[Pw_forum] Dynamical Matrix at the equivalent q-points in phonon dispersion calculations

[Zhong-Li Liu]

Dear Wang,

   Thank you for the quick reply. You are right, just as the normal method that
we usually use to calculate the phonon dispersion curve with ph.x, q2r.x
and matdyn.x, we can obtain the dispersion curve. However, I am trying another
way that the dynamical matrices are calculated using other methods such as lmto
linear-reponse code. The code just provide one of the dynamical matrices of
the same set of equivalent q-points, so I need reduce the known
dynamical matrices
to get the others' probably according to the symmetry operations of q-points.

Best wishes,
Z.Liu

On 24/09/2009, xirainbow  wrote:
> Dear Liu:
> If you just want to perform q2r calculation, I do not think you have to get
> daynamic matrix manually.
> You can follow example 06 to fulfill your calculation ??
>
> 
> Hui Wang
> School of physics, Nankai University, Tianjin, China
>


-- 
Dr. Liu, Luoyang Normal University, Luoyang, China
E-mail: zl.liu.caep at gmail.com

[Pw_forum] Pw_forum Digest, Vol 27, Issue 78

[wangqj1]

>Message: 3
>Date: Thu, 24 Sep 2009 08:52:09 +0200
>From: Gabriele Sclauzero 
>Subject: Re: [Pw_forum] Pw_forum Digest, Vol 27, Issue 76
>To: PWSCF Forum 
>Message-ID: <4ABB1719.7090605 at sissa.it>
>Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
>wangqj1 wrote:
>>  >Message: 2
>>  >Date: Wed, 23 Sep 2009 15:06:07 +0200
>>  >From: "Lorenzo Paulatto" 
>>  >Subject: Re: [Pw_forum] Pw_forum Digest, Vol 27, Issue 74
>>  >To: "PWSCF Forum" 
>>  >Message-ID: 
>>  >Content-Type: text/plain; charset=utf-8; format=flowed; delsp=yes
>>  >
>>  >In data 23 settembre 2009 alle ore 14:12:53, wangqj1  
>> ha  
>>  >scritto:
>>  >>> /home/wang/bin/pw.x -npool 8 -in ZnO.pw.inp>ZnO.pw.out
>>  >> It only print the output heander and not have iteration .
>> 
>>>Maybe it's not reading the input at all! You should specify the full path  
>>>to you input file, e.g.
>>>   mpirun ... bin/pw.x -in /where/is/is/ZnO.pw.inp
>>>just to be sure.
>> 
>> The output file is as following:
>>  Program PWSCF v.4.0.1  starts ...
>> 
>>  Today is  24Sep2009 at  8:49:30
>>   Parallel version (MPI)
>>   Number of processors in use:   8
>>  R & G space division:  proc/pool =8
>>   For Norm-Conserving or Ultrasoft (Vanderbilt) Pseudopotentials or PAW
>>  .
>>   Initial potential from superposition of free atoms
>>   starting charge  435.99565, renormalised to  436.0
>>   Starting wfc are  254 atomic +8 random wfc
>> 
>> It seems that it had read the input file  .
>
>I think so. Maybe you have problems with lack of memory or very slow disk 
>access (as 
>already pointed by previous responses). Have you tried running with smaller 
>system, or 
>increasing the number of processors, or using local scratch file system,...?

I had running with smaller system use  R & G space division,it runs quickly and 
soon finished the task .When I run bigger system (48 atoms),it turns up the 
phenomena as I said last letter.
>> When use K-point parallel ,it runs well.
>
>Can you specify better the conditions on which it runs well? What does it mean 
>that you 
>use "K-point parallel"?
 
I mean only I use K-points division,the big system can runs ,but very slow.
>
>> 
>>>
>>>> I am not the supperuser,I don't know how to Set the environment variable  
>>>> OPEN_MP_THREADS to 1,I can't find where is OPEN_MP_THREADS ?
>>>
>>>You don't need to be super-user (nor supper-user ;-) to set an environment  
>>>variable, you only have to add
>>>  export OMP_NUM_THREADS=1
>>>in your PBS script, before calling mpirun. To be sure it's propagated to  
>>>all the processors add the option
>>>  -x OMP_NUM_THREAD
>>>to mpirun arguments (BEFORE pw.x).
>> I want to know whether it is necessary to set environment variable 
>> OPEN_MP_THREADS (I installed MPICH2 not OPENMPI) ?
>> 
>
>In case of doubt (like yours), always specify it. It makes no harm, and it 
>ensures that 
>you're not running into troubles because of unwanted threads proliferation.
>
>HTH
>
>GS
>
>
>P.S.:Please, always sign your mails and put affiliation. It is not difficult 
>to let it be 
>done  automatically by your (web)mail program.
>Personally, I don't even like seeing mail which use the username as display 
>name in the 
>mail header, instead of the full (real) name... but that's my opinion.
>
Thank you !
Best regard 
-- next part --
An HTML attachment was scrubbed...
URL: 
http://www.democritos.it/pipermail/pw_forum/attachments/20090924/765882c4/attachment-0001.htm
 

[Pw_forum] Dynamical Matrix at the equivalent q-points in phonon dispersion calculations

[Zhong-Li Liu]

Dear all,

   Recently, I am doing the phonon dispersion calculations with lmto
linear-response code and
pwscf code. Using the lmto code, I can only obtain one of the matrices
of the equivalent q-points
in each set. For example, bcc Ta (one atom in unit cell) at q = (
-0.12500  -0.12500
0.5 ) in 8x8x8 q mesh, the matrix is

  0.16975011  0.0.01325182  0.   -0.03964828  0.
  0.01325182  0.0.16975011  0.   -0.03964828  0.
 -0.03964828  0.   -0.03964828  0.0.24323635  0.

How can I transform the existed matrix to obtain the matrices of the
others' equivalent q-points(
because the others' matrices in the same set of equivalent q-points
are needed by the q2r.x and
 matdyn.x code), such as

q = (0.12500   0.12500   0.5 )
q = (0.12500  -0.12500  -0.5 )
 ..
 ..
 ..
q = (   -0.5  -0.12500   0.12500 ) ?

Any information is appreciated very much!

Best wishes,
z.liu


-- 
Dr. Liu, Luoyang Normal University, Luoyang, China
E-mail: zl.liu.caep at gmail.com

[Pw_forum] from electrons : error # 1 charge is wrong

[dev sharma]

Thanks Sir,
Its neel here but i use my friend  Dev Sharma's email Id also because gmail
shows all reply in one window :):)
thank you very much sir,

Neel,
University of Delhi


On Thu, Sep 24, 2009 at 3:45 PM, Lorenzo Paulatto  wrote:

> In data 24 settembre 2009 alle ore 12:03:02, dev sharma
>  ha scritto:
>
> > Dear Sir,
> >  what i was find in my output file  ,  is that  the structure is
> > metallic and asking for smearing and nosym see output below. I am doing
> > calculation on ZnO doped with N, with one Zn replaced by N. Sir any
> > comment or
> > suggestion on this as ZnO is a insulator with band gap 3.32 eV approx.
> > And when i am giving the smearing and set nosym=.true., the error is
> > removed and positions are being releaxed.
>
> I'm not sure I've understood your problem correctly, but in general, if
> you replace an atom with another there is no guarantee that the resulting
> crystal will still be insulator!
>
> In particular, by replacing a Zn (12 electrons in valence) with a Nitrogen
> (5 electrons in valence) you will change the parity of the total number of
> electrons in the cell: if before you had an even number of electrons than
> it will become odd, i.e. if before you had an insulator than you will have
> a conductor. Keep in mind that you're not just replacing *one* atom,
> you're replacing one atom *per unit cell*.
>
> best regards
>
> P.S. I'm confused... are you Neel Sing?
>
>
> --
> Lorenzo Paulatto
> SISSA  &  DEMOCRITOS (Trieste)
> phone: +39 040 3787 511
> skype: paulatz
> www:   http://people.sissa.it/~paulatto/<http://people.sissa.it/%7Epaulatto/>
>
> *** save italian brains ***
>  http://saveitalianbrains.wordpress.com/
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
-- next part --
An HTML attachment was scrubbed...
URL: 
http://www.democritos.it/pipermail/pw_forum/attachments/20090924/afb83d99/attachment-0001.htm
 

[Pw_forum] from electrons : error # 1 charge is wrong

[dev sharma]

Dear Sir,
 what i was find in my output file  ,  is that  the structure is  metallic
and asking for smearing and nosym see output below. I am doing  calculation
on ZnO doped with N, with one Zn replaced by N. Sir any comment or
suggestion on this as ZnO is a insulator with band gap 3.32 eV approx. And
when i am giving the smearing and set nosym=.true., the error is removed and
positions are being releaxed.


 Program PWSCF v.4.0.2  starts ...
 Today is 24Sep2009 at 15:13:53

 Parallel version (MPI)

 Number of processors in use:   4
 R & G space division:  proc/pool =4

 For Norm-Conserving or Ultrasoft (Vanderbilt) Pseudopotentials or PAW

 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
 Message from routine setup:
 the system is metallic, specify occupations
 Message from routine setup:
 Dynamics, you should have no symmetries


Thanks In Advance,
Neel Singh ,
University of Delhi,
India



On Thu, Sep 24, 2009 at 1:41 PM, Lorenzo Paulatto  wrote:

> Dear Neel,
> I only wish to add one remark to what has been already said by Sreekar and
> Gabriele.
>
> > ecutwfc = 40.0
>
> you have specified ecutwfc, but not ecutrho, which will be set to
> 4*ecutwfc=160Ry. Nevertheless, as you are using ultrasoft pseudopotential
> your choice is not very wise; you can probably decrease ecutwfc a bit
> (like 25-30%), but your definitely should increase ecutrho consistently
> (about 8-12 times ecutwfc).
>
> best regards.
>
> --
> Lorenzo Paulatto
> SISSA  &  DEMOCRITOS (Trieste)
> phone: +39 040 3787 511
> skype: paulatz
> www:   http://people.sissa.it/~paulatto/<http://people.sissa.it/%7Epaulatto/>
>
> *** save italian brains ***
>  http://saveitalianbrains.wordpress.com/
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
-- next part ------
An HTML attachment was scrubbed...
URL: 
http://www.democritos.it/pipermail/pw_forum/attachments/20090924/90a64b37/attachment.htm
 

[Pw_forum] Fw: isolated atom

[Gabriele Sclauzero]

No need to specify nelup and neldw, because specifying tot_magnetization (or, 
equivalently,  multiplicity) is enough. Moreover the nelup and neldw are 
deprecated 
keywords and will be no more available in future versions of QE.

Regards,

GS

Duy Le wrote:
> nelec in  will solve this problem. This has been discussed many 
> time in this forum.
> 
> :)
> 
> On Thu, Sep 24, 2009 at 7:06 AM, ali kazempour  > wrote:
> 
> Dear Lorenzo
> I tried with this but I have error
> from  system_checkin  : error # 1
>   neldw out of range
> my input file is:
> 
>  calculation = 'scf' ,
> restart_mode = 'from_scratch' ,
>   outdir = '/home/kazempou/tmp/' ,
>   pseudo_dir = './' ,
>   prefix = 'iso-gga' ,
>etot_conv_thr = 0.001 ,
>forc_conv_thr = 0.001 ,
>  /
>  
>ibrav = 1,
>celldm(1) =30
>  nat = 1,
> ntyp = 1,
>  ecutwfc = 60,
>  ecutrho = 400 ,
>  nspin=2
>   occupations='fixed', tot_magnetization=2.0,nelup=4,neldw=2,
>  /
>  
> conv_thr = 1.0D-7 ,
>  /
> ATOMIC_SPECIES
> O   16  o.optgga1.fhi.UPF
> ATOMIC_POSITIONS crystal
> O  0.5 0.5 0.5
> K_POINTS gamma
> would you tell me where did I do mistake?
> 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
> 
> 
> 
> *From:* Lorenzo Paulatto mailto:paulatto at 
> sissa.it>>
> 
> *To:* PWSCF Forum mailto:pw_forum at pwscf.org>>
> *Sent:* Wednesday, September 23, 2009 4:47:56 PM
> 
> *Subject:* Re: [Pw_forum] Fw: isolated atom
> 
> In data 23 settembre 2009 alle ore 15:40:55, ali kazempour 
> mailto:kazempoor2000 at yahoo.com>> ha 
> scritto:
>  > But esspresso don't allow fixed occupation for spin-polarized
> 
> Dear Ali,
> it does! You have to specify the occupations for spin up then, on a
> new 
> line, for spin down.
> 
> that's all
> 
> cheers
> 
> -- 
> Lorenzo Paulatto
> SISSA  &  DEMOCRITOS (Trieste)
> phone: +39 040 3787 511
> skype: paulatz
> www:  http://people.sissa.it/~paulatto/
> 
> 
> *** save italian brains ***
>   http://saveitalianbrains.wordpress.com/
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org 
> http://www.democritos.it/mailman/listinfo/pw_forum
> 
> 
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org 
> http://www.democritos.it/mailman/listinfo/pw_forum
> 
> 
> 
> 
> -- 
> --
> Duy Le
> PhD Student
> Department of Physics
> University of Central Florida.
> 
> 
> 
> 
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum

-- 


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  |
| skype: gurlonotturno |
o  o

[Pw_forum] from electrons : error # 1 charge is wrong

[Lorenzo Paulatto]

In data 24 settembre 2009 alle ore 12:03:02, dev sharma  
 ha scritto:

> Dear Sir,
>  what i was find in my output file  ,  is that  the structure is   
> metallic and asking for smearing and nosym see output below. I am doing   
> calculation on ZnO doped with N, with one Zn replaced by N. Sir any  
> comment or
> suggestion on this as ZnO is a insulator with band gap 3.32 eV approx.  
> And when i am giving the smearing and set nosym=.true., the error is  
> removed and positions are being releaxed.

I'm not sure I've understood your problem correctly, but in general, if  
you replace an atom with another there is no guarantee that the resulting  
crystal will still be insulator!

In particular, by replacing a Zn (12 electrons in valence) with a Nitrogen  
(5 electrons in valence) you will change the parity of the total number of  
electrons in the cell: if before you had an even number of electrons than  
it will become odd, i.e. if before you had an insulator than you will have  
a conductor. Keep in mind that you're not just replacing *one* atom,  
you're replacing one atom *per unit cell*.

best regards

P.S. I'm confused... are you Neel Sing?


-- 
Lorenzo Paulatto
SISSA  &  DEMOCRITOS (Trieste)
phone: +39 040 3787 511
skype: paulatz
www:   http://people.sissa.it/~paulatto/

 *** save italian brains ***
  http://saveitalianbrains.wordpress.com/

[Pw_forum] from electrons : error # 1 charge is wrong

[sreekar guddeti]

>Hi,
Hi Neel

>?i am trying to relax a structure but after two iteration i am getting this
error,

 from electrons : error # 1
 charge is wrong

have a look at this
http://www.democritos.it/pipermail/pw_forum/2008-April/008784.html

occupations = 'fixed' is for insulators and # of bands computed = nelec/2
mostly during iteration electrons are crossing over to higher bands. hence
the underestimation of integrated charge.

u can always dig in through the archives which has a wealth of helpful
information
and we all would be grateful if u could specify your affiliation. it gives a
good estimate of the extent of the spread of our community, a community
which adheres to the philosophy of using, distributing and writing free
software.

sincerely,
Sreekar Guddeti
B.Tech + M.Tech
Physics Dept
IIT Bombay
India




-- 
Sreekar Guddeti
-- next part --
An HTML attachment was scrubbed...
URL: 
http://www.democritos.it/pipermail/pw_forum/attachments/20090924/0203126e/attachment.htm
 

[Pw_forum] Dynamical Matrix at the equivalent q-points in phonon dispersion calculations

[xirainbow]

Dear Liu:
If you just want to perform q2r calculation, I do not think you have to get
daynamic matrix manually.
You can follow example 06 to fulfill your calculation ??


Hui Wang
School of physics, Nankai University, Tianjin, China
-- next part --
An HTML attachment was scrubbed...
URL: 
http://www.democritos.it/pipermail/pw_forum/attachments/20090924/7660328e/attachment.htm
 

[Pw_forum] relaxating only z coordinate

[ambavale sagar]

Dear Manoj

i.e now in your input file the atomic position card will look like:

ATOMIC POSITIONS
Si 000001
Si0.50.50.5001
Si0.70.70.7100

This atomic position card allow you to displace  first two atoms in z direction 
while the third Si in x direction. 


Regards
Sagar Ambavale
The M. S. University of Baroda
India
===


Message: 8
Date: Wed, 23 Sep 2009 17:50:22 -0400 (EDT)
From: Manoj Srivastava <ma...@phys.ufl.edu>
Subject: [Pw_forum] relaxating only z coordinate?
To: PWSCF Forum 
Message-ID:

Content-Type: TEXT/PLAIN; charset=US-ASCII

Dear PWSCF users, 
This might have been answered previously, but I was unable to find
it. How can one relax only z coordinate of atoms inside unit cell using
PW? In other words how can I constrain x and y coordinates of atoms during
relaxation?


Regards, 
Manoj Srivastava
University of Florida 
Gainesville, FL 



--

Message: 9
Date: Thu, 24 Sep 2009 06:29:11 +0800
From: lan haiping <lanhaip...@gmail.com>
Subject: Re: [Pw_forum] relaxating only z coordinate?
To: PWSCF Forum 
Message-ID:

Content-Type: text/plain; charset="iso-8859-1"

Hi, Please check INPUT_PW document,  you will find below description:
if_pos(1), if_pos(2), if_pos(3) INTEGER  *Default:* 1

component i of the force for this atom is multiplied by if_pos(i),
which must be either 0 or 1.  Used to keep selected atoms and/or
selected components fixed in meta-dynamics, neb, smd, MD dynamics or
structural optimization run.

If you want to fix some atom or some direction , just set if_pos(i) =0 .

Regards,

Hai-Ping


  From cricket scores to your friends. Try the Yahoo! India Homepage! 
http://in.yahoo.com/trynew
-- next part --
An HTML attachment was scrubbed...
URL: 
http://www.democritos.it/pipermail/pw_forum/attachments/20090924/cd3a1dde/attachment-0001.htm
 

[Pw_forum] why SCF calculation for isolated atom is tricky

[udayagiri sai babu]

In the forum I have seen the statement like doing scf calculation for an
isolated atom is tricky. Can somebody explain me why is this so? and then
while testing a pseudo potential is it a good idea to calculate cohesive
energies (which involves isolated atom) and compare as we do for lattice
parameter and bulk modulus.
-- 
U.Saibabu
PhD student,
Deformation mechanisms modeling group,
Materials engineering department,
IISc Bangalore,
India.
-- next part --
An HTML attachment was scrubbed...
URL: 
http://www.democritos.it/pipermail/pw_forum/attachments/20090924/a3dc3f3a/attachment.htm
 

[Pw_forum] why SCF calculation for isolated atom is tricky

[Lorenzo Paulatto]

In data 24 settembre 2009 alle ore 06:53:06, udayagiri sai babu  
 ha scritto:
> In the forum I have seen the statement like doing scf calculation for an
> isolated atom is tricky. Can somebody explain me why is this so?

Because finding the ground-state of an isolated atom often involves  
breaking the symmetry, which requires reading the manual (hint:  
nosym=.true. and specify a starting magnetization).

The most serious problem is that the ground state is usually degenerate,  
e.g. Boron can put it's higher-energy electron in p_x, p_y or p_z or any  
linear combination of three and still get exactly the same energy.
As a consequence Self-consistency cycle can start to oscillate between  
degenerate ground-states and never converge. That's why an abundant number  
of bands and a small smearing is usually a good idea. Other people prefer  
to break  symmetry by hand, e.g. specifying a non-cubic unit cell, but I  
personally find it to be not very effective.

> and then
> while testing a pseudo potential is it a good idea to calculate cohesive
> energies (which involves isolated atom) and compare as we do for lattice
> parameter and bulk modulus.

Yes, it is good idea.

-- 
Lorenzo Paulatto
SISSA  &  DEMOCRITOS (Trieste)
phone: +39 040 3787 511
skype: paulatz
www:   http://people.sissa.it/~paulatto/

 *** save italian brains ***
  http://saveitalianbrains.wordpress.com/

[Pw_forum] from electrons : error # 1 charge is wrong

[Lorenzo Paulatto]

Dear Neel,
I only wish to add one remark to what has been already said by Sreekar and  
Gabriele.

> ecutwfc = 40.0

you have specified ecutwfc, but not ecutrho, which will be set to  
4*ecutwfc=160Ry. Nevertheless, as you are using ultrasoft pseudopotential  
your choice is not very wise; you can probably decrease ecutwfc a bit  
(like 25-30%), but your definitely should increase ecutrho consistently  
(about 8-12 times ecutwfc).

best regards.

-- 
Lorenzo Paulatto
SISSA  &  DEMOCRITOS (Trieste)
phone: +39 040 3787 511
skype: paulatz
www:   http://people.sissa.it/~paulatto/

 *** save italian brains ***
  http://saveitalianbrains.wordpress.com/

[Pw_forum] from electrons : error # 1 charge is wrong

[Neel Singh]

Hi,

?i am trying to relax a structure but after two iteration i am getting this 
error, Please help or advice, My input file is listed below.
Thanks in advance

?iteration #? 1 ecut=??? 40.00 Ry beta=0.20
 Davidson diagonalization with overlap
 ethr =? 1.00E-02,? avg # of iterations =? 1.0

 total cpu time spent up to now is??? 252.18 secs

 WARNING: integrated charge=?? 286.8000, expected=?? 287.

 total energy? = -2892.51662082 Ry
 Harris-Foulkes estimate?? = -2894.39255945 Ry
 estimated scf accuracy??? http://in.yahoo.com/trynew
-- next part --
An HTML attachment was scrubbed...
URL: 
http://www.democritos.it/pipermail/pw_forum/attachments/20090924/0c2bd514/attachment.htm
 

[Pw_forum] Geometry optimization does not converge

[Gunther Jegert]

Thanks for your support. I will follow your suggestions and keep you
informed.

 

Best wishes

Gunther

 

 

_
Dipl.-Phys. Gunther Jegert
Lehrstuhl f?r Nanoelektronik
Technische Universit?t M?nchen
Geb?ude N8, Raum 1820

Theresienstra?e 90
80333 M?nchen

 

Phone: +49 89 289 25370
Mail: <mailto:bernhard.fabel at tum.de> guntherjegert at mytum.de

Web:<http://www.nano.ei.tum.de/> http://www.nano.ei.tum.de
_

 

-- next part --
An HTML attachment was scrubbed...
URL: 
http://www.democritos.it/pipermail/pw_forum/attachments/20090924/f7047d8b/attachment.htm
 

[Pw_forum] Pw_forum Digest, Vol 27, Issue 76

[wangqj1]

>Message: 2
>Date: Wed, 23 Sep 2009 15:06:07 +0200
>From: "Lorenzo Paulatto" 
>Subject: Re: [Pw_forum] Pw_forum Digest, Vol 27, Issue 74
>To: "PWSCF Forum" 
>Message-ID: 
>Content-Type: text/plain; charset=utf-8; format=flowed; delsp=yes
>
>In data 23 settembre 2009 alle ore 14:12:53, wangqj1  ha  
>scritto:
>>> /home/wang/bin/pw.x -npool 8 -in ZnO.pw.inp>ZnO.pw.out
>> It only print the output heander and not have iteration .

>Maybe?it's?not?reading?the?input?at?all!?You?should?specify?the?full?path??
>to?you?input?file,?e.g.
>???mpirun?...?bin/pw.x?-in?/where/is/is/ZnO.pw.inp
>just?to?be?sure.

The output file is as following:
 Program PWSCF v.4.0.1  starts ...
 Today is  24Sep2009 at  8:49:30
  Parallel version (MPI)
  Number of processors in use:   8
 R & G space division:  proc/pool =8
  For Norm-Conserving or Ultrasoft (Vanderbilt) Pseudopotentials or PAW
 .
  Initial potential from superposition of free atoms
  starting charge  435.99565, renormalised to  436.0
  Starting wfc are  254 atomic +8 random wfc
It seems that it had read the input file  .When use K-point parallel ,it runs 
well.

>
>>?I?am?not?the?supperuser,I?don't?know?how?to?Set?the?environment?variable??
>>?OPEN_MP_THREADS?to?1,I?can't?find?where?is?OPEN_MP_THREADS??
>
>You?don't?need?to?be?super-user?(nor?supper-user?;-)?to?set?an?environment??
>variable,?you?only?have?to?add
>??export?OMP_NUM_THREADS=1
>in?your?PBS?script,?before?calling?mpirun.?To?be?sure?it's?propagated?to??
>all?the?processors?add?the?option
>??-x?OMP_NUM_THREAD
>to?mpirun?arguments?(BEFORE?pw.x).
I want to know whether it is necessary to set environment?variable 
OPEN_MP_THREADS?(I installed MPICH2 not OPENMPI) ?
Thanks very much for your help !
Best regards
?
?
-- next part --
An HTML attachment was scrubbed...
URL: 
http://www.democritos.it/pipermail/pw_forum/attachments/20090924/2f43cad8/attachment.htm
 

[Pw_forum] relaxating only z coordinate

[Manoj Srivastava]

Thanks Sagar!

On Thu, 24 Sep 2009, ambavale sagar wrote:

> Dear Manoj

i.e now in your input file the atomic position card will look like:

ATOMIC POSITIONS
Si 000001
Si0.50.50.5001
Si0.70.70.7100

This atomic position card allow you to displace  first two atoms in z direction 
while the third Si in x direction. 


Regards
Sagar Ambavale
The M. S. University of Baroda
India
===


Message: 8
Date: Wed, 23 Sep 2009 17:50:22 -0400 (EDT)
From: Manoj Srivastava 
Subject: [Pw_forum] relaxating only z coordinate?
To: PWSCF Forum 
Message-ID:

Content-Type: TEXT/PLAIN; charset=US-ASCII

Dear PWSCF users, 
This might have been answered previously, but I was unable to find
it. How can one relax only z coordinate of atoms inside unit cell using
PW? In other words how can I constrain x and y coordinates of atoms during
relaxation?


Regards, 
Manoj Srivastava
University of Florida 
Gainesville, FL 



--

Message: 9
Date: Thu, 24 Sep 2009 06:29:11 +0800
From: lan haiping 
Subject: Re: [Pw_forum] relaxating only z coordinate?
To: PWSCF Forum 
Message-ID:

Content-Type: text/plain; charset="iso-8859-1"

Hi, Please check INPUT_PW document,  you will find below description:
if_pos(1), if_pos(2), if_pos(3) INTEGER  *Default:* 1

component i of the force for this atom is multiplied by if_pos(i),
which must be either 0 or 1.  Used to keep selected atoms and/or
selected components fixed in meta-dynamics, neb, smd, MD dynamics or
structural optimization run.

If you want to fix some atom or some direction , just set if_pos(i) =0 .

Regards,

Hai-Ping


  From cricket scores to your friends. Try the Yahoo! India Homepage! 
http://in.yahoo.com/trynew

[Pw_forum] from electrons : error # 1 charge is wrong

[Gabriele Sclauzero]

This question as been asked n! times... please first check forum archives at
http://www.democritos.it/pipermail/pw_forum/

troubleshooting section of user guide,
http://www.quantum-espresso.org/user_guide/user_guide.html

FAQs,
http://www.quantum-espresso.org/wiki/index.php/Frequently_Asked_Questions

...

Posting an incomplete input file does not allow anyone to check if your 
structure is 
correct. Anyway you can do it by yourself using xcrysden, if you haven't yet.

Please, make an effort to put your name and affiliation at the bottom of your 
next mails. 
Thanks!

Regards,


Gabriele


Neel Singh wrote:
> Hi,
> 
>  i am trying to relax a structure but after two iteration i am getting 
> this error, Please help or advice, My input file is listed below.
> Thanks in advance
> 
>  iteration #  1 ecut=40.00 Ry beta=0.20
>  Davidson diagonalization with overlap
>  ethr =  1.00E-02,  avg # of iterations =  1.0
> 
>  total cpu time spent up to now is252.18 secs
> 
>  WARNING: integrated charge=   286.8000, expected=   287.
> 
>  total energy  = -2892.51662082 Ry
>  Harris-Foulkes estimate   = -2894.39255945 Ry
>  estimated scf accuracy< 6.18305675 Ry
> 
>  iteration #  2 ecut=40.00 Ry beta=0.20
>  Davidson diagonalization with overlap
>  ethr =  2.15E-03,  avg # of iterations =  2.0
> 
>  total cpu time spent up to now is438.77 secs
> 
>  WARNING: integrated charge=   286.60793701, expected=   287..
> 
>  
> %%
>  from electrons : error # 1
>  charge is wrong
>  
> %%
> 
>  stopping ...
> rank 2 in job 1  localhost.localdomain_55326   caused collective abort 
> of all ranks
>   exit status of rank 2: killed by signal 9
> 
> 
> Relax input file
> ==]
> 
> 
> calculation='relax',
> restart_mode='from_scratch',
> prefix='ZnO'
> wf_collect=.true.
> pseudo_dir = '/home/sushil/pseudo/',
> outdir='/home/sushil/kajal/dopedZnO/temp'
> tprnfor = ..true. ,
> 
>  /
>  
> ibrav = 4, nat=  32, ntyp=3,celldm(1)=12.280421,
> celldm(3) =1.60203 ,ecutwfc = 40.0,occupations='fixed',
> 
>  /
>  
> mixing_beta = 0.2
> conv_thr =  1.0e-6
> startingpot = 'atomic' ,
> startingwfc = 'atomic' ,
> diagonalization = 'david',
>   
>  /
> 
>   ion_dynamics='damp',
>   pot_extrapolation = "second_order",
>   /
> 
> ATOMIC_SPECIES
>   Zn65.39 Zn.pw91-n-van.UPF
>   O 15.9994   O.pw91-van_ak.UPF
>   N 14.00674  N.pw91-van_ak.UPF
> 
> ATOMIC_POSITIONS {crystal}
>   Zn0.1650.3350.000
>   /
>   /
>   Zn0.8350.6650.750
> 
> K_POINTS {automatic}
>   4 4 2 0 0 0
> 
> 
> 
>  From cricket scores to your friends. Try the Yahoo! India Homepage! 
> 
> 
> 
> 
> 
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum

-- 


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  |
| skype: gurlonotturno |
o  o

[Pw_forum] Pw_forum Digest, Vol 27, Issue 76

[Gabriele Sclauzero]

wangqj1 wrote:
>  >Message: 2
>  >Date: Wed, 23 Sep 2009 15:06:07 +0200
>  >From: "Lorenzo Paulatto" 
>  >Subject: Re: [Pw_forum] Pw_forum Digest, Vol 27, Issue 74
>  >To: "PWSCF Forum" 
>  >Message-ID: 
>  >Content-Type: text/plain; charset=utf-8; format=flowed; delsp=yes
>  >
>  >In data 23 settembre 2009 alle ore 14:12:53, wangqj1  
> ha  
>  >scritto:
>  >>> /home/wang/bin/pw.x -npool 8 -in ZnO.pw.inp>ZnO.pw.out
>  >> It only print the output heander and not have iteration .
> 
>>Maybe it's not reading the input at all! You should specify the full path  
>>to you input file, e.g.
>>   mpirun ... bin/pw.x -in /where/is/is/ZnO.pw.inp
>>just to be sure.
> 
> The output file is as following:
>  Program PWSCF v.4.0.1  starts ...
> 
>  Today is  24Sep2009 at  8:49:30
>   Parallel version (MPI)
>   Number of processors in use:   8
>  R & G space division:  proc/pool =8
>   For Norm-Conserving or Ultrasoft (Vanderbilt) Pseudopotentials or PAW
>  .
>   Initial potential from superposition of free atoms
>   starting charge  435.99565, renormalised to  436.0
>   Starting wfc are  254 atomic +8 random wfc
> 
> It seems that it had read the input file  .

I think so. Maybe you have problems with lack of memory or very slow disk 
access (as 
already pointed by previous responses). Have you tried running with smaller 
system, or 
increasing the number of processors, or using local scratch file system,...?

> When use K-point parallel ,it runs well.

Can you specify better the conditions on which it runs well? What does it mean 
that you 
use "K-point parallel"?

> 
>>
>>> I am not the supperuser,I don't know how to Set the environment variable  
>>> OPEN_MP_THREADS to 1,I can't find where is OPEN_MP_THREADS ?
>>
>>You don't need to be super-user (nor supper-user ;-) to set an environment  
>>variable, you only have to add
>>  export OMP_NUM_THREADS=1
>>in your PBS script, before calling mpirun. To be sure it's propagated to  
>>all the processors add the option
>>  -x OMP_NUM_THREAD
>>to mpirun arguments (BEFORE pw.x).
> I want to know whether it is necessary to set environment variable 
> OPEN_MP_THREADS (I installed MPICH2 not OPENMPI) ?
> 

In case of doubt (like yours), always specify it. It makes no harm, and it 
ensures that 
you're not running into troubles because of unwanted threads proliferation.

HTH

GS


P.S.:Please, always sign your mails and put affiliation. It is not difficult to 
let it be 
done  automatically by your (web)mail program.
Personally, I don't even like seeing mail which use the username as display 
name in the 
mail header, instead of the full (real) name... but that's my opinion.

-- 


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  |
| skype: gurlonotturno |
o  o

[Pw_forum] Fw: isolated atom

[Gabriele Sclauzero]

Maybe there is a bit of misunderstanding: I think that Stefano was referring to 
fixed 
occupations, while Lorenzo to occupations given from input. I just want to 
point out that 
these are two different options to the occupations keyword in the  
namelist (Ali, 
please read carefully the documentation in Doc/INPUT_PW). Anyway they are both 
allowed 
with spin-polarized calculations and should be both viable to get the desired 
GS of the 
molecule.

Cheers

GS

Lorenzo Paulatto wrote:
> In data 23 settembre 2009 alle ore 15:40:55, ali kazempour  
>  ha scritto:
>> But esspresso don't allow fixed occupation for spin-polarized
> 
> Dear Ali,
> it does! You have to specify the occupations for spin up then, on a new  
> line, for spin down.
> 
> that's all
> 
> cheers
> 

-- 


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  |
| skype: gurlonotturno |
o  o

[Pw_forum] Fw: isolated atom

[Duy Le]

nelec in  will solve this problem. This has been discussed many time
in this forum.
:)

On Thu, Sep 24, 2009 at 7:06 AM, ali kazempour wrote:

> Dear Lorenzo
> I tried with this but I have error
> from  system_checkin  : error # 1
>   neldw out of range
> my input file is:
> 
>  calculation = 'scf' ,
> restart_mode = 'from_scratch' ,
>   outdir = '/home/kazempou/tmp/' ,
>   pseudo_dir = './' ,
>   prefix = 'iso-gga' ,
>etot_conv_thr = 0.001 ,
>forc_conv_thr = 0.001 ,
>  /
>  
>ibrav = 1,
>celldm(1) =30
>  nat = 1,
> ntyp = 1,
>  ecutwfc = 60,
>  ecutrho = 400 ,
>  nspin=2
>   occupations='fixed', tot_magnetization=2.0,nelup=4,neldw=2,
>  /
>  
> conv_thr = 1.0D-7 ,
>  /
> ATOMIC_SPECIES
> O   16  o.optgga1.fhi.UPF
> ATOMIC_POSITIONS crystal
> O  0.5 0.5 0.5
> K_POINTS gamma
> would you tell me where did I do mistake?
> 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
>
> --
> *From:* Lorenzo Paulatto 
> *To:* PWSCF Forum 
> *Sent:* Wednesday, September 23, 2009 4:47:56 PM
> *Subject:* Re: [Pw_forum] Fw: isolated atom
>
> In data 23 settembre 2009 alle ore 15:40:55, ali kazempour
>  ha scritto:
> > But esspresso don't allow fixed occupation for spin-polarized
>
> Dear Ali,
> it does! You have to specify the occupations for spin up then, on a new
> line, for spin down.
>
> that's all
>
> cheers
>
> --
> Lorenzo Paulatto
> SISSA  &  DEMOCRITOS (Trieste)
> phone: +39 040 3787 511
> skype: paulatz
> www:  http://people.sissa.it/~paulatto/<http://people.sissa.it/%7Epaulatto/>
>
> *** save italian brains ***
>   http://saveitalianbrains.wordpress.com/
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>


-- 
--
Duy Le
PhD Student
Department of Physics
University of Central Florida.
-- next part --
An HTML attachment was scrubbed...
URL: 
http://www.democritos.it/pipermail/pw_forum/attachments/20090924/17395584/attachment.htm
 

[Pw_forum] relaxating only z coordinate?

[lan haiping]

Hi, Please check INPUT_PW document,  you will find below description:
if_pos(1), if_pos(2), if_pos(3) INTEGER  *Default:* 1

component i of the force for this atom is multiplied by if_pos(i),
which must be either 0 or 1.  Used to keep selected atoms and/or
selected components fixed in meta-dynamics, neb, smd, MD dynamics or
structural optimization run.

If you want to fix some atom or some direction , just set if_pos(i) =0 .

Regards,

Hai-Ping

On Thu, Sep 24, 2009 at 5:50 AM, Manoj Srivastava wrote:

> Dear PWSCF users,
>  This might have been answered previously, but I was unable to find
> it. How can one relax only z coordinate of atoms inside unit cell using
> PW? In other words how can I constrain x and y coordinates of atoms during
> relaxation?
>
>
> Regards,
> Manoj Srivastava
> University of Florida
> Gainesville, FL
>
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>



-- 
Hai-Ping Lan
Department of Electronics ,
Peking University , Bejing, 100871
lanhaiping at gmail.com, hplan at pku.edu.cn
-- next part --
An HTML attachment was scrubbed...
URL: 
http://www.democritos.it/pipermail/pw_forum/attachments/20090924/ac5c3cb0/attachment-0001.htm
 

[Pw_forum] Fw: isolated atom

[ali kazempour]

Dear Lorenzo
I tried with this but I have error
from  system_checkin  : error # 1
  neldw out of range
my input file is:

 calculation = 'scf' ,
restart_mode = 'from_scratch' ,
  outdir = '/home/kazempou/tmp/' ,
  pseudo_dir = './' ,
  prefix = 'iso-gga' ,
   etot_conv_thr = 0.001 ,
   forc_conv_thr = 0.001 ,
 /
 
   ibrav = 1,
   celldm(1) =30
 nat = 1,
ntyp = 1,
 ecutwfc = 60,
 ecutrho = 400 ,
 nspin=2
  occupations='fixed', tot_magnetization=2.0,nelup=4,neldw=2,
 /
 
conv_thr = 1.0D-7 ,
 /
ATOMIC_SPECIES
O   16  o.optgga1.fhi.UPF
ATOMIC_POSITIONS crystal
O  0.5 0.5 0.5
K_POINTS gamma
would you tell me where did I do mistake?
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





From: Lorenzo Paulatto <paula...@sissa.it>
To: PWSCF Forum 
Sent: Wednesday, September 23, 2009 4:47:56 PM
Subject: Re: [Pw_forum] Fw: isolated atom

In data 23 settembre 2009 alle ore 15:40:55, ali kazempour  
 ha scritto:
> But esspresso don't allow fixed occupation for spin-polarized

Dear Ali,
it does! You have to specify the occupations for spin up then, on a new  
line, for spin down.

that's all

cheers

-- 
Lorenzo Paulatto
SISSA  &  DEMOCRITOS (Trieste)
phone: +39 040 3787 511
skype: paulatz
www:  http://people.sissa.it/~paulatto/

 *** save italian brains ***
  http://saveitalianbrains.wordpress.com/
___
Pw_forum mailing list
Pw_forum at pwscf.org
http://www.democritos.it/mailman/listinfo/pw_forum



  
-- next part --
An HTML attachment was scrubbed...
URL: 
http://www.democritos.it/pipermail/pw_forum/attachments/20090924/bd1778c2/attachment.htm
 

[Pw_forum] relaxating only z coordinate?

[Manoj Srivastava]

Thanks Hai-Ping!

-Manoj

On Thu, 24 Sep 2009, lan haiping wrote:

> Hi, Please check INPUT_PW document,  you will find below description:
> if_pos(1), if_pos(2), if_pos(3) INTEGER  *Default:* 1
> 
> component i of the force for this atom is multiplied by if_pos(i),
> which must be either 0 or 1.  Used to keep selected atoms and/or
> selected components fixed in meta-dynamics, neb, smd, MD dynamics or
> structural optimization run.
> 
> If you want to fix some atom or some direction , just set if_pos(i) =0 .
> 
> Regards,
> 
> Hai-Ping
> 
> On Thu, Sep 24, 2009 at 5:50 AM, Manoj Srivastava  phys.ufl.edu>wrote:
> 
> > Dear PWSCF users,
> >  This might have been answered previously, but I was unable to find
> > it. How can one relax only z coordinate of atoms inside unit cell using
> > PW? In other words how can I constrain x and y coordinates of atoms during
> > relaxation?
> >
> >
> > Regards,
> > Manoj Srivastava
> > University of Florida
> > Gainesville, FL
> >
> > ___
> > Pw_forum mailing list
> > Pw_forum at pwscf.org
> > http://www.democritos.it/mailman/listinfo/pw_forum
> >
> 
> 
> 
> -- 
> Hai-Ping Lan
> Department of Electronics ,
> Peking University , Bejing, 100871
> lanhaiping at gmail.com, hplan at pku.edu.cn
>