[Pw_forum] nothing is written to the output file

[Hong LI]

Dear users,

We are using espresso to relax the atomic structures of an alloy, there is a 
problem that after several days of running the size of *.out is still zero, 
nothing is written to the output file. If we kill the job then the output file 
is not empty. Some small jobs run fine, I mean the information is updated from 
time to time during the calculation. It seems this is just an occasional case. 
Does anyone here encounter similar problem before, any suggestions to solve 
this problem ? Many thanks.

Best wishes.
Hong
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[Pw_forum] Charge ordering with QE

[Gabriele Sclauzero]

Dear Mattia,

Mulazzi Mattia wrote:
> In order to calculate the electronic structure of an orbitally-ordered  
> system I think I have to use a supercell and specify different  
> occupation numbers for the different Vanadium sites. The problem is  
> that I don't know how to do that. I tried specifying the  
> starting_ns_eigenvalue variable on different sites, but the converged  
> calculation is identical to the calculation with  
> starting_ns_eigenvalue left unspecified. In the INPUT_PW it is written  
> that the occupation matrices can be specified only when the LDA+U  
> scheme is used.

I don't understand a thing: starting_ns_eigenvalue is used only on the species 
on which 
you put +U (i.e. Hubbard_U(?)>0), so if you cannot not use LDA+U for V with 
your QE 
installation, how could you say that using starting_ns_eigenvalue does not 
change the result?

One other important point is that occupations are symmetrized according to the 
symmetry of 
the system. So that, perhaps, retrying after breaking some symmetry or using 
nosym=.TRUE. 
may change something.

> However, I cannot use the LDA+U on my system (Mac OS X 10.5.6) because  
> every time I use the Vanadium pseudopotential (either the one I  
> generated, ether the one on the QE database) I find a "segmentation  
> fault" that I  cannot solve. BTW, the segmentation fault error does  
> not appear for Co or Fe or Ni pseudopotentials.

Which version of QE are you using?
Please check if the Vanadium case has already been inserted in tabd.f90 and 
set_hubbard_l.f90 files.
If not pw.x should stop with an error message like
  "pseudopotential not yet inserted"
before causing any segmentation fault.
 From version 4.1 on, LDA+U should be working with any of the transition metal 
elements.
If you have previous versions, you can easily get it working modifying those 
two files.

Please report to us if the problem persists in v4.1 and if it is reproducible.

Thanks,


GS

> 
> Thanks everybody for the help,
> 
>  Mattia Mulazzi
> 
> 
> FPR Fellow of RIKEN at Spring8
> Excitation Order Research Team
> 1-1-1 Sayo-cho Sayo-gun, Hyogo
> Japan
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o  o

[Pw_forum] plane averaged local potential

[Gabriele Sclauzero]

Dear Eduardo and Ghosh,

Prasenjit Ghosh wrote:
> 
> 
> 2009/10/28 Eduardo Ariel Menendez Proupin  >
> 
> Hello,
> I need to calculate plane averaged local potentials, and charges,
> for a heterostructure. I.e., 
> V(z)=1/(Lx*Ly) \int\int V(x,y,z) dx dy  
> 
> I think I  can do it using PP to get V(x,y,z) in the 3D FFT grid and
> a write a program that makes the average. Then I want to obtain the
> macroscopic average, as defined in a triestine paper by Baldereschi,
> Baroni and Resta PRL 61 ,734 (1988).
> 
> Before spending one or two days  writing the program and become sure
> that is works fine, I would like to confirm that this is not already
> implemented in PP or in other utility of Quantum-ESPRESSO. 
> 
> Hi Eduardo,
> 
> The executable average.x can do the jobfor the input file  you 
> can see the example on Work function calculation..
> However, if you want to calculate the planar average of charge density, 
> you need to multiply it with the area of the xy plane, assuming you want 
> to plot along the z-direction.

I can confirm. I've been using that and it should give exactly the integral you 
wrote above.


> 
> Also I think (I'm not sure) it works only if the z- is perpendicular to 
> the xy-plane.

There is a variable that let's you chose the direction along which to plot the 
quantity 
(the other two are integrated up). Please read the header of PP/average.f90.

Cheers,

GS

> 
> With regards,
> Prasenjit.
> 
> 
> 
> -- 
> PRASENJIT GHOSH,
> POST-DOC,
> ROOM NO: 265, MAIN BUILDING,
> CM SECTION, ICTP,
> STRADA COSTERIA 11,
> TRIESTE, 34104,
> ITALY
> PHONE: +39 040 2240 369 (O)
>  +39 3807528672 (M)
> 
> 
> 
> 
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o  o
| Gabriele Sclauzero, PhD Student  |
| c/o:   SISSA & CNR-INFM Democritos,  |
|via Beirut 2-4, 34014 Trieste (Italy) |
| email: sclauzer at sissa.it |
| phone: +39 040 3787 511  |
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o  o

[Pw_forum] mpi-pwcond error

[Gabriele Sclauzero]

Dear Sagar,

ambavale sagar wrote:
> Dear PwScf users,
> I am getting MPI error during PWCOND run at particular point. The 
> standard output gives:
> 
> MPI_Allreduce: invalid communicator: Unknown error 2064 (rank 0, comm 16)
> Rank (0, MPI_COMM_WORLD) : Call stack within LAM:
> Rank (0, MPI_COMM_WORLD) : -MPI_Allreduce()
> Rank (0, MPI_COMM_WORLD) : -main()
> --
> One of the processes started by mpirun has exited with a nonzero 
> exit
> ...
> ..
> ..
> PID 16077 failed on node n1 (192.168.0.12) with exit status 1.
> -

Is the error reproducible? Have you managed to run in parallel pw.x+pwcond.x 
for a smaller 
system that, let's say, can be done on 2 cpus?

> 
> 
> I am running espresso-4.0 installed with lam-mpi 7.1.4 and ifort 10.1 on 
> dual cpu quad core xeon processors. There are 2 machines running in 
> parallel. Thus 4 cpus or 16 cores are available. However, this 
> calculation was ran on 4 cores only. The scf and relax calculations do 
> not crash. One more thing to note is: recently I have enhanced RAM on 
> both the machines. And after enhnacement did not do any reinstallation 
> or recompilation of any software including lam-mpi.

I don't think this is needed. You simply need to reboot the machine and see if 
the OS sees 
the new RAM banks, I suppose.

> 
> Note : Through search on forum archives I found a post by Derek :
> http://www.democritos.it/pipermail/pw_forum/2005-November/003219.html
> which indicates this might be a problem related to mpi or def.h..
> 
> 
> Thank you.
> 
> Regards
> Sagar Ambavale
> PhD Student
> The M.S. Uni. of Baroda
> India
> 
> 
> Now, send attachments up to 25MB with Yahoo! India Mail. Learn how 
> .
> 
> 
> 
> 
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o  o
| Gabriele Sclauzero, PhD Student  |
| c/o:   SISSA & CNR-INFM Democritos,  |
|via Beirut 2-4, 34014 Trieste (Italy) |
| email: sclauzer at sissa.it |
| phone: +39 040 3787 511  |
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o  o

[Pw_forum] Tetrahedra method

[Paolo Giannozzi]

I am not sure tetrahedron method works in the
noncolinear case. In any event, be careful because
its usage for self-consistency will lead to small errors
on forces. The main usage of tetrahedra is for
calculation of the DOS.

P.
---
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via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222

[Pw_forum] Left and right going Bloch's states from PWCOND

[Manoj Srivastava]

Just to add one more question. 
what is 'lorb' switch. I get following- 
  lorb,  &  ! if .t. calculate the scattering (or Bloch) states
so, i guess for transmission calculation i will have to set it to
't'. now- 
IF (lorb.and.ikind.eq.2) call errore('do_cond','lorb not working with
ikind = 2',1)
so, it seems that calculation for r and t for right and left going
state, when left and right leads are different doesnot work. Is that
correct? A possible work around may be rotating the whole system by 180
degree, which would be like treating left lead as right lead and
scattering region rotated. Can I do that?

Regards, 
Manoj

On Fri, 30 Oct 2009, Manoj Srivastava wrote:

> Dear Alexander,
> Thank you very much! I read the code, it seems that there are
> quiet a few changes in 4.1.1 compared to 4.0.4 :) .So, just to make sure,
> if I want to calculate r and t for left going Bloch's state as well as
> right going Bloch's state, I need to run the code two times, one time with
> 'left_to_right' switch true, and another time false. I dont need to change
> scattering region or interchange left and right leads. 
> 
> Regards, 
> Manoj Srivastava
>  On Thu, 29 Oct 2009, Alexander
> Smogunov wrote:
> 
> > Dear Manoj
> > 
> > On Wed, 2009-10-28 at 01:49 -0400, Manoj Srivastava wrote:
> > > Dear Alexander, 
> > >  You are correct, left and right moving states are in general not
> > > related. I was wrong about trying to create a pair. Thanks for
> > > clarification. 
> > >  I have a few more questions.  
> > >  1. I want to find out the reflection coefficient in the code. In
> > > transmit.f90, transmission coefficient is |tmat(ig,n)|^2, where tmat is
> > > vec1(ntran-n2d-npol*nocrosr+ig,n). (line 206, of version 4.0.5).
> > > Reflection is not explicitly calculated in the code, but it should be
> > > modulus square of vec1(2*n2d+npol*norbs+ig,n) (line 234). Am I correct?
> > 
> > in the 4.1 version there is output of both t and r.
> > 
> > 
> > > 
> > >  2. In the code reflection and transmission coefficients are calculated
> > > for one direction lets say t++ and t+-, which is transmission and
> > > reflection coefficient for Bloch' state moving from - to + , or in other
> > > words, left to right. To calculate transmission and reflection for Bloch's
> > > state going from right to left, what should I do? Should i just rotate my
> > > system 180 degree, that way leads get interchanged and also scattering
> > > area has orientation 180 different from before.
> > > 
> > 
> > again in the 4.1 version you have possibility to calculate t and r for
> > both directions, in the do_cond.f90 the transmit routine is called with 
> > an extra parameter which is true (false) if you want to calculate
> > scattering states propagating from the left (from the right). 
> > 
> > >  3. In the subroutine sunitary.f90, is raux measure of conservation of
> > > flux? If I sum all the transmission and reflecion coefficient for
> > > a particular Bloch's state, I should get 1, and computationally a number
> > > close to 1. How large could it be for S matrix not to be unitary, i m
> > > getting raux more than one e.g. 1.0011  but code still considers smatrix
> > > to be unitary. 
> > 
> > in the case when |R + T - 1| > 1.d-4 for some band, it should print out
> > the value of R+T but continues to run anyway.
> > 
> > All the best,
> > Alexander
> >  
> > 
> > 
> > > 
> > > Regards, 
> > > Manoj Srivastava
> > > University of Florida, Gainesville, FL
> > > 
> > > 
> > > 
> > >  
> > > 
> > > 
> > > On Thu, 22
> > > Oct 2009, Alexander Smogunov wrote:
> > > 
> > > > On Thu, 2009-10-22 at 11:34 -0400, Manoj Srivastava wrote:
> > > > > Dear Alexander, 
> > > > >  Thanks for your answer. I just want to make sure. Imagine we have 
> > > > > total
> > > > > number of channels in the left lead 2, so total number of Bloch's 
> > > > > state
> > > > > are 4. 2 of them left going say a and b, and 2 right going say c and 
> > > > > d.
> > > > > So, are you saying that for left going state a, the corresponding 
> > > > > right
> > > > > going state is c? Are they ordered this way?
> > > > 
> > > > what do you mean by corresponding? Left and right moving Bloch
> > > > states are in general not related one to another, you can even have
> > > > different number of them ... Only if you have some symmetry S which
> > > > brings kz to -kz conserving k_parallel, then the state with 
> > > > \psi_{-kz} will be S \psi{kz}. This is true for example at 2D G point
> > > > when you have time reversal operation.
> > > > 
> > > > Now the code simply arranges the propagating states in the order of 
> > > > increasing |k_z|...
> > > > 
> > > > Regards, Alexander
> > > >  
> > > > 
> > > > > 
> > > > > Regards, 
> > > > > Manoj
> > > > > 
> > > > >  
> > > > >  On Thu, 22 Oct 2009, Alexander
> > > > > Smogunov wrote:
> > > > > 
> > > > > > Dear Manoj.
> > > > > > 
> > > > > > The output of complex k vectors is performed in
> > > > > > summary_band.f90 routine. 

[Pw_forum] (no subject)

[Giuseppe Mattioli]

Are you sure that N atoms inserted into the ZnO lattice substitute Zn atoms? I 
would put the N atom at the O site, but you know what you're doing... 
Yours
Giuseppe Mattioli

On Thursday 29 October 2009 02:52:20 kajal jindal wrote:
> Hii,
>
> I am working on ZnO doped with Nitrogen .I have used 2*2*2 ZnO supercell
> ..If i replace 1 Zn atom by 1 N atom in that supercell,doped N atom does
> not make any bonds with the surrounding atoms even after optimizing the
> lattice constants and atomic positions..It remains at that position as an
> isolated atom only...So can anybody plz suggest me what should i do in this
> caseAlso i want to know that whether  this will affect my band
> structure calculations???
>
> sincerely,
> Miss Kajal
> (UTA)(University of Delhi)


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[Pw_forum] (no subject)

[Lorenzo Paulatto]

In data 29 ottobre 2009 alle ore 02:52:20, kajal jindal  
 ha scritto:
> make any bonds with the surrounding atoms even after optimizing the  
> lattice constants and atomic positions..It remains at that position as  
> an isolated atom only...So can anybody plz suggest me what should i do  
> in this
> case

Dear Kajal,
what do you mean precisely by it does not make any bond? If you just  
cannot see any bond in XCrysDen or similar graphic programs it does not  
mean it isn't bound. Also, if it is not feeling any force it may be due to  
symmetry, try to break it slightly.


> Also i want to know that whether this will affect my band structure  
> calculations???

Yes, of course.

best regards

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[Pw_forum] el-ph for vacancy

[ali kazempour]

 Hi all

I want to study vacancy problem in ionic material. When a vacancy forms in an 
ionic materials like ZnO, there is stronger electron-lattice coupling because 
of electrostatic interaction with nearly atom cores. These interaction repels 
the surrounding nearest neighbors away from empty lattice site. So electronic 
structure pictures can be affected by this type of interaction.
I want to know Does espresso help me to detect and calculate the effect of 
el-ph interaction on band renormalization. I saw in example07 for Al that is 
metal,  but I dont know that whether or not it can be  used for semiconductor ?


thanks a lot
Ali Kazempour
Physics department, Isfahan University of Technology
84156 Isfahan, Iran.Tel-1:  +98 311 391 3733
Fax: +98 311 391 2376  Tel-2:  +98 311 391 2375



  
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