[Pw_forum] Problem on pp.x

[Paolo Giannozzi]

On Friday 26 December 2008 04:48, Jiaye, Li wrote:
> I tried like this: mpirun -np 2 ~/bin/pp.x input.inp output.out

you should have tried like this:
  mpirun -np 2 ~/bin/pp.x < input.inp 
or
  mpirun -np 2 ~/bin/pp.x -in input.inp 
Paolo
-- 
Paolo Giannozzi, Democritos and Udine University

[Pw_forum] K_POINTS, tpiba or crystal

[giann...@democritos.it]

Quoting "Paul M. Grant" :

> Frankly, I don't understand what "crystal" means wrt to reciprocal space

it means "in units of the reciprocal lattice primitive vectors"

Paolo



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[Pw_forum] dynmat.x

[giann...@democritos.it]

Quoting Adam Jacobsson :

> My first thought was that the program wanted the direction from where 
> to approach the gamma point as a limit. Is that the case?

yes. If you specify a direction for q, dynmat.x will calculate the 
LO-TO splitting; if you specify q=0, it will not calculate it.

Paolo
--
Paolo Giannozzi, Democritos and Udine University



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[Pw_forum] K_POINTS, tpiba or crystal

[Paul M. Grant]

OK, let's get specific...suppose I want to generate a uniformly distributed
set of k-points for the reciprocal lattice of the primitive cell of an fcc
lattice.  The output of an scf run (and common sense matrix algebra) tells
me the reciprocal lattice is defined as

reciprocal axes: (cart. coord. in units 2 pi/a_0)
   b(1) = (  1.00  0.00  0.00 )  
   b(2) = (  0.00  1.00  0.00 )  
   b(3) = (  0.00  0.00  1.00 )  

OK (again)...I now generate a(n) uniformly distributed grid over the "b"
vectors, and plot the points via xcrysden with PRIMVEC as above and see that
grid fills the entire basic reciprocal cell (that is, with translation
vector = O).  No specification of celldm(1).

Now, I want to input this grid to an nscf run via K_POINTS...is my grid
"tpiba" or "crystal?"

BTW, we (this community) owe a huge debt to Paolo and Axel.

Paul M. Grant, PhD
Principal, W2AGZ Technologies
Visiting Scholar, Applied Physics, Stanford (2005-2008)
EPRI Science Fellow (Retired)
IBM Research Staff Member Emeritus
w2agz at pacbell.net
http://www.w2agz.com
?
?

-Original Message-
From: pw_forum-bounces at pwscf.org [mailto:pw_forum-boun...@pwscf.org] On
Behalf Of giannozz at democritos.it
Sent: Monday, December 29, 2008 12:29 PM
To: pw_forum at pwscf.org
Subject: Re: [Pw_forum] K_POINTS, tpiba or crystal

Quoting "Paul M. Grant" :

> Frankly, I don't understand what "crystal" means wrt to reciprocal space

it means "in units of the reciprocal lattice primitive vectors"

Paolo



This message was sent using IMP, the Internet Messaging Program.

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[Pw_forum] Problems in compiling pw.x and ph.x using XLF and ESSL on IBM-PPC

[Paolo Giannozzi]

On Wednesday 24 December 2008 13:54, Zhong-Li Liu wrote:

> So could you find some missettings of the compilation parameters and
> something wrong? 

use -D__LINUX_ESSL instead of -D__ESSL . For parallel execution,
add -D__PARA. For the rest, complain with IBM or better with 
whoever bought that machine

-- 
Paolo Giannozzi, Democritos and Udine University

[Pw_forum] electron-phonon interaction

[penghua]

Dear pwscf users, 

In example 07, how to calculate electron-phonon interaction is shown. But, why 
twice scf calculations are done in this calculation? What is the intention of 
each calculation?

Besides can I calculation the electron-phonon interaction of semiconductor?

Thank you in advance.

 

Penghua

Penghua8503 at 163.com

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[Pw_forum] problem about calculation with ph.x

[lzh-ming]

Hello everyone,
  I have tried to calculate the phonon disperation of CdCNi3.
I wrote in the file CdCNi3.ph.in as follow:
  
  ldisp=.true.,
  nq1=4, nq2=4, nq3=4,
  iq1=2, iq2=1, iq3=1,
 
but in the file CdCNi3.dyn0 , I got 
  4 4 4
  1
  0.0 0.0 0.0 
 
I changed the value of iq1,iq2,iq3 to 2,2,1, I still got 0.0 0.0 0.0.
I set the value as 3 3 2, I got 0.25 0.25 0.25.
When the value is 3 3 3, I got -0.5 -0.5 -0.5.(This is right.)
 
I tried all the 10 unequivalent points of 4*4*4 grid(simple cube),
I only got 3 different outputs.
 
What's the problem? Can you help me?
 
Thanks a lot!
 
li-ming-fan
 


 
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[Pw_forum] electron-phonon interaction

[Lorenzo Paulatto]

On Mon, 29 Dec 2008 13:20:24 +0100, penghua  wrote:
> But, why twice scf calculations are done in this calculation? What is  
> the intention of each calculation?

It is explained quite clearly in the README file in the example07 directory: 
the first one is for DOS calculation, the second for phonons. Please read the 
README file accurately, as it provides vital hints and answers your question in 
detail.


> Besides can I calculation the electron-phonon interaction of  
> semiconductor?

I don't see any problem with it, but I don't really know the matter in depth 
thus some technical problems may arise.

cheers

P.S. please provide your affiliation when writing to pw forum!


-- 
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] K_POINTS, tpiba or crystal

[Axel Kohlmeyer]

On Mon, 29 Dec 2008, Paul M. Grant wrote:


hi paul,

PG> When specifying a user generated mesh for an nscf run, should tpiba (the
PG> default) or crystal coordinates be designated on the  K_POINTS card?

most likely tpiba.

PG> Frankly, I don't understand what "crystal" means wrt to reciprocal space
PG> (ATOMIC_POSITIONS, yes), and it does seem to make a small difference

in my understanding, crystal would be multiples of the 
reciprocal lattice vectors, i.e. the "b"-matrix printed
out at the beginning of a job.

cheers,
   axel.

PG> depending on the application (e.g. Fermi surface generation).


PG> 
PG> A Merry Winter Solstice Break to All.
PG> 
PG> Paul M. Grant, PhD
PG> Principal, W2AGZ Technologies
PG> Visiting Scholar, Applied Physics, Stanford (2005-2008)
PG> EPRI Science Fellow (Retired)
PG> IBM Research Staff Member Emeritus
PG> w2agz at pacbell.net
PG> http://www.w2agz.com  
PG>  
PG>  
PG> 
PG> 
PG> 

-- 
===
Axel Kohlmeyer   akohlmey at cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
===
If you make something idiot-proof, the universe creates a better idiot.

[Pw_forum] Too many data communications between nodes when run pw.x in parallel?

[Axel Kohlmeyer]

On Tue, 30 Dec 2008, Wang Qinjing wrote:

QW> Dear all:

QW> I noted that if I made calculation by pw.x in paralllel, there were 
QW> too many data communications between nodes. That was attributed to 
QW> the data communication of wave functions. There is a severe delay to 
QW> get information from these nodes.

please provide more detail about the kind of job you 
are running, how you were running it and the kind of 
hardware you are running it on.

there are several ways how you can improve parallel efficiency.
please see the documentation and the many previous discussions
on this topic and then make some scaling and performance tests
to see how to run most efficiently. the best settings can vary
a lot between different inputs and calculation types.
 
QW> If I set disk_io='low', things are much better. But the main node 

this is only one option and indicates that you are most likely
not running your job in a very efficient manner.

QW> (or the first node) still has problem in net communication. I 
QW> noticed a charge density file is still written after each scf step. 
QW> Is that the problem?  Or is there anything I can do to improve this 
QW> situation?

there is a lot that can be done, but since you don't provide any
information on what you are already doing, it is impossible to
give any recommendation beyond urging you to (re-)read the 
documentation and FAQs.

cheers,
   axel.

QW> Thanks in advance.
QW> 
QW> Yours Wang
QW> 
QW> 
QW> 
QW> Wang Qinjing, Physics Department, 
QW> Fudan University

-- 
===
Axel Kohlmeyer   akohlmey at cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
===
If you make something idiot-proof, the universe creates a better idiot.

[Pw_forum] K_POINTS, tpiba or crystal

[Paul M. Grant]

When specifying a user generated mesh for an nscf run, should tpiba (the
default) or crystal coordinates be designated on the  K_POINTS card?
Frankly, I don't understand what "crystal" means wrt to reciprocal space
(ATOMIC_POSITIONS, yes), and it does seem to make a small difference
depending on the application (e.g. Fermi surface generation).

A Merry Winter Solstice Break to All.

Paul M. Grant, PhD
Principal, W2AGZ Technologies
Visiting Scholar, Applied Physics, Stanford (2005-2008)
EPRI Science Fellow (Retired)
IBM Research Staff Member Emeritus
w2agz at pacbell.net
http://www.w2agz.com <http://www.w2agz.com/> 
 
 


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[Pw_forum] can pwscf compute the phonon of properties of excited state?

[xu yuehua]

hi all
i face a problem when calculate the phonon at G  of  excited state?
 iter #  78 total cpu time : 20566.8 secs   av.it.: 141.6
  thresh= 0.100E-01 alpha_mix =  0.700 |ddv_scf|^2 =  0.430+113
  iter #  79 total cpu time : 21036.5 secs   av.it.: 144.1
  thresh= 0.100E-01 alpha_mix =  0.700 |ddv_scf|^2 =  0.236+115
  iter #  80 total cpu time : 21484.8 secs   av.it.: 146.4
  thresh= 0.100E-01 alpha_mix =  0.700 |ddv_scf|^2 =  0.198+119
  iter #  81 total cpu time : 21946.2 secs   av.it.: 151.2
  thresh= 0.100E-01 alpha_mix =  0.700 |ddv_scf|^2 =  0.311+122
 kpoint   1 ibnd  17 solve_e: root not converged  0.113E-01
 kpoint   1 ibnd  17 solve_e: root not converged  0.142E-01
  iter #  82 total cpu time : 22423.0 secs   av.it.: 155.6
  thresh= 0.100E-01 alpha_mix =  0.700 |ddv_scf|^2 =  0.207+127
 kpoint   1 ibnd  17 solve_e: root not converged  0.140E-01
 kpoint   1 ibnd  17 solve_e: root not converged  0.520E-01
 kpoint   1 ibnd  17 solve_e: root not converged  0.558E-01
 kpoint   2 ibnd  17 solve_e: root not converged  0.127E-01
 kpoint   2 ibnd  17 solve_e: root not converged  0.544E-02
 kpoint   2 ibnd  17 solve_e: root not converged  0.522E-02
so i want to ask can pwscf compute the phonon of properties of excited
state?

-- 
Xu Yuehua
physics Department of Nanjing university
China
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[Pw_forum] can pwscf compute the phonon of properties of excited state?

[Axel Kohlmeyer]

On Mon, 29 Dec 2008, xu yuehua wrote:

YX> hi all
YX> i face a problem when calculate the phonon at G  of  excited state?

what _kind_ of excited state? 
what are the inputs that you were using? 

as has been mentioned here _many_ times, the more details 
you provide, the better chances you have of getting a useful 
answer, or any answer at all.

axel.

YX>  iter #  78 total cpu time : 20566.8 secs   av.it.: 141.6

[...]


-- 
===
Axel Kohlmeyer   akohlmey at cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
===
If you make something idiot-proof, the universe creates a better idiot.

[Pw_forum] Problem on pp.x

[Jiaye, Li]

Hi

I think my input file should be correct, since I made it according to the
example. But when I submit a job, it always report:
 Program POST-PROC v.4.0.3  starts ...
 Today is 29Dec2008 at 17:36:39
 Parallel version (MPI)
 Number of processors in use:   2
 R & G space division:  proc/pool =2
 %%
 from postproc : error #   225
 reading inputpp namelist
 %%
As a previous post pointed out that it may be due to the input file error,
however, I think the input file should be a standard input file for surface
calculation, could you help me with pick out where the error is from my
input file? Thanks.

 
   outdir='/home/blade/jamesli/test/tmp',   # temp files
   plot_num=11  # the V_bare + V_H potential
   filplot = 'IO-O.pp'  # the quantity selected by plot_num
/
 
   iflag= 3,# 3D plot
   output_format=3  # format suitable for
XCRYSDEN  (1D, 2D, 3D)
/


-- 
Sincerely

Jiaye Li



==
Li, Jiaye

M.S. in designing and developing novel materials

Research experience:
*ALD precursor. ie. Metal complexes
*Surface modification. ie. Indium tin oxide, SiO2
*Gas storage and adsorption. ie. Ionic Liquids

Skills:
*ab-initial method, DFT simulation and Force Field simulation

Please contact me at:
1. jameslipd at gmail.com  or
2. jameslibd at gmail.com

==
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[Pw_forum] Problem on pp.x

[Lorenzo Paulatto]

On Mon, 29 Dec 2008 02:59:26 +0100, Jiaye, Li  wrote:
> I think my input file should be correct, since I made it according to the
> example. But when I submit a job, it always report:

Dear Li Jiaye,
you cannot use "#" as a comment marker in an input file; it works in the 
example because it is inserted in a bash script. Replace the "#" with "!" and 
it will work.

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] problem about calculation with ph.x

[Eyvaz Isaev]

Dear li-ming-fan,

In order to calculate phonon dispersion curves you need to calculate real space 
Interatomic Force Constants matrix F(R). This can be obtained via the FFT using 
the dynamical matricies F(q). 

In order to get F(q) set, you should use only nq1,nq2,nq3, but not iq1,iq2,iq3 
which are used to calculate F(q) for a given q-point(s).

After F(q)=> F(R) transformation you have to supply a list of q-points along 
high symmetry directions and calculate phonon modes for these points.

Bests,
Eyvaz.


---
Prof. Eyvaz Isaev, 
Theoretical Physics Department, Moscow State Institute of Steel & Alloys, 
Russia, 
Department of Physics, Chemistry, and Biology (IFM), Linkoping University, 
Sweden 
Condensed Matter Theory Group, Uppsala University, Sweden 
Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com


--- On Mon, 12/29/08, lzh-ming  wrote:

> From: lzh-ming 
> Subject: [Pw_forum] problem about calculation with ph.x
> To: "Pw_forum" 
> Date: Monday, December 29, 2008, 2:46 PM
> Hello everyone,
>   I have tried to calculate the phonon disperation of
> CdCNi3.
> I wrote in the file CdCNi3.ph.in as follow:
>   
>   ldisp=.true.,
>   nq1=4, nq2=4, nq3=4,
>   iq1=2, iq2=1, iq3=1,
>  
> but in the file CdCNi3.dyn0 , I got 
>   4 4 4
>   1
>   0.0 0.0 0.0 
>  
> I changed the value of iq1,iq2,iq3 to 2,2,1, I still got
> 0.0 0.0 0.0.
> I set the value as 3 3 2, I got 0.25 0.25 0.25.
> When the value is 3 3 3, I got -0.5 -0.5 -0.5.(This is
> right.)
>  
> I tried all the 10 unequivalent points of 4*4*4 grid(simple
> cube),
> I only got 3 different outputs.
>  
> What's the problem? Can you help me?
>  
> Thanks a lot!
>  
> li-ming-fan
>  
> 
> 
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