[Pw_forum] 回复： Can the result of relax mode be recongnized as one representive of snapshots of molecular dynamics?

[Huiqun Zhou]

shaofeng,

I don't think you can generally think that way, they are different.  

In short, the process of relaxation (structure optimization) is mathematical, 
while
the process of MD is physical. Putting it in a clearer way, the movement of 
ions in
a system during relaxation is ruled by the algorithms you are using, whether 
Newton-like, 
or conjugate gradient, and the trajectory of the movement is meaningless. In 
MD, the
movement of atoms in a system is assumed to obey classical mechanics, and the 
evolving 
trajectory of the system is obtained by solving a system of ordinary 
differential 
equations. This trajectory can be used to calculate various physical properties 
of the
system.

In case you are considering crystal structure of the system at T=0 K, the 
result of 
relaxation, ONLY the structure, is indeed coincident to the average of last a 
few 
snapshots of a MD trajectory in equilibrium at T=0 K. That's why there is 
option of MD 
for structural optimization in other DFT code.   


Huiqun Zhou@Earth Sciences
Nanjing University, China


- 原始邮件 -
发件人: "Shaofeng Wang" 
收件人: pw forum 
已发送邮件: Wed, 17 Jun 2015 00:33:19 +0800 (CST)
主题: [Pw_forum] Can the result of relax mode be recongnized as one
representive of snapshots of molecular dynamics?

Dear all,

Can the result of relax mode be recongnized as one representive of snapshots 
of molecular dynamics?

Regards,

Shaofeng



--
Shaofeng Wang, Ph.D
Environmental Molecular Science Group
Institute of Applied Ecology, Chinese Academy of Sciences
Shenyang, 110016, China
wangshaof...@iae.ac.cn
www.iae.cas.cn 


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[Pw_forum] 回复： espresso installation problem

[Huiqun Zhou]

Hi,

If your error message really indicates that fftw is the problem, I'd like to
guess that the way you linked your espresso programs is the issue. You may 
linked the programs with fftw dynamically, while your fftw is only installed
on your fronted, so that when the program is distributed to the compute nodes,
the program could not find where the .so file is at these nodes.

You may need to install fftw either on every compute nodes, or under a network
shared directory, or link quantum espresso with fftw statically.

As you didn't show us your error message, the above is just a guess.


Huiqun Zhou
@Earth Sciences, Nanjing University, China



-  -
???: Ajanta Maity 
???: pw forum 
?: Wed, 06 Aug 2014 02:57:24 +0800 (CST)
??: [Pw_forum] espresso installation problem

Hello all,
I am trying to configure espresso 5.1 on a cluster having Centos6. After
the make all command i get following error.

make[2]: *** [pw.x] Error 1
make[2]: Leaving directory `/c9gpfs/c9scratch/user/qe/espresso-5.1/PW/src'
make[1]: *** [pw] Error 1
make[1]: Leaving directory `/c9gpfs/c9scratch/user/qe/espresso-5.1/PW'
make: *** [pw] Error 1
It seems the some FFTW lib problem and i am very new to all this. Any help
will be greatly appreciated.
Thanks
Ajanta
Research Scholar
Harish Chandra Research Institute,
Allahabad,India

[Pw_forum] where is qe-gipaw?

[Huiqun Zhou]

Hi,

It'll download the qe-gipaw-5.0.tar.gz from 
http://ge-forge.org/frs/download.php/198/ge-gipaw-5.0.tar.gz
automatically when run 
  make gipaw

If your frontend has no direct internet connection, you have to download it 
from the above URL and put
it into "archive" directory, then make gipaw.

dr. zhou huiqun
@earth sciences, nanjing university, china

  - Original Message - 
  From: ??? 
  To: PWSCF Forum 
  Sent: Tuesday, June 26, 2012 3:27 PM
  Subject: [Pw_forum] where is qe-gipaw?


  Dear all,
  I tried to compile the gipaw for qe4.3.2 and 5.0.
  When I try to make gipaw, both two QE version can not download gipaw from 
qeforge.
  I checked the QEforge and find that the latest gipaw is for 4.3.1.
  How to compile gipaw for 4.3.2 or 5.0?
  Thank you in advance.
  Best,
  -- 
  Y. C. Cheng
  Department of Physics
  Nanjing University
  Nanjing 210093
  P. R. China
  Tel: 86-25-83592907
  Email: yccheng.nju at gmail.com



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[Pw_forum] Requesting for structural details

[Huiqun Zhou]

You just need to pick up a math textbook of high school. 
Given a vector a = (ax, ay, az), |a| = sqrt(ax^2+ay^2+az^2).
For the angle between two vectors, you need to know their dot product,
cos(angle) = a dot b /(|a||b|), where a dot b = ax*bx + ay*by + az*bz.

Hope you know which two lattice vectors correspond to which angle.

zhou huiqun
@earth sciences, nanjing university, china

  - Original Message - 
  From: Kondaiah Samudrala 
  To: pw_forum at pwscf.org 
  Sent: Sunday, January 29, 2012 4:31 AM
  Subject: [Pw_forum] Requesting for structural details


  Dear All,

  I am working on layered type material which crystallizes in rhombohedral 
structure with space group 166 ( ibrav =5). In the i/p file for VC-Relax, i 
used the lattice parameters and angle as  celldm(1)=7.4870 and 
celldm(4)=0.586005.

  In the first step of the of the o/p file shows the basis vectors as 
  0.454970 -0.262677 0.850884
  0.00 0.525354 0.850884
  -0.4504970 -0.262677 0.850884

  After completing the VC-Relax i got the basis vectors as


  CELL-PARAMETERS ( alat=7.4870)
  0.441119855 -0.254680667 0.78874941
  0.   0.509361335 0.78874941
  -0.441119855 -0.254680667 0.78874941

with this o/p values, how can i calculate lattice vector and angle for my 
material ( For orthorhombic and tetragonal structures i calculated lattice 
parametrs successfully but i am not able to do this structure ).


  i am requesting your favorable reply.

  with regards
  S.Appalakondaiah
  PhD Scholar
  University of Hyderabad
  Hyderabad
  India







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[Pw_forum] vc-relax for a Magnetic atom

[Huiqun Zhou]

I just can't understand why you need to do vc-relax to an single atom system.
Usually, you need to put the atom in a big enough supercell, do you think
there are any geometric parameters need to be optimized in such a case? 

What you need to do is to determine how big the supercell should be.


dr. zhou huiqun
@earth sciences, nanjing university, china 

  - Original Message - 
  From: Ali ALLAM 
  To: pw_forum at pwscf.org ; giannozz at democritos.it 
  Sent: Wednesday, November 23, 2011 4:06 PM
  Subject: [Pw_forum] vc-relax for a Magnetic atom




  Dear All
   
  I want to calculate the vc-relax for a magnetic atom, like the manganese Mn.
   
  I try to do it, but always , i obtain errors and the calculation is not good 
at all.
   
  So what should i add in my input to obtain a better calculation for Mn.
   
  Can anybody send for me to ali.allam2 at hotmail.com an example for the 
vc-relax for a magnetic atom.
   
  Thanks 
   
  Ali



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[Pw_forum] calculation of lattice parameter and angle of rhombohedral structure

[Huiqun Zhou]

I'm afraid the formula for calculating cosA should be
cosA = b (*) c / (|b| | c|)

dr. zhou huiqun
@earth sciences, nanjing university, china

  - Original Message - 
  From: GAO Zhe 
  To: PWSCF Forum 
  Sent: Wednesday, November 16, 2011 8:53 PM
  Subject: Re: [Pw_forum] calculation of lattice parameter and angle of 
rhombohedral structure


  the three basis vectors of rhombohedral are (after relaxation) :
  a = ( 0.636439417  -0.367448469   0.640642896 )
  b = ( 0.0   0.734896938   0.640642896 )
  c = ( -0.636439417  -0.367448469   0.640642896 )
  then the lattice paremeter should be: A = sqrt (a1^2+a2^2+a3^2) * alat = 
8.05092296 a.u. .
  The angle between two vectors can be calculated by:
  cosA = a (*) b / |a (*) b|,
  where a and b are basis vectors, (*) represents the dot product.


  --
  GAO Zhe
  CMC Lab, MSE, SNU, Seoul, S.Korea


  At 2011-11-16 20:14:38,"yedu kondalu"  wrote:

Dear users,

I did the optimization for a compound using variable cell approximation 
using PWSCF, which belongs to the space group R3m(160) Rhombohedral 
representation.  The primitive vectors in terms of lattice parameter a = 
8.25791360 a.u.  
   a(1) = (   0.619505  -0.357671   0.698774 )  
   a(2) = (   0.00   0.715343   0.698774 )  
   a(3) = (  -0.619505  -0.357671   0.698774 ) 

after completion of optimization step, the primitive vectors

CELL_PARAMETERS (alat=  8.25791360)
   0.636439417  -0.367448469   0.640642896
   0.0   0.734896938   0.640642896
  -0.636439417  -0.367448469   0.640642896

can u please explain me 

how can I calculate the lattice parameter a and the angle (alpha)  ???

Thanks in advance

 Regards
 Yedukondalu








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[Pw_forum] Query on Xcrysden

[Huiqun Zhou]

When you try to use XCrysden from PWgui, you still need to have a copy of
XCrysden to be installed in advance.


dr. zhou huiqun
@earth sciences, nanjing university, china

- Original Message - 
From: "Ren PJ" 
To: 
Sent: Monday, November 07, 2011 10:50 PM
Subject: Re: [Pw_forum] Query on Xcrysden


> 
> There is a executable file which need not to install. The latest version
> is 4.3. The url is: http://www-k3.ijs.si/kokalj/pwgui/
> 
> 
> 
> 
> Pengju Ren
> renpj at dicp.ac.cn
> State  Key Laboratory of Catalysis, 
> Dalian Institute of Chemical Physics, 
> Chinese Academy of Sciences 
> 457 zhongshan Road, Dalian, 116023, P.R. China  
> ___
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>

[Pw_forum] problem in scf run

[Huiqun Zhou]

Axel,

I noticed recently that you have come back to qe mailing list, warm welcome!

You are always a very valuable person at every forum you had and have been 
taking care of!

zhou huiqun
@earth sciences, nanjing university, china
  - Original Message - 
  From: Axel Kohlmeyer 
  To: PWSCF Forum 
  Sent: Thursday, November 03, 2011 10:19 PM
  Subject: Re: [Pw_forum] problem in scf run





  On Thu, Nov 3, 2011 at 8:50 AM, Pankaj Pankaj  
wrote:

Dear All,

  When i tried to run my scf cal, i got following message

At line 155 of file read_cards.f90
Fortran runtime error: End of file
At line 155 of file read_cards.f90
Fortran runtime error: End of file
At line 155 of file read_cards.f90
Fortran runtime error: End of file
At line 155 of file read_cards.f90
Fortran runtime error: End of file
--
mpirun has exited due to process rank 1 with PID 1914 on
node shiva exiting without calling "finalize". This may
have caused other processes in the application to be
terminated by signals sent by mpirun (as reported here).

Whereas for VERY SIMILAR file do not give any error. Where can be problem.



  your input is missing an essential part.
  and "end of file" error means, that the
  code is trying to read something, but
  it is not there.


  axel.


Thank you so much.

Kind Regards
Pankaj
Research Assistant
AU India

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  Dr. Axel Kohlmeyer   
  akohlmey at gmail.com  http://goo.gl/1wk0

  College of Science and Technology
  Temple University, Philadelphia PA, USA.



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[Pw_forum] Running an input file

[Huiqun Zhou]

Gulicin,

It seems you may be a totally beginner in using LINUX/UNIX OS, too.
If it's true, just forget the example script for a moment, and prepare an
input file of pwscf, then run
$ /bin/pw.x -input your_input_file.inp 
or if you have access to a parallel computer:
$ mpirun -np 4 /bin/pw.x -input 
your_input_file.inp 

hope this help you.

zhou huiqun
@earth sciences, nanjing university, china

  - Original Message - 
  From: Gulcin Kucukdalyan 
  To: pw_forum at pwscf.org 
  Sent: Thursday, October 20, 2011 4:52 AM
  Subject: [Pw_forum] Running an input file


  HI All,

  Could you please tell me how can i run an input file. It is the second time i 
am asking this question. Last time i was asked to read tutorials. It is not 
specified there if i have to prepare a text file or an executable file 
(run_example) like the ones in the examples. If i have to prepare a text file 
how can i run it.

  Thanks, 

  Gulcin



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[Pw_forum] Input file for MgB2C2.

[Huiqun Zhou]

You should have already got the crystal structure from the information
you provided, haven't you?

1/2a = 5.461
1/2b = 4.7305
c = 7.459

And because your structure is base centered orthorhombic (bco),
so your ibrav = 9.

Hope this help you.

zhou huiqun
@earth sciences, nanjing university, china


- Original Message - 
From: "Hongsheng Zhao" 
To: 
Sent: Sunday, July 17, 2011 3:54 PM
Subject: Re: [Pw_forum] Input file for MgB2C2.


On 07/17/2011 02:38 PM, Eyvaz Isaev wrote:
>
>  > I want to construct the corresponding crystal structure information for
>  > pwscf based on the above content. Any hints?
>
> You have all the information to build the crystal structure. Please read
> carefully the page info.

I've some puzzles on which are the lattice vectors should be used for
this case.  In detail, you can find the following information from the
webpage: http://cst-www.nrl.navy.mil/lattice/struk/mgb2c2.html

-
   Primitive Vectors:
A1 =  ? a X - ? b Y
A2 =  ? a X + ? b Y
A3 =  c Z
-

On the other hand, you can find the following information from within
the mgb2c2.pos file downloaded from here:
http://cst-www.nrl.navy.mil/lattice/struk.xmol/mgb2c2.pos:

--
Primitive vectors
a(1) =   5.4610 -4.7305  0.
a(2) =   5.4610  4.7305  0.
a(3) =   0.  0.  7.4590
--

So in this case, what's the lattice vectors should I used to construct
the unit cell, i.e., the [a(1),a(2), a(3)] or the [a,b,c] should be used?

Furthermore, you can find fourty basis vectors listed for MgB2C2 on the
webpage: http://cst-www.nrl.navy.mil/lattice/struk/mgb2c2.html.  What's
the usage of these basis vectors?

Regards
>
> Bests,
> Eyvaz.
> ---
> Prof. Eyvaz Isaev,
> Department of Physics, Chemistry, and Biology (IFM), Linkoping
> University, Sweden
> Theoretical Physics Department, Moscow State Institute of Steel &
> Alloys, Russia,
> isaev at ifm.liu.se, eyvaz_isaev at yahoo.com
> 
> *From:* Hongsheng Zhao 
> *To:* PWSCF Forum 
> *Sent:* Sunday, July 17, 2011 7:24 AM
> *Subject:* [Pw_forum] Input file for MgB2C2.
>
> Hi all,
>
> I obtain the xyz format crystal structure information for MgB2C2 - with
> the spacegroup of Cmca (#64) - from the following webpage:
>
> http://cst-www.nrl.navy.mil/lattice/struk.xmol/mgb2c2.pos
>
>
>
> I want to construct the corresponding crystal structure information for
> pwscf based on the above content. Any hints?
>
> Regards
> --
> Hongsheng Zhao mailto:zhaohscas at yahoo.com.cn>>
> School of Physics and Electrical Information Science,
> Ningxia University, Yinchuan 750021, China
>
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>
>
>
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-- 
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School of Physics and Electrical Information Science,
Ningxia University, Yinchuan 750021, China
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[Pw_forum] how to choose ibrav

[Huiqun Zhou]

Hi, 

It's your own responsibility to make clear what crystal class your system 
belongs to.
Do you know the symbol of space group of your system? For your case, if it's 
Pxxx, 
the system should be simple tetragonal (ibrav=6), if it's Ixxx, it should be 
base centered 
tetragonal (ibrav=7).


zhou huiqun
@earth sciences, nanjing university, china

  - Original Message - 
  From: tian kong 
  To: PWSCF Forum 
  Sent: Saturday, June 25, 2011 9:49 PM
  Subject: Re: [Pw_forum] how to choose ibrav


  yeah, i think you are right. but what really matters is how to set ibrav in 
pwscf. 

  ibravstructure   celldm(2)-celldm(6)

6  Tetragonal P (st)   celldm(3)=c/a
7  Tetragonal I (bct)  celldm(3)=c/asimple tetragonal 
(p)

   v1 = a(1,0,0),  v2 = a(0,1,0),  v3 = a(0,0,c/a)

body centered tetragonal (i)

   v1 = (a/2)(1,-1,c/a),  v2 = (a/2)(1,1,c/a),  v3 = (a/2)(-1,-1,c/a).
it seems that: if ibrav=6, then A=B?C. if ibrav=7, then A=B=C.but what i need 
is A?B=C. i don't know if i can choose ibrav=6 or 7, and should i need to 
change the atoms position after i choose ibrav=6 or 7 ?


  ?this is an email sent by tiankong?



  2011/6/24 GAO Zhe 

In your case, this structure must be simple tetragonal or body centered 
tetragonal. Please check your model more carefully from PDF-card or ICSD 
database.
P.S.: the choice of ibrav depends on the knowledge of crystallography, 
please learn it before you do ab-initio calculation, since symmetry is a very 
important and foundamental thing in this area.

--
GAO Zhe
CMC Lab, MSE, SNU, Seoul, S.Korea


At 2011-06-24 15:25:10?"tian kong"  wrote:

  i have read the help document about INPUT_PW.htm again and again, but 
since i'm a newbie, i still don't know whice one i should choose. can you help 
me?
  here is the problem:
  A=10, B=C=8, cosAB=cosBC=cosAC=0.
  can you tell me ibrav=?
  thx a lot !!!
  ?this is an email sent by tiankong?





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[Pw_forum] Reading fildvscf

[Huiqun Zhou]

Reading fildvscfYou need to find out the piece of source code that write the 
file fildvscf, then
you can mimic the code, for example, open the file as "old", replace "write"
with "read", and make use of the original "format" statements, to write your 
program to read the file in. It should be very simple even for those who have 
very little experience of programming.

zhou huiqun
@earth scieces, nanjing university, china

  - Original Message - 
  From: Siobhan O'Halloran 
  To: pw_forum at pwscf.org 
  Sent: Tuesday, June 21, 2011 7:12 PM
  Subject: [Pw_forum] Reading fildvscf


  Hi all,

  I would like to read the variation of the potential from fildvscf. As 
somebody who has little programming experience, how would I do that?

  Regards,

  Siobhan O Halloran

  Materials Theory Group
  Tyndall National Institute
  Cork, Ireland





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[Pw_forum] VC RELAX

[Huiqun Zhou]

Abolore,

There are two , actually one, "implicit" methods for defining the matrix:
1. set ibrav = 1 to 14 to define a suitable lattice, then celldm(i), i = 1 
to 6, to
define the cell parameters;
2. set ibrav again, as well as A, B, C, cosAB, cosAC and cosBC to define
cell parameters;

There is one explicit method for defining the cell vector matrix, too:
set ibrav = 0 with celldm(1) = alat or without celldm(1), then define the 
three
vectors as suitable for your purpose in the CELL_PARAMETER card.

For detail, please read the input_PW.html. Manual is always your first aid!

zhou huiqun
@earth sciences and engineering, nanjing university, china


- Original Message - 
From: "Abolore Musari" 
To: 
Sent: Sunday, June 19, 2011 6:51 PM
Subject: [Pw_forum] VC RELAX


> Dear all, In the vc relax example of the expresso l want to ask how
> the cell parameter (3x3 matrix) of the system are gotten. thanks in
> anticapation of your favourable reply. Abolore, Phy dept UNAAB
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[Pw_forum] to extract k-point from bilbao crystallographic server

[Huiqun Zhou]

They are just written down there in your mail, aren't they? For Fd-3m, they are
K, L, U, W, X.

You can click on the "Brillouin zone" to see the graph for further 
understanding what 
they present.


zhou huiqun
@earth sciences, nanjing university, china

  - Original Message - 
  From: Abolore Musari 
  To: PWSCF Forum 
  Sent: Friday, June 10, 2011 2:26 PM
  Subject: [Pw_forum] to extract k-point from bilbao crystallographic server





  Dear all QE users
  I am so sorry to ask this question I have been to crystallographic server to 
extract the coordinate for my  k-poiint card for space group Fd-3m. the page is 
displayed below but I dont know how to extract my k-point from this page i 
would be grateful if U can explain how I can get the coordinates for my k 
point. Please I would be grateful for your assistance.


  Abolore Musari
  Dept Of Physics
  University Of Agriculture, Nigeria.

  The k-vector types of space group 227 [Fd-3m]
  (Table for arithmetic crystal class m -3 mF)
  Fm-3m-Oh5 (225) to Fd-3c- Oh8(228)
  Reciprocal space group (Im-3m)*, No.229

  Brillouin zone


k-vector description Wyckoff Position ITA description 
CDML* Conventional-ITA ITA Coordinates 
Label Primitive 
GM 0,0,0 0,0,0 a 2 m-3m 0,0,0  
X 1/2,0,1/2 0,1,0 b 6 4/mm.m 0,1/2,0  
L 1/2,1/2,1/2 1/2,1/2,1/2 c 8 .-3m 1/4,1/4,1/4  
W 1/2,1/4,3/4 1/2,1,0 d 12 -4m.2 1/4,1/2,0  
DT u,0,u 0,2u,0 e 12 4m.m 0,y,0 : 0 < y < 1/2 
LD u,u,u u,u,u f 16 .3m x,x,x : 0 < x < 1/4 
V 1/2,u,1/2+u 2u,1,0 g 24 mm2.. x,1/2,0 : 0 < x < 1/4 
SM u,u,2u ex 2u,2u,0 h 24 m.m2 x,x,0 : 0 < x <= 3/8 
S 1/2+u,2u,1/2+u ex 2u,1,2u h 24 m.m2 x,1/2,x : 0 < x < 1/8 
S~SM1=[K M] h 24 m.m2 x,x,0 : 3/8 < x < 1/2 
SM SM1=[GM M] h 24 m.m2 x,x,0 : 0 < x < 1/2 
Q 1/2,1/4+u,3/4-u 1/2,1-2u,2u i 48 ..2 1/4,1/2-y,y : 0 < y < 1/4 
A u,-u+v,v ex -2u+2v,2u,0 j 48 m.. x,y,0 : 0 < x < y <= 3/8 U
U x,y,0 : 0 < x < 3/4-y < y < 1/2  
B 1/2+u,u+v,1/2+v ex 2v,1,2u j 48 m.. x,1/2,z : 0 < z < x <= 1/4-z 
B~B1=[K M W] j 48 m.. x,y,0 : 3/4-y <= x < y < 1/2 
A B1=[GM M X] j 48 m.. x,y,0 : 0 < x < y < 1/2 
C u,u,v ex v,v,-v+2u k 48 ..m x,x,z : 0 < z < x <= 3/8-z/2 
J u,v,u[GMXUL] ex v,-v+2u,v k 48 ..m x,y,x : 0 < x < y <= 1/2-x U
U x,y,x : 1/4 < y < 1/2, 1/2-y < x < 3/8-y/2  
J~J1=[GM L X3] + [L K M] k 48 ..m x,x,z : 0 < x < z <= 1/2-x U
U x,x,z : 0 < z < 1/4, 3/8-z/2 < x < 1/2-z  
C + J1=[GM M X3] \ [GM L] k 48 ..m x,x,z : 0 < z < 1/2 -x < 1/2, x!= z 
GP u,v,w -u+w+v,u+w-v,u-w+v l 96 1 x,y,z : 0 < z < x < y < 1/2-x U
U x,y,z : 0 < z < 1/2-y < x < y < 1/2 U
U x,y,1/2-y : 1/4 < y < 1/2; 1/2-y < x < 1/4.  





  * Cracknell, A. P., Davies, B.L., Miller, S. C., and Love, W. F. (1979). 
Kronecker Product Tables. Vol. 1. General Introduction and Tables of 
Irreducible Representations of Space Groups. New York: IFI/Plenum.


  The asymmetric unit of ITA is obtained from that used in these tables by 


  reflectionthrough the plane x,x,z . 


  The asymmetric unit is obtained from the representation domain of CDML by the 
equivalence 


  [L K W M] ~[L U W X] through the two-fold rotation around the axis Q. 


  Wing: [GM L X3] x,x,z: 0 < x < z < 1/2-x 




  The transformation matrix that relates the primitive (CDML) base with the 
conventional-ITA is -a+b+c, a-b+c, a+b-c



If you want to identify a k-vector you have to introduce: 
1. The reciprocal bases:  primitive (CDML) conventional dual (ITA)  
  2. The k-vector:  kxkykz
   
  






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[Pw_forum] espresso 4.3.1 - segmentation fault in file set_irr.f90

[Huiqun Zhou]

Andrea,

Could you please send me the related files for solving the problem, too?
I installed 4.3.1 and am working on a system with same structure as 
Meenakshi's.

 Or, if you prefer to recommend me to get the snapshot by svn, please let 
know.

Thanks!

zhou huiqun
@earth sciences, nanjing university, china

- Original Message - 
From: "Andrea Dal Corso" 
To: 
Sent: Friday, June 03, 2011 12:28 AM
Subject: Re: [Pw_forum] espresso 4.3.1 - segmentation fault in file 
set_irr.f90


> Thank you for reporting the problem. There was actually a bug in
> PW/divide_class.f90 that appears in your case.
> I have commited the correction in the svn version.
>
> HTH,
>
> Andrea
>
>
>
> On Thu, 2011-06-02 at 17:06 +0530, Meenakshi Sundaram wrote:
>> Dear all,
>>
>> I think that the input file for pw.x would also be necessary. I have
>> pasted it below:
>>
>> &control
>>  calculation = 'scf'
>>  restart_mode='from_scratch',
>>  prefix='SrSnO3',
>>  tstress = .true.
>>  tprnfor = .true.
>>  pseudo_dir = '/home/test/omkar/pseudo',
>>  outdir='/home/test/omkar/phonon/tmp'
>>   /
>> &system
>>  ibrav=  0,  nat=  5, ntyp= 3,celldm(1)=7.75862,
>>  ecutwfc =50.0, ecutrho=300.0,
>>  occupations='smearing', smearing='fermi-dirac', degauss=0.003
>>   /
>> &electrons
>>  mixing_mode = 'plain'
>>  mixing_beta = 0.5
>>  conv_thr =  1.0d-10
>>   /
>> &ions
>>   /
>>
>> CELL_PARAMETERS {cubic}
>>   1.000  0.000   0.000
>>   0.000  1.000   0.000
>>   0.000  0.000   1.000
>>
>>
>> ATOMIC_SPECIES
>> Sr87.62 Sr.pw91-nsp-van.UPF
>> Sn118.710   Sn.pw91-n-van.UPF
>> O 15.9994   O.pw91-van_ak.UPF
>>
>> ATOMIC_POSITIONS {crystal}
>>Sr0.000.000.00
>>Sn0.500.500.50
>> O0.500.500.00
>> O0.500.000.50
>> O0.000.500.50
>>
>> K_POINTS {automatic}
>>   14 14 14 0 0 0
>>
>> Regards
>> M. Meenakshi Sundaram
>> R&D Assistant
>> JNCASR
>>
>>
>> On 06/02/2011 04:48 PM, Meenakshi Sundaram wrote:
>> > Dear All,
>> > I am trying to run a phonon calculation using the following input file
>> > for ph.x
>> >
>> > phonon at all dynpoints
>> > &inputph
>> > tr2_ph=1.0d-14,
>> > prefix='SrSnO3',
>> > ldisp=.true.,
>> > nq1=4, nq2=4, nq3=4,
>> > amass(1)=87.62,
>> > amass(2)=118.710,
>> > amass(3)=15.9994,
>> > outdir='/home/test/omkar/phonon/tmp',
>> > fildyn='SrSnO3.dynpoint',
>> > /
>> >
>> > The error is pasted below:
>> > forrtl: severe (174): SIGSEGV, segmentation fault occurred
>> > Image PC Routine Line Source
>> > ph.x 00454B53 set_irr_ 292
>> > set_irr.f90
>> > ph.x 00428ACB init_representati 91
>> > init_representations.f90
>> > ph.x 004083EB check_initial_sta 156
>> > check_initial_status.f90
>> > ph.x 004050E0 MAIN__ 89
>> > phonon.f90
>> > ph.x 0040502C Unknown Unknown Unknown
>> > libc.so.6 003249C1D994 Unknown Unknown Unknown
>> > ph.x 00404F39 Unknown Unknown Unknown
>> >
>> > When I tried using a lower version 4.0.4 it ran fine.
>> >
>> > A couple of other observations. When I lowered or increased the size of
>> > the q point mesh, the program executed without any problems in 4.3.1
>> >
>> > I also tried localizing the problem, and I find that the 15th element 
>> > of
>> > num_rap_mode array gets some strange value of -1 after a call to
>> > find_mode_sym.
>> >
>> > Hope this information would be useful. If you need the input file for
>> > pw.x please let me know.
>> >
>> > Thank you for any help.
>> >
>> > Regards
>> > M. Meenakshi Sundaram
>> > R&D Assistant
>> > JNCASR
>> > ___
>> > Pw_forum mailing list
>> > Pw_forum at pwscf.org
>> > http://www.democritos.it/mailman/listinfo/pw_forum
>>
>> ___
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>> Pw_forum at pwscf.org
>> http://www.democritos.it/mailman/listinfo/pw_forum
>
> Andrea Dal CorsoTel. 0039-040-3787428
> SISSA, Via Bonomea 265  Fax. 0039-040-3787249
> I-34136 Trieste (Italy) e-mail: dalcorso at sissa.it
>
>
>
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[Pw_forum] compile MPI+OpenMP version

[Huiqun Zhou]

Paolo,

Yes, I had used that option. My question is that which library we should 
choose, the multi-thread
version, libmkl_intel_thread.a or the sequential version, 
libmkl_sequential.a, of Intel MKL when
compiling mixed MPI+OpenMP version of qe? Or, in other words, do we need to 
take advantage
of multi-threading functinality of Intel MKL when compiling MPI+OpenMP 
version?

Thanks!

zhou huiqun
@earth sciences, nanjing university, china


- Original Message - 
From: "Paolo Giannozzi" 
To: "PWSCF Forum" 
Sent: Wednesday, June 08, 2011 9:55 PM
Subject: Re: [Pw_forum] compile MPI+OpenMP version


>
> On Jun 8, 2011, at 11:39 , Huiqun Zhou wrote:
>
>> for MPI+OpenMP, should I use libmkl_intel_thread.a instead?
>
> you should use "./configure --enable-openmp [other options]"
>
> P.
> ---
> Paolo Giannozzi, Dept of Chemistry&Physics&Environment,
> Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
> Phone +39-0432-558216, fax +39-0432-558222
>
>
>
>
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> 

[Pw_forum] compile MPI+OpenMP version

[Huiqun Zhou]

Hi,

Just want to know which Intel MKL library is recommended for compiling 
MPI+OpenMP
version. For compiling pure MPI version, I usually use libmkl_sequential.a for 
avoiding the
trouble of the default multi-threading in MKL. But for MPI+OpenMP, should I use
libmkl_intel_thread.a instead?

Thanks!

zhou huiqun
@earth sciences, nanjing university, china
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[Pw_forum] Shirley interpolation

[Huiqun Zhou]

It's provided only internally to the "Molecular Foundry" users, I think.


zhou huiqun
@earth sciences, nanjing university, china

  - Original Message - 
  From: Mingxing Chen 
  To: pw_forum at pwscf.org 
  Sent: Tuesday, April 19, 2011 2:34 PM
  Subject: [Pw_forum] Shirley interpolation


  Dear all,

  As stated in PRB 80, 235126 (2009) by David Prendergast, the Shirley's 
interpolation scheme has been implemented as a post processing tool in QE. 
However, I did not find it in the latest version of QE, i.e., Version 4.3. Does 
anyone know that? Any suggestion would be appreciated. Thanks a lot.

  Best regards,

  Mingxing Chen

  -- 

Mingxing Chen,Institute for Physical ChemistryUniversity of ViennaEmail: 
mxchen.2011 at gmail.com




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[Pw_forum] problem with degauss and magnetization

[Huiqun Zhou]

If I were you, I would try degauss=0.006, 0.004, 0.002 with dense enough k 
points 
and see the tendency.

zhou huiqun
@earth sciences, nanjing university, china
  - Original Message - 
  From: Thaneshwor Kaloni 
  To: pw_forum at pwscf.org 
  Sent: Monday, March 14, 2011 12:22 AM
  Subject: [Pw_forum] problem with degauss and magnetization


  Dear Quantum Espresso users,


  I am trying to get the magnetization by creating one vacancy 
  in 5x5 supercell of graphene.
  With different values of degauss the total magnetization is 
  changing surprisingly. Is there anything wrong with my input ?.
  Could anybody please tell me  some references where I
  can read detail about smearing and degauss ?.


  The total magnetization with  different degauss are given as below,

  degauss  total magnetization
   0.05   0.00
   0.01   0.58
   0.001 0.88
   0.0001   0.88



  I am posting my input file below.



  &CONTROL
  calculation = 'scf' ,
  restart_mode = 'from_scratch' ,
  outdir = 'OUT/',
  pseudo_dir = '/home/kaloni/pseudo/',
  prefix = 'g',
  tstress=.true.,
  /
  &SYSTEM
  ibrav = 4, a=12.199359575, b= 12.199359575,
  c=19.999668786, cosab= -0.5, cosac =0.0 , cosbc=0.0,
  nat=  49, ntyp= 1,
  ecutwfc = 40,
  ecutrho = 400,
  nspin =2, starting_magnetization = 1.0,
  occupations='smearing', smearing=' gaussian', degauss=0.05,
  nosym = .true.,

  /
   &ELECTRONS
  mixing_beta = 0.3
  conv_thr = 1.0d-9
   /
  ATOMIC_SPECIES
  C12.0107 C.pz-rrkjus.UPF
  ATOMIC_POSITIONS (crystal)
  C   -0.000437574  -0.000580938   0.00015
  C0.000878501   0.200420327  -0.8
  C0.001210858   0.399950578  -0.00071
  C   -0.000312205   0.599509065   0.2
  C   -0.000716730   0.798976722   0.00025
  C0.199479935  -0.000986699  -0.00031
  C0.200591611   0.200243356   0.00020
  C0.204951004   0.399348478  -0.00039
  C0.200756083   0.599210178  -0.00027
  C0.199615366   0.799016660   0.00045
  C0.399828248  -0.000558044  -0.00011
  C0.399613916   0.200154971   0.00014
  C0.401785094   0.599046302  -0.00047
  C0.400264884   0.799510584   0.00019
  C0.600023737   0.000445858  -0.00037
  C0.599500576   0.200387180   0.00030
  C0.594152084   0.399266958   0.00290
  C0.597008286   0.598889370   0.00057
  C0.600448742   0.800956977  -0.00036
  C0.800386518   0.000445469  -0.00021
  C0.800217273   0.200473648  -0.00180
  C0.798607049   0.399927530   0.00120
  C0.798270617   0.599140827   0.00073
  C0.799080030   0.799392409  -0.00024
  C0.132951308   0.065395469   0.00019
  C0.133142262   0.266027786  -0.00014
  C0.135800585   0.466331814  -0.00062
  C0.133194345   0.665806346   0.00014
  C0.132633945   0.865364014   0.00018
  C0.332386006   0.065362305  -0.00012
  C0.329787525   0.259493844   0.3
  C0.336738546   0.468697263  -0.00042
  C0.333671463   0.665846245  -0.00020
  C0.333143624   0.865895587   0.00044
  C0.533078996   0.066642011  -0.00019
  C0.532824452   0.265959049   0.00110
  C0.531539380   0.468474465   0.00226
  C0.534652606   0.669416138  -0.00013
  C0.533415252   0.867317865  -0.00015
  C0.733533974   0.067101960  -0.00071
  C0.733185901   0.266889900  -0.7
  C0.730336277   0.466262841   0.00196
  C0.731928945   0.665704201   0.00020
  C0.733842050   0.867300592  -0.00017
  C0.933534511   0.066657775   0.00016
  C0.933667182   0.266910925  -0.00085
  C0.933067875   0.466263286   0.0
  C0.932454196   0.665766534   0.4
  C0.932632612   0.865835315   0.8
  K_POINTS AUTOMATIC
  4 4 1 1 1 1


  Thanks 

  Thaneshwor Prashad Kaloni
   



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[Pw_forum] НА: Re: problem in MPI running of QE (16 processors)

[Huiqun Zhou]

Alexander,

According to your reply to my message, you actually applied 64 CPU cores 
(16 nodes, 4 cores per node), this should have no problem unless the policy
of using your cluster prohibited it. Once upon a time, we had such a policy
on our cluster: an job occupies at most 32 CPU cores, otherwise put it into
sequential queue.

Maybe, you should ask your administrator whether there is such a policy ...

zhou huiqun
@earth sciences, nanjing university, china
 
  - Original Message - 
  From: Alexander G. Kvashnin 
  To: PWSCF Forum 
  Sent: Tuesday, March 08, 2011 12:24 AM
  Subject: Re: [Pw_forum] ??: Re: problem in MPI running of QE (16 processors)


  Dear all



  I tried to use full paths, but it didn't give positive results. It wrote an 
error message  


  application called MPI_Abort(MPI_COMM_WORLD, 0) - process 0




  On 7 March 2011 10:30, Alexander Kvashnin  wrote:

Thanks, I tried to use "<" instead of "-in" it also didn't work.
OK,I will try to use full paths for input and output, and answer about 
result.

-  ? -
??: Omololu Akin-Ojo 
??: 7 ? 2011 ?. 9:56
: PWSCF Forum 
: Re: [Pw_forum] ??: Re: problem in MPI running of QE (16 processors)

Try to see if specifying the full paths help.
E.g., try something like:

mpiexec /home/MyDir/bin/pw.x -in  /scratch/MyDir/graph.inp >
/scratch/MyDir/graph.out

(where /home/MyDir/bin is the full path to your pw.x and
/scratch/MyDir/graph.inp is the full path to your output )

( I see you use "-in" instead of "<" to indicate the input. I don't
know too much but _perhaps_ you could also _try_ using "<" instead of
"-in") .

o.

On Mon, Mar 7, 2011 at 7:31 AM, Alexander Kvashnin  wrote:
> Yes, I wrote
>
> #PBS -l nodes=16:ppn=4
>
> And in userguide of MIPT-60 wrote,that mpiexec must choose number of
> processors automatically, that's why I didn't write anything else
>
>
> 
> : Huiqun Zhou 
> : 7 ?? 2011 ??. 7:52
> : PWSCF Forum 
> : Re: [Pw_forum] problem in MPI running of QE (16 processors)
>
> How did you apply number of node, procs per node in your job
> script?
>
> #PBS -l nodes=?:ppn=?
>
> zhou huiqun
> @earth sciences, nanjing university, china
>
>
> - Original Message -
> From: Alexander G. Kvashnin
> To: PWSCF Forum
> Sent: Saturday, March 05, 2011 2:53 AM
> Subject: Re: [Pw_forum] problem in MPI running of QE (16 processors)
> I create PBS task on supercomputer MIPT-60 where I write
>
> mpiexec ../../espresso-4.2.1/bin/pw.x -in graph.inp > output.opt
> all other

[??? ??  ? ? ?]



  -- 

  Sincerely yours
  Alexander G. Kvashnin
  

  Student
  Moscow Institute of Physics and Technology  http://mipt.ru/
  141700, Institutsky lane 9, Dolgoprudny, Moscow Region, Russia



  Junior research scientist

  Technological Institute for Superhard 
  and Novel Carbon Materials   
http://www.ntcstm.troitsk.ru/
  142190, Central'naya St. 7a, Troitsk, Moscow Region, Russia
  




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[Pw_forum] problem in MPI running of QE (16 processors)

[Huiqun Zhou]

How did you apply number of node, procs per node in your job
script?

#PBS -l nodes=?:ppn=?

zhou huiqun
@earth sciences, nanjing university, china

  - Original Message - 
  From: Alexander G. Kvashnin 
  To: PWSCF Forum 
  Sent: Saturday, March 05, 2011 2:53 AM
  Subject: Re: [Pw_forum] problem in MPI running of QE (16 processors)


  I create PBS task on supercomputer MIPT-60 where I write 



  mpiexec ../../espresso-4.2.1/bin/pw.x -in graph.inp > output.opt


  all other types of this line such as 


  mpiexec -np 16 ../../espresso-4.2.1/bin/pw.x -in graph.inp > output.opt



  doesn't work.
  Maybe this number of processor too small for parallel calculation to QE? 






  On 4 March 2011 21:37, Eyvaz Isaev  wrote:

Dear  Alexander,

How do you run a job? You should launch a command like (some parameters are 
omitted) 
mpirun -np 16 -maxtime 30 ./pw.x < scf.in >scf.out

The easiest way to be added to the forum list  is subscribing  to this 
forum. Please visit 
http://www.pwscf.org/contacts.php

Please also provide your affiliation.
 
Best regards,

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






From: Alexander G. Kvashnin 
To: pw_forum at pwscf.org
Sent: Fri, March 4, 2011 9:07:46 PM
Subject: [Pw_forum] problem in MPI running of QE (16 processors)



Hello,



I have some problem when I ran parallel version of QE (16 procs), I saw 
next line in output file



Parallel version (MPI), running on 1 processors


And it works using only 1 processor, but there is MPI version.
Help me please in my problem
Thank you!
-- 

Sincerely yours
Alexander G. Kvashnin





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  -- 

  Sincerely yours
  Alexander G. Kvashnin




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[Pw_forum] temperature rescaling for vc-md

[Huiqun Zhou]

Giovanni,

Thanks for your quick response! I'll try to reduce the dt and
'restart' for restart_mode.

Thank you.

Huiqun

- Original Message - 
From: "Giovanni La Penna" 
To: "PWSCF Forum" 
Sent: Monday, February 28, 2011 5:31 PM
Subject: Re: [Pw_forum] temperature rescaling for vc-md


>
> I would suggest to heat the system slowly.
> restart='from_scratch'
> means that previous velocities are not loaded.
> So going from zero (for a hopefully relaxed system) to 300 K,
> with a time-step of 1 fs (if a remember correctly), may imply
> a huge time to converge at each time step.
> Even CP would not work properly this way: it runs, but temperature
> oscillations become huge and the fake electron
> kinetic energy would quickly increase, providing
> an uncontrolled dynamics.
> Other codes may have hidden controls on temperature,
> time-steps, etc..
>
> Giovanni
>
> 
> Giovanni La Penna - National research council (Cnr)
> Institute for chemistry of organo-metallic compounds (Iccom)
> via Madonna del Piano 10,
> I-50019 Sesto Fiorentino, Firenze, Italy
> tel.: +39 055 522-5264, fax: +39 055 522-5203
> e-mail: glapenna at iccom.cnr.it - http://www.iccom.cnr.it/lapenna
> skype: giovannilapenna
> 
>
> On Mon, 28 Feb 2011, Huiqun Zhou wrote:
>
>> ...
>> but the SCF convergence is always failed to reach after 20 or so ion 
>> steps
>> no matter
>> how I change mixing_beta from 0.5 to 0.05. One thing I noticed is that 
>> the
>> temperature
>> controling may be not in effect as the temperature remains as high as 6
>> digits. I used
>> ...





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[Pw_forum] temperature rescaling for vc-md

[Huiqun Zhou]

Hi,

I'm trying to run a vc-md simulation of a supercell with 80 atoms at 300 K and 
20 GPa,
but the SCF convergence is always failed to reach after 20 or so ion steps no 
matter 
how I change mixing_beta from 0.5 to 0.05. One thing I noticed is that the 
temperature
controling may be not in effect as the temperature remains as high as 6 digits. 
I used 
the 'rescaling' , the only setting available for vc-md, for ion_temperature, 
the default 
100.0 for tolp. 

Below is part of my input file, any comments are welcome. I would also like to 
know
which source file I need to look at for the rescaling function. 

The same system is running without any problem using CP dynamics in VASP and 
CASTEP. 

 &control
calculation = 'vc-md',
restart_mode = 'from_scratch',
prefix = 'mgsio3',
tstress = .true.,
tprnfor = .true.,
pseudo_dir = '/home/hqzhou/qe_pseudo/',
outdir = '/gpfsTMP/hqzhou/tmp/'
wf_collect = .true.
nstep = 100
dt = 20.0
 /
 &system
!ibrav = 0
!celldm(1) = 0.0
ibrav = 14
celldm(1) = 18.0484, celldm(2) = 1.0322, celldm(3) = 0.7221
celldm(4) = 0.0, celldm(5) = 0.0, celldm(6) = 0.0
nat = 80, ntyp = 3,
ecutwfc = 40.0, ecutrho = 400.0
nspin = 1
nosym = .true.
occupations = 'fixed'
 /
 &electrons
electron_maxstep = 200
diagonalization = david
mixing_mode = 'plain'
mixing_beta = 0.1
conv_thr = 1.0d-8
 /
 &ions
ion_dynamics = 'beeman'
pot_extrapolation = 'second_order'
wfc_extrapolation = 'second_order'
upscale = 100.0
ion_temperature = 'rescaling'
tempw = 300.0
refold_pos = .true.
 /
 &cell
cell_dynamics = 'pr'
press = 200.0
!wmass = 0.05
cell_factor = 1.6
press_conv_thr = 0.2
 /
..

Thanks in advance.

zhou huiqun
@earth sciences, nanjing university, china

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[Pw_forum] limit on atom count to compute total energy

[Huiqun Zhou]

LAMMPS, DL_POLY, ..., just name a few of them.


zhou huiqun
@earth sciences, nanjing university, china

  - Original Message - 
  From: sakthi kumaran 
  To: PWSCF Forum 
  Sent: Friday, January 14, 2011 2:22 PM
  Subject: Re: [Pw_forum] limit on atom count to compute total energy




  Dear all
Is there any open source molecular dynamics tool to get to know the 
energy of the 3000 atom count.Any open source molecular dynamics tool 
  suggestions are favourable


  Thank you,

  Kind regards,
  Sakthi




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[Pw_forum] (solved) Error in phonon calculation and duringtests also?

[Huiqun Zhou]

It's not nessarilly a problem of Intel compiler. I'm using Intel Compiler 11.1
064 and 072 on two different clusters and no problem occurred in compiling
qe-espresso.

You can try to clean your build and remove the folder S3DE, then compile 
again.

zhou huiqun
@earth sciences, nanjing university, china

  - Original Message - 
  From: sonu kumar 
  To: pw_forum at pwscf.org 
  Sent: Saturday, November 20, 2010 9:22 PM
  Subject: Re: [Pw_forum] (solved) Error in phonon calculation and duringtests 
also?


  Respected Prof. Paolo Giannozzi, Lorenzo Paulatto, Ali Tavana and all QE 
users,

  Thank you very much for your help.

  Problem is solved with gfortran compiler ( gcc version 4.4.1 ). 
  All the tests and phonon calculations are working fine.


  >did you pay real money for your compiler? complain with Intel.
  >If not, try a different compiler (or a different version of the
  >same compiler)

  I used latest non-commercial version of intel fortran compiler.
  Will try to check with other intel compilers.


  >About one year ago I met a very similar problem with the sun compiler.
  >After a long debugging session I was able to track it to a specific
  >compiler bug: loop counter was not incremented at loop exit (for
  >sufficiently complicated loops). Reducing optimization to 1 for compiling
  >iotk solved the problem.

  will try with -O1 flag.


  Sonu Kumar

  Phd Student
  Physics Department
  Indian Institute of Technology 
  Delhi-110016, India
  web:-http://www.iitd.ac.in/



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[Pw_forum] Bug in PlotPhon

[Huiqun Zhou]

Eyvaz,

There is a tiny bug or typo in ../PlotPhon/Scripts/Lines. When $cell == 8,
  b2a=`head -1 $FC_name.fc | cut -c 22-33 `
should be
  b2a=`head -1 $FC_name.fc | cut -c 23-33 `

I'm using PlotPhon in qe 4.2.1.


zhou huiqun
@earth sciences, nanjing university, china
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[Pw_forum] Re [8] : US-PP of Au

[Huiqun Zhou]

reza,

Another possibility is that you have flawed memory chip(s).

I trid your original (actually, changed to scf calculation) 13 Au cluster 
on my machine without anyproblem.

huiqun zhou
@earth sciences, nanjing university, china

  - Original Message - 
  From: reza shidpoor 
  To: pw_forum at pwscf.org 
  Sent: Wednesday, September 15, 2010 5:43 PM
  Subject: [Pw_forum] Re [8] : US-PP of Au


  Dear Lorenzo

  Thank you to reply.
  It is always segmentation fault. My system is 3-atoms Au cluster.
  this cluster forms a chain of atoms but the calculations never finished
  because of segmentation fault. 

  Dear Gabriele

  the work was completely don with kinetic-energy cutoff=32.  Ry and  
charge density cutoff  = 320.  Ry .


  Forces acting on atoms (Ry/au):

   atom   1 type  1   force =-0.9579   -0.95790.
   atom   2 type  1   force = 0.00013265   -0.36860.
   atom   3 type  1   force =-0.36860.000132650.

   Total force = 0.000237 Total SCF correction = 0.000290
   SCF correction compared to forces is too large, reduce conv_thr

   bfgs converged in  24 scf cycles and  19 bfgs steps
   (criteria: energy < 0.10E-03, force < 0.10E-02)

   End of BFGS Geometry Optimization

   Final energy   =-262.9046471560 Ry
  Begin final coordinates

  ATOMIC_POSITIONS (angstrom)
  Au   1.381049485   1.381049485   0.0
  Au   3.868137287  -1.139186772   0.0
  Au  -1.139186772   3.868137287   0.0
  End final coordinates


  Best wishes.
  Reza.Shidpour
  Institute for Nanoscienec and Nanotechnology,
  SUT



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[Pw_forum] ambiguous results with vc-relax

[Huiqun Zhou]

It's up to what kind of system you are studying. For a system with 
orthorhombic, monoclinic
or triclinic structure, my experience told me that vc-relax is much faster than 
the "static"
method because in those cases you need to do a series of calculations for each 
parameter,
b/a, c/a as well as volume for example of orthorhombic system.


huiqun zhou
@earth sciences, nanjing university, china

  - Original Message - 
  From: jia chen 
  To: pw_forum at pwscf.org 
  Sent: Wednesday, August 25, 2010 2:51 AM
  Subject: [Pw_forum] ambiguous results with vc-relax


  sorry for interrupting you guys, I didn't follow the whole post before. 
Pressure calculations need very high ecutoff. And,according to my experience, 
vc-relax is supposed to be slow. So, I usually avoid vc-relax if possible... 
Last but not least, I am a student, maybe very wrong. Have a good day.

  -- 
  Jia Chen

  Dept of Chemistry
  Princeton University
  Princeton, NJ 08544



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[Pw_forum] Test

[Huiqun Zhou]

Sorry, this is a test because I didn't see my several recent posts showed up
in the forum.

huiqun zhou
@earth sciences, nanjing university, china

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[Pw_forum] Speeding up the calculations

[Huiqun Zhou]

Mehmet,

Hope you are the same person who posted a very good tutorial on phonon 
calculation via
small displacement method (SDM) and DFPT at Siesta forum.

Interestingly, I noticed that in your tutorial DFPT (PW+PH: 328 sec at 8CPU) 
was much faster 
than SDM (Siesta+PHON: 520 sec at 8CPU, VASP+PHON: 1674 sec at 16CPU) for the 
case 
of graphene, at least by the criteria of getting identical phonon dispersion 
relation. So, your 
current recommendation means that was just a individual case for you, right? 

My feel (no concret numbers) with qe shows that for the previous version of qe 
(before 4.0 
or earllier?) PW+PH was somewhat slower than PW+PHON, but the situation is 
reversed 
with recent versions of qe.   

If you have further examples, please share with us.

Thank you in advance!

huiqun zhou
@earth sciences, nanjing university, china
 
  - Original Message - 
  From: Mehmet Topsakal 
  To: PWSCF Forum 
  Sent: Sunday, August 15, 2010 3:52 PM
  Subject: Re: [Pw_forum] Speeding up the calculations


  Dear  Bipul,


  You can try Small Displacement Method ( see 
http://www.homepages.ucl.ac.uk/~ucfbdxa/ ) which has different idea than DFPT.
  It requires you to make 2 displacement in a supercell and calculate the 
forces with single scf. You can run scf's at the same time.  
  For example, you need to calculate the forces in 5x5x1 graphene supercell 
having 50 carbon atoms for 2 displacemet.


  BUT you cannot observe LO-TO splitting in polar materials (such as honeycomb 
monolayer ZnO) by using SDM.


  Regards.


  On Sat, Aug 14, 2010 at 9:44 PM, Bipul Rakshit  wrote:

Hi PWSCF user,
I am mainly doing Phonon calculation, which generally is time consuming ( 
even in parallel). I just want to know if there is any possible way to speed up 
the calculations. i.e. by installing certain libraries or so. Or using some 
appropirate methods

The machine had many nodes, and each nodes have 8/16 processors. Some of 
the other details of the machines are as follows:

 Intel(R) Xeon(R) CPU  E5345  @ 2.33GHz, 64 bit
4GB RAM

compiler: mpif90 and icc

Thanks
-- 
Bipul Rakshit
Research Fellow
S N Bose Centre for Basic Sciences,
Salt Lake,
Kolkata 700 098
India

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  -- 

  Mehmet Topsakal  (Ph.D. Student)
  UNAM-Institute of Materials Science and Nanotechnology. 
  Bilkent University. 06800 Bilkent, Ankara/T?rkiye
  Tel: 0090 312 290 3527 ; Fax: 0090 312 266 4365
  UNAM-web  : www.nano.org.tr




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[Pw_forum] about the program style of pwscf

[Huiqun Zhou]

I guess you may have been familiar with programming in FORTRAN 77,
what you need is to find a textbook for FORTRAN 90/95 as the syntax
of FORTRAN 90/95 is to some extent different from that of FORTRAN 77.
The FORTRAN xx language itself is the same whether used under Linux
or Widows.

huiqun zhou
@earth sciences, nanjing university, china
 
  - Original Message - 
  From: Wei Zhou 
  To: pw_forum at pwscf.org 
  Sent: Wednesday, August 11, 2010 4:23 PM
  Subject: [Pw_forum] about the program style of pwscf


  Hello everyone.
  In face I have learned how to write fortran program, and also 
have writen small program, but when I try to read the program of pwscf, I feel 
puzzled,  is there some book about the write fortran in linux. I just want to 
learn write fortran in linux normally.
  any suggestion will be appreciated.

  -- 
  ZhouDawei
  JiLin Universiyt ,ChangChun ,China
  zdw2000 at gmail.com



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[Pw_forum] error in running the relaxation code

[Huiqun Zhou]

You have something wrong in your script. Check it yourself as you
didn't give any detail of it. I think that most probably the LSF system 
failed to find your input file. If you check your output file more carefully,
you should find information about the reason why it exited. You can try 
to change the line
mpirun -srun pw.x -input 01_Ni3Al.in
into
mpirun -srun pw.x -input ./01_Ni3Al.in


dr. huiqun zhou
@earth sciences, nanjing university, china
  
  - Original Message - 
  From: vicky singh 
  To: PWSCF Forum 
  Sent: Monday, August 02, 2010 8:18 PM
  Subject: [Pw_forum] error in running the relaxation code


  Hi
  I am running a code on Nickel for relaxation. the code is running fine on 
core 2 duo (my desktop) but when i am trying to run the code on to a cluster it 
is showing an error 

  Your job looked like:
  
  # LSBATCH: User inputYour job looked like:
  
  # LSBATCH: User input
  mpirun -srun pw.x -input 01_Ni3Al.in
  
  Exited with exit code 1.
  Resource usage summary:
  CPU time   :  0.16 sec.

  can anybody help me what is this exit code 1.

  with regards

  vickysingh10

  research student
  Bangalore




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[Pw_forum] starting_magnetization problem

[Huiqun Zhou]

The manual is a little bit misleading. It just says implicitly: don't
let both tot_magnetization and starting_magnetization appear in
your input file simutanously, they are mutual exclusive. For your
purpose, you just need to define starting_magnetization and don't
bother yourself with defining tot_magnetization = -1 in the input,
which is not allowed according to your practice although it should
be OK logically.

huiqun zhou
@earth sciences, nanjing university, china

- Original Message - 
From: "Weyl Fang" 
To: 
Sent: Sunday, July 25, 2010 1:29 PM
Subject: [Pw_forum] starting_magnetization problem


> Dear all,
>
> Recently i want to do a spin polarization calculation. After I read the
> pw.x input file description, i know if i set the tot_magnetization to
> unspecified the amount of electronic magnetization is determined during
> the self-consistent cycle. So i set the tot_magnetization to
> unspecified. But when i execute pw.x, i get a error message some
> starting_magnetization MUST be set. But i get the message" If you fix
> the magnetization with "tot_magnetization", you should not specify
> starting_magnetization." from the pw.x input file description. If i
> still should specify the starting_magnetization? And If i want the
> amount of electronic magnetization determined during the self-consistent
> cycle, how should i specify the starting_magnetization?
>
> Thanks for your help!
>
> Weyl
>
> ===
>
> Weyl FANG
> Graduate student in Chemical Engineering
> State Key Laboratory of Materials-oriented Chemical Engineering
> College of Chemistry and Chemical Engineering
> Nanjing University of Technology, 210009, Nanjing, Jiangsu, China
> 
> Email: weylfang at gmail.com
> Office: Room A705, Technical Innovation Building, Xinmofan Road 5#, 
> Nanjing, Jiangsu, China
> * 
> ***
>
>
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[Pw_forum] how does the quantum espresso scale with increasingthe number of nodes.

[Huiqun Zhou]

vicky,

If by node you mean a compute node with 4 or 8 CPU cores, I'm afraid you
used too much compute resource. I had ever successfully optimized a spin 
polarized structure with 56 atoms by vc-relax on one compute node with 8 
CPU cores within several hours. Although you didn't mention what system 
you are calculating, I strongly recommend you try to run on one or two nodes 
to see how much wall time it'll take.

Efficiency of parallel computing depends on many things, one of which is the
system size. Usually you need to do simpler calculations to determine how
many cpu cores are optimal for your job. 


huiqun zhou
@earth sciences, nanjing University, china

  - Original Message - 
  From: vicky singh 
  To: PWSCF Forum 
  Sent: Wednesday, July 21, 2010 5:50 PM
  Subject: Re: [Pw_forum] how does the quantum espresso scale with 
increasingthe number of nodes.


  Dear prof Giannozzi

  sorry to disturb you but i want to ask one question. the same work raran QE 
simulation with 40 atoms with 8 nodes and 12 nodes. the system got relaxed in 2 
days 11 hrs with 8 nodes but it could nod relax even in 3 days with 12 nodes. 
even it got relaxed with 16 nodes in 2 days 11 hrs but not relax in 6 days with 
32 nodes.

  can u help me out.

  with regards 




  vicky singh
  research student
  Bangalore




  On Tue, Jul 20, 2010 at 1:17 PM, Paolo Giannozzi  
wrote:

vicky singh wrote:

> Can anybody let me know how does the quantum espresso scale with
> increasing the number of nodes or number of processors.


short answer: it depends. Please read the documentation, in
particular sec.3 of the userguide; sec.5 of J.Phys. Condens.
Matter 21, 395502 (2009); the following slides:
http://www.fisica.uniud.it/~giannozz/QE-Tutorial/tutorial_para.pdf

P.
--
Paolo Giannozzi, Democritos and University of Udine, Italy

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[Pw_forum] Distributing phonon calculations todifferent machines

[Huiqun Zhou]

Andrea,

Below are what I have in q1/ directory, it includes everything, I think.

[hqzhou at c01n05 ~]$ ls -l /gpfsTMP/hqzhou/tmp/sill_1.04v0/q1/
total 405184
drwxrwxr-x  2 hqzhou hqzhou65536 Jul  9 18:17 _ph0sill_1.04v0.phsave
drwxrwxr-x 10 hqzhou hqzhou65536 Jul  6 07:54 sill_1.04v0.save
-rw-rw-r--  1 hqzhou hqzhou 52060160 Jul  9 18:14 sill_1.04v0.wfc1
-rw-rw-r--  1 hqzhou hqzhou 52224000 Jul  9 18:14 sill_1.04v0.wfc2
-rw-rw-r--  1 hqzhou hqzhou 51773440 Jul  9 18:14 sill_1.04v0.wfc3
-rw-rw-r--  1 hqzhou hqzhou 51814400 Jul  9 18:14 sill_1.04v0.wfc4
-rw-rw-r--  1 hqzhou hqzhou 51855360 Jul  9 18:14 sill_1.04v0.wfc5
-rw-rw-r--  1 hqzhou hqzhou 51363840 Jul  9 18:14 sill_1.04v0.wfc6
-rw-rw-r--  1 hqzhou hqzhou 51896320 Jul  9 18:14 sill_1.04v0.wfc7
-rw-rw-r--  1 hqzhou hqzhou 51609600 Jul  9 18:14 sill_1.04v0.wfc8

Thanks for your help.

huiqun zhou
@earth sciences, nanjing university, china

- Original Message - 
From: "Dal Corso Andrea" 
To: "PWSCF Forum" 
Sent: Thursday, July 08, 2010 2:40 PM
Subject: Re: [Pw_forum] Distributing phonon calculations todifferent 
machines


> On Thu, 2010-07-08 at 11:11 +0800, Huiqun Zhou wrote:
>> Andrea,
>>
>> I checked the directory, all files are there. See below,
>>
>> ls /gpfsTMP/hqzhou/tmp/sill_1.04v0/q1/_ph0sill_1.04v0.phsave/
>> data-file.xml  data-file.xml.2  data-file.xml.5  data-file.xml.8
>> data-file.xml.1data-file.xml.3  data-file.xml.6
>> data-file.xml.1.0  data-file.xml.4  data-file.xml.7
>>
>
> what about the directory /gpfsTMP/hqzhou/tmp/sill_1.04v0/q1 ?
> Are all the files there? and the directory
> /gpfsTMP/hqzhou/tmp/sill_1.04v0/q1/sill_1.04v0.save  ?
>
> Andrea
>
>> It's a little bit insane, this error only occurred when I compute the
>> first q point (gamma). ph.x worked fine while calculating other
>> q points. You can see the script snippet in my second post in this
>> thread, I had created neccessary directories and copied all needed
>> files in advance before distributing jobs.
>>
>> Any ideas?
>>
>> huiqun zhou
>> @earth sciences, nanjing university, china
>>
>> - Original Message - 
>> From: "Dal Corso Andrea" 
>> To: "PWSCF Forum" 
>> Sent: Wednesday, July 07, 2010 8:06 PM
>> Subject: Re: [Pw_forum] Distributing phonon calculations todifferent
>> machines
>>
>>
>> > On Tue, 2010-07-06 at 17:55 +0800, Huiqun Zhou wrote:
>> >> Thanks, Andrea.
>> >>
>> >> As indicated in the script below, I have copied all files and 
>> >> directories
>> >> created
>> >> by pw.x run.
>> >>
>> >> if test ! -d $TMP_DIR/${system}/q${i} ; then
>> >>  mkdir $TMP_DIR/${system}/q${i}
>> >>  cp -r $TMP_DIR/${system}/${system}.* $TMP_DIR/${system}/q${i}
>> >> fi
>> >>
>> >
>> > Are the files really there? If all the files are in the directory
>> > $TMP_DIR/${system}/q${i} there is no reason why the ph.x code stops.
>> > If they are not, I cannot help you. It is not a problem of ph.x.
>> >
>> >
>> >> BTW, could you please describe more in detail about the newly added
>> >> information
>> >> in INPUT_PH.html for distributing phonon calculations to cluster? If I
>> >> set
>> >> wf_collect
>> >> to true, there should be no relation in nproc and npool between pw.x 
>> >> run
>> >> and
>> >> later
>> >> two ph.x runs, right? Taking AlAs in the GRID_example as example, If I
>> >> want
>> >> to use
>> >> server with 8 CPU core to do calculations for each one q point (8 
>> >> servers
>> >> in
>> >> total),
>> >> what are the values of images and pools?
>> >>
>> >>
>> > You are right, the explanation refer only to the case
>> > wf_collect=.false.. However, image parallelization of ph.x is very
>> > experimental, so be patient. At the moment it divides both q and 
>> > irreps.
>> > Load balancing on q only is not implemented.
>> >
>> >
>> > Andrea
>> >
>> >
>> >
>> >> Huiqun Zhou
>> >> @Earth Sciences, Nanjing University, China
>> >>
>> >> - Original Message - 
>> >> From: "Dal Corso Andrea" 
>> >> To: "PWSCF Forum" 
>> >> Sent: Tuesday, July 06, 2010 4:14 PM
>> >> Subject: Re: [Pw_forum] Distributing phonon calculations todifferent
>> >> 

[Pw_forum] Distributing phonon calculations todifferent machines

[Huiqun Zhou]

Andrea,

I checked the directory, all files are there. See below,

ls /gpfsTMP/hqzhou/tmp/sill_1.04v0/q1/_ph0sill_1.04v0.phsave/
data-file.xml  data-file.xml.2  data-file.xml.5  data-file.xml.8
data-file.xml.1data-file.xml.3  data-file.xml.6
data-file.xml.1.0  data-file.xml.4  data-file.xml.7

It's a little bit insane, this error only occurred when I compute the
first q point (gamma). ph.x worked fine while calculating other
q points. You can see the script snippet in my second post in this
thread, I had created neccessary directories and copied all needed
files in advance before distributing jobs.

Any ideas?

huiqun zhou
@earth sciences, nanjing university, china

- Original Message - 
From: "Dal Corso Andrea" 
To: "PWSCF Forum" 
Sent: Wednesday, July 07, 2010 8:06 PM
Subject: Re: [Pw_forum] Distributing phonon calculations todifferent 
machines


> On Tue, 2010-07-06 at 17:55 +0800, Huiqun Zhou wrote:
>> Thanks, Andrea.
>>
>> As indicated in the script below, I have copied all files and directories
>> created
>> by pw.x run.
>>
>> if test ! -d $TMP_DIR/${system}/q${i} ; then
>>  mkdir $TMP_DIR/${system}/q${i}
>>  cp -r $TMP_DIR/${system}/${system}.* $TMP_DIR/${system}/q${i}
>> fi
>>
>
> Are the files really there? If all the files are in the directory
> $TMP_DIR/${system}/q${i} there is no reason why the ph.x code stops.
> If they are not, I cannot help you. It is not a problem of ph.x.
>
>
>> BTW, could you please describe more in detail about the newly added
>> information
>> in INPUT_PH.html for distributing phonon calculations to cluster? If I 
>> set
>> wf_collect
>> to true, there should be no relation in nproc and npool between pw.x run 
>> and
>> later
>> two ph.x runs, right? Taking AlAs in the GRID_example as example, If I 
>> want
>> to use
>> server with 8 CPU core to do calculations for each one q point (8 servers 
>> in
>> total),
>> what are the values of images and pools?
>>
>>
> You are right, the explanation refer only to the case
> wf_collect=.false.. However, image parallelization of ph.x is very
> experimental, so be patient. At the moment it divides both q and irreps.
> Load balancing on q only is not implemented.
>
>
> Andrea
>
>
>
>> Huiqun Zhou
>> @Earth Sciences, Nanjing University, China
>>
>> - Original Message - 
>> From: "Dal Corso Andrea" 
>> To: "PWSCF Forum" 
>> Sent: Tuesday, July 06, 2010 4:14 PM
>> Subject: Re: [Pw_forum] Distributing phonon calculations todifferent
>> machines
>>
>>
>> > On Tue, 2010-07-06 at 12:13 +0800, Huiqun Zhou wrote:
>> >> Sorry, I sent an unfinished message.
>> >>
>> >> When using _ph0{prefix}.phsave, I got the error message shown in the
>> >> previous
>> >> message.
>> >>
>> >> Here is the snippet of my script for distributing lsf tasks:
>> >>
>> >> ..
>> >> nq=`sed -n '2p' ./${system}_q${nq1}${nq2}${nq3}.dyn0`
>> >>
>> >> for ((i=1; i<=$nq; i++))
>> >> do
>> >> if test ! -d $TMP_DIR/${system}/q${i} ; then
>> >> mkdir $TMP_DIR/${system}/q${i}
>> >> cp -r $TMP_DIR/${system}/${system}.* $TMP_DIR/${system}/q${i}
>> >> fi
>> >> if test ! -d $TMP_DIR/${system}/q${i}/_ph0${system}.phsave ; then
>> >> mkdir $TMP_DIR/${system}/q${i}/_ph0${system}.phsave
>> >> cp -r $TMP_DIR/${system}/_ph0${system}.phsave/*
>> >> $TMP_DIR/${system}/q${i}/_ph0${system}.phsave
>> >> fi
>> >> done
>> >>
>> >> for ((i=1; i<=$nq; i++))
>> >> do
>> >> cat > ${system}_q${i}.in << EOF
>> >> phonons of ${system}
>> >>  &inputph
>> >>   tr2_ph = 1.0d-13,
>> >>   alpha_mix(1) = 0.2,
>> >>   prefix = '${system}',
>> >>   ldisp = .true.,
>> >>   recover = .true.
>> >>   nq1 = ${nq1}, nq2 = ${nq2}, nq3 = ${nq3}
>> >>   start_q = $i, last_q = $i
>> >>   outdir = '$TMP_DIR/${system}/q${i}',
>> >>   fildyn = '${system}_q${nq1}${nq2}${nq3}.dyn'
>> >> ..
>> >> EOF
>> >> $ECHO "calculation of q point $i"
>> >> bsub -a intelmpi -n $processes \
>> >>  -R "span[ptile=8]" \
>> >>  -J ${r}q${i}anda \
>> >>  -oo ${system}_q${i}.out \
>

[Pw_forum] Intel Compiler version needed in compiling qe 4.2

[Huiqun Zhou]

Paolo,

You are right. I don't know when I had an iotk directory created, instead of 
a
soft link to S3DE/iotk. Both "make clean" and "make distclean" failed 
toremove
*.o and *.mod files in the directory.

Sorry to disturb everyone.

huiqun zhou
@earth sciences, nanjing university, china

- Original Message - 
From: "Paolo Giannozzi" 
To: "PWSCF Forum" 
Sent: Wednesday, July 07, 2010 8:15 PM
Subject: Re: [Pw_forum] Intel Compiler version needed in compiling qe 4.2


>
> On Jul 7, 2010, at 11:58 , Huiqun Zhou wrote:
>
>> Here are the error messages, it's about format of a module file
>
> I have ifort v.10.1.008 and I never saw such an error. Most likely
> you have some "leftover" object from a previous compilation.
> Remove the iotk directory and recompile.
>
> Paolo
> ---
> Paolo Giannozzi, Dept of Physics, University of Udine
> via delle Scienze 208, 33100 Udine, Italy
> Phone +39-0432-558216, fax +39-0432-558222
>
>
>
> ___
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> http://www.democritos.it/mailman/listinfo/pw_forum
> 

[Pw_forum] Intel Compiler version needed in compiling qe 4.2

[Huiqun Zhou]

Gabriele,

Here are the error messages, it's about format of a module file:

mpiifort -O3 -mcmodel=medium -nomodule -fpp -D__INTEL -D__FFTW3 -D__MPI 
-D__PARA -I../include -I../iotk/src -I. -c metadyn_io.f90
fortcom: Error: metadyn_io.f90, line 18: The module file cannot be read.  Its 
format requires a more recent F90 compiler.   [IOTK_MODULE]
  USE iotk_module
--^
fortcom: Error: metadyn_io.f90, line 22: A specification expression object must 
be a dummy argument, a COMMON block object, or an object accessible through 
host or use association   [IOTK_ATTLENX]
  CHARACTER(iotk_attlenx) :: attr
^
fortcom: Error: metadyn_io.f90, line 22: An automatic object must not appear in 
the specification part of a module.   [ATTR]
  CHARACTER(iotk_attlenx) :: attr
-^
compilation aborted for metadyn_io.f90 (code 1)
make[1]: *** [metadyn_io.o] Error 1
make[1]: Leaving directory `/home/cook/espresso-4.2/Modules'
make: *** [mods] Error 2


Huiqun

  - Original Message - 
  From: Gabriele Sclauzero 
  To: PWSCF Forum 
  Sent: Wednesday, July 07, 2010 3:10 PM
  Subject: Re: [Pw_forum] Intel Compiler version needed in compiling qe 4.2


  Dear Huiqun,


 thanks for having reported this issue, but can you be more precise? 
Specifically, can you post the error messages from the compiler?


  I can tell you that I have recently compiled espresso-4.2 on Linux machines 
with Intel compilers versions 10.1.025, 11.0.081 and 11.1.056 without any 
difficulty.




  Regads,




  GS


  Il giorno 07/lug/2010, alle ore 08.16, Huiqun Zhou ha scritto:


This is just a memo, it may help others.

When I compiled quantum espresso 4.2 by Intel Compilers 10.1.018,
I got an error message about unsupported language features by the
current compiler. Switching to Intel Compiler 11.1.064, it's OK.

Versions before 4.2 can be compiled by 10.1.018.


Huiqun Zhou
@Earth Sciences, Nanjing University, China
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  ? Gabriele Sclauzero, EPFL SB ITP CSEA
 PH H2 462, Station 3, CH-1015 Lausanne




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[Pw_forum] Intel Compiler version needed in compiling qe 4.2

[Huiqun Zhou]

This is just a memo, it may help others.

When I compiled quantum espresso 4.2 by Intel Compilers 10.1.018,
I got an error message about unsupported language features by the 
current compiler. Switching to Intel Compiler 11.1.064, it's OK.

Versions before 4.2 can be compiled by 10.1.018.


Huiqun Zhou
@Earth Sciences, Nanjing University, China
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[Pw_forum] Distributing phonon calculations todifferent machines

[Huiqun Zhou]

Thanks, Andrea.

As indicated in the script below, I have copied all files and directories 
created
by pw.x run.

if test ! -d $TMP_DIR/${system}/q${i} ; then
 mkdir $TMP_DIR/${system}/q${i}
 cp -r $TMP_DIR/${system}/${system}.* $TMP_DIR/${system}/q${i}
fi

BTW, could you please describe more in detail about the newly added 
information
in INPUT_PH.html for distributing phonon calculations to cluster? If I set 
wf_collect
to true, there should be no relation in nproc and npool between pw.x run and 
later
two ph.x runs, right? Taking AlAs in the GRID_example as example, If I want 
to use
server with 8 CPU core to do calculations for each one q point (8 servers in 
total),
what are the values of images and pools?


Huiqun Zhou
@Earth Sciences, Nanjing University, China

- Original Message - 
From: "Dal Corso Andrea" 
To: "PWSCF Forum" 
Sent: Tuesday, July 06, 2010 4:14 PM
Subject: Re: [Pw_forum] Distributing phonon calculations todifferent 
machines


> On Tue, 2010-07-06 at 12:13 +0800, Huiqun Zhou wrote:
>> Sorry, I sent an unfinished message.
>>
>> When using _ph0{prefix}.phsave, I got the error message shown in the
>> previous
>> message.
>>
>> Here is the snippet of my script for distributing lsf tasks:
>>
>> ..
>> nq=`sed -n '2p' ./${system}_q${nq1}${nq2}${nq3}.dyn0`
>>
>> for ((i=1; i<=$nq; i++))
>> do
>> if test ! -d $TMP_DIR/${system}/q${i} ; then
>> mkdir $TMP_DIR/${system}/q${i}
>> cp -r $TMP_DIR/${system}/${system}.* $TMP_DIR/${system}/q${i}
>> fi
>> if test ! -d $TMP_DIR/${system}/q${i}/_ph0${system}.phsave ; then
>> mkdir $TMP_DIR/${system}/q${i}/_ph0${system}.phsave
>> cp -r $TMP_DIR/${system}/_ph0${system}.phsave/*
>> $TMP_DIR/${system}/q${i}/_ph0${system}.phsave
>> fi
>> done
>>
>> for ((i=1; i<=$nq; i++))
>> do
>> cat > ${system}_q${i}.in << EOF
>> phonons of ${system}
>>  &inputph
>>   tr2_ph = 1.0d-13,
>>   alpha_mix(1) = 0.2,
>>   prefix = '${system}',
>>   ldisp = .true.,
>>   recover = .true.
>>   nq1 = ${nq1}, nq2 = ${nq2}, nq3 = ${nq3}
>>   start_q = $i, last_q = $i
>>   outdir = '$TMP_DIR/${system}/q${i}',
>>   fildyn = '${system}_q${nq1}${nq2}${nq3}.dyn'
>> ..
>> EOF
>> $ECHO "calculation of q point $i"
>> bsub -a intelmpi -n $processes \
>>  -R "span[ptile=8]" \
>>  -J ${r}q${i}anda \
>>  -oo ${system}_q${i}.out \
>>  -eo ${system}_q${i}.err \
>>  $PH_COMMAND -input ./${system}_q${i}.in
>> done
>>
>>
>> Huiqun Zhou
>> @Earth Sciences, Nanjing University, China
>> - Original Message - 
>> From: Huiqun Zhou
>> To: pw_forum at pwscf.org
>> Sent: Tuesday, July 06, 2010 12:00 PM
>> Subject: [Pw_forum] Distributing phonon calculations to
>> different machines
>>
>>
>> dear developers,
>>
>> Please clarify what directory should be copied
>> for distributing phonon calculations
>> to different machines,  _ph{prefix}.phsave
>> or _ph0{prefix}.phsave? The former is
>> described in the manual INPUT_PH.html, the latter is used in
>> the GRID_example.
>> Although there is no _ph{prefix}.phsave existed after the
>> preparatory run with
>> start_irr=0 and last_irr=0, using the former works OK at the
>> cost of redundant
>> calculations.
>>
>>  Representation #  1 mode #   1
>>
>>  Self-consistent Calculation
>>
>>  %
>> %
>>  from davcio : error #25
>>  error while reading from file
>>  %
>> %
>>
>>  stopping ...
>
> Thank you for the message. I will correct the INPUT_PH documentation.
> The correct directory is _ph0{prefix}.phsave.
>
> This message usually means that you have not copied all the required
> files. Did you copy all the files produced by pw.x?
>
> HTH,
>
> Andrea
>
>
>
>>
>> __
>>
>> ___
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://www.democritos.it/mailman/listinfo/pw_forum
>> ___
>> Pw_forum mailing list
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>> http://www.democritos.it/mailman/listinfo/pw_forum
> -- 
> Andrea Dal CorsoTel. 0039-040-3787428
> SISSA, Via Beirut 2/4   Fax. 0039-040-3787528
> 34151 Trieste (Italy)   e-mail: dalcorso at sissa.it
>
>
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> 

[Pw_forum] Distributing phonon calculations to different machines

[Huiqun Zhou]

Sorry, I sent an unfinished message.

When using _ph0{prefix}.phsave, I got the error message shown in the previous
message.

Here is the snippet of my script for distributing lsf tasks:

..
nq=`sed -n '2p' ./${system}_q${nq1}${nq2}${nq3}.dyn0`
 
for ((i=1; i<=$nq; i++))
do
if test ! -d $TMP_DIR/${system}/q${i} ; then
mkdir $TMP_DIR/${system}/q${i}
cp -r $TMP_DIR/${system}/${system}.* $TMP_DIR/${system}/q${i}
fi
if test ! -d $TMP_DIR/${system}/q${i}/_ph0${system}.phsave ; then
mkdir $TMP_DIR/${system}/q${i}/_ph0${system}.phsave
cp -r $TMP_DIR/${system}/_ph0${system}.phsave/* 
$TMP_DIR/${system}/q${i}/_ph0${system}.phsave
fi
done
 
for ((i=1; i<=$nq; i++))
do
cat > ${system}_q${i}.in << EOF
phonons of ${system}
 &inputph
  tr2_ph = 1.0d-13,
  alpha_mix(1) = 0.2,
  prefix = '${system}',
  ldisp = .true.,
  recover = .true.
  nq1 = ${nq1}, nq2 = ${nq2}, nq3 = ${nq3}
  start_q = $i, last_q = $i
  outdir = '$TMP_DIR/${system}/q${i}',
  fildyn = '${system}_q${nq1}${nq2}${nq3}.dyn'
..
EOF
$ECHO "calculation of q point $i"
bsub -a intelmpi -n $processes \
 -R "span[ptile=8]" \
 -J ${r}q${i}anda \
 -oo ${system}_q${i}.out \
 -eo ${system}_q${i}.err \
 $PH_COMMAND -input ./${system}_q${i}.in
done


Huiqun Zhou
@Earth Sciences, Nanjing University, China
  - Original Message - 
  From: Huiqun Zhou 
  To: pw_forum at pwscf.org 
  Sent: Tuesday, July 06, 2010 12:00 PM
  Subject: [Pw_forum] Distributing phonon calculations to different machines


  dear developers,

  Please clarify what directory should be copied for distributing phonon 
calculations
  to different machines,  _ph{prefix}.phsave or _ph0{prefix}.phsave? The former 
is 
  described in the manual INPUT_PH.html, the latter is used in the 
GRID_example. 
  Although there is no _ph{prefix}.phsave existed after the preparatory run 
with 
  start_irr=0 and last_irr=0, using the former works OK at the cost of 
redundant 
  calculations. 

   Representation #  1 mode #   1
   
   Self-consistent Calculation
   
   
%%
   from davcio : error #25
   error while reading from file
   
%%
   
   stopping ...


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[Pw_forum] Distributing phonon calculations to different machines

[Huiqun Zhou]

dear developers,

Please clarify what directory should be copied for distributing phonon 
calculations
to different machines,  _ph{prefix}.phsave or _ph0{prefix}.phsave? The former 
is 
described in the manual INPUT_PH.html, the latter is used in the GRID_example. 
Although there is no _ph{prefix}.phsave existed after the preparatory run with 
start_irr=0 and last_irr=0, using the former works OK at the cost of redundant 
calculations. 

 Representation #  1 mode #   1
 
 Self-consistent Calculation
 
 %%
 from davcio : error #25
 error while reading from file
 %%
 
 stopping ...
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[Pw_forum] plumed for ESPRESSO-4.2 available

[Huiqun Zhou]

Layla,

Sorry for my ignorance about PLUMED. Could you please explain a little
about the differences between metadynamics in PLUMED and that in pwscf?

Any reference papers are welcome.


Huiqun Zhou
@Earth Sciences, Nanjing University, China

- Original Message - 
From: 
To: ; 
Sent: Friday, July 02, 2010 8:50 PM
Subject: [Pw_forum] plumed for ESPRESSO-4.2 available


> Dear All, the PLUMED plug-in for metadynamic calculations has been 
> adapted to Quantum ESPRESSO-4.2 and is available at
> 
> http://qe-forge.org/frs/?group_id=10
> 
> There is also an additional README (README.plumed.xlc_compiler) for 
> those that uses ibm machines with xlc compiler.
> 
> bests
> 
> 
> Layla
> 
> -- 
> Dr. L. Martin-Samos
> tel. +39 040 3787 429
> CNR-DEMOCRITOS and
> International School for Advanced Studies (ISAS-SISSA)
> via Beirut 2-4
> 34151 Trieste Italy
> 
> 
> This message was sent using IMP, the Internet Messaging Program.
> 
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>

[Pw_forum] Calculating multiple el-ph matrices simultaneously

[Huiqun Zhou]

Carefully read the "Additional information" of INPUT_PH.html, then you 
can do easilly what you want.

Huiqun Zhou
@Earth Sciences, Nanjing University, China
  - Original Message - 
  From: Hahnbidt Rhee 
  To: pw_forum at pwscf.org 
  Sent: Wednesday, June 09, 2010 8:56 AM
  Subject: [Pw_forum] Calculating multiple el-ph matrices simultaneously


  Hello, all. I am doing electron-phonon calculations, and my question pertains 
specifically to getting the el-ph matrices for each q-point. I have noticed 
that, although calculating a matrix of one q-point is independent of that of 
another q-point, the code calculates one q-point at a time--ie, one after the 
other--which makes for an inefficient and very time-consuming run. This is 
based on the elph.in input file (for ph.x), given in Example07 of the examples 
given by PWSCF, in which there is a line to specify the q-pt grid,


  nq1=4, nq2=4, nq3=4


  but not individual q-pts. So one run takes care of all the q-points. Is there 
an option (that I don't know of) to create separate jobs for each q-point so 
that I can calculate el-ph matrices of multiple inequivalent q-pts 
SIMULTANEOUSLY? I am using the parallel version of the latest code (v4.2), so 
it seems reasonable for there to be this option. Thank you!

  HB Rhee
  UC Davis



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[Pw_forum] My installation of Espresso 4.1/4.2 is not passingbenchmarks

[Huiqun Zhou]

If I were you, I'll ignore such minor differences in calculated pressure. In 
fact,
you should feel lucky that you got less number of SCF iterations (^o^)


Zhou Huiqun
@Earth Sciences, Nanjing University, China

- Original Message - 
From: "Christopher O'Brien" 
To: 
Sent: Tuesday, June 01, 2010 8:05 AM
Subject: [Pw_forum] My installation of Espresso 4.1/4.2 is not 
passingbenchmarks


> To all:
> I have successfully compiled Quantum Espresso 4.2 with the GCC v4.5 (April 
> 2010) on Mac 10.6.3 (64-bit kernel enabled). I have also installed 4.1 
> with ifort 9.0 on a red-had linux cluster. After completing the 
> installation, I ran the benchmarks included in the 'test' folder of the 
> distributions but saw many discrepancies. Perhaps the most disturbing were 
> those involving simple SCF calculations such as:
>> Checking atom-pbe...discrepancy in pressure detected
>> Reference: -14.44, You got: -14.43
> and
>> Checking atom-sigmapbe...discrepancy in pressure detected
>> Reference: -15.02, You got: -15.03
> Also, large errors were reported for
>> Checking lda+U_gamma...discrepancy in number of scf iterations detected
>> Reference: 46, You got: 40
>> discrepancy in force detected
>> Reference:   0.4682, You got:   0.4690
>> discrepancy in pressure detected
>> Reference: 549.51, You got: 551.15
>
> It seems that these discrepancies are due to more than numerical error. Is 
> this a common problem? Is this related to the fact that the reference 
> values are from v4.1a?
>
> Detailed error reports and my configuration file can be found at:
> https://sites.google.com/a/ncsu.edu/cjobrien/tutorials-and-guides/quantum-espresso-install-errors
>
> Thanks in advance.
> ===
> Christopher J. O'Brien
> Ph.D. Candidate
> Computational Materials Group
> Department of Materials Science & Engineering
> North Carolina State University
> ___
> Please send all documents in PDF, HTML, RTF, DVI, PS or plain text.
> For Word documents: Please use the 'Save as PDF' option before sending.
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[Pw_forum] How to specify spin for individual atoms

[Huiqun Zhou]

Hi,

Something look like below
...
 starting_magnetization(1) = 0.5
 starting_magnetization(2) = -0.5
..

ATOM_SPECIES
Mn1mass_of_mn  Mn.gga.upf
Mn2mass_of_mn  Mn.gga.upf




Huiqun Zhou
@Earth Sciences, Nanjing University, China

  - Original Message - 
  From: Bipul Rakshit 
  To: PWSCF Forum 
  Sent: Monday, May 17, 2010 4:11 PM
  Subject: Re: [Pw_forum] How to specify spin for individual atoms


  Dear Baris,
  thanks for your kind reply. I go through the "starting_magnetization" and the 
related documents. But with the help of that flag, we can specify the magnetic 
moment to particular type. But if u see the atomic co-ordinate i gave there i 
require the Mn1 spin up & down, and Mn2 spin up & down.

  So that's i didnt understand how do i specify the spins for particular atoms 
not with particular type.


  On Mon, May 17, 2010 at 1:21 PM, O. Baris Malcioglu  wrote:

Dear Bipul Rakshit,

Please take a glance at "starting_magnetization" under the system
namelist. You can find the relevant information in the supplied
documentation directory.

Best,
Baris


2010/5/17 Bipul Rakshit :

> Dear Users,
> I am doing a system in which i have 8 Mn.
> Following is the atomic positions in fractional co-ordinate.
>
> Mn1  0.125  0.250  0.2794000+
> Mn1  0.375  0.750  0.7206000+
> Mn2  0.125  0.250  0.7486000-
> Mn2  0.375  0.750  0.2514000-
> Mn1  0.625  0.250  0.2794000-
> Mn1  0.875  0.750  0.7206000-
> Mn2  0.625  0.250  0.7486000+
> Mn2  0.875  0.750  0.2514000+
>
>
> Now i want to specify the spin as shown by the last column, (with + & -
> signs).
> So can  you please tell me what flags i have to use to specify the 
magnetic
> spin for particular atom.
> --
>  Bipul Rakshit
> Research Fellow,
> S N Bose Centre for Basic Sciences,
> Salt Lake,
> Kolkata 700 098
> India
>

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[Pw_forum] MKL libraries

[Huiqun Zhou]

MKL librariesHi,

You'd better use sequential version of MKL for MPI parallelization. For example,
when you configure qe-espresso,

./configure ..
..
BLAS_LIBS="-L$(MKLROOT)/lib/em64t -lmkl_intel_lp64 -lmkl_sequential -lmkl_core"
LAPACK_LIBS=""
..


Huiqun Zhou
@Earth Sciences, Nanjing University

  - Original Message - 
  From: Vo, Trinh (388C) 
  To: PWSCF Forum 
  Sent: Wednesday, May 19, 2010 3:49 AM
  Subject: [Pw_forum] MKL libraries


  Dear PWSCF Users,

  I am compiling QE 4.1.2 with Intel compiler 11.1.038.   I go to the following 
link to find which libraries for my system.  I am not sure which of the 
following is the better choice for compiling with QE: sequential or 
multi-threaded version of Intel? MKL. If any of you have  experience with this, 
could you give me some advise.  

  Thank you very much in advance,

  Trinh Vo
  Computing Group
  JPL/CalTech 



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[Pw_forum] Low speed

[Huiqun Zhou]

mohsen,

Increasing speed is a difficult task unless you could find better algorithms 
and 
write better programs. Anyway, first thing is first, my recommendation is to
change your compiler to Intel FORTRAN and use Intel MKL instead of your
self-compiled BLAS and LAPACK.


Huiqun Zhou
@Earth Sciences, Nanjing University, China
  - Original Message - 
  From: mohsen modaresi 
  To: PWSCF Forum 
  Sent: Thursday, May 13, 2010 3:39 AM
  Subject: Re: [Pw_forum] Low speed


  Daer Ngoc,
  Thanks for your answer.
  This is "make.sys", Do any body have any suggestion for increasing speed?
  Thanks again for your answers,
  Mohsen Modaresi 



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[Pw_forum] a question about the name ESPRESSO

[Huiqun Zhou]

Although most chinese used to drink green tea, now we have vending machine that 
serves 
espresso on every floor of our teachoing building and Starbucks is spreading in 
the city, too. 

Let's further enjoy "espresso" in a coffee house or on our super computer!


Huiqun Zhou
@Earth Sciences, Nanjing University, China
  - Original Message - 
  From: Stefano Baroni 
  To: PWSCF Forum 
  Sent: Wednesday, May 05, 2010 4:02 AM
  Subject: Re: [Pw_forum] a question about the name ESPRESSO


  PPS: although a bit outdated, "espresso" is actually an adjective. It used to 
mean "made on purpose" or "made on demand". This is the origin of the 
expression (note the common root of the words!) "espresso coffee", which is 
made on demand, rather than filtered and kept hot in a kettle. I think that  it 
is because of its association with "coffee on demand" that at some pointthe 
word   "espresso" came to mean "swift", or "quick" (because brewing espresso 
coffee is much faster than making filter coffee). As a matter of fact, the 
fastest Italian trains when I was a kid were named "espresso". So, "Quantum 
ESPRESSO" alludes to a blend of all these meanings: tasty (as good coffee), 
fashionable (as many Italian goods), user friendly (ready on demand), swift and 
powerful (as espresso trains), tech savy (as Illy coffee), a bit understating 
(you don't drink espresso coffee in very elegant cafes, but you can find small 
coffee places with a great reputation for their espresso), keeping awake/alive 
(as strong coffee should: please, notice the contrast with "siesta"). SB


  On May 4, 2010, at 9:32 PM, Stefano Baroni wrote:


PS: the one hiding himself behind the camera is Roberto Car


On May 4, 2010, at 11:50 AM, Nicola Marzari wrote:




  Dear L F Huang,

  Trieste (where the code originates) is the main shipping port in Italy 
  for coffee
  imports, and the city has a long tradition of coffee houses and of 
  coffee producers
  (the beans themselves are grown elsewhere).

  The most famous of these companies is "Illy", that is extremely tech savy 
-
  this below is an article that the company founder wrote a few years ago 
  for "Scientific
  American": http://www.podmerchant.com/coffee/complexity-of-coffee.pdf

  What might intrigue you is that we invented the name while waiting in
  Beijing airport a flight to Xi'an - we were in Beijing for a summer school
  at the institute of physics (2004), and we decided to spend the weekend in
  the old capital.

  Here is the team at work - I believe Shobhana, Ralph and Carlo are
  missing, among those that were there :
  http://quasiamore.mit.edu/personal/xian/espresso.jpg

 nicola


  -- 
  -
  Prof Nicola Marzari   Department of Materials Science and Engineering
  13-5066   MIT   77 Massachusetts Avenue   Cambridge MA 02139-4307 USA
  tel 617.4522758 fax 2586534 marzari at mit.edu http://quasiamore.mit.edu 

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  http://stefano.baroni.me [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni 
(skype)


  La morale est une logique de l'action comme la logique est une morale de la 
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[Pw_forum] About q point parallelization

[Huiqun Zhou]

dear developers,

Just want someone clarifies that it's not neccessary to execute the "final run 
of ph.x"
if I only split q points (not irr) to different machines because the *.dyn# 
file has been
generated on each machine.

Thanks!

Huiqun Zhou
@Nanjing University, China
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[Pw_forum] Relaxation doesn't converge

[Huiqun Zhou]

Pablo,

Usually, setting conv_thr = 1d-8 is sufficient, please make sure if you
need such strict convergence criterion.


Huiqun Zhou
@Earth Sciences, Nanjing University, China


- Original Message - 
From: "Pablo Aguado" 
To: 
Sent: Tuesday, September 01, 2009 6:38 PM
Subject: [Pw_forum] Relaxation doesn't converge


> Dear all,
>
> I'm doing some tests on the structural optimization with pw. I'm
> currently testing with the tetragonal structure of PbTiO3, using the
> following input:
>
> &control
>calculation  = 'vc-relax'
>restart_mode = 'restart'
>pseudo_dir   = '//espresso-4.1/pseudo/'
>outdir   = '/***/tmp'
>forc_conv_thr = 1d-3
>nstep = 50
> /
> &system
>ibrav=6
>celldm(1)=7.3699
>celldm(3)=1.04
>nat=5
>ntyp=3
>nbnd=28
>ecutwfc=30.0
>occupations = 'fixed'
> /
> &electrons
>conv_thr = 1d-12,
>mixing_beta=0.4,
> /
> &ions
>ion_dynamics = 'bfgs'
>bfgs_ndim = 5
> /
> &cell
>cell_dynamics = 'damp-pr'
>press_conv_thr = 1.0d0
>cell_dofree = 'z'
> /
> ATOMIC_SPECIES
>  Pb   207.2  Pb.pz-d-van.UPF
>  Ti47.867Ti.pz-sp-van_ak.UPF
>  O 15.9994   O.pz-van_ak.UPF
> ATOMIC_POSITIONS crystal
>  Pb0.0000.0000.040   0 0 1
>  Ti0.5000.5000.520   0 0 1
>  O 0.0000.5000.500   0 0 1
>  O 0.5000.5000.000   0 0 1
>  O 0.5000.0000.500   0 0 1
> K_POINTS automatic
>  6 6 6 1 1 1
>
> The relaxation is taking forever so I've checked the output and I've
> found several steps where everything seems to be converged (notice I'm
> only relaxing out-of-plane lattice vector) but the code keeps running.
> An example:
>
> - Energy difference = 4e-7
> - Forces acting on atoms (Ry/au):
>
> atom   1 type  1   force = 0.0.0.00085679
> atom   2 type  2   force = 0.0.   -0.1779
> atom   3 type  3   force = 0.0.   -0.00024617
> atom   4 type  3   force = 0.0.   -0.00034665
> atom   5 type  3   force = 0.0.   -0.00024617
>
> Total force = 0.000988 Total SCF correction = 0.02
>
>  total   stress  (Ry/bohr**3)   (kbar) 
>   P=   -0.84
>  -0.1150   0.   0. -1.69  0.00  0.00
>   0.  -0.1150   0.  0.00 -1.69  0.00
>   0.   0.   0.0591  0.00  0.00  0.87
>
> Any idea of what's going on?
>
> Thank you very much
>
> Pablo
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[Pw_forum] problem in parallel running

[Huiqun Zhou]

Sharma,

Let me try to put it clearer. Paolo means that the compute nodes involved 
in the computation must be able to "see" the folder /home/devsharma/pseudo,
meaning the pseudo folder must be located on a NFS, which is shared
by the head node, the one you submitted your job, and compute nodes,
on which your job is executed.

If your job was submitted to the head node itself, that will be very strange. 
You need to let us know your cluster environment.

Huiqun Zhou
@Nanjing University, China  
  - Original Message - 
  From: dev sharma 
  To: PWSCF Forum 
  Sent: Monday, August 24, 2009 5:10 PM
  Subject: Re: [Pw_forum] problem in parallel running


  Dear Sir,
   I am sending all the terminal commands to you. Please guide me.,

  [devsharma at headnode ~]$ ls
  espresso-4.0.2  pseudo  tmp  work
  [devsharma at headnode ~]$ cd pseudo/
  [devsharma at headnode pseudo]$ ls

  0710.pdfCr.pw91-sp-van.info Li.pz-n-vbc.UPF   
 Pt.pw91-n-van.info
  Ag.pbe-d-rrkjus.infoCr.pw91-sp-van.UPF  Li.pz-s-mt.UPF
 Pt.pw91-n-van.UPF
  Ag.pbe-d-rrkjus.UPF Cs.pbe-mt_bw.info   Li.pz-s-van_ak.info   
 Pt.pz-nd-rrkjus.UPF
  Ag.pz-d-rrkjus.UPF  Cs.pbe-mt_bw.UPFLi.pz-s-van_ak.UPF
 Pt.pz-rrkjus.UPF
  Al.blyp-n-van_ak.info   C.tpss-mt.UPF   Mg.pw91-np-van.info   
 Pt.rel-pz-n-rrkjus.UPF
  Al.blyp-n-van_ak.UPFCu.blyp-n-van_ak.info   Mg.pw91-np-van.UPF
 Re.pw91-n-van.info
  Al.bp-n-van_ak.info Cu.blyp-n-van_ak.UPFMg.pz-bhs.UPF 
 Re.pw91-n-van.UPF
  Al.bp-n-van_ak.UPF  Cu.pbe-d-rrkjus.infoMg.pz-n-vbc.info  
 Rh.pbe-nd-rrkjus.UPF
  Al.pbe-n-van.info   Cu.pbe-d-rrkjus.UPF Mg.pz-n-vbc.UPF   
 Rh.pbe-rrkjus.UPF
  Al.pbe-n-van.UPFCu.pbe-n-van_ak.infoMn.pbe-sp-van.info
 Rh.pz-rrkjus.UPF
  Al.pbe-rrkj.UPF Cu.pbe-n-van_ak.UPF Mn.pbe-sp-van.UPF 
 Ru.pbe-n-van.info
  Al.pw91-n-van.info  Cu.pw91-n-van_ak.info   Mo.pw91-n-van.info
 Ru.pbe-n-van.UPF
  Al.pw91-n-van.UPF   Cu.pw91-n-van_ak.UPFMo.pw91-n-van.UPF 
 Ru.pw91-n-van.info
  Al.pz-vbc.UPF   Cu.pz-d-rrkjus.UPF  
Na.blyp-sp-van_ak.info Ru.pw91-n-van.UPF
  Ar.pz-rrkj.info Cu.pz-n-van_ak.info Na.blyp-sp-van_ak.UPF 
 S.blyp-mt.info
  Ar.pz-rrkj.UPF  Cu.pz-n-van_ak.UPF  Na.bp-sp-van_ak.info  
 S.blyp-mt.UPF
  As.pbe-n-van.info   Fe.blyp-sp-van_ak.info  Na.bp-sp-van_ak.UPF   
 S.blyp-van_ak.info
  As.pbe-n-van.UPFFe.blyp-sp-van_ak.UPF   Na.pbe-n-mt_bw.info   
 S.blyp-van_ak.UPF
  As.pw91-n-van.info  Fe.blyp-sp-van.info Na.pbe-n-mt_bw.UPF
 S.bp-van_ak.info
  As.pw91-n-van.UPF   Fe.blyp-sp-van.UPF  Na.pbe-n-van.UPF  
 S.bp-van_ak.UPF
  As.pz-bhs.info  Fe.bp-sp-van_ak.infoNa.pbe-sp-van_ak.info 
 Sb.pw91-n-van.info
  As.pz-bhs.UPF   Fe.bp-sp-van_ak.UPF Na.pbe-sp-van_ak.UPF  
 Sb.pw91-n-van.UPF
  Au.blyp-van_ak.info Fe.pbe-nd-rrkjus.UPFNa.pw91-n-mt.UPF  
 Sb.pz-bhs.info
  Au.blyp-van_ak.UPF  Fe.pbe-sp-van_ak.info   Na.pw91-n-van.UPF 
 Sb.pz-bhs.UPF
  Au.bp-van_ak.info   Fe.pbe-sp-van_ak.UPF
Na.pw91-sp-van_ak.info Sc.pbe-nsp-van.info
  Au.bp-van_ak.UPFFe.pbe-sp-van.info  Na.pw91-sp-van_ak.UPF 
 Sc.pbe-nsp-van.UPF
  Au.pbe-nd-rrkjus.UPFFe.pbe-sp-van_mit.info  Na.pz-n-vbc.info  
 Sc.pw91-nsp-van.info
  Au.pbe-nd-van.info  Fe.pbe-sp-van_mit.UPF   Na.pz-n-vbc.UPF   
 Sc.pw91-nsp-van.UPF
  Au.pbe-nd-van.UPF   Fe.pbe-sp-van.UPF   Na.pz-sp-van_ak.info  
 Se.pbe-van.info
  Au.pbe-van_ak.info  Fe.pw91-sp-van_ak.info  Na.pz-sp-van_ak.UPF   
 Se.pbe-van.UPF
  Au.pbe-van_ak.UPF   Fe.pw91-sp-van_ak.UPF   
Nb.elastic_constant_tests.pdf  Se.pz-bhs.info
  Au.pw91-d-van.UPF   Fe.pz-nd-rrkjus.UPF N.blyp-mt.info
 Se.pz-bhs.UPF
  Au.pw91-van_ak.info Fe.pz-sp-van_ak.infoN.blyp-mt.UPF 
 Si.pbe-n-van.info
  Au.pw91-van_ak.UPF  Fe.pz-sp-van_ak.UPF N.blyp-van_ak.info
 Si.pbe-n-van.UPF
  Au.pz-d-rrkjus.UPF  filename.upfN.blyp-van_ak.UPF 
 Si.pbe-rrkj.UPF
  Au.pz-d-van.UPF F.pbe-n-van.infoNb.pbe-nsp-van.info   
 Si.pw91-n-van.info
  Au.pz-van_ak.info   F.pbe-n-van.UPF Nb.pbe-nsp-van.UPF
 Si.pw91-n-van.UPF
  Au.pz-van_ak.UPFF.pw91-n-van.info   N.bp-van_ak.info  
 Si.pz-vbc.UPF
 

[Pw_forum] scf

[Huiqun Zhou]

Alvaro,

I think you need to test total energy or total magnetization against degauss,
the value of degauss should be small enough to make total energy converge.


Huiqun Zhou
@Earth Sciences, Nanjing University, China
  - Original Message - 
  From: ?lvaro Alves 
  To: PWSCF Forum 
  Sent: Friday, August 14, 2009 5:43 AM
  Subject: Re: [Pw_forum] scf


Hello. I am doing a scf calculation system and uses degauss = 0.003 and 
needed change it  for 0001. With this new value, the calculation does not 
converge. What may be happening?  

Regards, Alvaro

A. S. Santos

--- Em qui, 13/8/09, ?lvaro Alves  escreveu:


  De: ?lvaro Alves 
  Assunto: [Pw_forum] scf
  Para: "pw" 
  Data: Quinta-feira, 13 de Agosto de 2009, 17:30


Hello I am doing a scf calculation system and uses degauss = 
0.003 and needed change it paar 0001. With this new value, the calculation does 
not converge. What may be happening? 

Regards, Alvaro


   


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[Pw_forum] Stress calculation in quantum espresso

[Huiqun Zhou]

Thanks, Lorenzo, for your quick action. Anyway, English is not
our mother tongue(^o^)

BTW, there are other items need to check:
(1) ion_dynamics
 add 'bfgs' for the case of calculation = 'vc-relax'
(2) pot | wfc_extrapolation
 please clarify if 'first_order', 'second_order' can be used in calculations
 other than 'md' or 'vc-md'. I used these options in 'relax' and 'vc-relax'
 without any errors, too. Of course, I don't know if these were really in
 effect.
(3) ecfixed, qcutz and q2sigma
 in the original paper, the framework is an extension of PR dynamics to
 CP. Please clarify if these are effective in other dynamics (damp-w, bfgs).
 If possible, suggest a guide line how to set these options (there is only
 one example of carbon in the paper), say, qcutz should be at least N (2?)
 times of ecfixed, ecfixed should be ecutwfc plus alpha (5 Ry or so?),
 q2sigma should be one N-th of qcutz ...

Sorry for adtional requests.

Huiqun Zhou
@Earth Sciences, Nanjing University, China

- Original Message - 
From: "Lorenzo Paulatto" 
To: "PWSCF Forum" 
Sent: Tuesday, June 30, 2009 2:17 PM
Subject: Re: [Pw_forum] Stress calculation in quantum espresso


>
> On Tue, June 30, 2009 05:22, Huiqun Zhou wrote:
>>  But at least, this kind of description is a bit of  misleading.
>
> You are right, it is a bad translation from Italian. For an Italian
> speaker it apears to have has a certain meaning, while the real meaning is
> completely different! I'll fix it.
>
> cheers
>
> -- 
> Lorenzo Paulatto
> SISSA  &  DEMOCRITOS (Trieste)
> phone: +39 040 3787 511
> skype: paulatz
> www:   http://people.sissa.it/~paulatto/
>
>
>
> 
>  SISSA Webmail https://webmail.sissa.it/
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> 

[Pw_forum] Stress calculation in quantum espresso

[Huiqun Zhou]

But at least, this kind of description is a bit of  misleading. 


Huiqun Zhou
@Earth Sciences, Nanjing University, China

> +
>   Variable:   tstress
> 
>   Type:   LOGICAL
>   Description:calculate stress. Set to .TRUE. if calculation='vc-md'
>   +
> The last sentence does not mean that the variable applies just to a 
> vc-md calculation but  that
> it is by default set to .true. in that case.

[Pw_forum] what's the difference between 'md' in pw.x and cp.x

[Huiqun Zhou]

'md' in PWscf may most likely be BOMD.


Zhou Huiqun
  - Original Message - 
  From: vega lew 
  To: PWSCF Forum 
  Sent: Monday, June 22, 2009 4:39 PM
  Subject: [Pw_forum] what's the difference between 'md' in pw.x and cp.x


  Dear all,

  I want to perform ab initio molecular dynamics calculation via Q-E. I found 
both cp.x and pw.x could undertake this calculation.
  I wonder what's the difference between 'md' in pw.x and cp.x, and if I could 
achieve the same final geometry for same systems (the coordinates of atoms, 
temparature, box dimensions and K-ponits etc. are exactly the same) by this two 
methods.
  Do you think both 'md' calculation in pw.x and 'cp' in cp.x could be regard 
as the 'Car-Parrinello Molecular Dynamics' calculation and do the almost the 
same thing as the 'CPMD' codes copyrighted jointly by IBM Corp.

  thank you for reading 

  best,

  vega
  -- 
  
==
  Vega Lew ( weijia liu)
  PH.D Candidate in Chemical Engineering
  State Key Laboratory of Materials-oriented Chemical Engineering
  College of Chemistry and Chemical Engineering
  Nanjing University of Technology, 210009, Nanjing, Jiangsu, China
  
**
  Email: vegalew at gmail.com
  Office: Room A705, Technical Innovation Building, Xinmofan Road 5#, Nanjing, 
Jiangsu, China  
  
**
 



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[Pw_forum] Apology

[Huiqun Zhou]

Dear list users,

I apologize for sending out a post three times because of
a configuration problem in my mail client. I tried twice
so that there were already two unsent mails in my outbox.
After I fixed the setting problem, I forgot to delete the
two and tried again, so you may have received my three
equivalent posts.

I'm sorry for the inconvenience and apologize again.

Huiqun Zhou
@Earth Sciences, Nanjing University, China
   
   
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[Pw_forum] Elastic Constant.

[Huiqun Zhou]

Stefano,

The straightforward approach is tedious for orthorgonal, monolinic, trilinic
systems. Should the lost implementation gain in these respects?

Huiqun Zhou
@Earth Sciences, Nanjing University, China

- Original Message - 
From: "Stefano Baroni" 
To: "PWSCF Forum" 
Sent: Sunday, June 14, 2009 6:01 PM
Subject: Re: [Pw_forum] Elastic Constant.


> Dear Bipul,
> 
> long ago there used to be an implementation of the linear-response  
> approach to elastic constants by SB, Giannozzi, and Testa:
> % Copyright (C) 2009 The American Physical Society
> % Please report any problems to prola at aps.org
> 
> @Article{PhysRevLett.59.2662,
>   title = {Elastic Constants of Crystals from Linear-Response Theory},
>   author = {Baroni, Stefano  and Giannozzi, Paolo  and Testa, Andrea },
>   journal = {Phys. Rev. Lett.},
>   volume = {59},
>   number = {23},
>   pages = {2662--2665},
>   numpages = {3},
>   year = {1987},
>   month = {Dec},
>   doi = {10.1103/PhysRevLett.59.2662},
>   publisher = {American Physical Society}
> }
> This is no longer available, partly because of the programmers'  
> lazyness, partly because there is not much to be gained with respect  
> to the straightforward approach you are following.
> 
> Stefano B
> 
> 
> On Jun 13, 2009, at 10:00 PM, Bipul Rakshit wrote:
> 
>> Dear Pwscf user,
>> I want to calculate the elastic constants for cubic structure for
>> LaSb, which is having NaCl structure. Although I have written a small
>> script for doing that. But if anybody develop any code, do he/she like
>> to share, so that I can compare my results.
>> Thanks
>> -- 
>> Bipul Rakshit
>> PhD Student,
>> Barkatullah University,
>> Bhopal 462026,
>> MP, India
>> ___
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://www.democritos.it/mailman/listinfo/pw_forum
> 
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>

[Pw_forum] Elastic Constant.

[Huiqun Zhou]

Stefano,

The straightforward approach is tedious for orthorgonal, monolinic, trilinic
systems. Should the lost implementation gain in these respects?

Huiqun Zhou
@Earth Sciences, Nanjing University, China

- Original Message - 
From: "Stefano Baroni" 
To: "PWSCF Forum" 
Sent: Sunday, June 14, 2009 6:01 PM
Subject: Re: [Pw_forum] Elastic Constant.


> Dear Bipul,
> 
> long ago there used to be an implementation of the linear-response  
> approach to elastic constants by SB, Giannozzi, and Testa:
> % Copyright (C) 2009 The American Physical Society
> % Please report any problems to prola at aps.org
> 
> @Article{PhysRevLett.59.2662,
>   title = {Elastic Constants of Crystals from Linear-Response Theory},
>   author = {Baroni, Stefano  and Giannozzi, Paolo  and Testa, Andrea },
>   journal = {Phys. Rev. Lett.},
>   volume = {59},
>   number = {23},
>   pages = {2662--2665},
>   numpages = {3},
>   year = {1987},
>   month = {Dec},
>   doi = {10.1103/PhysRevLett.59.2662},
>   publisher = {American Physical Society}
> }
> This is no longer available, partly because of the programmers'  
> lazyness, partly because there is not much to be gained with respect  
> to the straightforward approach you are following.
> 
> Stefano B
> 
> 
> On Jun 13, 2009, at 10:00 PM, Bipul Rakshit wrote:
> 
>> Dear Pwscf user,
>> I want to calculate the elastic constants for cubic structure for
>> LaSb, which is having NaCl structure. Although I have written a small
>> script for doing that. But if anybody develop any code, do he/she like
>> to share, so that I can compare my results.
>> Thanks
>> -- 
>> Bipul Rakshit
>> PhD Student,
>> Barkatullah University,
>> Bhopal 462026,
>> MP, India
>> ___
>> 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
>

[Pw_forum] Elastic Constant.

[Huiqun Zhou]

Stefano,

The straightforward approach is tedious for orthorgonal, monolinic, trilinic
systems. Should the lost implementation gain in these respects?

Huiqun Zhou
@Earth Sciences, Nanjing University, China

- Original Message - 
From: "Stefano Baroni" 
To: "PWSCF Forum" 
Sent: Sunday, June 14, 2009 6:01 PM
Subject: Re: [Pw_forum] Elastic Constant.


> Dear Bipul,
> 
> long ago there used to be an implementation of the linear-response  
> approach to elastic constants by SB, Giannozzi, and Testa:
> % Copyright (C) 2009 The American Physical Society
> % Please report any problems to prola at aps.org
> 
> @Article{PhysRevLett.59.2662,
>   title = {Elastic Constants of Crystals from Linear-Response Theory},
>   author = {Baroni, Stefano  and Giannozzi, Paolo  and Testa, Andrea },
>   journal = {Phys. Rev. Lett.},
>   volume = {59},
>   number = {23},
>   pages = {2662--2665},
>   numpages = {3},
>   year = {1987},
>   month = {Dec},
>   doi = {10.1103/PhysRevLett.59.2662},
>   publisher = {American Physical Society}
> }
> This is no longer available, partly because of the programmers'  
> lazyness, partly because there is not much to be gained with respect  
> to the straightforward approach you are following.
> 
> Stefano B
> 
> 
> On Jun 13, 2009, at 10:00 PM, Bipul Rakshit wrote:
> 
>> Dear Pwscf user,
>> I want to calculate the elastic constants for cubic structure for
>> LaSb, which is having NaCl structure. Although I have written a small
>> script for doing that. But if anybody develop any code, do he/she like
>> to share, so that I can compare my results.
>> Thanks
>> -- 
>> Bipul Rakshit
>> PhD Student,
>> Barkatullah University,
>> Bhopal 462026,
>> MP, India
>> ___
>> 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
>

[Pw_forum] phonon calculation for large system

[Huiqun Zhou]

Gabriele,

I just downloaded the CVS version two days ago, but found no INPUT_PH
in Doc. Should you please post one, or let me know how to generate it?

Huiqun Zhou
@Earth Sciences, Nanjing University, China


- Original Message - 
From: "Gabriele Sclauzero" 
To: "PWSCF Forum" 
Sent: Thursday, April 30, 2009 3:46 PM
Subject: Re: [Pw_forum] phonon calculation for large system


>
>
> zq wu wrote:
>> Dear pwscf users,
>>
>> I need to do phonon calculation for large system (several hundreds atoms
>> per cell). Since i can use lots of processors, I plan to submit many
>> jobs,  each of which will calculate 1 phonon mode. But i do not know
>> whether it is available to get final dynamic matrix from these separate
>> runs and how to do it. Can any one help me?
>>
>>  Currently, phonon modes are calculated one by one in sequence in phonon
>> calculation. Can we do some parallelization here? Can we divide the
>> processors into several groups and let each group take care of one or
>> more modes in a way similar to K-points parallelization?  I think that
>> the parallel efficeincy for modes parallelization should also be close
>> to K-points parallelization since the phonon modes calculation is
>> independent of each other.  The modes parallelization should be very
>> useful for system with large numbers of atoms.  Does anyone have the
>> idea how hard it is to do the modes parallelization?
>
> If I correctly understood, i think that this kind of parallelization has 
> already been
> exploited in the latest versions of CVS, in order to use ph.x on the GRID. 
> I don't know if
> all the related problems have been fixed at this stage (have they, 
> Paolo?), but you can
> try to download the CVS and use the keywords start_q, last_q, start_irr, 
> last_irr (see
> INPUT_PH) to split your job in many independent jobs. Sorry, I don't know 
> the details, but
> at least now you're aware that there is this possibility available (though 
> not extensively
> tested, I think, so use _with_ _care_ and help debugging, please).
>
> HTH
>
> GS
>
>
>>
>> Thanks
>>
>> Zhongqing
>>
>> CACS  University of Southern California
>>
>>
>>
>> 
>>
>> ___
>> 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
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> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
> 

[Pw_forum] DMFT+LDA

[Huiqun Zhou]

Paolo,

Soory I might not make the question clearer. I mean, I used to access
CVS version from the server indicated in README.cvs. Just want to
confirm it's the same with that downloaded from qe-forge.org.

Huiqun Zhou

- Original Message - 
From: "Paolo Giannozzi" 
To: "PWSCF Forum" 
Sent: Friday, March 27, 2009 3:27 PM
Subject: Re: [Pw_forum] DMFT+LDA


> 
> On Mar 27, 2009, at 5:28 , Huiqun Zhou wrote:
> 
>> Does the snapshot you indicated the same as the cvs version
>> accessed from SISSA's cvs root?
> 
> please?
> 
> ---
> Paolo Giannozzi, Democritos and University of Udine, Italy
> 
> 
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> http://www.democritos.it/mailman/listinfo/pw_forum
>

[Pw_forum] DMFT+LDA

[Huiqun Zhou]

Paolo,

Does the snapshot you indicated the same as the cvs version accessed
from SISSA's cvs root?

Huiqun
@Earth Sciences, Nanjing University, China

- Original Message - 
From: "Paolo Giannozzi" 
To: "PWSCF Forum" 
Sent: Wednesday, March 25, 2009 5:12 PM
Subject: Re: [Pw_forum] DMFT+LDA


> DdrSmiLe wrote:
> 
>> Another problem is I could not compile w90 in espresso-4.1CVS package.
>> It showed that there are something loss in W90 package.
> 
> use the link "[Download The Nightly CVS Tree Snapshot]"
> from here: ttp://qe-forge.org/scm/?group_id=10
> The CVS package you mention wss an experiment and
> might not be complete
> 
> P.
> -- 
> Paolo Giannozzi, Democritos and University of Udine, Italy
> ___
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> http://www.democritos.it/mailman/listinfo/pw_forum
>

[Pw_forum] question about electron phonon calculation

[Huiqun Zhou]

Gabriele,

Sorry for my ignorance of developer's fast tempo. I asked a question about
q-point parallization in using ph.x nearly one year ago, and got the 
following
answer:

http://www.democritos.it/pipermail/pw_forum/2008-April/008667.html

It seems things change faster. Thnaks for the effort.

Huiqun Zhou


- Original Message - 
From: "Gabriele Sclauzero" 
To: "PWSCF Forum" 
Sent: Monday, March 09, 2009 5:04 PM
Subject: Re: [Pw_forum] question about electron phonon calculation


>
> hqzhou wrote:
>> It simply means that using pools in phonon calculation is meaningless.
>
> Why do you say this? Phonon calculations with pools parallelization is 
> implemented and
> works properly! Why should it be meaningless?
>
> The error message report you were refering to:
>
>  from elphsum : error # 1
>
>  pools and a2F not implemented
>
> does not come from a phonon calculation (which can be done using pools), 
> but from an
> electron-phonon coupling calculation, which has not yet been parallelized 
> with pools
> (while distributed FFT parallelization should be already working).
>
> GS
>
>> But it may not be the main cause of your error.
>>
>> Dr. Huiqun Zhou
>> @Earth Sciences, Nanjing University, China
>>
>>
>> ___
>> 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
> ___
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> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
> 

[Pw_forum] Use of pool

[Huiqun Zhou]

Axel and list-users,

I'm terribly sorry for my delayed response.  I personally want to
thank Axel for his thorough investigation, to-the-point analysis and
detailed report, every bit of experience will benefit us a lot in our
future life in computation.

As I said, the test maching I used is an AMD box with 2 way
quad core  Shanghai (opteron 23xx, 2.3 GHz) , which has only
1 MB L2 cache, the test case may make the CPU cache inefficient
more quickly than Intel ones (usually 4-6 MB L2 cache) according
to your findings.

BTW, the input file I sent you is absolutely the same as I used here.
AMD's shanghai and Intel's nehalem, which I have done several tests
on both platforms, are much better than their previous processors.
It seems Axel needs to connect more powerful machines with his
high-end infiniBand network(^o^)

Thanks again, Axel!

Dr. Huiqun Zhou
@Earth Sciences, Nanjing University, China


- Original Message - 
From: "Axel Kohlmeyer" 
To: "PWSCF Forum" 
Sent: Wednesday, March 04, 2009 10:51 AM
Subject: Re: [Pw_forum] Use of pool


> On Tue, Feb 24, 2009 at 1:45 AM, Huiqun Zhou  wrote:
>> Dear list users:
>
> hi all,
>
>> I happened to test duration times of calculating the system I'm
>> investigating against number of pools used. There are totally
>> 36 k points. But the results surprised me quite a lot.
>>
>> no pool:  6m21.02s CPU time, 6m45.88s wall time
>> 2 pools:  7m19.39s CPU time, 7m38.99s wall time
>> 4 pools: 11m59.09s CPU time,12m14.66s wall time
>> 8 pools: 21m28.77s CPU time,21m38.71s wall time
>>
>> The machine I'm using is an AMD box with 2 quad core shanghai.
>>
>> Is my understanding of usage of pool wrong?
>
> sorry for replying to an old mail in this thread, but it has the
> proper times to compare to. the input you sent me, does not
> seem to be the exactly the same as the one you used for the
> benchmarks (rather a bit larger). but i reduced the number of
> k-points to yield 36 and have some numbers here.
> this is on dual intel quad core E5430 @ 2.66GHz cpus with 8GB DDR2 ram.
> i also modified the input to set wfcdir to use the local scratch rather 
> than my
> working directory (as this is on an NFS server) and test with
> disk_io='high' and 'low'.
> on a single node (always with 8 MPI tasks) i get:
>
> 1node-1pools-high.out: PWSCF: 18m55.62s CPU time,26m
> 7.20s wall time
> 1node-2pools-high.out: PWSCF: 14m46.03s CPU time,18m
> 0.26s wall time
> 1node-4pools-high.out: PWSCF: 14m 5.27s CPU time,
> 16m44.03s wall time
> 1node-8pools-high.out: PWSCF: 32m29.71s CPU time,35m
> 0.35s wall time
>
> 1node-1pools-low.out: PWSCF: 18m36.88s CPU time,
> 19m24.71s wall time
> 1node-2pools-low.out: PWSCF: 15m 0.98s CPU time,
> 15m42.56s wall time
> 1node-4pools-low.out: PWSCF: 14m 6.97s CPU time,
> 14m55.57s wall time
> 1node-8pools-low.out: PWSCF: 31m51.68s CPU time,
> 32m46.77s wall time
>
> so the result is not quite as drastic, but with 8 pools on the node,
> the machine is suffering.
> one can also see that disk_io='low' is helping to reduce waiting time
> (disk_io='high' still
> writes files into the working directory, which is on slow NFS). so for
> my machine it looks
> as if 4 pools is the optimal compromise. to further investigate
> whether pools or gspace
> parallelization is more efficient i then started to run the same job
> across multiple nodes.
> this uses only 4 cores per node, i.e. the total number of mpi tasks is 
> still 8.
>
> 2node-1pools-high.out: PWSCF: 12m 0.88s CPU time,
> 17m42.01s wall time
> 2node-2pools-high.out: PWSCF:  8m42.96s CPU time,
> 11m44.88s wall time
> 2node-4pools-high.out: PWSCF:  6m26.72s CPU time,
> 8m54.83s wall time
> 2node-8pools-high.out: PWSCF: 12m47.61s CPU time,
> 15m18.67s wall time
>
> 2node-1pools-low.out: PWSCF: 10m53.87s CPU time,
> 11m35.94s wall time
> 2node-2pools-low.out: PWSCF:  8m37.37s CPU time,
> 9m23.17s wall time
> 2node-4pools-low.out: PWSCF:  6m22.87s CPU time,
> 7m11.22s wall time
> 2node-8pools-low.out: PWSCF: 13m 7.30s CPU time,
> 13m57.71s wall time
>
> in the next test, i doubled the number of nodes again, but this time
> kept 4 mpi tasks per node,
> also i'm only using disk_io='low'.
>
> 4node-4pools-low.out: PWSCF:  4m52.92s CPU time,
> 5m38.90s wall time
> 4node-8pools-low.out: PWSCF:  4m29.73s CPU time,
> 5m17.86s wall time
>
> interesting, now the striking differe

[Pw_forum] how to use fqha.x

[Huiqun Zhou]

lidonglin556,

everything in bin is soft link to the real excutable in relevant directiories, 
respectively.
The clever way to find where the code is is to run 
  ls -l bin
you can easily find fqha.x there linked to pwtools/fqha.x, then from there you 
can
find again a fqha.f90. Read the source code patiently, you can figure out how to
write input soon.

Huiqun Zhou
@Nanjing University, China
 
  - Original Message - 
  From: lidonglin556 
  To: pw_forum at pwscf.org 
  Sent: Wednesday, March 04, 2009 2:42 PM
  Subject: [Pw_forum] how to use fqha.x





  hi
  I want get the thermal properties, but I don't know how to do. Does fqha.x 
can deal with it? And how to write the input? where can I the code?
   many thanks !



--
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[Pw_forum] the dynmaical matrix are like "***********" when thephonons calculation at gama

[Huiqun Zhou]

Hi, Yuehua,

This is not an answer to your question, but I think if you have no special
reason to use espresso 3.2.3, you'd better upgrade to 4.0.4 and try again.

Since we are on the same campus and I guess you're using our Altix 4700,
if this is true and you're willing to, you can run the command below to get
the latest compiled copy from my home:

scp -r hqzhou at 210.119.46.90:/disk3/hqzhou/espresso-4.0.4 /your/home

Call me at 83686750, I'll let you know my password.

Huiqun Zhou
@Nanjing University, China

- Original Message - 
From: "xu yuehua" 
To: "PWSCF Forum" 
Sent: Tuesday, March 03, 2009 10:11 PM
Subject: Re: [Pw_forum] the dynmaical matrix are like "***" when 
thephonons calculation at gama


> my problem is not the "nan" , it has aready sovled,
>
> my problem is the original problem :
> i am facing unkonwn problem when i calculated the phonons
> at gama:
>
> the  dynamical matrix  file  wrote:
> 
>>>  Dynamical  Matrix in cartesian axes
>>>
>>>  q = (0.0   0.0   0.0 )
>>>
>>>   1  1
>>>   0.    0.
>>>   0.
>>>   0.    0.
>>>   0.
>>>   0.    0.
>>>   0.
>>>   1  2
>>>   0.    0.
>>>   0.
>>>   0.    0.
>>>   0.
>>>   0.    0.
>>>   0.
>>>   1  3
>>>   0.    0.
>>>   0.
>>>   0.    0.
>>>   0.
>>>   0.    0.
>>>   0.
>>>   1  4
>>>   0.    0.
>>>   0.
>>>   0.    0.
>>>   0.
>>>   0.    0.
>>>   0.
>>>   1  5
>>>   0.    0.
>>>   0.
>>>   0.    0.
>>>   0.
>>>   0.    0.
>>>   0.
>>>   1  6
>>>   0.    0.
>>>   0.
>>>   0.    0.
>>>   0.
>>>   0.    0.
>>>   0.
>>>   1  7
>>>   0.    0.
>>>   0.
>>>   0.    0.
>>>   0.
>>>   0.    0.
>>>   0.
>>>   1  8
>>>   0.    0.
>>>   0.
>>>   0.    0.
>>>   0.
>>>   0.    0.
>>>   0.
>>>   1  9
>>>   0.    0.
>>>   0.
>>> ...
>>>
>>> my phone input file :
>>> phonons at Gamma
>>>  &inputph
>>>   tr2_ph=1.0d-15,
>>>   prefix='scf_two_b_type',
>>>   epsil=.true.,
>>>   amass(1)=1.0,
>>>   amass(2)=15.999,
>>>   outdir='/disk2/xxx/xxx/espresso-3.2.3/tmp',
>>>   fildyn='fourringwater.dynG',
>>>  /
>>> 0.0 0.0 0.0
>>>
>>>
>>> and my scf input file is :&CONTROL
>>> calculation  = "scf",
>>>   prefix   = "scf_two_b_type"
>>>   pseudo_dir   =
>>> "/disk2/xxx/xxx/espresso-3.2.3/pseudo",
>>>   outdir   =
>>> "/disk2/jdong/xyh/espresso-3.2.3/tmp",
>>> /
>>> &SYSTEM
>>>   ibrav = 4,
>>>   a=20,b=20,c=5.60,cosab=-0.5,cosac=0,cosbc=0,
>>>   nat   = 24,
>>>   ntyp  = 2,
>>>   ecutwfc   =35 ,
>>>   ecutrho   =420

[Pw_forum] Use of pool

[Huiqun Zhou]

Liping,

Of course, my tests were made on 8 CPU cores.

Huiqun Zhou
@Nanjing University, China

- Original Message - 
From: "Liping Yu" 
To: "PWSCF Forum" 
Sent: Tuesday, February 24, 2009 9:49 PM
Subject: Re: [Pw_forum] Use of pool


> Dear Huiqun,
> 
> If your results are based on the same number of processes for different
> npools, they make sense to me.   To my understanding, the almost linear
> time scaling of using npool means that the computer time is almost
> linear to npool (and also the total number of procs) only when we fix
> the number of the processors at each pool.
> 
> Please correct me if I am wrong. Thanks!
> 
> Liping Yu
> Department of Physics
> NC State University, USA
> 
> 
> Huiqun Zhou wrote:
>> Dear list users:
>>
>> I happened to test duration times of calculating the system I'm 
>> investigating against number of pools used. There are totally
>> 36 k points. But the results surprised me quite a lot. 
>>
>> no pool:  6m21.02s CPU time, 6m45.88s wall time
>> 2 pools:  7m19.39s CPU time, 7m38.99s wall time
>> 4 pools: 11m59.09s CPU time,12m14.66s wall time
>> 8 pools: 21m28.77s CPU time,21m38.71s wall time
>>
>> The machine I'm using is an AMD box with 2 quad core shanghai.
>>
>> Is my understanding of usage of pool wrong?
>>
>> Huiqun Zhou
>> @Nanjing University, China
>> ___
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>>   
> 
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>

[Pw_forum] Use of pool

[Huiqun Zhou]

Dear list users:

I happened to test duration times of calculating the system I'm 
investigating against number of pools used. There are totally
36 k points. But the results surprised me quite a lot. 

no pool:  6m21.02s CPU time, 6m45.88s wall time
2 pools:  7m19.39s CPU time, 7m38.99s wall time
4 pools: 11m59.09s CPU time,12m14.66s wall time
8 pools: 21m28.77s CPU time,21m38.71s wall time

The machine I'm using is an AMD box with 2 quad core shanghai.

Is my understanding of usage of pool wrong?

Huiqun Zhou
@Nanjing University, China

[Pw_forum] About PWgui-4.0 and XCrySDen

[Huiqun Zhou]

You need to do right as the error message told you. A longer name for Itcl is 
[incr Tcl] and
it's an extension to the Tcl language. Go to download and install the package. 

www.activestate.com should be a good place. The standard edition is for free.


Dr. Huiqun Zhou
@Nanjing University, China

  - Original Message - 
  From: Fan Yang 
  To: pw_forum at pwscf.org 
  Sent: Saturday, May 31, 2008 10:30 AM
  Subject: [Pw_forum] About PWgui-4.0 and XCrySDen


  Dear everyone,

  I have two questions about the additional tools for espresso-4.0. 
First is the compilation of PWgui-4.0, namely, when executing ./pwui
  I got error message: Can't find package Itcl while executing.

 The second is about XCrySDen, when runing espresso-4.0, it seems that 
only the initial structure could be displayed, while the subsequent 
configurations could not be imported. If I use the previous version, 
espresso-3.2.3, then everything goes well.

 Does anyone have the same problem?

 Best Regards,

   
  ==
  Fan Yang
  PH.D Candidate in Electrochemistry  
  College of Chemistry and Molecular Science
  Wuhan University,430072,Hubei Province,China 
  E-mail:shrek_826 at yahoo.com.cn
  ==




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[Pw_forum] parallel run of phonon calculation (ph.x)

[Huiqun Zhou]

list-users,

I'm trying to run ph.x in the mode of q-point parallelization,
using 4 compute nodes with 4 cpu cores in each. The command is
sort of following 

mpiexec -n 16 ph.x -npool 4 < input > output

Say, it determined there are 8 q points according to the q-mesh
I set. I'm expecting it could parallelly compute 4 q points per 
time (so get *.dyn1-4 simultaneously), but I saw it still compute
q point one by one. Is my understanding of q point parallelization
wrong?

Thanks!

Huiqun Zhou
@Earth Sciences, Nanjing University, China 

[Pw_forum] compile error on Xeon with intel fortran

[Huiqun Zhou]

I used PWscf, Siesta and Wien2k quite often and checked the examples
and my own which gave comparable results to the experiments although
I didn't try other DFT code heavily. I only found that linking to fftw 3.x
when using 9.0 compiler could crash ph.x (and may be others, but not pw.x).

Maybe, compiler options used and OS version (?) make difference ("o")


Huiqun

 
- Original Message - 
From: "Axel Kohlmeyer" 
To: "PWSCF Forum" 
Cc: "lan haiping" 
Sent: Monday, April 07, 2008 1:32 PM
Subject: Re: [Pw_forum] compile error on Xeon with intel fortran


> On Sun, Apr 6, 2008 at 10:14 PM, Huiqun Zhou  wrote:
>> Axel,
>>
>>  9.0 (build 20050809) seems an exception. I have been using
>>  this version of Intel compiler since its release and successfully
>>  compiled all prevailing DFT code.
> 
> nope that one's broken as well. it miscompiles several codes.
> you have to have a newer patchlevel to have a working 9.0
> compiler. i had moderate success with the 20051020 build,
> but the correspondingly late patchlevels of 8.1 and 9.1 have
> been much more reliable.
> 
> the issue with miscompiled code is that the code not always
> crashes on you, but sometimes just gives the wrong result...
> 
> cheers,
>axel.
> 
>>
>>  Huiqun Zhou
>>  @Nanjing University, China
>>
>>
>>
>>  - Original Message -
>>  From: "Axel Kohlmeyer" 
>>  To: "lan haiping" 
>>  Cc: "PWSCF Forum" 
>>  Sent: Saturday, April 05, 2008 9:19 PM
>>  Subject: Re: [Pw_forum] compile error on Xeon with intel fortran
>>
>>
>>  > On Sat, 5 Apr 2008, lan haiping wrote:
>>  >
>>  > IH> Dear Min,
>>  > IH>   Some one else told me before that ifort v10 is not a stable
>>  > compiler..
>>  >
>>  > this is not correct. newer patchlevels of 10.1 are quite
>>  > reliable. 10.1.012 should be ok. the original 10.0 release
>>  > was bad, like almost all intel x.0 releases.
>>  >
>>  > cheers,
>>  >  axel.
>>  >
>>
>>
>> ___
>>  Pw_forum mailing list
>>  Pw_forum at pwscf.org
>>
>>
>> http://www.democritos.it/mailman/listinfo/pw_forum
>>
>>
> 
> 
> 
> -- 
> ===
> 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.
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>

[Pw_forum] compile error on Xeon with intel fortran

[Huiqun Zhou]

Axel,

9.0 (build 20050809) seems an exception. I have been using
this version of Intel compiler since its release and successfully
compiled all prevailing DFT code.

Huiqun Zhou
@Nanjing University, China


- Original Message - 
From: "Axel Kohlmeyer" 
To: "lan haiping" 
Cc: "PWSCF Forum" 
Sent: Saturday, April 05, 2008 9:19 PM
Subject: Re: [Pw_forum] compile error on Xeon with intel fortran


> On Sat, 5 Apr 2008, lan haiping wrote:
>
> IH> Dear Min,
> IH>   Some one else told me before that ifort v10 is not a stable 
> compiler..
>
> this is not correct. newer patchlevels of 10.1 are quite
> reliable. 10.1.012 should be ok. the original 10.0 release
> was bad, like almost all intel x.0 releases.
>
> cheers,
>  axel.
>

[Pw_forum] error when run example02 in 3.2.package

[Huiqun Zhou]

Yuehua,

Send a private mail to me, and let me know what kind of machine you're
using (hope it isn't our newly bought big iron, SGI Altix 4700, I haven't 
succeeded in compiling qe on it yet). I can help you to set an environment 
for you  as long as your machine is on our campus network and give me 
administrator's privilege temporarily.


Huiqun Zhou
@Nanjing University

  - Original Message - 
  From: xu yuehua 
  To: PWSCF Forum 
  Sent: Monday, March 24, 2008 5:56 PM
  Subject: Re: [Pw_forum] error when run example02 in 3.2.package


  in  fact ,a few days ago ,i submit the problem in the pwscf forum,
  you can seach it .
  "Presently, configure looks first for a fortran compiler,
  then for a mpif90 script. Configure assumes that the latter
  uses the former. If not, the fortran flags chosen for the mpif90
  scripts will not be the correct ones. In your case you have
  ifort as (serial) compiler but your mpif90 script uses pgi"

  i am now puzzled that my mpi is complied with pgi, so  ,i choose f90=pgi
  how to deal with problem.anyone could help me 


  2008/3/24, lan haiping :
Hi, actually, this is due to your compilor .
this glibc error probably comes from memory leakage ,
you can try with another compilor , such as Intel ifort,
as i guess yours now should be a pgi pack..


On Mon, Mar 24, 2008 at 11:02 AM, xu yuehua  
wrote:

  hi all here 
  i am trying to test example,but face the crash ,i did not know what is 
wrong .
  please help me 
  thank you a lot

  /home/xyh/home2/espresso-3.2.3/examples/example02 : starting

  This example shows how to use pw.x and ph.x to calculate phonon
  frequencies at Gamma and X for Si and C in the diamond structure and
  for fcc-Ni.

executables directory: /home/xyh/home2/espresso-3.2.3/bin
pseudo directory:  /home/xyh/home2/espresso-3.2.3/pseudo
temporary directory:   /home/xyh/home2/temp

checking that needed directories and files exist... done

running pw.x as:  /home/xyh/home2/espresso-3.2.3/bin/pw.x
running ph.x as:  /home/xyh/home2/espresso-3.2.3/bin/ph.x

cleaning /home/xyh/home2/temp... done
running the scf calculation...FORTRAN STOP
   done
running the phonon calculation at Gamma...*** glibc detected *** double 
free or corruption (!prev): 0x02df48e0 ***



   i fact ,that is the same problem when i run example1 .



  -- 
  Xu Yuehua
  physics Department of Nanjing university
  China 


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-- 
Hai-Ping Lan 
Department of Electronics ,
Peking University , Bejing, 100871
lanhaiping at gmail.com, hplan at pku.edu.cn 
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  -- 
  Xu Yuehua
  physics Department of Nanjing university
  China 


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[Pw_forum] why there is no code for the constant of e-p couplingfor nonmetal?is there any difficulty for nonmetal?

[Huiqun Zhou]

Yuehua,

Have you searched the mailing list archive? Stefano had an explanation 
to your question(^o^) about a year ago.

Huiqun Zhou
@Nanjing University

  - Original Message - 
  From: xu yuehua 
  To: PWSCF Forum 
  Sent: Friday, March 21, 2008 5:27 PM
  Subject: [Pw_forum] why there is no code for the constant of e-p couplingfor 
nonmetal?is there any difficulty for nonmetal?



  hello all 
  i have no answer when my boss ask this question .
  anyone can help me to cover this question .
  thank you 
  -- 
  Xu Yuehua
  physics Department of Nanjing university
  China 


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[Pw_forum] why there is no code for the constant of e-p couplingfor nonmetal?is there any difficulty for nonmetal?

[Huiqun Zhou]

I'll let your boss know you are not hard working (^o^).


Zhou Huiqun

  - Original Message - 
  From: xu yuehua 
  To: PWSCF Forum 
  Sent: Friday, March 21, 2008 5:27 PM
  Subject: [Pw_forum] why there is no code for the constant of e-p couplingfor 
nonmetal?is there any difficulty for nonmetal?



  hello all 
  i have no answer when my boss ask this question .
  anyone can help me to cover this question .
  thank you 
  -- 
  Xu Yuehua
  physics Department of Nanjing university
  China 


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[Pw_forum] A¡@question about LDA+U calculation aobut Vanadium ?

[Huiqun Zhou]

Didn't you find an explanation for occ_loc in the source code? It's "the 
total
number of d electrons", so occ_loc for V should be 3.0.

Cheers,

Dr. Huiqun Zhou
@Earth Sciences, Nanjing University, China


- Original Message - 
From: 
To: 
Sent: Friday, December 28, 2007 5:57 PM
Subject: [Pw_forum] A?@question about LDA+U calculation aobut Vanadium ?


> Dear all,
>   I would like to ask a question about the question i encounter
> .I calculated the transition metal element Vanadium "V" about LDA+U
> calculation ,the scf output file show
> 
> from tabd : error # 1
>  pseudopotential not yet inserted
> 
> I check the pwscf forum ,it suggest me to correct the  tabd.f90 file
> in PW.x code , so I would like to ask what is the "occ_loc" number for
> Vanadium "V" ?
>
> Thanks a lot
>  Bing-hong Chen
>Physics department,National Taiwan 
> Unverisity,Taiwan
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[Pw_forum] About ecutwfc and ecutrho again

[Huiqun Zhou]

Thanks, Nicola and Stefano,

Actually, I was thinking the choice should be the lagest or lagest plus 
alpha.
The pseudopotentials I'm testing are USPP for iron, chromium, oxygen and
others, and one of the materials I'm interested is chromite (FeCr2O4). I 
found
ecutwfc for iron and chromium is indeed around 35 Ry for convergence, but
over 55 Ry for oxygen. I haven't checked whether I did anything wrong when
creating potential for oxygen, but it's consistent with the results of 
convergence
test for chromite, in which ecutwfc should be set to 55 Ry (ecutrho=600) for
convergence.

Please comment.


Dr. Huiqun Zhou
@Earth Sciences, Nanjing University, China


- Original Message - 
From: "Nicola Marzari" 
To: "PWSCF Forum" 
Sent: Friday, December 21, 2007 12:52 PM
Subject: Re: [Pw_forum] About ecutwfc and ecutrho again


>
>
> Roughly speaking, the higher ecutwfc among the elements
> considered.
>
> Are these ultrasoft or norm conserving ? If the latter,
> ecutrho could have been safely kept to 240 Ry.
>
> If the former, my rule of thumb is that rarely a cutoff
> greater than 30 Ry is needed, unless subtle magnetic/spin
> propertes are sought. Thi sis to say that absolute convergence of
> the energy is not the most useful criterion - often one looks
> at lattice parameter, bulk modulus, or phonon frequencies as
> good indicators of convergence.
>
> nicola
>
> Huiqun Zhou wrote:
>> Dear PWscfers,
>>
>> I'm creating and testing pseudopotentials for severval
>> elements myself. I plotted the E-ecutwfc graphs for
>> each element, in which the ecutwfc was ranging from 20
>> to 60 with increament of 5 Ry and ecutrho was set to 600.
>> If take 1 mRy as convergence criterion, I find that the
>> total energy for some elements will be convergent at
>> ecutwfc = 35 Ry while some are around ecutwfc = 55 Ry.
>>
>> If the material I'm interested in is comprised from elements
>> with both lower and higher ecutwfc, what ecutwfc should I
>> set for the material, the higher one, the higher one plus
>> alpha, or a compromise between the lower and higher?
>>
>> Thnaks!
>>
>>
>> Dr. Huiqun Zhou
>> @Earth Sciences, Nanjing University, China
>
>
> -- 
> -
> Prof Nicola Marzari   Department of Materials Science and Engineering
> 13-5066   MIT   77 Massachusetts Avenue   Cambridge MA 02139-4307 USA
> tel 617.4522758 fax 2586534 marzari at mit.edu http://quasiamore.mit.edu
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> 

[Pw_forum] About ecutwfc and ecutrho again

[Huiqun Zhou]

Dear PWscfers,

I'm creating and testing pseudopotentials for severval
elements myself. I plotted the E-ecutwfc graphs for 
each element, in which the ecutwfc was ranging from 20
to 60 with increament of 5 Ry and ecutrho was set to 600.
If take 1 mRy as convergence criterion, I find that the
total energy for some elements will be convergent at
ecutwfc = 35 Ry while some are around ecutwfc = 55 Ry.

If the material I'm interested in is comprised from elements
with both lower and higher ecutwfc, what ecutwfc should I
set for the material, the higher one, the higher one plus
alpha, or a compromise between the lower and higher?

Thnaks!


Dr. Huiqun Zhou
@Earth Sciences, Nanjing University, China  

 

[Pw_forum] how to control the writing of wavefunction

[Huiqun Zhou]

Yuehua,

You don't need to issue mpirun command that way, just to point outdir
to a local directory, say /tmp/your_job, as Lorenzo suggested, but note
you must have read/write permission for the directory.

If you belong to the condensed matter physics group of Nanjing University,
the cluster you are using should be built using ROCKS. Then, everything is
easy, just run

$ cluster-fork mkdir /state/partition1/yuehua 

This command will create a folder on every compute nodes.
then, set "outdir = /state/partition1/yuehua/" in your input file.


Huiqun Zhou
@Earth Sciences, Nanjing University, China

  - Original Message - 
  From: xu yuehua 
  To: PWSCF Forum 
  Sent: Friday, December 14, 2007 4:36 PM
  Subject: Re: [Pw_forum] how to control the writing of wavefunction


  sorry, in fact ,"want" is  mpirun -np 8 mkdir -p /tmp/xy-job .and the error 
message :
  Warning: Command line arguments for program should be given
  after the program name.  Assuming that -p is a
  command line argument for the program.
  Warning: Command line arguments for program should be given
  after the program name.  Assuming that /tmp/xy-job is a
  command line argument for the program.
  Missing: program name
  Program mkdir either does not exist, is not 
  executable, or is an erroneous argument to mpirun. 



   
  2007/12/14, Paolo Giannozzi : 

On Dec 14, 2007, at 9:09 , xu yuehua wrote:

> thank you .although it does not work

what "does not work", and what do you mean by 
"does not work"?
---
Paolo Giannozzi, Dept of Physics, University of Udine
via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222



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  -- 
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  physics Department of Nanjing university
  China 


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[Pw_forum] bands_FS.x and spin polarized metals

[Huiqun Zhou]

Wow, what a "home computer"! Moor's law hadn't been invented 
at that time, right? :-)

Are there any copyright issue to prevent me from using it in my 
presentation about "concise history of personal computer"?

Thanks for sharing the precious picture with us!

Huiqun Zhou
@Earth Sciences, Nanjing University, China

- Original Message - 
From: "Paolo Giannozzi" 
To: "PWSCF Forum" 
Sent: Thursday, December 13, 2007 5:12 AM
Subject: Re: [Pw_forum] bands_FS.x and spin polarized metals


> 
> On Dec 12, 2007, at 21:58 , Nicola Marzari wrote:
> 
>>> I am old enough to have seen card punchers in action, so the term
>>> "abend" is not unknown to me, but I guess younger people don't
>>> know that it is a shorthand for "abnormal end", on IBM mainframes...
>>
>> What's a mainframe ? Is it like a really, really big ipod ?
> 
> do you remember the picture of the "home computer
> in 2004" you sent me some time ago ?
> http://www.fisica.uniud.it/~giannozz/public/pc2004.jpg
> :-)
> 
> P.
> ---
> Paolo Giannozzi, Dept of Physics, University of Udine
> via delle Scienze 208, 33100 Udine, Italy
> Phone +39-0432-558216, fax +39-0432-558222
> 
> 
> 
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[Pw_forum] how to continue my relax job

[Huiqun Zhou]

Yuehua,

You should continue (restart) the relaxation with increased nstep.
Basically, you can set nsetup to a bigger value, say, 100-200 as
it has no harm because relaxation will stop as soon as convergence
is reached. In my case, I always set nstep to 200 for my complex
structrue.


Huiqun Zhou
@Earth Sciences, Nanjing University

  - Original Message - 
  From: xu yuehua 
  To: PWSCF Forum 
  Sent: Friday, November 30, 2007 7:36 PM
  Subject: [Pw_forum] how to continue my relax job


  hi everyone here :
  i have another question about how to continue my relax job.for i set the 
  nstep is 50, too small ,and can not acheive convergence,and i want  to 
continue by adding the nstep,how to do with it ? 
  is it to add the restart option in input file?
  in general ,how many step i should to add?
  i wish your help 
  thank you ! 
  -- 
  Xu Yuehua
  physics Department of Nanjing university
  China 


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[Pw_forum] Convergence test

[Huiqun Zhou]

Axel,

Your advices are valuable, thanks a lot!. Seeing most of my calculations
(geometry optimization) are still effective, I can set my heart at rest :-).

Dr. Huiqun Zhou
@Nanjing University

- Original Message - 
From: "Axel Kohlmeyer" 
To: "Huiqun Zhou" 
Cc: 
Sent: Wednesday, November 14, 2007 1:31 PM
Subject: Re: [Pw_forum] Convergence test


> On Tue, 13 Nov 2007, Huiqun Zhou wrote:
>
> HZ> List users,
>
> dear huiqun zhou,
>
> HZ> I'm testing convergence on ecutwfc for chromite using USPP. Below are
> HZ> results of different ecutrho with different ecutwfc. I may be wrong, I 
> think
> HZ> I should watch the difference of total energy between successive runs 
> till
> HZ> it's less than 1-2 mRy. But the trend is not apparent in the results 
> below
> HZ> and it seems that the larger the ecutwfc, the lower the total energy.
>
> you are using an ultra-soft pseudopotential and for those
> actually the density cutoff is _much_ more important than
> the wavefunction cutoff. depending on the choice of the
> pseudopotential parameters, 35-40ry for the wavefunction
> cutoff should be a conservative choice, however a density
> cutoff of 250 is not. if you want to converge the energy
> very tightly, you may need to go up to 10x the wavefunction
> cutoff. you should also keep in mind that the total energy
> converges rather slowly, and that for most calculations
> you need energy differences or derivatives, which may converge
> faster, i.e. you may want to look at forces (use a non-symmetric
> input for that!!) or stress instead. what is sufficiently
> converged depends on your the kind of calculation you want
> to do. so for simple geometry optimization or MD 35/210
> or less may already be sufficient.
>
> HZ>
> HZ> I calculated E-V relations using two sets of ecutwfc and ecutrho:
> HZ> for ecutwfc = 35 ry and ecutrho = 240 ry, a = 8.405, B0 = 172.8, B0' = 
> 4.3
> HZ> for ecutwfc = 55 ry and ecutrho = 250 ry, a = 8.407, B0 = 178.6, B0' = 
> 3.6
> HZ>
> HZ> There are no big differences in unit cell parameter and elastic 
> properties.
> HZ> So, my questions are
> HZ> (1) usually, the ecutwfc of USPP should be around 35 ry or below, is 
> my
> HZ>   case an exception?
>
> no. it does not look like an exception.
>
> HZ> (2) how small the difference of total energy of successive runs should 
> be
> HZ>   in judging convergence against ecutwfc?
>
> total energy is not a good parameter. see above.
>
> cheers,
>  axel.
>
> HZ>
> HZ> Thank you in advance.
> HZ>
> HZ> Dr. Huiqun Zhou
> HZ> @Earth Sciences, Nanjing University, China
> HZ>
> HZ>
> HZ>
> HZ>
> HZ> ecutrho = 240 ry
> HZ> ecutwfc total energy
> HZ> 35 -1461.54573299 Ry
> HZ> 40 -1461.64206824 Ry
> HZ> 45 -1461.71978835 Ry
> HZ> 50 -1461.76587314 Ry
> HZ> 55 -1461.76316597 Ry
> HZ> 60 -1461.76692396 Ry
> HZ>
> HZ> ecutrho = 250 ry
> HZ> 40 -1461.64351876 Ry
> HZ> 45 -1461.70130510 Ry
> HZ> 50 -1461.74724764 Ry
> HZ> 55 -1461.76462943 Ry
> HZ> 60 -1461.76838812 Ry
> HZ>
> HZ> ecutrho = 280 ry
> HZ> 50 -1461.74778158 Ry
> HZ> 55 -1461.76516515 Ry
> HZ> 60 -1461.76892327 Ry
> HZ>
> HZ> ___
> HZ> Pw_forum mailing list
> HZ> Pw_forum at pwscf.org
> HZ> http://www.democritos.it/mailman/listinfo/pw_forum
> HZ>
>
> -- 
> ===
> 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] Convergence test

[Huiqun Zhou]

List users,

I'm testing convergence on ecutwfc for chromite using USPP. Below are
results of different ecutrho with different ecutwfc. I may be wrong, I think
I should watch the difference of total energy between successive runs till
it's less than 1-2 mRy. But the trend is not apparent in the results below
and it seems that the larger the ecutwfc, the lower the total energy.

I calculated E-V relations using two sets of ecutwfc and ecutrho:
for ecutwfc = 35 ry and ecutrho = 240 ry, a = 8.405, B0 = 172.8, B0' = 4.3
for ecutwfc = 55 ry and ecutrho = 250 ry, a = 8.407, B0 = 178.6, B0' = 3.6

There are no big differences in unit cell parameter and elastic properties.
So, my questions are
(1) usually, the ecutwfc of USPP should be around 35 ry or below, is my
  case an exception?
(2) how small the difference of total energy of successive runs should be
  in judging convergence against ecutwfc?

Thank you in advance.

Dr. Huiqun Zhou
@Earth Sciences, Nanjing University, China




ecutrho = 240 ry
ecutwfc total energy
35 -1461.54573299 Ry
40 -1461.64206824 Ry
45 -1461.71978835 Ry
50 -1461.76587314 Ry
55 -1461.76316597 Ry
60 -1461.76692396 Ry

ecutrho = 250 ry
40 -1461.64351876 Ry
45 -1461.70130510 Ry
50 -1461.74724764 Ry
55 -1461.76462943 Ry
60 -1461.76838812 Ry

ecutrho = 280 ry
50 -1461.74778158 Ry
55 -1461.76516515 Ry
60 -1461.76892327 Ry 

[Pw_forum] QHA code

[Huiqun Zhou]

I need it, Eyvaz.

Huiqun


- Original Message - 
From: "Eyvaz Isaev" 
To: 
Sent: Sunday, November 26, 2006 4:17 AM
Subject: [Pw_forum] QHA code


> Dear  users,
>
> Below is a sketch from a README file for quasiharmonic calculations with 
> provided force constants matrix.  Now all calculations can be done using 
> just  a script  which requires only  a few input paramters.
>
> 1) phonon_DOS.x - phonon DOS and atom projected phonon DOS with  g_x, g_y, 
> and g_zcomponents.
> 2) Atom_Integrated_DOS.x - integrates phonon DOS, and atom projected DOS 
> to find out 
> atom-specific  contribution to the zero point vibration energy, phonon 
> DOS, vibration energy, specific heat, entropy, internal energy
> NB!!! The limitation for the program is the presence of only one frequency 
> gap in the phonon spectrum, i.e. the program assumes that there are well 
> separated low-lying "acoustic" modes and optical branches.
>
> 3) Debye.x - calculates the Debye temperature
> 4) F_QHA.x - Total vibrational energy, the specific heat, entropy and 
> internal energy in  the
>   quasiharmonic  approximation
>
> If you find these features interesting then I can make the code available 
> for  the community , so that it can  be distributed  together with  our 
> lovely code.
>
> Bests,
> Eyvaz.
>
>
>
>
>
>
>
>
>
> 
> Want to start your own business?
> Learn how on Yahoo! Small Business.
> http://smallbusiness.yahoo.com/r-index
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
> 

[Pw_forum] use doual core

[Huiqun Zhou]

Have you set up you environment for using one the mpi libraries you installed 
in .bashrc?
For example, for openmpi you need to set following in your .bashrc if you are 
using bash
as your shell:
...
export PATH=/opt/openmpi/bin:$PATH
export LD_LIBRARY_PATH=/opt/openmpi/lib:$LD_LIBRARY_PATH
...

Note: you need to replace /opt/openmpi with the path of your installation.

Huiqun Zhou

  - Original Message - 
  From: Amin Babazadeh 
  To: pw_forum at pwscf.org 
  Sent: Sunday, November 26, 2006 6:11 PM
  Subject: Re: [Pw_forum] use doual core


  Dear Dr.Kohlmeyer
  Thanks a lot for your help.I did what you said.i installed 
  fftw-3.1.2.tar
  lam-7.1.2.tar
  mpich2-1.0.4p1.tar
  openmpi-1.1.2.tar
   on fedora core 5 and after that i configure the espresso but this error was 
written

  WARNING: the following problems were detected:
   unsupported C/Fortran compilers combination:
   CC=mpicc, F77=mpif77, F90=mpif90

  you may not be able to compile this program.
  i don't know what this problem means.would you please help me.
  Thanks a lot


   
  On 11/22/06, Axel Kohlmeyer  wrote: 
On 11/22/06, Amin Babazadeh < babazade at gmail.com> wrote:
> dear users 
> I use a computer with a dual core CPU.but my problem is that when i run a
> program only one of the CPU work but i like to share the work (solving k
> points) between cpus. 
> I think that i should install the parallel pwscf but when i run the 
> ./configure only single pwscf installed.

you have to install an MPI package (e.g. LAM/MPI, OpenMPI, MPICH)
first and then configure/compile quantum espresso with parallel support 
as explained in the provided installation instructions. 

please make sure that your MPI package is compatible with or compiled
for the fortran compiler you want to use to compiled quantum espresso with.
precompiled packages may be compiled for a different compiler and thus 
need special flags or environment variables set to use the compiler of
your choice.

axel.

> would you please tell me or give me a document that solve my problem.
>
>
> --
> AMIN 


--
===
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 mailing list 
Pw_forum at pwscf.org
http://www.democritos.it/mailman/listinfo/pw_forum




  -- 
  AMIN 
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[Pw_forum] Comparison of 3.1.1 and 3.2 (cvs)

[Huiqun Zhou]

Hi,

Here is the graph for the convergence patterns of v3.1.1 and v3.2.
I have reduced the size to about 13KB.

Huiqun

- Original Message - 
From: "degironc" 
To: 
Sent: Friday, November 24, 2006 4:39 PM
Subject: Re: [Pw_forum] Comparison of 3.1.1 and 3.2 (cvs)


> Dear Huiqun Zhou,
>a couple of changes have been made in the mixing routine (mainly to 
> reduce its
> huge memory requirement in certain cases) from 3.1.1 to 3.2. These might 
> be the reason for  the different behaviors. Could you please post your 
> input so that we can try to fgure out what happened ?
>Since every realization of an algorithm is the result of a compromise 
> between speed,
> memory use, work required to implement it, etc and since every compromise 
> will likely
> be more or less good depending on the particular application considered, a 
> comparison for
> different "typical" cases would also be useful in order to assess the 
> "average" performance
> (or loss of it) from 3.1.1 to 3.2
>Thank you,
> stefano
>
> Huiqun Zhou wrote:
>
>> Kostya,
>>
>> The number of SCF iterations is indeed the same regardless of the
>> number of CPU cores used for both versions. Furthermore, the process
>> of SCF convergence is precisely the same whatever we use 1, 2 or 4
>> CPU cores. This is true for both versions. And the final total energy 
>> found
>> by both version is the same. But, the behaviour of convergence of one
>> version compared to another is different if you watch the changes of
>> numbers after decimal point. It seems that the criteria of convergence of
>> each version are different.
>>
>> I have created three graphs for the pattern of convergence on 1, 2, 4 
>> cores
>> (but they are tottally the same as mentioned above). Each graph contains
>> a comparison of patterns of the two versions. Please let me know where
>> I can post the graphs, each of which is about 55KB, as I don't think this
>> forum permit posting a file with such large size.
>>
>> Here I first include the six data files extracted from the results. you 
>> can
>> plot the graph yourself, too.
>>
>> Please give me a pointer what kind of benchmarks you want me to run.
>> Do you think it's worth tring the same system with different type of run 
>> (relax, ...),
>> different method of diagonalization? Currently, all results I reported 
>> made use
>> of 'david' method for diagonalization.
>>
>> Regards,
>>
>> Huiqun
>>
>>
>> - Original Message - From: "Konstantin Kudin" 
>> 
>> To: 
>> Sent: Friday, November 24, 2006 1:42 AM
>> Subject: Re: [Pw_forum] Comparison of 3.1.1 and 3.2 (cvs)
>>
>>
>>>
>>> --- Huiqun Zhou  wrote:
>>>
>>>> (2) Version 3.1.1 is much faster than the cvs version as the former
>>>>   took only 13 scf iterations to reach convergence while the latter
>>>>   needed 16 iterations.
>>>
>>>
>>> Dear Huiqun,
>>>
>>> If the number of the SCF iterations is the same regardless of the
>>> number of cpus for both versions, then please post some kind of
>>> convergence pattern like for total energies. That would give developers
>>> a chance to evaluate if any of the recent changes might have caused
>>> this. Sometimes small numerical noise is a benign "feature", and
>>> sometimes it is a bug, so figuring out what is going on for your test
>>> would be useful.
>>>
>>> Also, perhaps you could try a different benchmark to see how things
>>> work there, if there are any differences found there as well.
>>>
>>> Kostya
>>>
>>>
>>>
>>> 
>>> Sponsored Link
>>>
>>> Compare mortgage rates for today.
>>> Get up to 5 free quotes.
>>> Www2.nextag.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
> 
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[Pw_forum] Comparison of 3.1.1 and 3.2 (cvs)

[Huiqun Zhou]

Stefano,

Here are the input file and a short script to run tests.

Huiqun

- Original Message - 
From: "degironc" 
To: 
Sent: Friday, November 24, 2006 4:39 PM
Subject: Re: [Pw_forum] Comparison of 3.1.1 and 3.2 (cvs)


> Dear Huiqun Zhou,
>a couple of changes have been made in the mixing routine (mainly to 
> reduce its
> huge memory requirement in certain cases) from 3.1.1 to 3.2. These might 
> be the reason for  the different behaviors. Could you please post your 
> input so that we can try to fgure out what happened ?
>Since every realization of an algorithm is the result of a compromise 
> between speed,
> memory use, work required to implement it, etc and since every compromise 
> will likely
> be more or less good depending on the particular application considered, a 
> comparison for
> different "typical" cases would also be useful in order to assess the 
> "average" performance
> (or loss of it) from 3.1.1 to 3.2
>Thank you,
> stefano
>
> Huiqun Zhou wrote:
>
>> Kostya,
>>
>> The number of SCF iterations is indeed the same regardless of the
>> number of CPU cores used for both versions. Furthermore, the process
>> of SCF convergence is precisely the same whatever we use 1, 2 or 4
>> CPU cores. This is true for both versions. And the final total energy 
>> found
>> by both version is the same. But, the behaviour of convergence of one
>> version compared to another is different if you watch the changes of
>> numbers after decimal point. It seems that the criteria of convergence of
>> each version are different.
>>
>> I have created three graphs for the pattern of convergence on 1, 2, 4 
>> cores
>> (but they are tottally the same as mentioned above). Each graph contains
>> a comparison of patterns of the two versions. Please let me know where
>> I can post the graphs, each of which is about 55KB, as I don't think this
>> forum permit posting a file with such large size.
>>
>> Here I first include the six data files extracted from the results. you 
>> can
>> plot the graph yourself, too.
>>
>> Please give me a pointer what kind of benchmarks you want me to run.
>> Do you think it's worth tring the same system with different type of run 
>> (relax, ...),
>> different method of diagonalization? Currently, all results I reported 
>> made use
>> of 'david' method for diagonalization.
>>
>> Regards,
>>
>> Huiqun
>>
>>
>> - Original Message - From: "Konstantin Kudin" 
>> 
>> To: 
>> Sent: Friday, November 24, 2006 1:42 AM
>> Subject: Re: [Pw_forum] Comparison of 3.1.1 and 3.2 (cvs)
>>
>>
>>>
>>> --- Huiqun Zhou  wrote:
>>>
>>>> (2) Version 3.1.1 is much faster than the cvs version as the former
>>>>   took only 13 scf iterations to reach convergence while the latter
>>>>   needed 16 iterations.
>>>
>>>
>>> Dear Huiqun,
>>>
>>> If the number of the SCF iterations is the same regardless of the
>>> number of cpus for both versions, then please post some kind of
>>> convergence pattern like for total energies. That would give developers
>>> a chance to evaluate if any of the recent changes might have caused
>>> this. Sometimes small numerical noise is a benign "feature", and
>>> sometimes it is a bug, so figuring out what is going on for your test
>>> would be useful.
>>>
>>> Also, perhaps you could try a different benchmark to see how things
>>> work there, if there are any differences found there as well.
>>>
>>> Kostya
>>>
>>>
>>>
>>> 
>>> Sponsored Link
>>>
>>> Compare mortgage rates for today.
>>> Get up to 5 free quotes.
>>> Www2.nextag.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
> 
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[Pw_forum] Comparison of 3.1.1 and 3.2 (cvs)

[Huiqun Zhou]

Kostya,

The number of SCF iterations is indeed the same regardless of the
number of CPU cores used for both versions. Furthermore, the process
of SCF convergence is precisely the same whatever we use 1, 2 or 4
CPU cores. This is true for both versions. And the final total energy found
by both version is the same. But, the behaviour of convergence of one
version compared to another is different if you watch the changes of
numbers after decimal point. It seems that the criteria of convergence of
each version are different.

I have created three graphs for the pattern of convergence on 1, 2, 4 cores
(but they are tottally the same as mentioned above). Each graph contains
a comparison of patterns of the two versions. Please let me know where
I can post the graphs, each of which is about 55KB, as I don't think this
forum permit posting a file with such large size.

Here I first include the six data files extracted from the results. you can
plot the graph yourself, too.

Please give me a pointer what kind of benchmarks you want me to run.
Do you think it's worth tring the same system with different type of run 
(relax, ...),
different method of diagonalization? Currently, all results I reported made 
use
of 'david' method for diagonalization.

Regards,

Huiqun


- Original Message - 
From: "Konstantin Kudin" 
To: 
Sent: Friday, November 24, 2006 1:42 AM
Subject: Re: [Pw_forum] Comparison of 3.1.1 and 3.2 (cvs)


>
> --- Huiqun Zhou  wrote:
>> (2) Version 3.1.1 is much faster than the cvs version as the former
>>   took only 13 scf iterations to reach convergence while the latter
>>   needed 16 iterations.
>
> Dear Huiqun,
>
> If the number of the SCF iterations is the same regardless of the
> number of cpus for both versions, then please post some kind of
> convergence pattern like for total energies. That would give developers
> a chance to evaluate if any of the recent changes might have caused
> this. Sometimes small numerical noise is a benign "feature", and
> sometimes it is a bug, so figuring out what is going on for your test
> would be useful.
>
> Also, perhaps you could try a different benchmark to see how things
> work there, if there are any differences found there as well.
>
> Kostya
>
>
>
> 
> Sponsored Link
>
> Compare mortgage rates for today.
> Get up to 5 free quotes.
> Www2.nextag.com
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
> 
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[Pw_forum] Comparison of 3.1.1 and 3.2 (cvs)

[Huiqun Zhou]

Dear list users,

10 days ago, I checked out the cvs version and compared
the speed of both versions against the same test case on
same machine.

pwscf was compiled using Intel Fortran 9.0 for x86_64, MPI
was Intel MPI-2 2.0, just the same environment for generating
the results of my previous tests on AMD opteron 285, Intel
Xeon 5060, 5140, 5150 platforms that I posted to this forum.

This test was carried on a Intel 5050 machine (dempsey 
3.0GHz/667MHz, 4GB memory). As my previous tests, the test case 
is still the one to calculate total energy of MgAl2O4 with 
calcium ferric structure, and 28 atoms in the unit cell. Here 
are the numbers:

(1) V3.1.1
1 core : 8m10s (8m09.52s)
2 cores: 4m57s (4m52.95s)
4 cores: 2m23s (2m17.68s)

(2) V3.2 (cvs, about 10 days ago)
1 core : 9m29.95s (9m11.09s)
2 cores: 6m03.24s (5m26.85s)
4 cores: 2m35.26s (2m04.52s)

There are two problems here:
(1) The differences between wall time and CPU time with version
  3.1.1 is small and seems reasonable while that between the two 
  with cvs version is relatively large. Why?
(2) Version 3.1.1 is much faster than the cvs version as the former
  took only 13 scf iterations to reach convergence while the latter
  needed 16 iterations.

Of course, it's just a cvs version and development is in progress.
I hope that developers have already noticed the difference.

Thanks to all developers for their great effort!


Huiqun Zhou

[Pw_forum] Another question about building a spinel structure

[Huiqun Zhou]

ibrav = 2 is correct, but you need to confirm if your atomic positions
are really those that in a PRIMITIVE cell.

Huiqun


- Original Message - 
From: "Chaohao Hu" 
To: 
Sent: Thursday, November 09, 2006 2:15 PM
Subject: Re: [Pw_forum] Another question about building a spinel structure


>I am sorry for my careless mistake. "ATOMIC_POSITIONS" should be set to 
>"crystal"
> option. Now this structure is OK. However, for the case of "ibrav= 0", I 
> still
> can not solve it.
>
>>Dear pwscf users,
>>Now I want to visualize a spinel structure Al2MgO4 (space group: F-3dm; 
>>227)
>>using XCrySDen. But I can not visualize it rightly. My input files are 
>>enclosed
>>here. Please you help me anlysis it.
>>===
>>cat > spinel.scf.in << EOF
>> &control
>>calculation='scf'
>>restart_mode='from_scratch',
>>tstress = .true.
>>tprnfor = .true.
>>prefix='spinel',
>>pseudo_dir = '$PSEUDO_DIR/',
>>outdir='$TMP_DIR/'
>> /
>> &system
>>ibrav=  2, celldm(1) =15.2595, nat=  14, ntyp= 3,
>>ecutwfc =36.0
>> /
>> &electrons
>>conv_thr =  1.0d-8
>>mixing_beta = 0.7
>> /
>>ATOMIC_SPECIES
>> Mg  24.305  Mg.pw91-np-van.UPF
>> Al  26.982  Al.pw91-n-van.UPF
>> O   15.9994 O.pbe-van_ak.UPF
>>ATOMIC_POSITIONS
>>Mg 0.125 0.125 0.125
>>Mg -0.125 -0.125 -0.125
>>Al 0.5 0.5 0.5
>>Al 0 0.5 0.5
>>Al 0.5 0 0.5
>>Al 0.5 0.5 0
>>O 0.236 0.236 0.236
>>O -0.208 0.236 0.236
>>O 0.236 -0.208 0.236
>>O 0.236 0.236 -0.208
>>O -0.236 -0.236 -0.236
>>O 0.208 -0.236 -0.236
>>O -0.236 0.208 -0.236
>>O -0.236 -0.236 0.208
>>K_POINTS {automatic}
>> 5 5 5 1 1 1
>>EOF
>>==
>>
>>However, when I change  "ibrav" from 2 to 0, some error information always
>>appears as following:
>>
>>invalid number: incomprehensible list input
>>apparent state: unit 5 (unnamed)
>>last format: list io
>>lately reading sequential formatted external IO
>>
>>
>>cat > spinel.scf.in << EOF
>> &control
>>calculation='scf'
>>restart_mode='from_scratch',
>>tstress = .true.
>>tprnfor = .true.
>>prefix='spinel',
>>pseudo_dir = '$PSEUDO_DIR/',
>>outdir='$TMP_DIR/'
>> /
>> &system
>>ibrav=  0, celldm(1) =15.259, nat=  14, ntyp= 3,
>>ecutwfc =36.0
>> /
>> &electrons
>>conv_thr =  1.0d-8
>>mixing_beta = 0.7
>> /
>>ATOMIC_SPECIES
>> Mg  24.305  Mg.pw91-np-van.UPF
>> Al  26.982  Al.pw91-n-van.UPF
>> O   15.9994 O.pbe-van_ak.UPF
>>ATOMIC_POSITIONS
>>Mg 0.125 0.125 0.125
>>Mg -0.125 -0.125 -0.125
>>Al 0.5 0.5 0.5
>>Al 0 0.5 0.5
>>Al 0.5 0 0.5
>>Al 0.5 0.5 0
>>O 0.236 0.236 0.236
>>O -0.208 0.236 0.236
>>O 0.236 -0.208 0.236
>>O 0.236 0.236 -0.208
>>O -0.236 -0.236 -0.236
>>O 0.208 -0.236 -0.236
>>O -0.236 0.208 -0.236
>>O -0.236 -0.236 0.208
>>K_POINTS {automatic}
>> 5 5 5 1 1 1
>>CELL_PARAMETERS
>> 0. 0.5000 0.5000
>> 0.5000 0. 0.5000
>> 0.5000 0.5000 0.
>>EOF
>>===
>>How to solve this problem?
>>
>>Best regards,
>>Chaohao
>>
>>
>>Dr. Chaohao Hu
>>Institute of Metal Research, Chinese Academy of Sciences--IMR
>>Wenhua Road, 72
>>110016, Shenyang, Liaoning (China)
>>Phone: +86-024-23971641
>>Email: chhu at imr.ac.cn
>>
>>
>>
>>___
>>Pw_forum mailing list
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>>http://www.democritos.it/mailman/listinfo/pw_forum
>>
>
> Thanks in advance.
> Best regards,
> Chaohao
>
> 
> Dr. Chaohao Hu
> Institute of Metal Research, Chinese Academy of Sciences--IMR
> Wenhua Road, 72
> 110016, Shenyang, Liaoning (China)
> Phone: +86-024-23971641
> Email: chhu at imr.ac.cn
>
>
>
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> http://www.democritos.it/mailman/listinfo/pw_forum
> 

[Pw_forum] Crash when running pw.x for relaxing a structure

[Huiqun Zhou]

Dear list-users,

I'm doing structural optimization for chromite with calcium ferrite 
structure
while changing b/a and c/a at fixed volume. But for every run with different
pair of b/a and c/a, I alway got following error ater 3-5 rounds of SCF
calculations:

..
 Writing output data file fecr2o4-cf-relax.save

 second order charge density extrapolation
rank 1 in job 170  woodcrest_32906   caused collective abort of all ranks
  exit status of rank 1: return code 220
...

The job was running parallely on one compute node with 4 CPU cores
(Intel woodcrest).

Did I do anything wrong?


Huiqun Zhou


Below is the snippet of my input file:

 &control
calculation = 'relax',
restart_mode = 'from_scratch',
prefix = 'fecr2o4-cf-relax',
tstress = .false.,
tprnfor = .false.,
pseudo_dir = '/home/geol/espresso-3.1.1/pseudo',
outdir = '/home/geol/espresso-3.1.1/tmp'
wf_collect = .true.
 /
 &system
ibrav = 8, celldm(1) = 16.9225, celldm(2) = 0., celldm(3) = 1.1065
nat = 28, ntyp = 3,
ecutwfc = 35.0, ecutrho = 240.0
nspin = 2, degauss = 0.08
occupations = 'smearing', smearing = 'gaussian'
starting_magnetization(1) = 0.5
starting_magnetization(2) = -0.5
starting_magnetization(3) = 0.1
 /
 &electrons
diagonalization = david
mixing_mode = 'plain'
mixing_beta = 0.1
conv_thr = 1.0d-6
 /
 &ions
ion_dynamics = 'bfgs'
pot_extrapolation = 'second_order'
wfc_extrapolation = 'second_order'
upscale = 100
 /
ATOMIC_SPECIES
 Fe  55.847  Fe.pw91-sp-van_ak.UPF
 Cr  51.996  Cr.pw91-sp-van.UPF
 O   15.999   O.pw91-van_ak.UPF
ATOMIC_POSITIONS crystal
 Fe 0.75600  0.25000  0.65400
 Fe 0.74400  0.75000  0.15400
 Fe 0.25600  0.25000  0.84600
 Fe 0.24400  0.75000  0.34600
 Cr 0.43300  0.25000  0.61000
 Cr 0.06700  0.75000  0.11000
 Cr 0.43300  0.25000  0.61000
 Cr 0.06700  0.75000  0.11000
 Cr 0.93300  0.25000  0.89000
 Cr 0.56700  0.75000  0.39000
..
  O 0.47900  0.75000  0.21600
  O 0.41900  0.25000  0.42400
  O 0.08100  0.75000  0.92400
  O 0.91900  0.25000  0.07600
  O 0.58100  0.75000  0.57600
K_POINTS automatic
1 3 1 1 1 1

[Pw_forum] Confused on nat definition

[Huiqun Zhou]

Hmm ..., because there are 4 lattice points, that are (0,0,0) and 3 end 
points of the
basis vectors as stated, in a diamond structure, and there are two primitive 
elements
which are located at (0,0,0) and (1/4,1/4,1/4) for this structure, so there 
should be
4 x 2 = 8 atoms in a conventional unit cell of diamond structure.

But because of periodicity, theoretically you can choose either only the 
primitive
elements (2 atoms) in an unit cell with appropriatelly selected large number 
of k points
for calculation, or the whole member (8 atoms) in an unit cell with less k 
points for
calculation. I may be wrong, please correct me.

Huiqun Zhou

- Original Message - 
From: "Eyvaz Isaev" 
To: 
Sent: Thursday, May 11, 2006 2:51 AM
Subject: Re: [Pw_forum] Confused on nat definition


> Hi,
>
>> This may seem silly, but I'm confused as to what
>> exactly the number of
>> atoms in a unit cell is (nat).  For example, the
>> Silicon example says
>> that nat is only two, yet a diamond structure such
>> as this should have
>> much more than two atoms per unit cell.
>
> Let us consider the diamond case. If you choose as
> basis vectors next 3 vectors (which are the standard
> choice)
>
> 1/2, 1/2, 0
> 1/2, 0  , 1/2
> 0  , 1/2, 1/2
>
> you have only 2 atoms in the unit cell
> (parallelepiped) spanned by these vectors:
> 0, 0, 0
> 1/4, 1/4, 1/4
>
> If you decide to choose as basis vectors next 3 ones
>
> 1 0 0
> 0 1 0
> 0 0 1
>
> you have 8 atoms in the unit cell which is now a cub.
> If your choice is the latter  for CaF2 structure you
> will have 12 atoms, but using the former - only 3.
>
> So, number of atoms (nat) in a unit cell depends on
> your unit cell choice defined by 3 basis vectors.
>
>> Is the definition of nat the  number of basis
>> vectors?
> To me it is not so clear, but see above.
>
> Bests,
> Eyvaz.
>
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>>
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[Pw_forum] questions about vc-relax

[Huiqun Zhou]

dear list-users,

I'm trying to run vc-relax or vc-md calculation on a mineral using pw.x, and my 
purpose is to
investigate what kind of structrues it would evolve into upon applying a serise 
of pressures.
I know that because of finite-size effect the transition pressure determined 
this way is 
meaningless. I just want to get the possible structures and then use total 
energy calculations
for different phases to determine the transition pressures at 0K. 

But firstly I need to make clear the following questions:

(1) I think, for my purpose, I may need to use vc-relax, but what's the 
differences between 
  vc-relax and vc-md method in the implementation because the PR dynamics is 
the same
  for both methods (am I wrong)?
(2) Should I always set ibrav = 14 (trilinic system) for variable cell 
calculation?
(3) Although in the manual INPUT_PW, tempw in &ION, press, wmass in &CELL are 
said to 
  be used in MD runs, they also can be used in vc-relax runs (for controlling 
temperature), right?

Thanks!

Huiqun Zhou
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[Pw_forum] Total number of d electrons of cobalt

[Huiqun Zhou]

dear developers and list users,

Just a simple question. What's the reason for setting cobalt's total number of 
d electrons 
to 9.0 but 7.0 in tabd.f90? Is it a typo, or a setting on purpose?


Huiqun Zhou
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[Pw_forum] Where to get CVS version of Q-Espresso?

[Huiqun Zhou]

Dear list-users,

I just checked the list archive and found there are quite some modifications in 
the cvs version,
which can solve some problems I encountered. 

Where can I get the cvs version? 

Huiqun Zhou
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[Pw_forum] Problem of compiling espresso 3.0 on AMD opteron cluster

[Huiqun Zhou]

Dear list-users,

I just downloaded espresso 3.0 and builded and run on Intel Xeon cluster very 
well.
But when I tried to compile it on my AMD opteron cluster, I got error below:

mpiifort -O3 -tpp7 -axP -unroll -pc64 -r8 -assume byterecl -nomodule -fpp 
-D__LINUX64 -D__INTEL -D__FFTW -D__MPI -D__PARA -I../include 
-I/usr/local/include -I. -I../Modules -I../PW -I../PH -I../iotk/src -c 
iotk_attr+COMPLEX1_0.f90
iotk_config.h(73): #error:  unknown Linux64 compiler, please add to 
iotk_config.h

iotk_config.h(73): #error:  unknown Linux64 compiler, please add to 
iotk_config.h

make[2]: *** [iotk_attr+COMPLEX1_0.o] Error 2
make[2]: Leaving directory `/home/hqzhou/espresso-3.0/iotk/src'
make[1]: *** [libiotk.a] Error 2
make[1]: Leaving directory `/home/hqzhou/espresso-3.0/iotk'
make: *** [libiotk] Error 2

I'm using Intel FORTRAN 9.0, Intel C/C++ 9.0 and Intel MKL 8.0.

Does anyone see the error too? It looks like that the option -D__INTEL was 
ignored.

Please help and thanks in advance.


Huiqun Zhou
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[Pw_forum] About compiling cd.x and fpmd.x

[Huiqun Zhou]

dear list users,

I have successfully compiled all programs of espresso 2.1.5 on a P4 cluster 
with very aggressive optimization
options (-O3 -tpp7 -xN -unroll -r8 -pc64). pw.x works very well both in serial 
and parallel runs but cp.x and fpmd.x
don't. Although cp.x works in serial run, it failed in parallel execution. 
fpmd.x is the worst, it fails in both serial
and parallel runs.

fpmd.x (example21)
both serial and parallel runs (serial is run on local computer) got same error 
message as below (memory 
addresses are different):

... some results of calculation (mostly initialization, I think) ...
running the calculation with 32 H2O molecules...
*** glibc detected *** free(): invalid next size (fast) : 0x1bebfad8 ***
forrtl: error (76): IOT trap signal

cp.x (example18)
serial run is OK. parallel run got error below:

... some results of calculation ...
forrtl: No such file or directory
forrtl: severe (29): file not found, unit 93, file 
/my/home/espresso-2.1.5/examples/example18/results/ .//fort.93
..

Note: the serial and parallel runs use same parallel version of cp.x and fpmd.x.

I also tried to compile a less optimized version with option -O2 -tpp7 -r8 
-pc64, but got same problem.
In both aggressive and less optimized versions, Intel MKL libraries were linked 
statically (-i-static option). Other 
libraries may be linked dynamically. But my compute nodes are homogenous 
architecture with precisely equivalent
OS and other stuff, including Intel icc, ifort, and MKL.


Thanks in advance.


Huiqun Zhou


Can anybody give me a pointer?
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