangling bonds on oxygens. Was this your
purpose?

  In principle you can later change your k point sampling in the direction
corresponding to the long axis of the unit cells. LDA, hmm, well if you
want. :)

Greetings from Paris,

   apsi

-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-
  Ari Paavo Seitsonen / ari.p.seitso...@iki.fi / http://www.iki.fi/~apsi/
Ecole Normale Supérieure (ENS), Département de Chimie, Paris
Mobile (F) : +33 789 37 24 25(CH) : +41 79 71 90 935


On Thu, 19 May 2016, Mofrad, Amir Mehdi (MU-Student) wrote:



Dear all QE users and developers,


So far I have been doing scf calculations on one unit cell of a specific type 
of zeolite (which is called SOD) and I have been
getting some good results. However, recently I wanted to extend my calculations 
on more than one unit cell (2x1x1 for
instance). The problem is when I do vc-relax it does not optimize the cell nor 
the internal coordinates of atoms. I put my
input file in case you might need to take a look at. Any help would be 
thoroughly appreciated.



 calculation = 'vc-relax' ,
 restart_mode = 'from_scratch' ,
 wf_collect = .true. ,
 outdir = './scratch' ,
 wfcdir = './scratch' ,
 pseudo_dir = '/global/espresso/pseudo' ,
 prefix = 'SOD' ,
 verbosity = 'high' ,
 etot_conv_thr = 1e-5 ,
 forc_conv_thr = 1e-4 ,
 nstep = 50 ,
 tstress = .true. ,
 tprnfor = .true. ,

 /


   ibrav = 0,
 nat = 70,
ntyp = 2,
 ecutwfc = 31 ,
 ecutrho = 310 ,


/

electron_maxstep = 100,
conv_thr = 3e-8 ,
 mixing_mode = 'plain' ,
 mixing_beta = 0.7 ,
 diagonalization = 'david' ,
 /

   ion_dynamics = 'bfgs' ,
   trust_radius_ini = 0.5 ,
/

cell_dynamics='bfgs',
cell_factor=5,
/

CELL_PARAMETERS angstrom
 18.   0.0   0.0
 0.0   9.0   0.0
 0.0   0.0   9.0
ATOMIC_SPECIES
 Si   28.08600 Si.pz-n-rrkjus_psl.0.1.UPF
 O15.99940 O.pz-n-rrkjus_psl.0.1.UPF

ATOMIC_POSITIONS angstrom
 O   1.31516   4.48250   7.64983
Si   2.24125   4.48250   0.0
 O   4.48250 

Re: [Pw_forum] H-L Pseudopotential generation:Reg

[Ari P Seitsonen]

Dear A Suresh,

  You could easily take an existing input file for the atomic code 
('ld1.x') for the elements that you want - for example from the PSLibrary 
- and just change the exchange-correlation functional to the one you want; 
seen in /Modules/funct.f90:


  !  "hl" Hedin-Lunqvist icorr=6

Greetings,

   apsi

-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-
  Ari Paavo Seitsonen / ari.p.seitso...@iki.fi / http://www.iki.fi/~apsi/
Ecole Normale Supérieure (ENS), Département de Chimie, Paris
Mobile (F) : +33 789 37 24 25(CH) : +41 79 71 90 935


On Mon, 23 May 2016, Suresh A wrote:


Respectected Sir/Friends,
  I would like to do band structure calculation for tio2 with 
Hedin-Lundquist exchange-correlational pseudopotential.
Can one get from other sources or produce via ATOM package?
    Thank You

  With Regards,
A.Suresh,
Research Scholar,
Madurai Kamaraj University,
Madurai.

___
Pw_forum mailing list
Pw_forum@pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum

Re: [Pw_forum] vc-relax doesn't seem to converged.

[Ari P Seitsonen]

Dear Amir,

  Did you check your geometry, for example visually (XCrysDen, VESTA, 
...)? To me it looks as if there are some Si atoms missing in the 
structure, and thus there are dangling bonds on oxygens. Was this your 
purpose?


  In principle you can later change your k point sampling in the direction 
corresponding to the long axis of the unit cells. LDA, hmm, well if you 
want. :)


Greetings from Paris,

   apsi

-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-
  Ari Paavo Seitsonen / ari.p.seitso...@iki.fi / http://www.iki.fi/~apsi/
Ecole Normale Supérieure (ENS), Département de Chimie, Paris
Mobile (F) : +33 789 37 24 25(CH) : +41 79 71 90 935


On Thu, 19 May 2016, Mofrad, Amir Mehdi (MU-Student) wrote:



Dear all QE users and developers,


So far I have been doing scf calculations on one unit cell of a specific type 
of zeolite (which is called SOD) and I have been
getting some good results. However, recently I wanted to extend my calculations 
on more than one unit cell (2x1x1 for
instance). The problem is when I do vc-relax it does not optimize the cell nor 
the internal coordinates of atoms. I put my
input file in case you might need to take a look at. Any help would be 
thoroughly appreciated.



 calculation = 'vc-relax' ,
 restart_mode = 'from_scratch' ,
 wf_collect = .true. ,
 outdir = './scratch' ,
 wfcdir = './scratch' ,
 pseudo_dir = '/global/espresso/pseudo' ,
 prefix = 'SOD' ,
 verbosity = 'high' ,
 etot_conv_thr = 1e-5 ,
 forc_conv_thr = 1e-4 ,
 nstep = 50 ,
 tstress = .true. ,
 tprnfor = .true. ,

 /


   ibrav = 0,
 nat = 70,
    ntyp = 2,
 ecutwfc = 31 ,
 ecutrho = 310 ,


/

    electron_maxstep = 100,
    conv_thr = 3e-8 ,
 mixing_mode = 'plain' ,
 mixing_beta = 0.7 ,
 diagonalization = 'david' ,
 /

   ion_dynamics = 'bfgs' ,
   trust_radius_ini = 0.5 ,
/

    cell_dynamics='bfgs',
    cell_factor=5,
/

CELL_PARAMETERS angstrom
 18.   0.0   0.0
 0.0   9.0   0.0
 0.0   0.0   9.0
ATOMIC_SPECIES
 Si   28.08600 Si.pz-n-rrkjus_psl.0.1.UPF
 O    15.99940 O.pz-n-rrkjus_psl.0.1.UPF

ATOMIC_POSITIONS angstrom
 O   1.31516   4.48250   7.64983
Si   2.24125   4.48250   0.0
 O   4.48250   1.31517   7.64983
 O   7.64983   4.48250   7.64983
 O   4.48250   7.64983   7.64983
 O   1.31517   4.48250   1.31517
 O   4.48250   1.31517   1.31517
 O   7.64983   4.48250   1.31517
 O   4.48250   7.64983   1.31517
 O   7.64983   1.31517   4.48250
 O   7.64983   7.64983   4.48250
 O   1.31516   7.64983   4.48250
 O   1.31517   1.31517   4.48250
 O   5.79767  -0.0   3.16733
 O  -0.0   5.79767   3.16733
 O   3.16733  -0.0   3.16733
 O  -0.0   3.16733   3.16733
 O   5.79767  -0.0   5.79767
 O  -0.0   5.79767   5.79767
 O   3.16733  -0.0   5.79767
 O  -0.0   3.16733   5.79767
 O   3.16733   5.79767   0.0
 O   3.16733   3.16733   0.0
 O   5.79767   3.16733   0.0
 O   5.79767   5.79767   0.0
Si   4.48250   2.24125   0.0
Si   6.72375   4.48250   0.0
Si   4.48250   6.72375   0.0
Si  -0.0   2.24125   4.48250
Si   6.72375  -0.0   4.48250
Si  -0.0   6.72375   4.48250
Si   2.24125  -0.0   4.48250
Si   4.48250  -0.0   2.24125
Si  -0.0   4.48250   2.24125
 O  10.28017   4.48250   7.64983
Si  11.20625   4.48250   0.0
 O  13.44750   1.31517   7.64983
 O  16.61483   4.48250   7.64983
 O  13.44750   7.64983   7.64983
 O  10.28017   4.48250   1.31517
 O  13.44750   1.31517   1.31517
 O  16.61483   4.48250   1.31517
 O  13.44750   7.64983   1.31517
 O  16.61483   1.31517   4.48250
 O  16.61483   7.64983   4.48250
 O  10.28017   7.64983   4.48250
 O  10.28017   1.31517   4.48250
 O  14.76267  -0.0   3.16733
 O   8.96500   5.79767   3.16733
 O  12.13233  -0.0   3.16733
 O   8.96500   3.16733   3.16733
 O  14.76267  -0.0   5.79767
 O   8.96500   5.79767   5.79767
 O  12.13233  -0.0   5.79767
 O   8.96500   3.16733   5.79767
 O  12.13233   5.79767   0.0
 O  12.13233   3.16733   0.0
 O  14.76267   3.16733   0.0
 O  14.76267   5.79767   0.0
Si  13.44750   2.24125   0.0
Si  15.68875   4.48250   0.0
Si  13.44750   6.72375   0.0
Si   8.96500   2.24125   4.48250
Si  15.68875  -0.0   4.48250
Si   8.96500   6.72375   4.48250
Si  11.20625  -0.0   4.48250
Si  13.44750  -0.0   6.72375
Si   8.96500   4.48250   6.72375
Si  13.44750  -0.0   2.24125
Si   8.96500   4.48250   2.24125

K_POINTS automatic
2 2 2 1 1 1

Best,


Amir M. Mofrad   

University of Missouri


___
Pw_forum mailing list
Pw_forum@pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum

Re: [Pw_forum] pdos

[Ari P Seitsonen]

Dear Ashkan Shekaari,

  Please check the documentation, for example in 
/PP/Doc/INPUT_PROJWFC.def:


  text {
  Order of m-components for each l in the output:
1, cos(phi), sin(phi), cos(2*phi), sin(2*phi), .., cos(l*phi), 
sin(l*phi)
  where phi is the polar angle:x=r cos(theta)cos(phi), y=r 
cos(theta)sin(phi)
  This is determined in file flib/ylmr2.f90 that calculates spherical 
harmonics.

  for l=1:
1 pz (m=0)
2 px (real combination of m=+/-1 with cosine)
3 py (real combination of m=+/-1 with sine)

  for l=2:
1 dz2(m=0)
2 dzx(real combination of m=+/-1 with cosine)
3 dzy(real combination of m=+/-1 with sine)
4 dx2-y2 (real combination of m=+/-2 with cosine)
5 dxy(real combination of m=+/-2 with sine)
}

Greetings from Paris,

   apsi

-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-
  Ari Paavo Seitsonen / ari.p.seitso...@iki.fi / http://www.iki.fi/~apsi/
Ecole Normale Supérieure (ENS), Département de Chimie, Paris
Mobile (F) : +33 789 37 24 25(CH) : +41 79 71 90 935


On Sun, 8 May 2016, ashkan shekaari wrote:


Dear experts,
in quantum mechanics, the quantum number m is between -l and l : -l<=m<=l

and so m=-1, 0, +1 for l=1. but in the output of a pdos calculation, values of 
m 

are seen as follows:

     state #   9: atom   1 (Mo ), wfc  5 (l=2 m= 1)
     state #  10: atom   1 (Mo ), wfc  5 (l=2 m= 2)
     state #  11: atom   1 (Mo ), wfc  5 (l=2 m= 3)
     state #  12: atom   1 (Mo ), wfc  5 (l=2 m= 4)
     state #  13: atom   1 (Mo ), wfc  5 (l=2 m= 5)

Is, for example,  (l=2 , m= 1) equivalent to m=-2 or 

     (l=2 m= 1)-->  m=-2
     (l=2 m= 2)-->  m=-1
      (l=2 m= 3)-->  m=0
      (l=2 m= 4)-->  m=1
      (l=2 m= 5)-->  m=2

?

--
All the best,
Ashkan Shekaari
Plasma Physics Research Center, Science and Research Branch, 
I A U, 14778-93855 Tehran, Iran.

On Sun, May 8, 2016 at 12:06 AM, ashkan shekaari  wrote:
  Dear experts,
in quantum mechanics, the quantum number m is between -l and l : -l<=m<=l

and so m=-1, 0, +1. but in the output of a pdos calculation, values of m 

are seen as follows:

     state #   9: atom   1 (Mo ), wfc  5 (l=2 m= 1)
     state #  10: atom   1 (Mo ), wfc  5 (l=2 m= 2)
     state #  11: atom   1 (Mo ), wfc  5 (l=2 m= 3)
     state #  12: atom   1 (Mo ), wfc  5 (l=2 m= 4)
     state #  13: atom   1 (Mo ), wfc  5 (l=2 m= 5)

Is, for example,  (l=2 , m= 1) equivalent to m=-2 or 

     (l=2 m= 1)-->  m=-2
     (l=2 m= 2)-->  m=-1
      (l=2 m= 3)-->  m=0
      (l=2 m= 4)-->  m=1
      (l=2 m= 5)-->  m=2

?

--
All the best,
Ashkan Shekaari
Plasma Physics Research Center, Science and Research Branch, 
I A U, 14778-93855 Tehran, Iran.



___
Pw_forum mailing list
Pw_forum@pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum

Re: [Pw_forum] Consulting for the calculation of band structure with pwscf

[Ari P Seitsonen]

Hello ???, [no affiation, not even name;
 http://www.quantum-espresso.org/forum/#1.0, "Sign your post with your name and 
affiliation."]

  Adding to the comment of Ridwan Agbaoye, I also agree that I did not 
fully understand for what you meant; I would at least specify the units of 
the k points in the calculation of the bands. Maybe you mean why no 
symmetries are found to each band (or, all bands have the simple 
representation 'A'), or that there are no degeneracies in the bands?


  To start with, did you look at the output of the self-consistent run? I 
tried your file (with reduced number of k points, to make it faster), and 
I see


  2 Sym. Ops., with inversion, found

I would have expected to see more, maybe there is a reason to that? 
Further down,


-
 Forces acting on atoms (Ry/au):

 atom1 type  2   force = 0.072954360.11942494   93.95848463
 atom2 type  2   force =-3.835456509.13148686  -74.40161511
 atom3 type  2   force =-0.07295436   -0.11942494  -93.95848463
 atom4 type  2   force = 3.83545650   -9.13148686   74.40161511
 atom5 type  1   force = 6.08077747  -11.27416034  -50.44274724
 atom6 type  1   force =-6.08077747   11.27416034   50.44274724

 Total force =   185.313058 Total SCF correction = 0.000351


 entering subroutine stress ...

  total   stress  (Ry/bohr**3)   (kbar) P=
   1.36208034   0.77578489  -0.05878813 200368.90 114121.88  -8648.03
   0.77578489   2.34432579   0.10345704 114121.88 344862.17  15219.05
  -0.05878813   0.10345704   4.69893799  -8648.03  15219.05 691237.53
-

These are astronomically large values, something must be wrong in your 
structure. Did you try to visualise your initial structure? (keyword 
"XCrysDen", for example)  They look wrong to me - maybe you got confused 
with the default units of the coordinates in 'pw.x'? Going to crystal 
coordinates looks more like it (there are also more symmetries, which 
usually means more physical structure). Still the atoms look to be very 
close - do you know what the units of length are when specifying 
'celldm()'? I tend to use 'a'/'b'/'c' for this reason - even if the 
meaning of 'celldm(2:6)' is different.


  Maybe those will help; after that I would still spend some time trying 
to understand what is the _expected_ symmetry group, and why you might 
have fewer symmetries than that (some further hint: "verbosity = 'high'" 
to have more output, also including longer output of the symmetry 
operations; and then the number of digits for the coordinates).


  And after these exercises, I wonder why you have coordinates 0.36 for a 
kpoints - is quite close to 1/3 though... ;)


Good Luck and Happy QE'ing,

   apsi

PS^1 I still do not understand why people want to run hexagonal cell with 
laterally shifted k points in self-consistent calculations. :)  Well, up 
to them


PS^2 I consider using "outdir = '.'" quite confusing, I would recommend 
you to use some specific directory (my favourite choice is './scratch/', 
which on computers with a dedicated/faster disc space is a symbolic link 
to that file system)


-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-
  Ari Paavo Seitsonen / ari.p.seitso...@iki.fi / http://www.iki.fi/~apsi/
Ecole Normale Supérieure (ENS), Département de Chimie, Paris
Mobile (F) : +33 789 37 24 25(CH) : +41 79 71 90 935


On Thu, 5 May 2016, mp...@ncsu.edu wrote:


  Hi,
I am trying to calculate the band structure of tungsten sulfide. Aattachments 
are my input files. I input these
commands:

    pw.x  ws2.cry.scf.out
    pw.x  ws2.cry.band.out
    bands.x  ws2.cry.bands.out
I understand my k path in the second input file in not symmetric, and I am 
learning how to generate a symmetric path.
But to my surprise, the k points in file ws2cry.dat have nothing to do with the 
k points in the second input file. I
tried to modify the k points for both input files for multiple times, and I 
found the k points of ws2cry.dat depends on
the first input file only, with some additionally points generated by ESPRESSO 
to satisfy symmetry. Besides, there are
26 bands in ws2cry.dat, which is different from my setting where nbnd = 28.
I tried the band structure of fcc Cu before, and the k points in my dat file 
are identical with those in the band input
file. I do not understand why it does not work for ws2.
I am a beginner, and I really need your help. Please forgive me if you think my 
questions are too silly.
Thank you for your help, and I am really looking forward to your reply.

__

Re: [Pw_forum] Data arrangement in cube file generated by QE

[Ari P Seitsonen]

Dear Reza [affiliation?],

  If you have not found it yet, please see for example the official 
documentation at Gaussian.com, or http://paulbourke.net/dataformats/cube/ 
seems to be very good. It is "funny" that the three loops over the grid 
are in the "wrong" order, or let us say that in the opposite order from 
that what one would usually expect.


Greetings from Paris,

   apsi

-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-
  Ari Paavo Seitsonen / ari.p.seitso...@iki.fi / http://www.iki.fi/~apsi/
Ecole Normale Supérieure (ENS), Département de Chimie, Paris
Mobile (F) : +33 789 37 24 25(CH) : +41 79 71 90 935


On Thu, 28 Apr 2016, reza vatan wrote:


Dear all,

I'm using Quantum Espresso to generate electrostatic potential map in a cube 
file format, but I'm not sure how the grid data 
is arranged in the generated cube file. Could any one please help me to 
understand these data arrangement?

Following is the typical format of the cube file generated by QE.

~~
. . .
. . .
. . .
0.64081E+00  0.61382E+00  0.47140E+00  0.26001E+00 -0.21555E-02 -0.28997E+00
 -0.38866E+00 -0.24394E+00  0.57880E-02  0.22743E+00  0.40169E+00  0.53083E+00
  0.60580E+00  0.65390E+00  0.69301E+00  0.69229E+00  0.65015E+00  0.54336E+00
  0.34993E+00  0.50902E-01 -0.44137E+00 -0.96727E+00 -0.11918E+01 -0.92172E+00
 -0.37681E+00  0.13135E+00  0.38158E+00  0.55621E+00  0.55922E+00  0.46486E+00
  0.34838E+00  0.27159E+00  0.27171E+00  0.34192E+00  0.43531E+00  0.53276E+00
  0.59288E+00  0.61644E+00  0.61473E+00  0.60359E+00  0.60592E+00  0.60949E+00
  0.62433E+00  0.64255E+00  0.64860E+00
  0.70080E+00  0.67077E+00  0.61035E+00  0.47476E+00  0.34814E+00  0.22304E+00
  0.17583E+00  0.15350E+00  0.20507E+00  0.30341E+00  0.40159E+00  0.49777E+00
  0.59071E+00  0.63163E+00  0.66700E+00  0.67871E+00  0.62231E+00  0.50685E+00
  0.26470E+00 -0.17819E+00 -0.94059E+00 -0.18196E+01 -0.22336E+01 -0.17183E+01
 -0.82710E+00 -0.81849E-01  0.30226E+00  0.50429E+00  0.46462E+00  0.30476E+00
  0.11341E+00 -0.50208E-01 -0.57036E-01  0.88787E-01  0.29274E+00  0.45146E+00
  0.57254E+00  0.60594E+00  0.64278E+00  0.65667E+00  0.67023E+00  0.68294E+00
  0.67795E+00  0.68056E+00  0.70079E+00
  0.73881E+00  0.69610E+00  0.67892E+00  0.60824E+00  0.53767E+00  0.43530E+00
  0.32806E+00  0.23262E+00  0.21444E+00  0.22629E+00  0.29974E+00  0.41133E+00
  0.53259E+00  0.60957E+00  0.65101E+00  0.66303E+00  0.60060E+00  0.48269E+00
  0.23573E+00 -0.23816E+00 -0.10918E+01 -0.21159E+01 -0.26154E+01 -0.19800E+01
 -0.95826E+00 -0.17024E+00  0.28844E+00  0.45849E+00  0.36552E+00  0.13739E+00
 -0.20048E+00 -0.49471E+00 -0.50082E+00 -0.23353E+00  0.12178E+00  0.36455E+00
  0.56008E+00  0.62601E+00  0.67359E+00  0.70136E+00  0.69873E+00  0.71362E+00
  0.71695E+00  0.72155E+00  0.73383E+00
 . . .
 . . .
 . . .
~~


Thanks in advances,
Reza

___
Pw_forum mailing list
Pw_forum@pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum

Re: [Pw_forum] too many g-vectors

[Ari P Seitsonen]

Dear Amir,

  First of all, I can give only very general answer. One point is that you 
are using the HGH pseudo potentials: I think that for oxygen you probably 
have to go to cut-off energies exceeding 100 Ry to get reasonable energies 
and forces, and the stress would probably need more; I do not know if Na 
would need even more, if it has the semi-core electrons in the valence. 
Have you tested that you have at least some kind of convergence in the 
values of the pressure?


  Getting these kind of errors as you receive might mean that the cell 
changes too much from the initial cell; did you check for how big the 
stresses are in the initial geometry, even after the calculation 'relax' 
(in case you printed out the stress tensor)? If those are veryveryvery 
large, you could try to relax the cell first "by hand", along the large 
components of the stress tensor. I do not know if increasing the value of 
the variable 'cell_factor' from the default 1.2 could help. I would start 
by increasing the cut-off energy (no need to specify 'ecutrho') and 
studying the stress tensor.


Greetings from Sunny Paris,

   apsi

-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-
  Ari Paavo Seitsonen / ari.p.seitso...@iki.fi / http://www.iki.fi/~apsi/
Ecole Normale Supérieure (ENS), Département de Chimie, Paris
Mobile (F) : +33 789 37 24 25(CH) : +41 79 71 90 935


On Tue, 26 Apr 2016, Mofrad, Amir Mehdi (MU-Student) wrote:



Dear all QE users and developers,


I want to do a cell optimization (vc-relax) but I keep getting the following 
error:

 task # 0
 from ggen : error #   150
 g-vectors missing !
I also have tried changing the ecutwfc as well yet, It gives me the same error. 
When I look at the output file it seems that
it has finished the optimization but it's not able to run the last SCF step 
using the final coordinates. Also when I visualize
it in Xcrysden, the structure distorts significantly which may not be 
reasonable.


Here is my input file in case you might need to take a look at. Any help would 
be thoroughly appreciated.

 
 calculation = 'vc-relax' ,
    restart_mode = 'from_scratch' ,
  wf_collect = .true. ,
  outdir = './scratch' ,
  wfcdir = './scratch' ,
  pseudo_dir = '/global/espresso/pseudo' ,
  prefix = 'SOD' ,
   verbosity = 'high' ,
   etot_conv_thr = 1e-5 ,
   forc_conv_thr = 1e-4 ,
   nstep = 50 ,
 tstress = .true. ,
 tprnfor = .true. ,
 /
 
   ibrav = 0,
 nat = 41,
    ntyp = 4,
 ecutwfc = 60 ,
 ecutrho = 240 ,
 /
 
    electron_maxstep = 100,
    conv_thr = 3e-8 ,
 mixing_mode = 'plain' ,
 mixing_beta = 0.2 ,
 diagonalization = 'david' ,
 /
 
    ion_dynamics = 'bfgs' ,
    trust_radius_ini = 0.5 ,
/

    cell_dynamics='bfgs',
    cell_factor=6,
 /
CELL_PARAMETERS angstrom
 9.000    0.000    0.000
 0.000    9.000    0.000
 0.000    0.000    9.000
ATOMIC_SPECIES
   Si   28.08600  Si.pz-hgh.UPF
    O   15.99940  O.pz-hgh.UPF
    Al  26.981539 Al.pz-hgh.UPF
    Na  22.989769 Na.pz-hgh.UPF
ATOMIC_POSITIONS angstrom
Si   2.21200   0.0   4.42400
Si   6.63600   0.0   4.42400
Si   4.42400   2.21200   0.0
Si   4.42400   6.63600   0.0
Si   0.0   4.42400   2.21200
Si   0.0   4.42400   6.63600
Si   2.21200   4.42400   0.0
Al   6.63600   4.42400   0.0
Al   0.0   2.21200   4.42400
Al   0.0   6.63600   4.42400
Al   4.42400   0.0   2.21200
Al   4.42400   0.0   6.63600
O   1.20864   3.83826   1.31835
O   7.63936   5.00974   1.31835
O   7.63936   3.83826   7.52965
O   1.20864   5.00974   7.52965
O   1.31835   1.20864   3.83826
O   1.31835   7.63936   5.00974
O   7.52965   7.63936   3.83826
O   7.52965   1.20864   5.00974
O   3.83826   1.31835   1.20864
O   5.00974   1.31835   7.63936
O   3.83826   7.52965   7.63936
O   5.00974   7.52965   1.20864
O   8.26226   5.63264   5.74235
O   0.58574   3.21536   5.74235
O   8.26226   3.21536   3.10565
O   0.58574   5.63264   3.10565
O   5.63264   5.74235   8.26226
O   3.21536   5.74235   0.58574
O   3.21536   3.10565   8.26226
O   5.63264   3.10565   0.58574
O   5.74235   8.26226   5.63264
O   5.74235   0.58574   3.21536
O   3.10565   8.26226   3.21536
O   3.10565   0.58574   5.63264
Na   7.51726   1.33074   7.51726
Na   1.33074   7.51726   7.51726
Na   5.75474   5.75474   5.75474
Na   5.75474   3.09326   3.09326
Na   3.09326   5.75474   3.09326

K_POINTS automatic
  2 2 2   1 1 1


P.S. When I do the same simulation with relax instead of vc-relax it runs well 
without any error. However, my task is to do
cell optimization 

Re: [Pw_forum] Phonon of ScN

[Ari P Seitsonen]

Dear Sohail Ahmad,

  Did you treat the LO-TO splitting? The material seems to have very large 
splitting, in the article that you cite 335 cm-1, even if the band gap 
is very small. If not, you can see for example the end of

http://people.sissa.it/~degironc/QE-Tutorial/tutorial_phon.htm
on how to calculate that with QE/pw.x+ph.x.

Greetings from Paris,

   apsi

-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-
  Ari Paavo Seitsonen / ari.p.seitso...@iki.fi / http://www.iki.fi/~apsi/
Ecole Normale Supérieure (ENS), Département de Chimie, Paris
Mobile (F) : +33 789 37 24 25(CH) : +41 79 71 90 935


On Sat, 23 Apr 2016, Sohail Ahmad wrote:


Dear All,
I am trying to calculate phonon frequencies of ScN,
but i am not getting as reported by Prof Umesh Waghmare group
Journal of Applied Physics, 107, 03715 (2010)
Electronic structure, phonons and thermal properties of ScN, ZrN and HfN

I am not getting any frequency around 600 cm-1.
Pls check and suggest any mistakes
-
Output (and input )of my calculation at Gamma for ScN is as follows

q = (    0.0   0.0   0.0 )

 **
 freq (    1) =   0.073720 [THz] =   2.459027 [cm-1]
 freq (    2) =   0.312948 [THz] =  10.438836 [cm-1]
 freq (    3) =   0.312948 [THz] =  10.438836 [cm-1]
 freq (    4) =  10.407119 [THz] = 347.144126 [cm-1]
 freq (    5) =  10.472361 [THz] = 349.320372 [cm-1]
 freq (    6) =  10.472361 [THz] = 349.320372 [cm-1]
 **

 Mode symmetry, C_3v (3m)   point group:

 freq (  1 -  1) =  2.5  [cm-1]   --> A_1  L_1    I+R
 freq (  2 -  3) = 10.4  [cm-1]   --> E    L_3    I+R
 freq (  4 -  4) =    347.1  [cm-1]   --> A_1  L_1    I+R
 freq (  5 -  6) =    349.3  [cm-1]   --> E    L_3    I+R
 
--

   ibrav=2,
   a=4.501,
   nat=2, ntyp=2,
   ecutwfc = 250, ecutrho = 1000,
   nbnd=15,
   occupations = 'smearing', smearing = 'gaussian', degauss = 0.001,
   nspin = 2,
   starting_magnetization(1)=0.1d0,
  /
 
    conv_thr =  1.0d-9,
    mixing_beta = 0.3,
 /
 ATOMIC_SPECIES
  Sc 44.956   Sc.pw91-nsp-van.UPF
  N  14.007   N.pw91-van_ak.UPF
 ATOMIC_POSITIONS {angstrom}
 Sc  -0.044377705  -0.044377705  -0.044377705
 N    2.294877705   2.294877705   2.294877705
 K_POINTS automatic
12 12 12 1 1 1

 
 tr2_ph = 1.0d-16,
 amass(1) = 44.956,
 amass(2) = 14.007,
 prefix = 'ScN',
 !epsil=.true.,  ! set this to true for polar semiconductors !
 outdir = '/scratch/ScN-scf-30591'
 fildyn = 'ScN.dynG',
/
0.0  0.0  0.0

-
Dr. Sohail Ahmad
King Khalid UniversityAbha, Saudi Arabia


___
Pw_forum mailing list
Pw_forum@pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum

Re: [Pw_forum] more patches

[Ari P Seitsonen]

Dear David [affiliation?], Paolo et alia,

  Just an innocent question: How many compilers do _not_ have an internal 
pre-processor these days or are not able to use an external one? I was 
compiling .F90 files some 10-15 years ago with automatic pre-processing, 
without the need of intermediate files, is it true that the compilers 
would not have adapted a default pre-processor up to now? Well, probably 
there are some compilers still around which might not have this built in, 
would it be possible to treat them as "special cases" and create these 
intermediate files for them as needed?


Greetings,

   apsi

-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-
  Ari Paavo Seitsonen / ari.p.seitso...@iki.fi / http://www.iki.fi/~apsi/
Ecole Normale Supérieure (ENS), Département de Chimie, Paris
Mobile (F) : +33 789 37 24 25(CH) : +41 79 71 90 935


On Sun, 24 Apr 2016, David Strubbe wrote:


Hi Paolo,
My point about cpp is: Octopus (and some other codes) have been using this 
approach for many years on a variety of platforms. So, I don't see any reason 
it would cause trouble
for any compilers. The issue for OSX I mention is related to the filesystem and 
is independent of the compiler.

David

On Fri, Apr 22, 2016 at 4:42 PM, Paolo Giannozzi  wrote:
  First two corrections done, thank you.

I recommend changing the name of your output from cpp runs to 
something other than .F90, since on a case-insensitive filesystem (default for 
Mac OSX)
this is the same as the .f90 input file, which makes the 
compilation fail. For example, in the Octopus project we use _oct.f90.


For this, we should figure out first if such change is harmless for all other 
compilers

Paolo

--
Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222


___
Pw_forum mailing list
Pw_forum@pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum



___
Pw_forum mailing list
Pw_forum@pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum

Re: [Pw_forum] phonon

[Ari P Seitsonen]

Dear [?? Please remember the name and affiliation next time]

  "perfix"?

Greetings from Paris,

   apsi

-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-
  Ari Paavo Seitsonen / ari.p.seitso...@iki.fi / http://www.iki.fi/~apsi/
Ecole Normale Supérieure (ENS), Département de Chimie, Paris
Mobile (F) : +33 789 37 24 25(CH) : +41 79 71 90 935

On Sat, 23 Apr 2016, azadeh aezami wrote:


HiPlease help me solve the following error


#phA.in

  
 
tr2_ph=1.0d-14,
 
perfix='LMO-SMO-phonon',
 
amass(1)=54.938045,
 
amass(2)=54.938045,
 
amass(3)=138.90547,
 
amass(4)=87.62,
 
amass(5)=15.9994,
 
outdir='/home/asus/Desktop/phonon/A/scratch/',
 
fildyn='LMO-SMO.dynA',
 
/ 
 
0.0 0.0 0.5
 



ERROR IS:

 Program PHONON v.4.3.2     
starts on 23Apr2016 at 16:50:22 

     
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/wiki/index.php/Citing_Quantum-ESPRESSO

     
Parallel version (MPI), running on     1 processors

     Ultrasoft (Vanderbilt) Pseudopotentials

 %%
     
from phq_readin : error #      5010
     
reading inputph namelist
 %%

   
  stopping ...



___
Pw_forum mailing list
Pw_forum@pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum

Re: [Pw_forum] the symmetry problem in calculating phonon frequency of wurtzite AlN

[Ari P Seitsonen]

Dear ??, [ Please notice the humble rules how to post to the list: 
Affiliation ]


  I am not the best expert here, but I presume that you refer to the space 
group C_6v, but QE/pw.x only finds the point group C_3v. I am not sure 
whether the phonon code could handle the translations (probably not), but 
I do not think that this should lead to any serious differences between 
the two symmetry groups (in particular since you are using a 
more-than-sufficient 'ecutwfc'; well, I do not know whether it would be 
better to reduce that and use a value for 'ecutrho' of typical 6-8 times 
'ecutwfc'). How large is your deviation from the "reference" (what do you 
use as reference?)? Did you consider the LO-TO splitting? You have quite 
few k points - and once again, using the lateral shift of k points in a 
hexagonal cell "spoils" the symmetries - sorry for repeating this, but it 
does not seems to be clear to the wide community.


Greetings from Sunny Paris,

   apsi

-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-
  Ari Paavo Seitsonen / ari.p.seitso...@iki.fi / http://www.iki.fi/~apsi/
Ecole Normale Supérieure (ENS), Département de Chimie, Paris
Mobile (F) : +33 789 37 24 25(CH) : +41 79 71 90 935


On Tue, 12 Apr 2016, wz wrote:


Dear all,

I am trying to calculate the phonon frequency of wurtzite AlN in gamma
point?? i try to use the input files as PHonon/examples/example01/ in
Quantum Espresso. The symmetry of wurtzite AlN is C6v, but in the output of
my calculation, the symmetry is C3v so that the phonon frequency get by my
work do not correspond with that get by reference.  
I want to know that if there is a way in quantum espresso to specify the
symmetry? or some other method to get the right symmetry in phonon
calculation?
===
pw input
 
    ibrav= 4, celldm(1)= 5.8804, nat= 4, ntyp= 2,
    celldm(3) = 1.600724
    ecutwfc = 160
 /
 
    conv_thr =  1.0d-8
    mixing_beta = 0.7
 /
ATOMIC_SPECIES
    Al   26.982  Al.pbesol-n-kjpaw_psl.0.1.UPF
    N    14.007  N.pbesol-n-kjpaw_psl.0.1.UPF
ATOMIC_POSITIONS crystal
    Al  0.33343         0.66687         0.0
    Al  0.66627         0.33313         0.5
    N   0.33343         0.66687         0.381929994
    N   0.66627         0.33313         0.881929994
       
K_POINTS automatic
2 2 1 1 1 1  
--
ph input

phonons of aln at Gamma
 
  tr2_ph=1.0d-14,
  prefix='aln',
  epsil=.true.,
   outdir='/tmp',
   fildyn='aln.dyn',
 /
0.0 0.0 0.0

___
Pw_forum mailing list
Pw_forum@pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum

Re: [Pw_forum] mos2

[Ari P Seitsonen]

Dear Ashkan,

  First on your band structures, apparently you have aligned the zero of 
energy, on the vertical axis, somewhat differently. But overall, maybe 
they are correct. I guess that in the "super-cell" you refer the k points 
(Gamma, M, K) to the corresponding reciprocal lattice vectors, so that 
actually M_sc = 1/2 M_uc. And at K_sc you obtain the same gap as at K_uc, 
because the latter is actually K'_sc; shortly, K = (1/3,1/3,0) and K' = 
(-1/3,-1/3,0) = (2/3,2/3,0) (in units of the reciprocal lattice vectors), 
and since K_sc = 1/2 K_uc, also K'_sc = 1/2 K'_uc = K_sc. It might need a 
bit of drawing hexagons, before this become clear. :)


  Back-folding, since in a super-cell your lattice vectors in real space 
are longer, in reciprocal space they are correspondingly shorter (let us 
call them b1_sc and b2_sc). And since you have the periodicity also in the 
reciprocal space, the Brillouin zone is smaller and you have for 
example many more "Gamma points", Gamma_sc, in the original Brillouin 
zone of the "unit cell". So for example in your case, 2x2, b1_sc = 1/2 
b1_uc = M_uc. So you should obtain the same bands in the super-cell at the 
point Gamma_sc as M_uc. Thus I would see the bands at ca -1.6 and -2.1 eV 
at M_uc as the bands -1.3 and -1.7 eV at Gamma_sc. The band beginning at 
Gamma_uc and going toward 1/2 K_uc, that is also seen Gamma_sc-K_sc. And 
so on. But not only those, you see more bands because of the two 
two-dimensionality of your band structure.


  But to start understanding back-folding I would start by looking at a 
band structure in one dimension: You can take for example a cos(k) 
function, which mimics the dispersion of the s-type band (one can look up 
in a solid-state book why so). When you double the real-space unit cell, 
you can divide the reciprocal unit cell, so you cut the band at mid-point 
between the minimum at Gamma and maximum at X (if that is 1/2 b, you 
reciprocal lattice vector, or if you want to call it "M") and "fold it 
back", going away from the 1/2 X point toward Gamma again but with the 
same energy dependence as before: e(k) = e(X-k). Thus you get two bands in 
the new Brillouin zone, and they have the same energy at the point 1/2 X. 
Or you can go through the exercise of having a super-cell consisting of 
two atoms in the real-space cell, and when you make the atoms as 
identical, the band structure will be as the one of the super-cell, 
naturally.


  Well, this is certainly much more clearly explained in some text books 
or lecture notes. :)


Greetings,

   apsi

PS Indeed, I would also learn how to use a consistent alignment of 
energies in the case of periodic systems with a band gap. Hint: Either 
mid-gap or top of valence band as the reference


-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-
  Ari Paavo Seitsonen / ari.p.seitso...@iki.fi / http://www.iki.fi/~apsi/
Ecole Normale Supérieure (ENS), Département de Chimie, Paris
Mobile (F) : +33 789 37 24 25(CH) : +41 79 71 90 935


On Wed, 6 Apr 2016, ashkan shekaari wrote:


Dear Ari,
I obtained the bands below via routine calculations (without back-folding). Is 
something wrong with my calculations?

What do you mean back-folding?

On Wed, Apr 6, 2016 at 9:30 PM, Ari P Seitsonen <ari.p.seitso...@iki.fi> wrote:

  Dear Ashkan,

    Yes, due to back-folding - unless you perform the "back-folding". Jonas 
Björk told me that they have a public code for doing this and it should
  also work with QE (I have not tried it myself though, even if I should 
have applied it recently - sorry Jonas!)

      Greetings,

         apsi

  
-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-
    Ari Paavo Seitsonen / ari.p.seitso...@iki.fi / http://www.iki.fi/~apsi/
      Ecole Normale Supérieure (ENS), Département de Chimie, Paris
      Mobile (F) : +33 789 37 24 25    (CH) : +41 79 71 90 935


  On Wed, 6 Apr 2016, ashkan shekaari wrote:

Dear QE users,
Does the 2*2 supercell of mos2 monolayer have a different band 
structure than that of the single unit cell?


--
Best regards,
Ashkan Shekaari
Plasma Physics Research Center, Science and Research Branch, 
I A U, 14778-93855 Tehran, Iran.
Mobile: +98 (933) 459 7122


___
Pw_forum mailing list
Pw_forum@pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum




--
Best regards,
Ashkan Shekaari
Plasma Physics Research Center, Science and Research Branch, 
I A U, 14778-93855 Tehran, Iran.
Mobile: +98 (933) 459 7122

___
Pw_forum mailing list
Pw_forum@pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum

Re: [Pw_forum] mos2

[Ari P Seitsonen]

Dear Ashkan,

  Yes, due to back-folding - unless you perform the "back-folding". Jonas 
Björk told me that they have a public code for doing this and it should 
also work with QE (I have not tried it myself though, even if I should 
have applied it recently - sorry Jonas!)


Greetings,

   apsi

-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-
  Ari Paavo Seitsonen / ari.p.seitso...@iki.fi / http://www.iki.fi/~apsi/
Ecole Normale Supérieure (ENS), Département de Chimie, Paris
Mobile (F) : +33 789 37 24 25(CH) : +41 79 71 90 935


On Wed, 6 Apr 2016, ashkan shekaari wrote:


Dear QE users,
Does the 2*2 supercell of mos2 monolayer have a different band structure than 
that of the single unit cell?


--
Best regards,
Ashkan Shekaari
Plasma Physics Research Center, Science and Research Branch, 
I A U, 14778-93855 Tehran, Iran.
Mobile: +98 (933) 459 7122
___
Pw_forum mailing list
Pw_forum@pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum

Re: [Pw_forum] VC_relax

[Ari P Seitsonen]

Dear Vishal Gupta,

  Your cut-off energy looks _very_ low, no matter which elements/pseudo 
potentials you do employ. Probably your system becomes metallic upon the 
relaxation, so I would include some kind of broadening of the occupation 
numbers, in addition possibly using the mixing mode 'local-TF', if you 
have vacuum in your system.


Greetings,

   apsi

-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-
  Ari Paavo Seitsonen / ari.p.seitso...@iki.fi / http://www.iki.fi/~apsi/
Ecole Normale Supérieure (ENS), Département de Chimie, Paris
Mobile (F) : +33 789 37 24 25(CH) : +41 79 71 90 935


On Thu, 31 Mar 2016, Vishal Gupta wrote:


Hi all,I've been running a vc_relax calculation on a 40 atom system. The 
calculation works fine for some
cycles. The total force had come down to 0.108. After some time. the force 
started increasing and now the
iterations don't converge even in 400 steps. The input file is
 /
 
                       ibrav = 0,
                         nat = 40,
                        ntyp = 1,
                     ecutwfc = 12 ,
 /
 
                 mixing_beta = 0.3 ,
             diagonalization = 'david' ,
             electron_maxstep = 200 ,
 /

[/]
/

cell_dynamics= 'sd' ,
cell_dofree='xy' ,
/

CELL_PARAMETERS angstrom
    22.265358047804796    0.000    0.000
     0.000   11.131216979724510    0.000
     0.000    0.000   10.000

P.S. Ive tried changing cell dynamics to 'damp-pr' , 'sd' and 'damp-w', but the 
same problem persists.
Can anybody Please help me identifying the mistake ?
Thank You.
Best Regards,
Vishal Gupta

B.Tech. 3rd year Mechanical

Indian Institute of Technology Ropar
Rupnagar (140001), Punjab, India.
Email :- vishal.gu...@iitrpr.ac.in
RMML, IIT Ropar



[487a748cedfb942f92401d52262f336d11784524388949.png]

___
Pw_forum mailing list
Pw_forum@pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum

Re: [Pw_forum] Generating K points for Wurzite Structure using crystal_b

[Ari P Seitsonen]

Dear Mustapha,

  Adding to the comment of M V Kondrin, some comments: I also do not 
understand why you no longer have the exact hexagonal symmetry laterally; 
further, ecutrho => 4 * ecutwfc, otherwise you might get some nasty 
effects (your input does not reveal which pseudo potentials/PAW data sets 
you were employing); why using the cold smearing if the system would 
probably be semi-conducting or even insulating; and the k point with high 
symmetry would actually be (1/3,1/3,0), not (0.3,0.3,0).


Greetings from Paris,

   apsi

-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-
  Ari Paavo Seitsonen / ari.p.seitso...@iki.fi / http://www.iki.fi/~apsi/
Ecole Normale Supérieure (ENS), Département de Chimie, Paris
Mobile (F) : +33 789 37 24 25(CH) : +41 79 71 90 935


On Thu, 31 Mar 2016, lateef mustapha wrote:


Dear QE Users, I just successfully generated the k points for plotting the band 
structure of a wurzite structure. The crystal direction of the calculated are 
approximated and I guess that was the reason why my band dispersion were fairly 
distorted. Any advice ?
see Input file below

Reading   16 bands at 91 k-points
Range:   -9.1640   28.7880eV  Emin, Emax > -9.164 28.788
high-symmetry point:  0. 0. 0.   x coordinate   0.
high-symmetry point:  0. 0. 0.3019   x coordinate   0.3019
high-symmetry point:  0.4993 0.2883 0.3019   x coordinate   0.8784
high-symmetry point:  0.4993 0.2883 0.   x coordinate   1.1803
high-symmetry point:  0. 0. 0.   x coordinate   1.7569
high-symmetry point:  0.2996 0.5189 0.   x coordinate   2.3561
high-symmetry point:  0.2996 0.5189 0.3019   x coordinate   2.6580


   restart_mode = 'from_scratch'
   tstress = .TRUE.,
   tprnfor = .TRUE. ,
   calculation = 'bands'
   pseudo_dir  = '/home/musty/esp/pseudo/PW91'
   prefix = 'BN'
/

   ibrav =  4,
   celldm(1) = 4.82,
   celldm(3) = 1.65,
   occupations='smearing' ,
   smearing='mp',
   nat =  4,
   ntyp = 2,
   nbnd = 16,
   degauss=0.06,
   ecutwfc = 65,
   ecutrho = 200,
/

   diagonalization='david'
   mixing_mode = 'plain'
   mixing_beta = 0.7
   conv_thr =  1.0d-8
/
ATOMIC_SPECIES
B  10.811
N  14.001

CELL_PARAMETERS (alat=  4.8200)
  1.001361289   0.0   0.0
 -0.500680645   0.867204315   0.0
  0.0   0.0   1.656271159

ATOMIC_POSITIONS (crystal)
B0.0   0.0   0.000317468
B0.66700   0.33300   0.500317468
N0.0   0.0   0.374682532
N0.66700   0.33300   0.874682532

K_POINTS crystal_b
7
0.0 0.0 0.0 10
0.0 0.0 0.5 20
0.5 0.0 0.5 10
0.5 0.0 0.0 20
0.0 0.0 0.0 20
0.3 0.3 0.0 10
0.3 0.3 0.5 1

Mustapha L.O
Graduate Student, University of Ibadan. Nigeria
___
Pw_forum mailing list
Pw_forum@pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum
___
Pw_forum mailing list
Pw_forum@pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum

Re: [Pw_forum] Fiorentini-Methefessel: Surface energy

[Ari P Seitsonen]

Dear Elliot,

  I am not sure if I understood correctly your description, but basically: 
You plot the energy per layer as a function of the inverse of number of 
layers, so starting from the definition


E_surf = [ E_slab(N) - N * E_bulk ] / ( 2 A ) ,

where

  Esurf = surface energy per unit area A - sometimes one plots the surface 
energy per unit cell; 2 because the slab has two surfaces,


  E_slab(N) = total energy of the slab of N layers

  E_bulk = the "unknown" bulk energy

Rewriting à la Fiorentini et Methfessel,

E_slab(N)/N = 2A (1/N) E_surf + E_bulk

which is equivalent of an equation

y = 2A E_surf x + E_bulk ^= a x + b

where E_surf and E_bulk are the unknowns, obtained from the fit. So how do 
you find E_bulk from this equation (hint: What happens when N -> 
infinity?)? And what does the slope yield?


Greetings from Paris,

   apsi

-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-
  Ari Paavo Seitsonen / ari.p.seitso...@iki.fi / http://www.iki.fi/~apsi/
Ecole Normale Supérieure (ENS), Département de Chimie, Paris
Mobile (F) : +33 789 37 24 25(CH) : +41 79 71 90 935


On Fri, 25 Mar 2016, Elliot S. MENKAH wrote:



Hello Everyone,

In reference to the papers Extracting convergent surface energies from slab 
calculations, 1996, and Surface e
nergies, work functions, and surface relaxations of low index metallic surfaces 
from first-principles, 2009,
 I'm trying to compute surface energies with the Fiorentini-Methefessel technique. 


I'm extracting the bulk energy from a linear plot of total energy vrs N.

I computed the total energies of nickel surface (100) with 12, 14, 16,
18 and 20 atomic layers.

I made a plot of total energies vrs N(Number of layers) and i got the
equation  y = 0.24897 - 171.79x

With the slope being -171.79, am I right to say the bulk energy is
-171.79Ry?

Is this the right way of going about the Fiorentini-Methfessel technique?

Can someone please point me in the right direction

Thank you.

Kind Regards,

Elliot.

--
Elliot Sarpong Menkah
Graduate Student - Computational Chemistry / Computational Material Science.
Theoretical and Computational Chemistry
Dept. of Chemistry
Kwame Nkrumah University of Science and Technology (KNUST),
Private Mail Bag,
Kumasi,
Ghana.
Mobile:+233-243-055-717,+233-202-929-058


Alt. Email: esmen...@knust.edu.gh
elliotsmen...@gmail.com
elliotsmen...@hotmail.com

webpage: http://chemistry.knust.edu.gh/MMC/group-members/ESMenkah

___
Pw_forum mailing list
Pw_forum@pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum

Re: [Pw_forum] cannot get .projwfc.x bin in 5.x version

[Ari P Seitsonen]

Dear Efi Dwi Indari,

  You could execute 'make pwall' or just 'make pw pp' instead of 'make 
all' (or 'make link'/'make neb' etc), that should be enough to give you 
the 'projwfc.x'.


  I am not sure if I understood the rest of your email... We have been 
conducting calculations on Ubuntu 14.04 for some time, well with 
self-compiled OpenMPI, SCALAPACK, BLAS/LAPACK etc, trying to minimise 
using the packages from Ubuntu itself (in the hope of better performance 
and to avoid all the confusion between different versions of MPIs).


Greetins from Sunny Paris,

   apsi

-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-
  Ari Paavo Seitsonen / ari.p.seitso...@iki.fi / http://www.iki.fi/~apsi/
Ecole Normale Supérieure (ENS), Département de Chimie, Paris
Mobile (F) : +33 789 37 24 25(CH) : +41 79 71 90 935


On Fri, 11 Mar 2016, efi dwi indari wrote:


Dear all,

*First of all I would like to mention that I use Ubuntu 14.04 OS*

I am now almost in the end of my calculation target. I would like to obtain
pdos graphs with projwfc.x bin. In the middle of calculation, I was running
out of memory then I moved all files from /home/... to /media/... After
moving, I executed the bin but permission was denied. Then I was thinking
that the execution should be in /home/... Thus, I cleaned up all files in my
/home/.. directory but it gave me the same warning: permission was denied.

Afterwards, I started all over from the very beginning. I downloaded the
.tar.gz from download page. Unfortunately, after ./configure and make all,
all 5.x versions did not give me projwfc.x executable bin.

The error is like these (I copied from warning error since the previous
lines are a lot and seems nothing going wrong):

fortran -O3 -g -x f95-cpp-input -D__GFORTRAN -D__STD_F95 -D__FFTW  
-I../include -I../../iotk/src -I../../Modules -I../src -I.  -c dist.f90
Warning: Nonexistent include directory "../include"

...

if test ! -d ../NEB; then \
    (gzip -dc ../archive/neb-5.2.0.tar.gz | (cd ../ ; tar -xvf -)) ; fi

gzip: ../archive/neb-5.2.0.tar.gz: not in gzip format
tar: This does not look like a tar archive
tar: Exiting with failure status due to previous errors
make[1]: *** [uncompress-neb] Error 2
make[1]: Leaving directory
`/home/efidwiindari/Downloads/espresso-5.2.0/install'
make: *** [neb] Error 1


Then I moved to espresso-4.3.2 and yes, I got it but after several
modification in the input file, (e.g.  as the namelist and
lsym=.true.) there was still error on the output file as shown below:

# FROM IOTK LIBRARY, VERSION 1.2.0
# UNRECOVERABLE ERROR (ierr=-1)
# ERROR IN: iotk_scan_dat (iotk_dat+CHARACTER1_0.f90:546)
# CVS Revision: 1.27
# Dat not found
name=CELL_SYMMETRY

and below is the input file


 outdir='/home/efidwiindari/Downloads/espresso-4.3.2/tempdir/FAPIks/',
 prefix='FAPIks',
 ngauss=-1,
 Emin=-19.0,
 Emax=8.0,
 deltaE=0.1,
 lsym=.true.
 filpdos='FAPIks.pdos'
/

I also have tried to copy the bin and after ./configure, I typed make links
since the link is broken (shown on the file type in the explorer). 

following is the error message on the terminal:

test -d bin || mkdir bin
( cd bin/ ; \
    rm -f *.x ; \
    for exe in ../*/*/*.x ../*/bin/* ; do \
        if test ! -L $exe ; then ln -fs $exe . ; fi \
    done ; \
    [ -f ../WANT/wannier/dos.x ] &&  ln -fs ../WANT/wannier/dos.x
../bin/dos_want.x ; \
    [ -f ../PP/src/dos.x ] &&  ln -fs ../PP/src/dos.x ../bin/dos.x ; \
    [ -f ../WANT/wannier/bands.x ] &&  ln -fs ../WANT/wannier/bands.x
../bin/bands_want.x ; \
    [ -f ../PP/src/dos.x ] &&  ln -fs ../PP/src/bands.x ../bin/bands.x ; \
    [ -f ../W90/wannier90.x ] &&  ln -fs ../W90/wannier90.x
../bin/wannier90.x ; \
    )
make: *** [links] Error 1

Any comment and/or suggestion on this issue would be really appreciated.
Thank you all for your time.

Best Regards,

Efi Dwi Indari
Research Assistant, Bandung Institute of Technology



___
Pw_forum mailing list
Pw_forum@pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum

Re: [Pw_forum] Shifted_Vs_Unshifted

[Ari P Seitsonen]

Dear Amir-who-is-missing-the-affiliation-in-the-post,

  A small clarification to Lorenzo's-who-did-not-even-sign-the-post 
answer, in principle both would mathematically give the same accuracy, but 
due to the pecularities in the density of states in particular regions of 
the Brillouin zone one or the other could lead to faster convergence, like 
Lorenzo wrote. Traditionally one tries to avoid the Gamma point, as one 
thinks that it is an "extreme point" in the band structure (it is a local 
minimum or maximum of each band, as their derivatives with respect to any 
direction in k space is zero). Earlier this was of more importance, when 
one could afford few k points and/or the systems were small, nowadays 
choosing one or the other is no longer that important, as the increased 
computing power makes the inclusion of more k points or larger cell 
easier.


  And just to bore all the reader of the Forum, I remind you that in 
hexagonal cell it is better to keep a Gamma-centred Monkhorst-Pack grid, 
as otherwise the k point grid will get symmetrised (if this would not be 
done, the grid would have a lower symmetry than the hexagonal cell 
itself).


  And for historical note, the original Monkhorst-Pack grid corresponds to 
the case "1 1 1", the shift was actually introduced later (when they were 
indeed notified about the problem in the hexagonal case; references are a 
Comment and Reply to Comment to the original Article of Monkhorst and 
Pack). So in this sense the convention in QE of "shifted" and "unshifted" 
k point sets are opposite to the ones of the original literature. :)


Greetings from Paris,

   apsi

-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-
  Ari Paavo Seitsonen / ari.p.seitso...@iki.fi / http://www.iki.fi/~apsi/
Ecole Normale Supérieure (ENS), Département de Chimie, Paris
Mobile (F) : +33 789 37 24 25(CH) : +41 79 71 90 935


On Tue, 8 Mar 2016, Lorenzo Paulatto wrote:



If you use 1's the grid will be shifted by half its step, this makes the 
integrals of the grid convergence faster in some cases.

On 8 Mar 2016 8:51 p.m., "Mofrad, Amir Mehdi (MU-Student)" 
 wrote:

  Dear all QE users and developers,


  I have a question about the K_POINTS card in the input file. What is the 
difference between using shifted (1 1 1) and unshifted (0 0 0)?


  Best,



  Amir M. Mofrad


___
Pw_forum mailing list
Pw_forum@pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum


___
Pw_forum mailing list
Pw_forum@pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum

Re: [Pw_forum] Binding Energy for H2O with PAW

[Ari P Seitsonen]

Dear Felix,

  Just a quick comment on PANG Rui's response: It is true that those 
approximations should be closer to the correct value, but at most only 
about 20-25 %; this is how much Hartree-Fock exchange is mixed to the GGA 
exchange. The correlation functional remains the same, so the "gain" might 
be even smaller. And not to mention the HUGE computational effort one 
would spend; in such cases plane wave basis set is not a good idea for an 
isolated water molecule, better would be a code based on localised basis 
sets.


  Just my small note.

Greetings,

   apsi

-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-
  Ari Paavo Seitsonen / ari.p.seitso...@iki.fi / http://www.iki.fi/~apsi/
Ecole Normale Supérieure (ENS), Département de Chimie, Paris
Mobile (F) : +33 789 37 24 25(CH) : +41 79 71 90 935


On Fri, 26 Feb 2016, 庞瑞(PANG Rui) wrote:


Dear Felix
If I am correct, PBE contains self-interaction error, that means it may give a 
wrong number when you use it to calculate a single electron system such as 
hydrogen. Mayben you
could try B3LYP or HSE.
Best wishes





--
[viewfile?type=logo=sustc.edu.cn]

庞瑞(PANG Rui)

South University of Science and Technology of China/Department of Physics

No.1088,Xueyuan Road, Shenzhen,Guangdong

 
 
 
-- Original --
From:  "Felix Brockherde";
Date:  Fri, Feb 26, 2016 09:31 PM
To:  "Pw_forum";
Subject:  [Pw_forum] Binding Energy for H2O with PAW
 
Dear all,

We would like to calculate the binding energy for non-equilibrium H2O 
geometries with PAW pseudo potentials.

The initial thought was to calculate the single-atom energies. However, for H 
the system becomes metallic. We used smearing but the results seem too far from 
the experimental
value for us to use them (-0.91784682 Ry).

Now, we would like to calculate the binding energy by separating the H2O 
molecule as far as necessary. We would thus avoid inaccuracies caused by 
smearing because it is not a
metallic system. However, when pulling H2O apart, the DFT calculations do not 
converge.
Can anybody help with either how to get the separated H2O converged or a 
different approach to get the binding energy with PAW pseudo potentials?

We used PWSCF v.5.1.1 and I attached an input file where QE does not converge.

Best regards,
Felix Brockherde
TU Berlin

 
    calculation = 'scf',
    wfcdir = 'tmp',
    pseudo_dir = '/home/user/pseudo_potentials',
    tprnfor = .true.,
    prefix = 'prefix',
    tstress = .false.,
    outdir = './',
    wf_collect = .true.,
 /
 
    nat = 3,
    ntyp = 2,
    ecutwfc = 90,
    ecutrho = 360,
    celldm(1) = 30,
    ibrav = 1,
 /
 
 /
ATOMIC_SPECIES
    H 1.00794 H_pbe-kjpaw_psl.0.1.UPF
    O 15.9994 O_pbe-kjpaw_psl.0.1.UPF
ATOMIC_POSITIONS alat
    O 0.5 0.3 0.5
    H 0.5 0.7 0.3
    H 0.5 0.7 0.7
K_POINTS automatic
   1 1 1   0 0 0

___
Pw_forum mailing list
Pw_forum@pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum

Re: [Pw_forum] Binding Energy for H2O with PAW

[Ari P Seitsonen]

Dear Felix,

  First of all, the "hydrogen becomes metallic" probably means that you 
should apply spin polarisation as you have only one atom. Please remember 
that the absolute energies do not make sense, the total energy of the atom 
should be calculated by removing the energy difference between a pseudo 
atom and the all-electron atom, but this is prone to numerical 
(convergence) errors.


  Second, dissociating a water molecule by pulling one hydrogen apart 
would in principle lead to a double radical; well, in practise it would 
lead to two non-neutral constituents (in one calculation the electrons can 
move freely, in "metallic language" the Fermi level is global and same 
everywhere, even if the atoms would be 1 km apart). And further, most of 
the approximations, in particular GGAs, have a problem when pulling apart 
atoms, they give wrong asymptotics (famous examples are dissociating H_2).


  As I do not know what your target goal is, I would once more look at the 
literature on DFT and these asymptotic failures, whether the DFT (and the 
XC functional that you plan to use) is able to capture the correct 
asymptotics.


Greetings from the Austrian Alps,

   apsi

PS Indeed, the quantity you would be calculating is rather dissociating 
energy, or?


-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-
  Ari Paavo Seitsonen / ari.p.seitso...@iki.fi / http://www.iki.fi/~apsi/
Ecole Normale Supérieure (ENS), Département de Chimie, Paris
Mobile (F) : +33 789 37 24 25(CH) : +41 79 71 90 935


On Fri, 26 Feb 2016, Felix Brockherde wrote:


Dear all,

We would like to calculate the binding energy for non-equilibrium H2O 
geometries with PAW pseudo potentials.

The initial thought was to calculate the single-atom energies. However, for H 
the system becomes metallic. We used smearing but the results seem too far from 
the experimental
value for us to use them (-0.91784682 Ry).

Now, we would like to calculate the binding energy by separating the H2O 
molecule as far as necessary. We would thus avoid inaccuracies caused by 
smearing because it is not a
metallic system. However, when pulling H2O apart, the DFT calculations do not 
converge.
Can anybody help with either how to get the separated H2O converged or a 
different approach to get the binding energy with PAW pseudo potentials?

We used PWSCF v.5.1.1 and I attached an input file where QE does not converge.

Best regards,
Felix Brockherde
TU Berlin

 
    calculation = 'scf',
    wfcdir = 'tmp',
    pseudo_dir = '/home/user/pseudo_potentials',
    tprnfor = .true.,
    prefix = 'prefix',
    tstress = .false.,
    outdir = './',
    wf_collect = .true.,
 /
 
    nat = 3,
    ntyp = 2,
    ecutwfc = 90,
    ecutrho = 360,
    celldm(1) = 30,
    ibrav = 1,
 /
 
 /
ATOMIC_SPECIES
    H 1.00794 H_pbe-kjpaw_psl.0.1.UPF
    O 15.9994 O_pbe-kjpaw_psl.0.1.UPF
ATOMIC_POSITIONS alat
    O 0.5 0.3 0.5
    H 0.5 0.7 0.3
    H 0.5 0.7 0.7
K_POINTS automatic
   1 1 1   0 0 0

___
Pw_forum mailing list
Pw_forum@pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum

Re: [Pw_forum] Convergence test on big model

[Ari P Seitsonen]

Dear Yangchuan Li,

  In principle the values of cut-off are fully transferable, for the same 
kind of pseudo potential: As the highest Fourier components are required 
due to more localised (ie fastly varying) electronic wave functions close 
to the nuclei and there the changes going from one chemical environment to 
a different one are small, in most cases the cut-off tested in one system 
are indeed transferable (a reminder: using the same pseudo potential, so 
the recommended values for the cut-off energies are not strictly element- 
but even pseudo potential-specific).


  About the k points, rather the bigger the system, less k points: That is 
"hidden" in the word "reciprocal" space. Please have a look in the 
discussions on the back-folding of k points etc. The bottom line is, to 
get the same kind of accuracy in systems of different sizes the distance 
between the k points should be more or less the same (as they are used to 
approximate an integral). And if the cell in real space gets bigger, the 
Brillouin zone gets smaller: Thus less k points needed if the distance 
between the points is kept the same.


  And the density depends on the kind of system: In general one needs more 
points in metallic systems (in order to integrate the states close to the 
Fermi level accurately) than in semi-conducting or insulating systems. But 
if in the latter there are some more exotic bands somewhere needing higher 
integration sampling in the reciprocal space, more k points are also 
needed there. So shortly, no, one cannot give a general "preferred" number 
of k points; also because that depends on the quantity one is looking at 
(the structure converges faster than for example the phonon modes etc).


Greetings from Sleepy Paris,

   apsi

-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-
  Ari Paavo Seitsonen / ari.p.seitso...@iki.fi / http://www.iki.fi/~apsi/
Ecole Normale Supérieure (ENS), Département de Chimie, Paris
Mobile (F) : +33 789 37 24 25(CH) : +41 79 71 90 935


On Thu, 18 Feb 2016, Yangchuan Li wrote:


Hi everyone,

I want to ask whether a converged Ecut and smearing width can be used in 
another model. I have a big model (functionalized carbon nanotube) and it's 
time-consuming to do scf
calculation. I notice Stefano mentioned that Ecut is not strongly depended on 
particular configuration. (In topic Technique for converging Ecut and K-points?)

So can I used small model like diamond, nitrogen gas to do convergence test and 
then use the preferred parameter in my big model? Why I can or can't do that?

Also, if the dimension of the system is big. Is it necessary to select a very 
dense k-mesh? Is there a preferred k-point density in reciprocal space?

Thank you for your time. Any comment will be appreciated.

Yangchuan Li
UT Austin | ME



___
Pw_forum mailing list
Pw_forum@pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum

Re: [Pw_forum] Volume Optimisation :-Reg

[Ari P Seitsonen]

Dear A Suresh,

  My standard answer, sorry for that - did you check that the value of 
'ecutwfc' is sufficient? In the Good Old Days (at FHI) we used to use 
something more like 80-100 Ry for FHI-pseudos of oxygen, and that in 
ionc relaxations-only: The 'vc-relax' requires yet-a higher value. Did you 
try to start a new calculation from the lattice+ionic geometry that you 
obtained, _without_ restarting the electronic structure (ie copying the 
new values lattice vectors and ionic coordinates into the input file and 
keeping the "restart_mode = 'from_scratch'"): If the lattice constants 
start to change a lot, the cut-off energy is too low. Or you look at the 
value of the stress at the end of your previous calculation: The final 
step is done with re-generated plane waves, so if your lattice changed a 
lot and the cut-off was too low, there suddenly is a large value of 
stress.


  On the other hand I do not know about the accuracy of the pseudo 
potential for Ti: I remember there were some problems with a 
norm-conserving one, at least if the number of valence electrons is four. 
Maybe this one would work better, I do not know this one, but I would 
start checking the value of the cut-off energy.


Greetings from Sunny Paris,

   apsi

PS Why this "exxdiv_treatment" in your input...?

-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-
  Ari Paavo Seitsonen / ari.p.seitso...@iki.fi / http://www.iki.fi/~apsi/
Ecole Normale Supérieure (ENS), Département de Chimie, Paris
Mobile (F) : +33 789 37 24 25(CH) : +41 79 71 90 935


On Tue, 16 Feb 2016, Suresh A wrote:


Dear All,
    I have optimized the structure for anatase simple tetragonal. The 
optimiized lattice parameters are a= 3.754336A. c=9.193631522694A. but the 
experimental values are
a= 3.785A, c=9.514A. There is big difference in c value for optimised 
strucutre.But the same calculation for GGA pseudo potential gives the lattice 
parameter values which are
good with  experimental values. In literature  previous results for LDA has 
good lattice parameter values.
 Which parameter I have to  change in order to get good results for LDA?
  Below is my input and the version i have used is 5.2.1

 
   title = 'anatase' ,
 calculation = 'vc-relax' ,
    restart_mode = 'from_scratch' ,
  pseudo_dir = '/home/suresh/GN2/',
  outdir ='/home/suresh/Desktop/ashahicheck/asahiopt/tmp/',
  prefix = 'anatase' ,
 tstress = .true. ,
 tprnfor = .true. ,
 /
 
   ibrav = 6,
   A = 3.692,
   C = 9.471 ,
 nat = 12,
    ntyp = 2,
 ecutwfc = 60 ,
    exxdiv_treatment = 'none' ,
 /
 
 /
 
  ion_dynamics = 'bfgs' ,
 /
 
   cell_dynamics = 'bfgs' ,
 /
ATOMIC_SPECIES
   Ti   47.86700  Ti.pz-mt_fhi.UPF
    O   15.99940  O.pz-mt_fhi.UPF
ATOMIC_POSITIONS (crystal)
Ti  0.000   0.000   0.000
Ti  0.500   0.000   0.750
Ti  0.000   0.500   0.250
Ti  0.500   0.500   0.500
O   0.000   0.000   0.2066000
O   0.500   0.000   0.5434000
O   0.000   0.500   0.4566000
O   0.500   0.000   0.9566000
O   0.000   0.500   0.0434000
O   0.000   0.000   0.7934000
O   0.500   0.500   0.7066000
O   0.500   0.500   0.2934000
K_POINTS automatic
4 4 2 1 1 1


Thanks in advance.


  With Regards,
A.Suresh,
Research Scholar,
Madurai Kamaraj University,
Madurai.

___
Pw_forum mailing list
Pw_forum@pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum

Re: [Pw_forum] Geometry_Optimization_ERROR

[Ari P Seitsonen]

Dear Amir M. Mofrad, [ next time please with affiliation ]

  Since no qualified expert has answered so far, I give some quick 
comments:


 - Do you know what you are doing with the variable 'nr1'/'nr2'/'nr3'?

 - I found only 107 atoms in your input file, 'nat = 108'

 - I would actually find it easier to use 'ibrav = 4' and 'a = 13.6750', 
'c = 14.76700'; now you do not give many digits in the second, y 
coordinate of the second lattice vector, so a hexagonal cell is maybe not 
found; the alternative would be to more digits [13.6750/2*sqrt(3) = ...]


 - It is not a good idea to shift the k points laterally away from the 
Gamma point, unless there is a good reason (please see either my previous 
comments on the Forum or the appendix of my PhD thesis; the latter shows 
in practise how the Monkhort-Pack points, if not including the Gamma 
point, have a lower symmetry than the hexagonal cell and more k points 
need to be generated)


 - I do not know if the pseudo potential that you want to use have been 
improved in the later versions of PSLibrary; personally I would try to use 
the latest versions, if there is no specific reason for employing the 
elder ones


 - I would also check if you can symmetrise the coordinates; 'pw.x' gives 
coordinates that resemble having some "nice numbers" inside. But for 
'pw.x' to find symmetries the coordinates have to be very close to being 
symmetric, some five digits or so (I know of some other programs where one 
can ask the code to symmetrise the coordinates if found to be withing some 
given epsilon); symmetries would further reduce the number of k points 
that are generated with your input


 - ... and I would begin with less k points than the 4x4x4, as your cell 
is a bit bigger (lattice vectors ~10 Å) and your base material probably 
has a band gap (metallic systems usually require more k points); once you 
have the relaxation converging you might shift to more k points


  I do not know if these are of any help; Good Luck in any case. :)

Greetings from Montrouge,

   apsi

-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-
  Ari Paavo Seitsonen / ari.p.seitso...@iki.fi / http://www.iki.fi/~apsi/
Ecole Normale Supérieure (ENS), Département de Chimie, Paris
Mobile (F) : +33 789 37 24 25(CH) : +41 79 71 90 935


On Fri, 12 Feb 2016, Mofrad, Amir Mehdi (MU-Student) wrote:



Dear all QE experts and developers,


I want to do a geometry optimization on a zeolite but I get the following
error:

 task # 0
 from sym_rho_init_shell : error # 2
 lone vector
Here is my input file in case you need it.



 calculation = 'relax' ,
 restart_mode = 'from_scratch' ,
 wf_collect = .true. ,
 outdir = './scratch' ,
 wfcdir = './scratch' ,
 pseudo_dir = '/global/espresso/pseudo' ,
 prefix = 'CHA' ,
 verbosity = 'high' ,
 etot_conv_thr = 1e-5 ,
 forc_conv_thr = 1e-4 ,
 nstep = 50 ,
 tstress = .true. ,
 tprnfor = .true. ,

 /


 ibrav = 0,
 nat = 108,
 ntyp = 2,
 nr1= 32,
 nr2=32,
 nr3=32,
 ecutwfc = 30 ,
 ecutrho = 300 ,

/

  electron_maxstep = 100,
  conv_thr = 3e-8 ,
  mixing_mode = 'plain' ,
  mixing_beta = 0.7 ,
  diagonalization = 'david' ,

/


    ion_dynamics = 'bfgs' ,
    trust_radius_ini = 0.5 ,
 /
CELL_PARAMETERS angstrom
 13.6750   0.00   0.00
-6.83750  11.84290   0.00
-0.0  -0.0   14.76700

ATOMIC_SPECIES
    Si   28.08600  Si.pbe-n-rrkjus_psl.0.1.UPF
    O   15.99940  O.pbe-n-rrkjus_psl.0.1.UPF
ATOMIC_POSITIONS angstrom
 O  11.66477   1.16060   1.81191
 O  11.23606   3.67248   2.46166
 O   0.00068   2.84822   1.94186
...
Si   1.54596   5.21048  11.39668

K_POINTS automatic
4 4 4 1 1 1

Any help would be thoroughly appreciated.


Best,


Amir M. Mofrad   
___
Pw_forum mailing list
Pw_forum@pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum

Re: [Pw_forum] About getting Raman Spectrum for a 24 atom-hybrid halide perovskite

[Ari P Seitsonen]

Dear Josue Clavijo,

  Do you mind sending the input for both 'pw.x' and 'ph.x'? Then we would 
better understand - for example which pseudo potentials you use etc - what 
you are doing and if we find some aspect that should be improved to get 
the calculations running normally; it is not common, at least in my 
limited experience, that one should increase the 'tr2_ph' that much, as 
this is also a material with quite a band gap, isn't it?


Greetings from Sunny Montrouge,

   apsi

-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-
  Ari Paavo Seitsonen / ari.p.seitso...@iki.fi / http://www.iki.fi/~apsi/
Ecole Normale Supérieure (ENS), Département de Chimie, Paris
Mobile (F) : +33 789 37 24 25(CH) : +41 79 71 90 935


On Tue, 9 Feb 2016, Josue Itsman Clavijo Penagos wrote:


Dear all, I apologize for sending a former e-mail from another account other
than the subscribed one.

So, here is my post again:

I’m having trouble to replicate the result for the raman spectra for some
hybrid perovskite, namely CH3NH3PbI3, a.k.a MAPbI3 (4 MAPbI3 molecules/unit
cell). I'm using the relaxed cell and atomic coordinates as in J. Phys.
Chem. Lett., 2014, 5 (2), pp 279–284.

So, I’d really thank you any advice and words of correction regarding to the
following issues:

1-The thing is that my phonon calculations never converge, even using an
energy cutoff in the scf previous calculations of 1D-12. (Using
Norm-conserving LDA-level PZ PPs). WIll be necessary to lower the tr2_ph
value in ph.x to something greater than 1D-12 since the system is somewhat
huge (24 atoms)?

2- In a latter ph.x run attemp, I set the tr2_ph value to 1D-8 and the the
initial convergence was achieved, but at the stage of calculation the second
derivatives, roots never converged, so i can not get the dynamical matrix
anytime.

So, for as a huge system as MAPbI3 is, It is likely to exist special
constraints, adjustments or requirements i'm missing, in order to get the
dynamical matrix and, using dynmat.x and other plotting tools, to simulate
the raman spectrum with the quantum espresso suite?

Excuse me if i’m missing several important theoretical or QE-related
aspects, but i really need some advice about all of this stuff.

Best regards,

---
Dr.Sc. JOSUÉ CLAVIJO, Chem.
Christian, born again

Assistant Professor
Universidad Nacional de Colombia
Science College
Chemistry Department




___
Pw_forum mailing list
Pw_forum@pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum